bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variational Inference of Population Structure in Large SNP Datasets
Authors: Raj Anil , Stephens Matthew , Pritchard Jonathan K. 
Published: December 2013

AbstractTools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a dataset and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data, and illustrate using genotype data from the CEPH-Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias towards detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online athttp://pritchardlab.stanford.edu/structure.html.
U2AF1mutations alter splice site recognition in hematological malignancies
Authors: Ilagan Janine O. , Ramakrishnan Aravind , Hayes Brian , Murphy Michele E. , Zebari Ahmad S. , Bradley Philip , Bradley Robert K. 
Published: December 2013

AbstractWhole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3′ splice site recognition factor U2AF1 alter its normal role in RNA splicing. We find thatU2AF1mutations influence the similarity of splicing programs in leukemias, but do not give rise to widespread splicing failure.U2AF1mutations cause differential splicing of hundreds of genes, affecting biological pathways such as DNA methylation (DNMT3B), X chromosome inactivation (H2AFY), the DNA damage response (ATR, FANCA), and apoptosis (CASP8). We show thatU2AF1mutations alter the preferred 3′ splice site motif in patients, in cell culture, andin vitro. Mutations affecting the first and second zinc fingers give rise to different alterations in splice site preference and largely distinct downstream splicing programs. These allele-specific effects are consistent with a computationally predicted model of U2AF1 in complex with RNA. Our findings suggest thatU2AF1mutations contribute to pathogenesis by causing quantitative changes in splicing that affect diverse cellular pathways, and give insight into the normal function of U2AF1’s zinc finger domains.
Analysis of the study of the cerebellar pinceau by Korn and Axelrad
Authors: Blot Antonin , Barbour Boris 
Published: December 2013

AbstractThe axon initial segment of each cerebellar Purkinje cell is ensheathed by basket cell axons in a structure called the pinceau, which is largely devoid of chemical synapses and gap junctions. These facts and ultrastructural similarities with the axon cap of the teleost Mauthner cell led to the conjecture that the pinceau mediatesephaptic(via the extracellular field) inhibition. Korn and Axelrad published a study in 1980 in which they reported confirmation of this conjecture. We have analysed their results and show that most are likely to be explained by an artefactual signal arising from the massive stimulation of parallel fibres they employed. We reproduce their experiments and confirm that all of their results are consistent with this artefact. Their data therefore provide no evidence regarding the operation of the pinceau.
Granulocyte and monocyte adsorption apheresis for Behçet's disease in a pregnant woman
Authors: Higashi Yuko , Shimokawa Mitsuyoshi , Kawai Kazuhiro , Kanekura Takuro 
Published: December 2013

AbstractWe present a 39‐year‐old pregnant woman with Behçet's disease who was treated successfully with granulocyte and monocyte adsorption apheresis (GMA). There were no complications or adverse effects during her pregnancy and delivery. The neonate manifested no abnormalities.
Case of immunoglobulin G4‐related skin disease: Possible immunoglobulin G4‐related skin disease cases in cutaneous pseudolymphoma only by immunohistochemical analysis
Authors: Iwata Yohei , Mizoguchi Yoshikazu , Takahashi Masayuki , Tanaka Beni , Kuroda Makoto , Yagami Akiko , Matsunaga Kayoko 
Published: December 2013

AbstractImmunoglobulin G4‐related disease (IgG4‐RD) is a newly recognized disease characterized by elevated serum IgG4 levels, tissue infiltration rich in IgG4+ plasma cells. We report on a case which was first considered as pseudolymphoma from the histopathological analysis, but finally diagnosed as IgG4‐related skin lesions. As the morphological features of cutaneous involvement of IgG4‐RD are consistent with those of cutaneous pseudolymphoma, we tried immunostaining past potential cases of IgG4‐RD. Thirty‐two skin specimens (15 men and 17 women; mean age, 53 years) diagnosed as having pseudolymphoma were retrieved from the archives to conduct hematoxylin–eosin, IgG and IgG4 staining. Out of the 32 cases of cutaneous pseudolymphoma, germinal center formation was seen in 22 cases, and moderate–severe fibrosis was seen in seven cases. Eleven cases showed more than 10 IgG4+ plasma cell infiltration/high‐power field, and among these 11 cases, seven cases (22%) showed A ratio of IgG4+/IgG+ cells of more than 40%. Thus, out of the 32 cases of cutaneous pseudolymphomas, two cases (6.3%) satisfied IgG4‐RD histopathological diagnostic criteria. As clinical presentations and histopathological features of skin involvement of IgG4‐RD are analogous to cutaneous B‐cell pseudolymphoma, careful identification is required through systemic examination, serum IgG4 measurement and other means.
Supporting Insurance in European Agriculture: Experience of Mutuals in the Netherlands
Authors: Meuwissen Miranda P.M. , Assefa Tsion Taye , van Asseldonk Marcel A.P.M. 
Published: December 2013

SummaryThe Common Agricultural Policy currently allows the support of agricultural insurance, with a particular focus on mutuals. This article analyses the experience of mutuals in the Netherlands over the past 20 years. A total of nine mutuals are reviewed, some operating on a purely private basis, others receiving some form of public support. Results illustrate that mutuals are well equipped to insure risks that are uninsurable in the commercial market. This is especially true for animal and crop disease risks. Mutuals are furthermore able to fulfil the EU conditions for receiving premium support hence opening up the opportunity for farmers to insure against multi‐peril weather risks. Experience has however demonstrated that mutuals are not always successful, even with substantial public support. Lack of members caused several mutuals to be discontinued only a few years after their foundation. In order to secure the benefits of mutuals, it is shown that there is a need to carefully balance size of risk, affordability of premiums, financial robustness and solidarity. These issues are even more important in the case of mutuals providing income stabilisation tools as these have the added responsibility of data and (classified) market information management.
A New Era in the European Union: Time to Reform the Cyprus National Food Safety System
Authors: Hadjigeorgiou Andreas 
Published: December 2013

SummaryThis article critically examines the current National Food Safety System (NFSS) of Cyprus and identifies its main shortcomings related mainly to duplication and overlapping of food safety responsibilities between competent agencies. Although food supply in Cyprus is generally safe, the country does not have a single and independent National Food Safety Authority (NFSA), but a multi‐level, fragmented system divided among several ministries and governmental agencies based on different food inspection tasks. On the contrary, the European Union (EU) and the majority of EU Member States have re‐organised their systems and established stand‐alone authorities at the central or national level. Within this context, the limitations and strengths of a proposed draft law for the establishment of a Cyprus NFSA embedded in the current environment of economic crisis are also discussed. Finally, the findings of a population‐based survey, which was carried out to determine the beliefs and attitudes of interested parties (regular consumers, food business operators and public service directors or head officers) concerning the operation of the NFSS in Cyprus, are presented. The findings are highlighted in relation to the different practices employed in the EU Member States to rebuild their corresponding NFSS.
Management of benign biliary strictures with a novel retrievable self‐expandable metal stent
Authors: Hu Bing , Leung Joseph W , Gao Dao Jian , Wang Tian Tian , Wu Jun 
Published: December 2013

ObjectiveEndoscopic placement of covered self‐expandable metal stent (SEMS) has gained popularity in the management of benign biliary strictures (BBS). The existing SEMS has been designed primarily to palliate malignant biliary obstruction and has a high frequency of stent migration, difficulty in retrieval and stricture recurrence after stent removal. This study aimed to design a novel retrievable SEMS dedicated to the treatment of extrahepatic BBS and evaluate its clinical efficacy and safety.MethodsA short fully covered SEMS (FCSEMS) with a retrieval lasso was designed for the specific treatment of BBS. A total of 45 patients with segmental extrahepatic BBS were included in this study. The stent was placed entirely inside the bile duct with only the retrieval lasso extending from the papilla. The stents were recommended to be in situ for 6 to 12 months before removal.ResultsThe FCSEMS was successfully placed in all 45 patients. In all, 33 patients had their FCSEMS successfully removed after a mean period of 8.6 ± 3.7 (range 2–15.5) months. Stent migration occurred in 9.1% of the patients. During a mean follow‐up of 18.9 months after stent removal, recurrent stricture was found in 2 (6.1%) patients and was successfully treated with a second FCSEMS. Overall, the strictures resolved in 30/33 (90.9%) patients.ConclusionsIntraductal placement of a short FCSEMS is suitable for the treatment of segmental extrahepatic BBS. This new removable design offered prolonged stenting and drainage for BBS for up to one year with minimal complications.
Incidence of clinically silent malrotation detected on barium swallow examination in children
Authors: Atkin Karen L , Chowdhury Moti M , Bartlett Murray 
Published: December 2013

AbstractIntroductionDuodenojejunal flexure (DJF) orientation is often examined routinely during contrast swallow studies, including those performed for purely oesophageal queries. We examine the radiation burden and the incidence of malrotation in patients undergoing contrast swallow, without clinical suspicion for malrotation.MethodsTwo hundred eighteen consecutive contrast swallow studies were reviewed. Patients whose history may potentially suggest malrotation were identified (n = 90), and remaining children were grouped based on whether DJF was examined (Group 1; n = 88) or not (Group 2; n = 40). Data extracted include demographics, radiographic parameters (dosage, screening time, number of images obtained) and examination findings. Outcome measures comprised: (i) prevalence of clinically incidental malrotation; and (ii) influence of additional evaluation of DJF on patient dosage (mean ± SEM).ResultsMalrotation was identified in 2 of 90 patients (2.2%) examined with clinical indications for possible malrotation, but none in Group 1 (13% already had normal DJF confirmed on previous examinations). Groups 1 and 2 were comparable with respect to age and gender (P = ns). Additional evaluation of DJF (Group 1) meant that 54% more images were acquired (48.5 ± 2.9 vs. 31.4 ± 3.4 images in group 2; P = 0.0002) and 24.9% increased screening time (130.8 ± 9.3 vs. 104.7 ± 13.0 seconds in group 2; P = 0.089), resulting in 32.6% increased patient dosage (1.36 ± 0.21 vs. 1.02 ± 0.16 microGym2/kg in group 2; P = 0.19).ConclusionsThis study highlights the increased radiation exposures involved with routine screening for DJF position in those patients without clinical suspicion of malrotation, and raises questions about the validity of this practice; however, further research is needed.
Role of 3D sonohysterography in the investigation of uterine synechiae/asherman's syndrome: Pictorial assay
Authors: Ahmadi Firoozeh , Javam Maryam 
Published: December 2013

SummarySeveral imaging methods have been applied for evaluation of suspected uterine synechiae; however, sonohysterography is yet recognised as a valid and accurate modality. Performing three‐dimensional (3D) imaging along with sonohysterography enables evaluation of the uterus in the coronal plane to detect and grade the adhesions that characterise this condition. Thus, 3D sonohysterography is a minimally invasive and cost‐effective tool for investigating suspected synechiae and is particularly useful when the transvaginal sonography findings are normal.
Access to Finance Thresholds and the Finance‐Growth Nexus
Authors: Abdmoulah Walid , Jelili Riadh Ben 
Published: December 2013

Based on Aghion et al. (), this article provides new insights regarding whether financial development can affect economic growth non‐linearly by adopting the concept of threshold effects. The empirical approach adopted in this article allows for the finance‐growth relationship to be piecewise linear with a set of indicators including access to finance acting as a regime‐switching trigger. Using cross‐country observations from 144 countries stretching from 1985 to 2009, strong evidence of threshold effects in finance‐growth link is found. It is suggested that financial development in general, and access to finance in particular, is among the important forces contributing to cross‐country (non)‐convergences in growth rates.
Mesenchymal Stem Cells Seeded on Cross‐Linked and Noncross‐Linked Acellular Porcine Dermal Scaffolds for Long‐Term Full‐Thickness Hernia Repair in a Small Animal Model
Authors: Mestak Ondrej , Matouskova Eva , Spurkova Zuzana , Benkova Kamila , Vesely Pavel , Mestak Jan , Molitor Martin , Pombinho Antonio , Sukop Andrej 
Published: December 2013

AbstractBiological meshes are biomaterials consisting of extracellular matrix that are used in surgery particularly for hernia treatment, thoracic wall reconstruction, or silicone implant‐based breast reconstruction. We hypothesized that combination of extracellular matrices with autologous mesenchymal stem cells used for hernia repair would result in increased vascularization and increased strength of incorporation. We cultured autologous adipose‐derived stem cells harvested from the inguinal region of Wistar rats on cross‐linked and noncross‐linked porcine extracellular matrices. In 24 Wistar rats, a standardized 2 × 4 cm fascial defect was created and repaired with either cross‐linked or noncross‐linked grafts enriched with stem cells. Non‐MSC‐enriched grafts were used as controls. The rats were sacrificed at 3 months of age. The specimens were examined for the strength of incorporation, vascularization, cell invasion, foreign body reaction, and capsule formation. Both materials showed cellular ingrowth and neovascularization. Comparison of both tested groups with the controls showed no significant differences in the capsule thickness, foreign body reaction, cellularization, or vascularization. The strength of incorporation of the stem cell‐enriched cross‐linked extracellular matrix specimens was higher than in acellular specimens, but this result was statistically nonsignificant. In the noncross‐linked extracellular matrix, the strength of incorporation was significantly higher in the stem cell group than in the acellular group. Seeding of biological meshes with stem cells does not significantly contribute to their increased vascularization. In cross‐linked materials, it does not ensure increased strength of incorporation, in contrast to noncross‐linked materials. Owing to the fact that isolation and seeding of stem cells is a very complex procedure, we do not see sufficient benefits for its use in the clinical setting.
Twentieth century shifts in abundance and composition of vegetation types of theSierraNevada, CA,US
Authors: Dolanc Christopher R. , Safford Hugh D. , Dobrowski Solomon Z. , Thorne James H. 
Published: December 2013

AbstractQuestionsHas tree density changed consistently across vegetation types? Do changes in component species correspond with changes across vegetation types? Do patterns of changes suggest potential drivers of change?LocationNorthern two‐thirds of theSierraNevada,CA,USA, ca. 45 000 km2.MethodsUsing two data sets that cover the span of elevations and land jurisdictions in the study area, we classified 4321 historical plots and 1000 modern plots into nine broad groups of vegetation types that are widely used by land managers and researchers in the region. We compared tree density and composition between historical and modern plots across and within these nine types.ResultsIn the modern data set, tree density was significantly higher in eight of nine vegetation types. Total density was significantly higher in modern plots for all west slope types, especially for montane hardwood, where modern forests are 128% denser, and mixed conifer forests, which are 69% denser. Relative density of component species was also very different between data sets in these forests, and suggests a shift in dominance toward shade‐tolerant conifers and evergreen oaks. Fire suppression is likely a driving factor in these types but density was also significantly higher in high‐elevation types such as sub‐alpine forest (+20%), where neither fire suppression nor logging have had major impacts on structure. East slope forest types (eastsideP. jeffreyiforest and piñon‐juniper woodland) were very similar in both modern and historical data sets, with no significant differences in density or composition.ConclusionWest slope forest types, especially montane hardwood and mixed conifer forest, appear the most altered types of the mountain range. These types are more productive but have also been subject to greater disturbance than high‐elevation and east slope forest types. Climate change may also be driving changes across the study area. Species such asQuercus chrysolepisandCalocedrus decurrens, which have each increased markedly in abundance, appear well positioned to dominate in the near future, especially under continued fire suppression and a warmer climate.
Restoration dynamics evaluation by vegetation mapping and transition matrix modelling: analysis of 20 yr of restoration and management at the megalithic site of Carnac (Brittany, France)
Authors: Gallet Sébastien , Sawtschuk Jérôme 
Published: December 2013

AbstractQuestionThe main aim of this study is to consider how long‐term spatial vegetation surveys can be optimized via a simple quantitative statistical model to assess, and potentially predict, restoration success. How can modelling be used as a decision‐making tool?LocationThe study was conducted in the megalithic site of Carnac (Brittany, France). Due to over‐frequentation (more than 500 000 visitors·yr−1) and lack of adapted management, the vegetation (heathlands and grasslands) of the site, which constitutes not only the framework of the monument, but also an essential protection for archaeological soils, was highly damaged during the 1980s. In order to initiate restoration of the vegetation, the whole site was fenced at the beginning of the 1990s, and a management plan (including vegetation management and frequentation control) was initiated in 2001.MethodsThe site has been mapped (with the same methodology) in 1985 (before enclosure), 1997 (5 yrs after fencing), 2006 (after 5 yrs of management plan application) and in 2012. GIS analysis and transition matrix modelling were used to describe vegetation dynamics changes in both time and space. Restoration trajectories were considered in two specific parts of the study site, which are analysed both together and separately in order to show potential spatial heterogeneity in vegetation dynamics.ResultsThe matrices approach underlined the heterogeneity of restoration process within the study site. The restoration process leads to the establishment of a complex of grassland with a potential dynamic toward broom thicket in one area, and to a heathland complex in the other area. These differences are needed to refine restoration goals, first defined as heathland for the whole site.ConclusionsThe matrix approach used on vegetation maps allows a more precise description of restoration processes than analysis only based on the evolution of the extent of each vegetation type. It notably includes the spatial heterogeneity of vegetation dynamics at site scale. It provides large data sets for qualitative assessment of restoration operations, and could potentially be used to build up prediction models. Indeed, maps, which are one of the main survey methods used in natural areas management, can offer much scientific knowledge for research in restoration ecology.
HarnessingSDandCSRwithin Corporate Self‐regulation of Weak Economies— A Meta‐regulation Approach
Authors: Rahim Mia Mahmudur 
Published: December 2013

AbstractThe semantic of the terms “sustainable development” and “corporate social responsibility” have changed over time to a point where these concepts have become two interrelated processes for ensuring the far‐reaching development of society. Their convergence has given dimension to the environmental and corporate regulation mechanisms in strong economies. This article deals with the question of how the ethos of this convergence could be incorporated into the self‐regulation of businesses in weak economies where nonlegal drivers are either inadequate or inefficient. It proposes that the policies for this incorporation should be based on the precepts of meta‐regulation that have the potential to hold force majeure, economic incentives, and assistance‐related strategies to reach an objective from the perspective of weak economies.
Ignorance and historical geographies of Aboriginal exclusion: Evidence from the 2007 Bouchard‐Taylor Commission on Reasonable Accommodation
Authors: Schaefli Laura M. , Godlewska Anne M.C. 
Published: December 2013

AbstractIgnorance is linked to colonialism and is deeply implicated in the maintenance of unequal social relations. The authors theorize ignorance as structural and self‐interested, and undertake a geographically sensitive analysis of Quebec's 2007 Bouchard‐Taylor Commission to demonstrate how ignorance of Aboriginal realities works strategically to sustain unequally occupied rhetorical and material space. The Bouchard‐Taylor Commission was a public inquiry into Quebec citizens' opinions on the degree to which cultural difference should be accommodated in the province. Through both geographic decisions about where to hold public meetings and in its very mandate, the Commission restricted participation to Quebecers of French‐Canadian descent and immigrants of long and more recent standing. The authors analyze how the law, and ignorance of how it applies to Aboriginal peoples, was mobilized by the Commissioners to create a space from which Aboriginal peoples could be excluded, and highlight the continuity of this strategy with past debates over Quebec identity. The case of the Bouchard‐Taylor Commission demonstrates how ignorance operates in highly sophisticated and often readily justifiable ways to uphold settler interests.