bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of post-alignment processing in variant discovery from whole exome data
Authors: Tian Shulan , Yan Huihuang , Kalmbach Michael , Slager Susan L. 
Published: October 2016

Abstract
Background
GATK Best Practices workflows are widely used in large-scale sequencing projects and recommend post-alignment processing before variant calling. Two key post-processing steps include the computationally intensive local realignment around known INDELs and base quality score recalibration (BQSR). Both have been shown to reduce erroneous calls; however, the findings are mainly supported by the analytical pipeline that incorporates BWA and GATK UnifiedGenotyper. It is not known whether there is any benefit of post-processing and to what extent the benefit might be for pipelines implementing other methods, especially given that both mappers and callers are typically updated. Moreover, because sequencing platforms are upgraded regularly and the new platforms provide better estimations of read quality scores, the need for post-processing is also unknown. Finally, some regions in the human genome show high sequence divergence from the reference genome; it is unclear whether there is benefit from post-processing in these regions.

Results
We used both simulated and NA12878 exome data to comprehensively assess the impact of post-processing for five or six popular mappers together with five callers. Focusing on chromosome 6p21.3, which is a region of high sequence divergence harboring the human leukocyte antigen (HLA) system, we found that local realignment had little or no impact on SNP calling, but increased sensitivity was observed in INDEL calling for the Stampy + GATK UnifiedGenotyper pipeline. No or only a modest effect of local realignment was detected on the three haplotype-based callers and no evidence of effect on Novoalign. BQSR had virtually negligible effect on INDEL calling and generally reduced sensitivity for SNP calling that depended on caller, coverage and level of divergence. Specifically, for SAMtools and FreeBayes calling in the regions with low divergence, BQSR reduced the SNP calling sensitivity but improved the precision when the coverage is insufficient. However, in regions of high divergence (e.g., the HLA region), BQSR reduced the sensitivity of both callers with little gain in precision rate. For the other three callers, BQSR reduced the sensitivity without increasing the precision rate regardless of coverage and divergence level.

Conclusions
We demonstrated that the gain from post-processing is not universal; rather, it depends on mapper and caller combination, and the benefit is influenced further by sequencing depth and divergence level. Our analysis highlights the importance of considering these key factors in deciding to apply the computationally intensive post-processing to Illumina exome data.
VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams
Authors: Lam Felix , Lalansingh Christopher M. , Babaran Holly E. , Wang Zhiyuan , Prokopec Stephenie D. , Fox Natalie S. , Boutros Paul C. 
Published: October 2016

Abstract
Background
Visualization of data generated by high-throughput, high-dimensionality experiments is rapidly becoming a rate-limiting step in computational biology. There is an ongoing need to quickly develop high-quality visualizations that can be easily customized or incorporated into automated pipelines. This often requires an interface for manual plot modification, rapid cycles of tweaking visualization parameters, and the generation of graphics code. To facilitate this process for the generation of highly-customizable, high-resolution Venn and Euler diagrams, we introduce VennDiagramWeb: a web application for the widely used VennDiagram R package. VennDiagramWeb is hosted at http://venndiagram.res.oicr.on.ca/.

Results
VennDiagramWeb allows real-time modification of Venn and Euler diagrams, with parameter setting through a web interface and immediate visualization of results. It allows customization of essentially all aspects of figures, but also supports integration into computational pipelines via download of R code. Users can upload data and download figures in a range of formats, and there is exhaustive support documentation.

Conclusions
VennDiagramWeb allows the easy creation of Venn and Euler diagrams for computational biologists, and indeed many other fields. Its ability to support real-time graphics changes that are linked to downloadable code that can be integrated into automated pipelines will greatly facilitate the improved visualization of complex datasets. For application support please contact Paul.Boutros@oicr.on.ca.
Contributions to the fixed point theory of diagonal operators
Authors: Petruşel Adrian , Rus Ioan A , Şerban Marcel-Adrian 
Published: October 2016

AbstractIn this paper, we introduce the notion of diagonal operator, we present the historical roots of diagonal operators and we give some fixed point theorems for this class of operators. Our approaches are based on the weakly Picard operator technique, difference equation techniques, and some fixed point theorems for multi-valued operators. Some applications to differential and integral equations are given. We also present some research directions.
Efficiency of metaphase II oocytes following minimal/mild ovarian stimulation in vitro fertilization
Authors: Zhang John J. , Yang Mingxue , Merhi Zaher 
Published: October 2016

Abstract
Background
An inverse relationship between oocyte efficiency and ovarian response was reported in conventional IVF. The purpose of this study was to report metaphase II (MII) oocyte efficiency according to oocyte yield in minimal/mild stimulation IVF (mIVF) and to assess whether oocyte yield affects live birth rate (LBR).

Methods
Infertile women (n = 264) aged < 39 years old with normal ovarian reserve who had mIVF were recruited. All participants received the same protocol for ovarian stimulation. All the embryos were cultured to the blastocyst stage and vitrified using a freeze-all approach. This was followed by a single blastocyst transferred to each participant in subsequent cycles over a 6-month period. Ovarian response was categorized according to the number of MII oocyte yield (low: 1–2, intermediate: 3–6 and high ≥ 7 MII oocytes). MII oocyte utilization rate was calculated as the number of live births divided by the number of MII oocytes produced after only one oocyte retrieval and subsequent transfers of vitrified/warmed blastocysts. The main outcome measure was cumulative LBR over a 6-month period.

Results
Among all the participants, 1173 total retrieved oocytes (4.4 ± 0.2 per patient) resulted in 1019 (3.9 ± 0.2 per patient) total MII oocytes, a clinical pregnancy rate of 48.1 % and a LBR of 41.2 %. Oocyte utilization rate was inversely related to ovarian response where it was 30.3 % in the “low” vs. 9.3 % in the “intermediate” vs. 4.3 % in the “high” oocyte yield groups (p < 0.05). Implantation rate significantly dropped as the number of MII oocytes increased and was highest in the “low” oocyte yield group (p < 0.0001). Cumulative LBR was similar in “low,” “intermediate,” and “high” oocyte yield groups (p > 0.05). The number of MII oocytes had poor sensitivity and specificity for predicting a live birth.

Conclusion
These data extend the hypothesis of oocyte efficiency reported in conventional IVF protocols to mIVF protocols.

Trial registration
Registration clinicaltrials.gov: NCT00799929.
Narratives of experience of mental health and illness on healthtalk.org
Authors: Kidd Jo , Ziebland Sue 
Published: October 2016

SummaryOnline health information is increasingly popular and may bring both benefits and potential harm to users with mental health problems. The encouragement of harmful behaviour among this population is a particular concern. The website healthtalk.org provides the benefits of shared experience by publishing excerpts from rigorous research interviews with patients, contextualised with medical information. This article sets out evidence for the positive and negative effects of online mental health information and describes the methodology behind healthtalk.org, with an overview of the mental health information it provides and how it can benefit patients and health professionals.
mTOR Inhibitors for the Treatment of Severe Congenital Hyperinsulinism: Perspectives on Limited Therapeutic Success
Authors: Szymanowski Marie , Estebanez Maria Salomon , Padidela Raja , Han Bing , Mosinska Karolina , Stevens Adam , Damaj Lena , Pihan-Le Bars Florence , Lascouts Emilie , Reynaud Rachel , Ferreira Catherine , Bansept Claire , de Lonlay Pascale , Saint-Martin Cécile , Dunne Mark J. , Banerjee Indraneel , Arnoux Jean-Baptiste 
Published: October 2016

Context:
Congenital hyperinsulinism (CHI) is the most common cause of persistent hypoglycemia in neonates and infants. In medically unresponsive CHI, subtotal pancreatectomy is performed to achieve euglycemia with consequent diabetes in later life. Sirolimus, a mammalian target of rapamycin (mTOR) inhibitor, has been reported to obviate the need for pancreatectomy, but experience is limited.

Objective:
We have investigated the efficacy and adverse effect profile of mTOR inhibitors in the treatment of severe CHI.

Design, Setting, and Patients:
This was an observational review of 10 severe CHI patients treated with mTOR inhibitors, in France and the United Kingdom, with the intention of achieving glycemic control without pancreatectomy. Safety information was recorded.

Main Outcome Measure(s):
We examined whether mTOR inhibitors achieved glycemic control, fasting tolerance, and weaning of supportive medical therapy.

Results:
mTOR inhibition achieved euglycemia, fasting tolerance, and reduced medical therapy in only three patients (30%). Triglyceride levels were elevated in five patients (50%). One child required a blood transfusion for anemia, four had stomatitis, two had sepsis, one developed varicella zoster, and two patients developed gut dysmotility in association with exocrine pancreatic insufficiency. In silico analysis of transcriptome arrays from CHI patients revealed no significant association between mTOR signaling and disease. Pancreatic tissue from two patients who did not respond to sirolimus showed no reduction in cell proliferation, further suggesting that mTOR signaling did not down-regulate proliferation in the CHI pancreas.

Conclusion:
mTOR inhibitor treatment is associated with very limited success and must be used with caution in children with severe CHI.
A Struggle for Trust: The Comcáac (Seris) of Sonora Under Colonial and Republican Rule, 1650–1850
Authors: Hölck Lasse 
Published: October 2016

Abstract
This study examines the historical relationship between Comcáac foragers of Sonora, Mexico, and the Spanish/Mexican society between 1650 and 1850. To do so, the concept of trust is introduced, adapted for ethnohistorical research, and discussed as a frequent term in the primary sources. The social organization of foragers is outlined to localize the place of trust within it and to analyze its meaning for interethnic relations. Finally, historical examples are given throughout the article to illustrate and expand the theoretical findings. This article highlights the nonviolent relations in contrast to the commonplace view of perennial conflict between the societies, as given in secondary literature, and aims to provide an alternative reading of this particular ethnohistory.
Meeting with Resistance: Early Spanish Encounters in the Americas, 1492–1524
Authors: Redmond Elsa M. 
Published: October 2016

AbstractThis examination of the earliest Spanish-Amerindian encounters on Hispaniola and in Tierra Firme adopts a historical perspective on indigenous warfare. A chronological timeline monitors the recorded encounters and hostilities between the native Amerindian societies and the Spaniards from Columbus’s 1492 voyage until the destruction of the first permanent Spanish settlement of Santa María de la Antigua del Darién in 1524. The timeline evaluates the proposition that Amerindian societies intensified their warfare practices in response to European incursions. The available information about the size, composition, preparedness, and organization of the native forces is juxtaposed against that of the Spanish forces. The warfare strategies and tactics are examined, both offensive and defensive measures, as well as the actions of the opposing forces in the aftermath of a confrontation. The findings do not support the proposition that Amerindian warfare practices changed significantly in the face of European incursions. The study concludes with a consideration of the unexpected innovations and consequences of the military encounters between late fifteenth- and early sixteenth-century Europeans and Amerindian chiefdoms.
O USO INDISCRIMINADO DO CLORIDRATO DE METILFENIDATO COMO ESTIMULANTE POR ESTUDANTES DA ÁREA DA SAÚDE DA FACULDADE ANHANGUERA DE BRASÍLIA (FAB)
Authors: Affonso Raphael da Silva , Lima Karine silva , Oyama Yasmine Mithiê de Oliveira , Deuner Melissa Cardoso , Garcia Danielle Rodrigues , Barboza Larissa Leite , França Tanos Celmar Costa 
Published: October 2016

A presente pesquisa de campo refere-se ao uso indiscriminado de psicoestimulantes, com ênfase no cloridrato de metilfenidato. Este medicamento é indicado para o tratamento do Transtorno de Déficit de Atenção e Hiperatividade (TDAH) e da narcolepsia. O cloridrato de metilfenidato é um fármaco que age no sistema nervoso central, inibindo a recaptação de dopamina e noradrenalina dos terminais sinápticos. Ele vem sendo usado, sem a orientação medica, de forma a potencializar as funções cognitivas de indivíduos que não possuem nenhum tipo de distúrbio. O objetivo desta pesquisa foi identificar e quantificar o uso não terapêutico do cloridrato de metilfenidato, analisar os efeitos colaterais provocados por tal medicamento e fazer um levantamento do uso de outros psicoestimulantes. A pesquisa foi realizada na Faculdade Anhanguera de Brasília (FAB), com a aplicação de um questionário sobre o uso indiscriminado do cloridrato de metilfenidato ou outros psicoestimulantes pelos estudantes dos cursos de Biomedicina, Enfermagem, Farmácia e Nutrição. A análise dos dados coletados demonstrou que, de um total de 400 entrevistados, 6,0% (n=24) relataram o uso de metilfenidato. Dentre os estudantes que relataram o uso, somente 16,7% (n=4) possuíam o diagnóstico médico de TDAH para o uso terapêutico. Outros autores apontam um aumento crescente na produção e na utilização do cloridrato de metilfenidato. De acordo com a avaliação do questionário respondido pelos alunos da FAB 19,5% dos estudantes revelaram já terem feito uso de algum medicamento para auxiliar os estudos e 57% dos alunos que usaram o cloridrato de metilfenidato como psicoestimulantes o fizeram sem a orientação de um médico.
Effects of Moringa oleifera aqueous leaf extract in alloxan induced diabetic mice
Authors: Tuorkey Muobarak J. 
Published: October 2016

Objective
There is a lack of knowledge regarding the underlying mechanisms of the antidiabetic activity of Moringa oleifera. This study investigates the antidiabetic effect of M. oleifera and its impact on the immune tolerance.

Methods
Alloxan-induced diabetes model for mice was used. A dose of 100 mg/kg of Moringa extract was orally administered to diabetic treated mice. Glucose and insulin levels were evaluated to calculate insulin resistance. Total antioxidant capacity (TAC), creatinine, and blood urea nitrogen (BUN) levels were measured. The relative percentage of CD44, CD69, and IFN-γ was investigated by flow cytometry.

Results
In diabetic mice, insulin resistance by homeostasis model assessment of insulin resistance (HOMA-IR) was increased 4.5-fold than in the control group, and HOMA-IR was decreased 1.3-fold in the Moringa treatment group. The level of TAC was declined 1.94-fold in diabetic mice, and increased 1.67-fold in diabetic treated group. In diabetic mice, creatinine and BUN levels were significantly reduced 1.42- and 1.2-fold, respectively, in Moringa treatment mice. The relative percentage of CD44 was not changed in diabetic mice, but the relative percentage of CD69 was found to be increased. INF-γ was decreased 2.4-fold in diabetic mice and elevated in treated groups.

Conclusion
Moringa may ameliorate insulin resistance, increase TAC, and improve immune tolerance.
DISTRIBUSI UKURAN DAN PARAMETER POPULASI LOBSTER PASIR (Panulirus homarus) DI PERAIRAN ACEH BARAT
Authors: Kembaren Duranta D , Nurdin Erfind 
Published: October 2016

Penelitian tentang distribusi ukuran dan parameter populasi lobster pasir di perairan Aceh Barat dilakukan pada bulanApril sampai November 2013. Penelitian ini bertujuan untukmengkaji status lobster di perairan Aceh Barat dilihat dari aspek distribusi ukuran dan parameter populasinya. Pengamatan dan pengukuran lobster dilakukan di tempat pengumpul lobster dengan sistem sampling acak. Sebaran frekuensi panjang karapas selanjutnya ditabulasikan dan dianalisa dengan metode kurva logistik. Struktur ukuran lobster yang tertangkap menunjukkan bahwa lobster jantan dominan tertangkap dibawah ukuran nilai tengah 72,5 mm dan sebaliknya diatas ukuran nilai tengah 72,5 mm yang didominasi jenis kelamin betina. Lobster terlebih dahulu tertangkap sebelum mencapai ukuran matang gonad (Lc = 65,8mm< Lm= 76,8 mm). Puncak musim pemijahan terjadi pada bulan Mei dan Agustus. Panjang asimtosis (CL∞ ) sebesar 119,5 mm dengan laju pertumbuhan (K) 0,39/tahun serta laju kematian total (Z) 1,44/tahun, laju kematian alamiah (M) 0,67/tahun dan laju keamatian akibat penangkapan (F) 0,77/tahun. Laju eksploitasi sudah mengarah kepada penangkapan yang berlebih (E=0,54), oleh karena itu perlu dilakukan tindakan pengelolaan perikanan lobster yang berkelanjutan. Salah satu upaya yang dapat di tempuh adalah dengan menerapkan sistem penutupan musim penangkapan lobster pada saat terjadinya puncak musim pemijahan.Research on the length distribution and population parameters of scalloped spiny lobster conducted in the Aceh Barat waters during April to November 2013. The aim of this study was to assess lobster fishery status in this waters from the point of view their length size and population parameters. Sampel collected randomly in the lobster landing site. Distribution of carapace length frequency was tabulated and analysed using logistic curve method. Length composition of male lobster was dominated under 72,5 mm midlenght, while female lobster was dominated above 72,5 mm midlength. This study found that the scalloped spiny lobster was caught before their reach the size of maturity (Lc = 65,8 mm < Lm = 76,8 mm). The peak season of spawning was indicated on May and August. Asimtotic length (CL∞) of scalloped spiny lobster was 119,5 mm with the growth rate (K) 0,39/year, total mortality (Z) 1,44/year, natural mortality (M) 0,67/year, and fishing mortality (F) 0,77/year. Exploitation rate was leading to the overfishing condition (E=0,54). Thus, it is needed to manage the lobster fishery in this area to gain the sustainability. We suggest that closing system season should be applied, especially in the peak spawning season.
Climate, habitat associations and the potential distributions of Neotropical birds: Implications for diversification across the Andes
Authors: Cadena Carlos Daniel , Pedraza Carlos A. , Brumfield Robb T. 
Published: October 2016

En contraste con la visión tradicional de que el levantamiento de los Andes impulsó la diversificación biótica causando vicarianza en varios grupos con distribuciones que antes eran continuas, investigaciones recientes sugieren que eventos de dispersión a través de los Andes sucedidos después de los principales episodios de levantamiento fueron catalizadores principales de la especiación en aves neotropicales, y que la habilidad de los linajes para persistir y dispersarse en el paisaje predice fuertemente los patrones de especiación. Sin embargo, se desconoce cuándo y dónde sucedieron dichos eventos de dispersión, y el papel de las fluctuaciones climáticas y el consecuente desplazamiento de la vegetación como promotores de la dispersión a través de los Andes en distintos momentos no ha sido estudiado. Empleamos modelos de la distribución potencial de especies basados en datos de clima actual e histórico para examinar escenarios de dispersión a través de los Andes en 41 especies de aves neotropicales de tierras bajas con diferentes afinidades de hábitat. Nuestros resultados indican que la conectividad ecológica que favorecería la dispersión a través de los Andes en el presente es mayor en pasos bajos de la cordillera del sur de Ecuador y el norte de Perú que en pasos bajos de Colombia, y este patrón espacial parece haberse mantenido en cuatro momentos diferentes de los últimos 130,000 años. También encontramos que aunque algunas áreas actualmente no serían propicias para la dispersión de las aves a través de los Andes, bajo condiciones climáticas del pasado (i.e. durante períodos más fríos y secos) presentaron condiciones climáticas sustancialmente más idóneas para permitir la conectividad ecológica de poblaciones a través de la cordillera. No encontramos diferencias consistentes en la conectividad ecológica presente y pasada a través de los Andes entre especies de diferentes tipos de hábitat. Sugerimos que los valles andinos impulsan la diversificación evolutiva no solo porque aíslan las poblaciones de especies de montaña, sino porque permiten la dispersión episódica de especies de las tierras bajas. Nuestros modelos permiten hacer predicciones sobre flujo genético que pueden ser evaluadas en estudios futuros que examinen patrones de intercambio genético a escala fina usando herramientas de genética del paisaje. © Acad. Colomb. Cienc. Ex. Fis. Nat. 2016.
Wireless Smart Node and Private Cloud Based Environmental Noise Monitoring System
Authors: Song Hao 
Published: October 2016

<p class="p1"><span class="s1">This paper introduces a wireless smart node and private cloud based city ambient noise detection and processing system. With the function of noise data preprocessing and storage, self-diagnostics, and power management, the smart node implements a high-precision, wide-area and continuous noise data acquisition in urban environment. Data are send back from smart node all-round the city to processing center running on private cloud through public mobile communication networks. Applications on the private cloud manage, analyzing and do a data fusion job with geographic information system. The system requires less setting and maintenance cost, and has more flexibility for update and extension. </span></p>
Deep Knowledge: A Strategy For University Budgetary Cuts
Authors: Reynolds Douglas B. 
Published: October 2016

During and after the Financial Crisis of 2008, many institutions of higher learning have had revenue and budgetary reductions, forcing them to make severe university budget cuts and university reductions in force. Often the university cuts are preceded by a process of evaluation of academic programs where institutions determine what they stand for and value. One option, when forced to downsize, is to use a business model, such as Sullivan (2004) explains, where high-value, low-cost programs are kept and low-value, high-cost programs are cut. However, a business model of education does not reflect the true social value of education or the importance of arts, sciences and humanities, where students learn how to struggle with, write about and understand the world. John Henry Cardinal Newman’s (1852) treatise, The Idea of a University, suggests an alternative strategy of cost cutting that has to do with deep knowledge, i.e. keep the oldest programs in existence on a given university. Using the deep knowledge concept, a university will cut young (junior programs) first and retain old (senior) programs until the very last, rather than deciding cuts based on a business model. The deep knowledge concept emphasizes a Socratic ideal where professors and students wrestle over concepts, such as the meaning of “beauty.”