bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tectonic Evolution of the Western Margin of the Burma Microplate Based on New Fossil and Radiometric Age Constraints
Authors: Aitchison Jonathan C. , Ao Aliba , Bhowmik Santanu , Clarke Geoffrey L. , Ireland Trevor R. , Kachovich Sarah , Lokho Kapesa , Stojanovic Denis , Roeder Tara , Truscott Naomi , Zhen Yan , Zhou Renjie 
Published: April 2019

AbstractResults of biostratigraphic and geochronological investigations in eastern Nagaland and Manipur, NE India, provide new constraints on the tectonic evolution of the western margin of the Burma microplate. U/Pb zircon ages indicate that the Naga Hills ophiolite developed in a suprasubduction zone setting as part of an intraoceanic island arc developed during late Early Cretaceous (mid‐Aptian) time and is younger than similar rocks exposed along the Indus‐Yarlung Tsangpo suture zone. Radiolarian microfossils provide Jurassic and Cretaceous age constraints for Tethyan ocean floor sediments that were subducted beneath the forming ophiolite. Timing of the emplacement of these rocks onto the passive margin of eastern India is constrained by Paleocene/Eocene radiolarians in sediments over which the ophiolitic assemblage has been thrust. Previously undated schists and gneisses in the Naga Metamorphics are of Early Ordovician age, and their sedimentary protolith was most likely derived from sources in the south of Western Australian and East Antarctica. After Barrovian‐style metamorphism, these rocks were uplifted and eroded becoming an important source of detritus shed into the Eocene Phokphur Formation. This unit also contains abundant clasts sourced from the disrupted basement of the Naga Hills ophiolite, which it overlies. It also contains Permo‐Triassic‐aged detritus eroded off an enigmatic source that was possibly a continental convergent margin arc system somewhere along the northern margin of Gondwana.
The Stat3-Fam3a axis promotes muscle stem cell myogenic lineage progression by inducing mitochondrial respiration
Authors: Sala David , Cunningham Thomas J. , Stec Michael J. , Etxaniz Usue , Nicoletti Chiara , Dall’Agnese Alessandra , Puri Pier Lorenzo , Duester Gregg , Latella Lucia , Sacco Alessandra 
Published: April 2019

AbstractMetabolic reprogramming is an active regulator of stem cell fate choices, and successful stem cell differentiation in different compartments requires the induction of oxidative phosphorylation. However, the mechanisms that promote mitochondrial respiration during stem cell differentiation are poorly understood. Here we demonstrate that Stat3 promotes muscle stem cell myogenic lineage progression by stimulating mitochondrial respiration in mice. We identify Fam3a, a cytokine-like protein, as a major Stat3 downstream effector in muscle stem cells. We demonstrate that Fam3a is required for muscle stem cell commitment and skeletal muscle development. We show that myogenic cells secrete Fam3a, and exposure of Stat3-ablated muscle stem cells to recombinant Fam3a in vitro and in vivo rescues their defects in mitochondrial respiration and myogenic commitment. Together, these findings indicate that Fam3a is a Stat3-regulated secreted factor that promotes muscle stem cell oxidative metabolism and differentiation, and suggests that Fam3a is a potential tool to modulate cell fate choices.
Design of a 100 kHz wide bandgap inverter for motor applications with active damped sine wave filter
Authors: Maislinger Franz , Ertl Hans , Stojcic Goran , Lagler Christoph , Holzner Florian 
Published: April 2019

In this study, a three‐phase motor inverter with sinusoidal output voltages based on the application of gallium nitride transistors and advanced control is analysed. In comparison to standard silicon‐insulated gate bipolar transistors much higher feasible switching frequencies of 100 kHz and above are possible and reduce the output sine filter component size such that the filter can be directly included into the inverter. This considerably improves the electromagnetic interference (EMI) behaviour of the drive system as well as the acoustic noise, eases the inverter‐to‐motor wiring and protects the motor isolation against high du /dt rates. The study describes the dimensioning and design of the used two‐stage LC filter including motor current control based on proportional‐integral‐type phase current controllers. The LC filter damping is performed actively by capacitor current feedback. Using this active damping scheme avoids additional losses of conventional sine filters and guarantees high system efficiency up to 98%. Finally, experimental results of a laboratory prototype verify the proper behaviour of the proposed concept.
The combination of 13N-ammonia and
18F-FDG PET/CT in the identification of metabolic phenotype of
primary human brain tumors
Authors: Yi Chang , Shi Xinchong , Yu Donglan , Luo Ganhua , Zhang Bing , He Qiao , Zhang Xiangsong 
Published: April 2019

Abstract
Aim This pilot study made a preliminary attempt to distinguish different
metabolic phenotypes of primary human brain tumors with dual tracer
13N-ammonia and 18F-FDG.
Methods 74 patients were included in this study including 12 benign
meningiomas (B-MEN), 4 malignant meningiomas (M-MEN), 15 low-grade gliomas
(LGG), 32 high-grade gliomas (HGG) and 11 primary central nervous system
lymphomas (PCNSL). All patients underwent 13N-ammonia and
18F-FDG PET imaging. Semi-quantification analysis by
tumor-to-gray matter (T/G) ratios was used for the evaluation of tracer uptakes.
After the calculation of canonical discriminant functions, cross validation was
done for all cases to evaluate the differential efficacy of dual tracers.
Results According to the visual analysis, B-MEN were characterized by
lower uptake of 18F-FDG and higher uptake of 13N-ammonia,
while PCNSLs displayed contrary results. Both M-MEN and HGG had higher uptake of
18F-FDG and 13N-ammonia, while LGG displayed negative
results for both tracers. According to the T/G ratios analysis, the accuracy of
predicted tumor classification by means of canonical discriminant analysis for
B-MEN, LGG, HGG and PCNSL was 91.7 %, 100 %, 84.4 % and 93.3 % respectively; the
overall accuracy was 90.5 %.
Conclusion The combination of dual tracer 13N-ammonia and
18F-FDG has a certain potential in distinguishing different types
of brain tumors (meningiomas, gliomas and PCNSL). However, an advantage of the
additional use of 13N-ammonia PET compared to a combined diagnosis
with MRI and 18F-FDG PET could not be demonstrated and requires
further studies.
Characterization of Major and Clinically Relevant Non-Major Bleeds in the APEX Trial
Authors: Yee Megan , Gibson C. , Nafee Tarek , Kerneis Mathieu , Daaboul Yazan , Korjian Serge , Chi Gerald , AlKhalfan Fahad , Hernandez Adrian , Hull Russell , Cohen Alexander , Goldhaber Samuel 
Published: April 2019

Background Among medically ill patients treated with thromboprophylaxis, betrixaban was not associated with an increase in major bleeding compared with enoxaparin, but an increase in clinically relevant non-major (CRNM) bleeding was observed. The aim of this analysis is to describe the severity and clinical consequences of major and CRNM bleeding in the APEX trial.
Methods The APEX trial randomized 7,513 hospitalized acutely ill medical patients to receive either enoxaparin for 6 to 14 days or betrixaban for 35 to 42 days. Subjects receiving a concomitant strong p-glycoprotein inhibitor or with creatinine clearance <30 mL/min were administered a reduced dose of study drug.
Results A total of 25 (0.7%) and 21 (0.6%) major bleeds occurred in the betrixaban and enoxaparin arms, respectively (p = NS) and a total of 91 (2.5%) and 38 (1.0%) CRNM bleeds occurred in the betrixaban and enoxaparin arm (p < 0.001), respectively. Most major bleeds were considered moderate or severe and most CRNM bleeds were considered mild and moderate (p = NS). One fatal major bleed occurred in each treatment arm. Rates of major or CRNM bleeds resulting in new or prolonged hospitalization (major: 44.0 vs. 28.6%; CRNM: 12.1 vs. 21.1%) or study treatment interruption or cessation (major: 72.0 vs. 71.4%; CRNM: 71.3 vs. 68.4%) were similar between treatment arms (p = NS).
Conclusions In the APEX trial, CRNM bleeds were mild or moderate in nature and had less of a clinical impact than major bleeds. The severity and clinical sequela of bleeds in the betrixaban arm were comparable to those in the enoxaparin arm.
Clinical Trial Registration URL: http://www.clinicaltrials.gov.; Unique identifier: NCT01583218.
S-shaped microfiber based diaphragm supported optical microphone
Authors: Dass Sumit , Kachhap Santosh , Jha Rajan 
Published: April 2019

Abstract
We propose and demonstrate a simple and highly sensitive optical microphone based on S-shaped tapered fibre (STF). The short pigtailed end of the STF is attached to the centre of a thin circular nitrile diaphragm. The applied acoustic signal deforms the nitrile diaphragm and due to the affixation, the STF structure gets modified leading to change in the bending angles of the two STF bends. As a consequence, the photodetector output, detecting the reflected light intensity of the STF, varies in accordance with the applied acoustic signal. Various properties of the proposed sensing setup can be easily tailored by changing the diaphragm diameter and thickness, and the shapes and size of the STF. For an optimized configuration, the proposed sensor achieves a sensitivity of 3.07 mV Pa−1 and a minimum detectable pressure of 36.48 mPa Hz−1. The sensor shows a linear behaviour up to 1300 Hz and the experimental value of its first order natural frequency is 1455 Hz.
NGSEP3: accurate variant calling across species and sequencing protocols
Authors: Tello Daniel , Gil Juanita , Loaiza Cristian D , Riascos John J , Cardozo Nicolás , Duitama Jorge 
Published: April 2019

AbstractMotivationAccurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features.ResultsUnderstanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algorithms for realignment and haplotype clustering of reads spanning indels and short tandem repeats. We performed extensive benchmark experiments comparing NGSEP to state-of-the-art software using real data from three sequencing protocols and four species with different distributions of repetitive elements. NGSEP consistently shows comparative accuracy and better efficiency compared to the existing solutions. We expect that this work will contribute to the continuous improvement of quality in variant calling needed for modern applications in medicine and agriculture.Availability and implementationNGSEP is available as open source software at http://ngsep.sf.net.Supplementary informationSupplementary data are available at Bioinformatics online.
sbgntikz—a TikZ library to draw SBGN maps
Authors: Rougny Adrien 
Published: April 2019

Abstract

Summary
The systems biology graphical notation (SBGN) has emerged as the main standard to represent biological maps graphically. It comprises three complementary languages: Process Description, for detailed biomolecular processes; Activity Flow, for influences of biological activities and Entity Relationship, for independent relations shared among biological entities. On the other hand, TikZ is one of the most commonly used package to ‘program’ graphics within TEX/LATEX. Here, we present sbgntikz, a TikZ library that allows drawing and customizing SBGN maps directly into TEX/LATEX documents, using the TikZ language. sbgntikz supports all glyphs of the three SBGN languages, and offers options that facilitate the drawing of complex glyph assembly within TikZ. Furthermore, sbgntikz is provided together with a converter that allows transforming any SBGN map stored under the SBGN Markup Language into a TikZ picture, or rendering it directly into a PDF file.

Availability and implementation
sbgntikz, the SBGN-ML to sbgntikz converter, as well as a complete documentation can be freely downloaded from https://github.com/Adrienrougny/sbgntikz/. The library and the converter are compatible with all recent operating systems, including Windows, MacOS, and all common Linux distributions.

Supplementary information
Supplementary material is available at Bioinformatics online.
A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery
Authors: Watson Oliver P , Cortes-Ciriano Isidro , Taylor Aimee R , Watson James A 
Published: April 2019

AbstractMotivationArtificial intelligence, trained via machine learning (e.g. neural nets, random forests) or computational statistical algorithms (e.g. support vector machines, ridge regression), holds much promise for the improvement of small-molecule drug discovery. However, small-molecule structure-activity data are high dimensional with low signal-to-noise ratios and proper validation of predictive methods is difficult. It is poorly understood which, if any, of the currently available machine learning algorithms will best predict new candidate drugs.ResultsThe quantile-activity bootstrap is proposed as a new model validation framework using quantile splits on the activity distribution function to construct training and testing sets. In addition, we propose two novel rank-based loss functions which penalize only the out-of-sample predicted ranks of high-activity molecules. The combination of these methods was used to assess the performance of neural nets, random forests, support vector machines (regression) and ridge regression applied to 25 diverse high-quality structure-activity datasets publicly available on ChEMBL. Model validation based on random partitioning of available data favours models that overfit and ‘memorize’ the training set, namely random forests and deep neural nets. Partitioning based on quantiles of the activity distribution correctly penalizes extrapolation of models onto structurally different molecules outside of the training data. Simpler, traditional statistical methods such as ridge regression can outperform state-of-the-art machine learning methods in this setting. In addition, our new rank-based loss functions give considerably different results from mean squared error highlighting the necessity to define model optimality with respect to the decision task at hand.Availability and implementationAll software and data are available as Jupyter notebooks found at https://github.com/owatson/QuantileBootstrap.Supplementary informationSupplementary data are available at Bioinformatics online.
Diagnostic Accuracy of Transabdominal Ultrasound in Detecting Intestinal Inflammation in Paediatric IBD Patients—a Systematic Review
Authors: van Wassenaer Elsa A , de Voogd Floris A E , van Rijn Rick R , van der Lee Johanna H , Tabbers Merit M , van Etten-Jamaludin Faridi S , Gecse Krisztina B , Kindermann Angelika , de Meij Tim G J , D’Haens Geert R , Benninga Marc A , Koot Bart G P 
Published: April 2019

Abstract

Background and Aims
Currently used non-invasive tools for monitoring children with inflammatory bowel disease [IBD], such as faecal calprotectin, do not accurately reflect the degree of intestinal inflammation and do not provide information on disease location. Ultrasound [US] might be of added value. This systematic review aimed to assess the diagnostic test accuracy of transabdominal US in detecting intestinal inflammation in children with IBD in both diagnostic and follow-up settings.

Methods
We systematically searched PubMed, Embase [Ovid], Cochrane Library, and CINAHL [EBSCO] databases for studies assessing diagnostic accuracy of transabdominal US for detection of intestinal inflammation in patients diagnosed or suspected of IBD, aged 0–18 years, with ileo-colonoscopy and/or magnetic resonance enterography [MRE] as reference standards. Studies using US contrast were excluded. Risk of bias was assessed with QUADAS-2.

Results
The search yielded 276 records of which 14 were included. No meta-analysis was performed, because of heterogeneity in study design and methodological quality. Only four studies gave a clear description of their definition for an abnormal US result. The sensitivity and specificity of US ranged from 39-93% and 90–100% for diagnosing de novo IBD, and 48–93% and 83–93% for detecting active disease during follow-up, respectively.

Conclusions
The diagnostic accuracy of US in detecting intestinal inflammation as seen on MRE and/or ileo-colonoscopy in paediatric IBD patients remains inconclusive, and there is currently no consensus on defining an US result as abnormal. Prospective studies with adequate sample size and methodology are needed before US can be used in the diagnostics and monitoring of paediatric IBD.
Performance study of coal-fired power generation system combined with renewable solar energy source based on thermodynamic analysis
Authors: Wang Juan 
Published: April 2019

Abstract
China’s coal resources are abundant, so the total amount of carbon emissions is large. In order to achieve ecologically sustainable development, clean energy such as solar energy is used to generate electricity. This study briefly introduced the composition and working process of solar energy and coal-fired power generation system, analyzed its working principle with thermodynamics, established the corresponding thermodynamic model to simulate and then analyzed the change of the photoelectric conversion efficiency and the levelized cost of energy (LCOE) with the change of collector area under different loads of solar energy and coal-fired power generation system. The results showed that the photoelectric conversion efficiency increased first and then decreased with the increase of the collector area under different loads, and the higher the load was, the higher the photoelectric conversion efficiency would be; the LCOE decreased first and then increased with the increase of the collector area under different loads, and the higher the load was, the lower the LCOE would be.
Cognitive Psychology and the Metaphysics of Meaning
Authors: Johnston Mark , Leslie Sarah-Jane 
Published: April 2019

Abstract
This chapter distinguishes the clusters of psychologically real heuristics that govern our use of terms—the “psi-concepts”—from the “phi-concepts” or meanings that are the semantic determinants of the extensions of the terms in question, and hence of the truth-conditions of the sentences that contain those terms. Concerning the psi-concepts the chapter proposes a new, empirically motivated, and philosophically consequential amendment to both the theory-theory and the prototype theory, namely the generic encoding hypothesis: the heuristics which typically guide our use of terms by exploiting prevalence, cue-validity, and causal explanatory structure are properly formulated in generic terms. The chapter then explores the philosophical consequences of the generic encoding hypothesis, exploring its destructive impact on the method of cases (with particular attention to its use in the philosophy of personal identity), philosophical analysis, the “normativity of meaning,” and the idea that we know how to use terms by grasping meanings.
Confessors
Authors: Bugyis Katie Ann-Marie 
Published: April 2019

Abstract
The chief aim of Chapter 4 is to reassess the impact of both local and more universal reform efforts to clericalize the practice of penance in communities of Benedictine nuns during the central Middle Ages. According to the prevailing historiography, various reform efforts over the tenth, eleventh, and twelfth centuries effectively charged priests with hearing nuns’ confessions. Yet, as this chapter shows, study of the extant prayer books and psalters, produced by or altered for nuns’ use, demonstrates that they served as confessors not only for their consorors but also for visiting pilgrims and laity affiliated with their communities. Several of these prayers are adaptations of mass-texts traditionally said by priests within the context of the Mass and would have cast the women who recited them in markedly sacerdotal roles and even recognized their performance of ministries around the altars of their churches, including handling the eucharistic vessels and consecrated elements.
Conclusion
Authors: Bugyis Katie Ann-Marie 
Published: April 2019

Abstract
The Conclusion offers a final assessment of the use of the term “ministry” in the preceding chapters to comprehend the variety of liturgical and pastoral roles and responsibilities—both in their idealized forms and in their actual practices—that Benedictine nuns in England assumed during the central Middle Ages according to the sources that preserve their lives. It also stresses the need for future scholarship to pursue the threads of continuity in Benedictine nuns’ ministries across the central and later Middle Ages. Close studies of the extant documents of practice and other material remains from women’s communities in late medieval England may yet unveil more ministers of Christ, charged with the spiritual care of fellow sisters, laity, vowed religious, and clerics who sought their hospitality, counsel, instruction, healing, absolution, and intercession.
Tethered Fates
Authors: Hertel Shareen 
Published: April 2019

Abstract
Global supply chains extend throughout the developing world, but we know surprisingly little about company–community interaction. This book engages multiple sources of data to map the evolution and contemporary scope of “stakeholder dialogue” in the business and human rights arena. It draws on the 7,000-company database of the Business and Human Rights Resource Centre, and on original interviews with community members in two factory towns in the Dominican Republic, to illustrate economic rights challenges in light manufacturing communities. Tethered Fates maps trends in stakeholder dialogue by region and industry sector globally. It demonstrates that companies tend to engage stakeholders in sectors where the sunk costs are high (such as the extractive sector) rather than in sectors where the threat of exit looms large (such as light manufacturing). The book then offers a view into local community members’ perceptions of the prospects for dialogue with companies and the challenges of everyday life, through comparative case studies of two textile manufacturing towns in the Dominican Republic. Tethered Fates does more than simply explain why stakeholder dialogue often falls short as a vehicle for safeguarding economic rights and promoting community development; it also offers an assessment of the varieties of emerging policy alternatives for moving beyond the current state of practice.