bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virtual‐reality exergaming improves performance during high‐intensity interval training
Authors: Farrow Matthew , Lutteroth Christof , Rouse Peter C. , Bilzon James L. J. 
Published: November 2018

AbstractPurpose: To determine if: (i) mean power output and enjoyment of high‐intensity interval training (HIIT) are enhanced by virtual‐reality (VR)‐exergaming (track mode) compared to standard ergometry (blank mode), (ii) if mean power output of HIIT can be increased by allowing participants to race against their own performance (ghost mode) or by increasing the resistance (hard mode), without compromising exercise enjoyment.Methods: Sixteen participants (8 males, 8 females, VO2max: 41.2 ± 10.8 ml−1·kg−1·min−1) completed four VR‐HIIT conditions in a partially‐randomised cross‐over study; (1a) blank, (1b) track, (2a) ghost, and (2b) hard. VR‐HIIT sessions consisted of eight 60 s high‐intensity intervals at a resistance equivalent to 70% (77% for hard) maximum power output (PMAX), interspersed by 60 s recovery intervals at 12.5% PMAX, at a self‐selected cadence. Expired gases were collected and VO2 measured continuously. Post‐exercise questionnaires were administered to identify differences in indices related to intrinsic motivation, subjective vitality, and future exercise intentions.Results: Enjoyment was higher for track vs. blank (difference: 0.9; 95% CI: 0.6, 1.3) with no other differences between conditions. There was no difference in mean power output for track vs. blank, however it was higher for track vs. ghost (difference: 5 Watts; CI: 3, 7), and hard vs. ghost (difference: 19 Watts; 95% CI: 15, 23).Conclusions: These findings demonstrate that VR‐exergaming is an effective intervention to increase enjoyment during a single bout of HIIT in untrained individuals. The presence of a ghost may be an effective method to increase exercise intensity of VR‐HIIT.
Comparison of the standards for absorbed dose to water of the VSL, The Netherlands, and the BIPM for 60Co γ rays
Authors: Kessler C , Burns D , Jansen B J , Pooter J A de , Prez L A de 
Published: November 2018

A key comparison of the standards for absorbed dose to water of the VSL, Dutch Metrology Institute, Delft, The Netherlands and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in December 2017. The comparison result, based on the calibration coefficients for two transfer standards and expressed as a ratio of the VSL and the BIPM standards for absorbed dose to water, is 0.9960 with a combined standard uncertainty of 4.8 x 10-3. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.
KEY WORDS FOR SEARCH
Absorbed dose to water, 60Co, key comparison, radiation dosimetry

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
CCQM-K121 - Monoterpenes in nitrogen at 2.5 nmol mol-1 final report
Authors: Liaskos Christina , Rhoderick George , Hodges Joseph , Possolo Antonio , Goodman Cassie , Kim Yong Doo , Kim Dal Ho , Lee Sangil , Allen Nicholas , Corbel Marivon , Worton David , Brown Richard , Brewer Paul 
Published: November 2018

Main text

The growing awareness of climate change, and continuing concerns regarding tropospheric and stratospheric chemistry, will require future measurements and standards for compounds linked to these issues. To globally monitor and control the emissions of these species in the atmosphere, it is necessary to demonstrate measurement equivalence at the highest levels of accuracy for assigned values of standards. This report describes the results of a key comparison for several important monoterpene species, which are relevant to atmospheric chemistry and climate. The comparison samples include α-pinene, 3-carene, R-limonene and 1,8-cineole in a nitrogen matrix gas, at a 2.5 nmol mol-1 amount of substance fraction. The objective of this key comparison is to evaluate the participants' capabilities to measure trace level monoterpenes using their own calibration techniques.
KEY WORDS FOR SEARCH
VOCs, terpenes, metrology, gas standards

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Combined Non-Ablative Laser and Microfat Grafting for Burn Scar Treatment
Authors: Onur Erol O , Agaoglu Galip , Jawad Mohammad Ali 
Published: November 2018

AbstractBackgroundBurn scar treatment persists as an unsolved problem, involving thousands of affected patients disfigured for life.ObjectivesWe sought to present our experience with the use of combined treatments for patients with burn scars.MethodsThis was a case series report of the senior author’s experience during 8 years utilizing the combined treatments of Fraxel Restore (fractional laser) and microfat graft injection for 288 patients with burn scars.ResultsLaser treatment reduced scar intensity and attenuated skin irregularities and hyperpigmentation. All patients demonstrated marked improvement of skin texture and an increase in scar softness after 3 sessions of microfat grafting. However, the degree of improvement varied between patients and was related to the severity of the scar and the type of tissue. Overall, a 40% to 80% improvement was noted in our patients. All patients and their families expressed satisfaction with the results.ConclusionsThe combined treatment of Fraxel and microfat grafting is an effective technique for improving the appearance of a hypertrophic scar or keloid on burn patients. Fat tissue stem cells may have helped to repair the damaged skin.Level of Evidence: 4
Clusterdv: a simple density-based clustering method that is robust, general and automatic
Authors: Marques João C , Orger Michael B 
Published: November 2018

Abstract

Motivation
How to partition a dataset into a set of distinct clusters is a ubiquitous and challenging problem. The fact that data vary widely in features such as cluster shape, cluster number, density distribution, background noise, outliers and degree of overlap, makes it difficult to find a single algorithm that can be broadly applied. One recent method, clusterdp, based on search of density peaks, can be applied successfully to cluster many kinds of data, but it is not fully automatic, and fails on some simple data distributions.

Results
We propose an alternative approach, clusterdv, which estimates density dips between points, and allows robust determination of cluster number and distribution across a wide range of data, without any manual parameter adjustment. We show that this method is able to solve a range of synthetic and experimental datasets, where the underlying structure is known, and identifies consistent and meaningful clusters in new behavioral data.

Availability and implementation
The clusterdv is implemented in Matlab. Its source code, together with example datasets are available on: https://github.com/jcbmarques/clusterdv.

Supplementary information
Supplementary data are available at Bioinformatics online.
High efficiency referential genome compression algorithm
Authors: Shi Wei , Chen Jianhua , Luo Mao , Chen Min 
Published: November 2018

AbstractMotivationWith the development and the gradually popularized application of next-generation sequencing technologies (NGS), genome sequencing has been becoming faster and cheaper, creating a massive amount of genome sequence data which still grows at an explosive rate. The time and cost of transmission, storage, processing and analysis of these genetic data have become bottlenecks that hinder the development of genetics and biomedicine. Although there are many common data compression algorithms, they are not effective for genome sequences due to their inability to consider and exploit the inherent characteristics of genome sequence data. Therefore, the development of a fast and efficient compression algorithm specific to genome data is an important and pressing issue.ResultsWe have developed a referential lossless genome data compression algorithm with better performance than previous algorithms. According to a carefully designed matching strategy selection mechanism, the advantages of local matching and global matching are reasonably combined together to improve the description efficiency of the matched sub-strings. The effects of the length and the position of matched sub-strings to the compression efficiency are jointly taken into consideration. The proposed algorithm can compress the FASTA data of complete human genomes, each of which is about 3 GB, in about 18 min. The compressed file sizes are ranging from a few megabytes to about forty megabytes. The averaged compression ratio is higher than that of the state-of-the-art genome compression algorithms, the time complexity is at the same order of the best-known algorithms.Availability and implementationhttps://github.com/jhchen5/SCCGSupplementary informationSupplementary data are available at Bioinformatics online.
Index suffix–prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression
Authors: Liu Yuansheng , Yu Zuguo , Dinger Marcel E , Li Jinyan 
Published: November 2018

Abstract

Motivation
Advanced high-throughput sequencing technologies have produced massive amount of reads data, and algorithms have been specially designed to contract the size of these datasets for efficient storage and transmission. Reordering reads with regard to their positions in de novo assembled contigs or in explicit reference sequences has been proven to be one of the most effective reads compression approach. As there is usually no good prior knowledge about the reference sequence, current focus is on the novel construction of de novo assembled contigs.

Results
We introduce a new de novo compression algorithm named minicom. This algorithm uses large k-minimizers to index the reads and subgroup those that have the same minimizer. Within each subgroup, a contig is constructed. Then some pairs of the contigs derived from the subgroups are merged into longer contigs according to a (w, k)-minimizer-indexed suffix–prefix overlap similarity between two contigs. This merging process is repeated after the longer contigs are formed until no pair of contigs can be merged. We compare the performance of minicom with two reference-based methods and four de novo methods on 18 datasets (13 RNA-seq datasets and 5 whole genome sequencing datasets). In the compression of single-end reads, minicom obtained the smallest file size for 22 of 34 cases with significant improvement. In the compression of paired-end reads, minicom achieved 20–80% compression gain over the best state-of-the-art algorithm. Our method also achieved a 10% size reduction of compressed files in comparison with the best algorithm under the reads-order preserving mode. These excellent performances are mainly attributed to the exploit of the redundancy of the repetitive substrings in the long contigs.

Availability and implementation
https://github.com/yuansliu/minicom

Supplementary information
Supplementary data are available at Bioinformatics online.
Identifying antimicrobial peptides using word embedding with deep recurrent neural networks
Authors: Hamid Md-Nafiz , Friedberg Iddo 
Published: November 2018

Abstract

Motivation
Antibiotic resistance constitutes a major public health crisis, and finding new sources of antimicrobial drugs is crucial to solving it. Bacteriocins, which are bacterially produced antimicrobial peptide products, are candidates for broadening the available choices of antimicrobials. However, the discovery of new bacteriocins by genomic mining is hampered by their sequences’ low complexity and high variance, which frustrates sequence similarity-based searches.

Results
Here we use word embeddings of protein sequences to represent bacteriocins, and apply a word embedding method that accounts for amino acid order in protein sequences, to predict novel bacteriocins from protein sequences without using sequence similarity. Our method predicts, with a high probability, six yet unknown putative bacteriocins in Lactobacillus. Generalized, the representation of sequences with word embeddings preserving sequence order information can be applied to peptide and protein classification problems for which sequence similarity cannot be used.

Availability and implementation
Data and source code for this project are freely available at: https://github.com/nafizh/NeuBI.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Mortality Burden of Multidrug-resistant Pathogens in India: A Retrospective, Observational Study
Authors: Gandra Sumanth , Tseng Katie K , Arora Anita , Bhowmik Bhaskar , Robinson Matthew L , Panigrahi Bishnu , Laxminarayan Ramanan , Klein Eili Y 
Published: November 2018

Abstract

Background
The threat posed by antibiotic resistance is of increasing concern in low- and middle-income countries (LMICs) as their rates of antibiotic use increase. However, an understanding of the burden of resistance is lacking in LMICs, particularly for multidrug-resistant (MDR) pathogens.

Methods
We conducted a retrospective, 10-hospital study of the relationship between MDR pathogens and mortality in India. Patient-level antimicrobial susceptibility test (AST) results for Enterococcus spp., Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. were analyzed for their association with patient mortality outcomes.

Results
We analyzed data on 5103 AST results from 10 hospitals. The overall mortality rate of patients was 13.1% (n = 581), and there was a significant relationship between MDR and mortality. Infections with MDR and extensively drug resistant (XDR) E. coli, XDR K. pneumoniae, and MDR A. baumannii were associated with 2–3 times higher mortality. Mortality due to methicillin-resistant S. aureus (MRSA) was significantly higher than susceptible strains when the MRSA isolate was resistant to aminoglycosides.

Conclusions
This is one of the largest studies undertaken in an LMIC to measure the burden of antibiotic resistance. We found that MDR bacterial infections pose a significant risk to patients. While consistent with prior studies, the variations in drug resistance and associated mortality outcomes by pathogen are different from those observed in high-income countries and provide a baseline for studies in other LMICs. Future research should aim to elucidate the burden of resistance and the differential transmission mechanisms that drive this public health crisis.
Maternal work and exclusive breastfeeding in Mansoura, Egypt
Authors: Abou-ElWafa Hala Samir , El-Gilany Abdel-Hady 
Published: November 2018

AbstractBackgroundWorking mothers face unique barriers to breastfeeding, despite the compelling evidence of its benefits. The aim of this study was to describe exclusive breastfeeding (EBF) rate of working mothers and associated factors.MethodsCross-sectional study was carried out in Mansoura District, Egypt from 1 July to 31 December 2017 among working mothers attending health care facilities for vaccinating their infants aged 6 months. Data were collected using a questionnaire covering sociodemographic and occupational data; breastfeeding supportive workplace facilities; antenatal and natal care; infant’s data; and EBF practice.ResultsEBF rate was 14.1%. Independent predictors were being still on work leave, return to work 4 months after childbirth, working as farmer/manual worker and in trades and business, and being self/family employed.ConclusionsEBF rate is low among working mothers. There is a need to extend maternity leave and provide promoting workplace facilities.
Super-Earths in the TW Hya disc
Authors: Mentiplay Daniel , Price Daniel J , Pinte Christophe 
Published: November 2018

ABSTRACT
We test the hypothesis that the sub-millimetre thermal emission and scattered light gaps seen in recent observations of TW Hya are caused by planet–disc interactions. We perform global three-dimensional dusty smoothed particle hydrodynamics simulations, comparing synthetic observations of our models with dust thermal emission, CO emission, and scattered light observations. We find that the dust gaps observed at 24 au and 41 au can be explained by two super-Earths (∼ 4 M⊕). A planet of approximately Saturn-mass can explain the CO emission and the depth and width of the gap seen in scattered light at 94 au. Our model produces a prominent spiral arm while there are only hints of this in the data. To avoid runaway growth and migration of the planets we require a disc mass of ${\lesssim } 10^{-2}\, \mathrm{M}_{\odot }{}$ in agreement with CO observations but 10–100 times lower than the estimate from HD line emission.
Transcriptional modulation of the T helper 17/interleukin 17 axis ameliorates renal ischemia-reperfusion injury
Authors: Lee Jae Wook , Bae Eunjin , Kwon Sun-Ho , Yu Mi-Yeon , Cha Ran-Hui , Lee Hajeong , Kim Dong Ki , Lee Jung Pyo , Ye Sang-Kyu , Yoo Joo-Yeon , Park Dong Jun , Kim Yon Su , Yang Seung Hee 
Published: November 2018

AbstractBackgroundSignal transducer and activator of transcription 3 (STAT3) is a latent transcription factor critical for T-cell function. Although inhibition of the Janus kinase 2 (JAK2)/STAT3 pathway has been reported to be protective against ischemia-reperfusion injury (IRI), the role of T cell–associated STAT3 in the pathogenesis of renal IRI has not been specifically defined.MethodsWe induced renal IRI in both mice with T cell–specific STAT3 knockout (Lck-Cre;STAT3flox/flox) and wild-type controls (C57BL/6) and assessed renal damage and inflammation at 48 h after IRI. Human proximal tubular epithelial cells grown under hypoxia were treated with a JAK2 inhibitor, caffeic acid 3,4-dihydroxy-phenylethyl ester, to determine the effect of JAK2/STAT3 inhibition on renal epithelia. Independently, we disrupted Cln 3-requiring 9 (Ctr9) to inhibit T helper 17 (Th17) activation via RNA interference and determined if Ctr9 inhibition aggravates renal injury through upregulated Th17 activation.ResultsThe Lck-Cre;STAT3flox/flox mice exhibited significantly reduced kidney damage compared with controls. This protective effect was associated with reduced intrarenal Th17 infiltration and proinflammatory cytokines. Human proximal tubular epithelial cells under hypoxia exhibited significant upregulation of interleukin 17 receptors, and pharmacologic inhibition of JAK2 significantly ameliorated this change. RNA interference with Ctr9 in splenocytes enhanced differentiation into Th17 cells. In vivo knockdown of Ctr9 in mice with renal IRI further aggravated Th17-associated inflammation and kidney injury.ConclusionsSTAT3 in T cells contributes to renal IRI through Th17 activation. Inhibition of Ctr9 further enhances Th17 activation and aggravates kidney injury, further supporting the role of Th17 cells in renal IRI.
Youth Access to Tobacco Products in the United States: Findings From Wave 1 (2013–2014) of the Population Assessment of Tobacco and Health Study
Authors: Tanski Susanne , Emond Jennifer , Stanton Cassandra , Kirchner Thomas , Choi Kelvin , Yang Ling , Ryant Chase , Robinson Joelle , Hyland Andrew 
Published: November 2018

Abstract

Objectives
Tobacco products in the US market are growing in diversity. Little is known about how youth access tobacco products given this current landscape.

Methods
Data were drawn from 15- to 17-year-olds from the Wave 1 youth sample of the US nationally representative Population Assessment of Tobacco and Health (PATH) Study. Past 30-day tobacco users were asked about usual sources of access to 12 different tobacco products, and if they had been refused sale because of their age.

Results
Among 15- to 17-year-olds, social sources (“someone offered” or “asked someone”) were the predominant usual source of access for each tobacco product. “Bought by self” was the usual source of access for users of smokeless (excluding snus, 23.2%), cigarillos (21.0%), cigarettes (13.8%), hookah (12.0%), and electronic cigarettes (10.5%). Convenience stores and/or gas stations were the most often selected retail source for all products except hookah. Among youth who attempted purchase, 24.3% were refused sale of cigarettes, 23.9% cigarillos, and 13.8% smokeless tobacco.

Conclusions
Most 15- to 17-year-old tobacco users obtain tobacco products through social sources; however, among those who purchased tobacco, the majority report not being refused sale because of age. At the time of survey, cigarette and cigar sales to under 18 years were prohibited in all 50 states, and electronic cigarettes sales in 47 states and two territories. 2014 Annual Synar Reports signaled increasing trends in retail violations of state and/or district laws prohibiting tobacco product sales to under 18 years. Monitoring illicit youth sales, conducting compliance check inspections, and penalizing violations remain important to reduce youth tobacco access at retail venues.

Implications
Access to the spectrum of tobacco products by youth in the United States remains predominantly through social sources. However, of the minority of youth tobacco users in 2014 who purchased tobacco themselves, a few reported being refused sale: Convenience stores and/or gas stations were the most common retail source for tobacco products. The strategies of monitoring illicit youth sales, conducting compliance checks, and penalizing violations remain important to reduce youth tobacco access at retail venues. Limiting sources of youth tobacco access remains an important focus to reduce the burden of tobacco on the public health.
THE IMPACT OF OBESITY ON ABDOMINAL CT RADIATION DOSE AND IMAGE QUALITY
Authors: Qurashi Abdulaziz A , Rainford Louise A , Alshamrani Khalid M , Foley Shane J 
Published: November 2018

Abstract
The aim of this study was to evaluate how iterative reconstruction can compensate for the noise increase in low radiation dose abdominal computed tomography (CT) technique for large size patients and the general impact of obesity on abdominal organ doses and image quality in CT. An anthropomorphic phantom layered with either none or a single layer of 3-cm- thick circumferential animal fat packs to simulate obese patients was imaged using a 128MDCT scanner. Abdominal protocols (n = 12) were applied using automatic tube current modulation (ATCM) with various quality reference mAs (150, 200, 250 and 300). kVs of 100, 120 and 140 were used for each mAs selection. Metal oxide semiconductor field effect transistor dosimeters (MOSFET) measured internal organ dose. All images produced were reconstructed with filtered back projection (FBP) and sinogram affirmed iterative reconstruction (SAFIRE) (3, 4 and 5) and objective noise was measured within three regions of interest at the level of L4–L5. Organ doses varied from 0.12 to 41.9 mGy, the spleen received the highest doses for both phantom sizes. Compared to the phantom simulating average size, the obese phantom was associated with up to twofold increase in delivered mAs, dose length product (DLP) and computed tomography dose index (CTDIvol) for the matched mAs selection (p < 0.05). However, organ dose increased by 50% only. The use of 100 kV resulted in a 40% lower dose (p < 0.05) compared to 120 kV and the associated noise increase was improved by SAFIRE (5) use, which resulted in 60% noise reduction compared to FBP (p < 0.05). When combined with iterative reconstruction, low kV is feasible for obese patients to optimise radiation dose and maintain objective image quality.