Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation of Balneolaceae as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new class Saprospiria from Chitinophagia. Epilithonimonas is nested within the older genus Chryseobacterium and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, Vitellibacter is proposed to be included in Aequorivita. Flexibacter is confirmed as being heterogeneous and dissected, yielding six distinct genera. Hallella seregens is a later heterotypic synonym of Prevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification of Bacteroidetes is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.The bacterial phylum  Bacteroidetes comprise bacteria widespread in the biosphere and isolated from many distinct habitats, including temperate, tropical and polar ecosystems saline environments only , whereas Cryomorphaceae mostly live in cold, marine environments  and gene cluster (polysaccharide utilization loci) transfer between environmental and gut Bacteroidetes  from the Bacteroidetes as the novel phylum Rhodothermaeota. Nevertheless, many unsatisfactory aspects of Bacteroidetes classification might still persist.g Woese, . Before chenbach . The anaIndeed, only monophyletic taxa can be accepted in a taxonomic classification because its purpose is to summarize the phylogeny of the classified organisms Hennig, , and genBacteroidetes, it is strongly recommended to include the G+C content especially when describing every species of Flavobacteriaceae  pilot phase as well as the One Thousand Microbial Genomes phase 1 (KMG-1) projects  What is the relationship between the phylogenomic trees and the proposed taxonomic classifications or the 16S rRNA gene phylogenies? (ii) Which taxa need to be revised because they are evidently non-monophyletic? (iii) Which taxon descriptions that lack G+C values should be augmented with information from genome sequences? (iv) Which taxon descriptions deviate from G+C content values calculated from genome sequences and should now be emended accordingly? (v) Does the correction of G+C values improve their fit to the phylogeny?The Genomic Encyclopedia of Bacteroidetes (ingroup), Chlorobi, Planctomycetes, and Verrucomicrobia (outgroup) type-strain genomes originating from the GEBA pilot phase and the KMG-1  number of identities within BLAST hits (high-scoring segment pairs) to the overall length of these hits and thus is unaffected by incomplete genome sequencing, and subjected to 100 pseudo-bootstrap replicates   calculation of the G+C content from genome sequences was done as in a previous study , based on the priority of the respective genus names. A comparable situation has been solved recently for the Ignavibacteriaceae  differ from Bacteroidetes by a considerable number of phenotypic characters. The large amount of phospholipids  found in Rhodothermus (and its relatives) is unusual for aerobic Bacteroidetes  rather than ester-linked polar lipids . Three branches with weak to moderate  support, respectively, would need to be wrong to obtain monophyletic Chitinophagia and Chitinophagales. The UCT and CCT show a distinct picture with a monophyletic Chitinophagia and Chitinophagales with 94–99% support under ML and <60–79% support under MP. Thus, regarding the monophyly criterion, it might or might not be adequate to place Saprospiraceae in Chitinophagales according to our analyses. The monophyly of the family itself, including the type genus Saprospira, is supported by the 16S rRNA gene trees with 95–100%. Thus, given its uncertain position relative to the remaining Chitinophagia and Chitinophagales, the taxonomic placement of Saprospiraceae should be reconsidered.With the y Figure  with theSaprospiraceae has been proposed first in Bergey's manual  that form long filaments (up to 500 μm) and do not possess sphingophospholipids. Moreover, the 16S rRNA gene trees indicate that the group comprising both Saprospiraceae and Chitinophagaceae . Lewinella, Saprospira and Aureispira exhibit gliding motility, but only Saprospira and Aureispira form helical filaments  tolerates up to 6% NaCl and 70°C  thrive in salt lakes and crystallizer ponds and grow at maximum temperatures of 50°C in medium with at least 5% NaCl and up to saturation  contain PG, but no glycolipids  with 99% support in the GBDP analysis. Flexithrix and Rapidithrix formed a clade with reasonable bootstrap support  in the UCT and CCT. Marivirga and Roseivirga did not form a clade either, with a conflicting branch supported by 94% in the GBDP tree. Because of their overall lower resolution, the 16S rRNA gene trees do not indicate in which of these three distinct groups of Flammeovirgaceae its type genus, Flammeovirga, is placed. For this reason, further revisions of Flammeovirgaceae have to be postponed until more genome sequences are available. Based on phylogenetic results , and Thermonema lapsum (Flammeovirgaceae) was used as an outgroup for the 16S rRNA gene sequence-based phylogeny. A similar set of strains was investigated in the description of the two other Marivirga species, M. lumbricoides , hence no taxonomic consequences will be undertaken in our study.Within s Figure , as all Butyricimonas and Odoribacter from Porphyromonadaceae to place them in the new family Odoribacteraceae  appeared paraphyletic because Pseudopedobacter saltans was placed as sister group of Pedobacter glucosidilyticus with 100% support and Pedobacter oryzae as sister group of Arcticibacter svalbardensis and Mucilaginibacter paludis with <50% support  appeared paraphyletic with high confidence in the phylogenomic tree because the clade comprising F. litoralis and F. roseolus (separated by long branches) occurred in clades with 77 and 99% support together with other genera, to the exclusion of F. elegans, which formed the sister group of Microscilla marina with maximum support , which was placed in an uncertain position. Apart from tree topology, the branch lengths in the whole-genome and 16S rRNA gene tree indicated that the Flexibacter species are too divergent to be placed in a single genus. Additionally, Microscilla marina and F. elegans appear to be too divergent to be placed in a single genus , but it was emphasized that Flexibacter is still heterogeneous and should be subdivided based on additional molecular taxonomic data   to obtain monophyletic groups. The solution to merge the two genera is thus more conservative. Moreover, the overall divergence of the clade comprising the two genera is lower than the divergence of other clades comprising only a single genus  appeared paraphyletic in the phylogenomic tree because Croceitalea dokdonensis was placed as sister group of M. lutaonensis. Support was weak (<60%), however, and in the UCT and CCT Croceitalea and Muricauda appear as separate groups with moderate support. Thus, even though in the description of the moderate thermophile M. lutaonens the genus Croceitalea was not considered  also appeared paraphyletic in the phylogenomic tree because two Vitellibacter species were placed as sister group of Aequorivita sublithincola with 94% support. In the UCT and CCT the clade comprising both genera is maximally supported, but within the clade the two genera are intermixed without much support. The genomic divergence of the clade comprising both genera appears as lower than the divergences of many clades that contain only a single genus  and Chlostridia are considered as halotolerant or halophilic Bacteria  or halotolerant   or halophilic .Our phylogenetic analysis revealed much agreement between genome-scale data and the current classification of ia Oren, . The recRhodothermaeota and Balneolaeota, but also of other groups reclassified here, it is likely that ecological studies using metagenomic binning or similar techniques will benefit from the further improved classification. Studies that do not distinguish between Rhodothermaeota, Balneolaeota, and Bacteroidetes may insufficiently describe microbial compositions of environmental habitats and perhaps make misleading assumptions on environmental conditions , and thus environmental studies using this probe are not influenced by the mentioned reclassifications.In other areas such as medicine and industry, the risk classification of a prokaryotic species to cause infectious diseases is based on its taxonomic classification ABAS, . Given tBacteroidetes species descriptions needs to be corrected. The according emendations proposed below are numerous but by no means excessive. Indeed, we do not propose to correct all G+C content values whose precision or accuracy could be improved but only those that are too imprecise or inaccurate given that the within-species deviation in G+C content is at most 1%  superphylum,” considering the recent proposal to include the phylum rank in taxonomy .Bal.ne.o.lae.o'ta  order of the phylum is The description is the same as given by Munoz et al.  with theBalneolia from the phylum Rhodothermaeota.This change was necessary due to the removal of Balneolia is part of the phylum Balneolaeota and has been additionally circumscribed on the basis of whole-genome phylogenetic analysis.The description is the same as given by Munoz et al.  with theBalneolia from the phylum Rhodothermaeota. The description is the same as for the order Balneolales.This change was necessary due to the removal of The description is the same as given by Nakagawa  with theBalneola from Cytophagia.This change was necessary due to the removal of Saprospira, type genus of the type order of the class, -ia ending to denote a class; N.L. fem. pl. n. Saprospiria, the class of the order Saprospirales).Sa.pros.pi'ri.a .Sa.pro.spi.ra'les .Le.wi.nel.la'ce.ae . Seawater is required for growth. Flexirubin-type pigments are not produced. Carotenoid-type pigments are produced. The respiratory quinone is MK-7. The genomic G+C content is around 45–53%.Cells are ensheathed, Gram-stain negative flexible rods (up to 3 μm) that form long filaments (up to 150 μm) and are motile by gliding. Typical fatty acids are iso-CBacteroidetes, order Saprospirales ord. nov., class Saprospiria class. nov., and currently comprises only the type genus, Lewinella.This family belongs to the phylum Haliscomenobacter type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Haliscomenobacteraceae the Haliscomenobacter family).Ha.lis.co.me.no.bac.te.ra'ce.ae . Typical fatty acids are iso-C15:0, summed feature 3 (either C16:1 ω7c/C16:1 ω6c or C16:1 ω7c/iso-C15:0 2-OH) and either iso-C17:0 3-OH or iso-C15:0 3-OH. Flexirubin-type pigments are not produced. Carotenoid-type pigments are produced. The respiratory quinone is MK-7. Cells are oxidase-positive. The genomic G+C content is around 47–54%.Cells are Gram-stain negative, non-motile long rods (up to 5 μm) that form long needle-like filaments (up to 300 μm). Some are enclosed by a narrow, hardly visible hyaline sheath , Phaeodactylibacter and Portibacter.This family belongs to the phylum Microscilla type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Microscillaceae the Microscilla family).Mi.cros.cil.la'ce.ae  and Eisenibacter gen. nov.This family belongs to the phylum Bernardetia type genus of the family; -aceae ending to denote a family; N.L. fem. pl. n. Bernardetiaceae the Bernardetia family).Ber.nar.de.ti.a'ce.ae , Hugenholtzia, and tentatively also Garritya.This family belongs to the phylum The description is the same as given by Munoz et al.  with the15:0 and other non-hydroxy branched-chain fatty acids. Major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and either phosphatidylglycerol  or phosphatidylcholine . The major menaquinone is MK-7. The genomic G+C content varies around 45%.Cells are non-motile or motile by means of flagella. The dominant fatty acids are iso-CThe description is the same as given by Munoz et al.  with the15:0, C18:1 ω7c, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c).Major polar lipids are diphosphatidylglycerol (cardiolipid) and diphosphatidylcholin. Some species possess halocapnines. The major fatty acids are iso-CThe description is the same as given by Ludwig et al.  with the16:0, iso-C17:0, anteiso-C17:0. The genomic G+C content varies around 65%.Major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major fatty acids are iso-CThe description is the same as given by Munoz et al.  with the15:0, with a low ratio of anteiso-C15:0 to iso-C15:0. The genomic G+C content varies around 40–50%.Cells are non-motile. Metabolism fermentative, major end products are diverse organic acids. Major menaquinones are MK-9 and MK-10. Major fatty acid iso-CThe description is as given by Krieg et al. , with thCells are long rods (up to 3.5 μm) that form long helical filaments (up to 500 μm) and are motile by gliding. NaCl is required for growth and some can be tolerate NaCl at a concentration of up to 9% (w/v). Cytochrome oxidase and catalase activities are variable. Flexirubin-type pigments are not produced. Carotenoid-type pigments are produced. The respiratory quinone is MK-7. The genomic G+C content is around 33–48%.Bacteroidetes, order Saprospirales ord. nov., class Saprospiria class. nov., and currently comprises the genera Saprospira (the type genus) and Aureispira.This family belongs to the phylum Bernardet named after Jean-François Bernardet, researcher at INRA Research Center, Jouy-en-Josas, France, and chairman of ICSP subcommittee on the taxonomy of aerobic Bacteroidetes; N.L. fem. n. Bernardetia a genus named after Jean-François Bernardet).Ber.nar.de'ti.a .B. li.to.ra'lis .Gar.ri'ty.a  species of the genus is Garritya polymorpha.On the basis of 16S rRNA gene sequence and phylogenomic analysis, the genus represents a separate branch within the order polymorpha, variable in form).G. po.ly.mor'pha .Hu.gen.hol'tzi.a .H. ro.se'o.la  species of the genus is Thermoflexibacter ruber.On the basis of 16S rRNA gene sequence analysis as well as previously published physiological and morphological data, the genus represents a branch of uncertain affiliation within the order rubra, red).T. ru'bra .Ei.se.ni.bac'ter  species of the genus is Eisenibacter elegans.On the basis of 16S rRNA gene sequence analysis as well as previously published physiological and morphological data, the genus represents a separate branch within the order E. e'le.gans .Flexibacter elegans  Reichenbach 1989b, 2067ALBasonym: Flexibacter elegans .A. aes.tu.a'ri.i .A. e.chi.no.i.de.o'rum .A. ni.o.nen'sis A. soe.sok.ka.ken'sis Vitellibacter vladivostokensis Nedashkovskaya et al. 2003Basonym: Vitellibacter vladivostokensis .C. gin.sen.gi.ter'rae Basonym: Epilithonimonas ginsengisoli .C. hal.per'ni.ae Basonym: Epilithonimonas lactis .C. psy.chro.to'le.rans. .C. te'nax .C. xi.xi.so'li (N.L. n. Epilithonimonas xixisoli Feng et al. 2014Basonym: Epilithonimonas xixisoli (Feng et al., The description is the same as for Flexibacter flexilis, as its known features, while scarce, already differentiate at the genus level.The description is the same as for the species Cytophagales, and must be separated from all other species formerly classified in Flexibacter. 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(Tenreiro et al., The description is as given by Zhang et al.  with theThe genome sequence-derived G+C content was reported earlier (Lang et al., The description is as given by Begum et al.  with theHK prepared genomic DNA. TW sequenced the genomes. MH, NI, NK, and SM annotated the genomes. JM and MG phylogenetically analyzed the data. MGL and MG collected the G+C content information. RH, MGL, and MG collected the phenotypic information. RH, JM, MGL, and MG interpreted the results. All authors read and approved the final manuscript.This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231. RH was supported by the German Bundesministerium für Ernährung und Landwirtschaft, grant No. 22016812 for Brian J. Tindall.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.


Dry socket is one of the most common complications that develops after the extraction of a permanent tooth, and its prevention is more effective than its treatment.Analyze the efficacy of different methods used in preventing dry socket in order to decrease its incidence after tooth extraction.A Cochrane and PubMed-MEDLINE database search was conducted with the search terms “dry socket”, “prevention”, “risk factors”, “alveolar osteitis” and “fibrynolitic alveolitis”, both individually and using the Boolean operator “AND”. The inclusion criteria were: clinical studies including at least 30 patients, articles published from 2005 to 2015 and written in English. The exclusion criteria were case reports and nonhuman studies.30 publications were selected from a total of 250. Six of the 30 were excluded after reading the full text. The final review included 24 articles: 9 prospective studies, 2 retrospective studies and 13 clinical trials. They were stratified according to their level of scientific evidence using SIGN criteria (Scottish Intercollegiate Guidelines Network).All treatments included in the review were aimed at decreasing the incidence of dry socket. Locally administering chlorhexidine or applying platelet-rich plasma reduces the likelihood of developing this complication. Antibiotic prescription does not avoid postoperative complications after lower third molar surgery. With regard to risk factors, all of the articles selected suggest that patient age, history of previous infection and the difficulty of the extraction are the most common predisposing factors for developing dry socket. There is no consensus that smoking, gender or menstrual cycles are risk factors.Taking the scientific quality of the articles evaluated into account, a level B recommendation has been given for the proposed-procedures in the prevention of dry socket. Key words:Dry socket, prevention, alveolar osteitis, risk factors. Dry socket is the most common complication following tooth extraction  and one Its incidence is approximately 3% for all routine extractions and can exceed 30% for impacted mandibular third molars , and manIt has been suggested that increased local fibrinolytic activity is the main etiological factor in developing dry socket. Increased in fibrinolytic activity could result in the premature loss of the intraalveolar blood clot after extraction . The fibThe treatment of alveolitis depends on each professional’s clinical experience  primarilThe Cochrane Collaboration published a review on local procedures for managing dry socket, and concluded there was no evidence to support any of the procedures should be included in its treatment .The aim of this systematic review is to analyze the different methods used for preventing dry socket. The following question emerged: what is the most effective method for preventing dry socket and reducing its incidence? In addition, would identifying the risk factors for dry socket reduce its incidence?A Cochrane and PubMed-MEDLINE databases search of articles was conducted between May 2015 and December 2015. The key words “dry socket”, “risk factors”, “alveolar osteitis” and “fibrynolitic alveolitis” were used. After that, the terms were combined using the Boolean operator “AND”, in order to obtain the articles that included two or more of the words used in the search.The inclusion criteria were clinical studies that included at least 30 patients published from 2005 to 2015 and written in English. The exclusion criteria were case reports and nonhuman studies.Articles were selected by one of the authors first reading the titles and abstracts and then reading the full text of the articles that met the inclusion criteria Fig. . The PRIThe complete texts of 30 articles were analyzed out of the 250 studies initially obtained from the search. Six of these 30 articles were excluded because they had no direct relationship with the subject and 24 relevant articles were finally selected to be included in our systematic review: 9 prospective studies, 2 retrospective studies and 13 clinical trials    Table , Table 2The articles we reviewed analyzed three different methods for preventing dry socket: chlorhexidine -23, antiThe concentration and formulation of chlorhexidine in preventing dry socket used 0.12%, 0.2% and 1% gel formulation -21,23 oret al.  one of the most studied medications, in 500 mg or 2 g doses. Bortoluzzi et al.  studied et al. , tetracyet al.  and topiet al. . It must  with another preventive method like eugenol (Alvogyl®) , the latet al. (With respect to antibiotic prescription, there is a consensus between the eight articles included in the review. Seven of them conclude that the prophylactic regimen is unnecessary, since it does not prevent dry socket. Even so, Halpern and Dodson  do descret al.  concludeet al. (Platelet-rich plasma may also have a preventive effect as well as being efficient in dry socket management . The twoet al.  points oIn relation to the other methods described for dry socket prevention, the results were diverse. Both warm saline mouth rinse  and abso- Risk factorset al. (Regarding dry socket risk factors, Chuang et al.  makes a et al. (These authors point out that the only modifiable factor is the pre- surgical infection site that could be inoculated with microorganisms from the external environment in the newly exposed socket after extraction . Partharet al.  goes on et al. (Another modifiable factor may be tobacco use, even though there is no clear data indicating a higher predisposition in smoking patients. Three articles ,43,45 deet al.  found siet al. , althougOnly Eshghpour and Nejat  describeet al. (et al. (With respect to the menstrual cycles and oral contraceptive use, Eshghpour et al.  found a  (et al.  did not  (et al. .et al. (et al. (Abu Younis et al.  believeset al. -45 suppoet al. . Parhasa (et al.  also poi (et al. .et al. (Professional experience was only analyzed in one article , showinget al.  were theOnly Oginni  states tet al. (Finally, with reference to age and gender as risk factors, all of the authors except Eshghpour and Nejat  describeet al.  found a Some limitations encountered during the review process were the lack of consensus in the preventive methods used in the articles included in the review, being the formulation and dosage of the method studied different in each article, and therefore their comparison was quite challenging. Also, the diversity of the risk factors considered in the articles included made it difficult to compare all the studies with accuracy.Chlorhexidine administration or platelet rich plasma reduce dry socket development. Antibiotic prescriptions do not have a preventive effect on postoperative inflammatory complications.Age, history of previous infection and difficulty of extraction are risk factors for developing dry socket and should therefore be taken into account by the clinician when carrying out the procedure. There is no consensus that tobacco use and menstrual cycles play a role in the development of dry socket.After the article’s analysis and according to their scientific quality, a level C recommendation is given to all the therapeutic procedures proposed for preventing dry socket.


The 2015 World Health Organization (WHO) Guidelines on when to start antiretroviral (ARV) therapy and on pre-exposure prophylaxis (PrEP) for HIV  have shoOn 8 June 2016, the UN General Assembly signed the political declaration on HIV and AIDS: on the fast-track to accelerate the fight against HIV and to end the AIDS epidemic by 2030 . To fulfDespite recent progress and these aspirational goals, actual roll-out at a global scale is just beginning, and considerable challenges remain unmet. The planning and organization of demonstration studies beyond MSM in the United States and the UK has been slow, and implementation-relevant information for both the general population and specific key populations  is still lacking. While concerns about adherence and effectiveness (particularly among MSM) have abated, some other issues have emerged, including 1) the preferred ARV agent, although tenofovir–emtricitabine is the only licensed agent at present; 2) potential of less frequent dosing, cost and sustainability (as much in lower-middle income as in higher-income countries); and 3) a long list of implementation questions that vary by setting and target population. The latter may make monitoring of impact and outcome more complex.NEMUS, in collaboration with UNAIDS, has followed its first supplement on PrEP beyond clinical trials  with thiet al. [A paper by Cáceres et al.  discusseet al. [The contribution by McGillen et al.  examineset al. [Also focusing on sub-Saharan Africa, Cowan et al.  state thet al. [A paper by Zablotska-Manos et al.  discusseet al. [Ravasi et al.  discuss et al. [® is a major barrier to PrEP implementation, together with inadequate health systems and a weakening civil society.The final regional paper by McCormack et al.  focuses et al. [This special issue includes three papers focused on specific populations. One contribution by Sevelius et al.  focuses et al. [® as daily PrEP in adolescents. A number of general and unique challenges have arisen in this age group. Prime among these is adherence to daily medication, which is particularly challenging among younger populations, but other individual level barriers  and structural challenges  are also described.Hosek et al.  focus onIn turn, Coleman and McLean  provide Finally, Cairns and Race  present Given the need presented in this series and the promise and potential of the clinical trials and recommendations from WHO, it is hoped that we will see an impressive expansion of combination prevention including PrEP in the next 2–5 years. With just 14 short years before the UNAIDS target to end AIDS by 2030, unless we urgently, actively and extensively deploy all of the effective interventions at our disposal, this goal will slip away from our grasp. No one should be left behind .


Pediatric femoral shaft fractures account for less than 2% of all fractures in children. However, these are the most common pediatric fractures necessitating hospitalization and are associated with prolonged hospital stay, prolonged immobilization and impose a significant burden on the healthcare system as well as caregivers. In this paper, the authors present a comprehensive review of epidemiology, aetiology, classification and managemement options of pediatric femoral shaft fractures. Pediatric femoral shaft fractures are uncommon, constituting less than 2% of all fractures in children; yet they are a significant burden on healthcare systems and families as they are the most common fractures requiring hospitalization in children , 2. Theset al. ..1) [44].External fixator application is associated with complications manifold -48. The Fixator removal is usually done after 3-4 months when bridging callus is noted in at least 3 of the 4 cortices on AP and lateral views. An alternative strategy (“portable traction”) is to remove fixator at around 6-8 weeks when early callus is noted and to apply a walking spica. This method minimises stress shielding and allows pin tracts to ossify with the spica acting as a protective splint .ii)Developed by the Nancy group in France , 59 in t2) [et al. [The preferred technique for insertion of these nails is a retrograde technique with 2 small incisions  just above the distal femoral physis  . Antegra2) . The dia2) . During 2) , 60, 63.2) , 60, 63. [et al.  observedComplications include excessive shortening which leads to nail protrusion and limb length discrepancy. The most common complication is pain or skin irritation at the nail insertion site caused by a prominent nail end , 66. HigAntegrade vs retrograde insertion of flexible nails• et al. [Frick et al.  conducteet al. .et al. [et al. demonstrated that given satisfactory cortical starting points in the distal fragment, retrograde insertion provides greater stability [Mehlman et al.  conductetability .Steel vs titanium flexible nails• et al. [et al. [Wall et al.  compared [et al.  it was n [et al. .Flexible interlocked nailing• et al. [Linhart and Roposch  describeet al.  reportedet al. .et al. [Ellis et al.  conducteet al. .3), which has reduced the chances of osteonecrosis, the use of rigid intramedullary nails in adolescents is on the rise again [Rigid intramedullary nails initially fell out of favour compared to flexible intramedullary nails as these nails had a piriformis entry and hence were associated with avascular necrosis (AVN) of the femur head and with injuries to the growth plate leading to growth arrest . Howeverse again , 87.Current literature suggests that rigid intramedullary nail with a trochanteric entry point is the preferred mode of fixation of shaft femur fractures in adolescents . Howeveriii)Pediatric trauma surgeons have largely moved away from the traditional open reduction and compression plating to the more modern submuscular bridge plating which offers stability without disturbing the vascularity of the fracture fragments hence leading to early union.4) [Submuscular bridge plating provides excellent stability; it is especially useful in the management of proximal/distal fractures that are not suitable for IM nailing/external fixation  , 94. Thi4) -100.Femoral shaft fractures in children are amongst the commonest fractures necessitating hospitalization. The major determinant of treatment modality is age of the child. Fractures in children below 6 years of age can be managed non-operatively with excellent outcomes. Elastic stable intramedullary nails are preferred for children < 11 years of age or those with body weight < 50 kg with a length stable transverse or short oblique fracture. Length unstable fractures and fractures at the proximal ends of femur may be managed by submuscular plating or external fixation. For children above 11 years of age or those with body weight > 50 kg, rigid intramedullary nailing or submuscular plating is preferred. Piriformis fossa entry nails should be avoided to prevent the complication of avascular necrosis of femoral head.The authors confirm that this article content has no conflicts of interest.


The aim of this study was to compare the shear bond strength of a self-adhering flowable composite (SAFC) and resin-modified glass ionomer (RMGI) to mineral trioxide aggregate (MTA) and calcium-enriched mixture (CEM) cement. A total of 72 acrylic blocks with a central hole (4 mm in diameter and 2 mm in depth) were prepared. The holes were filled with MTA (sub group A) and CEM cement. The specimens of both restorative materials were divided into 6 groups; overall there were 12 groups. In groups 1 and 4, SAFC was used without bonding while in groups 2 and 5 SAFC was used with bonding agent. In all these groups the material was placed into the plastic mold and light cured. In groups 3 and 6, after surface conditioning with poly acrylic acid and rinsing, RMGI was placed into the mold and photo polymerized. After 24 h, the shear bond strength values were measured and fracture patterns were examined by a stereomicroscope. Data were analyzed using the two-way ANOVA and student’s t-test.P=0.008 and 0.00, respectively). In both materials, RMGI had the lowest shear bond strength values (2.25 Mpa in MTA and 1.32 Mpa in CEM). The mean shear bond strength were significantly higher in MTA specimen than CEM cement (P=0.003). There was a significant differences between fracture patterns among groups (P=0.001). Most failures were adhesive/mix in MTA specimen but in CEM cement groups the cohesive failures were observed in most of the samples. The use of bonding agent significantly increased the shear bond strength of FC to MTA and CEM cement (The bond strength of self-adhering flowable composite resin to MTA and CEM cement was higher than RMGI which was improved after the additional application of adhesive. Following traumatic injuries or restorative procedure, normal dental pulp exposure may occur inadvertently. In this situation, vital pulp therapy (VPT) is performed by placing the direct pulp capping biocompatible materials to maintain the health and vitality of dental pulp . It is oCalcium-enriched mixture (CEM) cement is suggested biocompatible pulp capping material produced to overcome the drawbacks of MTA . These bet al. [et al. [et al. [After VPT a definite leakage free restoration  should be used. Different studies showed that acid etching before composite build up and nature of solvent in the adhesives may influence the mechanical properties and bond strength of pulp covering agent to composite resin , 9. Hashet al.  also demet al. . Oskoee  [et al.  and Ajam [et al.  showed tet al. [Vertise Flow  is a self-adhering flowable composite which combines an all-in-one adhesive system and a flowable composite for a step-less system . The preet al.  revealedThere is no information on the adhesion of SAFC to MTA or CEM cement. Therefore, the purposes of this study was to determine the shear bond strength of SAFC alone and in conjunction with a self-etch adhesive to MTA and CEM cement and also compare it with RMGI cement. The null hypothesis was that there would be no differences between the bond strength values in different study groups.n=36). RootMTA  and CEM  were mixed according to their manufacturers’ instructions. The pastes were poured into the holes in the center of acrylic blocks, flattened with a spatula, covered with a moist cotton pellet and temporary filling materials . Then, the specimens were stored for 72 h at 37°C temperature and 100% humidity. After storage, the temporary materials and cotton pellets were removed without interfering with the surfaces of the pulp capping materials. Then, the specimens of each material were divided into the six groups (n=12). In this study, 72 acrylic blocks  were with a central hole measuring 4 mm in diameter and 2 mm in depth. The samples were divided into two groups  for 40 sec. In groups 1 and 4, after air drying of the specimen, the SAFC  was actively applied directly over MTA or CEM with no adhesive. The SAFC was placed into the plastic mold with 3 mm diameter and 2 mm height in one increment. Then the SAFC was light cured with light density 600 mw/cm In groups 2 and 5, after air drying of the specimen, Opti-Bond all-in-one adhesive  was actively applied on the surfaces with a brush and after air thinning, was light cured for 20sec. Then SAFC was subsequently applied to the conditioned surfaces, similar to the previous groups.In groups 3 and 6, the surfaces of pulp capping agents were conditioned with 10% poly acrylic acid  for 20 sec, then rinsed for 30 sec and air dried. After that, the powder and liquid of RMGI  was mixed according to the manufacturer’s instructions; the paste was placed into the plastic mold and light cured for 40 sec similar to above mentioned groups.°C temperature for 24 h. After that, the plastic molds were carefully removed from the specimen before the shear bond strength test.The prepared specimens were kept in 100% relative humidity at 37The specimens were mounted in the universal testing machine  and shear forces were applied at the crosshead speed of 0.5 mm/min until the fracture occurred. The maximum loads at failure were recorded in Newton and were then converted into the Mps.The fractured specimens were observed under a stereomicroscope under 40× magnification to determine the failure mode. The failure types were categorize as adhesive , cohesive (any deficiency in the pulp capping agent surface) and mixed (combination the adhesive residue and deficiency in the pulp capping surfaces).The two-way ANOVA analysis was applied to determine the interaction effect between the experimental groups and if it was applicable, the post hoc comparison and t-test was used to compare the shear bond strength results among groups. Also, the chi-square and Fissure’s exact test were used to compare the fracture surface pattern between groups. The level of significance was set at 0.05.P=0.008, 0.000, respectively). In both pulp capping agents, RMGI had the lowest shear bond strength values (P=0.05). For all intermediate materials in this study, the mean shear bond strength values were significantly higher in MTA than CEM; however, these difference was not obvious in RMGI than other intermediate materials (P=0.003). There were a significant difference between fracture patterns between groups (P=0.001). Most failures in MTA specimens were adhesive/mix, but in CEM cement specimens, the cohesive failure was the predominant mode of fracture except for RMGI materials which adhesive failures were also observed. All groups showed significant differences with CEM/SAFC with no bonding ( bonding .The results of our study showed that SAFC (with or without application of adhesive) had superior bond strength compared to RMGI, either over MTA or CEM cement. The null hypothesis was rejected, because the bond strength changed in relation to adhesive application and filling materials. More researches have shown that, both MTA and CEM cement can be used effectively as pulp capping agents because they have the ability to stimulate the differentiation of dental pulp stem cells to odontoblast like cells and ultimately initiate the formation of dentinal bridge which is thicker, less porous along with less pulp inflammation than the calcium hydroxide material , 16, 17.In this study, we used SAFC as an intermediate material before permanent composite restoration over Root MTA or CEM cement. The SAFC used in this experiments a novel flowable resin based composite that eliminates the etching, priming and bonding steps in order to simplify the adhesive procedures to dentin and enamel . et al. [et al. [et al. [vs. self-etch) did not have a significant effect on the shear bond strength of composite resin to pulp capping biomaterials [et al. [The results of our study demonstrated that surface treatment with an all-in-one adhesive before SAFC significantly increased the shear bond strength of SAFC to Root MTA and CEM cement. It was in consistent with the results of the study by Tuloglu et al. . Also, t [et al.  showed t [et al. . However [et al.  indicateaterials , 22. Kay [et al. , evaluat [et al. , 23. In  [et al. . In our  [et al. . Thus, iet al. [As mentioned previously, the additional application of self-etching bonding would enhance the shear bond strength of SAFC to MTA and CEM cement. However, the results were in argue with Yesilyurk et al.  who concet al. . In our et al. . This faet al. .et al. [et al. [In this study, SAFC had significantly higher mean of shear bond strength values than RMGI for both MTA and CEM cement. This results were contrary to the results reported by Ajami et al.  that sho [et al.  revealedet al. [et al. [According to the manufacturers, SAFC used in this study consists of phosphate functional monomer (GPDM) which may interact with the calcium ions . Both MTet al.  revealed [et al.  reported [et al. , 31. In  [et al. . Bond st [et al. . Because [et al. . Furtherin vitro study, it was found that the application of a self-etch adhesive improves the bond quality of Vertise Flow to MTA and CEM cement. Moreover, the bond strength of Vertise Flow was significantly greater than resin-modified-glass ionomer in both materials. All materials had significantly higher bond strength in MTA group than CEM cement after 72 h setting.Within the limitation of this


The microbial biofilm is an important factor for human infection. Finding effective antimicrobial strategies should be considered for decreasing antimicrobial resistance and controlling the infectious diseases. Treatment of infected canal systems may not be able to remove all bacteria and so bacterial persistence after treatment may occur. Application of antibacterial nanoparticles may be a potential strategy to improve the elimination of bacteria from the canal. Furthermore, mechanism of action and applications of photodynamic therapy and Photon-induced photoacoustic streaming (PIPS) and GentleWave system was reviewed. Different anatomy and complexities of the canal, in addition to dentin composition, are key challenges for effective disinfection in endodontics . AntimicIn order to overcome the limitations of ordinary root canal irrigants and medicaments, using nanoparticles to disinfect the canal system has been proposed.Antibacterial nanoparticles (NPs) Nanomaterial denotes a natural or manufactured material containing unbound particles in which half or more of the particles in number and size is in the size range of 1-100 nm . These mThe electrostatic interaction between negatively charged bacterial cells and positively charged NPs, and also accumulation of increased number of NPs on the cell membrane of the bacteria have been associated with the loss of membrane permeability and unsuitable membrane function . Enterococcus faecalis biofilm comparing camphorated phenol and chlorhexidine (CHX) gluconate [in vitro study showed that nanosilver gel is not efficient enough against Enterococcus faecalis; however, triple antibiotic paste and CHX gel showed better antibacterial activity than calcium hydroxide (CH) and so can be used as an alternative medicaments in endodontic treatment [et al. [Enterococcus faecalis and showed that silver NPs with CH has a significant inhibitory effect on the biofilm of Enterococcus faecalis. Antibacterial NPs show a broad spectrum of antimicrobial activity. According to Vier and Figueiredo , 10 metaluconate . An in vreatment . Zhang e [et al.  assessedet al. [et al. [in vitro study showed that adding silver NPs to MTA and CEM increased their antibacterial activity [et al. [Enterococcus faecalis and concluded that it may exhibit strong antibacterial activity against planktonic Enterococcus faecalis and better residual inhibition effects against Enterococcus faecalis growth on dentin than CH.Barreras et al.  indicate [et al.  showed tactivity . Fan et  [et al.  investigAntimicrobial photodynamic therapy (APDT) APDT is a two-step procedure that involves the application of a photosensitizer, followed by light illumination of the sensitized tissues, which would generate a toxic photochemistry on target cells, leading to killing of microorganisms -20. Nowaet al. [et al. [et al. [Enterococcus faecalis with the optical fiber is better than when the laser light is applied directed at the access cavity. APDT may be combined with the usual mechanical instrumentation and chemical antimicrobials , 22. Garet al.  compared [et al.  evaluate [et al.  also shoet al. [Enterococcus faecalis. They concluded that NaOCl was the most effective in Enterococcus faecalis elimination, while Er:YAG laser also resulted in great decrease in viable counts. The use of both commercial APDT systems resulted in a weak reduction in the number of bacteria. The worth option was Nd:YAG irradiation.Meire et al.  comparedEnterococcus faecalis. The volume of damage on these targets is influenced by the photosensitizer solvent used during APDT. Soukos et al. [Enterococcus faecalis (53%). William et al. [Peptostreptococcus micros, Streptococcus intermedius, Fusobacterium nucleatum and Prevotella intermedia, and concluded that PAD killed these bacteria at statistically significant levels compared to controls.According to George and Kishen , 28, APDs et al.  conductem et al.  measuredet al. [Effect of PAD on bacterial endotoxins has also been studied. Endotoxin, a part of the cell wall of gram-negative bacteria, is composed of lipids, polysaccharides, and proteins and is referred to as lipopolysaccharide -33. Shreet al.  evaluatePhoton-induced photoacoustic streaming (PIPS)PIPS is based on the radial firing stripped tip with laser impulses of subablative energies of 20 mJ at 15 Hz for an average power of 0.3W at 50 μs impulses. These impulses induce interaction of water molecules with peak powers of 400W. This creates successive shock waves leading to formation of a powerful streaming of the antibacterial fluid located inside the canal, with no temperature rising , 36.Unlike the conventional laser applications, the unique tapered PIPS tip is not mandatory to be placed inside the canal itself but rather in the pulp chamber only. This can reduce the need for using larger instruments to create larger canals so that irrigation solutions used during treatment can effectively reach to the apical part of the canal and also canal ramifications. This procedure can effectively remove both vital and nonvital tissues, kill bacteria, and disinfect dentin tubules , 38.et al. [et al. [via PIPS and 6% NaOCl has great effect in inhibiting Enterococcus faecalis. Peters et al.  showed t [et al.  concludeet al. [in vitro biofilm and showed an improved cleaning of the infected dentin on PIPS groups when compared to the PUI group. The extraordinary result from this study was the fact PIPS tip was placed 22 mm away from the target area, while sonic, ultrasonic, and passive irrigation were made at the exact target area. Jaramillo et al. [versus 100% disinfection on PIPS, with a total of 1 min of irrigation with the same solution. Alshahrani et al. [Ordinola et al.  evaluateo et al.  showed 8i et al.  also shoin vitro study, Zhu et al. [et al. [In an u et al.  compared [et al.  showed tGentlewave irrigation Gentlewave (GW)  system aims to clean the root canal through generation of different physiochemical mechanisms including a broad spectrum of sound waves. Multisonic waves are initiated at the tip of GentleWave™ handpiece, which is positioned inside the pulp chamber . It deliet al. [et al. [et al. [According to Haapasalo et al.  the GW Set al. . Accordi [et al. , the GW  [et al. . In a mu [et al.  reportedRecent advances in root canal disinfection using new technology and on the basis of recent studies may improve the ability to disinfect the root canal system. However, conventional methods are still helpful for obtaining good prognosis.


In addition, Parkinson’s disease comprised only 3.2% of our cohort of 1363 post mortem brains [et al. [Substantia nigra, despite not being directly sampled. If the mtDNA variants we detected were contributing to the pathogenesis of neurodegeneration, we would have expected to see a difference between diseases cases and controls. If mtDNA mutations are contributing to cell loss, then one might even expect to see a reduction in the mutation burden in affected tissue - but this was not the case in our study (including DLB-PD, Fig. 3 & Supplementary Fig. 12 in Wei et al. [et al. [As Simon ur study  was not m brains . However [et al. , and are [et al. .et al., point out, they have shown that neurons containing mtDNA mutations are present in early and pre-clinical Lewy body disorders [Substantia nigra, and is not just an innocent bystander in a toxic cellular environment at a particular phase of the disorder.As Simon isorders , thus deisorders  (and bee


Apple trees are often subject to severe salt stress in China as well as in the world that results in significant loss of apple production. Therefore this study was carried out to evaluate the response of apple seedlings inoculated with abuscular mycorrhizal fungi under 0, 2‰, 4‰ and 6‰ salinity stress levels and further to conclude the upper threshold of mycorrhizal salinity tolerance.− and Na+ concentrations clearly increased and K+ contents obviously decreased in non-mycorrhizal roots in comparison to mycorrhizal plants, this caused mycorrhizal plants had a relatively higher K+/Na+ ratio in root. In contrast to zero salinity level, although ascorbate peroxidase and catalase activities in non-inoculated and inoculated leaf improved under all saline levels, the extent of which these enzymes increased was greater in mycorrhizal than in non-mycorrhizal plants. The numbers of survived tree with non-mycorrhization were 40, 20 and 0  on the days of 30, 60 and 90 under 4‰ salinity, similarly in mycorrhization under 6‰ salinity 40, 30 and 0  respectively.The results shows that abuscular mycorrhizal fungi significantly increased the root length colonization of mycorrhizal apple plants with exposure time period to 0, 2‰ and 4‰ salinity levels as compared to non-mycorrhizal plants, however, percent root colonization reduced as saline stress increased. Salinity levels were found to negatively correlate with leaf relative turgidity, osmotic potential irrespective of non-mycorrhizal and mycorrhizal apple plants, but the decreased mycorrhizal leaf turgidity maintained relative normal values at 2‰ and 4‰ salt concentrations. Under salt stress condition, ClThese results suggest that 2‰ and 4‰ salt concentrations may be the upper thresholds of salinity tolerance in non-mycorrhizal and mycorrhizal apple plants, respectively.The online version of this article (doi:10.1186/s40529-014-0070-6) contains supplementary material, which is available to authorized users. Generaet al. ). Under et al. ). In add [et al. ).Malus × domestica Borkh.) is one of the most valuable horticultural fruit crops in the world. Although it produces the highest yield in China, it is not a halophyte species and sensitive to salinity, therefore it is subject to severe salt stress in many areas . To dea [et al. ; Bouksil [et al. ). Thoughet al. [et al. [et al. [et al. [et al. [et al. [et al.  fungi are associated with the roots of over 90% of terrestrial plant species . Many iet al. ; Mena-Vi [et al. ; Miransa [et al. ). Munns  [et al. ) demonst [et al. ; Marulan [et al. ). AM col [et al. ; Harisna [et al. ; He et a [et al. ). Althou[et al.  tested At present, few researches focus on mechanisms in mycorrhizal apple plants to alleviate salt stress. Therefore, this study is undertaken to identify the potential interaction between AM fungi and apple plants in salinity environment and further to define the upper threshold of mycorrhizal salinity tolerance of apple seedlings.Malus hupehensis Rehd. root stock) with trunk diameter of 0.7 cm and height of 50 cm. The selected mycorrhizal inoculum of Glomus versiforme consisted of 15 isolated spores per milliliter and was provided by Qingdao Agricultural University, Shandong Province, China. It was derived from pot culture prepared with Trifolium repens L. grown in 1:9 sterilized soil-sand and contained colonized pieces of root, soil and spores.Experimental plants were one-year-old Red Fuji apple seedlings (3 in volume), each filled with 25 kg of brawn soil sterilized at 121°C for 2‰hours and its chemical properties were as followings: organic matter 7.64‰g kg−1, available nitrogen 24.36‰mg kg−1, available phosphorus 3.17 mg kg−1, available potassium 61.24‰mg kg−1, salinity 0.093‰ and pH 7.2 . In the transplantation process, in order to assure a rapid colonization the root systems of AM treatment were uniformly sprinkled with 100 ml Glomus versiforme inoculum. Counterparts of non-AM treatment were received volumetric sterilized soil-sand free of spores. After apple seedlings survived, the pots were watered with 1000 ml saline solution every 15 days throughout the experiment, fresh water was added as necessary to make up for losses by evaporation or transpiration. Determination was conducted at 30, 60 and 90 days after salt treatment.The experimental design consisted of four treatments with four salinity levels , each treatment involved in 10 non-AM inoculated and 10 AM inoculated plants and replicated six times. Apple seedlings were transplanted in plastic pots . Leaf pet al.  and proet al. . Catalaet al.  respecttion (Lu ). The ostion (Lu ). Leaf rtion (Lu ).LeafrelLSD (least significant difference) test at the 0.05 probability level.All experiments were repeated as indicated. Values presented are means. The effects of the treatments were tested by one-way analysis of variance (ANOVA). Means were compared between the treatments using the In non-mycorrhizal plants root length colonization rate was always zero, however, mycorrhizal plants presented a trend in increase in percent root colonization at zero, low (2‰), moderate (4‰) and high (6‰) salinity levels. Table Under no saline condition, leaf relative turgidities in non-mycorrhizal and mycorrhizal plants remained a comparative steady-state level from 53.75% to 54.56% throughout the experiment Figure A. As salThere were similar trends between non-mycorrhizal and mycorrhizal plants in increase in ascorbate peroxidase and catalase activities under different salt stress levels, nevertheless the increase rate was higher in mycorrhizal plants as compared to non-mycorrhizal plants Figure A, B. The- and Na+ in plant root, regardless of non-mycorrhizal and mycorrhizal plants, but the extent of which they raised was diverse. When apple trees were stressed under zero salt level, the Cl- and Na+ contents in non-mycorrhhizal and mycorrhizal roots ranged from about 0.08 to 0.09 g kg-1 at 30 and 60 days, but they increased to 0.1272 and 0.093 g kg-1 at 90 days, respectively. With an increasing salinity stress level and exposure time period to salinity stress, the increase rates of Cl- and Na+ concentration in non-mycorrhhizal plants were apparently higher than in mycorrhizal plants. Compared to non-mycorrhizal plants, K+ concentrations in mycorrhizal roots slightly increased under zero salt level and were obviously higher under moderate and high salinity stress. Due to lower Na+ concentration and higher K+ concentration in mycorrhizal roots in comparison to non-mycorrhhizal roots, therefore ratios of K+ to Na+ ions in roots were higher than in non-mycorrhizal plants.Table Results in Figure The finding that AM fungi inoculation with apple seedlings could improve salt tolerance of host plants under stress condition is very important information for saline areas in China as well as in the world. These results evidence that, to reduce the unfavorable effects of salinity on apple plant growth, the use of AM inoculation ought to be considered as biological method to alleviate salinity stress.et al. [et al. [et al. [et al. [Root length colonization rate is an important indicator suggesting plants become mycorrhizal. In the present study root colonization rate was found to negatively correlate with salinity stress. This conclusion is consistent with previous report that soil salinity can affect AM fungi by slowing down root colonization, spore germination (Juniper and Abbott ). Howeveet al. ; Yamato  [et al. ; Peng et [et al. ). The di [et al. ).+ and Cl- ions bind water that is needed to be mobilized by the plants . In they et al. ; Kothari [et al. ). In our [et al. ). The fu [et al. ).et al. [There is accumulating evidence that production of reactive oxygen species is a major damaging factor in plants exposed to different environmental stresses, including salinity . Result- and Na+, because NaCl was used to develop a salinity gradient. Root Cl- and Na+ concentrations were lower in mycorrhizal than in non-mycorrhizal plants under given salinity conditions, resulting from dilution effects due to growth enhancement by AM fungi colonization . In thii et al. ). The nui et al. ). The redhalter  Maintenn et al. ). The coThe data in survived apple seedlings verifies that 4‰ and 6‰ salt concentration were the limits of salinity tolerance in non-mycorrhizal and mycorrhizal apple seedlings, respectively. This further confirmed that AM fungi increased salinity tolerance of mycorrhizal apple seedlings as compared to non-mycorrhizal counterparts exposed to salinity stress.+/Na+ ratio, the number of survival and induced antioxidant enzymes, but the extents of which they responded to salinity stress were not the completely same. 2‰ and 4‰ salt concentrations may be the upper thresholds of salinity tolerance in non-mycorrhizal and mycorrhizal apple plants, respectively.In conclusion, non-mycorrhizal and mycorrhizal apple seedlings existed similar performances with respect to salinity stress such as reduced leaf turgidity, osmotic potential, K


Nanoporous anodic alumina (NAA) has become one of the most promising nanomaterials in optical biosensing as a result of its unique physical and chemical properties. Many studies have demonstrated the outstanding capabilities of NAA for developing optical biosensors in combination with different optical techniques. These results reveal that NAA is a promising alternative to other widely explored nanoporous platforms, such as porous silicon. This review is aimed at reporting on the recent advances and current stage of development of NAA-based optical biosensing devices. The different optical detection techniques, principles and concepts are described in detail along with relevant examples of optical biosensing devices using NAA sensing platforms. Furthermore, we summarise the performance of these devices and provide a future perspective on this promising research field. Recently, the combination of different optical techniques  with sensing platforms based on nanomaterials has received notorious attention. These nanostructures can confine, guide, transmit and enhance optical signals when they interact with light, as well as working as containers capable of accommodating and immobilising analyte molecules in a selective manner. This has enabled the design and development of ultra-sensitive optical biosensing systems for a broad range of analytes and applications  . Amid th) [etc.) . Further) [etc.) .In this scenario, this review is aimed at compiling and summarising the most relevant advances and developments of optical biosensors based on NAA. First, we will introduce a brief description of the fabrication process of NAA and the different electrochemical approaches used to develop optical platforms based on NAA. Second, we will describe the most relevant and recent developments of optical biosensing systems based on NAA, providing a detailed description about their sensing principles, performances and practical applications. Finally, we will provide a prospective outlook on this field.etc.). Since the first decades of the 20th century, this electrochemical process has been intensively used for a broad range of industrial applications, including surface finishing, automobile engineering, machinery, corrosion protection, and so on [2O3)) featuring close-packed arrays of hexagonally arranged cells containing a cylindrical nanopore at the centre, which grows perpendicularly to the underlying aluminium substrate (2SO4), oxalic (H2C2O4) or phosphoric acids (H3PO4), in which both electrodes, the anode ) and cathode ), are immersed  and dissolution  throughout the anodisation process. First, aluminium oxide grows at the aluminium-alumina interface, due to the countermigration of ionic species  through the oxide barrier layer. Second, Al2O3 is dissolved at the alumina-electrolyte interface. This electrochemical process can be described by the following reduction-oxidation  equations:(i)Formation of alumina )(ii)Dissolution of alumina )(iii)Diffusion of aluminium cations (within oxide barrier layer (anode))(iv)Hydrogen evolution (electrolyte-cathode interface (cathode))NAA is produced by electrochemical anodisation of aluminium in different acid electrolytes  evolve throughout the anodisation process. For this reason, the experimental anodic current efficiency is always lower than 100%.i.e., from 3 to 8 µm·h−1) and exponentially decreasing and fast in the HA regime . Pore geometry in NAA can be defined by such structural parameters as pore diameter (dp), pore length (Lp) and interpore distance (dint)  or hard anodisation (HA) regimes ,12,13,14e (dint) a. These  decades . In thati.e., Al3+ and O2−) across the aluminium-alumina interface, the alumina barrier layer and the alumina-electrolyte interface [i.e., HO− and O2−) from the bulk electrolyte to the reaction interface  [i.e., the longer the pore length, the slower the mass transport of oxygen-containing anionic species from the bulk electrolyte to the reaction interface)  . This phterface) b.2O3) contaminated with impurities incorporated into the NAA structure from the acid electrolyte during the anodisation process. The latter, however, is basically composed of pure Al2O3. Nevertheless, it is worth stressing that, as other studies have pointed out, the real chemical structure of NAA is composed of more than two chemical layers. For instance, Yamamoto et al. [i.e., close to the central pore) to the inner one .As for its chemical structure, NAA presents an onion-like structure distributed in a layered fashion . Previouo et al.  analysedo et al. . We founi.e., pore diameter, pore length and interpore distance) and its chemical composition . Therefore, the fabrication conditions and the structural design of the NAA structure become crucial factors to produce optical sensing platforms based on NAA with enhanced capabilities for biosensing applications.The optical properties of NAA are directly related with its pore nanoporous structure  [3PO4 0.4 M at 110 V and 10 °C for 15 min. Next, the acid electrolyte was replaced by an aqueous solution of H2C2O4 0.015 M, and the anodisation voltage was set to 137 V. The electrolyte temperature was kept at 0.5 °C during this anodisation step to prevent NAA from burning. The time length of this step was 2 min. Highly uniform periodic modulations of the pore diameter in NAA were obtained by repeating this procedure. Notice that, in this process, the interpore distance in both layers  remains constant due to the anodisation voltages being set to yield the same interpore distance in the MA and HA conditions. This prevented NAA from pore branching. The pore diameter of each segment was established by the acid electrolyte and the anodisation voltage, while the length of each segment was controlled by the anodisation time, making it possible to modulate the pore diameter in depth. This work was the origin of a flood of studies about different electrochemical approaches to generate pore diameter modulations in NAA [Electrochemical approaches aimed at producing pore diameter modulations in NAA have been intensively researched due to the interesting optical properties of the resulting NAA structures. The most widespread method used to generate pore diameter modulations in NAA is to switch the anodisation regime from MA and HA in an alternating fashion a. Pore d latter) . In thiss in NAA ,21,22.etc.) in order to engineer the effective medium of NAA in depth [et al. [et al. [et al. [et al. [et al. [Multilayered NAA structures consist of stacks of layers of NAA featuring different levels of porosity ,31,32,33in depth ,31,32,33 [et al.  reported [et al.  demonstri.e., an integrated current passed through the system), the pore diameter in that segment is engineered by the pore widening time. This enables the structural engineering of the nanoporous structure of NAA in depth and the replication of nanostructures based on different materials with optical properties. For example, He et al. [et al. [et al. [et al. [et al. [i.e., linear cones, whorl-embedded cones, funnels, pencils, parabolas and trumpets) by the fabrication parameters  within distances of several hundreds of nanometres. Therefore, any change in the effective medium inside the NAA matrix can be quantified. As a result of its outstanding capabilities, SPR is one of the most widespread analytical methods used to detect biological events . This technique is capable of monitoring any dynamic change in the effective medium of NAA in real time and in situ. Furthermore, a suitable design of the nanoporous structure of NAA makes it possible to confine and guide light and to minimise scattering losses, which are key parameters to develop optical systems with enhanced sensitivity [et al. [et al. [et al. [et al. [et al. [SPR is an optical technique based on the generation of surface plasmons by an evanescent electromagnetic wave, which takes place when light is shined on the surface of a prism coated with metal. Typically, this system is implemented in a Kretschmann configuration, where an NAA layer is grown by anodising a thin aluminium film grown on the prism . The plasitivity . Figure  [et al.  combined [et al. , who cha [et al. . In this [et al.  used a S [et al.  engineer [et al.  deposite6 of the Raman signal from molecules adsorbed onto the surface of a metal substrate with nanometric roughness, known as “hot spots” or “hot junctions”. SERS is an ultra-sensitive technique able to detect, identify and quantify trace amounts of analyte molecules. NAA has been demonstrated to be an excellent platform to develop SERS substrates, due to its organised nanostructure and cost-competitive and scalable fabrication process. Typically, SERS-NAA platforms are fabricated by sputtering or evaporating metals, basically gold and silver, on the top or bottom surface of NAA substrates, although other options, such as embedded nanowires, decorative nanoparticles and metallic membranes, have been explored, too. As a result of its versatility in terms of geometry, SERS-NAA platforms can be broadly engineered by the anodisation parameters and the metal deposition conditions to provide optimised SERS signals for specific sensing applications. SERS-NAA platforms featuring gold or silver nanoparticles on their surface have been demonstrated to provide strong Raman signal enhancements of up to the order of 106.Surface-enhanced Raman scattering (SERS) is a surface-sensitive optical technique that enhances Raman scattering by molecules adsorbed on rough metal surfaces or nanostructures. The most likely mechanism that explains the enhancement effect of SERS is associated with the excitation of localised surface plasmons. Nevertheless, the real mechanism of SERS is still a matter of debate. The SERS effect is translated into an enhancement of the order of 10et al. [et al. [3)2+. The size and density of silver nanoparticles was tuned to optimise SERS signals. The sensing performance of this SERS-NAA platform was assessed by detecting p-aminothiophenol. A point-by-point SERS mapping of this analyte on the NAA platform was acquired to characterise the homogeneity of the adsorbed molecules. Ji et al. [et al. [i.e., the distance between adjacent nanowires in the NAA matrix) was assessed when detecting 4-aminobenzenethiol. They found that the SERS intensity signal can be increased over 200-fold when the interwire gap distance is reduced from 35 to 10 nm. Another type of SERS-NAA platform was developed by Valleman et al. [et al. [For instance, Ko et al.  decorate [et al.  used sili et al.  used a s [et al.  grew siln et al. , who car [et al.  decorate+ centres associated with ionised oxygen vacancies in the amorphous structure of NAA [et al. [Although the photoluminescence (PL) properties of NAA were reported several decades ago and extensive studies have been carried out since then, their origin is still in doubt ,70,71. Ie of NAA ,73,74. P [et al.  used PL-et al. [et al. [i.e., by changing the effective medium). These PL-NAA platforms have been tested with success for detecting biological substances, such as organic dyes, enzymes and glucose ; where neff is the effective refractive index of NAA; Lp is the pore length; and m is the order of the RIfS fringe; the maximum of which is located at the wavelength, λ. These RIfS peaks are the base of label-free optical biosensors capable of monitoring in real time and in situ binding events of biomolecules. These can be detected through changes in the effective optical thickness of NAA, which are translated into shifts in the RIfS peak positions [et al. [et al. [et al. [Reflectometric interference spectroscopy (RIfS) is a highly sensitive optical sensing technique based on the interaction of white light with thin films . In the ositions ,79. Thesositions ,82. For  [et al.  demonstr [et al.  reported [et al.  develope [et al. . This de [et al. .et al. [et al. [et al. [et al. [et al. [i.e., refractive index). The obtained results were validated by a theoretical model , demonstrating that the control over the nanoporous structure makes it possible to optimise optical signals in RIfS for biosensing applications.Dronov et al.  develope [et al. , who com [et al.  have pre [et al.  demonstr [et al.  demonstret al. [in vitro drug release techniques performed under static conditions.Notice that RIfS-NAA platforms not only can be used to monitor binding events between analyte molecules and surface functional groups, but also to study the release of molecules from NAA platforms. Kumeria et al.  used thietc.) make them an outstanding and promising alternative to widely used porous silicon platforms. NAA is a highly attractive nanomaterial for developing a broad range of optical biosensing systems for clinical, industrial and environmental analyses. NAA can be structurally engineered to provide complex nanostructures with optimised optical properties. Furthermore, this material can be modified with desired functionalities to endow optical biosensors with high selectivity towards target analytes. It is expected that further development and progress in structural and chemical modifications of NAA will enable the development of innovative optical sensing systems based on NAA, featuring up-to-the-minute capabilities. Finally, this review has demonstrated that there is still an excellent opportunity for further advances and developments of optical sensing systems based on NAA, in particular through further miniaturisation and integration into lab-on-chip systems for real-life applications.This review has summarised recent progress in the use of NAA platforms to develop optical biosensing systems. We have presented in detail the fundamental aspects of each optical technique used in combination with these nanoporous platforms and provided relevant concepts and examples of devices based on different optical sensing principles. As these studies have demonstrated, the key features of NAA platforms (e.g., cost-competitive and scalable fabrication process, well-defined and versatile nanoporous structure, chemical and physical stability, optical activity,


Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between the individuals in a population. It is an important source of genetic variation in an individual which is now being utilized rather than single nucleotide polymorphisms (SNPs), as it covers the more genomic region. CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs). Earlier, researchers extensively utilized SNPs as the main source of genetic variation. But now, the focus is on identification of CNVs associated with complex traits. With the recent advances and reduction in the cost of sequencing, arrays are developed for genotyping which cover the maximum number of SNPs at a time that can be used for detection of CNVRs and underlying quantitative trait loci (QTL) for the complex traits to accelerate genetic improvement. CNV studies are also being carried out to understand the evolutionary mechanism in the domestication of livestock and their adaptation to the different environmental conditions. The main aim of the study is to review the available data on CNV and its role in genetic variation among the livestock. The copy number variants (CNVs) are a structural variation in the genome of an individual in the form of losses or gains of DNA fragments. CNV is an important source of genetic and phenotypic variation . Union oNon-allelic homologous recombination (NAHR), non-homologous end-joining (NHEJ), fork stalling and template switching (FoSTeS), and L1-mediated retro transposition are some of the mechanisms which generate rearrangements in the genome and possibly account for the majority of CNV formation ,6. NAHR SNP arrays are being used normally for CNV detection and analysis in humans because of its availability and economic feasibility . In geneIt is a Hidden Markov Model (HMM) algorithm which integrates multiple parameters such as LRR, BAF, the population frequency of the B allele (PFB) of SNPs, the distance between neighboring SNPs and the allele frequency of SNPs -27. It iCnvPartition is based on a different proprietary sliding window approach which detects CNVs by processing LRR and BAF. Only those homozygous deletion events segregating in different animals were reported by this algorithm due to concern quality calls .The cn.MOPS (Mixture of PoissonS) algorithm is based on the Bayesian approach for the detection of CNV in multiple samples for NGS data. It decomposes read variations across multiple samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. The advantages of using this method are- it identifies overlapping sequences and estimates allele-specific copy numbers .QuantiSNP uses different HMMs unlike PennCNV. QuantiSNP uses both LRR and BAF frequency independently whereas in pennCNV treat them as combined. It uses a fixed rate of heterozygosity for each SNP .It is a python package for CNV detection on whole exome sequencing data from amplicon-based enrichment technologies. This program uses SDe termed as experimental variability, in the LRR distribution .et al. [taurine cattle is higher than the overlap between taurine and indicine cattle. Largest CNV diversity was reported among the zebu cattle [Upadhyay et al.  using thet al. ,35,36. Iu cattle .et al. [indicine and African taurine cattle breeds than in European taurine using Vst for population differentiation which indicates the breed divergence and population history. Pezer et al. [et al. [Recent studies reported that CNVs evolved 2.5 folds faster than SNPs and helped to promote a better adaptation in different environments . Liu et et al.  reportedr et al.  suggeste [et al.  in their [et al. . Differeet al. [indicine than in African groups and taurine breeds. This observation may suggest the independent domestication events of cattle in Europe, Africa, and Southeast Asia [et al. [et al. [et al. [Hou et al.  reportedast Asia ,41. Hou  [et al.  using ar [et al.  identifi [et al. . Bae et  [et al.  also ide [et al. -37,42-46 [et al. ,16,47-52et al. [BTG3, PTGS1, and PSPH) which are involved in the fetal muscle development, prostaglandin (PG) synthesis, and bone color. Ma et al. [et al. [Yang et al.  identifia et al.  identifi [et al.  using a  [et al. .et al. [Fontanesi et al.  identifiet al. . Differeet al. .et al. [Copy number variants account for about 1-3% of the horse genome and mostly of intragenic than those located in intergenic regions . Ghosh eet al.  using 40et al. [Chicken has a unique genome arrangement due to the presence of micro- and macro-chromosome . Griffinet al.  first stet al. ,58. Receet al. , 59-66.et al. [CATHL4) in the Nellore cattle sample, but these genes were found only in a single copy in human and mice. CNV overlapping with KIT gene was found to be associated with color-sidedness in English Longhorn cattle [et al. [MTHFSD and GTF2I in the CNVRs. Yoshida et al. [et al. [CIITA gene that showed nematode resistance in Angus cattle. MTHFSD gene covering the CNVR1206 found to be associated with milk protein yield in Spanish HF cattle [et al. [MSH4 gene was found to be associated with impaired gamete formations in laboratory mice and recombination rate in cattle [et al. [Bickhart et al.  reportedn cattle . Severaln cattle . Upadhya [et al.  found gea et al.  found th [et al.  found thF cattle . Reyer e [et al.  found GTn cattle , 70, 71. [et al.  suggesteASIP) gene, the itchy E3 ubiquitin protein ligase homolog (mouse) (ITCH), and the adenosylhomocysteinase (AHCY) loci [et al. [ORAOV1 gene in Rhodesian and Thai Ridgeback dogs which is responsible for characteristic dorsal hair ridge. A different pattern of white coat color was reported due to the duplication of the KIT gene in pig and in some cattle breeds [The dominant white coat in sheep is associated with duplication of 190 kb genomic fragment which encompasses three genes viz. the agouti signaling protein (CY) loci . Hillber [et al.  identifie breeds .et al. [et al. [BTG3, PTGS1, and PSPH) in diverse sheep breeds which were involved in fetal muscle development, PG synthesis, and bone color.GO analysis and functional studies in sheep reported that many CNVRs are associated with genes related to environmental response and biological functions . Liu et et al.  indicateet al. . Yang et [et al.  found seAKR1C gene may be a possible cause of disorders of sexual development such as male-pseudohermaphroditism due to its role in testicular androgen production and sexual development [et al. [CSMD1 gene which encodes for a transmembrane and a candidate tumor suppressor protein [A homozygous deletion in the elopment . GO analelopment . Ghosh e [et al.  confirme protein .SOX5 transcription factor interferes with SOX5 expression, and the regulation of gene expression is critical during cell differentiation for the development of the comb and wattles [et al. [PRLR and SPEF2 genes [et al. [SOX6 gene in chicken also has a similar function as reported in many species for the proliferation and differentiation of skeletal muscle cells. SOX6 gene expression is positively correlated with the number of CNV for CNP13 region in the chicken genome.Duplication of segment of DNA at intron 1 non-coding region of the  wattles . Luo et  [et al.  suggesteF2 genes . Lin et  [et al.  suggesteRecent studies for CNV detection have enabled the construction of CNV map which in turn helps in identification of CNVs associated with economically important traits. With the advancement in the techniques and reduced cost of sequencing, researchers are now focusing on the CNV study for detecting the genetic variations, as CNV shows more inclusions and complex genetic variants than SNP sites. Current research for the identification of the CNV regions (CNVRs) throughout the genome in domestic species will change the concept of breeding for genetic improvement. Development of robust and convenient CNV detection techniques could further facilitate unveiling of genetic secrets for molecular breeding of poultry and other farm animals.MP conceptualized and designed the manuscript. BV, SC, and MP prepared manuscript draft and reviewed. CR contributed in literature collection. MP, DRP, and KA edited and made critical comments on the manuscript. MP and BV made critical comments on the revised manuscript and edited for final submission. All authors read and approved the final version.