bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Age, Joint Angle, and Test Modality on Strength Production and Functional Outcomes
Authors: Thompson Brennan , Whitson Morgan , Sobolewski Eric , Stock Matt 
Published: November 2017

AbstractThis study investigated the impact of age, knee joint angle, and strength testing modality on lower body maximal and rapid strength production and assessed the transferability of these characteristics to mobility-related function. Twenty young (age=21.9 yrs) and eighteen elderly (71.1 yrs) adults performed single-joint and multiple-joint isometric maximal voluntary contractions at three knee angles. Outcome measures included peak torque (PT), rate of torque development (RTD), jump height, power, 10 and 400 m walk, and timed chair stand. Older adults exhibited greater reductions in RTD for the multiple-joint (45%) than for the single-joint mode (18%). The 10 m walk was best predicted by multiple-joint RTD at 90°, the 400 m walk by jump height, and the chair stand by single-joint PT at 20°. Single-joint strength tests may underestimate age-related rapid strength impairments, likely due to requirements to exert muscular force in excess of one’s body mass in an upright position.
Does Metabolic Rate Increase Linearly with Running Speed in all Distance Runners?
Authors: Batliner Matthew , Kipp Shalaya , Grabowski Alena , Kram Rodger , Byrnes William 
Published: November 2017

AbstractRunning economy (oxygen uptake or metabolic rate for running at a submaximal speed) is one of the key determinants of distance running performance. Previous studies reported linear relationships between oxygen uptake or metabolic rate and speed, and an invariant cost of transport across speed. We quantified oxygen uptake, metabolic rate, and cost of transport in 10 average and 10 sub-elite runners. We increased treadmill speed by 0.45 m·s−1 from 1.78 m·s−1 (day 1) and 2.01 m·s−1 (day 2) during each subsequent 4-min stage until reaching a speed that elicited a rating of perceived exertion of 15. Average runners’ oxygen uptake and metabolic rate vs. speed relationships were best described by linear fits. In contrast, the sub-elite runners’ relationships were best described by increasing curvilinear fits. For the sub-elites, oxygen cost of transport and energy cost of transport increased by 12.8% and 9.6%, respectively, from 3.58 to 5.14 m·s−1. Our results indicate that it is not possible to accurately predict metabolic rates at race pace for sub-elite competitive runners from data collected at moderate submaximal running speeds (2.68–3.58 m·s−1). To do so, metabolic rate should be measured at speeds that approach competitive race pace and curvilinear fits should be used for extrapolation to race pace.
Thyroid Stimulating Hormone Within the Reference Range is Associated with Visceral Adiposity Index and Lipid Accumulation Product: A Population-Based Study of SPECT-China
Authors: Chen Yi , Chen Yingchao , Wang Ningjian , Chen Chi , Nie Xiaomin , Li Qin , Han Bing , Lu Yingli 
Published: November 2017

AbstractFew studies about the relationship of thyroid stimulating hormone (TSH) level with visceral adiposity index (VAI) and lipid accumulation product (LAP) in large Chinese population are available. The aim of this study was to explore whether TSH level within the reference range was associated with these two newer reliable cardiovascular risk factors. The data were obtained from a cross-sectional study (SPECT-China study, 2014–2015), which was based on the population. Participants underwent several checkups, which included anthropometric parameters, blood pressure, TSH levels, and glucose and lipid profiles. VAI and LAP were calculated. A total of 8727 subjects were enrolled in this study. The mean age was 53.00±13.05 years. Age, female to male ratio, BMI, systolic pressure, and HOMA-IR increased along with the increasing levels of TSH (p<0.01). Analysis of lipid profile showed significantly higher serum triglycerides and LDL cholesterol levels in the higher TSH quartile (p<0.001 and p=0.028, respectively). The levels of VAI and LAP were all increased along with increasing TSH level (all p<0.001). After full adjustment, TSH levels were positively associated with VAI, LAP, and TG/HDL levels significantly (B=0.041, 0.028 and 0.037, respectively, all p<0.01). Higher TSH concentrations among the reference range were common in older people as well as in women subjects, and they were positively associated with VAI and LAP. This highlighted that even subtle variations of serum TSH within the normal range may be potential risk factors for cardiovascular diseases.
A subset of extracellular vesicles carries the bulk of microRNAs in commercial dairy cow's milk
Authors: Benmoussa Abderrahim , Ly Sophia , Shan Si Ting , Laugier Jonathan , Boilard Eric , Gilbert Caroline , Provost Patrick 
Published: November 2017

ABSTRACTMicroRNAs are small gene‐regulatory RNAs that are found in various biological fluids, including milk, where they are often contained inside extracellular vesicles (EVs), like exosomes. In a previous study, we reported that commercial dairy cow's milk microRNAs resisted simulated digestion and were not exclusively associated with canonical exosomes. Here, we report the characterization of a milk EV subset that sediments at lower ultracentrifugation speeds and that contains the bulk of microRNAs. Milk EVs were isolated by differential ultracentrifugation and Iodixanol density gradient (IDG), and analysed for (1) microRNA enrichment by reverse transcription and quantitative polymerase chain reaction (RT‐qPCR), and (2) EV‐associated proteins by Western blot. Milk EVs were characterized further by dynamic light scattering (DLS), density measurements, fluorescent DiR and RNA labelling, high‐sensitivity flow cytometry (HS‐FCM), transmission electron microscopy (TEM), proteinase K and RNase A assay, and liquid chromatography tandem‐mass spectrometry (LC‐MS/MS). We found that the bulk of milk microRNAs (e.g., bta‐miR‐125b, bta‐miR‐148a, etc.) sediment at 12,000 g and 35,000 g. Their distribution pattern was different from that of exosome‐enriched proteins, but similar to that of several proteins commonly found in milk fat globule membranes (MFGM), including xanthine dehydrogenase (XDH). These low‐speed ultracentrifugation pellets contained cytoplasm‐enclosing phospholipid bilayered membrane vesicles of a density comprised between 1.11 and 1.14 g/mL in Iodixanol. This milk EV subset of ~100 nm in diameter/~200 nm hydrodynamic size resisted to proteinase K digestion and protected their microRNA content from RNase A digestion. Our results support the existence of a milk EV subset pelleting at low ultracentrifugations speeds, with a protein coating comparable with MFGM, which contains and protects the bulk of milk microRNAs from degradation. This milk EV subset may represent a new EV population of interest, whose content in microRNAs and proteins supports its potential bioactivity.
CALQ: compression of quality values of aligned sequencing data
Authors: Voges Jan , Ostermann Jörn , Hernaez Mikel 
Published: November 2017

Abstract

Motivation
Recent advancements in high-throughput sequencing technology have led to a rapid growth of genomic data. Several lossless compression schemes have been proposed for the coding of such data present in the form of raw FASTQ files and aligned SAM/BAM files. However, due to their high entropy, losslessly compressed quality values account for about 80% of the size of compressed files. For the quality values, we present a novel lossy compression scheme named CALQ. By controlling the coarseness of quality value quantization with a statistical genotyping model, we minimize the impact of the introduced distortion on downstream analyses.

Results
We analyze the performance of several lossy compressors for quality values in terms of trade-off between the achieved compressed size (in bits per quality value) and the Precision and Recall achieved after running a variant calling pipeline over sequencing data of the well-known NA12878 individual. By compressing and reconstructing quality values with CALQ, we observe a better average variant calling performance than with the original data while achieving a size reduction of about one order of magnitude with respect to the state-of-the-art lossless compressors. Furthermore, we show that CALQ performs as good as or better than the state-of-the-art lossy compressors in terms of variant calling Recall and Precision for most of the analyzed datasets.

Availability and implementation
CALQ is written in C ++ and can be downloaded from https://github.com/voges/calq.

Supplementary information
Supplementary data are available at Bioinformatics online.
scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data
Authors: Liu Tong , Wang Zheng 
Published: November 2017

Abstract

Summary
We build a software package scHiCNorm that uses zero-inflated and hurdle models to remove biases from single-cell Hi-C data. Our evaluations prove that our models can effectively eliminate systematic biases for single-cell Hi-C data, which better reveal cell-to-cell variances in terms of chromosomal structures.

Availability and implementation
scHiCNorm is available at http://dna.cs.miami.edu/scHiCNorm/. Perl scripts are provided that can generate bias features. Pre-built bias features for human (hg19 and hg38) and mouse (mm9 and mm10) are available to download. R scripts can be downloaded to remove biases.

Supplementary information
Supplementary data are available at Bioinformatics online.
Reactome diagram viewer: data structures and strategies to boost performance
Authors: Fabregat Antonio , Sidiropoulos Konstantinos , Viteri Guilherme , Marin-Garcia Pablo , Ping Peipei , Stein Lincoln , D’Eustachio Peter , Hermjakob Henning 
Published: November 2017

Abstract

Motivation
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community.

Results
The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources.

Availability and implementation
Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram.

Supplementary information
Supplementary data are available at Bioinformatics online.
PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool
Authors: Zhou Anbo , Zhang Yeting , Sun Yazhou , Xing Jinchuan 
Published: November 2017

Abstract

Summary
Analysis pipelines are an essential part of bioinformatics research, and ad hoc pipelines are frequently created by researchers for prototyping and proof-of-concept purposes. However, most existing pipeline management system or workflow engines are too complex for rapid prototyping or learning the pipeline concept. A lightweight, user-friendly and flexible solution is thus desirable. In this study, we developed a new pipeline construction and maintenance tool, PipelineDog. This is a web-based integrated development environment with a modern web graphical user interface. It offers cross-platform compatibility, project management capabilities, code formatting and error checking functions and an online repository. It uses an easy-to-read/write script system that encourages code reuse. With the online repository, it also encourages sharing of pipelines, which enhances analysis reproducibility and accountability. For most users, PipelineDog requires no software installation. Overall, this web application provides a way to rapidly create and easily manage pipelines.

Availability and implementation
PipelineDog web app is freely available at http://web.pipeline.dog. The command line version is available at http://www.npmjs.com/package/pipelinedog and online repository at http://repo.pipeline.dog.

Supplementary information
Supplementary data are available at Bioinformatics online.
SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles
Authors: Koehorst Jasper J , van Dam Jesse C J , Saccenti Edoardo , Martins dos Santos Vitor A P , Suarez-Diez Maria , Schaap Peter J 
Published: November 2017

AbstractSummaryTo unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used to process and analyze existing genome annotations. SAPP automatically predicts, tracks and stores structural and functional annotations and associated dataset- and element-wise provenance in a Linked Data format, thereby enabling information mining and retrieval with Semantic Web technologies. This greatly reduces the administrative burden of handling multiple analysis tools and versions thereof and facilitates multi-level large scale comparative analysis.Availability and implementationSAPP is written in JAVA and freely available at https://gitlab.com/sapp and runs on Unix-like operating systems. The documentation, examples and a tutorial are available at https://sapp.gitlab.io.
Resolution of Balance-of-Payments Crises
Authors: Ocampo José Antonio 
Published: November 2017

AbstractThis chapter analyses the history and effectiveness of the two major mechanisms of resolution of balance-of-payments crises: IMF emergency financing and complementary mechanisms, and sovereign debt workouts. It argues that IMF lending has historically met its counter-cyclical objectives and has been improving in recent decades in terms of providing adequate lending facilities as well as focusing conditionality on macro-relevant areas. Swap arrangements among central banks constitute the most important complementary mechanism, but benefit mainly developed countries. In contrast to advances in IMF financing, the need to have a better framework for debt resolution remains one of the major gaps of the international financial architecture. In this regard, this chapter proposes a multilateral mechanism that would lie between the voluntary and statutory solutions that have been proposed in the global debate. This mechanism would offer a sequence of voluntary negotiations, mediation, and eventual arbitration that would take place with pre-established deadlines.
Introduction
Authors: Ludwig Kirk 
Published: November 2017

AbstractChapter 1 sets out the problem of institutional agency, explains the project and its methodology, describes the structure of the book, and gives advice to readers on navigating through it. The central problem of institutional action is to understand how the structure of institutions is grounded in more primitive forms of joint intentional action, and how those more primitive forms of joint intentional action are expressed through those institutional structures. The project aims to uncover the conceptual structure of institutional agency, taking as examples familiar institutions. It starts with the question of the logical form of grammatically singular group action sentences, that is, action sentences about mobs and organizations and institutions, and then provides reductive analyses of key notions in understanding institutional action in particular, namely, constitutive rules, status functions and roles, institutional membership, and proxy agency.
Status Functions as Agentive Functions
Authors: Ludwig Kirk 
Published: November 2017

AbstractChapter 8 begins the analysis of status functions by locating them within the broader category of agentive functions. It starts with a taxonomy of agentive functions that relies on the different bases on which we attribute them and places them in relation to the overlapping category of artefacts. Then it identifies status functions as a subcategory and analyzes them as arising from the need for agents to coordinate on, or collectively accept, the same things as filling roles in joint activities defined by constitutive rules. It distinguishes between status functions attached to types and to tokens. Finally, it considers the status of counterfeits, how we understand activities into which they are introduced, and what to say when an agent intends to introduce a counterfeit but mistakenly uses the real thing.
Kinds of Status Functions
Authors: Ludwig Kirk 
Published: November 2017

AbstractChapter 10 first discusses a subcategory of status function, the status role, which is occupied by an agent, and partially defined in terms of how the agent is to exercise her agency in that role. Second, it discusses the nature of the rights and responsibilities associated with status roles, and then whether role responsibilities generate desire-independent reasons for action. Third, it describes the role of status indicators, which are themselves status functions whose role is to make identification of other functions and roles more perspicuous. Fourth, it distinguishes between determinable and determinate status functions. Last, it discusses the relation of status functions to design functions and our ordinary terminology for the sorts of things we press into service as bearers of status functions.
Group Membership
Authors: Ludwig Kirk 
Published: November 2017

AbstractChapter 11 is concerned with the nature of the membership relation relevant to sorting agents under the concept of a mob or organization and the nature of groups organized under such relations. First, it develops a taxonomy of different sorts of groups, distinguishing natural groups, institutions or organizations, and mobs and crowds. Second, it provides an account of membership in institutions, the key idea of which is that membership is a matter of having a determinable status role characterized by the nature of the relevant institution. Third, it takes up a counting puzzle connected with the reductive view of organizations. If an organization at a time is nothing but its members, then two clubs with the same members are the same, but this seems counterintuitive. Finally, it gives an analysis of membership specifically in mobs and crowds.
The Division of Labor and Proxy Agency
Authors: Ludwig Kirk 
Published: November 2017

AbstractChapter 13 first lays out the problem of proxy agency. An example of a proxy agent is a spokesperson for an organization. When the spokesperson, appropriately authorized, in the right conditions, with the right intention and message, speaks, we count the group as announcing something. Thus, it appears that the group does something but only one of its members acts. Proxy agency appears then to be inconsistent with the multiple agents analysis of collective action. Chapter 13 provides an account of proxy agency, focusing on the case of a spokesperson, that draws on the notion of a status function and constitutive agency to show it can be compatible with the multiple agents account of institutional action. Then it clarifies and extends the account by defending it against objections. Finally, it discusses the systematic use of the same terms in different senses in relation to individual and institutional agency.
Introduction
Authors: Allen Michael P. , Tildesley Dominic J. 
Published: November 2017

Abstract
This chapter contains a short review of the development of computer simulation, and its place in research as a complement to experiment and theory. This is followed by an introduction to intermolecular interactions, and the way that they are modelled on a computer, complete with examples of program code. Force fields are introduced to describe the full range of interactions in atomic and molecular fluids and a number of coarsegrained models for exploring liquid-crystalline and polymer systems are also considered. The consequences of performing bulk simulations using finite-size systems are described, along with the way that these problems can be mitigated by the use of periodic boundary conditions.
Ancient Near Eastern Sources
Authors: Nissinen Martti 
Published: November 2017

AbstractThis chapter constitutes a comprehensive and up-to-date overview of the available sources of the prophetic phenomenon in the ancient Near East. The texts are presented according to textual genres, which yield different kinds of information on prophets, their activities, prophetic oracles, and their interpretation. Lexical lists and omen texts associate prophets with temple personnel and people with liminal roles. Legal and administrative texts as well as ritual texts document the presence of prophets in temple communities, whereas letters report their performances to kings of Mari and Assyria. Written oracles provide examples of early transcripts of spoken oracles, whereas texts containing literary prophecy document their use and interpretation. Most of the texts are written in Akkadian, but even some West Semitic, Luwian (Tell Ahmar stele) and Egyptian texts (Report of Wenamun) are available.
Perioperative Complications of Cesarean Delivery Myomectomy
Authors: Pergialiotis Vasilios , Sinanidis Ilias , Louloudis Ioannis-Evangelos , Vichos Theodoros , Perrea Despina N. , Doumouchtsis Stergios K. 
Published: November 2017

OBJECTIVE:
To assess the association of myomectomy during cesarean delivery with intraoperative and perioperative maternal morbidity.

DATA SOURCES:
We searched MEDLINE (1966–2017), Scopus (2004–2017), ClinicalTrials.gov (2008–2017), EMBASE (1980–2017), and Cochrane Central Register of Controlled Trials CENTRAL (1999–2017) databases.

METHODS OF STUDY SELECTION:
We selected all observational studies that reported outcomes on patients undergoing myomectomy at the time of cesarean delivery. Statistical meta-analysis was performed with RevMan 5.3.

RESULTS:
Nineteen studies were included in our systematic review with a total number of 3,900 women. Among them, 2,301 women had myomectomy during cesarean delivery and 1,599 had cesarean delivery only. Women undergoing concomitant myomectomy had a mild decline in hemoglobin compared with those who had cesarean delivery only (mean difference 0.25 mg/dL, 95% CI 0.06–0.45). Myomectomy at the time of cesarean delivery is associated with longer surgical time compared with cesarean delivery alone (mean difference 13.87 minutes, 95% CI 4.78–22.95). Blood transfusion (odds ratio [OR] 1.41, 95% CI 0.96–2.07) and postoperative fever (OR 1.12, 95% CI 0.80–1.56) rates did not differ between the two groups (myomectomy compared with no myomectomy). A statistically, but not clinically, significant increase in postoperative hospitalization was evident in the myomectomy group (mean difference 0.35 days, 95% CI 0.25–0.46).

CONCLUSION:
This systematic review and meta-analysis of observational studies demonstrated an association with increased operative time and hemoglobin drop in patients who underwent cesarean myomectomy compared with cesarean delivery alone. No increased rate of major hemorrhage or need for transfusion was identified. Cesarean myomectomy may be considered in cases of isolated myomas, although randomized trials are needed.