Health educators need rigorously developed instruments to evaluate cognitive skills relating to evidence based practice (EBP). Previous EBP evaluation instruments have focused on the acquisition and appraisal of the evidence and are largely based in the medical profession. The aim of this study was to develop and validate an EBP evaluation instrument to assess EBP cognitive skills for entry-level health professional disciplines.The Fresno test of competence in evidence based medicine was considered in the development of the 'Knowledge of Research Evidence Competencies' instrument (K-REC). The K-REC was reviewed for content validity. Two cohorts of entry-level students were recruited for the pilot study, those who had been exposed to EBP training , and who had not been exposed to EBP training . The K-REC was administered to one cohort of students (n = 24) on two testing occasions to evaluate test-retest reliability. Two raters independently scored the first test occasion (n = 24) to evaluate the inter-rater reliability of the marking guidelines. Construct validity was assessed by comparison of the two groups, 'exposed' and 'non-exposed', and the percentage of students achieving a 'pass' score in each of these groups. Item difficulty was established.p < 0.0001) difference in the total K-REC scores. The test-retest and inter-rater reliability of the individual items and total scores ranged from moderate to excellent .Among the 100 participants , there was a statistically significant (The K-REC instrument is a valid and reliable evaluation instrument of cognitive skills of EBP in entry-level student health professionals. The instrument is quick to disseminate and easy to score, making it a suitable instrument for health educators to employ to evaluate students' knowledge of EBP or in the evaluation of entry-level EBP training. The most widely accepted definition of evidence based practice (EBP) involves three components: the integration of the best research evidence with patient values and clinical expertise . EvidencIt has been proposed that EBP consists of a five step process ,5,6. PreA previous systematic review  identifiA further 10 instruments evaluating cognitive EBP skills have been published since the 2006  systematp < 0.0001) [At the time of the current study 2008), the instrument developed in this study, the 'Knowledge of Research Evidence Competencies' instrument (K-REC) was the first known tool prospectively designed to collect data on cognitive EBP skills of entry-level allied health students. Since the initial literature search and development of the K-REC, two further instruments have been published that evaluated cognitive skills of EBP in the allied health disciplines 08, the i. The 'Ad 0.0001) .While the Fresno test has been recognised as the current best available instrument to comprehensively assess cognitive skills of EBP , the insDue to the focus of this study on the assessment of entry-level education (novice rather than postgraduate learners or clinicians), the instrument was intended to evaluate the first three fundamental steps of the EBP process model , rather than assessment of the fourth step involving the application of knowledge and skills in clinical practice. The aim of this study was to develop an instrument to evaluate entry-level respondents' cognitive skills regarding the research evidence component of EBP that:• could be used across the health professions;• was quick to complete and easy to score; and• was underpinned by a transparent and defensible psychometric testing process.The development of the instrument was completed in two stages. The first stage involved the development of the instrument and the second stage comprised the processes used to psychometrically evaluate the instrument.Ethical approval for the study was obtained from the University of South Australia Human Research Ethics Committee (protocol number P067/08).Firstly, the research team considered the content of the Fresno test in the drafting of the instrument. The first seven items of the Fresno test were relevant for application to health professions external to medicine and were considered in the development of the K-REC instrument. The remaining Fresno items (8-12) involved advanced statistical calculations , and questions about diagnosis and prognosis. While these skills are pertinent to all health professions, the instrument was intended for use with entry-level health professional students with varying degrees of exposure to EBP education (novice learners rather than graduates of professions). Therefore, a choice to focus on what might reasonably be expected to be taught generically across a range of degrees/stages of programs and across disciplines was required. In both forms of the modified Fresno test ,21, the One clinical scenario template was designed for the K-REC, with specific inclusion of each of the PICO components. The clinical scenario needed to be relevant to a variety of health professional disciplines and was therefore deliberately designed around the topic of a chronic condition (cystic fibrosis) and two possible types of intervention for this condition. The interventions included in the scenario (exercise and breathing exercises) were intentionally chosen to be understood by a number of health professional disciplines .Given the time and scoring related limitations of the Fresno test, the K-REC was designed to be relatively quick for respondents to complete and easy to score. The K-REC therefore consisted of a combination of short answer, multiple choice and true/false type questions rather than conforming to the open ended short essay answer style of the Fresno test. The final draft of the K-REC instrument was distributed to three senior academics with expertise in research methods and EBP and two entry-level physiotherapy students at the University of South Australia to review the clarity and formatting of the items and instructions. The instrument underwent three rounds of review and minor revision to the wording, instructions and layout of the instrument.entry-level respondents' cognitive skills regarding the research evidence component of EBP. The instrument therefore covered the first three steps of the five step EBP process model relevant to cognitive skill , but did not consider the last two steps involving the application of evidence into practice (APPLY and ASSESS) [The K-REC instrument was designed to evaluate cognitive skills of EBP, with a combination of items evaluating either knowledge, or skills in the application of knowledge . The K-REC instrument was intended to assess  ASSESS) . The finThe 'correct' answers for each item of the K-REC were determined through review of the Fresno test, and consultation and consensus of the research team and senior academics during the development procedure. The two open-ended items (1 and 7) were scored according to the presence or absence of set criteria. For item one, respondents were allocated half a mark for each of the PICO  components provided in their question. In item seven, respondents were required to list four characteristics of randomised controlled trials that would increase their confidence that the research was methodologically sound. Half a mark was awarded for any characteristic that was consistent with the Physiotherapy Evidence Database (PEDro) scale  which isThe aims of Stage 2 of the instrument development process were to explore the practicalities of the survey process , establish test-retest and inter-rater reliability, investigate the validity of the K-REC, and seek informal feedback from the participants about the appearance, layout and general user friendliness of the instrument.The recruitment strategy aimed to enlist two main types of participants:Exposed': participants who were representative of the target population for the K-REC and who could be reasonably expected to have a good understanding of EBP through exposure to formal EBP training, and,• 'Non-exposed': participants who could be reasonably expected to have minimal understanding of EBP through minimal or no exposure to formal EBP training.• 'Third year physiotherapy students (n = 24) were invited to participate as the 'exposed' group. At the time of the study (2008), these students had completed either a mandatory stand-alone EBP course (13 weeks) or an Honours research preparation course (2 weeks and ongoing supervision within a research team) where they were taught and assessed on the different components of EBP. Therefore, these students had prior exposure to formal training and were expected to have a foundation knowledge and understanding of EBP.Human movement students (n = 89) were invited to participate as the 'non-exposed group'. Rather than compare first and third year students from the same professional discipline (physiotherapy), human movement students were selected as they would have been exposed to similar information technology literacy  and were at the same time point in their entry-level programs as the physiotherapy students (third year). The human movement students were expected to have minimal knowledge of EBP, as at the time of the study these students were not required to enroll or be assessed in any EBP or research training course and were therefore not exposed to any formal standardised EBP or research instruction.The entire group of 24 physiotherapy students was invited to complete the K-REC instrument at a face to face class. Students were requested to write their student identification number on the survey to be used to match the second round of surveys (test-retest). A second administration to the participating physiotherapy students (n = 24) was completed three days after the first testing occasion. The completed surveys from the first testing occasion (n = 24) were independently scored by two raters to establish the inter-rater reliability of the instrument. In order to establish the discriminative validity of the K-REC, the 'non-exposed' cohort of human movement (n = 89) students were invited to participate at a face to face class. The mean item and total K-REC scores of each of the student groups ('exposed' and 'non-exposed') were compared to establish discriminant validity.Test-retest and inter-rater reliability was assessed by using the intraclass correlation coefficient (ICC) for items with interval data or those with ordinal data where the intervals between measurements were assumed as equivalent . The reliability of the remaining items was assessed using Cohen's Kappa coefficient (un-weighted) for categorical data  and percentage agreement (items 1 and 3). Agreement of less than 0.50 was classified as poor, between 0.50 and 0.75 as moderate, and greater than 0.75 was classified as a good level of reliability .Discriminative validity was assessed by comparison of the individual item and total scores from the two student groups (human movement and physiotherapy) with calculation of unpaired t tests, and the z-test for comparing proportions (two-tailed) for the differences between the percentage of students achieving a pass (≥ 50% score) mark for each of the survey items in both student groups . ProbabiThe K-REC achieved an overall response rate of 88 per cent . The average completion time for the K-REC was approximately 10 minutes.All K-REC items and the total score achieved a moderate level of test-retest reliability or above Table . All parp < 0.0001) in the mean total K-REC scores between the 'exposed' and 'non-exposed' students.Discriminative validity of the K-REC was determined by the comparison of two student groups, one group with prior exposure to EBP training (expected to have an understanding of EBP process), and one group with no prior exposure to formal EBP training . The results of the total and individual survey item scores of the K-REC for both groups are shown in Table Considering the mean scores of each group of students for each K-REC item, for nine out of 10 (item eight has two sections which were considered separately) instrument items a higher proportion of 'exposed' than 'non-exposed' students passed. A z-test for comparing proportions (two-tailed) was performed to investigate the differences between the groups resulting in a statistically significant difference between groups for seven of the 10 instrument items Table .The values presented in Table The K-REC met the basic psychometric requirements for reliability, validity and usability of a standard instrument for collecting data on respondents' cognitive skills of EBP. The information gained through testing the instrument on two health professional discipline areas at one institution suggests that if the instrument is disseminated in a similar fashion, a reasonable response rate should be achieved.There are a variety of instruments available to assess EBP cognitive skills, some of which have been demonstrated to discriminate between novice and expert learners. The issue with pre-existing tools is that for novice learners, the relevance of the scenario questions and a floor effect is likely to be the issue especially with entry-level students in the early years of their programs. The K-REC instrument was designed to assess the cognitive EBP skills of novice learners (entry-level students) irrespective of their professional discipline. That is, the anticipated target audience of this instrument was predominantly entry-level health professional students, who could range from pre-novice , novice and intermediate EBP learners. While the K-REC could be used for expert learners, we suspect that a ceiling effect is likely to occur which may make it a useful tool for comparison between participants of varying EBP exposure but it is likely to be insensitive to change in EBP experts .The K-REC differed from existing instruments in terms of design, length, content and psychometric properties. The K-REC contains a clinical scenario template that may be relevant to a variety of health professional disciplines and individual items relating to the scenario. The K-REC therefore has the potential to be applicable to a variety of health disciplines, rather than being specific to one discipline. In contrast to the original Fresno test , and twop < 0.001, effect size 1.13). When comparing the psychometric properties of the K-REC to the other two instruments developed for allied health  or professional discipline versus optional, advanced or profession specific knowledge. This might explain why there is such a profusion of derivative instruments from the original Fresno test which modify, exclude or add items concerning statistical concepts, scenarios relevant to various professional groups, or focus upon questions of intervention rather than giving equal weight to questions of prognosis or diagnosis. Where instruments have been developed to assess the learning outcomes of specific EBP training courses, it is likely that the key items included within the assessment are reflected within the specific EBP education program. For example, the content of the Fresno test [Developers of instruments assessing EBP knowledge face a number of philosophical and practical issues. While the Sicily Statement clearly conveys the five fundamental steps of EBP, no similar consensus statements exist to guide which specific knowledge and skills might be considered essential to sno test  was desisno test  was devep value, effect size and confidence intervals) and questions relating to intervention (rather than prognosis/diagnosis).While it is clear that entry-level students should be able to critically analyse and evaluate the usefulness of research in disciplines such as physiotherapy and occupational therapy ,27, therAn additional issue concerning development of EBP evaluation instruments is whether the instrument is intended for repeated use with the same group of participants (eg pre and post EBP training). Where the identical instrument is used on repeated occasions with the same group, concerns arise over respondent familiarity with the items and expected answers. In a number of instruments, provision has been made for alternate items to be used on repeated occasions . The clinical scenario for a question of intervention developed for the K-REC was intended to comprise a template where the specific condition, intervention, comparator and outcome could be modified without altering the intent of the questions relating to the scenario . For example, the PICO components relevant in the scenario included within this tested version of the K-REC were:16 year old girl who has cystic fibrosis (POPULATION) and she has recently been admitted to hospital with a chest infection. Jane normally self treats at home with breathing exercises (INTERVENTION) taught to her by a physiotherapist. One of her friends also has cystic fibrosis (POPULATION) but she treats herself with exercise (COMPARATOR), not breathing exercises. Jane wants to know whether her lung condition (OUTCOME) would be more effectively managed with an exercise program. You have no experience of either breathing exercises or exercise programs for cystic fibrosis and are not sure what to recommend.""Jane is a This scenario could be modified to be relevant to any health professional discipline by altering the PICO components, for example, based on one of the clinical scenarios within the AFT , the sce16 year old girl who has a traumatic brain injury (POPULATION), currently completing her final year exams and referred to you for memory rehabilitation. Jane has a number of usual strategies (INTERVENTION) but one of her friends also has had a traumatic brain injury (POPULATION) but she manages her memory issues with a diary (COMPARATOR). Jane wants to know whether she would function better at school (OUTCOME) with a diary. You have no experience of the usual strategies or diaries for memory problems in traumatic brain injury and are not sure what to recommend.""Jane is a When the K-REC instrument with the above alternate clinical scenario was completed by a sample of entry-level physiotherapy students (n = 15), the inter-rater reliability of the marking guidelines remained high . The K-REC currently consists of a clinical scenario template, with two 'tested' scenarios. If the instrument were to be applied longitudinally, it would be necessary to develop and test a 'bank' of alternate clinical scenarios. While the option is there for users of the K-REC instrument to modify the clinical scenario template to suit various health professional disciplines, it is important to note that any modified scenario would need to be tested appropriately. It is also worth considering that the clinical scenarios contained in the original Fresno test, two modified versions and the instrument developed in the current study were all based on intervention style questions. The Centre of Evidence Based Medicine Levels of Evidence  currentlIt is possible that the three days between test occasions resulted in a degree of respondent familiarity with the items in the K-REC instrument for the test-retest reliability testing. The choice of how long to wait before retesting knowledge items requires a trade-off between the likelihood of participant recall and learning. In test-retest situations where the intent is to determine stability of respondent's answers, a longer duration is likely to reduce the potential for participants to simply recall the answers they provided during the first test occasion but increases the possibility of ongoing learning of the specific knowledge concepts included in the original test. In the current study, participants were university students currently engaged in courses where it was likely that there would be ongoing exposure to EBP principles and knowledge. The choice of a shorter period between test occasions was selected as a compromise between recall and learning.The predominant multiple choice question design of the K-REC has both advantages and disadvantages. By providing a list of possible answers, it may encourage respondents to complete the question (rather than omit the question) due to the fact that the 'correct' answer is somewhere in the list of options. The answers in the list may also act to prompt respondents if they are unsure or having difficulty remembering the answer to a particular question. It is possible that if the same items were designed as 'fill in the blank' type questions, respondents may be less likely to guess the answer. It is not possible to know from the data collected in this study whether respondents were influenced by the provision of answers in the multiple choice items in the K-REC.The items in the K-REC that related to the second step of the EBP process (ACQUIRE) did not discriminate between the groups with differing exposures to formal EBP training . The ability to effectively search the literature is an essential step in the EBP process . IdentifThe K-REC instrument was designed to evaluate the EBP cognitive skills of novice learners . It was therefore appropriate that the testing of the instrument compared the two extremes that could be present in entry-level training of health professionals, that is, those with no exposure to formal EBP training versus those with exposure to formal EBP training. While comparisons between novice, intermediate and expert learners would be useful to undertake with the K-REC instrument, it is unknown whether a ceiling effect might exist for the expert group, rendering this instrument inappropriate for this group.The Sicily Consensus Statement on EBP  highlighPrevious EBP instruments have most commonly contained items evaluating the 'ACQUIRE' and 'APPRAISE' steps of EBP . The tenThe K-REC instrument captures cognitive EBP skills relating to the first three steps of the five step EBP process model . The instrument has demonstrated very good reliability, and the validity findings show promise in the application of the instrument for evaluating change at an undergraduate health professional level.The authors declare that they have no competing interests.LKL, MTW and TSO all instigated and conceived of the study, and participated in the drafting and editing of the manuscript. All authors read and approved the final version of the manuscript. All authors contributed equally to this workLKL is a Lecturer in the School of Health Sciences at the University of South Australia. She has recently completed a PhD in the area of EBP and entry-level physiotherapy education. Her research interests are in health professional education, and the teaching of EBP process and best research evidence to undergraduate students.MTW is an Associate Professor in the School of Health Sciences at the University of South Australia. Her research interests included EBP education, with particular reference to educational processes for best research evidence, and the sensation of breathlessness in people with chronic pulmonary conditions.TSO is a Professor in the School of Health Sciences at the University of South Australia. His research interests include the links between time use and health outcomes, mathematical modelling of sports performance, anthropometry and historical trends in fitness, fatness, food intake and sleep of children.The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1472-6920/11/77/prepubK-REC instrument.Click here for fileK-REC marking guidelines.Click here for file


The techniques of structural biology currently play an important role in the development of novel therapeutic agents including cancer chemotherapies. X-ray crystallography has proved to be a particularly powerful tool for both the discovery of novel compounds and their subsequent development. In this review of the literature, the steps involved in the determination of a crystal structure will be described, including how to obtain good quality crystals, how to perform the X-ray diffraction experiment itself and how to solve the phase problem and refine the final structure. Emphasis will be placed on how the end-user should be aware of the limitations of the techniques involved and the potential errors present in proteins structure deposited in the Protein Data Base. Fragment-based ligand discovery and theoretical docking offer alternative approaches for focusing the structural biologist’s weaponry onto drug design problems. Of the many applications described in the literature inhibitors of HSP90 and Protein Kinase B will be used as examples of the ways in which improving specific protein-ligand interactions can be used to improve binding and pharmacokinetic properties. On the other hand, a complex structure involving a migrastatin analogue will exemplify the risks of over-interpretation of crystallographic data.There are no competing interests in this presentation.


Our results, based on demographic and osteometric data, indicate that full domestication of both cattle and suids occurred at the site during the 8th millennium. Importantly, domestication was preceded in both taxa by demographic and metric population parameters indicating severe overhunting. The possible role of overhunting in shaping the characteristics of domesticated animals and the social infrastructure to ownership of herds is then explored.The faunal assemblage from the 9 In this respect we part with older approaches seeking clear cut-off points between domesticated livestock species and their wild progenitors in the region, approaches which are being replaced by more nuanced documentation of the selective pressures introduced in the process of domestication Understanding of the role of humans as constant modifiers of their ecological niches is reshaping at present our understanding on the beginning of agriculture th millennium BP onwards. Age-at-death and sex ratio analyses of early livestock taxa show increasing departure from the prime-adult pattern that typified Palaeolithic and Epipalaeolithic hunting to selective culling of younger male animals. This pattern can be seen in a wide region stretching from the Taurus-Zagros arc to the Upper Euphrates th millennium BP Cyprus, brought there by Neolithic colonists, is a striking demonstration of such human involvement This documentation involves the decoding of genetic, metric and demographic markers that can be directly linked to an evolving human-animal relationship Genetic studies further revealed the occurrence of multiple domestication events for suids th to 8th millennium BP . This region, here defined as extending from the confluence of the Rivers Yarmuk and Jordan in the south to the Hula Valley in the North  evidence for the fully-domesticated status of cattle th millennium BP. This is evidenced by both demographic and metric data th millennium In the late 9th millennium BP, it is reasonable to search for evidence of intensified human exploitation of these animals in the preceding millennium. The zooarchaeological assemblages from the key site of Sha'ar Hagolan fill this gap. Located in the Jordan Valley, south of the Sea of Galilee (th millennium BP (Pre-Pottery Neolithic C), reaching its impressive florescence in the early 8th millennium BP (Early Pottery Neolithic Yarmukian culture), under the ameliorated climate of the early Holocene. The excavation of the PN strata at the site revealed a street system, a water well, courtyard houses and large assemblage of portable art, flint and pottery. Faunal and floral investigations conducted at Sha'ar Hagolan show an economy dominated by domesticated caprine herding and founder crop agriculture in the PPN If cattle and pigs are fully-domesticated in the northern Jordan Valley by the early 7The alluvial habitats modified by human agricultural activities around Sha'ar Hagolan facilitated encounters between humans and wild cattle and boar. That interaction is important for understanding the observed demographic and biometric changes associated with the domestication of cattle and pigs The faunal assemblage of Sha'ar Hagolan consists of two chronostratigraphical phases. The PN phase was radiocarbon dated to 6400–5800 cal. BCE All necessary permits were obtained for the described studies. Permission to analyze and published the animal bone assemblage from Sha'ar Hagolan was granted to us by Prof. Yosef Garfinkel, who headed the expedition of the Hebrew University of Jerusalem to that site. Permission to use data from Mishmar Ha'Emeq was granted by Dr. Omry Barzilai and N. Getzov, who directed the excavations at the site on behalf of the Israel Antiquity Authority.The animal bones from Sha'ar Hagolan presented in this study were recovered using a 2 mm mesh during eleven excavation seasons . Identification to taxon was carried out using the comparative collection of the Laboratory of Archaeozoology at the University of Haifa. The faunal assemblage from Sha'ar Hagolan is now curated in the Israeli Antiquity Authority storage facilities in Bet-Shemesh, Israel.Both fused and unfused specimens were measured using Vernier calipers to the nearest 0.1 mm following von den Driesch th millennium BP (Pre Pottery Neolithic B) site of Mishmar Ha'Emeq in the Jezreel Valley, excavated by Omry Barzilai and Nimrod Getzov of the Israel Antiquity Authority The log-transformed measurements were used to compare body-sizes between the PPN and PN suid and cattle bones from Sha'ar Hagolan. We used as a control a sample of wild cattle and boar from the 10Age-at-death was determined by epiphyseal fusion The interpretation of survivorship curves called for monitoring density-mediated attrition that could differentially delete juvenile bones from the assemblage The taxonomic composition of the faunal samples from the PPN and the PN of Sha'ar Hagolan are presented in th millennium , cattle measurements are positively skewed (Pearson's skewness = 0.66), indicating that most values cluster at the lower half of the range and that, therefore, we likely observe a female-dominated sample . In contThe survivorship curve of PPN cattle is far steeper than the PN, to such an extent that very few mature animals appear to be present . The PN th millennium BP population . Survival to later adulthood appears to have been a rare occurrence in PPN populations. This is apparently not the result of a conservative herding strategy for either cattle or pigs, if we also take into account the female-dominated sex ratio, since it means very early culling of the reproductive core of the herd In the PN, the steep cattle mortality curve changes drastically in the direction of delayed culling: nearly half the population survives to older age. Also notable is the change in male-dominated sex ratio. This observation is in line with the measurements of unfused specimens, which are not large in relation to the cattle population average and preclude selective culling of young males. The small population of animals that were retained to an older age—in marked contrast with that reflected in the PPN sample—speaks for the presence of fully-domesticated cattle. Pig demography in the PN also demonstrates a sharp break with the previous millennium's culling practices. For pigs, the transition to the PN meant a younger age-at-death, with a sharp culling peak at the first and second years of life. The sharp positive skew in the PPN metric data, interpreted in terms of female dominance, disappears. In ordinal terms, more males are present. This very young age-at-death for pigs and the larger number of males present in the assemblage argues in favor of the presence of domesticated suids in the PN.th millennium followed a few centuries later by similar events further to the west in the Carmel region When combined with the evidence from the two sites where documentation of demography exists for the time period in the study region th millennium of the southern Levant is a solidly-based hypothesis th millennium Sha'ar Hagolan are in accord with the south Levantine context. It is also apparent that the transition to the PN at the site saw a sharp change in the mortality profiles of both taxa towards well-documented patterns for fully-domesticated animals, which do not match the steep mortality curves of the PPN at the site.The existence of domesticated cattle during the 8Whereas the conclusions on the domesticated state of cattle and suids in the PN settlement of Sha'ar Hagolan accord well with the expectations and data of previous research, which relied on shifts in taxonomic frequencies and metric data One of the consequences of overhunting is a reduction in mean body-size that can be observed in faunal assemblages Overhunted ungulate populations will also display steep mortality profiles, with high juvenile attrition—the result of high recruitment rate brought about by reduced intra-taxon competition and lower chances of survival to maturity. Such populations are expected to show higher female frequency due to the general human preference to hunt the larger male animals th and 9th millennia BP, intensive hunting of wild cattle and wild boar was practiced in the northern Jordan Valley, departing from the emphasis on gazelles and deer observed in the preceding hunting cultures of the region During the 10From an optimal-foraging perspective, if the body-size of the hunted cattle and pigs was reduced to the point where the adult female body-size was incorporated in the diet – i.e., when preferential hunting of males ceases, adult females will become more dominant in the diet. This preference is especially true if very few territorial adult males remained and the majority of the population is aggregated in nursery herds composed of adult females and young males and females. Since the measurements from PPN Sha'ar Hagolan do not include young individuals, an observed pattern of female domination emerges. This pattern was first noted and interpreted by Grigson [15: 98]: “However although the cattle of the seventh millennium bc sites were of wild size, there is a suggestion that in the western part of the area there was a stress on females; this could be interpreted as predation upon nursery herds and possibly as a first step towards domestication”.Both overhunting and domestication manifest in the metric data in a similar way, by population mean body-size reduction and by a low proportion of adult males. Therefore, it is pertinent to explore the consequences of overhunting as possible candidates for shaping the archaeozoological signature of domestication. Further, overhunting may have caused domestication, as both motivation and an unconscious selective mechanism that pre-adapted prospective domesticates to full-fledged husbandry. Reduced body-size, sexual dimorphism, and enhanced fertility, when combined with selection against aggressively territorial individuals  are pre-adaptations to domestication caused by a simple, non-conscious process Alvard and Kuznar Under this scenario , the shiThe possibility of an ‘overhunting’ trajectory to domestication affects the interpretation of demographic and metric data as markers for domestication. It would suggest that in some cases body-size reduction could precede intentional demographic management of herd animals, and may be the result of a non-intentional process that was pre-adaptive to it—as suggested some years ago by Tchernov and Kolska-Horwitz


Stat5a gene of MLV integration has been already reported by us [There have been a few reports that the HIV-1 genome can be selectively integrated into the genomic DNA of host cell. However, actual target sequence of integration has not been reported. The target sequence within the second intron of ed by us 6(ACTGGGAAGGGAC)6-3’ and a set of modified sequence DNAs by deletion of CAGT in the repeat unit. This CAGT and ACTG  in the repeat units originated from the HIV-1 proviral genome ends. We devised in vitro integration by using these sequence DNAs, HIV-1 provirus DNA, and recombinant HIV-1 integrase.On basis of the CA-rich sequence motif that was observed in MLV integration target sequence, we prepared a substrate repeat sequence DNA for In vitro integration occurred at the target sequence DNA at significant higher frequency and selectivity in comparison to random-sequence DNAs. Although the target sequence consisted of repeat segments, in vitro integration selectively occurred in the middle segment of the repeat sequence. On the other hand, both frequency and selectivity decreased markedly when using sequences with deletion of CAGT in the middle segment of the target sequence. Moreover, on incubation with the CAGT-deleted DNAs and target sequence, the integration efficiency and selectivity for the target sequence were significantly reduced. This interesting data indicated interference effects by the mixed sequence CAGT-deleted DNAs. Besides, efficiency and selectivity of integration into the target repeat sequence was found to vary discontinuously with changes in manganese dichloride concentration in the reaction buffer for in vitro integration. Because the structure transition at the critical concentration was exclusively observed in the target sequence DNA by electrophoresis, these discontinuous changes in in vitro integration were probably due to fluctuation in the secondary structure of the target DNA segment. Such structural isomers may be favorable for selective integration into the target sequence DNA.in vitro HIV-integration into the specified sequence. Similar DNA sequences can interfere with the process of selective integration. Dependency of in vitro integration upon the secondary structure of the target DNA is one of the models of in vivo integration that is promoted by open chromatin structure that is induced by transcriptional factor bound to the neighboring DNA segment. In addition, the present in vitro integration system can be useful for monitoring the integration activity or test of integrase inhibitor [There is a considerable selectivity in nhibitor .


The aim of many microarray experiments is to build discriminatory diagnosis and prognosis models. Given the huge number of features and the small number of examples, model validity which refers to the precision of error estimation is a critical issue. Previous studies have addressed this issue via the deviation distribution (estimated error minus true error), in particular, the deterioration of cross-validation precision in high-dimensional settings where feature selection is used to mitigate the peaking phenomenon (overfitting). Because classifier design is based upon random samples, both the true and estimated errors are sample-dependent random variables, and one would expect a loss of precision if the estimated and true errors are not well correlated, so that natural questions arise as to the degree of correlation and the manner in which lack of correlation impacts error estimation. We demonstrate the effect of correlation on error precision via a decomposition of the variance of the deviation distribution, observe that the correlation is often severely decreased in high-dimensional settings, and show that the effect of high dimensionality on error estimation tends to result more from its decorrelating effects than from its impact on the variance of the estimated error. We consider the correlation between the true and estimated errors under different experimental conditions using both synthetic and real data, several feature-selection methods, different classification rules, and three error estimators commonly used (leave-one-out cross-validation,


Soluble guanylate cyclase (sGC), the receptor for nitric oxide (NO), is one component of the nitric oxide (NO)-sGC-cGMP signaling pathway, which plays a key role in the cardiovascular system regulating smooth muscle relaxation and vasodilation and has been implicated in remodeling events in the heart and vasculature. Triggered by the binding endothelial-derived NO to the prosthetic heme group, sGC in smooth muscle cells converts GTP to the secondary messenger cGMP. Small molecule activators of sGC have been identified that either have the ability to activate the native heme-containing form of the enzyme (Heme-Dependent activators) or have the ability to activate to heme-free or oxidized form of the enzyme (Heme-Independent activators). The therapeutic potential of activators of sGC is illustrated by the successful clinical evaluation by Bayer of a Heme-dependent activator riociguat in pulmonary arterial hypertension . The cha


This study compared the benefit of the novel one- step procedure for the managment of calculous biliary disease.A retrospective review of 25 geriatric patients was conducted one-step procedure with positionament of loop in digiuno for reductions a little bowel distenction. In 24 of the patients, the one-step technique was successful (96 %); in the remaining 1 patient (4%), conversion open technique was necessary; in this case not positionament of loop in jejunum. We define the one-step procedure to be a laparoscopic cholecystectomy whit IOC to confirm the presence of stone, to be a gold standard; intraoperative ERCP whit stone extraction was conected if necessary as part of the one-step procedure.This technique evidence a statistically significant difference of the hospital cost, such us the length of the stay and pre operative day and reduce the high conversion rate with alternatively technique in two-step. The incidence of overall complications was lower in the one-step technique. The findings showed that one-step technique was associated with less clinical pancreatitis respect at the two-stage technique.A laparoscopic cholecystectomy after ES is lengthier and more difficult then in uncomplicated cholelithiasis and should therefore be performed by an experienced surgeon. This new technique appears to be a significant conversion reduction versus two step procedure, and reduce the cost of hospitality and length of stay and preoperative days. Further research with a larger study population is necessary to determine the additional benefits of this procedure.


Anemia some of the most cutting-edge research outcomes pertaining to the latest complications and the novel treatment strategies in iron-chelation therapy. We also study the effects of these interventions on the quality of life of patients. It is studies like these that serve as the basis of evidence-based medicine and guide clinicians through their process of decision making. Beta-thalassemia is considered one of the most common genetic disorders which mass migration is introducing to countries worldwide and challenging them with its management. Advanced and improved medical care has allowed us to prolong the lives of thalassemia patients, simultaneously uncovering novel complications and outlining new challenges. We herein present in this special issue of One article of this special issue addresses the new method of using transactional Doppler ultrasonography for measuring intracranial blood flow velocity in patients with beta-thalassemia intermedia. This study shows higher blood flow velocity in these patients compared to the control group, which may point to a higher risk of ischemic events in the future. Another paper discusses that thalassemic DNA-containing red blood cells are under oxidative stress, which induces externalization of phosphatidylserine. This mechanism is involved in the removal of these cells from the circulation by the spleen, similar to that of the removal of senescent red blood cells.This special issue also includes a paper explaining the pathophysiology of bone modifications in beta-thalassemia. Imbalance in mineral turnover resulting in abnormal regulation of bone metabolism may be related to hormonal and genetic factors, iron overload, and iron chelation therapy. These factors and their contribution are addressed.β-thalassemia major is presented. It is the result of oxidative stress from free radical production, altered antioxidant enzymes, and its interaction with other essential trace element levels.Moreover, a review article that addresses the mechanism of tissue damage arising from iron overload in patients with β-thalassemia major and myelodysplastic syndrome with iron-overload treated either with deferasirox or deferoxamine injections. The results show that deferasirox can improve health-related quality of life treatment satisfaction and adherence compared to subcutaneous deferoxamine injection. This issue is crucial and often neglected in the long-term treatment of patients with iron overload.The last paper presented is a study comparing the quality of life in patients with Mehran KarimiSezaneh HaghpanahAli T. TaherMaria Domenica Cappellini


P. falciparum malaria is close to licensure, having shown moderate levels of protection in clinical trials. Several analyses have shown the vaccine to be likely to be an effective and cost-effective addition to currently used control strategies. We previously used individual-based computer simulations  to analyze uncertainties in the predicted cost-effectiveness of introducing a malaria vaccine into the expanded programme on immunization in sub-Saharan Africa. We now extend these studies to include insecticide treated nets, a currently existing intervention. In addition, we also address model uncertainty in the current analysis.The first vaccine against We used techniques of probabilistic sensitivity analysis, involving randomly sampling the parameter vectors, to analyze the contributions of the different sources of uncertainty to the predicted cost-effectiveness. One specific aspect of these analyses of uncertainty is quantification of the value of acquiring additional information on these parameters by computation of expected value of perfect information (EVPI).Among the most important predictors of the cost-effectiveness of a control program are the cost of the intervention program and the transmission intensity at the time of the start of the program. EVPI is shown to be substantial, and in particular the accrual of up-to-date information on local endemicity would seem an efficient way to inform decisions about local deployment.Probabilistic sensitivity analysis and value of information analysis using computer simulation models provide a powerful way to identify data gaps hindering rational resource allocation in malaria control.


The arterial Switch operation (ASO) is now performed routinely for the repair of transposition of the great arteries (TGA). Neo-aortic root dilatation and reduced elasticity of the ascending aorta have been shown to impact the long-term outcomes of these patients.The aim of this study was to assess the effect of the ASO with the Lecompte maneuver on the dynamic behavior and dimensions of the aortic root, and the shape and curvature of the ascending aorta and aortic arch.Data was reviewed from nineteen TGA subjects  and twenty matched control subjects , who had undergone cardiovascular magnetic resonance (CMR) imaging for clinical indications at our Institution. Aortic flows at the root level and 3D Whole-Heart bSSFP were obtained using standard CMR sequences. Both groups had non-invasive brachial blood pressure cuff measurements. 3D Whole-Heart bSSFP images were used to create 3D models for each patient using commercial software  and the volume 3D centerline from ventricular apex to the descending aorta was calculated in order to better describe aortic geometry. Aortic flows and area changes were then analyzed from magnitude and phase-contrast images with an in-house written plugin  using an automatic propagation algorithm based on non-rigid registration.ASO subjects showed an abnormal aorta from the root to the arch with dilated aortic root and a more fragmented curvature of the ascending aorta with acute angulation of the aortic arch Figure . DilatatChanges in morphology, dimensions and dynamics observed in the ASO group suggest overall increased impedance, which is likely to be the mechanistic explanation for the long-term outcomes of this procedure.Carnegie Foundation, Fondation Leducq, UK National Institute of Health Research (NIHR), Royal Academy of Engineering and EPSRC.


Tuberculosis control in sub-Saharan Africa has long been hampered by poor diagnostics and weak health systems. New molecular diagnostics, such as the Xpert® MTB/RIF assay, have the potential to improve patient outcomes. We present a cluster randomised trial designed to evaluate whether the positioning of this diagnostic system within the health system has an impact on important patient-level outcomes.This pragmatic cluster randomised clinical trial compared two positioning strategies for the Xpert MTB/RIF system: centralised laboratory versus primary health care clinic. The cluster (unit of randomisation) is a 2-week time block at the trial clinic. Adult pulmonary tuberculosis suspects with confirmed human immunodeficiency virus infection and/or at high risk of multidrug-resistant tuberculosis are enrolled from the primary health care clinic. The primary outcome measure is the proportion of culture-confirmed pulmonary tuberculosis cases initiated on appropriate treatment within 30 days of initial clinic visit. Univariate logistic regression will be performed as the primary analysis using generalised estimating equations with a binomial distribution function and a logit link.Diagnostic research tends to focus only on performance of diagnostic tests rather than on patient-important outcomes. This trial has been designed to improve the quality of evidence around diagnostic strategies and to inform the scale-up of new tuberculosis diagnostics within public health systems in high-burden settings.ISRCTN18642314; South African National Clinical Trials Registry DOH-27-0711-3568.Current Controlled Trials  Mycobacterium tuberculosis strains leading to high mortality rates . Th. Th27]. misation . Hazard M. tuberculosis against the reference standard of single MGIT culture will be based on complete case analysis  and will only include individuals not on TB treatment at the time of enrolment. Estimation of sensitivity and specificity of Xpert MTB/RIF for the detection of rifampicin resistance against the reference standard of genotypic ± phenotypic DST on the culture isolate will be based on participants with M. tuberculosis detected by Xpert MTB/RIF and with a positive MGIT culture and valid drug susceptibility test (LPA ± phenotypic DST) results. This will include individuals on TB treatment at the time of enrolment (e.g. participants with AFB smear non-conversion or treatment failure).The diagnostic performance of Xpert MTB/RIF will be compared between the two arms. Estimation of sensitivity and specificity of Xpert MTB/RIF for the detection of In addition to evaluating the effectiveness of point-of-care positioning of Xpert MTB/RIF, data from the trial will be combined with those from a costing analysis to explore the cost-effectiveness of point-of-care placement. Health system costs will be obtained through monitoring of study expenditure and interviews with health service management. Collection of data relating to patient and household costs will be nested within the trial—this will involve additional data collected from a subset of patients at baseline and at the 2-month follow-up to determine direct and indirect costs incurred during the diagnostic process. The framework for costing analysis is presented in Table The study will also compare the operational feasibility of Xpert MTB/RIF implementation at the hospital laboratory and at the primary health care clinic. This encompasses an assessment of the performance and robustness of the system, as well as evaluation of the practicality of operating the system at the laboratory and at the clinic. The key indicators to be assessed are displayed in Table The study has been approved by the Biomedical Research Ethics Committee of the University of KwaZulu-Natal (BF033/11), the Ethics Committee of the London School of Hygiene and Tropical Medicine (5926), and the Health Research Committee of the KwaZulu-Natal Department of Health (HRKM084/11). Permission for the study was granted by Hlabisa Hospital and by the Community Advisory Board of the Africa Centre for Health and Population Studies.Given that the units of randomisation are time blocks, it is not possible for individuals to consent to randomisation. Individual consent for participation remains important given that the intervention is delivered to individuals and that individual-level data are collected at enrolment and at follow-up.There are TB suspects who are not eligible for this study and therefore will not have access to Xpert MTB/RIF testing within the study (suspects who are neither HIV-infected nor at high risk for MDR-TB). The justification for this is that these groups were a lower priority for this intervention given the much lower mortality rates and these suspects continue to receive diagnostic evaluation including sputum microscopy ± culture/LPA/DST according to national guidelines. At the time of study design it was predicted that, were Xpert MTB/RIF to be implemented in South Africa, the WHO recommendations would be followed (use in HIV-infected and those at high risk of MDR-TB). Although the national roll-out plan went beyond this in incorporating its use for all TB suspects, Xpert MTB/RIF has not yet been installed in Hlabisa sub-district and is therefore not yet available in the sub-district outside the trial.Evaluation of diagnostic tools provides different challenges than those of therapeutic interventions. Diagnostic accuracy studies are usually the starting point for evaluation of new technologies, yet to inform public health policies and implementation it is crucial to evaluate patient-important outcomes . The ultBlinding of patients or of health care workers is not feasible in this pragmatic diagnostic trial because allocation to trial arms involves different actions by the patient and the clinical staff. As a result of this, the outcomes are as objective as possible to limit potential bias from differential ascertainment of outcomes in the two arms. The possibility of differential recruitment into the trial arms exists but will be minimised by standardised referral criteria for the clinic health care workers; recruitment will be monitored by reviewing the clinic records to ascertain what proportion of patients with cough were referred to the study during each 2-week block. This will be reported if there is a major imbalance in recruitment to the two trial arms. There is a further risk of selection bias if there is differential non-participation. The proportions of eligible subjects consenting by trial arm will be monitored and will be reported accurately at the conclusion of the trial. There is some risk of contamination between the arms if, over time with point-of-care testing, the health workers see the importance and the effect of receiving the test result in a timely fashion and this then improves their ability to encourage all suspects to return and receive their result. This would tend to bias the findings towards the null hypothesis. We will explore this by assessment of the variability in the proportion returning for their test result by cluster and by time period.The evaluation of diagnostic accuracy is not the primary focus of the trial and the reference standard of a single culture could be considered an imperfect gold standard. In the initial Xpert MTB/RIF clinical validity studies, the reference standard used results of liquid and solid culture on two specimens  . ConversThere are a number of trials evaluating the impact of Xpert MTB/RIF in different settings and with different research hypotheses. Information about research projects is collated by the TREAT TB Xpert Research Mapping Project . SeveralThe study received final ethical approval in June 2011. Enrolment commenced on 22 August 2011. Enrolment is scheduled to complete in March 2013 and follow-up will be complete in May 2013.ART: Antiretroviral therapy; DST: Drug susceptibility testing; GEE: Generalised estimating equation; HIV: Human immunodeficiency virus; MDR-TB: Multidrug-resistant TB; MGIT: Mycobacterial growth indicator tube; NHLS: National Health Laboratory Service; PCR: Polymerase chain reaction; PHC: Primary health care; TB: Tuberculosis; WHO: World Health Organization; XDR-TB: Extensively drug-resistant TB.The authors declare that they have no competing interests.RJL and PGF conceived and designed the trial, with additional input from GSC, NM, MPN and MLN. NM helped with the statistical design and analysis plan. RJL wrote the first draft of the manuscript. All authors contributed to revision of the manuscript and approved the final version.


An isocentric superconducting rotating-gantry for heavy-ion therapy is being developed . This roAll of the superconducting magnets were designed, and their magnetic fields were calculated using the Opera-3d code . With thThe design study as well as major tests of the superconducting magnets was completed, and the construction of the superconducting rotating-gantry is in progress. The construction of the superconducting rotating-gantry will be completed at the end of FY2014, and be commissioned within FY2015.


Trypanosoma cruzi. This accounts for the absence of RNA interference phenomena in these parasites. In the present work we have cloned and characterized the small RNA population from T. cruzi, in two of its life cycle forms: epimastigotes and metacyclic stages. Our results showed a highly represented population of small RNAs derived from de cleavage of mature tRNAs representing about 30% in epimastigotes and 40% in trypomastigotes of small RNA fraction which we dubbed mini-tRNAs. Surprisingly, more than 98% of mini-tRNAs derived from the 5' half of tRNA for Asp and Glu and localize to particular granular structures in the cytoplasm of T.cruzi at all stages of its life cycle. These tRNA halves seem to be related with an Argonaute protein distinctive of trypanosomatids which was recently cloned and sequenced in our laboratory. This Argonaute protein was differentially expressed through the life cycle of T. cruzi and its expression was accentuated by starvation. Whereas their biological significance is currently unknown this mini-tRNAs population it has been described in the last year in other organisms as Giardia lamblia, Aspergillus fumigatus and many mammalian cancer cells. These mini-tRNAs have also been found in the supernatant of culture of T. cruzi as forming part of the secretome of these organisms, which led us to speculate about a putative role of these molecules in intercellular communication. This could represent a new family of small RNAs with relevance in gene expression regulation in particular for these unicellular parasites where gene regulation is achieved principally by post-transcriptional mechanisms. The complete knowledge of gene expression regulatory pathways in this kind of parasites that concern human health could be a source of study for development of vaccines or anti-parasitic treatment in base new tools as the RNA vaccines or biotechnological drugs.In the last decade a new family of small regulatory RNAs (sRNAs) of 20-30 nt in length, were recognized as key players in the regulation of gene expression at the transcriptional and post-transcriptional levels. The enzymatic machinery associated with the biogenesis and effector functions of these "sRNAs" has been found in the majority of the organisms studied. The exceptions for this are some species of trypanosomatids including


With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention. The ENCODE consortium's large scale analysis of transcription factor binding and epigenetic marks as well as concordant work on ChIP-seq by other laboratories has established a new generation of ChIP-seq quality control measures. The use of these metrics alongside common processing steps has however not been evaluated. In this study, we investigate the effects of blacklisting and removal of duplicated reads on established metrics of ChIP-seq quality and show that the interpretation of these metrics is highly dependent on the ChIP-seq preprocessing steps applied. Further to this we perform the first investigation of the use of these metrics for ChIP-exo data and make recommendations for the adaptation of the NSC statistic to allow for the assessment of ChIP-exo efficiency. ChIP-seq couples chromatin immunoprecipitation with high throughput sequencing technologies to allow for the genome wide identification of transcription factor (TF) binding sites and epigenetic marks. The use of high throughput sequencing circumvents many of the limitations seen previously with ChIP-chip array based methods including probe specific biases and the physical limitations on the proportions of genomes which may be represented . Polymerase data was omitted from this study due to differential pattern of binding across transcriptional start sites and genes. ENA and SRA accession numbers for ENCODE/SYDH, CRUK ChIP-seq, and CRUK ChIP-exo datasets used in this study are included in the Supplementary Materials.TF and histone ChIP-seq was selected from the ENCODE/SYDH  . Analysis of overlaps and read counts within blacklisted regions was performed using the GenomicRanges Bioconductor package version 1.8.13 with R 2.15.1 .ChIP-seq and ChIP-exo reads were aligned to UCSC GRCh37 genome (February 2009 build) using BWA version 0.5.9   regions derived from a subset of the ENCODE open chromatin and input sequence data  were counted within all blacklists' regions for the ENCODE, CRUK, and ChIP-exo data sets. All data sets showed an enrichment of reads within blacklisted regions Figure , with ~1Across all datasets and blacklists there is enrichment for reads mapping to more than one location in keeping with repeat classes constituting large portions of the blacklists  is calculated from the weighted mean of the standard deviation of the depth of coverage across chromosomes normalized to the total number of reads sequenced  which may supersede that of the fragment length when assessing shift with maximum correlation for ChIP-seq as well as result in paired peaks on the Watson and Crick stand separated by the read length, thus leading to the incorrect prediction of the fragment length as the read length.The use of cross-correlation to predict fragment length provides further information about the overall quality of a ChIP-sample  typically achieve higher SSD and lower NSC or RSC scores than those with sharper signal enrichment over narrow regions .The cross-correlation profile for c-Myc (SRR568130; Figure In order to investigate the effects of differing filtering steps on cross-correlation profiles and hence NSC/RSC scores, reads were separated into those overlapping peaks, overlapping blacklists and duplicated reads. Whereas cross-correlation profiles derived from reads in peaks show the expected hump around the fragment length, the cross-correlation profile obtained by considering solely the DAC blacklist shows only the read-length spike illustrating the presence of the artifact signal within blacklisted regions and its influence in the read-length cross-correlation spikes for ChIP and input samples Figure . InteresTo systematically evaluate the effect of filtering steps on ChIP and background signal, cross-correlation profiles and their fragment-length and relative strand cross-correlation scores were assessed after blacklisting, duplicate removal and both simultaneously.The effect of blacklisting and/or duplicate removal on FSC scores is shown in Figure In keeping with the observations of DAC blacklisted reads contributing to the read-length cross-correlation peak, an increase in RSC scores across both ENCODE Figure  and CRUKThe use of cross-correlation analysis and NSC/RSC metrics for ChIP-exo data has not been previously investigated. Due to the enzymatic digestion of DNA fragments around binding sites cross-correlation profiles are expected to have a very different shape to that of successful ChIP. Neither the ER Figure  or FoxA1Cross-correlation profiles for ChIP-exo can be seen to be distinct between ER and FoxA1 ChIP. ER shows a broad enrichment over the read-length cross-correlation peak Figure  shows a Assessment of the effects of filtering on ChIP-exo shows that duplicate filtering has a dramatic effect on the overall cross-correlation profile whereas blacklisting has a specific effect in FoxA1 at the 28 bp cross-correlation peak and little effect at the 12 bp peak Figure . In thisFollowing the removal of aberrant signal and the contribution of this to the read-length cross-correlation peak, the ratio between the highest and minimum values of cross-correlation may replace the use of typical NSC scoring for ChIP-exo quality and so provide an equivalent measure of ChIP efficiency. The use of a metric equivalent to RSC's evaluation of signal to noise in ChIP-seq however is confounded by the overlap between read-length and fragment-length cross-correlation peaks. Nonetheless, in ChIP-exo data the observation of loss of a defined read-length cross-correlation peak after removal of artifact signal can act as an indication of successful removal of artifact signal.The processing of ChIP-seq data and the evaluation of ChIP quality remains an area of continued research. Following recent publications of ChIP quality metrics and analysis standards, we have performed the first systematic evaluation of the effects of ChIP-seq pre-processing steps on such metrics and an assessment of their application to the emerging technology of ChIP-exo sequencing.The assessment of ChIP-quality by the visualization of ChIP signal within genome browsers can be subjective to the investigator and is prohibitive of large scale evaluation of quality. The use of metrics of ChIP-quality therefore provides more objective methods to evaluate ChIP success as well as allows for high throughput classification of ChIP data. These metrics are however dependent on processing and filtering steps applied and therefore their interpretation must be made in their context.The removal of artifact signal can improve fragment length estimation and between sample normalization (Kharchenko et al., The SSD metric of signal inequality is highly sensitive to high signal artifact regions and so to evaluate ChIP enrichment masking of such regions is required prior to assessment of SSD. Furthermore, due its sensitivity to artifact regions, the SSD metric can be used as a flag for the persistence of artifact regions in input samples where higher scores for the input sample when compared to the ChIPed sample highlights the requirements for further artifact removal.The RSC metric provides a measure of ChIP to artifact signal, however the removal of blacklisted regions has been shown to eliminate the presence of the artifact peak and so the interpretation of RSC after blacklisting is obscured. In contrast to SSD, the assessment of RSC should be performed prior to blacklisting and the inspection of cross-correlation profiles be made after blacklisting to confirm the loss of the read-length peak within the cross-correlation profile.The treatment of duplicated reads in ChIP-seq varies between applications and the inclusion of duplicated reads is often performed in the context of differential affinity analysis (Ross-Innes et al., From these finding, we show the importance of the iterative assessment of quality over the masking of blacklisted regions and removal of duplicated reads. We recommend the assessment of RSC and NSC prior to blacklisting or duplicate removal and SSD before and after these steps to capture the extent and success of blacklisting.ChIP-exo sequencing presents a new methodology for genome wide ChIP analysis and provides a higher resolution and greater efficiency than seen for conventional ChIP (Serandour et al., The presence of artifact signal from blacklisted regions may be seen in ChIP-exo data but the degree of blacklisted signal was found to be consistently lower for this technology Figure . The sigThe use of standard cross-correlation analysis in the evaluation of ChIP-exo quality is confounded by the co-occurrence of both the read-length and the fragment-length cross-correlation peaks. Although this prohibits the use of the RSC metric, by identifying the expected cross-correlation profile of enriched regions, an adapted NSC metric may be generated as the extent of maximum cross-correlation within this profile over the background cross-correlation following the blacklisting of aberrant signal.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


In aerobically grown cells, iron homeostasis and oxidative stress are tightly linked processes implicated in a growing number of diseases. The deregulation of iron homeostasis due to gene defects or environmental stresses leads to a wide range of diseases with consequences for cellular metabolism that remain poorly understood. The modelling of iron homeostasis in relation to the main features of metabolism, energy production and oxidative stress may provide new clues to the ways in which changes in biological processes in a normal cell lead to disease.in silico mutants. The simulations of the different mutants gave rise to a remarkably accurate qualitative description of most of the experimental phenotype . A second validation involved analysing the anaerobiosis to aerobiosis transition. Therefore, we compared the simulations of our model with different levels of oxygen to experimental metabolic flux data. The simulations reproducted accurately ten out of the eleven metabolic fluxes. We show here that our probabilistic Boolean modelling strategy provides a useful description of the dynamics of a complex biological system. A clustering analysis of the simulations of all in silico mutations led to the identification of clear phenotypic profiles, thus providing new insights into some metabolic response to stress conditions. Finally, the model was also used to explore several new hypothesis in order to better understand some unexpected phenotypes in given mutants.Using a methodology based on probabilistic Boolean modelling, we constructed the first model of yeast iron homeostasis including oxygen-related reactions in the frame of central metabolism. The resulting model of 642 elements and 1007 reactions was validated by comparing simulations with a large body of experimental results (147 phenotypes and 11 metabolic flux experiments). We removed every gene, thus generating All these results show that this model, and the underlying modelling strategy, are powerful tools for improving our understanding of complex biological problems. A large body of data suggests that mitochondrial abnormalities may link gene defects and/or environmental challenges to many pathologies including several neurodegenerative processes . MitoDue to its unique redox properties and chemical reactivity, iron appears to be a key player in abnormal ROS generation, principally as a catalyst of the Fenton and Haber-Weiss reactions . This esIn the growing field of systems biology, several attempts have been made to model cellular processes. For complex systems, these models can be classified into static ,17 and dOur understanding of the relations between oxidative metabolism and iron homeostasis is based on a large body of qualitative knowledge from heterogeneous sources, often lacking numerical data. It is therefore not possible to derive mathematical relationships based on biological knowledge for the entire system, and the model has to include uncertain knowledge. As a consequence, despite several attempts to construct models accurately describing certain aspects of iron homeostasis  similar to those of mammalian cells. We first validated the model by simulating 198 in silico mutations resulting from the deletion of individual genes from the model . An independent validation was provided by analysing the key transition from anaerobic to aerobic metabolism, by comparing in silico reactions frequencies with experimental fluxomic data  = > B  3) A = > (A is degraded) 4) A < = > B (reversible reaction).Click here for fileSensitivity analysis of the outputs of the model (PoP at steady state) when the weights of the reactions are modified.Click here for filePoP of elements in simulated mutants versus phenotypes manually curated by SGD in the corresponding mutants. The spreadsheet le is composed of 6 sheets (one for each type of phenotype). Each sheet contains the simulated PoP on the left and the SGD phenotypes on the right panel . One phenotype can be represented by multiple lines when multiple articles reproduced it. ND = no difference between the WT and the mutant were observed. Red cells mean that the differences observed in the in silico mutant is not in agreement with the experimental observations. Yellow cells mean that the differences observed in the in silico mutant is not in agreement with the experimental observations as referenced by SGD but that a more recent publication is in agreement with our simulations . Columns in the "SGD Reference" section: - Reference  -PMID: #### SGD REF: #### (separated by pipe)(one reference per row) - Experiment Type (Mandatory) -The method used to detect and analyze the phenotype - Mutant Type (Mandatory) -Description of the impact of the mutation on activity of the gene product - Allele  -Allele name and description, if applicable - Strain Background  -Genetic background in which the phenotype was analyzed - Phenotype (Mandatory) -The feature observed and the direction of change relative to wild type - Chemical  -Any chemicals relevant to the phenotype - Condition  -Condition under which the phenotype was observed - Details  -Details about the phenotype - Reporter  -The protein(s) or RNA(s) used in an experiment to track a processClick here for fileList of the elements of the model that are always "ON" during the simulations.Click here for fileThe WT model implementing the first hypothesis. The WT model implementing the first hypothesis explored in "Results/Exploration of alternative hypothesis: an example of a use of the model".Click here for fileClustering presented in Figure Click here for file


Over the past years the ongoing human brain activity at rest came into focus, emphasizing the role of the rest-state activity for brain functions such as planning and perception in both healthy and diseased brains. For instance, it has been shown that the alpha rhythm during rest can be affected  using stimulations such as sensory or Transcranial Magnetic Stimulations (TMS). However, the origin and the mechanisms underlying the rest-state activity are not yet well understood.In this study, we focus on the propagation of large-scale brain responses to stimulations such as TMS to identify sub-networks involved in the rest-state.2 of the cortical surface. A sub-threshold Hopf oscillator with a Van der Pol term describes the temporal behavior of each NM and a Gaussian kernel defines the spatial interactions among the NMs. We also consider the connections through the white matter extracted from a combination of diffusion spectrum MRI tractography and the CoCoMac database. We systematically stimulate different brain areas and analyze the spatiotemporal responses of the model, using Principal Component Analysis.Using The Virtual Brain  we modelThe results provide evidence for the existence of a low dimensional set of networks during rest. Stimulations of brain areas involved in resting-state networks produce stronger and longer lasting responses than stimulations of other areas. We found overlapping of the networks with the dominant connectivity structures as well as with experimentally known resting-state networks (see Figure


To describe a novel hardware MR-perfusion phantom to model first-pass of a bolus of contrast in the cardiac cavities and large thoracic vessels  and in the myocardium, allowing for the acquisition of dynamic first-pass MR-perfusion data and for a precise control of cardiac output and myocardial perfusion for true validation of perfusion quantification.Development of quantitative MR-perfusion would benefit from the availability of a MR-compatible harware phantom allowing for a realistic simulation of the AIF and of the myocardial signal intensity curves. So far, mathematical phantoms or static samples with different T1 values have been described and a tool for development and true validation of MR-perfusion is lacking.Our MR-compatible phantom resembles the anatomy of the heart and of the thoracic vessels of a 60 kg subject. Water flow (2-4 l/min) is driven into the system by a pump located outside the MR room. Gadolinium injections  are performed in the vena cava by a power-injector . Progressive dilution of the Gadolinium bolus across the chambers generates the AIF. A fraction of the cardiac output perfuses two myocardial compartments  where perfusion can be controlled precisely and independently. Outside the MR room, a control unit allows for precise measurement and control of cardiac output and myocardial perfusion. The phantom was tested in a 3T-scanner . Acquisition of the perfusion sequence was repeated multiple times with a k-t SENSE sequence  using similar flow conditions to demonstrate the reproducibility of the measurements. Different flow conditions were used to assess the response of the system to different myocardial perfusion rates. Quantification was performed by Fermi deconvolution.The system produced realistic dynamic first-pass perfusion data Figure  and reacThis novel hardware perfusion phantom allows reliable, reproducible and efficient simulation of myocardial perfusion. The availability of a direct comparison between the image data and reference values of flow and perfusion will allow for rapid development and validation of accurate quantification methods.


Today's scoring functions are one of the main reasons that state-of-the-art protein-ligand dockings fail in about 20 % to 40 % of the targets due to the sometimes severe approximations they make. However these approximations are necessary for performance reasons. One possibility to overcome these problems is the inclusion of additional, preferably experimental information in the docking process. Especially ligand-based NMR experiments that are far less demanding than the solution of the whole complex structure are helpful.Here we present the inclusion of three different types of NMR-data into the ChemPLP  scoring In the second part the usefulness of INPHARMA data ,5 is sho


This issue includes a series of papers from the second special issue of the Standards in Genomic Sciences (SIGS) journal organized by the Genomic Standards Consortium (GSC).With this special issue, SIGS makes a significant advance towards its goal of providing a unique forum for publishing standards-compliant literature. With the publication of these articles SIGS is continuing to expand its scope and relevance to the wider scientific community working in the areas of genomes, metagenomes, metagenetics, 'omics and standard ways of describing, analyzing, distributing and publishing data.While the content of SIGS to date has largely consisted of reports on genome sequencing projects - making SIGS the 3rd ranked journal for total number of genome publications to date - the longer-term goal of SIGS is to serve as an open-access, standards-supportive publication for all consensus-building communities working to develop standards and related infrastructure. Joint publication is a key step in the defining the shared interests and goals of communities. This issue contains a suite of multi-author, consensus-driven articles.The papers in this special issue include a series of workshop reports, calls for adoption of new minimum information checklists, and a community call for open access to metagenomic samples. We look forward to seeing the international standards community continue to grow,  and we thank SIGS for providing a novel forum in which to publish critical advances in this field.


Acanthamoeba is opportunistic protozoan pathogen and is known to be one of the most ubiquitous organisms that can produce keratitis and rare but fatal encephalitis. Infections due to Acanthamoeba have increased over the year, which is due to presence of Acanthamoeba in the natural environment and have a direct contact with human in everyday life and is responsible for human diseases. Given the free-living nature of the organisms, it is anticipated that we encounter Acanthamoeba during our normal life. The aim of the present study was to investigate anti-Acanthamoeba antibodies in Pakistani healthy population to combat this pathogen in normal situation.Acanthamoeba isolation from environmental sources  was done using plating assay. Acanthamoeba identification from environmental samples was based on the morphology of cyst and trophozoite forms by non-nutrient agar plates seeded with E. coli K12 and PCR amplification with a genus specific primer pair. The presence of anti-Acanthamoeba sIgA in mucosal secretions of tribal Pakistani population  were determined using Enzyme-linked immunosorbent assays (ELISA).Acanthamoeba was successfully isolated from the water sources of Pakistan during this study. ELISA demonstrated the presence of Acanthamoeba-specific sIgA in mucosal secretions of in different age groups and both genders. A total of 524 samples of 45 tribes, were collected from different age groups ranged from 15 to 60 years. The overall prevalence was 78.8% in males and 73.8% in females. No significant difference was observed between genders. The high level of anti-Acanthamoeba antibodies was observed among the people in 25-30 years of age. Furthermore the prevalence of antibodies was observed high in tribal population of Khyber Pakhtunkhwa province as compared to rest of the country.Here, we for the first time isolated Acanthamoeba from the natural environment of Pakistan and presented the prevalence level of anti-Acanthamoeba secretory IgA antibody in mucosal secretions of the normal Pakistani population.


Despite the promising paradigm offered by high-content screening, the concrete execution of hundred of thousands of visual cell-based experiments has remained highly challenging in terms of both statistical robustness and speed. An efficient computational method for cellular microarrays was developed at Institut Pasteur-Korea that allow for high speed, high content genome-wide siRNA screening. Details of the method and examples of data from genome-wide analyses will be featured in this presentation. In particular, we will demonstrate that the sudden ability to dramatically increase the number of experiments has created the opportunity for automated identification of a drug’s target.


The common sense model of illness (CSM) has been shown to be a useful model to help understand the psychological influences on diabetes-related behaviour and health outcomes. Using the CSM, the aim of this study was to investigate the relationship between cognitive and emotional representations of peripheral neuropathy and diabetes-related foot ulceration in adults with diabetes.One-hundred and twenty-one people with diabetes and peripheral neuropathy were recruited into this one-year prospective cohort study. At baseline, the participants completed two questionnaires- the Patients’ Interpretation of Neuropathy questionnaire and a short questionnaire asking about preventative foot-care behaviour. Basic diabetes and demographic information was also collected. Sequential logistic regression was used to investigate the influence of cognitive and emotional representations of peripheral neuropathy as measured by the PIN and the development of incident foot ulceration.One-hundred and seventeen participants completed the study. The incidence of new foot ulceration was 34.2%. Only two statistically significant independent risk factors for foot ulceration were detected: prior history of foot ulceration  and severity of neuropathy .A consistent association between cognitive and emotional representations of peripheral neuropathy and incident foot pathology was not found. If the CSM is to be clinically useful for people with diabetes and peripheral neuropathy the mediational role of preventative foot-care behaviour should be further investigated.


The sixth sentence of the last paragraph of the Introduction is incorrect. The correct sentence is: AtWRKY11, AtbZIP63 and the DNA-binding domain of AtWRKY33 and revealed their full binding spectra.""We applied this approach to the already known DNA-binding proteins


To develop a model for determining the level of dose adherence of Antiretroviral Therapy (ART) clients from the first day of ART to the day of interview and to determine the dose adherence levels of the ART clients using the model.A cross-sectional study was conducted using pre-tested standardized questionnaires in exitinterviews in three ART centres and eleven social support groups to determine the dose adherence levels of ART clients in the Eastern Region of Ghana. A dose-adherence model was developed from three types of dose records; the observed doses, the expected doses and the missed doses and the frequency at which clients defaulted since commencement of ART. This model encapsulated the short-term recall of missed doses and the long-term default frequency of ART clients to arrive at the observed / expected adherence level ratio; the expected doses being the theoretical number of doses to be taken from the first day of ART to the time of interview and the observed doses being the difference between the expected doses and the missed doses.Standard adherence levels derived from the model based on literature were 25% , 50% [2]The dose-adherence model complements other methods for deducing client's level of dose adherence by considering the long-term default frequency as an addition to the short-term recall of missed doses or self-report.


Arabidopsis with a special focus on their role in vascular development and functioning.In higher plants phloem and xylem are responsible for long-distance transport of water, nutrients, and signals that act systemically at short or long-distance to coordinate developmental processes. The formation of the plant vascular system is a complex process that integrates signaling events and gene regulation at transcriptional and posttranscriptional levels. Thanks to transcriptomic and proteomic analysis we start to better understand the mechanisms underlying the formation and the functioning of the vascular system. The role of the DNA-binding with one finger (Dof TFs), a group of plant-specific transcription factors, recently emerged as part of the transcriptional regulatory networks acting on the formation and functioning of the vascular tissues. More than half of the members of this TF family are expressed in the vascular system. In addition some of them have been proposed to be mobile proteins, suggesting a possible role in the control of short- or long-distance signaling as well. This review summarizes the current knowledge on Dof TFs family in  The gradual colonization of the land through plant evolution has been possible thanks to the differentiation of complex vascular tissues that provide mechanical support and allow long-distance transport of water and nutrients. In land plants, vascular tissues are comprised of two conducting tissues the phloem and the xylem, and intervening cambium that can generate the different conducting cell types  transcription factor has been identified in maize (ZmDof1) and was shown to be involved in light response and transcriptional regulation of genes involved in carbon metabolism AAAG-3′ core . Along plant evolution, Dof transcription factors might have originated from a common ancestor, likely represented by the single Chlamydomonas reinhardtii gene, and then expanded in the different taxonomic groups of vascular plants through recurrent duplication events  so far analyzed eight to nine Dof TF genes are found     present only in the phloem of infected plants allowed the identification of a virus promoter functional in plants  to confer phloem-specific expression   potentially expressed in vascular tissue at different step of its development.The mining of RNA profiling datasets at the resolution of the vascular tissue  and vascular cell type  , or through plasmodesmata in a short distance (between cell types)  are potential mobile transcription factor RNAs.In addition, cell-type specific expression maps from A direct experimental proof of the intercellular movement of a non-cell-autonomous Dof TFs has recently been brought by Chen et al.  who showDof genes have been found expressed in the phloem, there is so far no evidence for long-distance transport since neither RNAs nor Dof proteins have been found in transcriptome and proteome datasets of phloem sap ], a differentiation-promoting transcription factor of the vascular system , which shows a precocious formation of the interfascicular cambium and its subsequent cell division, Guo et al. cambium initiation and activity  are suspected to be involved in the control of the maintenance of the cambium and/or cambial activity by controlling the cell cycle , and while looking for direct targets of AtDof3.4/OBP1 several core cell cycle genes and transcription factors were identified , CONSTANS (CO), and FLOWERING LOCUS T (FT) genes  have been shown to be expressed in the vasculature throughout the plant and were shown to negatively regulate the transcription of CO  specific H+-sucrose symporter  . Altogether these data suggest that interactions between Dof TFs and TFs belonging to other families are theoretically possible. Experimentally, OBP1 was shown to directly interact with the promoter of a bZIP transcription factor but also with the promoter of a member of the same family AtDof2.3 (Zhang et al., Arabidopsis (Zhao et al., REVOLUTA have also been demonstrated (Kim et al., Arabidopsis vein formation (Gardiner et al., Structurally, like for other zinc fingers, the Dof domain is known to be a bi-functional domain that mediates not only DNA-binding but also protein–protein interactions (Yanagisawa, In the context of the vascular system development and functioning, which integrates a large variety of internal or external stimuli, regulators are needed to fine-tune the responses to changes in the environment. In this review, we present evidences that the Dof TFs family is likely to participate in such fine-tuning of the responses to the different stimuli in the vascular system. By modulating a variety of transcription factors, by protein-DNA and/or protein–protein interactions, the Dof TFs could therefore act at the cross-talk of various developmental pathways directly or indirectly linked to the vascular development and/or functioning. One of the next challenges, besides the functional characterization of the still undescribed Dofs TFs, will therefore be identifying the actors involved in an integrated regulatory network. Combination of the high-throughput data collection at the resolution of the vascular cell types and developmental stages as well as the use of the next generation sequencing technology will certainly allow identifying genes network regulating the fundamental features of the vascular development.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


There has been transition in the profile of health risks from traditional risks such as under nutrition and low sanitation towards modern risks such as obesity and overweight. This has resulted in a high burden of non-communicable diseases such as diabetes, cardiovascular diseases, cancers and chronic respiratory diseases. Cross sectional studies, case-control studies and randomised controlled trials have significant challenges in exposure assessments and studying their long-term effects with respect to non-communicable diseases. Cohort studies are ideal for the study of long term effects on NCD outcomes, to study temporal sequence of exposure and potential outcomes, to study changes in exposure and may allow nested case-control studies with prospective exposure assessment.Physical activity plays an important role in non-communicable diseases and despite the initial success, more evidence based advocacy is necessary. There are concerns whether the resolutions of the UN NCD summit can be implemented speedily and physical inactivity is not included in the first set of targets currently under discussion for WHO's monitoring framework. Better methods for quantification of levels of physical activity and assessment of different domains of physical activity are now available and more trans-cultural research in physical activity and health is necessary. Indo-Swiss partnership in this area assumes importance in the above context.