bluuebunny/crossref_metadata_2025_split huggingface dataset:
BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures
Authors: Bondarev Stanislav A , Bondareva Olga V , Zhouravleva Galina A , Kajava Andrey V 
Published: October 2017

Abstract

Motivation
Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics.

Results
We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments.

Availability and implementation
BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine).

Supplementary information
Supplementary data are available at Bioinformatics online.
Towards unified quality verification of synthetic count data with countsimQC
Authors: Soneson Charlotte , Robinson Mark D 
Published: October 2017

Abstract

Summary
Statistical tools for biological data analysis are often evaluated using synthetic data, designed to mimic the features of a specific type of experimental data. The generalizability of such evaluations depends on how well the synthetic data reproduce the main characteristics of the experimental data, and we argue that an assessment of this similarity should accompany any synthetic dataset used for method evaluation. We describe countsimQC, which provides a straightforward way to generate a stand-alone report that shows the main characteristics of (e.g. RNA-seq) count data and can be provided alongside a publication as verification of the appropriateness of any utilized synthetic data.

Availability and implementation
countsimQC is implemented as an R package (for R versions ≥ 3.4) and is available from https://github.com/csoneson/countsimQC under a GPL (≥2) license.
Reflections on using a community-led research methodology to explore experiences of living with food insecurity
Authors: Greenaway Lesley , McDowell Jacqui 
Published: October 2017

AbstractThis article explores how community-led research in practice relates to the theory and aspirations of a community-led research methodology and how this approach can provide a unique opportunity to increase our understanding about the lived experiences of food insecurity. As an approach, community-led research has growing influence and relevance for communities, organizations, research commissioners, funders and policy makers. This article provides insights and learning for these stakeholders that we discovered in our experience of the ‘Living with food insecurity’ community-led research project. We draw on a range of sources including: community-led research literature, materials developed to support the project, feedback from the research teams, and reflective conversations between the research commissioner and the research specialist who was engaged to support the process. We start by setting out the context for food insecurity in Scotland and identify the research gap that led to the research project. We then discuss some pertinent research challenges in the context of this project, and explore how each of three distinct communities developed different models of community-led research. Learning from this project suggests that community-led research design needs to embrace divergence and facilitate research partnerships that are flexible, open and find ways to ‘live’ out the principles of community-led research in ways that are meaningful to a particular community and its stakeholders.
Investigating the spatiotemporal variation of fish choruses to help identify important foraging habitat for Indo-Pacific humpback dolphins, Sousa chinensis
Authors: Pine Matthew K , Wang Ding , Porter Lindsay , Wang Kexiong 
Published: October 2017

AbstractGiven the common physical overlapping between coastal developments and important marine mammal habitats, there is a need to identify potentially important foraging grounds for dolphins when informing marine spatial planning and management of underwater noise. Hydrophones were deployed at four locations either side of the mainland China–Hong Kong Special Administrative Region border to monitor the presence of soniferous fishes; a key prey item for Indo-Pacific humpback dolphins. Five distinct chorus-types were identified; each showing spatiotemporal variability. Each chorus-type was assumed to represent a separate species. Chorus-type diversity also differed between sites, with SP4 and SP5 types only being detected within Hong Kong waters where bottom trawling is illegal. Chorus-type SP1 was only detected at the recording sites in mainland Chinese waters. Call rates and chorus duration were highest during the spring and summer months. Given these dolphins show a predator-prey relationship, these data provide new information on the local fish communities at a much finer-scale than fish landing records and a baseline of fish activity in an environment that is challenging to explore. Overlaid with acoustic detections of foraging dolphins, these data form a basis for identifying potentially important foraging habitats that should be afforded the highest priority for protection.
Ultrasmall Superparamagnetic Iron Oxide Imaging Identifies Tissue and Nerve Inflammation in Pain Conditions
Authors: Shen Shiqian , Ding Weihua , Ahmed Shihab , Hu Ranliang , Opalacz Arissa , Roth Sarah , You Zerong , Wotjkiewicz Gregory R , Lim Grewo , Chen Lucy , Mao Jianren , Chen John W , Zhang Yi 
Published: October 2017

AbstractObjectiveCorrelation between radiologic structural abnormalities and clinical symptoms in low back pain patients is poor. There is an unmet clinical need to image inflammation in pain conditions to aid diagnosis and guide treatment. Ferumoxytol, an ultrasmall superparamagnetic iron oxide (USPIO) nanoparticle, is clinically used to treat iron deficiency anemia and showed promise in imaging tissue inflammation in human. We explored whether ferumoxytol can be used to identify tissue and nerve inflammation in pain conditions in animals and humans.MethodsComplete Freud’s adjuvant (CFA) or saline was injected into mice hind paws to establish an inflammatory pain model. Ferumoxytol (20 mg/kg) was injected intravenously. Magnetic resonance imaging (MRI) was performed prior to injection and 72 hours postinjection. The changes in the transverse relaxation time (T2) before and after ferumoxytol injection were compared between mice that received CFA vs saline injection. In the human study, we administered ferumoxytol (4 mg/kg) to a human subject with clinical symptoms of lumbar radiculopathy and compared the patient with a healthy subject.ResultsMice that received CFA exhibited tissue inflammation and pain behaviors. The changes in T2 before and after ferumoxytol injection were significantly higher in mice that received CFA vs saline (20.8 ± 3.6 vs 2.2 ± 2.5, P = 0.005). In the human study, ferumoxytol-enhanced MRI identified the nerve root corresponding to the patient’s symptoms, but the nerve root was not impinged by structural abnormalities, suggesting the potential superiority of this approach over conventional structural imaging techniques.ConclusionsFerumoxytol-enhanced MRI can identify tissue and nerve inflammation and may provide a promising diagnostic tool in assessing pain conditions in humans.
Aligning Education With Health Care Transformation: Identifying a Shared Mental Model of “New” Faculty Competencies for Academic Faculty
Authors: Gonzalo Jed D. , Ahluwalia Amarpreet , Hamilton Maria , Wolf Heidi , Wolpaw Daniel R. , Thompson Britta M. 
Published: October 2017

Purpose
To develop a potential competency framework for faculty development programs aligned with the needs of faculty in academic health centers (AHCs).

Method
In 2014 and 2015, the authors interviewed 23 health system leaders and analyzed transcripts using constant comparative analysis and thematic analysis. They coded competencies and curricular concepts into subcategories. Lead investigators reviewed drafts of the categorization themes and subthemes related to gaps in faculty knowledge and skills, collapsed and combined competency domains, and resolved disagreements via discussion.

Results
Through analysis, the authors identified four themes. The first was core functional competencies and curricular domains for conceptual learning, including patient-centered care, health care processes, clinical informatics, population and public health, policy and payment, value-based care, and health system improvement. The second was the need for foundational competency domains, including systems thinking, change agency/management, teaming, and leadership. The third theme was paradigm shifts in how academic faculty should approach health care, categorized into four areas: delivery, transformation, provider characteristics and skills, and education. The fourth theme was the need for faculty to be aware of challenges in the culture of AHCs as an influential context for change.

Conclusions
This broad competency framework for faculty development programs expands existing curricula by including a comprehensive scope of health systems science content and skills. AHC leaders can use these results to better align faculty education with the real-time needs of their health systems. Future work should focus on optimal prioritization and methods for teaching.
A Multi-Institutional Longitudinal Faculty Development Program in Humanism Supports the Professional Development of Faculty Teachers
Authors: Branch William T. , Frankel Richard M. , Hafler Janet P. , Weil Amy B. , Gilligan MaryAnn C. , Litzelman Debra K. , Plews-Ogan Margaret , Rider Elizabeth A. , Osterberg Lars G. , Dunne Dana , May Natalie B. , Derse Arthur R. 
Published: October 2017

The authors describe the first 11 academic years (2005–2006 through 2016–2017) of a longitudinal, small-group faculty development program for strengthening humanistic teaching and role modeling at 30 U.S. and Canadian medical schools that continues today. During the yearlong program, small groups of participating faculty met twice monthly with a local facilitator for exercises in humanistic teaching, role modeling, and related topics that combined narrative reflection with skills training using experiential learning techniques. The program focused on the professional development of its participants. Thirty schools participated; 993 faculty, including some residents, completed the program.
In evaluations, participating faculty at 13 of the schools scored significantly more positively as rated by learners on all dimensions of medical humanism than did matched controls. Qualitative analyses from several cohorts suggest many participants had progressed to more advanced stages of professional identity formation after completing the program. Strong engagement and attendance by faculty participants as well as the multimodal evaluation suggest that the program may serve as a model for others. Recently, most schools adopting the program have offered the curriculum annually to two or more groups of faculty participants to create sufficient numbers of trained faculty to positively influence humanistic teaching at the institution.
The authors discuss the program’s learning theory, outline its curriculum, reflect on the program’s accomplishments and plans for the future, and state how faculty trained in such programs could lead institutional initiatives and foster positive change in humanistic professional development at all levels of medical education.
Right Ventricular Perfusion
Authors: Crystal George J. , Pagel Paul S. 
Published: October 2017

Abstract
Regulation of blood flow to the right ventricle differs significantly from that to the left ventricle. The right ventricle develops a lower systolic pressure than the left ventricle, resulting in reduced extravascular compressive forces and myocardial oxygen demand. Right ventricular perfusion has eight major characteristics that distinguish it from left ventricular perfusion: (1) appreciable perfusion throughout the entire cardiac cycle; (2) reduced myocardial oxygen uptake, blood flow, and oxygen extraction; (3) an oxygen extraction reserve that can be recruited to at least partially offset a reduction in coronary blood flow; (4) less effective pressure–flow autoregulation; (5) the ability to downregulate its metabolic demand during coronary hypoperfusion and thereby maintain contractile function and energy stores; (6) a transmurally uniform reduction in myocardial perfusion in the presence of a hemodynamically significant epicardial coronary stenosis; (7) extensive collateral connections from the left coronary circulation; and (8) possible retrograde perfusion from the right ventricular cavity through the Thebesian veins. These differences promote the maintenance of right ventricular oxygen supply–demand balance and provide relative resistance to ischemia-induced contractile dysfunction and infarction, but they may be compromised during acute or chronic increases in right ventricle afterload resulting from pulmonary arterial hypertension. Contractile function of the thin-walled right ventricle is exquisitely sensitive to afterload. Acute increases in pulmonary arterial pressure reduce right ventricular stroke volume and, if sufficiently large and prolonged, result in right ventricular failure. Right ventricular ischemia plays a prominent role in these effects. The risk of right ventricular ischemia is also heightened during chronic elevations in right ventricular afterload because microvascular growth fails to match myocyte hypertrophy and because microvascular dysfunction is present. The right coronary circulation is more sensitive than the left to α-adrenergic–mediated constriction, which may contribute to its greater propensity for coronary vasospasm. This characteristic of the right coronary circulation may increase its vulnerability to coronary vasoconstriction and impaired right ventricular perfusion during administration of α-adrenergic receptor agonists.
A Comparison of Back Pain Functional Scale With Roland Morris Disability Questionnaire, Oswestry Disability Index, and Short Form 36-Health Survey
Authors: Koç Meltem , Bayar Banu , Bayar Kılıçhan 
Published: October 2017

Study Design.
A comparison study of Back Pain Functional Scale (BPFS) with Roland Morris Questionnaire (RMQ), Oswestry Disability Index (ODI), and Short Form 36-Health Survey (SF-36).

Objective.
The aim of this study is to investigate the correlation of BPFS with RMQ, ODI, and SF-36.

Summary of Background Data.
The primary goal in the treatment of patients with low back pain is to improve the patients’ levels of activities and participation. Many questionnaires focusing on function have been developed in patients with low back pain. BPFS is one of these questionnaires. No studies have investigated the correlation of BPFS with ODI and SF-36.

Methods.
This study was conducted with 120 patients receiving outpatient and inpatient treatment in physiotherapy and rehabilitation units of a state hospital. BPFS, RMQ, ODI, and SF-36 questionnaires were used to assess the disability in low back pain. Spearman and Pearson Correlation were used to compare the data obtained in the study.

Results.
There was a good correlation among the 5 functional outcome measures (correlation r = −0.693 for BPFS/RMQ, r = −0.794 for BPFS/ODI, r = 0.697 for BPFS/SF-36 Physical function and r = 0.540 for BPFS/SF-36 Pain).

Conclusion.
BPFS demonstrated good correlation with RMQ, ODI, SF-36 physical function, and SF-36 pain.

Level of Evidence: 2
Cartilage Endplate Thickness Variation Measured by Ultrashort Echo-Time MRI Is Associated With Adjacent Disc Degeneration
Authors: Berg-Johansen Britta , Han Misung , Fields Aaron J. , Liebenberg Ellen C. , Lim Brandon J. , Larson Peder EZ , Gunduz-Demir Cigdem , Kazakia Galateia J. , Krug Roland , Lotz Jeffrey C. 
Published: October 2017

Study Design.
A magnetic resonance imaging study of human cadaver spines.

Objective.
To investigate associations between cartilage endplate (CEP) thickness and disc degeneration.

Summary of Background Data.
Damage to the CEP is associated with spinal injury and back pain. However, CEP morphology and its association with disc degeneration have not been well characterized.

Methods.
Ten lumbar motion segments with varying degrees of disc degeneration were harvested from six cadaveric spines and scanned with magnetic resonance imaging in the sagittal plane using a T2-weighted two-dimensional (2D) sequence, a three-dimensional (3D) ultrashort echo-time (UTE) imaging sequence, and a 3D T1ρ mapping sequence. CEP thicknesses were calculated from 3D UTE image data using a custom, automated algorithm, and these values were validated against histology measurements. Pfirrmann grades and T1ρ values in the disc were assessed and correlated with CEP thickness.

Results.
The mean CEP thickness calculated from UTE images was 0.74 ± 0.04 mm. Statistical comparisons between histology and UTE-derived measurements of CEP thickness showed significant agreement, with the mean difference not significantly different from zero (P = 0.32). Within-disc variation of T1ρ (standard deviation) was significantly lower for Pfirrmann grade 4 than Pfirrmann grade 3 (P < 0.05). Within-disc variation of T1ρ and adjacent CEP thickness heterogeneity (coefficient of variation) had a significant negative correlation (r = −0.65, P = 0.04). The standard deviation of T1ρand the mean CEP thickness showed a moderate positive correlation (r = 0.40, P = 0.26).

Conclusion.
This study demonstrates that quantitative measurements of CEP thickness measured from UTE magnetic resonance imaging are associated with disc degeneration. Our results suggest that variability in CEP thickness and T1ρ, rather than their mean values, may serve as valuable diagnostic markers for disc degeneration.

Level of Evidence: N/A
Predictive Performance of Vancomycin Trough Concentrations in Patients With Diabetes With Microalbuminuria
Authors: Kimura Hiroshi , Shigematsu Marie , Tanaka Akihiro , Watanabe Shinichi , Takatori Shingo , Tanaka Mamoru , Mizuma Takashi , Araki Hiroaki 
Published: October 2017

Background:
The performance of a population pharmacokinetic model in predicting trough concentrations after the initial vancomycin dose was evaluated in patients with albuminuria compared with patients who did not have albuminuria.

Methods:
Data were collected from 52 patients infected with methicillin-resistant Staphylococcus aureus (excluding patients undergoing dialysis and acute kidney injury) and treated with vancomycin. The data included urinary albumin concentration.

Results:
The calculated mean prediction error and mean absolute error for the serum trough concentrations of vancomycin (with 95% confidence intervals) were 4.65 (4.13–5.17) and 6.1 (5.65–6.51), respectively, in microalbuminuria and 0.33 (−0.2 to 0.86) and 4.02 (3.59–4.45), respectively, in those without. There was no significant difference observed in serum creatinine concentration, age, weight, estimation of vancomycin trough concentration in serum, and actual trough concentration of vancomycin in serum between individuals with microalbuminuria and those without albuminuria.

Conclusions:
Microalbuminuria in patients with diabetes is a marker of the difference between predicted vancomycin trough concentrations and actual vancomycin trough concentrations.
ARTERIAL OXYGEN SATURATION IN NEOVASCULARIZATIONS IN PROLIFERATIVE DIABETIC RETINOPATHY
Authors: Bek Toke 
Published: October 2017

Purpose:
Retinal neovascularizations in proliferative diabetic retinopathy have been proposed to develop from larger retinal venules. However, angiographic evidence suggests that the new vessels may originate from both arterioles and venules, and the vitreous oxygen tension near retinal neovascularizations is similar to that of retinal arterioles. An assessment of the oxygen saturation in neovascularizations may help characterizing the vascular origin of these vessels in proliferative diabetic retinopathy.

Methods:
Dual wavelength oximetry was used to study the oxygen saturation in arterioles, venules, and retinal neovascularizations in 40 eyes from 40 patients with proliferative diabetic retinopathy.

Results:
The oxygen saturation was significantly lower in retinal venules than in arterioles and neovascularizations (P < 0.0001), and after a correction for the influence of vessel diameter, there was no significant difference between the oxygen saturation in retinal arterioles and neovascularizations (P = 0.71). Age at onset and duration of diabetes mellitus contributed significantly to the variation in oxygen saturation of the venules, whereas none of the clinical background parameters contributed to the variation in oxygen saturation in arterioles and neovascularizations.

Conclusion:
The oxygen saturation in retinal neovascularizations in proliferative diabetic retinopathy is similar to that of the arterioles. Neovascularizations may act as shunts to bypass areas of capillary occlusion.
Genomic Organization of TBK1 Copy Number Variations in Glaucoma Patients
Authors: DeLuca Adam P. , Alward Wallace L.M. , Liebmann Jeffrey , Ritch Robert , Kawase Kazuhide , Kwon Young H. , Robin Alan L. , Stone Edwin M. , Scheetz Todd E. , Fingert John H. 
Published: October 2017

Background:
Approximately 1% of normal tension glaucoma (NTG) cases are caused by TANK-binding kinase 1 (TBK1) gene duplications and triplications. However, the precise borders and orientation of these TBK1 gene copy number variations (CNVs) on chromosome 12 are unknown.

Methods:
We determined the exact borders of TBK1 CNVs and the orientation of duplicated or triplicated DNA segments in 5 NTG patients with different TBK1 mutations using whole-genome sequencing.

Results:
Tandemly duplicated chromosome segments spanning the TBK1 gene were detected in 4 NTG patients, each with unique borders. Four of 5 CNVs had borders located within interspersed repetitive DNA sequences (Alu and long interspersed nuclear element-L1 elements), suggesting that mismatched homologous recombinations likely generated these CNVs. A fifth NTG patient had a complex rearrangement including triplication of a chromosome segment spanning the TBK1 gene.

Conclusions:
No specific mutation hotspots for TBK1 CNVs were detected, however, interspersed repetitive sequences (ie, Alu elements) were identified at the borders of TBK1 CNVs, which suggest that mismatch of these elements during meiosis may be the mechanism that generated TBK1 gene dosage mutations.