bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-scale MRI spectrum detects differences in myelin integrity between MS lesion types
Authors: Zhang Yunyan , Jonkman Laura , Klauser Antoine , Barkhof Frederik , Yong V Wee , Metz Luanne M , Geurts Jeroen JG 
Published: January 2016

Background: Lesions with different extents of myelin pathology are found at autopsy in multiple sclerosis (MS), but the differences are not discernible in magnetic resonance imaging (MRI). Objective: To determine whether analysis of the local spectrum in MRI is sensitive to lesion differences in myelin integrity. Methods: We imaged fresh brain slices from 21 MS patients using 1.5T scanners. White matter lesions were identified in T2-weighted MRI, matched to corresponding specimens, and then classified into five categories in histology: pre-active (intact myelin); active, chronic active, chronic inactive (complete demyelination); and remyelinated lesions. Voxel-based frequency spectrum was calculated using T2-weighted MRI to characterize lesion structure (image texture). Results: MRI texture heterogeneity resulting from all spectral scales was greater in completely demyelinated lesions than in myelin-preserved lesions ( p = 0.02) and normal-appearing white matter ( p < 0.01). Moreover, the spectral distribution pattern over low-frequency scales differentiated demyelinated lesions from remyelinated and pre-active lesions ( p < 0.01), where different lesion types also showed distinct texture scales. Conclusion: Using multi-scale spectral analysis, it may be possible for standard MRI to evaluate myelin integrity in MS lesions. This can be critical for monitoring disease activity and assessing remyelination therapies for MS patients.
Extra- and within-system electoral volatility
Authors: Mainwaring Scott , Gervasoni Carlos , España-Najera Annabella 
Published: January 2016

We analyze the remarkable differences in the electoral success of new parties and compare the determinants of electoral volatility attributable to new versus established parties. We base our findings on an original data set of total volatility, extra-system volatility, and within-system volatility for 67 democratic countries across all regions of the world since 1945. The article makes three contributions. First, we show that it is important to distinguish between electoral volatility that represents vote shifts among established parties (within-system volatility) and shifts to new parties (extra-system volatility). Second, we provide descriptive information about total, within-system, and extra-system volatility for 67 countries. Third, we analyze the determinants of volatility. Our results show that the causes of within- and extra-system volatility differ markedly. In contrast to Powell and Tucker, for our broader range of countries and longer time period, there are several statistically robust positive findings.
Parallel morpho-orthographic and morpho-semantic activation in processing second language morphologically complex words: Evidence from Chinese-English bilinguals
Authors: Zhang Qingge , Liang Lijuan , Yao Panpan , Hu Shanshan , Chen Baoguo 
Published: January 2016

Objectives/research questions: The present study focused on the performance of Chinese learners of English to investigate the activation of morpho-semantic information in the early processing of second language (L2) morphologically complex words when participants’ first language (L1) and L2 are typologically different. Methodology: We used forward masked priming paradigm to compare the priming effect in three prime conditions, semantically transparent, semantically opaque and semantically related. In Experiment 1, the stimulus onset asynchrony (SOA) was 40 milliseconds (ms), while, In Experiment 2, the SOA was extended to 80 ms. Data and analysis: Reaction time and comprehension accuracy data were analysed using the linear mixed-effects model. Findings/conclusions: In Experiment 1, we only found a priming effect in the semantically transparent condition. In Experiment 2, we found a reliable priming effect in the semantically opaque condition, but not in the semantically related condition. These results suggest even Chinese learners of English whose native language is typologically different from English can employ the rule-based decomposing mechanism. The decomposition is based on the interplay of morpho-orthographic and morpho-semantic information, adding new evidence to the assumption of parallel orthography-semantics activation. Originality: We manipulated SOAs to investigate the role of the morpho-semantic factor in the early processing of morphologically complex L2 words when participants’ L1 and L2 are typologically different.
Development of the UK Vessel Health and Preservation (VHP) framework: a multi-organisational collaborative
Authors: Hallam Carole , Weston Valya , Denton Andrea , Hill Steve , Bodenham Andrew , Dunn Helen , Jackson Tim 
Published: January 2016

Vascular access is an important part of many patient care management plans but has some unwanted risks. Previous work published by Moureau et al. (2012) inspired a working group led by the UK Infection Prevention Society (IPS) to produce a vessel health and preservation (VHP) framework. This was with the intention of producing a resource for frontline staff to be able to assess and select the best vascular access device to meet the individual patient’s needs and to preserve veins for future use. The working group produced a framework that used available evidence, expert opinion and some small scale testing of the components of the framework. The work so far has received positive feedback but further work is required to formally evaluate the VHP framework in clinical practice to measure both staff knowledge and patient outcomes.
Full-Contact Practice and Injuries in College Football
Authors: Steiner Mark E. , Berkstresser Brant D. , Richardson Lars , Elia Greg , Wang Frank 
Published: January 2016

Background: Despite recent restrictions being placed on practice in college football, there are little data to correlate such changes with injuries. Hypothesis: Football injuries will correlate with a team’s exposure to full-contact practice, total practice, and total games. Study Design: Descriptive epidemiological study. Methods: All injuries and athlete injury exposures (AE × Min = athletes exposed × activity duration in minutes) were recorded for an intercollegiate football team over 4 consecutive fall seasons. Weekly injuries and injury rates (injuries per athletic injury exposure) were correlated with the weekly exposures to full-contact practices, total practices, formal scrimmages, and games. Results: The preseason practice injury rate was over twice the in-season practice injury rate ( P < 0.001). For preseason, injury exposures were higher for full-contact practice ( P = 0.0166), total practices ( P = 0.015), and scrimmages/games ( P = 0.034) compared with in-season. Preseason and in-season practice injuries correlated with exposure to full-contact practice combined with scrimmages for preseason ( P < 0.008) and full-contact practice combined with games for in-season ( P = 0.0325). The game injury rate was over 6 times greater than the practice injury rate ( P < 0.0001). Concussions constituted 14.5% of all injuries, and the incidence of concussions correlated with the incidence of all injuries ( P = 0.0001). Strength training did not correlate with injuries. Conclusion: Decreased exposure to full-contact practice may decrease the incidence of practice injuries and practice concussions. However, the game injury rate was over 6 times greater than the practice injury rate and had an inverse correlation with full-contact practice.
Imaging features of spinal tanycytic ependymoma
Authors: Tomek Michal , Jayajothi Anandapadmanabhan , Brandner Sebastian , Jaunmuktane Zane , Lee Cheong Hung , Davagnanam Indran 
Published: January 2016

Tanycytic ependymoma is an unusual morphological variant of WHO grade II ependymoma, typically arising from the cervical or thoracic spinal cord. Although the literature deals extensively with pathological features of this tumour entity, imaging features have not been well characterised. The purpose of this study was to review magnetic resonance imaging (MRI) features of spinal tanycytic ependymomas reported in the literature to date, exemplified by a case of a patient with tanycytic ependymoma of the conus medullaris presenting to our hospital. A Medline search of the English literature for all previously published cases of spinal tanycytic ependymoma was carried out and the reported MRI features reviewed. The tumours were found to be typically well-demarcated masses, predominantly showing isointensity on T1-weighted signal, and T2-weighted hyperintensity, with variable patterns of contrast enhancement. A cystic component was seen in half of the cases, and in a minority a mural nodule was present within the cyst wall. Associated syrinx formation was observed in one-third of the cases and haemorrhage was rare, which may be helpful pointers in differentiating the lesion from other ependymoma subtypes. In conclusion, MRI characteristics of spinal tanycytic ependymoma are variable and non-specific, and radiological diagnosis thus remains challenging, although certain predominant features are identified in this report. Knowledge of these is important in the diagnostic differentiation from other intramedullary and extramedullary spinal tumours in order to guide appropriate surgical management.
MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature
Authors: Shivashankar Nithin , Patil Sonali , Bhosle Amrisha , Chandra Nagasuma , Natarajan Vijay 
Published: January 2016

Abstract
Background
Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily constructed from various forms of molecular data such as 3D atomic coordinates (PDB) and Electron Microscopy (EM) data.

Methods
We present a Multi-Scale Morse-Smale Molecular-Surface Alignment tool, MS3ALIGN, which aligns molecular surfaces based on significant protrusions on the molecular surface. The input is a pair of molecular surfaces represented as triangle meshes. A key advantage of MS3ALIGN is computational efficiency that is achieved because it processes only a few carefully chosen protrusions on the molecular surface. Furthermore, the alignments are partial in nature and therefore allows for inexact surfaces to be aligned.

Results
The method is evaluated in four settings. First, we establish performance using known alignments with varying overlap and noise values. Second, we compare the method with SurfComp, an existing surface alignment method. We show that we are able to determine alignments reported by SurfComp, as well as report relevant alignments not found by SurfComp. Third, we validate the ability of MS3ALIGN to determine alignments in the case of structurally dissimilar binding sites. Fourth, we demonstrate the ability of MS3ALIGN to align iso-surfaces derived from cryo-electron microscopy scans.

Conclusions
We have presented an algorithm that aligns Molecular Surfaces based on the topology of surface curvature. A webserver and standalone software implementation of the algorithm available at http://vgl.serc.iisc.ernet.in/ms3align.
Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice (Oryza sativa L.)
Authors: Zhang Yubo , Ding Yi 
Published: January 2016

Abstract
Background
Rice (Oryza sativa L.) is one of the most important cereal crops in the world and its yield is closely related to the photosynthesis efficiency. The chloroplast stromal ridge complex consisting of PsaC-PsaD-PsaE plays an important role in plant photosynthesis, which has been a subject of many studies. Till now, the recognition mechanism between PsaC and PsaD in rice is still not fully understood.

Results
Here, we present the interaction features of OsPsaC and OsPsaD by molecular dynamics simulations and bioinformatics. Firstly, we identified interacting residues in the OsPsaC-OsPsaD complex during simulations. Significantly, important hydrogen bonds were observed in residue pairs R19-E103, D47-K62, R53-E63, Y81-R20, Y81-R61 and L26-V105. Free energy calculations suggested two salt bridges R19-E103 and D47-K62 were essential to maintain the OsPsaC-OsPsaD interaction. Supportively, electrostatic potentials surfaces of OsPsaD exhibited electrostatic attraction helped to stabilize the residue pairs R19-E103 and D47-K62. In particular, the importance of R19 was further verified by two 500 ns CG-MD simulations. Secondly, this study compared the stromal ridge complex in rice with that in other organisms. Notably, alignments of amino acids showed these two salt bridges R19-E103 and D47-K62 also existed in other organisms. Electrostatic potentials surfaces and X-ray structural analysis strongly suggested the stromal ridge complex in other organisms adopted a similar and general recognition mechanism.

Conclusions
These results together provided structure basis and dynamics behavior to understand recognition and assembly of the stromal ridge complex in rice.
GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data
Authors: Melo Arthur T. O. , Bartaula Radhika , Hale Iago 
Published: January 2016

Abstract
Background
With its simple library preparation and robust approach to genome reduction, genotyping-by-sequencing (GBS) is a flexible and cost-effective strategy for SNP discovery and genotyping, provided an appropriate reference genome is available. For resource-limited curation, research, and breeding programs of underutilized plant genetic resources, however, even low-depth references may not be within reach, despite declining sequencing costs. Such programs would find value in an open-source bioinformatics pipeline that can maximize GBS data usage and perform high-density SNP genotyping in the absence of a reference.

Results
The GBS SNP-Calling Reference Optional Pipeline (GBS-SNP-CROP) developed and presented here adopts a clustering strategy to build a population-tailored “Mock Reference” from the same GBS data used for downstream SNP calling and genotyping. Designed for libraries of paired-end (PE) reads, GBS-SNP-CROP maximizes data usage by eliminating unnecessary data culling due to imposed read-length uniformity requirements. Using 150 bp PE reads from a GBS library of 48 accessions of tetraploid kiwiberry (Actinidia arguta), GBS-SNP-CROP yielded on average three times as many SNPs as TASSEL-GBS analyses (32 and 64 bp tag lengths) and over 18 times as many as TASSEL-UNEAK, with fewer genotyping errors in all cases, as evidenced by comparing the genotypic characterizations of biological replicates. Using the published reference genome of a related diploid species (A. chinensis), the reference-based version of GBS-SNP-CROP behaved similarly to TASSEL-GBS in terms of the number of SNPs called but had an improved read depth distribution and fewer genotyping errors. Our results also indicate that the sets of SNPs detected by the different pipelines above are largely orthogonal to one another; thus GBS-SNP-CROP may be used to augment the results of alternative analyses, whether or not a reference is available.

Conclusions
By achieving high-density SNP genotyping in populations for which no reference genome is available, GBS-SNP-CROP is worth consideration by curators, researchers, and breeders of under-researched plant genetic resources. In cases where a reference is available, especially if from a related species or when the target population is particularly diverse, GBS-SNP-CROP may complement other reference-based pipelines by extracting more information per sequencing dollar spent. The current version of GBS-SNP-CROP is available at https://github.com/halelab/GBS-SNP-CROP.git
Long-term recovery from acute cold shock in Caenorhabditis elegans
Authors: Robinson Joseph D. , Powell Jennifer R. 
Published: January 2016

Abstract
Background
Animals are exposed to a wide range of environmental stresses that can cause potentially fatal cellular damage. The ability to survive the period of stress as well as to repair any damage incurred is essential for fitness. Exposure to 2 °C for 24 h or longer is rapidly fatal to the nematode Caenorhabditis elegans, but the process of recovery from a shorter, initially non-lethal, cold shock is poorly understood.

Results
We report that cold shock of less than 12-hour duration does not initially kill C. elegans, but these worms experience a progression of devastating phenotypes over the next 96 h that correlate with their eventual fate: successful recovery from the cold shock and survival, or failure to recover and death. Cold-shocked worms experience a marked loss of pigmentation, decrease in the size of their intestine and gonads, and disruption to the vulva. Those worms who will successfully recover from the cold shock regain their pigmentation and much of the integrity of their intestine and gonads. Those who will die do so with a distinct phenotype from worms dying during or immediately following cold shock, suggesting independent mechanisms. Worms lacking the G-protein coupled receptor FSHR-1 are resistant to acute death from longer cold shocks, and are more successful in their recovery from shorter sub-lethal cold shocks.

Conclusions
We have defined two distinct phases of death associated with cold shock and described a progression of phenotypes that accompanies the course of recovery from that cold shock. The G-protein coupled receptor FSHR-1 antagonizes these novel processes of damage and recovery.
TREM-like transcript 2 is stored in human neutrophil primary granules and is up-regulated in response to inflammatory mediators
Authors: Thomas Kimberly A , King R Glenn , Sestero Christine M , Justement Louis B 
Published: January 2016

Abstract
The triggering receptor expressed on myeloid cell locus encodes a family of receptors that is emerging as an important class of molecules involved in modulating the innate immune response and inflammation. Of the 4 conserved members, including triggering receptor expressed on myeloid cells 1 and 2 and triggering receptor expressed on myeloid cell-like transcripts 1 and 2, relatively little is known about triggering receptor expressed on myeloid cell-like transcript 2 expression and function, particularly in humans. In this study, experiments were performed to determine if triggering receptor expressed on myeloid cell-like transcript 2 expression is conserved between mouse and human, demonstrating that human triggering receptor expressed on myeloid cell-like transcript 2 is expressed on cells of the lymphoid, as well as myeloid/granuloid lineages, similar to murine triggering receptor expressed on myeloid cell-like transcript 2. Consistent with studies in the mouse, triggering receptor expressed on myeloid cell-like transcript 2 expression is up-regulated in response to inflammatory mediators on human neutrophils. Importantly, it was shown that triggering receptor expressed on myeloid cell-like transcript 2, in resting human neutrophils, is predominantly localized to intracellular vesicles, including secretory vesicles and primary granules; with the majority of triggering receptor expressed on myeloid cell-like transcript 2 stored in primary granules. In contrast to other primary granule proteins, triggering receptor expressed on myeloid cell-like transcript 2 is not expelled on neutrophil extracellular traps but is retained in the plasma membrane following primary granule exocytosis. In summary, these findings establish that triggering receptor expressed on myeloid cell-like transcript 2 expression is conserved between species and is likely to be important in regulating neutrophil antimicrobial function following primary granule exocytosis.
Volasertib Versus Chemotherapy in Platinum-Resistant or -Refractory Ovarian Cancer: A Randomized Phase II Groupe des Investigateurs Nationaux pour l'Etude des Cancers de l'Ovaire Study
Authors: Pujade-Lauraine Eric , Selle Frédéric , Weber Béatrice , Ray-Coquard Isabelle-Laure , Vergote Ignace , Sufliarsky Jozef , Del Campo Josep Maria , Lortholary Alain , Lesoin Anne , Follana Philippe , Freyer Gilles , Pardo Beatriz , Vidal Laura , Tholander Bengt , Gladieff Laurence , Sassi Mouna , Garin-Chesa Pilar , Nazabadioko Serge , Marzin Kristell , Pilz Korinna , Joly Florence 
Published: January 2016

Purpose Volasertib is a potent and selective cell-cycle kinase inhibitor that induces mitotic arrest and apoptosis by targeting Polo-like kinase. This phase II trial evaluated volasertib or single-agent chemotherapy in patients with platinum-resistant or -refractory ovarian cancer who experienced failure after treatment with two or three therapy lines. Patients and Methods Patients were randomly assigned to receive either volasertib 300 mg by intravenous infusion every 3 weeks or an investigator’s choice of single-agent, nonplatinum, cytotoxic chemotherapy. The primary end point was 24-week disease control rate. Secondary end points included best overall response, progression-free survival (PFS), safety, quality of life, and exploratory biomarker analyses. Results Of the 109 patients receiving treatment, 54 received volasertib and 55 received chemotherapy; demographics were well balanced. The 24-week disease control rates for volasertib and chemotherapy were 30.6% (95% CI, 18.0% to 43.2%) and 43.1% (95% CI, 29.6% to 56.7%), respectively, with partial responses in seven (13.0%) and eight (14.5%) patients, respectively. Median PFS was 13.1 weeks and 20.6 weeks for volasertib and chemotherapy (hazard ratio, 1.01; 95% CI, 0.66 to 1.53). Six patients (11%) receiving volasertib achieved PFS fore more than 1 year, whereas no patient receiving chemotherapy achieved PFS greater than 1 year. No relationship between the expression of the biomarkers tested and their response was determined. Patients treated with volasertib experienced more grade 3 and 4 drug-related hematologic adverse events (AEs) and fewer nonhematologic AEs than did patients receiving chemotherapy. Discontinuation resulting from AEs occurred in seven (13.0%) and 15 (27.3%) patients in the volasertib and chemotherapy arms, respectively. Both arms showed similar effects on quality of life. Conclusion Single-agent volasertib showed antitumor activity in patients with ovarian cancer. AEs in patients receiving volasertib were mainly hematologic and manageable.