bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utility and reliability of non‐invasive muscle function tests in high‐fat‐fed mice
Authors: Martinez‐Huenchullan Sergio F. , McLennan Susan V. , Ban Linda A. , Morsch Marco , Twigg Stephen M. , Tam Charmaine S. 
Published: May 2017

New Findings
What is the central question of this study?
Non‐invasive muscle function tests have not been validated for use in the study of muscle performance in high‐fat‐fed mice.

What is the main finding and its importance?
This study shows that grip strength, hang wire and four‐limb hanging tests are able to discriminate the muscle performance between chow‐fed and high‐fat‐fed mice at different time points, with grip strength being reliable after 5, 10 and 20 weeks of dietary intervention.

Non‐invasive tests are commonly used for assessing muscle function in animal models. The value of these tests in obesity, a condition where muscle strength is reduced, is unclear. We investigated the utility of three non‐invasive muscle function tests, namely grip strength (GS), hang wire (HW) and four‐limb hanging (FLH), in C57BL/6 mice fed chow (chow group, n = 48) or a high‐fat diet (HFD group, n = 48) for 20 weeks. Muscle function tests were performed at 5, 10 and 20 weeks. After 10 and 20 weeks, HFD mice had significantly reduced GS (in newtons; mean ± SD: 10 weeks chow, 1.89 ± 0.1 and HFD, 1.79 ± 0.1; 20 weeks chow, 1.99 ± 0.1 and HFD, 1.75 ± 0.1), FLH [in seconds per gram body weight; median (interquartile range): 10 weeks chow, 2552 (1337–4964) and HFD, 1230 (749–1994); 20 weeks chow, 2048 (765–3864) and HFD, 1036 (717–1855)] and HW reaches [n; median (interquartile range): 10 weeks chow, 4 (2–5) and HFD, 2 (1–3); 20 weeks chow, 3 (1–5) and HFD, 1 (0–2)] and higher falls [n; median (interquartile range): 10 weeks chow, 0 (0–2) and HFD, 3 (1–7); 20 weeks chow, 1 (0–4) and HFD, 8 (5–10)]. Grip strength was reliable in both dietary groups [intraclass correlation coefficient (ICC) = 0.5–0.8; P < 0.05], whereas FLH showed good reliability in chow (ICC = 0.7; P < 0.05) but not in HFD mice after 10 weeks (ICC < 0.5). Our data demonstrate that non‐invasive muscle function tests are valuable and reliable tools for assessment of muscle strength and function in high‐fat‐fed mice.
Draft Genome Sequences of Enterohemorrhagic Escherichia coli O103:H2 Strains Isolated from Feces of Feedlot Cattle
Authors: Noll Lance W. , Worley Jay N. , Yang Xun , Shridhar Pragathi B. , Bai Jianfa , Meng Jianghong , Caragea Doina , Nagaraja T. G. 
Published: May 2017

ABSTRACT

The enterohemorrhagic pathotype represents a minor proportion of the
Escherichia coli
O103 strains shed in the feces of cattle. We report here the genome sequences of 43 strains of enterohemorrhagic
E. coli
(EHEC) O103:H2 isolated from feedlot cattle feces. The genomic analysis will provide information on the genetic diversity and virulence potential of bovine EHEC O103.
Draft Genome Sequences of Serratia marcescens Strains CAPREx SY13 and CAPREx SY21 Isolated from Yams
Authors: Honger Joseph , Monson Rita E. , Rawlinson Alison , Salmond George P. C. 
Published: May 2017

ABSTRACT

Serratia marcescens
strains CAPREx SY13 and CAPREx SY21 were isolated from Ghanaian yams from a London market. The draft genomes suggest that the strains are similar, with genomes of 5,308,004 and 5,157,134 bp and 59.35 and 59.62 G+C%, respectively. The genes necessary for prodigiosin biosynthesis were present in both strains.
Complete Genome Sequence of Bacteriophage SEN8, a Temperate Phage Isolated from Salmonella enterica subsp.
salamae
Authors: Bosák Juraj , Mikalová Lenka , Čejková Darina , Šmarda Jan , Šmajs David 
Published: May 2017

ABSTRACT

A temperate phage, SEN8, having a broad activity against pathogenic
Salmonella
serovars, was isolated from
Salmonella enterica
subsp.
salamae
strain Sen8. The complete genome sequence of phage SEN8 was determined (35,203 bp) and showed relatedness to P2-like phages (
Salmonella
phages Fels-2 and RE-2010).
Complete Genome Sequence of an Enterovirus 71 Strain Isolated from the Cerebrospinal Fluid of a Child with Severe Hand-Foot-and-Mouth Disease in Yunnan, China, 2013
Authors: Lin Keqin , Zhang Haihao , Bai Wei , Zhao Yiling , Liu Hongbo , Huang Xiaoqin , Yang Zhaoqing , Ma Shaohui 
Published: May 2017

ABSTRACT
The complete genome sequence of the enterovirus 71 strain CSF15/YN/CHN/2013, first isolated from cerebrospinal fluid of a child in Yunnan, China, in 2013, was determined. According to the phylogenetic and homogeneity analyses, the isolate was assigned to subgenotype C4a.
Complete Genome Sequence of the Bacterium Bacillus circulans Jordan Strain 32352
Authors: Middleton Dustin R. , Lorenz Walter , Avci Fikri Y. 
Published: May 2017

ABSTRACTHere, we report the complete genome sequence for theBacillus circulansJordan strain 32352. This species is a soil dwelling bacterium that expresses glycosyl hydrolase enzymes degrading pneumococcal capsular polysaccharides.
Complete Annotated Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains and One Atypical Enteropathogenic E. coli Strain, Isolated from Naturally Colonized Cattle of German Origin
Authors: Geue Lutz , Menge Christian , Berens Christian , Barth Stefanie A. 
Published: May 2017

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) are important zoonotic enteric pathogens with the main reservoir in cattle. Here, we present the genomes of two STEC strains and one atypical enteropathogenic
E. coli
strain from cattle origin, obtained during a longitudinal study in German cattle herds.
Genome Sequences of Listeria monocytogenes Strains with Resistance to Arsenic
Authors: Dutta Vikrant , Lee Sangmi , Ward Todd J. , Orwig Nathane , Altermann Eric , Jima Dereje D. , Parsons Cameron , Kathariou Sophia 
Published: May 2017

ABSTRACT

Listeria monocytogenes
frequently exhibits resistance to arsenic. We report here the draft genome sequences of eight genetically diverse arsenic-resistant
L. monocytogenes
strains from human listeriosis and food-associated environments. The availability of these genomes will help elucidate the role of heavy-metal resistance in the ecology of
L. monocytogenes
.
Draft Genome Sequence of Staphylococcus fleurettii Strain MBTS-1 Isolated from Cucumber
Authors: Li Bo , Brinks Erik , Franz Charles M. A. P. , Cho Gyu-Sung 
Published: May 2017

ABSTRACT

The draft genome of
Staphylococcus fleurettii
MBTS-1, isolated from cucumber in northern Germany, was sequenced. Analysis showed that the assembled genome had a size of 2,582,128 bp with a predicted total of 2,491 protein-encoding genes, 9 rRNAs, 5 ncRNAs, and 44 tRNAs. This strain did not contain plasmid DNA.
Assessing total retinal blood flow in diabetic retinopathy using multiplane en face Doppler optical coherence tomography
Authors: Pechauer Alex D , Hwang Thomas S , Hagag Ahmed M , Liu Liang , Tan Ou , Zhang Xinbo , Parker Maria , Huang David , Wilson David J , Jia Yali 
Published: May 2017

AimTo assess total retinal blood flow (TRBF) in diabetic retinopathy (DR) using multiplane en face Doppler optical coherence tomography (OCT).MethodsA 70 kHz spectral-domain OCT system scanned a 2×2 mm area centred at the optic disc of the eyes with DR and healthy participants. The multiplane en face Doppler OCT algorithm generated a three-dimensional volumetric data set consisting of 195 en face planes. The TRBF was calculated from the maximum flow values of each branching retinal vein at an optimised en face plane. DR severity was graded according to the international clinical classification system. The generalised linear model method was used to compare flow values between DR groups and the control group.ResultsA total of 71 eyes from 71 participants were included. Ten eyes were excluded due to poor image quality. The within-visit repeatability of scans was 4.1% (coefficient of variation). There was no significant difference in the TRBF between the healthy (46.7±10.2 µL/min) and mild/moderate non-proliferative DR (44.9±12.6 µL/min) groups. The TRBF in severe non-proliferative DR (39.1±12.6 µL/min) and proliferative DR (28.9±8.85 µL/min) groups were significantly lower (p=0.04 and p<0.0001, respectively) than that of the healthy group. TRBF was correlated with DR disease severity (p<0.0001, linear trend test).ConclusionThe novel multiplane en face Doppler OCT method provided reliable measurements of TRBF in DR eyes. This may be a useful tool in understanding the pathophysiology of DR.
Sham surgery versus labral repair or biceps tenodesis for type II SLAP lesions of the shoulder: a three-armed randomised clinical trial
Authors: Schrøder Cecilie Piene , Skare Øystein , Reikerås Olav , Mowinckel Petter , Brox Jens Ivar 
Published: May 2017

BackgroundLabral repair and biceps tenodesis are routine operations for superior labrum anterior posterior (SLAP) lesion of the shoulder, but evidence of their efficacy is lacking. We evaluated the effect of labral repair, biceps tenodesis and sham surgery on SLAP lesions.MethodsA double-blind, sham-controlled trial was conducted with 118 surgical candidates (mean age 40 years), with patient history, clinical symptoms and MRI arthrography indicating an isolated type II SLAP lesion. Patients were randomly assigned to either labral repair (n=40), biceps tenodesis (n=39) or sham surgery (n=39) if arthroscopy revealed an isolated SLAP II lesion. Primary outcomes at 6 and 24 months were clinical Rowe score ranging from 0 to 100 (best possible) and Western Ontario Shoulder Instability Index (WOSI) ranging from 0 (best possible) to 2100. Secondary outcomes were Oxford Instability Shoulder Score, change in main symptoms, EuroQol (EQ-5D and EQ-VAS), patient satisfaction and complications.ResultsThere were no significant between-group differences at any follow-up in any outcome. Between-group differences in Rowe scores at 2 years were: biceps tenodesis versus labral repair: 1.0 (95% CI −5.4 to 7.4), p=0.76; biceps tenodesis versus sham surgery: 1.6 (95% CI −5.0 to 8.1), p=0.64; and labral repair versus sham surgery: 0.6 (95% CI −5.9 to 7.0), p=0.86. Similar results—no differences between groups—were found for WOSI scores. Postoperative stiffness occurred in five patients after labral repair and in four patients after tenodesis.ConclusionNeither labral repair nor biceps tenodesis had any significant clinical benefit over sham surgery for patients with SLAP II lesions in the population studied.Trial registration numberClinicalTrials.gov identifier:NCT00586742
Randomised controlled trial of online continuing education for health professionals to improve the management of chronic fatigue syndrome: a study protocol
Authors: Li Sophie H , Sandler Carolina X , Casson Sally M , Cassar Joanne , Bogg Tina , Lloyd Andrew R , Barry Benjamin K 
Published: May 2017

IntroductionChronic fatigue syndrome (CFS) is a serious and debilitating illness that affects between 0.2%–2.6% of the world’s population. Although there is level 1 evidence of the benefit of cognitive behaviour therapy (CBT) and graded exercise therapy (GET) for some people with CFS, uptake of these interventions is low or at best untimely. This can be partly attributed to poor clinician awareness and knowledge of CFS and related CBT and GET interventions. This trial aims to evaluate the effect of participation in an online education programme, compared with a wait-list control group, on allied health professionals’ knowledge about evidence-based CFS interventions and their levels of confidence to engage in the dissemination of these interventions.Methods and analysisA randomised controlled trial consisting of 180 consenting allied health professionals will be conducted. Participants will be randomised into an intervention group (n=90) that will receive access to the online education programme, or a wait-list control group (n=90). The primary outcomes will be: 1) knowledge and clinical reasoning skills regarding CFS and its management, measured at baseline, postintervention and follow-up, and 2) self-reported confidence in knowledge and clinical reasoning skills related to CFS. Secondary outcomes include retention of knowledge and satisfaction with the online education programme. The influence of the education programme on clinical practice behaviour, and self-reported success in the management of people with CFS, will also be assessed in a cohort study design with participants from the intervention and control groups combined.Ethics and disseminationThe study protocol has been approved by the Human Research Ethics Committee at The University of New South Wales (approval number HC16419). Results will be disseminated via peer-reviewed journal articles and presentations at scientific conferences and meetings.Trial registrationACTRN12616000296437.
Determinants of treatment duration in the prevention of recurrent venous thromboembolism: a protocol for a balanced vignette experiment
Authors: Ten Cate Vincent , Essers Brigitte AB , Prins Martin H 
Published: May 2017

IntroductionVenous thromboembolism (VTE) is a condition that annually occurs in approximately 1‰ of the world’s population. Patients who have already had a VTE are at elevated risk for a recurrent VTE. Recurrent events increase the risk of long-term sequelae and can be fatal. Adequate secondary prophylaxis is thus needed to prevent such events. Patients with VTE are often prone to bleeding, and pharmacological prophylaxis exacerbates bleeding risk. Expert opinions on the optimum duration of secondary prophylaxis in VTE still vary substantially. The existence of treatment guidelines has not led to uniformity of VTE secondary prophylaxis strategies, which means that physicians still adhere to individual risk calculi in determining treatment duration.Methods and analysisThe aim of this study is to establish what factors lie at the root of this variance in VTE secondary prophylactic treatment strategies, and what risk factors are deemed of particular importance in determining the perceived risks and benefits of variable treatment durations. To do this, we created a survey based on a D-efficient and G-efficient balanced experimental vignette design. This protocol covers all aspects of how this survey was set up and how it was implemented. The analysis of the experimental data will be carried out using mixed-effects methods, which are beneficial in scenarios with high interindividual variance and correlated (eg, repeated-measures) responses. We propose the use of maximal random effects structures insofar as possible.Ethics and disseminationAll data are de-identified, and any identifying characteristics of the respondents will not be reported in a final manuscript or elsewhere. A paper describing the expert interviews is currently under peer review. A manuscript that contains the analysis of the results of the experiment described in this protocol is being drafted, and will also be submitted to a peer-reviewed journal.
Estimating the prevalence, hospitalisation and mortality from type 2 diabetes mellitus in Nigeria: a systematic review and meta-analysis
Authors: Adeloye Davies , Ige Janet O , Aderemi Adewale V , Adeleye Ngozi , Amoo Emmanuel O , Auta Asa , Oni Gbolahan 
Published: May 2017

BackgroundThere is not yet a comprehensive evidence-based epidemiological report on type 2 diabetes mellitus (T2DM) in Nigeria. We aimed to estimate country-wide and zonal prevalence, hospitalisation and mortality rates of T2DM in Nigeria.MethodsWe searched MEDLINE, EMBASE, Global Health, Africa Journals Online (AJOL) and Google Scholar for population and hospital-based studies on T2DM in Nigeria. We conducted a random-effects meta-analysis on extracted crude estimates, and applied a meta-regression epidemiological model, using the United Nations demographics for Nigeria in 1990 and 2015 to determine estimates of diabetes in Nigeria for the two years.Results42 studies, with a total population of 91 320, met our selection criteria. Most of the studies selected were of medium quality (90.5%). The age-adjusted prevalence rates of T2DM in Nigeria among persons aged 20–79 years increased from 2.0% (95% CI 1.9% to 2.1%) in 1990 to 5.7% (95% CI 5.5% to 5.8%) in 2015, accounting for over 874 000 and 4.7 million cases, respectively. The pooled prevalence rate of impaired glucose tolerance was 10.0% (95% CI 4.5% to 15.6%), while impaired fasting glucose was 5.8% (95% CI 3.8% to 7.8%). Hospital admission rate for T2DM was 222.6 (95% CI 133.1 to 312.1) per 100 000 population with hyperglycaemic emergencies, diabetic foot and cardiovascular diseases being most common complications. The overall mortality rate was 30.2 (95% CI 14.6 to 45.8) per 100 000 population, with a case fatality rate of 22.0% (95% CI 8.0% to 36.0%).ConclusionOur findings suggest an increasing burden of T2DM in Nigeria with many persons currently undiagnosed, and few known cases on treatment.
The exp-log normal form of types: decomposing extensional equality and representing terms compactly
Authors: Ilik Danko 
Published: May 2017

Lambda calculi with algebraic data types lie at the core of functional programming languages and proof assistants, but conceal at least two fundamental theoretical problems already in the presence of the simplest non-trivial data type, the sum type. First, we do not know of an explicit and implemented algorithm for deciding the beta-eta-equality of terms---and this in spite of the first decidability results proven two decades ago. Second, it is not clear how to decide when two types are essentially the same, i.e. isomorphic, in spite of the meta-theoretic results on decidability of the isomorphism.
In this paper, we present the exp-log normal form of types---derived from the representation of exponential polynomials via the unary exponential and logarithmic functions---that any type built from arrows, products, and sums, can be isomorphically mapped to. The type normal form can be used as a simple heuristic for deciding type isomorphism, thanks to the fact that it is a systematic application of the high-school identities.
We then show that the type normal form allows to reduce the standard beta-eta equational theory of the lambda calculus to a specialized version of itself, while preserving completeness of the equality on terms.
We end by describing an alternative representation of normal terms of the lambda calculus with sums, together with a Coq-implemented converter into/from our new term calculus. The difference with the only other previously implemented heuristic for deciding interesting instances of eta-equality by Balat, Di Cosmo, and Fiore, is that we exploits the type information of terms substantially and this often allows us to obtain a canonical representation of terms without performing a sophisticated term analyses.
Fencing off go: liveness and safety for channel-based programming
Authors: Lange Julien , Ng Nicholas , Toninho Bernardo , Yoshida Nobuko 
Published: May 2017

Go is a production-level statically typed programming language whose design features explicit message-passing primitives and lightweight threads, enabling (and encouraging) programmers to develop concurrent systems where components interact through communication more so than by lock-based shared memory concurrency. Go can only detect global deadlocks at runtime, but provides no compile-time protection against all too common communication mismatches or partial deadlocks.
This work develops a static verification framework for bounded liveness and safety in Go programs, able to detect communication errors and partial deadlocks in a general class of realistic concurrent programs, including those with dynamic channel creation and infinite recursion. Our approach infers from a Go program a faithful representation of its communication patterns as a behavioural type. By checking a syntactic restriction on channel usage, dubbed fencing, we ensure that programs are made up of finitely many different communication patterns that may be repeated infinitely many times. This restriction allows us to implement bounded verification procedures (akin to bounded model checking) to check for liveness and safety in types which in turn approximates liveness and safety in Go programs. We have implemented a type inference and liveness and safety checks in a tool-chain and tested it against publicly available Go programs.
Updated on 27th Feb 2017. See Comments.
Computational higher-dimensional type theory
Authors: Angiuli Carlo , Harper Robert , Wilson Todd 
Published: May 2017

Formal constructive type theory has proved to be an effective language for mechanized proof. By avoiding non-constructive principles, such as the law of the excluded middle, type theory admits sharper proofs and broader interpretations of results. From a computer science perspective, interest in type theory arises from its applications to programming languages. Standard constructive type theories used in mechanization admit computational interpretations based on meta-mathematical normalization theorems. These proofs are notoriously brittle; any change to the theory potentially invalidates its computational meaning. As a case in point, Voevodsky's univalence axiom raises questions about the computational meaning of proofs.
We consider the question: Can higher-dimensional type theory be construed as a programming language? We answer this question affirmatively by providing a direct, deterministic operational interpretation for a representative higher-dimensional dependent type theory with higher inductive types and an instance of univalence. Rather than being a formal type theory defined by rules, it is instead a computational type theory in the sense of Martin-Löf's meaning explanations and of the NuPRL semantics. The definition of the type theory starts with programs; types are specifications of program behavior. The main result is a canonicity theorem stating that closed programs of boolean type evaluate to true or false.
Complexity verification using guided theorem enumeration
Authors: Srikanth Akhilesh , Sahin Burak , Harris William R. 
Published: May 2017

Determining if a given program satisfies a given bound on the amount of resources that it may use is a fundamental problem with critical practical applications. Conventional automatic verifiers for safety properties cannot be applied to address this problem directly because such verifiers target properties expressed in decidable theories; however, many practical bounds are expressed in nonlinear theories, which are undecidable.
In this work, we introduce an automatic verification algorithm, CAMPY, that determines if a given program P satisfies a given resource bound B, which may be expressed using polynomial, exponential, and logarithmic terms. The key technical contribution behind our verifier is an interpolating theorem prover for non-linear theories that lazily learns a sufficiently accurate approximation of non-linear theories by selectively grounding theorems of the nonlinear theory that are relevant to proving that P satisfies B. To evaluate CAMPY, we implemented it to target Java Virtual Machine bytecode. We applied CAMPY to verify that over 20 solutions submitted for programming problems hosted on popular online coding platforms satisfy or do not satisfy expected complexity bounds.