bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prioritising candidate genes causing QTL using hierarchical orthologous groups
Authors: Warwick Vesztrocy Alex , Dessimoz Christophe , Redestig Henning 
Published: July 2018

AbstractMotivationA key goal in plant biotechnology applications is the identification of genes associated to particular phenotypic traits (for example: yield, fruit size, root length). Quantitative Trait Loci (QTL) studies identify genomic regions associated with a trait of interest. However, to infer potential causal genes in these regions, each of which can contain hundreds of genes, these data are usually intersected with prior functional knowledge of the genes. This process is however laborious, particularly if the experiment is performed in a non-model species, and the statistical significance of the inferred candidates is typically unknown.ResultsThis paper introduces QTLSearch, a method and software tool to search for candidate causal genes in QTL studies by combining Gene Ontology annotations across many species, leveraging hierarchical orthologous groups. The usefulness of this approach is demonstrated by re-analysing two metabolic QTL studies: one in Arabidopsis thaliana, the other in Oryza sativa subsp. indica. Even after controlling for statistical significance, QTLSearch inferred potential causal genes for more QTL than BLAST-based functional propagation against UniProtKB/Swiss-Prot, and for more QTL than in the original studies.Availability and implementationQTLSearch is distributed under the LGPLv3 license. It is available to install from the Python Package Index (as qtlsearch), with the source available from https://bitbucket.org/alex-warwickvesztrocy/qtlsearch.Supplementary informationSupplementary data are available at Bioinformatics online.
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations
Authors: Tang Haiming , Finn Robert D , Thomas Paul D 
Published: July 2018

Abstract

Summary
TreeGrafter is a new software tool for annotating protein sequences using pre-annotated phylogenetic trees. Currently, the tool provides annotations to Gene Ontology (GO) terms, and PANTHER family and subfamily. The approach is generalizable to any annotations that have been made to internal nodes of a reference phylogenetic tree. TreeGrafter takes each input query protein sequence, finds the best matching homologous family in a library of pre-calculated, pre-annotated gene trees, and then grafts it to the best location in the tree. It then annotates the sequence by propagating annotations from ancestral nodes in the reference tree. We show that TreeGrafter outperforms subfamily HMM scoring for correctly assigning subfamily membership, and that it produces highly specific annotations of GO terms based on annotated reference phylogenetic trees. This method will be further integrated into InterProScan, enabling an even broader user community.

Availability and implementation
TreeGrafter is freely available on the web at https://github.com/pantherdb/TreeGrafter, including as a Docker image.

Supplementary information
Supplementary data are available at Bioinformatics online.
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics
Authors: Sun Chen , Medvedev Paul 
Published: July 2018

Abstract

Motivation
Genotyping a set of variants from a database is an important step for identifying known genetic traits and disease-related variants within an individual. The growing size of variant databases as well as the high depth of sequencing data poses an efficiency challenge. In clinical applications, where time is crucial, alignment-based methods are often not fast enough. To fill the gap, Shajii et al. propose LAVA, an alignment-free genotyping method which is able to more quickly genotype single nucleotide polymorphisms (SNPs); however, there remains large room for improvements in running time and accuracy.

Results
We present the VarGeno method for SNP genotyping from Illumina whole genome sequencing data. VarGeno builds upon LAVA by improving the speed of k-mer querying as well as the accuracy of the genotyping strategy. We evaluate VarGeno on several read datasets using different genotyping SNP lists. VarGeno performs 7–13 times faster than LAVA with similar memory usage, while improving accuracy.

Availability and implementation
VarGeno is freely available at: https://github.com/medvedevgroup/vargeno.

Supplementary information
Supplementary data are available at Bioinformatics online.
Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples
Authors: Yu Hua , Lu Lu , Jiao Bingke , Liang Chengzhi 
Published: July 2018

Abstract

Motivation
The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism.

Results
Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, we discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. We explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, we discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. Our study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding.

Availability and implementation
The analyzed gene expression data, reconstructed GCNs, modules and detailed annotations can be freely downloaded from ftp://47.94.193.106/pub.

Supplementary information
Supplementary data are available at Bioinformatics online.
Re-identification of individuals in genomic data-sharing beacons via allele inference
Authors: von Thenen Nora , Ayday Erman , Cicek A Ercument 
Published: July 2018

Abstract

Motivation
Genomic data-sharing beacons aim to provide a secure, easy to implement and standardized interface for data-sharing by only allowing yes/no queries on the presence of specific alleles in the dataset. Previously deemed secure against re-identification attacks, beacons were shown to be vulnerable despite their stringent policy. Recent studies have demonstrated that it is possible to determine whether the victim is in the dataset, by repeatedly querying the beacon for his/her single-nucleotide polymorphisms (SNPs). Here, we propose a novel re-identification attack and show that the privacy risk is more serious than previously thought.

Results
Using the proposed attack, even if the victim systematically hides informative SNPs, it is possible to infer the alleles at positions of interest as well as the beacon query results with very high confidence. Our method is based on the fact that alleles at different loci are not necessarily independent. We use linkage disequilibrium and a high-order Markov chain-based algorithm for inference. We show that in a simulated beacon with 65 individuals from the European population, we can infer membership of individuals with 95% confidence with only 5 queries, even when SNPs with MAF &lt;0.05 are hidden. We need less than 0.5% of the number of queries that existing works require, to determine beacon membership under the same conditions. We show that countermeasures such as hiding certain parts of the genome or setting a query budget for the user would fail to protect the privacy of the participants.

Availability and implementation
Software is available at http://ciceklab.cs.bilkent.edu.tr/beacon_attack.

Supplementary information
Supplementary data are available at Bioinformatics online.
StackDPPred: a stacking based prediction of DNA-binding protein from sequence
Authors: Mishra Avdesh , Pokhrel Pujan , Hoque Md Tamjidul 
Published: July 2018

AbstractMotivationIdentification of DNA-binding proteins from only sequence information is one of the most challenging problems in the field of genome annotation. DNA-binding proteins play an important role in various biological processes such as DNA replication, repair, transcription and splicing. Existing experimental techniques for identifying DNA-binding proteins are time-consuming and expensive. Thus, prediction of DNA-binding proteins from sequences alone using computational methods can be useful to quickly annotate and guide the experimental process. Most of the methods developed for predicting DNA-binding proteins use the information from the evolutionary profile, called the position-specific scoring matrix (PSSM) profile, alone and the accuracies of such methods have been limited. Here, we propose a method, called StackDPPred, which utilizes features extracted from PSSM and residue specific contact-energy to help train a stacking based machine learning method for the effective prediction of DNA-binding proteins.ResultsBased on benchmark sequences of 1063 (518 DNA-binding and 545 non DNA-binding) proteins and using jackknife validation, StackDPPred achieved an ACC of 89.96%, MCC of 0.799 and AUC of 94.50%. This outcome outperforms several state-of-the-art approaches. Furthermore, when tested on recently designed two independent test datasets, StackDPPred outperforms existing approaches consistently. The proposed StackDPPred can be used for effective prediction of DNA-binding proteins from sequence alone.Availability and implementationOnline server is at http://bmll.cs.uno.edu/add and code-data is at http://cs.uno.edu/∼tamjid/Software/StackDPPred/code_data.zip.Supplementary informationSupplementary data are available at Bioinformatics online.
Posterior Fusiform and Midfusiform Contribute to Distinct Stages of Facial Expression Processing
Authors: Li Yuanning , Richardson R Mark , Ghuman Avniel Singh 
Published: July 2018

Abstract
Though the fusiform is well-established as a key node in the face perception network, its role in facial expression processing remains unclear, due to competing models and discrepant findings. To help resolve this debate, we recorded from 17 subjects with intracranial electrodes implanted in face sensitive patches of the fusiform. Multivariate classification analysis showed that facial expression information is represented in fusiform activity and in the same regions that represent identity, though with a smaller effect size. Examination of the spatiotemporal dynamics revealed a functional distinction between posterior fusiform and midfusiform expression coding, with posterior fusiform showing an early peak of facial expression sensitivity at around 180 ms after subjects viewed a face and midfusiform showing a later and extended peak between 230 and 460 ms. These results support the hypothesis that the fusiform plays a role in facial expression perception and highlight a qualitative functional distinction between processing in posterior fusiform and midfusiform, with each contributing to temporally segregated stages of expression perception.
IgE repertoire and immunological memory: compartmental regulation and antibody function
Authors: Gould Hannah J , Wu Yu-Chang Bryan 
Published: July 2018

AbstractIt is now generally recognized that bone marrow is the survival niche for antigen-specific plasma cells with long-term immunological memory. These cells release antibodies into the circulation, needed to prime effector cells in the secondary immune response. These antibodies participate in the surveillance for antigen and afford immune defence against pathogens and toxins previously encountered in the primary immune response. IgE antibodies function together with their effector cells, mast cells, to exert ‘immediate hypersensitivity’ in mucosal tissues at the front line of immune defence. The constant supply of IgE antibodies from bone marrow plasma cells allows the rapid ‘recall response’ by mast cells upon re-exposure to antigen even after periods of antigen absence. The speed and sensitivity of the IgE recall response and potency of the effector cell functions are advantageous in the early detection and elimination of pathogens and toxins at the sites of attack. Local antigen provocation also stimulates de novo synthesis of IgE or its precursors of other isotypes that undergo IgE switching in the mucosa. This process, however, introduces a delay before mast cells can be sensitized and resume activity; this is terminated shortly after the antigen is eliminated. Recent results from adaptive immune receptor repertoire sequencing of immunoglobulin genes suggest that the mucosal IgE+ plasmablasts, which have undergone affinity maturation in the course of their evolution in vivo, are a source of long-lived IgE+ plasma cells in the bone marrow that are already fully functional.
Clinical and Genomic Features of the First Cases of Elizabethkingia anophelis Infection in New York, Including the First Case in a Healthy Infant Without Previous Nosocomial Exposure
Authors: Snesrud Erik , McGann Patrick , Walsh Edward , Ong Ana , Maybank Rosslyn , Kwak Yoon , Campbell Jean , Jones Anthony , Vore Kelly , Hinkle Mary , Lesho Emil 
Published: July 2018

Abstract
Elizabethkingia spp are Gram-negative bacteria associated with neonatal meningitis. In 2015–2016, an outbreak of Elizabethkingia anophelis infection that involved 63 patients and 18 deaths occurred in Wisconsin. Despite a multistate investigation, as of September 2016 the source remained undetermined, and experts warned of reemergence. We describe here the first cases of E anophelis infection in New York, including the case of a healthy infant without previous healthcare contact.
Comforts, Clubs, and the Casino: Food and the Perpetuation of the British Class System in First World War Civilian Internment Camps
Authors: Durbach Nadja 
Published: July 2018

Abstract
Internment in camps for enemy aliens during the First World War might have led to a commonality of experience given that all civilian prisoners of war (POWs) were theoretically enduring the same material conditions. However, the privileges associated with social rank and with wealth led to profoundly different bodily regimes within these camps. The British class system was in fact perpetuated within the civilian internment camps established in the United Kingdom and among British subjects interned by the enemy, particularly in relation to the consumption of additional and superior food and drink that arrived in parcels from home and was provided at camp facilities for the privileged. These class distinctions had tangible material consequences for the interned, as not all bodies were equally subjected to the privations of the camp regime. That some POWs had access to more and better food throughout much of the First World War underscores the British state’s lack of commitment to the ideal of equality of bodily sacrifice. Instead the British government was complicit in perpetuating class inequalities both among its own subjects and those it had interned, even during a moment of international crisis when the social order was clearly being upended.
Plasma potassium ranges associated with mortality across stages of chronic kidney disease: the Stockholm CREAtinine Measurements (SCREAM) project
Authors: Gasparini Alessandro , Evans Marie , Barany Peter , Xu Hairong , Jernberg Tomas , Ärnlöv Johan , Lund Lars H , Carrero Juan-Jesús 
Published: July 2018

AbstractBackgroundSmall-scale studies suggest that hyperkalaemia is a less threatening condition in chronic kidney disease (CKD), arguing adaptation/tolerance to potassium (K+) retention. This study formally evaluates this hypothesis by estimating the distribution of plasma K+ and its association with mortality across CKD stages.MethodsThis observational study included all patients undergoing plasma K+ testing in Stockholm during 2006–11. We randomly selected one K+ measurement per patient and constructed a cross-sectional cohort with mortality follow-up. Covariates included demographics, comorbidities, medications and estimated glomerular filtration rate (eGFR). We estimated K+ distribution and defined K+ ranges associated with 90-, 180- and 365-day mortality.ResultsIncluded were 831 760 participants, of which 70 403 (8.5%) had CKD G3 (eGFR &lt;60–30 mL/min) and 8594 (1.1%) had CKD G4–G5 (eGFR &lt;30 mL/min). About 66 317 deaths occurred within a year. Adjusted plasma K+ increased across worse CKD stages: from median 3.98 (95% confidence interval 3.49–4.59) for eGFR &gt;90 to 4.43 (3.22–5.65) mmol/L for eGFR ≤15 mL/min/1.73 m2. The association between K+ and mortality was U-shaped, but it flattened at lower eGFR strata and shifted upwards. For instance, the range where the 90-day mortality risk increased by no more than 100% was 3.45–4.94 mmol/L in eGFR &gt;60 mL/min, but was 3.36–5.18  in G3 and 3.26–5.53 mmol/L in G4–G5. In conclusion, CKD stage modifies K+ distribution and the ranges that predict mortality in the community.ConclusionAlthough this study supports the view that hyperkalaemia is better tolerated with worse CKD, it challenges the current use of a single optimal K+ range for all patients.
Electronic Cigarette Use and Understanding Among a National Sample of Australian Aboriginal and Torres Strait Islander Smokers
Authors: Thomas David P , Lusis Nadia , Van der Sterren Anke E , Borland Ron 
Published: July 2018

Abstract

Introduction
Adult daily smoking prevalence in the Aboriginal and Torres Strait Islander population is 2.8 times that of other Australians. There is little data on prevalence of electronic cigarette (e-cigarette) use among Aboriginal and Torres Strait Islander peoples. We measured e-cigarette use and beliefs about their harmfulness in national samples of Aboriginal and Torres Strait Islander smokers and of all Australian smokers.

Methods
The Talking About the Smokes project interviewed a nationally representative quota sample of 1301 Aboriginal and Torres Strait Islander smokers between August 2013 and August 2014. The Australian Wave 9 survey of the long-running International Tobacco Control Project interviewed 1093 smokers between February and May 2013. Estimates for all Australian smokers were standardized to the age and sex distribution of Aboriginal and Torres Strait Islander smokers.

Results
Fewer Aboriginal and Torres Strait Islander than all Australian smokers had tried an e-cigarette (21% vs. 30%). This was in part because of more Aboriginal and Torres Strait Islander smokers having not heard of e-cigarettes. Fewer Aboriginal and Torres Strait Islander smokers than all Australian smokers agreed that e-cigarettes are less harmful than conventional cigarettes (22% vs. 50%).

Conclusions
Many Aboriginal and Torres Strait Islander smokers have used e-cigarettes. However, there is considerable misunderstanding about the relative harm of e-cigarettes compared with conventional cigarettes, in part because of the tight regulatory environment in Australia.

Implications
The study describes e-cigarette use and understanding in national samples of Aboriginal and Torres Strait Islander smokers and of all Australian smokers. Only small studies have reported on e-cigarette use in this high smoking prevalence population. Fewer Aboriginal and Torres Strait Islander smokers than all Australian smokers had tried an e-cigarette and fewer agreed that e-cigarettes are less harmful than conventional cigarettes. Australian governments, health authorities, health professionals, and e-cigarette regulations should provide clearer messages that e-cigarettes are less harmful.
Enhanced Recovery After Surgery™ Awake Minimally-Invasive Transforaminal Lumbar Interbody Fusion: 2-Dimensional Operative Video
Authors: Chang Hsuan-Kan , Kolcun John Paul G , Chang Peng-Yuan , Wang Michael Y 
Published: July 2018

Abstract
This video demonstrates the awake endoscopic minimally-invasive transforaminal lumbar interbody fusion (MIS-TLIF) used in our institution's developing Enhanced Recovery After Surgery program. This technique relies on 6 key components, including (1) conscious sedation, (2) endoscopic visualization, (3) long-acting local anesthesia, (4) an expandable interbody device, (5) osteobiologics, and (6) percutaneous instrumentation. In joining these technologies, this procedure embodies the principles of minimally invasive surgery while achieving excellent clinical outcomes. We have previously described this procedure in detail, as well as its impact at our institution, including significant reductions in operative time, blood loss, postoperative length of stay, and hospital costs.
The procedure depicted in this video involves the off-label use of bone morphogenetic protein-2 and the Spineology Optimesh allograft containment device.
All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.
The patient gave direct consent for the use of the video footage and associated information from this surgery for the making and publication of this surgical video.
The Zapatista Movement and Mexico's Democratic Transition
Authors: Inclán María 
Published: July 2018

AbstractWhat happens to insurgent social movements that emerge during a democratic transition but fail to achieve their goals? How influential are they? Are they able to survive their initial mobilizing boom? Using the development of the Zapatista movement during Mexico’s democratic transition in the 1990s, this book seeks to answer these questions. The Zapatista movement is probably the best example of an influential and salient insurgent social movement emerging during a democratic transition that successfully mobilized sympathy and support for the indigenous agenda inside and outside of the country, yet failed to achieve its goals vis-à-vis the Mexican state. Why did such an influential movement fail to have its demands fully met? The answer is illustrated using a sliding door analogy to explain how the Zapatista movement developed within almost simultaneous openings and closings of political opportunities for its mobilization, success, and survival. Framing the relative achievements and failures of the movement within Mexico’s democratization is essential to understanding how social movements develop and survive and how responsive an electoral democracy can actually become. As such, this book offers a test of the quality of Mexico’s democracy and the resilience of the Zapatista movement, identifying the extent to which emerging political forces have incorporated dissident and previously excluded political actors into the new polity.
Democratic Transitions and Political Opportunities
Authors: Inclán María 
Published: July 2018

AbstractThis chapter presents the theoretical arguments of the book, which come from the literatures on political opportunities and democratic transitions, in particular protracted transitions and transitions from below. The chapter first compares Mexico’s democratic transition to other democratization processes in which insurgent social movements play a crucial role, such as the cases of El Salvador and South Africa. Then it provides an analysis of the opportunities that democratic transitions may open for the mobilization, success, and survival of an insurgent social movement. Third, hypotheses contextualized to the Mexican case illustrate how these expectations may influence the development of a specific movement’s cycle of protests, negotiating success, and chances of survival within a protracted democratic transition.