Chemical inducers such as 5-azacytidine (AzaC) and 5'-iodo-2'deoxyuridine (lUdR) have been used to discover and characterize endogenous retroviruses from rodent and avian speciecs, for example KBALB mouse cells. We found that induction conditions that have been optimized for mouse cells were not successful in inducing retrovirus from cell lines of other species, including nonhuman primates. Therefore, we developed a step-wise strategy based upon identification of critical parameters for endogenous retrovirus induction in mouse cells for optimizing induction conditions for non-murine cells. Using this approach, we have determined optimum conditions for investigating inducible endogenous retroviruses from Vero cells, which are of African green monkey (AGM) origin, a species that has never been reported to produce endogenous retroviruses .Based upon a step-wise induction strategy , Vero cegag, pol, and env regions related to endogenous SERV and BaEV sequences previously reported in the AGM DNA. Biological studies showed no evidence of replication-competent particles using several target cell lines. Similarly, an RT activity could be induced from a dog cell line, which is another species with no evidence of retrovirus isolation. This is currently under investigation for further characterization.The results demonstrated that endogenous retrovirus particles could be induced from Vero cells under optimized cell growth and drug treatment conditions. Molecular analysis indicated that the particles contained The induction of retrovirus particles from Vero cells was low and detected in cell-free supernatant only by using a highly sensitive PCR-based RT assay and virus-specific PCR assays. Further investigations of various emerging virus detection technologies used for novel virus discovery has demonstrated that induced viral RNAs could be detected in drug-treated cells using high throughput 454-massively parallel or deep sequencing: investigations with virus microarrays and long range PCR with mass spectrometry are ongoing. The results support that the combination of chemical induction strategy with sensitive broad virus detection technologies may be used for the discovery of novel endogenous retroviruses.


Vision loss degrades the quality of life of aged individuals. The major cause in industrialized countries is age-related macular degeneration (AMD), a blinding eye disease due to death of photoreceptors in the macula, a specialized retinal region responsible for high acuity vision. Photoreceptor death in AMD is thought to follow damage to the retinal pigment epithelium (RPE) , a monolRobust mTOR activation in the context of OXPHOS deficiency is counterintuitive because mTOR integrates trophic factor and nutrient availability signals to regulate cell growth and proliferation , and poiOXPHOS deficiency leads eventually to RPE atrophy, which is seen more commonly in AMD than RPE hypertrophy. Our findings suggest that RPE hypertrophy may be present at earlier stages of AMD. Indeed, ocular coherence tomography imaging demonstrated thickened macular RPE more frequently in early AMD eyes than in advanced AMD or control eyes . RPE hypertrophy may be less prominent in advanced AMD because drusen and diminished transport through aged Bruch's basement membrane  may restIntriguingly, pharmacological inhibition of mTORC1 with rapamycin blunted RPE dedifferentiation and hypertrophy and preserved photoreceptor numbers and function for both the metabolic and oxidative stress models . Rapamyc


In order to generate more accurate consensus sequences from ESTs, tools are needed to reduce or eliminate errors from de novo assemblies.Expressed Sequence Tags (ESTs) have played significant roles in gene discovery and gene functional analysis, especially for non-model organisms. For organisms with no full genome sequences available, ESTs are normally assembled into longer consensus sequences for further downstream analysis. However current We present iAssembler, a pipeline that can assemble large-scale ESTs into consensus sequences with significantly higher accuracy than current existing assemblers. iAssembler employs MIRA and CAP3 assemblers to generate initial assemblies, followed by identifying and correcting two common types of transcriptome assembly errors: 1) ESTs from different transcripts  are incorrectly assembled into same contigs; and 2) ESTs from same transcripts fail to be assembled together. iAssembler can be used to assemble ESTs generated using the traditional Sanger method and/or the Roche-454 massive parallel pyrosequencing technology.de novo EST assembly programs using both Roche-454 and Sanger EST datasets. It demonstrated that iAssembler generated significantly more accurate consensus sequences than other assembly programs.We compared performances of iAssembler and several other  We demonstrate the utility and performance of this program by performing assemblies on different EST datasets with different sets of parameters.iAssembler is implemented in Perl and can be executed under either 32-bit or 64-bit Linux systems with Bioperl  installede novo assemblies of EST sequences. As shown in Figure iAssembler employs an iterative assembly strategy and automated assembly error corrections to deliver highly accurate The unique feature of iAssembler is its ability to detect and automatically correct all possible assembly errors. Following initial assemblies by MIRA and CAP3, all-versus-all pairwise sequence alignments of resulting unigenes are performed using the NCBI megablast program. Unigenes whose overlapped sequence length and identity, and overhang length meet user-defined cutoffs are identified as type II assembly errors, i.e., sequences from same transcripts fail to be assembled together. The megablast assembler then utilizes the pairwise sequence alignment information to join the unigenes into new contigs. Next, the type I error corrector module maps individual EST members to their corresponding contigs using megablast. ESTs that have sequence similarities to their corresponding contigs less than and/or overhang lengths larger than the corresponding user-defined cutoffs are identified as type I assembly errors, i.e., two different transcripts are incorrectly assembled together. These misassembled ESTs are then extracted by the type I error corrector and together with unigenes derived from the current round of assembly and error correction, are used as the input sequences in the next round of assembly and error correction Figure .The iterative assembly strategy employed by iAssembler can result in loss of accuracy in final unigene base calling since later assemblies are performed on unigenes generated from previous assemblies, instead of ESTs; thus during assemblies by CAP3 and megablast assemblers, the information of depth of coverage by individual EST members at each unigene position will be lost and thus not used in base calling of assembled sequences. This will cause significant number of wrongly called bases in unigenes. iAssembler provides a unigene base error correction module Figure  which reFollowing corrections of type I and II assembly and unigene base calling errors, iAssembler reevaluates the resulting unigenes and identifies and corrects new assembly and base calling errors. The error identification and correction steps will be iterated until no new errors can be identified or corrected.It is worth noting that not all identified assembly errors can be corrected by iAssembler. A simple such example is illustrated in Figure iAssembler is designed to generate highly accurate assemblies of EST sequences by performing iterative assembly strategy and automated error detection and correction. The three assemblers in iAssembler, MIRA, CAP3 and megablast assemblers, are all base on the overlap-layout-consensus strategy thus iAssembler is applicable for ESTs with relative long sequences, such as those generated using Sanger and/or Roche-454 platforms.The workflow of iAssembler is shown in Figure Cleaned EST sequences are first supplied to iAssembler with appropriate user-defined parameters. iAssembler first employs MIRA to assemble EST sequences, followed by assembling the resulting MIRA unigenes using CAP3. These two open source assemblers were chosen because we have observed that MIRA is efficient in handling large-scale and relatively short Roche-454 reads while CAP3 can complement MIRA by correcting certain type II assembly errors. Following initial assemblies by MIRA and CAP3, type II assembly errors (unigenes belonging to same transcripts) are then identified by performing all-versus-all pairwise sequence alignments of the resulting unigenes using the NCBI megablast program. iAssembler then utilizes the pair-wise alignment information to assemble these unigenes into new contigs using the megablast assembler module. Next, iAssembler identifies type I assembly errors by aligning individual EST members to their corresponding unigenes. The misassembled ESTs, whose alignments to their corresponding unigenes do not satisfy cutoffs of user-specified parameters such as minimum percent identity or maximum overhang, were then extracted and used in the next round of assembly and error correction. Finally, unigene base calling errors are corrected based on alignment information of individual ESTs to their corresponding unigenes contained in the SAM output file. iAssembler iterates through error identification and correction steps until no new errors can be identified or corrected.The main output of iAssembler includes 1) the final assembled unigene sequence file in FASTA format, 2) a text file summarizing the statistics of alignments of ESTs against their corresponding unigenes, which provides necessary information to assess the quality of the assembly, and 3) a file containing detailed alignment information of individual EST sequences against their corresponding unigenes in SAM format. SAM format is a generic alignment format for storing read alignments against reference sequences  and has E. coli genome sequences, which resulted in a total of 246,993 olive ESTs with an average length of 196 bp and 362,445 tomato ESTs with an average length of 579 bp. EST assemblies were performed using a single CPU on a server with six Quad-core 2.93 GHz Intel Xeon processor and 64 GB of RAM. The following parameters were used for all the tested assembly programs, if applicable: minimum overlap length of 40 bp, minimum overlap percent identity of 97%, and maximum overhang length of 30 bp. Detailed commands and parameters used for these assemblers are listed in Table We compared the performance of iAssembler to that of several commonly used EST assembly programs including MIRA, CAP3, TGICL, Phrap, and Newbler. An olive EST dataset generated using the Roche-454 platform as described in Alagna et al.  and a toAs shown in Table We then tested performances of these assemblers using another set of parameters: minimum overlap length of 50 bp, minimum overlap percent identity of 95%, and maximum overhang length of 20 bp. The results also indicated that iAssembler generated much higher quality of assemblies than other assembly programs we investigated  using the megablast program with a minimum percent identity of 99 and a word size of 20. Only ESTs aligned to Arabidopsis cDNAs in their entire length were kept and the final collection contained 394,298 ESTs. These ESTs were assembled de novo using the six assemblers with the following parameters: minimum overlap length of 40 bp, minimum overlap percent identity of 97%, and maximum overhang length of 10 bp : LinuxProgramming language: PerlOther requirements: Bioperl version 1.006 or higherThird-party tools: BLAST, CAP3 and MIRA. These tools are already integrated into the iAssembler package.License: NoneAny restrictions to use by non-academics: noneZF conceived the general idea of this project and provided the guidance on the whole study. YZ developed the software and performed comparison with other assemblers. JG and LZ helped with design and evaluation of the software. ZF, YZ, and JG wrote the manuscript. All authors have read and approved the manuscript.Examples of common EST assembly errors. The file provides several examples of common EST assembly errors.Click here for filePerformances of EST assembly programs. The file provides evaluation results on performances of several EST assembly programs.Click here for file


Tropheus sp., a Lake Tanganyika endemic with rich geographical colour pattern variation, in which the strength of sexual isolation varies between populations. We conducted two-way mate choice experiments to compare behaviour of males of a red-bodied morph (population Moliro) towards females from their own population with behaviour towards females from four allopatric populations at different stages of phylogenetic and phenotypic divergence. Males courted same-population females significantly more intensely than females of other populations, and reduced their heteromorphic courtship efforts both with increasing genetic and increasing phenotypic distinctness of the females. In particular, females of a closely related red-bodied population received significantly more courtship than either genetically distinct, similarly coloured females (‘Kirschfleck’ morph) or genetically related, differently coloured females (‘yellow-blotch’ morph), both of which were courted similarly. Genetically and phenotypically distinct females (Tropheus polli) were not courted at all. Consistent with previous female-choice experiments, female courtship activity also decreased with increasing genetic distance from the males’ population. Given successful experimental and natural introgression between colour morphs and the pervasive allopatry of related variants, we consider it unlikely that assortative preferences of both sexes were driven by direct selection during periods of secondary contact or, in turn, drove colour pattern differentiation in allopatry. Rather, we suggest that sexual isolation evolved as by-product of allopatric divergence.Whether premating isolation is achieved by male-specific, female-specific or sex-independent assortative preferences often depends on the underlying evolutionary processes. Here we test mate preferences of males presented with females of different allopatric colour variants of the cichlid fish  Assortative and conspecific mate preferences play an important role in maintaining reproductive isolation between species or among morphs within a species . It has Tropheus comprises another cichlid species complex with rich allopatric colour pattern variation  dates back to approximately 1.5 million years ago  on the extent of phenotypic and genetic differentiation , 2012. WIn the previous mate choice experiments, females were offered a two-way choice between a homomorphic and a heteromorphic male, and interactions of females with the males were scored in categories representing aggression and mate preference. Although designed as female choice experiments, both male and female preferences could have contributed to the observed patterns, for instance because the intensity of male courtship apparently influences female preferences in within-population interactions (Tropheus sp. ‘red’ (Tropheus moorii (T. moorii), a genetically distinct population with a red ‘Kirschfleck’ (cherry-blotch) colour pattern  equipped with internal box filters, heaters and hollow bricks and illuminated with overhead white light in a 12:12 h light:dark cycle.Tropheus by Experimental setup was analogous to the female-choice design developed for n = 15 males) were given a choice of one female from the Moliro population  and one female from one of the four other populations , resulting in four experiments with the four different heteromorphic populations. Heteromorphic stimulus females were from Ndole , Chiseketi , a location north of Mabilibili  and a location south of Isonga . Logistic constraints limited the numbers of stimulus females that could be used in the experiments. Males of the Moliro population  with package glmmADMB.To account for the repeated use of individual males and females, we employed generalized linear mixed models (GLMM) with male and female identities as crossed random factors. As male behaviour towards homomorphic females did not differ between experiments (see Results), data from all four experiments were combined to build models testing for morph-dependent differences in male and female behaviour. As the response variables were tallies of events, models were fitted with negative binomial error distributions  and log link functions, and included total observation time as offset. Analyses were conducted in R v. 2.15.0  aggressive and courtship behaviour of males towards homomorphic females was independent of the morph of the alternative stimulus female, (ii) males behaved differently towards homomorphic and heteromorphic females in the contexts of both courtship and aggression, and addressed significantly more courtship and significantly less aggression to homomorphic females, and (iii) the intensity of male heteromorphic courtship, but not of aggression, depended on the females’ population, as genetically and phenotypically similar females received significantly more courtship than females of genetically and/or phenotypically distant populations. Females from genetically distant populations also showed reduced courtship activity towards Moliro males, but an opposite trend in the allocation of aggression, which they only displayed in homomorphic encounters. Aggression between males and females reflects competition for feeding territories , and mayTropheus, which demonstrated that discrimination against foreign populations is not universal and amongst other possible factors dependent on the similarity between the involved morphs  and previously , genetically related females with distinct colour pattern (Chiseketi) and genetically distinct but similarly coloured females (‘Kirschfleck’). Males did not differentiate in their courtship rates between the latter two heteromorphic populations (Chiseketi and ‘Kirschfleck’), whereas they displayed significantly more courtship quivers to the genetically and phenotypically similar population (Ndole), and significantly less courtship towards the genetically and phenotypically distinct T. polli. Apparently, male discrimination was influenced not only by colour pattern differences but also by divergence in other, for example olfactory or acoustic, cues , which did not discriminate between homo- and heteromorphic males in laboratory two-way female choice tests against a bluish morph , and hence the maximum divergence between populations, dates to approximately 1.5 Ma , the time span within which sexual isolation evolved among Tropheus populations fits well with the haplochromine model.Overall, mate choice data of la flies  and haplTropheus populations at their various stages of phylogenetic and phenotypic divergence has the potential to improve our general understanding of how allopatric populations evolve premating isolation on their way to speciation.In conclusion, males of the Moliro population discriminate between females of different populations, and even vary their courtship behaviour between females of the same population and a phenotypically and genetically similar population. Discrimination among populations appears to increase with both, genetic distance and colour pattern dissimilarity. On the basis of current evidence, we consider it likely that assortative mate preferences evolved in both sexes as a by-product of allopatric divergence under natural or social selection. Experiments testing the effects of learning and sensory environments on mate choice are warranted to address the mechanisms underlying sexual isolation within this species complex. Understanding assortative mate preferences among


Rubiaceae (coffee), Violaceae (violet), Cucurbitaceae (cucurbit), Fabaceae (bean) and recently Solanaceae (potato family), but it is very likely that cyclotides are more widely distributed since their predicted number in Rubiaceae alone is ~50.000. Additionally, the pharmacological validation of plants used in traditional medicines may trigger the discovery of novel uterotonic compounds [Drug discovery from natural products is still one of the biggest sources of novel lead compounds. In particular, plant cyclotides, disulfide-rich peptides comprising three conserved disulfide bonds in a knotted arrangement, known as cyclic cystine knot motif, and a head-to-tail cyclization, have been extensively investigated over the last four decades for their use as scaffolds in drug development. However, their distribution among flowering plants still remains limited to few species of the families of ompounds .de novo sequencing and automated database identification. The aqueous extracts and semipure peptide fractions have been tested further in a collagen gel contractility assay model and showed varying ability to induce contractions in human myometrial smooth muscle cells.Based on the use of plants in traditional Nigerian medicine during pregnancy and childbirth, we analyzed several plants from different families to evaluate their uterotonic properties at cellular level and to identify cyclotides as active molecules. Using a MALDI-TOF/TOF-based screening protocol we were able to identify many novel cyclotide-containing species which was confirmed by manual In conclusion, our results underpin earlier suggestions that cyclotides are one of the largest peptide classes within plants, covering a large chemical space based on their high sequence diversity. The evaluation of contractile properties of plants used in traditional medicines offers new starting points for the discovery and development of peptide-based uterotonic drug leads.


Arterial embolism with lower limb ischemia is a rare manifestation of paraneoplastic hypercoagulability in cancer patients. We report a unique case of fatal thromboembolism involving both circulations associated with a poorly differentiated neuroendocrine tumor of the lung with rapid progress despite high doses of unfractioned heparin and review the current literature on anticoagulative regimen in tumour patients.  Limb ischemia due to arterial embolism in cancer patients has been reported for phaeochromocytoma, malignant melanoma, angiosarcoma, or cardiac tumour patients –3. SinglVascular tumour invasion, metastatic spread, and fragmentation of cardiac masses need to be distinguished from paraneoplastic effects like catecholamine associated vasospasm, protein precipitation, and hypercoagulability . The latEmbolism suggestive of Trousseau syndrome may occur as initial symptom resulting in tumour diagnosis, as complication alongside disease progression or may be triggered by specific chemotherapy agents , 12. ThrHere we report the unique case of a patient diagnosed with a multilocular metastasized neuroendocrine tumour (NET) of the lung suffering from progressive arterial embolisms in both circulations leading to bilateral lower limb ischemia, pulmonary embolism, stroke, and finally death five weeks after the initial bout of chemotherapy despite high doses of unfractioned heparin.A 58-year-old Caucasian male was admitted to the Oncology Department with polyuria and weight loss of seven kilos in the last two weeks. Risk factors were arterial hypertension and cigarette smoking. Syndrome of inappropriate antidiuretic hormone secretion (SIADH) with hyponatremia was noticed and tumour search detected metastatic liver disease and enlarged hilar lymph nodes. Blood analysis revealed elevated levels for neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), cytokeratin-fragment (Cyfra), and liver biopsy specified metastases of a small cellular, poorly differentiated neuroendocrine tumour (NET). Further staging via FDG PET disclosed the primary tumour near the left lung hilus with positive mediastinal and hilar lymph nodes, diffuse osseous filiarisation, and a sole metastasis in the right adrenal gland. Oncology board consensus decision was made for palliative chemotherapy with cisplatin and etoposid  as common for dedifferentiated NET.Two weeks after the initial bout of chemotherapy the patient presented in the Surgical Department with incomplete ischemia of the left lower limb. Immediate interventional recanalization failed and open embolectomy of the tibiofibular trunk with consecutive venous patch plasty was performed. Histological examination of the embolus showed no malignancy. Three days later reischemia of the same leg occurred and the operative procedure was repeated. Search for embolic origin by CT-scan disclosed clinically inapparent pulmonary embolism in three lobes. Mural thrombus of the infrarenal aorta with perifocal aortic wall calcifications appeared identical to the initial staging CT . All tumAgain four days later, transfemoral and pedal embolectomy with multilocular patch plasties of all native crural arteries as ultima ratio due to complete ischemia had to be performed. Decision was made for major amputation as symptoms recurred again two days later. After clinical signs of ischemia of the contralateral limb and respiratory impairment, all parties agreed upon the best supportive care concept. The patient died three days later after an additional stroke with left-sided hemiplegia. Autopsy revealed right-sided heart failure due to new severe pulmonary embolism as cause of death, as well as heavy thrombotic alterations of all major arterial vessels .To our best knowledge this is the first case with fulminant arterial embolisms involving the lung, brain, and both legs within a two-week period despite high doses of unfractioned heparins as paraneoplastic symptoms of a multilocular metastasized NET.Initially, calcifications of the infrarenal aorta with intraluminal thrombus were suggested as origin of embolism and protective stenting was discussed but not conducted due to the rapid chain of events Figures  and 2. RConclusively, paraneoplastic or chemotherapy-triggered hypercoagulability remains as possible explanations for generalized thromboembolic disease.Paraneoplastic syndromes occur in about 10% of malignant diseases and are defined as symptom complexes that cannot be readily explained by either the local or distant spread of cancer cells or specific secretory products . ConstitCisplatin, as part of the chemotherapeutic regimen among other substances such as thalidomide, is known to trigger thromboembolism in cancer patients with different nonrelated tumour entities –21. The 9/litre as the patient worsened rapidly.Some authors have reported secondary heparin-induced thrombocytopenia (HIT) of type II in cancer patients suggesting a higher incidence due to bone marrow infiltration , 25. HITIn terms of which anticoagulant drug to administer in paraneoplastic embolism, low-molecular-weight heparin (LMWH) seems to be superior compared to unfractioned heparin (UFH) and vitamin K antagonists. This assumption is mainly supported by studies with patients suffering from deep vein thrombosis , 28. RegLower limb ischemia in tumour patients is a severe paraneoplastic complication and might be the first clinical sign in a fast chain of overwhelming thromboembolic events. Tumours of neural crest origin seem to bear a high risk of hypercoagulation. Adequate surgical intervention and sufficient anticoagulation are the only treatment options and may be still too late. Further substantial research on anticoagulative treatment in tumour patients suffering from severe thromboembolic complications is needed.


Effort thrombosis refers to axillary-subclavian vein thrombosis associated with strenuous and repetitive activity of the upper extremities. Spontaneous thrombosis of upper extremity veins, subsequently termed the Paget-Schroetter syndrome, is relatively rare.A 26 -year-old woman presented with progressive left arm swelling that had started one week before admission. Her past medical history was unremarkable for trauma to the shoulder or arm, venous catheter insertion or intravenous drug usage. She was otherwise healthy and did not report any personal or family history of hematological disorders and denied using oral contraceptives. On further questioning, the patient gave a history of knitting daily, at continuous stretches of 4–6 hours. Physical examination revealed nonpitting edema involving the entire left upper extremity. The left upper limb showed normal arterial pulses and there was no neurological deficit or bony injury. A color Doppler and duplex ultrasound scan of the left upper limb showed acute deep vein thrombosis involving the left axillary and subclavian veins.Blood was taken for factor V Leiden-factor II (G20210A) mutations and antinuclear antibody concentrations, all of which were normal. The coagulation profile revealed activated partial thromboplastin time and prothrombin time within normal range. Anticoagulation was then started with heparin and continued with warfarin. As an outpatient, she completed 8 weeks of anticoagulation therapy. A repeat ultrasound examination showed that the thrombus had resolved completely and the left subclavian vein appeared intact. After having excluded other possible predisposing factors for upper limb deep vein thrombosis, we concluded that our patient`s thrombosis was primarily prolonged knitting induced.The upper limb is an uncommon site for deep vein thrombosis. Primary axillary-subclavian vein thrombosis is, however, well described and is also called Paget-Schroetter syndrome.6In 1894, von Schroetter was the first to identify vascular trauma from muscle strain as a potential etiologic factor. It is believed that retroversion, hyperabduction and extension of the arm involved with these activities impose undue strain on the subclavian vein leading to microtrauma of the endothelium and activation of the coagulation cascade. Substantial evidence now supports the role of anatomical abnormalities involving the thoracic outlet in the pathogenesis of effort thrombosis.7Effort thrombosis of the upper extremity has been described in athletes involved in a wide variety of sports, including ball games, combatant sport and heavy athletics, games with rackets or clubs, push-up exercise and aquatic sports.Hand knitting might be a potential risk for upper limb thrombosis. Effort thrombosis should be suspected in women who perform repeated hand knitting and present with symptoms characteristic of effort thrombosis.


Leptospira infection or icterohemorrhagic disease (LIR) are not rare entities. Our study introduces a patient infected with LIR following repeated professional underwater dives.Because of disturbances in visual acuity, the patient initially turned to the services of the Timişoara Ophthalmological Clinic in 2011, and was later sent to the Infectious Diseases Clinic of Timişoara, showing low grade fever, moderate hepatosplenomegaly, discreet subicteric sclera and a severely increasing deterioration of visual acuity.Direct ophthalmoscopy revealed disseminated bilateral chorioretinitis foci. The Infectious Diseases Clinic Laboratory confirmed hematological and serological diagnosis of LIR.The ocular chorioretinal determination of LIR is not frequent. In such situations, inoculation particularities along with evolving clinical and biological characteristics invite the clinician to extend the area of investigation.


Genome-wide association studies (GWAS) have achieved great success in identifying common genetics variants associated with increased risk for developing breast cancer. More recently, advances in next-generation sequencing (NGS) have made possible identification of mutations associated with breast cancer. However, to date, the information generated by GWAS and NGS has not been maximally leveraged and integrated with gene expression data to identify biomarkers associated with the most aggressive subset of breast cancer: the triple-negative breast cancer (TNBC). Here we present results from an integrative genomics approach that combines GWAS and sequence information with gene expression data to identify functionally related genes and biological pathways enriched for expression-associated genetic loci and mutations associated with TNBC using publicly available data.We used publicly available data derived from 60 GWAS involving over 400,000 cases and over 400,000 cancer-free controls to identify SNPs and associated genes with increased risk of developing breast cancer. Specifically, we first identified SNPs in population-based human cohorts that are associated with the expression of genes in TNBC. Mutations and associated genes were identified by mining publicly available RNA-Seq and whole exome/ genome sequencing data derived from 104 TNBC patients. Gene expression data were from 124 TNBC tumors and 142 cancer-free controls. We performed supervised and unsupervised analysis on gene expression data from genes containing genetic variants and mutations to identify functionally related genes. Additionally, we performed pathway prediction and network modeling using Ingenuity. For each predicted pathway and network, we counted the number of SNPs and mutation events by direct enumeration.We identified 600 SNPs mapped to 205 genes, and 250 genes with mutations that included inserts, deletions (Indels) and copy number variants. Hierarchical clustering revealed functional relationships and similarity in patterns of expression profiles between SNP-containing genes and genes containing mutations. We identified multi-gene biological pathways enriched for SNPs and mutations. Many of the pathways identified have been proposed as important candidate pathways for TNBC, including the p53, NFkB, apoptosis, BRCA, DNA repair and DNA mismatch repair pathways.The results provide convincing evidence that integrating GWAS and sequence information with gene expression data provides a unified and powerful approach for biomarker discovery in TNBC. Furthermore, the results provide insights about the broader context in which genetic variants and mutations operate in TNBC.


A new study provides information on another possible mechanistic pathway by revealing that cadmium impairs NAT-dependent carcinogen metabolism as demonstrated by altered biotransformation of environmental aromatic amines (AAs) N-acetyltransferases, are metabolic enzymes known to play a major role in the biotransformation of exogenous chemicals including AAs, many of which are known or suspected human carcinogens.Cadmium accumulates in body tissues and causes disease of the lungs, kidneys, liver, testes, prostate, and bladder. It also is thought to potentiate the carcinogenicity of many common workplace chemicals. NATs, or arylamine In the current study the authors exposed purified NAT enzymes to cadmium and found the exposure led to rapid and irreversible functional impairment—removing the cadmium could not restore enzyme activities. They also exposed lung epithelial cells and laboratory mice to cadmium, then assessed NAT acetylation activity in the cells and mouse tissue samples. Biologically relevant concentrations of cadmium similar to those found in the lung tissue of heavy smokers impaired the NAT-dependent acetylation of carcinogenic AAs in lung epithelial cells, and NAT activity was strongly impaired in multiple tissues of mice exposed to cadmium.These findings indicate acute cadmium exposure can alter the metabolism of carcinogenic AAs through impairment of the NAT-dependent pathway, with potentially important toxicologic effects—especially considering AAs are commonly found in cigarette smoke along with cadmium. The authors recommend further studies to address whether chronic cadmium exposure leads to similar effects.


The disruption of mother-infant interactions can have life-long detrimental consequences for offspring and mothers. Recently, science has begun to emphasize translational research including preclinical and neurobiological research that may have direct implications for clinical populations and issues (see Figure


Nowadays, the use of cardiopulmonary bypass (CPB) followed by systemic hypothermia is common in cardiac surgery procedures. CPB causes a systemic inflammatory response syndrome (SIRS) that is markedly expressed in congenital caridiosurgical surgery programe resulting with deleterious consequences. Those effects are mediated through cytokines and others mediators of acute inflammatory response in circulation, which may lead to low cardiac output syndrome, multiorgan failure and lethal outcome after surgical total correction of congenital heart disease. The best method for SIRS prevention remains unclear, although some authors suggest perioperative use of corticosteroids. The study sough to evaluate the impact of perioperative corticosteroids on SIRS extent as well as clinical outcomes following total correction of congenital heart disease.The study was conducted as prospective randomized controlled trial. We enrolled 60 patients who were scheduled for total correction of congenital heart disease.In this study we examine the effects of corticosteroids in different doses and different time. Patients were divided into three groups with respect to perioperative corticosteroids administration regime.More favorable clinical outcomes as well as laboratory findings were obtained in group of patients receiving high doses of corticosteroids. The best clinical outcome was observed in group receiving (30mg/kg metilprednisolon after induction in anesthesia), where we found the shortest ICU stay , the lowest requirements for inotropic support , the shortest ventilation time .Our study presumably described that perioperative corticosteroids provide more favorable outcomes in group of patients who undergo total correction of congenital disease. However, further prospective multicentric randomized trials are required with aim to elucidate optimal timing and dosing regimens of perioperative corticosteroids.


Astatotilapia latifasciata (Figure Haplochromis obliquidens. This species was described as Haplochromis latifasciatus [Astatotilapia [Haplochromis "zebra obliquidens" in the aquarium trade. Astatotilapia latifasciata has been reported to occur in Lake Nawampasa a small satellite lake of the much larger Lake Kyoga, and in Lake Kyoga located north of Lake Victoria in Uganda [After the publication of our work , we detea Figure , was errasciatus  and lateotilapia . Our misn Uganda .


Vancomycin-resistant Enterococci (VRE) is one of the most important hospital pathogens.The aim of the study was to evaluate the VRE colonization in patients hospitalized at the Hematology Intensive Care Unit and associated risk factors.Enterococci were isolated by standard microbiological methods. Isolate sensitivity was tested by disk-diffusion test using the 30μg/ml (BBL) Vancomycin plates according to CLSI standard.Prospective cohort study involved 70 patients hospitalized at the Intensive Care Unit (ICU), Clinic for Hematology, during three months. Demographic data and data risk factors for VRE colonization during present and previous hospitalization (within 6 months) were recorded for each patient using the questionnaire. Feces or rectal swab was collected for culture from patients on admission and at discharge in case when VRE was not isolated on admission. The Upon admission, 7% of patients were already colonized with VRE. The rate of VRE colonization during present hospitalization was 41.5%. Univariate logistic regression demonstrated statistical significant differences of acute myeloid leukemia (AML) diagnosis , length of present stay , use of aminoglycosides , and pip/tazobactam  in present hospitalization, duration of use of carbapenem  and pip/tazobactam  in present hospitalization between the VRE-colonized and non-colonized patients. AML, use of carbapenem in previous hospitalization and duration of use of piperacillin/tazobactam in present hospitalization were independent risk factors of VRE-colonized patients according to multivariate logistic regression.VRE colonization rate was high among patients admitted to hematology ICU. Rational use of antibiotics and an active surveillance may be helpful preventive measures for development of bacterial resistance to antimicrobial agents.None declared


Dendroctonus ponderasae Hopkins) and its associated pathogenic fungi  in western North America has resulted in the loss of more than 13 million hectares of pines since 1999 in British Columbia alone [Pinus contorta Dougl. ex Loud. var. latifolia) in British Columbia. However, since 2006 MPB has spread into northern Alberta, where lodgepole pine hybridizes with jack pine (Pinus banksiana Lamb.) [G. clavigera differ, and that water deficit affects these responses.The ongoing outbreak of mountain pine beetle  two year old lodgepole and jack pine seedlings in growth rooms, and (2) ca. sixty year old lodgepole x jack pine hybrids in naturally regenerated, thinned stands. Soil relative water content was monitored using time-domain reflectometry. Seedlings were subjected to watering or water deficit for one week prior to wounding or wounding plus Tree physiological status was evaluated by measuring gas exchange and stomatal conductance using a LiCor 6400, stem hydraulic conductivity using a low-pressure flow meter and safranin dye xylem perfusion, and HPLC. Defense responses were assessed by lesion measurements histochemistry, and qRT-PCR.Stomatal conductance and photosynthesis significantly decreased under water deficit for both lodgepole and jack pine seedlings, but seedling hydraulic conductivity was not affected. The mild water deficit applied to the mature trees reduced stomatal conductance and photosynthesis, but not significantly.G. clavigera-induced lesions developed more slowly in jack pine than lodgepole pine seedlings. Stem hydraulic conductivity decreased in inoculated lodgepole but not jack pine seedlings, likely because of greater tracheid occlusion caused by increased fungal growth and/or resin production in lodgepole pine [G. clavigera in the co-evolved lodgepole pine host than in the new jack pine host, and (2) defense responses are slowed by water limitation.Stem lesions are a means of killing and compartmentalizing invading organisms . G. clavole pine . Water dole pine , with loole pine . Accordiaquaporin and five DREB genes, families associated with water stress responses. Although the mild water deficit did not significantly alter expression of these genes, expression of one aquaporin and one DREB decreased in response to G. clavigera inoculation. We then profiled five chitinase and four terpene synthase defense-associated genes. Expression of two chitinases was significantly induced by water deficit but not G. clavigera. Expression of other chitinases significantly increased in response to fungalinoculation, but the response was attenuated by water deficit. Expression of one terpene synthase significantly increased with fungal inoculation, but this response was also attenuated under water deficit. In contrast, water deficit increased constitutive expression of another terpene synthase. Higher constitutive expression of the monoterpene synthase under mild water stress suggests a pre-emptive defense via higher biosynthesis of volatile monoterpenes. Microarray and qRT-PCR analyses of the lodgepole and jack pine seedling experiment are underway.We then examined the effect of water deficit on transcript abundance corresponding to genes classically associated with drought and defense responses. We conducted qRT-PCR transcript abundance profiling of secondary phloem from mature lodgepole x jack pine hybrids. We first profiled four Our analyses suggest that defense responses of jack pine differ from those of lodgepole pine. Molecular analyses are underway to further characterize these differences. Both constitutive and induced defense responses are modulated in pines by water deficit, and this response appears to be gene-specific. This study shows evidence of cross talk between the water stress and defense responses of pine trees.


Brain stem arteriovenous malformations (AVMs) are rare and their clinical management is controversial. A location in highly eloquent areas and a greater risk of radionecrosis are both serious issues for radiosurgery of this entity. We report a case of a pontine AVM treated successfully with gamma knife therapy. At 3 years angiographic follow-up, imaging demonstrated complete thrombosis and there were no new neurological deficits, and at 7 years clinical follow-up, the patient continued to be neurologically stable. Although all treatments carry risk of neurological compromise, gamma knife therapy may offer the best treatment option for brain stem AVMs as seen in the case presented herein. This case illustrates a rare case of holo-pontine AVM tolerating gamma radiation with complete angiographical response and minimal neurological sequalae. Arteriovenous malformations (AVM) are congenital vascular malformations with direct arterial to venous connections without an intervening capillary network Doppman . The abrThe main diagnostic tools for these pathologic entities are magnetic resonance imaging (MRI), CT angiogram, and angiography , where single treatment of a pontine AVM with overlapping isodoses led to complete obliteration without any new neurological deficit.Any treatment of brain stem AVMs offers considerable risk for neurological compromise. Radiosurgery in highly selected cases may offer a treatment option with reasonable risks.


Overproduction of insulin and associated hypoglycemia are hallmark features of this disease. Diagnosis can be made through demonstration of hypoglycemia and elevated plasma levels of insulin or C-Peptide. Metastatic disease can be detected through computerized tomography (CT) scans, magnetic resonance imaging (MRI), and positron emission tomography (PET)/CT. Somatostatin receptor scintigraphy can be used not only to document metastatic disease but also as a predictive marker of the benefit from therapy with radiolabeled somatostatin analog. Unresectable metastatic insulinomas may present as a major therapeutic challenge for the treating physician. When feasible, resection is the mainstay of treatment. Prevention of hypoglycemia is a crucial goal of therapy for unresectable/metastatic tumors. Diazoxide, hydrochlorothiazide, glucagon, and intravenous glucose infusions have been used for glycemic control yielding temporary and inconsistent results. Sandostatin and its long-acting depot forms have occasionally been used in the treatment of Octreoscan-positive insulinomas. Herein, we report a case of metastatic insulinoma with very difficult glycemic control successfully treated with the radiolabeled somatostatin analog lutetium ( Insulinoma is a rare pancreatic neuroendocrine tumor . OverproThe treatment of unresectable metastatic insulinoma is associated with prolonged hospitalization for intravenous glucose infusion. The management of recurrent hypoglycemia also encompasses the administration of diazoxide, hydrochlorothiazide, and glucagon.Sandostatin and its long-acting depot form (Sandostatin LAR) are an adjunct therapy to neuroendocrine tumors. There are a few reports of glycemic control in patients with insulinoma treated with radio labeled somatostatin analogs , 5.The m-TOR inhibitor everolimus has been used to control hypoglycemia in this group of patients –7. Moreo177LU).Herein, we report a case of metastatic insulinoma successfully treated with the radiolabeled somatostatin analog lutetium . Computerized tomography (CT) scan of the abdomen was performed confirming the sonographic findings. The patient underwent a liver biopsy. Histopathology and immunohistochemistry results were consistent with low-grade neuroendocrine neoplasia (positive stain for chromogranin A) . InsulinThe patient received continuous intravenous glucose because of recurrent episodes of hypoglycemia throughout the hospital stay . GlucagoOctreoscan was performed showing a high uptake in focal areas of the liver, left lower quadrant of the abdomen, and cervicothoracic area .177LU) 8 weeks apart beginning on hospital day 56. By the second administration of the radiopharmaceutical, Octreoscan SPECT/CT had already shown objective metabolic and radiologic response to treatment  has been successfully tested in the treatment of gastroenteropancreatic neuroendocrine tumors [Radiolabeled somatostatin analog lutetium  did show clear evidence of objective response in line with other reports.After results of Octreoscan became available, we decided to use radiolabeled somatostatin analog because of previous reports of glycemic control and objective responses. Glucose levels steadily improved, as shown in 177LU) may represent an option for glycemic and systemic disease control, as shown in the case presented here.In summary, unresectable metastatic insulinomas may present as a major therapeutic challenge for the treating physician. For Octreoscan-positive tumors, radiolabeled somatostatin analog lutetium (


Pulse wave velocity (PWV) is an indirect measure of vascular stiffness. Higher PWV is a recognised cardiovascular risk marker. Magnetic resonance imaging (MRI) is a non-invasive method of assessing PWV. Assessing maternal influences on offspring PWV is important as reduced fetal nutrient supply and impaired early development are linked with an increased risk of cardiovascular disease in adulthood. In multiparous women, changes in the uterine spiral arteries arising during previous pregnancies result in increased fetal nutrient supply. Rat studies have shown that changes in maternal fatty acid intake in pregnancy are associated with increased offspring arterial stiffness. Some studies of human adults suggest omega-3 fish oils reduce arterial stiffness. The objective of the study was to measure vascular stiffness using MRI, and examine maternal influences on vascular structure in children aged 9 years.Aortic PWV was assessed in 125 children aged 9 years  using velocity-encoded MRI as part of a study of developmental influences on cardiovascular structure and function. Maternal diet had been assessed in early and late pregnancy, and the child's diet at age 9 years, using administered food frequency questionnaires.PWV values fell within previously reported childhood ranges. Childhood aortic PWV was lower in offspring of multiparous mothers . Higher maternal oily fish intake in pregnancy was associated with lower childhood aortic PWV , but there was no association with the child’s current fish intake.MRI measurements of childhood aortic PWV indicate that the mother’s parity, and normal variations in maternal oily fish intake in pregnancy, may alter vascular development in utero - changing arterial structure and function with long-term consequences for cardiovascular risk in later life.This work was supported by funding from the British Heart Foundation and the National Institute for Health Research .


Introduction. The mechanisms underlying the association between insulin resistance and intrahepatic lipid (IHL) accumulation are not completely understood. We sought to determine whether this association was explained by differences in fasting non-esterified fatty acid (NEFA) levels and/or NEFA suppression after oral glucose loading. Materials and Methods. We performed a cross-sectional analysis of 70 healthy participants in the Hertfordshire Physical Activity Trial  who underwent oral glucose tolerance testing with glucose, insulin, and NEFA levels measured over two hours. IHL was quantified with magnetic resonance spectroscopy. Insulin sensitivity was measured with the oral glucose insulin sensitivity (OGIS) model, the leptin: adiponectin ratio (LAR), and the homeostasis model assessment (HOMA). Results. Measures of insulin sensitivity were not associated with fasting NEFA levels, but OGIS was strongly associated with NEFA suppression at 30 minutes and strongly inversely associated with IHL. Moreover, LAR was strongly inversely associated with NEFA suppression and strongly associated with IHL. This latter association  was explained by reduced NEFA suppression (P = 0.24 after adjustment). Conclusions. Impaired postprandial NEFA suppression, but not fasting NEFA, contributes to the strong and well-established association between whole body insulin resistance and liver fat accumulation. Excess intrahepatic lipid (IHL) accumulation  is an important component of the spectrum of metabolic derangements associated with central obesity and insulin resistance . StudiesNEFA suppression is impaired in type 2 diabetes  and NAFLThe rationale and design for the Hertfordshire Physical Activity Trial ISRCTN 60986572) have been described previously 8], and o


The spiking state is thought to be maintained by a positive feedback loop between a nonspecific, calcium-sensitive cationic current (ICAN) carried by canonical transient receptor potential (TRPC) channels and heightened intracellular calcium levels sustained during sufficiently fast spiking. Bistable persistent spiking (PSB) has been observed across layers and cell types in mEC and has been implicated in working memory and grid cell function, so cholinergic modulation of TRPC channels represents a potentially fundamental mechanism shaping the spiking output of mEC neurons. However, spiking of mEC neurons during navigation and goal directed behavior in vivo is strongly theta modulated (4-12 Hz), and it is not known how the PSB mechanism may interact with theta oscillations. In the present study we evaluated the effect of muscarinic modulation on input-output processing of mEC neurons to tonic, slowly varying, and oscillatory inputs. First, we investigated the frequency to injected current (FI) relationship using step and ramp current injection protocols in the presence of the muscarinic agonist carbachol (CCh). FI measures made following suprathreshold pre-pulse current injections exhibited higher spike frequencies than when measured following subthreshold pre-pulses, illustrating a spike-history dependence of the FI relationship. The instantaneous spike frequency measured during a range of current steps showed a positive slope for most PSB neurons, indicating that ICAN acts as a reverse spike frequency adaptation mechanism. In response to linearly increasing ramp current stimuli, mEC neurons showed a steep acceleration followed by a plateau of spike frequency. Spike frequency hysteresis during decreasing ramp stimuli demonstrated significant adaptation for higher input levels, but spiking was often maintained at lower levels of injected current. Next, using different combinations of theta frequency sinewave current injections and DC holding currents, we were able to generate a range of spiking patterns where spikes were elicited on different proportions of theta cycles and at different phases of the theta input. With muscarinic activation, spiking was elicited on a higher proportion of theta cycles and at earlier phases of the oscillatory input for lower levels of tonic current input. A subset of recorded neurons exhibitted repeated sequences of intrinsic phase precessing spiking behavior. Similar to the plateau in spike rate observed with ramp stimuli, in response to stimuli composed of sinewaves superimposed on ramps, spiking phase rapidly advanced and maintained an 'early-phase plateau' as DC current continued to increase. Taken together, we demonstrate that muscarinic modulation of TRPC channels determines the gain of the frequency to injected current relationship of mEC neurons, interacts with adaptation mechanisms to generate spike history dependencies of spike rate including hysteresis, and shapes the distribution of spiking phases relative to oscillatory input. We propose that increasing activation of ICAN by spike-triggered calcium influx as an animal enters a firing field may provide a cellular mechanism contributing to theta phase precession of mEC grid cells.In the presence of muscarinic cholinergic modulation


To the Editor: Rift Valley fever (RVF) virus causes severe disease, abortion, and death in domestic animals  in Africa and the Arabian Peninsula. Humans are infected by mosquitoes, which maintain epizootic transmission, or through exposure to infected animal tissue. Although human disease may be mild, sometimes severe retinitis, meningoencephalitis, or hemorrhagic fever syndromes may develop in patients. In Africa, epizootics and associated human epidemics usually follow heavy rainfall  and Kenya (1997), which suggests that the virus was imported through infected mosquitoes or livestock from East Africa  and the Department of Defense Global Emerging Infections Surveillance and Response System (DoD-GEIS) monitor the satellite-derived normalized difference vegetation index (NDVI), which reflects recent rainfall and other ecologic and climatic factors – panel A Satellite-derived rainfall estimates show that widespread rainfall occurred over most of western Saudi Arabia and Yemen from mid-April to mid-June 2005 (No human cases of RVF have been reported in Saudi Arabia and Yemen since the 2000 outbreak, but in September 2004 the Saudi Ministry of Agriculture reported that 5 RVF-seropositive sheep had been identified during routine surveillance in Jizan where most infected persons were exposed during the outbreak in 2000 (Since RVF virus can be maintained in mosquito eggs for extended periods and transmitted under favorable conditions (


Zosterisessor ophiocephalus), thornback ray (Raja clavata), and scorpionfish (Scorpaena scrofa) were studied. At least four caseinolytic proteases bands were observed in zymogram of each enzyme preparation. These proteolytic preparations were successfully used in the deproteinization of shrimp wastes for chitin extraction. Furthermore, a trypsin was purified from the pyloric ceca of Pacific cod  using chromatographic methods. The cod trypsin was successfully applied to catalyze dipeptide synthesis using series of “inverse substrates.” A Mackerel trypsin was also purified from defatted viscera by supercritical carbon dioxide, and its biochemical properties were studied.Sea products are valuable resources of natural substances such as lipids, polysaccharides, enzymes, vitamins, and proteins. In this issue, a variety of fish proteases  have been characterized and sometimes purified. Many of these enzymes display potentially interesting new biochemical properties for industrial applications. Their potential adequacy for biotechnological applications such as chitin extraction was demonstrated. Biochemical characteristics of crude alkaline protease extracts from the viscera of goby . Sea products proteins digestion using bacterial proteases generated protein hydrolysates displaying interesting biochemical properties and antioxidant activity. Antioxidative activities and biochemical properties of protein hydrolysates with different hydrolysis degrees, prepared from cuttlefish  using an Alcalase and This issue highlights the potential of sea products as valuable resources of bioactive peptides and proteins such as hydrolytic enzymes, lectins, and antioxidants. These resources might be of great interest for industrial biotechnological processes using safe and natural materials such as peptides or enzymes. Dicer is an RNase III enzyme with two catalytic subunits, which catalyzes the cleavage of double-stranded RNA to small interfering RNAs and micro-RNAs, which are mainly involved in invasive nucleic acid defense and endogenous genes regulation. In addition, Dicer is thought to be involved in defense mechanism against foreign nucleic acids such as viruses. A paper focused on the recent progress of Dicer-related research and discussed potential RNA interference pathways in aquatic species. Dicer is abundantly expressed in embryos, indicating the importance of the protein in early embryonic development. Nabil MiledNabil MiledMoncef NasriMoncef NasriHideki KishimuraHideki KishimuraFaouzi Ben RebahFaouzi Ben Rebah


University course processes have recently changed with student enrolments increasing, ultimately placing new demands on student placements within the healthcare setting. In response to the changing university curriculum and in line with the Victorian Department of Health, Clinical Placement Networks and Health Workforce Australia, Northern Health (NH) Podiatry department identified a unique opportunity in provision of clinical placement education.NH developed an innovative and exciting approach to the management and delivery of podiatry student clinical placements in order to increase capacity. Recruitment to a new Podiatry Clinical Educator (CE) position allowed implementation of strategies to significantly increase capacity, ensure provision of high quality, evidenced based and safe clinical education whilst supporting podiatrists and students.To increase student capacity with limited resources, NH created a Podiatry CE position. This facilitated developments including; 2:1 Model of Supervision with peer learning and incorporating a focus on student feedback and reflection, integrating simulation into traditional clinical education, evidenced based tutorials and support to podiatrists and students.Preliminary evaluation findings show significant increase in capacity with high student and podiatrist satisfaction. Results of student placement evaluations will be presented including perspectives on simulation, peer learning and specific podiatrist professional experiences.With a Podiatry CE position and great team functioning; strategies implemented allow consistent provision of efficient, high quality, evidence based podiatry student clinical placements enabling increased capacity.


Prosthodontists can serve as productive members of the craniofacial team and can help coordinate multidisciplinary treatment of patients with congenital anomalies. Often there are few, if any, evidence-based criteria to assist them in developing “correct” clinical protocols. When syndromes involve hypodontia, oligodontia, or anodontia, coordinating prosthetic treatment through phases of three-dimensional growth and development can be daunting.Early implant intervention with anodontia patients is acceptable in some treatment centers. Correcting previously untreated adolescent oligodontia can be extremely challenging and removal of strategic teeth with immediate implant placement is surely controversial. Understanding the morbidity of grafting in these patients and the questionable long-term survival of overdenture abutment teeth will lend to an active discussion of the advocated aggressive therapeutic approach.


Neuronal death and subsequent denervation of target areas is a major feature of several neurological conditions such as brain trauma, ischemia or neurodegeneration. The denervation-induced axonal loss results in reorganization of the dendritic tree of denervated neurons. Dendritic reorganization of denervated neurons has been previously studied using entorhinal cortex lesion (ECL).ECL leads to shortening and loss of dendritic segments in the denervated outer molecular layer of the dentate gyrus . HoweverTo perform comparative electrotonic analysis we used computer simulations in anatomically and biophysically realistic compartmental models of 3D-reconstructed healthy and denervated granule cells. Our results show that somatofugal and somatopetal voltage attenuation due to passive cable properties was strongly reduced in denervated granule cells. In line with these predictions, the attenuation of simulated backpropagating action potentials and forward propagating EPSPs was significantly reduced in dendrites of denervated neurons. In addition, simulations of somatic and dendritic frequency-current (f-I) curves revealed increased excitability in deafferentated granule cells.Taken together, our results indicate that unless counterbalanced by a compensatory adjustment of passive and/or active membrane properties, the plastic remodeling of dendrites following lesion of entorhinal cortex inputs to granule cells will boost their electrotonic compactness and excitability.


Mammalian gene regulation is often mediated by distal enhancer elements. Despite this, mechanistic investigations of correlated expression have thus far been focused on proximal promoter regions, mainly because distal enhancers are not known for a vast majority of genes. However, distal enhancers of co-regulated genes are likely to have correlated activity.cis) and from different chromosomes, after accounting for HS autocorrelation affecting cis-pairs. Using non-parametric tests and controlling for dependencies, highly correlated pairs are compared with background pairs for: enrichment of co-occurring binding motifs; for correlated gene expression across the 15 cell samples sourced for HS data; for shared gene function; for evidence of interactions between shared enhancer-binding transcription factors (TFs) and chromatin-modifying enzymes; and for Hi-C evidence of pair co-localization. The relationship between correlated enhancers now established, we conclude by scaling this pairs perspective to the building and validating of an enhancer network.Using P300-bound regions as putative enhancers  and usinWe find that correlated enhancers tend to share common TF-binding motifs, and that several chromatin modification enzymes preferentially interact with these TFs. We show that we can predict correlated enhancers with 73% accuracy based only on the presence of shared motifs for specific TFs. Also, genes near correlated enhancers have correlated expression and share common function. Correlated enhancers coincide with spatially proximal genomic regions assayed by Hi-C in two different cell types. Finally we construct an enhancer network based on shared motifs and correlated activity, and show its high overlap with biological processes and pathways.Overall, our analysis suggests that functionally linked genes may be co-regulated by distal enhancers whose activities are regulated by common sets of TFs and mediated by both 3D chromatin structure as well as chromatin modification enzymes. Our work represents the first investigation of enhancer networks based on correlated activity across multiple cell types.


Nocardia infections; ganciclovir, valganciclovir, or acyclovir for cytomegalovirus related complications in at-risk recipients; and lamivudine for prevention of progressive liver disease in HBsAg positive recipients. Viral load monitoring and pre-emptive treatment is used for BK virus infection. Infection with new organisms has recently been reported, mostly due to inadvertent transmission via the donor organ.Infections are the leading cause of hospitalization in transplant recipients. The increased risk of new onset diabetes after transplantation, cardiovascular disease, post-transplant lymphoproliferative disorders adversely affects allograft outcomes. Risk is determined by epidemiologic exposure, immunosuppressive therapy and prophylaxis. The predictable sequence of appearance of infections helps in making management decisions. High likelihood of infections with unusual and multiple organisms necessitates aggressive use of imaging techniques and invasive procedures. Serologic tests depend upon antibody response and are unreliable. Nucleic acid based assays are sensitive, rapid, and allow detection of subclinical infection and assessment of response to therapy. Preventive steps include screening of donors and recipients and vaccination. All indicated vaccines should be administered before transplantation. Inactivated vaccines can be administered after transplantation but produce weak and transient antibody response. Boosters may be required once antibody titers wane. Post-transplant chemoprophylaxis includes cotrimoxazole for preventing urinary tract infections, pneumocystis and  Optimal use of immunosuppressive drugs in a renal transplant recipient (RTR) requires a careful balancing act. Availability of potent and specific immunosuppressive agents has reduced the incidence of acute rejection to about 10–15% in most centers. However, despite refinements in diagnostic techniques and discovery of new anti-microbial drugs, the risk of infection amongst transplant recipients has not come down. showed iInfection risk is even greater in the pediatric transplant population. Data from the North American Pediatric Renal Transplant Cooperative study show that 38–42% patients transplanted between 1987 and 2002 required hospitalization for infections. Infection was the primary cause of hospitalization in the first 2 years after transplantation, exceeding that for rejection. Cl55 Cl5455In conclusion, infections remain a major problem in the transplant population. They are a main cause of death with functioning graft, and cause a number of other complications that increase morbidity. Molecular diagnostic techniques have allowed earlier identification and better monitoring of infections. Prophylactic strategies include vaccination and targeted post-transplant chemoprophylaxis. Use of drugs carries the risk of late and resistant infections. A high index of suspicion and early and aggressive use of diagnostic techniques are essential for accurate diagnosis and improved outcomes.


WebGimm is a free cluster analysis web-service, and an open source general purpose clustering web-server infrastructure designed to facilitate easy deployment of integrated cluster analysis servers based on clustering and functional annotation algorithms implemented in R. Integrated functional analyses and interactive browsing of both, clustering structure and functional annotations provides a complete analytical environment for cluster analysis and interpretation of results. The Java Web Start client-based interface is modeled after the familiar cluster/treeview packages making its use intuitive to a wide array of biomedical researchers. For biomedical researchers, WebGimm provides an avenue to access state of the art clustering procedures. For Bioinformatics methods developers, WebGimm offers a convenient avenue to deploy their newly developed clustering methods. WebGimm server, software and manuals can be freely accessed at  Identifying groups of co-expressed genes through cluster analysis has been successfully used to elucidate affected biological pathways and postulate transcriptional regulatory mechanisms. Methods for co-expression analysis of gene expression data have been extensively researched, and numerous clustering algorithms have been developed. New clustering algorithms often have been implemented as stand-alone computer programs, R packages, or both . NumerouThe rationale for developing WebGimm is two-fold. First, sophisticated and better performing clustering methods are likely to be used more often if they are accessible through a streamlined and familiar interface requiring only minimal computational resources and no local installation. Second, an integrated web-based cluster/treeview-like platform that also incorporates functional enrichment analysis will further improve the utility of even simple hierarchical clustering procedures. We aimed to combine the "wrapper" model to facilitate access to clustering algorithms implemented in R, with the web-server model of deployment that obviates any local software installation.cluster/treeview package. The version of the software deployed on our server implements multiple infinite mixture model based clustering procedures [k-means clustering). In addition, functional analysis using the CLEAN framework and FTreeView browser [To achieve these goals, we developed WebGimm, an open source general purpose clustering web-server infrastructure designed to facilitate the easy deployment of integrated cluster analysis servers based on clustering algorithms implemented in R. The design of our Java Web Start (JWS) client was modeled after the familiar ocedures ,8-11 as  browser  are inteWebGimm is an open source general purpose clustering web-server infrastructure designed to facilitate the easy deployment of integrated cluster analysis servers based on clustering algorithms implemented in R. The system consists of a Java GUI client deployed using the Java Web Start (JWS), and the server-side infrastructure designed around Java-based WebGimm server and multiple computing R servers. The server architecture is shown in Figure Rserve infrastructure http://www.rforge.net/Rserve/. R servers perform all computational tasks associated with cluster analysis and functional enrichment analysis by executing an R script with parameters supplied by the WebGimm server. R servers provide clients with feedback about the progress being made and also send a notification once the computation completes. Jobs are assigned to the servers in a round-robin fashion to evenly distribute the load among a "farm" of R servers.The design of the Java client is modeled after the familiar cluster/treeview package. The client's function is to pass user-specified analysis parameters and data to the server for analysis, and to facilitate viewing and downloading of analysis results. The server facilitates simple data centering and scaling, executing various clustering algorithms, performing functional enrichment analysis using CLEAN and viewing results of functionally annotated clustering results using Functional TreeView (FTreeView) . The Webk-means clustering). In addition to providing a convenient tool for using GIMM, the integrated functional analysis and FTreeView browser provide a strong incentive to use the tool even when applying simple clustering procedures. The simplicity of deployment and the interface allows anybody with only conceptual understanding of cluster analysis to start using it with little effort.WebGimm serves as an integrated platform for cluster analysis, functional annotation of clustering results, and for exploring analytical results using the (FTreeView). The version of the software deployed on our server implements Gaussian Infinite Mixture Model (GIMM) based clustering procedures ,8-10 as Figure The WebGimm infrastructure also provides a convenient way to implement and distribute newly developed clustering procedures. The complete code for client and server-side software, as well as instructions for deploying the server, can be downloaded from the support web site. By making simple modifications to the client GUI and the backend R scripts, Bioinformatics developers can deploy their own methods on their own servers in a way that is accessible to users without technical Bioinformatics expertise. Such deployment will likely increase the impact of their procedures, while allowing biomedical researchers to easily test state of the art analytical procedures and choose the one producing most meaningful results for their dataset at hand. Furthermore, separating the computational infrastructure from the user interface allows for a straightforward adoption of advanced computational paradigms. For example, the recent implementation of the hierarchical clustering using CUDA general purpose programming tools for NVIDIA Graphical Processing Units achieved 48-fold speed-up over typical desktop CPU using traditional sequential algorithm . ImplemeProject name: WebGimmhttp://ClusterAnalysis.orgProject home page: Operating system: platform independent client , Linux-based web-server, platform-independent R packagesProgramming language: Java, C++, MySQL, ROther requirements: NoneLicense: The tool is available online free of charge, and code is available based on GNU GPL.Any restrictions to use by non-academics: NoneCLEAN: Clustering Enrichment Analysis; DAVID: Database for Annotation, Visualization and Integrated Discovery; GIMM: Gaussian Infinite Mixture Model; JWS: Java Web Start.'The authors declare that they have no competing interests.VJ developed the complete server infrastructure and the JWS client. MM conceived and led the development of the software and the web-server. JF developed the server-side R scripts for performing cluster analysis and functional analysis. ZH develops and maintains the c++ GIMM code, VJ and MM wrote the paper. All authors read and approved the final manuscript.


Female genital tuberculosis remains as a major cause of tubal obstruction leadingto infertility, especially in developing countries. The global prevalence of genital tuberculosis has increased during the past two decades due to increasing acquired immunodeficiencysyndrome. Genital tuberculosis (TB) is commonly asymptomatic and it is diagnosed duringinfertility investigations. Despite of recent advances in imaging tools such as computed tomography (CT) scan, magnetic resonance imaging (MRI) and ultrasongraphy, hysterosalpinography has been considered as the standard screening test for evaluation of tubal infertilityand as a valuable tool for diagnosis of female genital tuberculosis. Tuberculosis gives rise tovarious appearances on hysterosalpingography (HSG) from non-specific changes to specificfindings. The present pictorial review illustrates and describes specific and non-specific radiographic features of female genital tuberculosis in two parts. Part I presents specific findings oftuberculosis related to tubes such as "beaded tube", "golf club tube", "pipestem tube", "cobblestone tube" and the "leopard skin tube". Part II will describe adverse effects of tuberculosison structure of endometrium and radiological specific findings, such as "T-shaped" tuberculosis uterus, "pseudo-unicornuate "uterus, "collar-stud abscess" and "dwarfed" uterus withlymphatic intravasation and occluded tubes which have not been encountered in the majorityof non-tuberculosis cases. Female genital tuberculosis (FGTB) is one formof extrapulmonary manifestations of tuberculosisand includes 5% of all female pelvic infections, 2. It iThe reported prevalence of genital tuberculosis hasshown a descending trend in developed countries, butrecently, its rate has started to increase again due toco-infection with human immunodeficiency virus(HIV) and the development of drug resistants trains ofMycobacterium tuberculosis -6. PrimaDiagnosis of genital TB may be difficult becausemajority of cases are asymptomatic; furthermore, inhigh prevalence-countries, culture facilities for mycobacterium and histopathologic diagnosisare limited-11. In tThis part of pictorial review illustrates and describes endometrial changes following genital tuberculosis detected by HSG. Tubal tuberculosis is disseminated to the endometrium in approximately 50% of cases  and persThe pathognomonic findings for tuberculosisinclude specific and non-specific features. Specificradiographic features are "collar-stud abscess","T-shaped" uterus and unicornuate uterus-likeappearance (the "pseudounicornuate" uterus). Otheruterine changes due to tuberculosis known as nonspecific features include endometritis, synechiae,distortion of uterine contour, and venous and lymphatic intravasations , 15.Uterine manifestations in tuberculosis may varyfrom mild endometritis to severe scarring and deformity leading to total obliteration of the uterinecavity  16). In. In16). Later with progression of TB, caseation and ulceration of endometrium occur, and intrauterine scarring may result in synechiae and intrauterineadhesions. In this stage, the uterine cavity is usually normal in size, but irregularity of uterine contour, filling defects, lack of uterine contractilityand tubal patency may be seen .With progression of disease, irregularity ofuterine contour and filling defects may resultin a denticulate cavity  18, 19), 1918, 1A dwarfed uterus which is characterized witha small and shrived uterus with irregularity anddisproportion between uterine cavity and cervix,while trifoliate shaped uterus are other presentations of uterine tuberculosis  (17).After long duration of infection, extensive destruction of endometrium and myometriumfollowed by fibrosis and complete obliteration of the uterine cavity may occur as the"Netter syndrome" (21). Hysterosalpingographic characteristic of Netters syndrome iscalled "glove’s finger" consisted of a cervical canal and a small part of the uterus  (21). Other radiographic findings of tubercular affection of the uterus include theformation of a "collar-stud abscess", whichis pathognomonic for tuberculosis (14).This feature should be differentiated fromintracavitary changes due to necrosis in anadjacent uterine leiomyoma. A collar-studabscess classically has a narrow neck with abroader base which is away from the endometrial cavity.The venous and lymphatic intravasation inuterine and adnexal vessels is acomplicateddisorder which occurs due to progressive destruction and ulceration of endometrium.Themost important cause of intravasation is the entry of contrast medium to the venous andlymphatic canals through unprotected ves-sels. Although this feature is not specific fortuberculosis, it can be detected by HSGs performed early in the menstrual cycle, shortlyafter endometrial instrumentation or pathological deficiency of endometrium . It isaIn hysterosalpingography filling of multiple,parallel beaded channels are seen.Contrast in thin delicate lymphatics are differentiated from blood vessels by their narrower caliber and reduced draining of contrast.  Cervical tuberculosis is rare due to the nature of stratified squamous epithelium of theectocervix which causes to be resistance tobacterial penetration - 26. TheIn the cervix, the tuberculous lesion can beulcerative or proliferative. In the ulcerativeform, the ulcers have wavy borders, clean cutedges and a yellow base. The proliferative lesion has papillary formations which may bepedunculated or sessile.On HSG, caseous ulceration of the mucosaproduces ragged irregular contours and diverticular outpouching with a feathery appearance . The other various featuressuch as adhesions, distortion and a serratedendocervical canal have also seen in somecases.There are useful differential diagnostic criteria suggested by Klein et al.  for diag Calcified lymph nodes or smaller irregularcalcifications in the adnexal area.Obstruction of the fallopian tube in the zoneof transition between the isthmus and the ampulla.Multiple constrictions along the course ofthe fallopian tube.Endometrial adhesion and/or deformity orobliteration of the endometrial cavity in theabsence of curettage or of surgical terminationof pregnancy.Uterine tuberculosis may show a range of mildto severe endometritis, restricted to superficiallayers of endometrium or endometrial ulcer leading to progressive destruction, obliteration anddeformity of the uterus in the late stages.Some of the hysterosalpingographic findings ofuterine tuberculosis, such as "T-shaped" tuberculosis uterus, "pseudounicornuate" uterus, "collarstud abscess" and "dwarfed" uterus with lymphatic intravasation and occluded tubes, are specificfor female genital tuberculosis and have not beenencountered in the majority of non-tuberculosiscases. Diagnosis of these radiographic characteristics is reliable evidence of genital tuberculosisand iscrucial in the infertility workup in order tomake a proper decision.


Platelet-derived growth factor (PDGF) has ample evidence to support its importance in pulmonary fibrosis. Expression of PDGF in the lungs of IPF patients as well as in BAL samples from animal models of lung fibrosis support its involvement during disease development. Vascular endothelial growth factor (VEGF) being a key regulator of angiogenesis and its receptors have been shown to be involved in the pathogenesis of pulmonary sarcoidosis and fibrosis. The hypothesis under investigation is that receptor tyrosine kinase inhibitors (e.g. Sutent) will slow both the fibrotic processes associated with PDGF signaling and the angiogenic processes regulated by VEGF. We tested two RTKi compounds from Pfizer’s internal portfolio (SU-11248 (Sutent), SU-14813) in the bleomycin-induced pulmonary fibrosis mouse model. Prophylactic as well as therapeutic dosing protocols were conducted. Endpoints included histology, body weights, wet lung weights, lung HO-Pro levels and tissue and serum samples for biomarker and lung exposure analyses. Statistically significant reductions in histological changes were demonstrated in lungs treated with both RTK inhibitors in both percentage of total collagen and inflammatory collagen present. RTK inhibitors demonstrated a statistically significant reduction in both wet lung weight and lung HO-Pro content when dosed prophylactically and therapeutically compared to controls. We have demonstrated that broad-spectrum RTK inhibition is efficacious in inhibiting established pulmonary fibrosis in the bleomycin-induced mouse model. Sutent and other broad spectrum RTKis may provide therapeutic benefit to IPF patients by slowing both the fibrotic and angiogenic processes regulated by tyrosine kinases.


The National Cancer Institute (NCI) supports a Cancer Centers Program (CCP) including 66 NCI-designated cancer centers. Several CCPs have associations with Integrative Medicine Programs (IMPs). However, limited information is available regarding cancer-CAM research and collaborations between them. An inventory by NCI’s Office of Cancer Complementary and Alternative Medicine (OCCAM) was conducted to learn about CAM related services and resources at NCI’s CCPs and IMPs, including members of the Consortium of Academic Health Centers for Integrative Medicine (CAHCIM).Sixty-six NCI-designated cancer centers of the CCP and 41 IMPs were eligible to participate in a brief inventory about clinical services, education, and research. This project examines the CCP-IMP cancer research results of this inventory.Most CCPs and IMPs indicated collaborating with each other and also working independently. CCPs conducted more independent research (38%) than IMPs (28%). Types of research collaborations included mainly clinical research . International collaborations were higher among CCPs (27%) compared to IMPs (11%). Both CCPs and IMPs reported NIH as their major source of funding . About 70% of CCPs and IMPs reported having CAM research experts in their centers. When asked if their institutions would find an NCI training on cancer CAM research grants beneficial, both CCP (85%) and IMP (94%) respondents were interested in such training and considered it to be beneficial.This inventory shows that research collaborations between CCPs and IMPs are ongoing. However, additional in depth details are needed. Research training on cancer CAM grants can be beneficial in fostering research collaborations and in advancing cancer CAM research among CCPs and IMPs.


Diabetic peripheral neuropathy (DPN) affects the sensory, motor, and autonomic nervous system. The biomechanical changes resulting from DPN may translate to increased plantar pressures in the foot, which contributes to the pathogenesis and development of foot ulcers. This review aims to investigate the existing biomechanical literature associated with gait, dynamic electromyography and plantar pressure of patients with DPN.Electronic databases  were searched for papers reporting observational studies on patients with DPN in gait, dynamic electromyography or plantar pressure. Exclusion criteria were papers investigating children, interventional studies or studies published prior to 2000.Twenty-five papers met the inclusion criteria and were reviewed. Overall there were disparities between studies due to methodological differences in reporting such as the disease duration and degree of neuropathy of participants. DPN subjects walked slower, with smaller stride length and reduced knee extension and active ankle plantar/dorsiflexion compared to healthy and diabetes controls. Dynamic electromyography studies suggested an early activation of lateral gastrocnemius, whilst findings in the tibialis anterior and vastus lateralis muscles were inconsistent. Markedly elevated forefoot peak plantar pressures (PPP) were observed in those with a history of ulceration.This review suggests marked biomechanical  variation in DPN patients compared to controls. Studies investigating kinematic (description of movement) variables of the foot are lacking and further studies are needed. It is recommended that future DPN biomechanical studies should document the duration and degree of DPN.


Ostracism—being ignored and excluded—causes distress and threatens psychological needs ? We will review the emerging research on vicarious ostracism, highlighting the neural correlates of this phenomenon. Finally, we posit future research questions to strengthen the theoretical understanding of vicarious ostracism from social cognitive and evolutionary psychological perspectives.Empathy research suggests that individuals vicariously experience others' pain. Most of this research has focused on vicarious physical pain, but might observers also experience vicarious We are aware of nine experimental studies demonstrating vicarious ostracism. These studies find that observers recognize an ostracized individual's distress and also feel ostracized themselves  and anterior insula (AI), two brain regions activated by directly experiencing ostracism  popular? When participants are eliminated, they are openly rejected . Schadenfreude research has found feelings of dislike, anger, or resentment can lead to perceived deservingness and pleasure at another's misfortune, both in self-reports and neurological measures (Weiner, Williams  argues a Weiner, . If ostr


The aim of this study was to assess the clinical implications of reversed ophthalmic artery flow (ROAF) for stroke risk and outcomes in subjects with unilateral severe cervical carotid stenosis/occlusion.We investigated 128 subjects (101 with acute stroke and 27 without), selected from a large hospital patients base , identified with unilateral high-grade cervical carotid stenosis/occlusion by using duplex ultrasonography and brain magnetic resonance imaging. All clinical characteristics were compared for stroke risk between acute stroke and nonstroke groups. Patients with acute stroke were divided into 4 subgroups according to ophthalmic artery flow direction and intracranial stenosis severity, and stroke outcomes were evaluated.The acute stroke group had significantly higher percentages of ROAF , carotid occlusion , and severe intracranial stenosis . However, multivariate analysis demonstrated that intracranial stenosis was the only significant risk factor . Analysis of functional outcomes among the 4 subgroups of patients with stroke showed significant trends (p  =  0.018 to 0.001) for better stroke outcomes from ROAF and mild or no intracranial stenosis. ROAF improved 10–20% stroke outcomes, as compared to forward ophthalmic artery flow, among the patients with stroke and the same degree of severities of intracranial stenosis.Patients with acute stroke and severe unilateral cervical carotid stenosis/occlusion significantly have high incidence of intracranial stenosis and ROAF. Intracranial stenosis is a major stroke risk indicator as well as a predictor for worse stroke outcomes, and ROAF may provide partial compensation for improving stroke outcomes. Extracranial severe carotid stenosis or occlusion is a well-known pathogenic factor for ischemic stroke. The risk of stroke increases in patients with concurrent severe stenosis of extra- and intracranial vessels To address this question, we selected patients with acute ischemic stroke and unilateral high-grade cervical carotid stenosis/occlusion and evaluated clinical functional outcomes in the presence of ROAF and intracranial stenosis. We hypothesized that intracranial stenosis would be a predictor for stroke risk and poor stroke outcomes and that the presence of ROAF would provide compensation for improving stroke outcomes in patients with ischemic stroke and severe unilateral cervical carotid stenosis/occlusion.This retrospective cohort study was carried out within the certificated Neurovascular Ultrasound Laboratory in Tri-Service General Hospital, Taipei, Taiwan. Written consent was given by every subject before the examination. The study was approved by the hospital's Institutional Review Board for Human Studies. Between January 1, 2005 and July 31, 2012, 3 certified sonographers screened 14,701 consecutive subjects for carotid stenosis  or occlusion (100%) of the cervical segment of the ICA. They underwent a detailed neurological examination and provided clinical history based on a structured checklist Head MRI  was performed to differentiate stroke type when clinically indicated. The 128 selected patients underwent cranial MRI with multiple modalities, including fluid-attenuated inversion recovery, diffusion-weighted imaging, and three-dimensional time-of-flight magnetic resonance angiography, to differentiate stroke pattern and type if appropriate. The grade of intracranial vascular stenosis was classified into 2 groups: normal to mild stenosis (≤50%) or moderate stenosis to occlusion (>50%), as described in previous reports Continuous variables were calculated as mean ± standard deviation. Categorical variables were expressed as numbers and percentages. Categorical or continuous variables were patient age, gender, vascular risk factors, ROAF, and cervical and intracranial stenosis. Odds ratios (ORs) were used to estimate multivariate relative risks, and 95% confidence intervals (CIs) were evaluated with age-adjusted logistic regression analyses. The multivariate logistic regression with a forward selection model was performed to identify significantly independent contribution factors for acute stroke. Attributable risk difference was calculated between the acute stroke and non-stroke groups for investigating the risk of ROAF in patients with acute stroke and severe intracranial stenosis. Fisher's exact tests for categorical variables and Mantel–Haenszel extension tests for trend analyses were conducted for stroke outcome evaluation to assess the compensation effect of ROAF on intracranial stenosis severity. Statistical analyses were performed with SPSS version 19 . Values were considered statistically significant at p<0.05.Out of 14,701 consecutive subjects, only 128 met the study criteria. Among them, 27 subjects had not experienced strokes and had no evidence of stroke as assessed clinically and with brain MRI, and these subjects were considered as the non-stroke group. The remaining 101 subjects had experienced acute ischemic strokes, including 58 with first-ever onset and 43 with recurrent strokes. There were no statistically significant differences in clinical characteristics after age-adjusted univariate analysis between the 2 subgroups, and they were hence collectively considered as the acute stroke group. Statistical analysis revealed that acute stroke group was younger  than the non-stroke group. The reason may be that the lack of symptoms in the non-stroke group delayed their decision to screen for the risk of carotid stenosis. To further determine acute stroke risk factors in patients with unilateral high-grade cervical carotid stenosis/occlusion, we compared clinical characteristics between the non-stroke and acute stroke groups with age-adjusted univariate logistic analysis. Among the 81 patients with intracranial stenosis , 80 had ipsilateral severe intracranial stenosis/occlusion in the anterior circulation, and 33 patients had other concomitant critical lesions in the contralateral anterior or posterior circulation. However, no difference of ROAF occurrence was observed between patients with ipsilateral severe intracranial stenosis/occlusion in the anterior circulation and those with multiple severe intracranial stenoses at other locations.To evaluate the roles of individual risk factors in predisposition to acute stroke in patients with unilateral high-grade cervical carotid stenosis/occlusion, we performed multivariate analyses with a forward selection model . The comWe employed logistical regression analysis to explore the role of severe intracranial stenosis in ROAF occurrence. To evaluate the relationship between OA flow direction and intracranial stenosis severity in the context of stroke outcomes, 4 acute stroke subgroups were analyzed by Fisher's exact tests for categorical variables and Mantel–Haenszel extension tests for trend analyses. However, regardless of blood flow direction of OA, the patients with intracranial stenosis had worse stroke outcomes than those without. This study demonstrated that intracranial stenosis was the major risk factor for the development of acute stroke in patients with severe unilateral cervical carotid stenosis/occlusion. Patients with acute ischemic stroke and concurrent severe cervical carotid stenosis/occlusion and intracranial stenosis had a higher rate of ROAF and worse stroke outcomes compared to those with extracranial severe carotid stenosis alone. However, ROAF partially compensated for cerebral insufficiency and was associated with improved stroke outcome.Angiographic and pathologic evidence has previously demonstrated racial differences in the distribution of cervicocerebral atherosclerosis In The strengths of this study are that the included patients were strictly selected using CCDU and brain MR angiography data from a large patient pool , and the patients with ischemic stroke all had the large artery atherosclerosis stroke type. However, the novel findings and potential implications of ROAF are limited by the lack of conventional digital subtraction angiography, which is the gold standard for confirming the diagnosis of extra- and intracranial stenosis and for imaging the cerebral collateral vessels. In addition, some medications in patients with ischemic stroke have been linked to better collateral circulation Our study found that patients with acute ischemic stroke and unilateral severe cervical carotid stenosis/occlusion had a significantly higher occurrence of severe intracranial stenosis and ROAF. Regardless of blood flow direction of OA, the patients with severe intracranial stenosis have worse stroke outcomes as compared to those without. ROAF may act as a secondary collateral when brain tissues receive insufficient blood supply from the primary collaterals, thereby providing patients a valuable, but limited, compensation for partial improvement of stroke outcomes. The results of this study revealed an important implication for clinical practice. It suggested that patients with ischemic stroke should undergo advanced brain imagining and cerebral hemodynamic evaluation when they were detected with unilateral severe cervical carotid stenosis/occlusion and ROAF by CCDU. Early identification of the intracranial pathological vascular lesions and hemodynamic compromise are essential for determining optimal therapeutic strategies for improving stroke outcomes.