bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Assessment of the Robustness of the COSHH-Essentials (C-E) Target Airborne Concentration Ranges 15 Years on, and Their Usefulness for Determining Control Measures
Authors: Vaughan Nicholas P. , Rajan-Sithamparanadarajah Rajadurai 
Published: February 2017

Abstract
The Health and Safety Executive (HSE) in Great Britain (GB), in association with its stakeholders, developed the Control of Substances Hazardous to Health (COSHH)-Essentials (C-E) control banding tool in 1998. The objective was to provide a simple tool for employers, particularly small and medium-sized enterprises (SMEs), to help select and apply appropriate measures for the adequate control of exposure to hazardous substances. The tool used hazard classification information (R-phrases) to assign substances to one of five health hazard groups, each with its respective ‘target airborne concentration range’. The validity of the allocation of substances to a target airborne concentration range was demonstrated at the time using 111 substances that had a current health-based Occupational Exposure Limit (OEL) in GB. The C-E control banding approach remains an important tool to complement exposure assessment/monitoring and the selection and use of suitable control measures for hazardous substances. These include engineering controls and personal protective equipment (PPE). The C-E based control banding approach has been adopted around the world. This paper extends the original validation exercise, using a greater number of chemical substances, to establish whether the target airborne concentration ranges remain appropriate. This is of particular interest in light of the introduction of the Globally Harmonized System (GHS) for classification, in which R-phrases have now been replaced by hazard-statements (H-statements). The validation exercise includes substances with OELs published by nine bodies internationally; and the Derived No-Effect Levels (DNELs) assigned by registrants under the European Union—Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) Regulations. When compared against 8-hour TWA OELs for 850 substances drawn from nine bodies and a limited number of DNELS, the C-E target airborne concentration ranges remain valid. This comparative work also informs a wider consideration around the practicality and the applicability of the C-E generic approach to facilitate the implementation of good practice control for a wide range of substances (more than 95%) which do not have any recognized OEL.
A multi-scale convolutional neural network for phenotyping high-content cellular images
Authors: Godinez William J , Hossain Imtiaz , Lazic Stanley E , Davies John W , Zhang Xian 
Published: February 2017

Abstract

Motivation
Identifying phenotypes based on high-content cellular images is challenging. Conventional image analysis pipelines for phenotype identification comprise multiple independent steps, with each step requiring method customization and adjustment of multiple parameters.

Results
Here, we present an approach based on a multi-scale convolutional neural network (M-CNN) that classifies, in a single cohesive step, cellular images into phenotypes by using directly and solely the images’ pixel intensity values. The only parameters in the approach are the weights of the neural network, which are automatically optimized based on training images. The approach requires no a priori knowledge or manual customization, and is applicable to single- or multi-channel images displaying single or multiple cells. We evaluated the classification performance of the approach on eight diverse benchmark datasets. The approach yielded overall a higher classification accuracy compared with state-of-the-art results, including those of other deep CNN architectures. In addition to using the network to simply obtain a yes-or-no prediction for a given phenotype, we use the probability outputs calculated by the network to quantitatively describe the phenotypes. This study shows that these probability values correlate with chemical treatment concentrations. This finding validates further our approach and enables chemical treatment potency estimation via CNNs.

Availability and Implementation
The network specifications and solver definitions are provided in Supplementary Software 1.

Supplementary information
Supplementary data are available at Bioinformatics online.
Empirical comparison of web-based antimicrobial peptide prediction tools
Authors: Gabere Musa Nur , Noble William Stafford 
Published: February 2017

Abstract

Motivation
Antimicrobial peptides (AMPs) are innate immune molecules that exhibit activities against a range of microbes, including bacteria, fungi, viruses and protozoa. Recent increases in microbial resistance against current drugs has led to a concomitant increase in the need for novel antimicrobial agents. Over the last decade, a number of AMP prediction tools have been designed and made freely available online. These AMP prediction tools show potential to discriminate AMPs from non-AMPs, but the relative quality of the predictions produced by the various tools is difficult to quantify.

Results
We compiled two sets of AMP and non-AMP peptides, separated into three categories—antimicrobial, antibacterial and bacteriocins. Using these benchmark data sets, we carried out a systematic evaluation of ten publicly available AMP prediction methods. Among the six general AMP prediction tools—ADAM, CAMPR3(RF), CAMPR3(SVM), MLAMP, DBAASP and MLAMP—we find that CAMPR3(RF) provides a statistically significant improvement in performance, as measured by the area under the receiver operating characteristic (ROC) curve, relative to the other five methods. Surprisingly, for antibacterial prediction, the original AntiBP method significantly outperforms its successor, AntiBP2 based on one benchmark dataset. The two bacteriocin prediction tools, BAGEL3 and BACTIBASE, both provide very good performance and BAGEL3 outperforms its predecessor, BACTIBASE, on the larger of the two benchmarks.

Supplementary information
Supplementary data are available at Bioinformatics online.
SANA: simulated annealing far outperforms many other search algorithms for biological network alignment
Authors: Mamano Nil , Hayes Wayne B 
Published: February 2017

Abstract

Summary
Every alignment algorithm consists of two orthogonal components: an objective function M measuring the quality of an alignment, and a search algorithm that explores the space of alignments looking for ones scoring well according to M. We introduce a new search algorithm called SANA (Simulated Annealing Network Aligner) and apply it to protein-protein interaction networks using S3 as the topological measure. Compared against 12 recent algorithms, SANA produces 5–10 times as many correct node pairings as the others when the correct answer is known. We expose an anti-correlation in many existing aligners between their ability to produce good topological vs. functional similarity scores, whereas SANA usually outscores other methods in both measures. If given the perfect objective function encoding the identity mapping, SANA quickly converges to the perfect solution while many other algorithms falter. We observe that when aligning networks with a known mapping and optimizing only S3, SANA creates alignments that are not perfect and yet whose S3 scores match that of the perfect alignment. We call this phenomenon saturation of the topological score. Saturation implies that a measure’s correlation with alignment correctness falters before the perfect alignment is reached. This, combined with SANA’s ability to produce the perfect alignment if given the perfect objective function, suggests that better objective functions may lead to dramatically better alignments. We conclude that future work should focus on finding better objective functions, and offer SANA as the search algorithm of choice.

Availability and Implementation
Software available at http://sana.ics.uci.edu.

Supplementary information
Supplementary data are available at Bioinformatics online.
Penalized likelihood estimation of a trivariate additive probit model
Authors: Filippou Panagiota , Marra Giampiero , Radice Rosalba 
Published: February 2017

SUMMARY
This article proposes a penalized likelihood method to estimate a trivariate probit model, which accounts for several types of covariate effects (such as linear, nonlinear, random, and spatial effects), as well as error correlations. The proposed approach also addresses the difficulty in estimating accurately the correlation coefficients, which characterize the dependence of binary responses conditional on covariates. The parameters of the model are estimated within a penalized likelihood framework based on a carefully structured trust region algorithm with integrated automatic multiple smoothing parameter selection. The relevant numerical computation can be easily carried out using the SemiParTRIV() function in a freely available R package. The proposed method is illustrated through a case study whose aim is to model jointly adverse birth binary outcomes in North Carolina.
A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus
Authors: Geng Xiaofang , Li Wanshun , Shang Haitao , Gou Qiang , Zhang Fuchun , Zang Xiayan , Zeng Benhua , Li Jiang , Wang Ying , Ma Ji , Guo Jianlin , Jian Jianbo , Chen Bing , Qiao Zhigang , Zhou Minghui , Wei Hong , Fang Xiaodong , Xu Cunshuan 
Published: February 2017

Abstract

Background
Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources leads to fewer study progresses in these fields, due to its huge genome of ~50 GB making it extremely difficult to be assembled.

Results
We reported the sequenced transcriptome of more than 20 tissues from adult CGS using Illumina Hiseq 2000 technology, and a total of 93 366 no-redundancy transcripts with a mean length of 1326 bp were obtained. We developed for the first time an efficient pipeline to construct a high-quality reference gene set of CGS and obtained 26 135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6% of vertebrate universal single-copy orthologs, and this coding gene set had a higher proportion of completeness CDS with comparable quality of the protein sets of Tibetan frog.

Conclusions
These highest quality data will provide a valuable reference gene set to the subsequent research of CGS. In addition, our strategy of de novo transcriptome assembly and protein identification is applicable to similar studies.
Managing marine socio-ecological systems: picturing the future
Authors: Thébaud Olivier , Link Jason S. , Kohler Bas , Kraan Marloes , López Romain , Poos Jan Jaap , Schmidt Jörn O. , Smith David C. 
Published: February 2017

Abstract
What do you get when a lawyer, a modeller, an economist, a social scientist and an ecologist talk about the ocean? Besides an interesting conversation, it is likely there will be some consideration of how to solve many of the problems facing marine ecosystems around the world. That is precisely what the MSEAS 2016 symposium on understanding marine socio-ecological systems aimed to do. From 30 May to 3 June in Brest, France, the symposium gathered over 230 participants from around the world and from multiple disciplines to discuss the challenge of explicitly considering the human component in producing synoptic assessments of marine social-ecological systems. The symposium fostered dynamic debates on the inter-disciplinary collaborations needed to support management of ongoing and anticipated growth in multiple ocean uses, with particular consideration of the triple bottom line of ecological, economic and social sustainability. Building on the illustrations produced by a professional cartoonist during the meeting, this graphic novel summarizes the key challenges ahead in understanding marine socio-ecological systems and draws a path for future research endeavours in this domain.
New Perspectives on Collective Labour Law: Trade Union Recognition and Collective Bargaining
Authors: Ewing Keith , Hendy John 
Published: February 2017

Abstract
Drawing on the Manifesto for Labour Law published earlier this year, we consider Kahn-Freund’s assessment of British labour law (for the first three quarters of the twentieth century) as voluntarist, abstentionist collective laissez faire as espoused by Bob Simpson. In contrast (and utilising Simpson’s tool of ‘law in context’), we point up the role of the state during this period in implementing labour law policy in support of extensive collective bargaining by the use of public law powers (in the contemporaneous sense in which such law was understood). Drawing on this legacy, we set out the measures by which collective bargaining, in particular at sectoral level, might be restored. We deal with the establishment of Sectoral Employment Commissions consisting of equal numbers of employers and union representatives (similar to the old Joint Industrial Councils). In default, tripartite bodies based on the extinct Wages Councils would be established. We propose the (re) use of ‘fair wages clauses’ (ie public procurement arrangements) to require participation in collective bargaining and the observance of collective agreements. We consider the reciprocal issues of representation at the workplace, union access thereto and reform of the recognition machinery, taking in Simpson’s analysis of the current and earlier recognition legislation.
A ward-based time study of paper and electronic documentation for recording vital sign observations
Authors: Wong David , Bonnici Timothy , Knight Julia , Gerry Stephen , Turton James , Watkinson Peter 
Published: February 2017

Abstract
Objective: To investigate time differences in recording observations and an early warning score using traditional paper charts and a novel e-Obs system in clinical practice.
Methods: Researchers observed the process of recording observations and early warning scores across 3 wards in 2 university teaching hospitals immediately before and after introduction of the e-Obs system. The process of recording observations included both measurement and documentation of vital signs. Interruptions were timed and subtracted from the measured process duration. Multilevel modeling was used to compensate for potential confounding factors.
Results: In all, 577 nurse events were observed (281 paper, 296 e-Obs). The geometric mean time to take a complete set of vital signs was 215 s (95% confidence interval [CI], 177 s–262 s) on paper, and 150 s (95% CI, 130 s–172 s) electronically. The treatment effect ratio was 0.70 (95% CI, 0.57–0.85, P &lt; .001). The treatment effect ratio in ward 1 was 0.37 (95% CI, 0.26–0.53), in ward 2 was 0.98 (95% CI, 0.70–1.38), and in ward 3 was 0.93 (95% CI, 0.66–1.33).
Discussion: Introduction of an e-Obs system was associated with a statistically significant reduction in overall time to measure and document vital signs electronically compared to paper documentation. The reductions in time varied among wards and were of clinical significance on only 1 of 3 wards studied.
Conclusion: Our results suggest that introduction of an e-Obs system could lower nursing workload as well as increase documentation quality.
Effect of acute millimeter wave exposure on dopamine metabolism of NGF-treated PC12 cells
Authors: Haas Alexis J. , Le Page Yann , Zhadobov Maxim , Sauleau Ronan , Dréan Yves Le , Saligaut Christian 
Published: February 2017

Abstract
Several forthcoming wireless telecommunication systems will use electromagnetic frequencies at millimeter waves (MMWs), and technologies developed around the 60-GHz band will soon know a widespread distribution. Free nerve endings within the skin have been suggested to be the targets of MMW therapy which has been used in the former Soviet Union. So far, no studies have assessed the impact of MMW exposure on neuronal metabolism. Here, we investigated the effects of a 24-h MMW exposure at 60.4 GHz, with an incident power density (IPD) of 5 mW/cm², on the dopaminergic turnover of NGF-treated PC12 cells. After MMW exposure, both intracellular and extracellular contents of dopamine (DA) and 3,4-dihydroxyphenylacetic acid (DOPAC) were studied using high performance liquid chromatography. Impact of exposure on the dopamine transporter (DAT) expression was also assessed by immunocytochemistry. We analyzed the dopamine turnover by assessing the ratio of DOPAC to DA, and measuring DOPAC accumulation in the medium. Neither dopamine turnover nor DAT protein expression level were impacted by MMW exposure. However, extracellular accumulation of DOPAC was found to be slightly increased, but not significantly. This result was related to the thermal effect, and overall, no evidence of non-thermal effects of MMW exposure were observed on dopamine metabolism.
Stylometry and collaborative authorship: Eddy, Lovecraft, and ‘The Loved Dead’
Authors: Eldin Addison , Lavin Matthew J. , Look Daniel M. 
Published: February 2017

Abstract
The authorship of the 1924 short story ‘The Loved Dead’ has been contested by family members of Clifford Martin Eddy, Jr. and Sunand Tryambak Joshi, a leading scholar on Howard Phillips Lovecraft. The authors of this article use stylometric methods to provide evidence for a claim about the authorship of the story and to analyze the nature of Eddy’s collaboration with Lovecraft. Further, we extend Rybicki, Hoover, and Kestemont’s (Collaborative authorship: Conrad, Ford, and rolling delta. Literary and Linguistic Computing, 2014; 29, 422–31) analysis of stylometry as it relates to collaborations in order to reveal the necessary considerations for employing a stylometric approach to authorial collaboration.
Direct evidence for Ly$\boldsymbol{\alpha }$ depletion in the protocluster core
Authors: Shimakawa Rhythm , Kodama Tadayuki , Hayashi Masao , Tanaka Ichi , Matsuda Yuichi , Kashikawa Nobunari , Shibuya Takatoshi , Tadaki Ken-ichi , Koyama Yusei , Suzuki Tomoko L. , Yamamoto Moegi 
Published: February 2017

Abstract
We have carried out panoramic Lyα narrow-band imaging with Suprime-Cam on Subaru towards the known protocluster USS1558−003 at z = 2.53. Our previous narrow-band imaging in the near-infrared identified multiple dense groups of Hα emitters (HAEs) within the protocluster. We have now identified the large-scale structures across a ∼50 comoving Mpc scale traced by Lyα emitters (LAEs) in which the protocluster traced by the HAEs is embedded. On a smaller scale, however, there are remarkably few LAEs in the regions of HAE overdensities. Moreover, the stacking analyses of the images show that HAEs in higher-density regions show systematically lower escape fractions of Lyα photons than those of HAEs in lower-density regions. These phenomena may be driven by the extra depletion of Lyα emission lines along our line of sight by more intervening cold circumgalactic/intergalactic medium and/or dust in the dense core. We also caution that all the previous high-z protocluster surveys using LAEs as tracers would have largely missed galaxies in the very dense cores of the protoclusters where we would expect to see any early environmental effects.
Concordance cosmology without dark energy
Authors: Rácz Gábor , Dobos László , Beck Róbert , Szapudi István , Csabai István 
Published: February 2017

Abstract
According to the separate universe conjecture, spherically symmetric sub-regions in an isotropic universe behave like mini-universes with their own cosmological parameters. This is an excellent approximation in both Newtonian and general relativistic theories. We estimate local expansion rates for a large number of such regions, and use a scale parameter calculated from the volume-averaged increments of local scale parameters at each time step in an otherwise standard cosmological N-body simulation. The particle mass, corresponding to a coarse graining scale, is an adjustable parameter. This mean field approximation neglects tidal forces and boundary effects, but it is the first step towards a non-perturbative statistical estimation of the effect of non-linear evolution of structure on the expansion rate. Using our algorithm, a simulation with an initial Ωm = 1 Einstein–de Sitter setting closely tracks the expansion and structure growth history of the Λ cold dark matter (ΛCDM) cosmology. Due to small but characteristic differences, our model can be distinguished from the ΛCDM model by future precision observations. Moreover, our model can resolve the emerging tension between local Hubble constant measurements and the Planck best-fitting cosmology. Further improvements to the simulation are necessary to investigate light propagation and confirm full consistency with cosmic microwave background observations.
Intramedullary Lesion Length on Postoperative Magnetic Resonance Imaging is a Strong Predictor of ASIA Impairment Scale Grade Conversion Following Decompressive Surgery in Cervical Spinal Cord Injury
Authors: Aarabi Bizhan , Sansur Charles A. , Ibrahimi David M. , Simard J. Marc , Hersh David S. , Le Elizabeth , Diaz Cara , Massetti Jennifer , Akhtar-Danesh Noori 
Published: February 2017

Abstract

BACKGROUND: Evidence indicates that, over time, patients with spinal cord injury (SCI) improve neurologically in various degrees. We sought to further investigate indicators of grade conversion in cervical SCI.

OBJECTIVE: To detect predictors of ASIA impairment scale (AIS) grade conversion in SCI following surgical decompression.

METHODS: In a retrospective study, demographics, clinical, imaging, and surgical data from 100 consecutive patients were assessed for predictors of AIS grade conversion.

RESULTS: American Spinal Injury Association motor score was 17.1. AIS grade was A in 52%, B in 29%, and C in 19% of patients. Surgical decompression took place on an average of 17.6 h following trauma (≤12 h in 51 and >12 h in 49). Complete decompression was verified by magnetic resonance imaging (MRI) in 73 patients. Intramedullary lesion length (IMLL) on postoperative MRI measured 72.8 mm, and hemorrhage at the injury epicenter was noted in 71 patients. Grade conversion took place in 26.9% of AIS grade A patients, 65.5% of AIS grade B, and 78.9% of AIS grade C. AIS grade conversion had statistical relationship with injury severity score, admission AIS grade, extent of decompression, presence of intramedullary hemorrhage, American Spinal Injury Association motor score, and IMLL. A stepwise multiple logistic regression analysis indicated IMLL was the sole and strongest indicator of AIS grade conversion (odds ratio 0.950, 95% CI 0.931-0.969). For 1- and 10-mm increases in IMLL, the model indicates 4% and 40% decreases, respectively, in the odds of AIS grade conversion.

CONCLUSION: Compared with other surrogates, IMLL remained as the only predictor of AIS grade conversion.