bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Dead Sea Scrolls as cultural icon
Authors: Lim Timothy H. 
Published: April 2017

Abstract
‘The Dead Sea Scrolls as cultural icon’ asks: how did the Dead Sea Scrolls become so popular? Discovered in 1947 and published fully in 1991, the term ‘Dead Sea Scrolls’ has become a catch-all term for ancient manuscripts. The media played an important part in the popularization of the scrolls, but advances in computer and digital technology have improved access to the scrolls. Dead Sea Scroll tourism is popular even during unrest in the Middle East. The discovery of the scrolls coincided with the founding of Israel, giving the documents a profound political importance. Vatican conspiracy theories and copyright lawsuits have also captured the public’s imagination.
The archaeological site and caves
Authors: Lim Timothy H. 
Published: April 2017

Abstract
‘The archaeological site and caves’ examines the archaeological evidence found at the Khirbet Qumran site. Palestinian archaeology was previously dominated by the biblical agenda, but Khirbet Qumran is not mentioned in the Bible, and was only excavated because of the Dead Sea Scrolls. The occupation of the site is generally divided into three phases: the Israelite phase, the communal phase (occupation by the Essenes), and the Second Revolt phase. A cemetery also exists at the site. This was the burial ground of the Qumran people (mixed with some later Bedouin burials), and arguments have raged over the importance of the different sections of the cemetery.
On scrolls and fragments
Authors: Lim Timothy H. 
Published: April 2017

Abstract
‘On scrolls and fragments’ explores the physical difficulties in working with the Dead Sea Scrolls. Firstly: how does one define a scroll? There is not a single, complete scroll in the entire collection, and questions exist about how many scrolls there were originally. Counting the scrolls is also difficult—are two fragments of the same scroll distinct? The scroll fragments are grouped together according to language, content, and handwriting, with obvious joins between fragments providing definitive proof that they are related. Handwriting was taught through scribal traditions, and as such palaeography is difficult but not impossible. Radiocarbon dating using accelerometer mass spectrometry has accurately dated the scrolls.
New light on the Hebrew Bible
Authors: Lim Timothy H. 
Published: April 2017

Abstract
‘New light on the Hebrew Bible’ investigates what the Dead Sea Scrolls can tell us about the textual diversity and canonicity of the Hebrew Bible. Before the scrolls were discovered, Hebrew manuscripts generally dated back to the medieval period. The Qumran texts, dating to between 250 bce and 100 ce, tell us what the Bible was like before its standardization. Errors from copying gave rise to different text-types, and the Dead Sea Scrolls showed that there were far more text-types than previously thought. Variations in readings of the Hebrew Bible and other ancient sources show there was greater diversity in biblical texts than previously realized.
Who owned the scrolls?
Authors: Lim Timothy H. 
Published: April 2017

Abstract
‘Who owned the scrolls?’ attempts to determine the ancient ownership of the Dead Sea Scrolls. The prevailing theory, with some modifications, is the Qumran–Essene theory, which posits that the Essene people lived in the site and were responsible for the creation of the Dead Sea Scrolls. Various evidence from the scrolls themselves, the archaeological Khirbet Qumran site, and primary historical sources support this. For instance, Pliny the Elder located a tribe living at Qumran during his travels in his Historia Naturalis that matched historical descriptions. Handwriting matches between the scrolls and inscriptions at Khirbet Qumran have also been found. Alternative but refuted theories suggest different uses for the site.
The religious beliefs of the sectarian communities
Authors: Lim Timothy H. 
Published: April 2017

Abstract
‘The religious beliefs of the sectarian communities’ explores Jewish beliefs in the Second Temple period. Judaism is a way of life rather than a common faith, but common beliefs are held. The Doctrine of the Two Spirits says that God divided men into those with good and those with evil spirits. Sectarians believed that a man’s spirit could be judged physically. The Jews believe that they are God’s chosen people, and as such they have a series of covenants with Yahweh. The sectarians believe that they are a remnant of true believers that have not strayed from God. Thus, the ‘New Covenant’ is actually a renewal of their existing agreement.
The inequalities of eugenics
Authors: Levine Philippa 
Published: April 2017

Abstract
The goal of eugenic fitness was intended, at its most utopian, to improve lives, to help eradicate disease and disability, and to foster productivity. In practice, however, eugenics mostly reinforced rather than dissolved existing class prejudices. ‘The inequalities of eugenics’ shows that it was frequently the poor, ill-educated, and minorities whose reproductive capacity and lifestyle came under attack, and it was women’s sexuality rather than men’s that was closely policed. The disparity between falling birthrates in the developed world and rising rates elsewhere also created racial inequalities in eugenic policies. Reproductive fitness was being undermined as those considered unfit outbred their superiors. Class, gender, and race differences were thus all central eugenic concerns.
The Jews: Religion or Nation?
Authors: Stanislawski Michael 
Published: April 2017

Abstract
Zionism—the nationalist movement calling for the establishment and support of an independent Jewish state in its ancient homeland—is one of the world’s most controversial ideologies. Its supporters see it as the national liberation movement of the Jewish people that came to fruition in the creation of the State of Israel in 1948. Its opponents regard it as one of the last forms of colonial oppression in the world, defined by Israel’s occupation of the West Bank in the name of a racist ideology increasingly turning Israel into an apartheid state. “The Jews: Religion or Nation?” outlines the aims of this VSI, which does not promote any particular position on Zionism.
Swing to the right, 1977–1995
Authors: Stanislawski Michael 
Published: April 2017

Abstract
Menachem Begin became prime minister of Israel on June 20, 1977, with a clear goal: to implement as quickly and as extensively as possible the policies of Revisionist Zionism as articulated by his mentor and hero, Vladimir Jabotinsky. “Swing to the right: 1977–1995” outlines the key events in Israeli politics that led to a decisive swing to the right in Zionist ideology, including the 1978 peace treaty with Egypt that returned the Sinai Peninsula, the Declaration of Principles on Interim Self-Government Arrangements with the Palestinian Liberation Organization in 1993, and the assassination of Prime Minister Yitzhak Rabin in November 1995 by a member of the ultra-right-wing religious Zionist movement.
Epitope Preservation Methods for Tissue Microarrays
Authors: Andeen Nicole K , Bowman Regina , Baullinger Toni , Brooks J Mathew , Tretiakova Maria S 
Published: April 2017

AbstractObjectivesWe sought to test recent guidelines for preserving immunoreactivity of precut slides, to quantify loss of immunoreactivity, and to determine potential for preservation by altering storage conditions.MethodsPrecut slides from tissue microarrays were stored under one of several conditions: exposed to ambient air at room temperature, 4°C, or –20°C or in a vacuum-sealed container at room temperature, –20°C, –80°C, or with paraffin coating. At multiple intervals over 1 year, slides were stained with antibodies against p53, isocitrate dehydrogenase 1, Ki-67, synaptophysin, and androgen receptor and evaluated.ResultsCompared with time 0, the overall median percentage immunoreactivity was 66% at 6 months and 51% at 1 year. During the experiment, this was as low as 55% for precut slides stored in paraffin coating and up to 87% for those stored at –20°C. Vacuum sealing was an effective preservative for some antibody targets and detrimental for others. Storage at –80°C did not have added value.ConclusionsFor precut slides, there is a time, storage condition, and antibody-dependent loss of immunoreactivity that could compromise analysis of prognostic, predictive, and diagnostic markers. Our findings support previous recommendations and suggest that the best storage conditions are at –20°C, without paraffin coating or vacuum sealing.
Modelling haplotypes with respect to reference cohort variation graphs
Authors: Rosen Yohei , Eizenga Jordan , Paten Benedict 
Published: April 2017

Abstract

Motivation
Current statistical models of haplotypes are limited to panels of haplotypes whose genetic variation can be represented by arrays of values at linearly ordered bi- or multiallelic loci. These methods cannot model structural variants or variants that nest or overlap.

Results
A variation graph is a mathematical structure that can encode arbitrarily complex genetic variation. We present the first haplotype model that operates on a variation graph-embedded population reference cohort. We describe an algorithm to calculate the likelihood that a haplotype arose from this cohort through recombinations and demonstrate time complexity linear in haplotype length and sublinear in population size. We furthermore demonstrate a method of rapidly calculating likelihoods for related haplotypes. We describe mathematical extensions to allow modelling of mutations. This work is an important incremental step for clinical genomics and genetic epidemiology since it is the first haplotype model which can represent all sorts of variation in the population.

Availability and Implementation
Available on GitHub at https://github.com/yoheirosen/vg.

Supplementary information
Supplementary data are available at Bioinformatics online.
Association testing of bisulfite-sequencing methylation data via a Laplace approximation
Authors: Weissbrod Omer , Rahmani Elior , Schweiger Regev , Rosset Saharon , Halperin Eran 
Published: April 2017

Abstract

Motivation
Epigenome-wide association studies can provide novel insights into the regulation of genes involved in traits and diseases. The rapid emergence of bisulfite-sequencing technologies enables performing such genome-wide studies at the resolution of single nucleotides. However, analysis of data produced by bisulfite-sequencing poses statistical challenges owing to low and uneven sequencing depth, as well as the presence of confounding factors. The recently introduced Mixed model Association for Count data via data AUgmentation (MACAU) can address these challenges via a generalized linear mixed model when confounding can be encoded via a single variance component. However, MACAU cannot be used in the presence of multiple variance components. Additionally, MACAU uses a computationally expensive Markov Chain Monte Carlo (MCMC) procedure, which cannot directly approximate the model likelihood.

Results
We present a new method, Mixed model Association via a Laplace ApproXimation (MALAX), that is more computationally efficient than MACAU and allows to model multiple variance components. MALAX uses a Laplace approximation rather than MCMC based approximations, which enables to directly approximate the model likelihood. Through an extensive analysis of simulated and real data, we demonstrate that MALAX successfully addresses statistical challenges introduced by bisulfite-sequencing while controlling for complex sources of confounding, and can be over 50% faster than the state of the art.

Availability and Implementation
The full source code of MALAX is available at https://github.com/omerwe/MALAX.

Supplementary information
Supplementary data are available at Bioinformatics online.
HLA class I binding prediction via convolutional neural networks
Authors: Vang Yeeleng S , Xie Xiaohui 
Published: April 2017

Abstract

Motivation
Many biological processes are governed by protein–ligand interactions. One such example is the recognition of self and non-self cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases.

Results
We apply machine learning techniques from the natural language processing (NLP) domain to address the task of MHC-peptide binding prediction. More specifically, we introduce a new distributed representation of amino acids, name HLA-Vec, that can be used for a variety of downstream proteomic machine learning tasks. We then propose a deep convolutional neural network architecture, name HLA-CNN, for the task of HLA class I-peptide binding prediction. Experimental results show combining the new distributed representation with our HLA-CNN architecture achieves state-of-the-art results in the majority of the latest two Immune Epitope Database (IEDB) weekly automated benchmark datasets. We further apply our model to predict binding on the human genome and identify 15 genes with potential for self binding.

Availability and Implementation
Codes to generate the HLA-Vec and HLA-CNN are publicly available at: https://github.com/uci-cbcl/HLA-bind.

Supplementary information
Supplementary data are available at Bioinformatics online.
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression
Authors: Ammad-ud-din Muhammad , Khan Suleiman A , Wennerberg Krister , Aittokallio Tero 
Published: April 2017

Abstract

Motivation
A prime challenge in precision cancer medicine is to identify genomic and molecular features that are predictive of drug treatment responses in cancer cells. Although there are several computational models for accurate drug response prediction, these often lack the ability to infer which feature combinations are the most predictive, particularly for high-dimensional molecular datasets. As increasing amounts of diverse genome-wide data sources are becoming available, there is a need to build new computational models that can effectively combine these data sources and identify maximally predictive feature combinations.

Results
We present a novel approach that leverages on systematic integration of data sources to identify response predictive features of multiple drugs. To solve the modeling task we implement a Bayesian linear regression method. To further improve the usefulness of the proposed model, we exploit the known human cancer kinome for identifying biologically relevant feature combinations. In case studies with a synthetic dataset and two publicly available cancer cell line datasets, we demonstrate the improved accuracy of our method compared to the widely used approaches in drug response analysis. As key examples, our model identifies meaningful combinations of features for the well known EGFR, ALK, PLK and PDGFR inhibitors.

Availability and Implementation
The source code of the method is available at https://github.com/suleimank/mvlr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Sharing and helping: predictors of adolescents’ willingness to share diabetes personal health information with peers
Authors: Vaala Sarah E , Lee Joyce M , Hood Korey K , Mulvaney Shelagh A 
Published: April 2017

Abstract

Objective
Sharing personal information about type 1 diabetes (T1D) can help adolescents obtain social support, enhance social learning, and improve self-care. Diabetes technologies, online communities, and health interventions increasingly feature data-sharing components. This study examines factors underlying adolescents’ willingness to share personal T1D information with peers.

Materials and Methods
Participants were 134 adolescents (12–17 years of age; 56% female) who completed an online survey regarding experiences helping others with T1D, perceived social resources, beliefs about the value of sharing information and helping others, and willingness to share T1D information. Hemoglobin A1c values were obtained from medical records.

Results
Adolescents were more willing to share how they accomplished T1D tasks than how often they completed them, and least willing to share glucose control status. In multivariate analyses, sharing/helping beliefs (β = 0.26, P &lt; .01) and glucose control (HbA1c value; β = −0.26, P &lt; .01) were related to greater willingness to share personal health information. Glucose control moderated relationships such that adolescents with worse A1c values had stronger relationships between sharing/helping beliefs and willingness to share (β = 0.18, P &lt; .05) but weaker relationships between helping experience and willingness to share (β = −0.22, P = .07).

Discussion
Many adolescents with T1D are willing to share personal health information, particularly if they have better diabetes health status and a stronger belief in the benefits of sharing.

Conclusion
Social learning and social media components may improve intervention participation, engagement, and outcomes by boosting adolescents’ beliefs about the benefits of sharing information and helping others.
Immediate dense circumstellar environment of supernova progenitors caused by wind acceleration: its effect on supernova light curves
Authors: Moriya Takashi J. , Yoon Sung-Chul , Gräfener Götz , Blinnikov Sergei I. 
Published: April 2017

Abstract
Type IIP supernova progenitors are often surrounded by dense circumstellar media that may result from mass-loss enhancement of the progenitors shortly before their explosions. Previous light-curve studies suggest that the mass-loss rates are enhanced up to ∼0.1 M⊙ yr−1, assuming a constant wind velocity. However, the density of circumstellar media at the immediate stellar vicinity can be much higher than previously inferred for a given mass-loss rate if wind acceleration is taken into account. We show that the wind acceleration has a huge impact when we estimate mass-loss rates from early light curves of Type IIP supernovae by taking SN 2013fs as an example. We perform numerical calculations of the interaction between supernova ejecta and circumstellar media with a constant mass-loss rate but with a β-law wind velocity profile. We find that the mass-loss rate of the progenitor of SN 2013fs shortly before the explosion, which was inferred to be ∼0.1 M⊙ yr−1 with a constant wind velocity of 10 km s−1 by a previous light-curve modelling, can be as low as ∼10−3 M⊙ yr−1 with the same terminal wind velocity of 10 km s−1 but with a wind velocity profile with β ≃ 5. In both cases, the mass of the circumstellar medium is similar (≃0.5 M⊙). Therefore, the beginning of the progenitor’s mass-loss enhancement in our interpretation is ∼100 yr before the explosion, not several years. Our result indicates that the immediate dense environment of Type II supernova progenitors may be significantly influenced by wind acceleration.
Mitochondrial Recombination and Introgression during Speciation by Hybridization
Authors: Leducq Jean-Baptiste , Henault Mathieu , Charron Guillaume , Nielly-Thibault Lou , Terrat Yves , Fiumera Heather L. , Shapiro B. Jesse , Landry Christian R. 
Published: April 2017

AbstractGenome recombination is a major source of genotypic diversity and contributes to adaptation and speciation following interspecies hybridization. The contribution of recombination in these processes has been thought to be largely limited to the nuclear genome because organelles are mostly uniparentally inherited in animals and plants, which prevents recombination. Unicellular eukaryotes such as budding yeasts do, however, transmit mitochondria biparentally, suggesting that during hybridization, both parents could provide alleles that contribute to mitochondrial functions such as respiration and metabolism in hybrid populations or hybrid species. We examined the dynamics of mitochondrial genome transmission and evolution during speciation by hybridization in the natural budding yeast Saccharomyces paradoxus. Using population-scale mitochondrial genome sequencing in two endemic North American incipient species SpB and SpC and their hybrid species SpC*, we found that both parental species contributed to the hybrid mitochondrial genome through recombination. We support our findings by showing that mitochondrial recombination between parental types is frequent in experimental crosses that recreate the early step of this speciation event. In these artificial hybrids, we observed that mitochondrial genome recombination enhances phenotypic variation among diploid hybrids, suggesting that it could play a role in the phenotypic differentiation of hybrid species. Like the nuclear genome, the mitochondrial genome can, therefore, also play a role in hybrid speciation.
The Role of Extent of Resection in IDH1 Wild-Type or Mutant Low-Grade Gliomas
Authors: Patel Toral , Bander Evan D , Venn Rachael A , Powell Tiffany , Cederquist Gustav Young-Min , Schaefer Peter M , Puchi Luis A , Akhmerov Akbarshakh , Ogilvie Shahiba , Reiner Anne S , Moussazadeh Nelson , Tabar Viviane 
Published: April 2017

Abstract

BACKGROUND
Maximizing extent of resection (EOR) improves outcomes in adults with World Health Organization (WHO) grade II low-grade gliomas (LGG). However, recent studies demonstrate that LGGs bearing a mutation in the isocitrate dehydrogenase 1 (IDH1) gene are a distinct molecular and clinical entity. It remains unclear whether maximizing EOR confers an equivalent clinical benefit in IDH mutated (mtIDH) and IDH wild-type (wtIDH) LGGs.

OBJECTIVE
To assess the impact of EOR on malignant progression-free survival (MPFS) and overall survival (OS) in mtIDH and wtIDH LGGs.

METHODS
We performed a retrospective review of 74 patients with WHO grade II gliomas and known IDH mutational status undergoing resection at a single institution. EOR was assessed with quantitative 3-dimensional volumetric analysis. The effect of predictor variables on MPFS and OS was analyzed with Cox regression models and the Kaplan–Meier method.

RESULTS
Fifty-two (70%) mtIDH patients and 22 (30%) wtIDH patients were included. Median preoperative tumor volume was 37.4 cm3; median EOR of 57.6% was achieved. Univariate Cox regression analysis confirmed EOR as a prognostic factor for the entire cohort. However, stratifying by IDH status demonstrates that greater EOR independently prolonged MPFS and OS for wtIDH patients (hazard ratio [HR] = 0.002 [95% confidence interval {CI} 0.000-0.074] and HR = 0.001 [95% CI 0.00-0.108], respectively), but not for mtIDH patients (HR = 0.84 [95% CI 0.17-4.13] and HR = 2.99 [95% CI 0.15-61.66], respectively).

CONCLUSION
Increasing EOR confers oncologic and survival benefits in IDH1 wtLGGs, but the impact on IDH1 mtLGGs requires further study.