bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ginseng oligopeptides protect against irradiation-induced immune dysfunction and intestinal injury
Authors: He Li-Xia , Zhang Zhao-Feng , Zhao Jian , Li Lin , Xu Teng , Bin Sun  , Ren Jin-Wei , Liu Rui , Chen Qi-He , Wang Jun-Bo , Salem Mohamed M. , Pettinato Giuseppe , Zhou Jin-Rong , Li Yong 
Published: September 2018

AbstractIntestinal injury and immune dysfunction are commonly encountered after irradiation therapy. While the curative abilities of ginseng root have been reported in prior studies, there is little known regarding its role in immunoregulation of intestinal repairability in cancer patients treated with irradiation. Our current study aims to closely examine the protective effects of ginseng-derived small molecule oligopeptides (Panax ginseng C. A. Mey.) (GOP) against irradiation-induced immune dysfunction and subsequent intestinal injury, using in vitro and in vivo models. Expectedly, irradiation treatment resulted in increased intestinal permeability along with mucosal injury in both Caco-2 cells and mice, probably due to disruption of the intestinal epithelial barrier, leading to high plasma lipopolysaccharide (LPS) and pro-inflammatory cytokines levels. However, when the cells were treated with GOP, this led to diminished concentration of plasma LPS and cytokines (IL-1 and TNF-α), suggesting its dampening effect on inflammatory and oxidative stress, and potential role in restoring normal baseline intestinal permeability. Moreover, the Caco-2 cells treated with GOP showed high trans-epithelial electrical resistance (TEER) and low FITC-dextran paracellular permeability when compared to the control group. This could be explained by the higher levels of tight junction proteins (ZO-1 and Occludin) expression along with reduced expression of the apoptosis-related proteins (Bax and Caspase-3) noticed in the GOP-treated cells, highlighting its role in preserving intestinal permeability, through prevention of their degradation while maintaining normal levels of expression. Further confirmatory in vivo data showed that GOP-treated mice exhibited high concentrations of lymphocytes (CD3+, CD4+, CD8+) in the intestine, to rescue the irradiation-induced damage and restore baseline intestinal integrity. Therefore, we propose that GOP can be used as an adjuvant therapy to attenuate irradiation-induced immune dysfunction and intestinal injury in cancer patients.
High‐precision differential time integrator based on time adder
Authors: Zhu Kai , Feng Jianhua , Lyu Yinxuan , He Ai 
Published: September 2018

A high‐precision time integrator is presented whose output is the accumulation of sequence of time inputs. A novel time adder with time‐domain differential structure is proposed to avoid common‐mode errors such as supply noise and leakage current. The performance under various process, voltage and temperature conditions is examined in detail. By using two time adders in parallel, a differential synchronous time integrator is proposed, which is easier to cascade with other time‐mode arithmetic circuit. Implemented in 65 nm 1.2 V CMOS technology, the proposed time integrator achieves a gain of 27.97 dB with a 317 kHz 30 ps peak‐to‐peak sinusoidal input, and consumes with 50 MHz sampling rate. The experimental results confirm the integration operation is realised properly and accurately.
Validation of a PMU‐based fault location identification method for smart distribution network with photovoltaics using real‐time data
Authors: Usman Muhammad Usama , Faruque Md. Omar 
Published: September 2018

A fault location (FL) identification method for smart distribution network is presented and validated using a digital real‐time simulator (DRTS). The method can accurately identify the FL in a distribution network in the presence of distributed generation (DG). This method is based on state estimation (SE) algorithm which uses real‐time data from simulated phasor measurement units (PMUs), placed in the distribution network. SE needs the fault currents of the generators and voltage measurements of an optimal number of nodes to perform the FL algorithm. The method was validated using the IEEE 37 node test feeder with DGs. PMUs are placed on the real‐time model of the system. The real‐time model was implemented on a DRTS which streams phasor data over the Internet using C37.118 protocol. OpenPDC is used to collect real‐time PMU data coming from the DRTS. Microsoft SQL is used as a database management server to store data coming from OpenPDC. In the last step of the FL process, data stored in OpenPDC is fed into a FL identification algorithm to locate the fault. Both balanced and unbalanced fault types are applied to different nodes and an accurate estimation of the FL (over 90% of the cases) is achieved.
Multiplicity and clustering in Taurus star forming region
Authors: Joncour Isabelle , Duchêne Gaspard , Moraux Estelle , Motte Frédérique 
Published: September 2018

Context. Multiplicity and clustering of young pre-main sequence stars appear as critical clues to understand and constrain the star formation process. Taurus is the archetypical example of the most quiescent star forming regions that may still retain primeval signatures of star formation.
Aims. This work identifies local overdense stellar structures as a critical scale between wide pairs and loose groups in Taurus.
Methods. Using the density-based spatial clustering of applications with noise (dbscan) algorithm, and setting its free parameters based on the one-point correlation function and the k-nearest neighbor statistics, we have extracted reliably overdense structures from the sky-projected spatial distribution of stars.
Results. Nearly half of the entire stellar population in Taurus is found to be concentrated in 20 very dense, tiny and prolate regions called NESTs (for Nested Elementary STructures). They are regularly spaced (≈2 pc) and mainly oriented along the principal gas filaments axes. Each NEST contains between four and 23 stars. Inside NESTs, the surface density of stars may be as high as 2500 pc−2 and the mean value is 340 pc−2. Nearly half (11) of these NESTs contain about 75% of the class 0 and I objects. The balance between Class I, II, and, III fraction within the NESTs suggests that they may be ordered as an evolutionary temporal scheme, some of them getting infertile with time, while other still giving birth to young stars. We have inferred that only 20% of stars in Taurus do not belong to any kind of stellar groups (either multiple system, ultra wide pairs or NESTs). The mass-size relation for stellar NESTs is very close to the Bonnor–Ebert expectation. The range in mass is about the same as that of dense molecular cores. The distribution in size is bimodal peaking at 12.5 and 50 kAU and the distribution of the number of YSOs in NESTs as a function of size exhibits two regimes.
Conclusions. We propose that the NESTs in their two size regimes represent the spatial imprints of stellar distribution at birth as they may have emerged within few millions years from their natal cloud either from a single core or from a chain of cores. We have identified them as the preferred sites of star formation in Taurus. These NESTs are the regions of highest stellar density and intermediate spatial scale structures between ultra-wide pairs and loose groups.
Upper Extremity Pain and Pitching Mechanics in National Collegiate Athletic Association (NCAA) Division I Softball
Authors: Oliver Gretchen , Gilmer Gabrielle , Anz Adam , Friesen Kenzie , Brittain Abigail , Goodlett Michael , Dugas Jeffrey , Andrews James 
Published: September 2018

AbstractThe purpose of this study was to evaluate pitching mechanics between female softball pitchers with upper extremity pain and those without upper extremity pain. Specifically, the trunk, shoulder and elbow kinematics and shoulder kinetics during the change-up softball pitch were examined. Fifty-five collegiate softball pitchers participated, divided into those with upper extremity pain (20.0±1.3 yrs.; 174.4±6.9 cm; 82.9±12.4 kg; 11.1±2.6 yrs. of experience; n=23) and those who were pain-free (19.9±1.4 yrs.; 173.8±6.9 cm; 81.4±12.5 kg; 10.0±2.5 yrs. of experience; n=32). Pitching mechanics were obtained via the trakSTAR™ electromagnetic tracking system (Ascension Technologies, Inc., Burlington, VT, USA). Mann-Whitney U tests revealed significant differences in shoulder horizontal abduction at foot contact (p=0.014, U=153, Z=2.450) and trunk lateral flexion at ball release (p=0.012, U=150, Z=–2.515); and between shoulder distraction force at ball release (p=0.034, U=168, Z=–2.124). The pain group illustrated greater shoulder horizontal abduction at foot contact, less trunk lateral flexion towards the throwing side at ball release, and greater shoulder distraction at ball release than the pain-free group. The differences in trunk and shoulder kinematics, and shoulder kinetics between groups allows for insight into further studies examining injury pervasiveness in softball pitching.
Prevalence and Precipitating Factors of Migraine in Secondary School Students in Thailand
Authors: Saengow Vitchayaporn , Tangcheewinsirikul Sirikarn 
Published: September 2018

Introduction Migraine is the most common primary headache in children which leads to disturbance of school performance and impaired quality of life. The prevalence of migraine is different between countries and ethnicities; this study determines the prevalence and precipitating factors of migraine in Thailand.
Method This cross-sectional school-based study was conducted in Nakhon Ratchasima. The children aged between 12 and 18 years from four secondary schools were selected by stratified randomization method. The screening questionnaire and directed interview with physical examination were done and migraine was diagnosed based on the criteria of International Classification of Headache Disorders III. The prevalence of migraine was identified and baseline characteristic of disease with precipitating factors was evaluated.
Results A total of 2,744 students aged between 12 and 18 years (900 males, 1,844 females) were recruited; mean age was 14.3 ± 1.75 years. Fifty-five students were diagnosed with migraine (20 males [36.36%], 35 females [63.64%], mean age: 15.1 ± 1.6 years). The prevalence of migraine was 1.98%. Migraine prevalence was predominant in female adolescents with a common feature being migraine without aura. The important precipitating factor in this study was stress from academic achievement.
Conclusion Migraine is a common disease in children and under-recognized in school students, and stress is the major precipitating factor.
Neurourbanistik – ein methodischer Schulterschluss zwischen Stadtplanung und Neurowissenschaften
Authors: Adli M. , Berger M. , Brakemeier E.-L. , Engel L. , Fingerhut J. , Hehl R. , Heinz A. , Mayer H J. , Matussek T. , Mehran N. , Tolaas S. , Walter H. , Weiland U. , Stollmann J. 
Published: September 2018

Zusammenfassung
Hintergrund: Urbanisierung gehört zu den wichtigsten globalen Veränderungen, denen die Menschheit in den kommenden Jahrzehnten ausgesetzt sein wird. Diese Entwicklung ist rasant – und sie ist gesundheitsrelevant, mit weit reichenden Konsequenzen für unser psychisches Befinden. Einige stressassoziierte psychische Erkrankungen zeigen ein erhöhtes Auftreten bei Stadtbewohnern. Methode: Es ist daher höchste Zeit, den Einfluss von Stadtleben auf das psychische Wohlbefinden sowie die Rolle urbaner Stressoren besser zu verstehen. Hierzu ist ein methodischer Schulterschluss zwischen Architektur, Stadtplanung, Neurowissenschaften und Medizin notwendig, für den wir den Begriff der „Neurourbanistik“ vorschlagen. Neurourbanistik als neue akademische Perspektive kann dazu beitragen, angemessen und effektiv auf die Herausforderungen einer urbanisierten Welt zu reagieren. Die Themen neurourbanistischer Forschung umfassen dabei Grundlagenforschung, Epidemiologie und Public Health genauso wie experimentelle Stressforschung und Präventionsforschung. Ziel: Ziel ist, ein Lebensumfeld zu schaffen, welches die Resilienz und psychische Gesundheit von Stadtbewohnern und urbaner Gemeinschaften stärkt.
The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices
Authors: Enache Oana M , Lahr David L , Natoli Ted E , Litichevskiy Lev , Wadden David , Flynn Corey , Gould Joshua , Asiedu Jacob K , Narayan Rajiv , Subramanian Aravind 
Published: September 2018

Abstract

Motivation
Facilitated by technological improvements, pharmacologic and genetic perturbational datasets have grown in recent years to include millions of experiments. Sharing and publicly distributing these diverse data creates many opportunities for discovery, but in recent years the unprecedented size of data generated and its complex associated metadata have also created data storage and integration challenges.

Results
We present the GCTx file format and a suite of open-source packages for the efficient storage, serialization and analysis of dense two-dimensional matrices. We have extensively used the format in the Connectivity Map to assemble and share massive datasets currently comprising 1.3 million experiments, and we anticipate that the format’s generalizability, paired with code libraries that we provide, will lower barriers for integrated cross-assay analysis and algorithm development.

Availability and implementation
Software packages (available in Python, R, Matlab and Java) are freely available at https://github.com/cmap. Additional instructions, tutorials and datasets are available at clue.io/code.

Supplementary information
Supplementary data are available at Bioinformatics online.
KeggExp: a web server for visual integration of KEGG pathways and expression profile data
Authors: Liu Xian , Han Mingfei , Zhao Chen , Chang Cheng , Zhu Yunping , Ge Changhui , Yin Ronghua , Zhan Yiqun , Li Changyan , Yu Miao , He Fuchu , Yang Xiaoming 
Published: September 2018

Abstract

Summary
Effective visualization is important for knowledge discovery when analysing expression profile data. However, existing tools for visually integrating expression profile data with KEGG pathway maps lack extensive interactive visualization operations. KeggExp simultaneously presents the pathway map of one pathway, dendrogram and heatmap of the genes in the pathway and scatter map of one gene; and also provides interactive operations for highlighting specific genes on the pathway map, including differentially-expressed genes, co-expressed genes selected from the heatmap and user-input genes. With KeggExp, researchers, including those without programming skills, can take advantage of its interactive operations to determine key genes or pathways when analysing expression profile data.

Availability and implementation
Freely available at http://www.fgvis.com/expressvis/KeggExp/. Language: JavaScript, python; Libraries: D3.js, Rxjs, Angular, Django, Django rest frame work, Scipy.

Supplementary information
Supplementary data are available at Bioinformatics online.
In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes
Authors: Giancarlo Raffaele , Rombo Simona E , Utro Filippo 
Published: September 2018

Abstract

Motivation
Although the nucleosome occupancy along a genome can be in part predicted by in vitro experiments, it has been recently observed that the chromatin organization presents important differences in vitro with respect to in vivo. Such differences mainly regard the hierarchical and regular structures of the nucleosome fiber, whose existence has long been assumed, and in part also observed in vitro, but that does not apparently occur in vivo. It is also well known that the DNA sequence has a role in determining the nucleosome occupancy. Therefore, an important issue is to understand if, and to what extent, the structural differences in the chromatin organization between in vitro and in vivo have a counterpart in terms of the underlying genomic sequences.

Results
We present the first quantitative comparison between the in vitro and in vivo nucleosome maps of two model organisms (S. cerevisiae and C. elegans). The comparison is based on the construction of weighted k-mer dictionaries. Our findings show that there is a good level of sequence conservation between in vitro and in vivo in both the two organisms, in contrast to the abovementioned important differences in chromatin structural organization. Moreover, our results provide evidence that the two organisms predispose themselves differently, in terms of sequence composition and both in vitro and in vivo, for the nucleosome occupancy. This leads to the conclusion that, although the notion of a genome encoding for its own nucleosome occupancy is general, the intrinsic histone k-mer sequence preferences tend to be species-specific.

Availability and implementation
The files containing the dictionaries and the main results of the analysis are available at http://math.unipa.it/rombo/material.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Enabling Reduction of Low-Grade Inflammation in Seniors (ENRGISE) Pilot Study: Screening Methods and Recruitment Results
Authors: Cauley Jane A , Manini Todd M , Lovato Laura , Talton Jennifer , Anton Steven D , Domanchuk Kathryn , Kennedy Kimberly , Stowe Cynthia L , Walkup Michael , Fielding Roger A , Kritchevsky Stephen B , McDermott Mary M , Newman Anne B , Ambrosius Walter T , Pahor Marco ,   ENRGISE Investigators
Published: September 2018

AbstractBackgroundThe Enabling Reduction of Low-grade Inflammation in Seniors (ENRGISE) Pilot Study is a multicenter randomized clinical trial examining the feasibility of testing whether omega-3 fish oil (ω-3) and the angiotensin receptor blocker losartan alone or in combination can reduce inflammation and improve walking speed in older adults with mobility impairment. We describe recruitment methods and results.MethodsEligible participants were 70 years and older, had elevated interleukin-6 levels (2.5–30 pg/mL) and mobility impairment.ResultsOf those who responded to recruitment, 83% responded to mailings. A total of 5,424 telephone screens were completed; of these, 2,011 (37.1%) were eligible for further screening. The most common reasons for ineligibility at the telephone screens were lack of mobility impairment or use of angiotensin receptor blockers or angiotensin-converting enzyme inhibitors (n=1.789). Of the 1,305 initial screening visits, 1,087 participants had slow gait speed (&lt;1 m/s). Of these, 701 (64%) had elevated interleukin-6 and were eligible for second screening visits. Of the 582 second screening visits, 335 (57.6%) were eligible to be randomized. A total of 289 participants (96% of goal) were randomized: 180 in the ω-3 stratum (240% of goal); 43 in the losartan (57% of goal), and 66 in the combination (44% of goal). The telephone screen and first screening visit to randomization ratio was 19 to 1 and 4.5 to 1, respectively. The estimated cost of recruitment per randomized participant was $1,782.ConclusionRecruitment for ω-3 exceeded goals, but goals for the losartan and combination strata were not met due to the high proportion of participants taking angiotensin receptor blockers or angiotensin-converting enzyme inhibitors.
The Association Between Physical Activity, Including Physical Activity Intensity, and Fear of Falling Differs by Fear Severity in Older Adults Living in the Community
Authors: Sawa Ryuichi , Asai Tsuyoshi , Doi Takehiko , Misu Shogo , Murata Shunsuke , Ono Rei 
Published: September 2018

Abstract

Objectives
Fear of falling (FoF) is common in older adults. Physical activity decreases as FoF increases. However, this association between physical activity and FoF may vary depending on activity intensity. The current study was performed to explore the associations between FoF and step count, light-intensity physical activity (LPA), and moderate/vigorous-intensity physical activity (MVPA) in community-dwelling older adults.

Methods
This cross-sectional observational study was held at a local community association center, with 242 older adults living independently in the community (mean age: 75.1 ± 5.4 years). FoF was defined using the Falls Efficacy Scale-International and categorized into three levels (low, moderate, and high). Physical activity was measured using a uniaxial accelerometer worn for 7 consecutive days, and by calculating daily step count, LPA, and MVPA, over this period.

Results
Step count and physical activity intensity showed significant linear trends across FoF severity (p &lt; .01, respectively). High FoF decreased step count by approximately 2,000 steps/day. Further, high FoF was significantly associated with short durations of both LPA and MVPA. In addition, moderate FoF was associated with decreased LPA duration, even after adjustment for confounding variables.

Discussion
Physical activity decreased concomitantly with a rise in FoF severity. Moreover, the association between physical activity and FoF differed by physical activity intensity level in community-dwelling older adults. Further studies are needed to investigate the causal relationship between FoF and objective physical activity in this population.
Continuous learning, teamwork, and lessons for young scientists
Authors: Peterman Randall M 
Published: September 2018

AbstractThis paper describes my research on fish population dynamics, which has aimed to improve the information available for management and conservation. Through numerous collaborations, my research program addressed three main objectives. (1) Increase the understanding of spatial and temporal variation in productivity of fish populations. (2) Quantify uncertainties and risks in fishery systems and their implications for management and conservation. (3) Develop methods to reduce those uncertainties and risks. To help young scientists, I present 11 general lessons, as well as some specific advice, that emerged from that research. The general lessons include pursuing a path of continuous learning, going beyond your comfort zone to broaden your skills and knowledge, and collaborating with others. More specific advice for fisheries scientists includes evaluating the bias and precision of parameter estimation methods via Monte Carlo simulations, and considering multiple models of whole fishery systems. This paper also illustrates, with examples, how the understanding of some aspects of fish population dynamics has evolved, at least from the limited perspective of my own group's research.