bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fractional differentiability for solutions of the inhomogeneous 𝑝-Laplace system
Authors: Miśkiewicz Michał 
Published: October 2017

It is shown that if

p
⩾
3

p \geqslant 3

and

u
∈

W

1
,
p

(
Ω
,

R

N

)

u \in W^{1,p}(\Omega ,\mathbb {R}^N)

solves the inhomogeneous

p
p

-Laplace system
\[

div
⁡
(

|

∇
u

|

p
−
2

∇
u
)
=
f
,

f
∈

W

1
,

p
′

(
Ω
,

R

N

)
,

\operatorname {div} (|\nabla u|^{p-2} \nabla u) = f, \qquad f \in W^{1,p’}(\Omega ,\mathbb {R}^N),

\]
then locally the gradient

∇
u

\nabla u

lies in the fractional Nikol’skiĭ space

N

θ
,
2

/

θ

\mathcal {N}^{\theta ,2/\theta }

with any

θ
∈
[

2
p

,

2

p
−
1

)

\theta \in [ \tfrac {2}{p}, \tfrac {2}{p-1} )

. To the author’s knowledge, this result is new even in the case of

p
p

-harmonic functions, slightly improving known

N

2

/

p
,
p

\mathcal {N}^{2/p,p}

estimates. The method used here is an extension of the one used by A. Cellina in the case

2
⩽
p
>
3

2 \leqslant p > 3

to show

W

1
,
2

W^{1,2}

regularity.
ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data
Authors: Huang Xiaosan , Zhang Shaoling , Li Kongqing , Thimmapuram Jyothi , Xie Shaojun 
Published: October 2017

Abstract

Motivation
High throughput bisulfite sequencing (BS-seq) is an important technology to generate single-base DNA methylomes in both plants and animals. In order to accelerate the data analysis of BS-seq data, toolkits for visualization are required.

Results
ViewBS, an open-source toolkit, can extract and visualize the DNA methylome data easily and with flexibility. By using Tabix, ViewBS can visualize BS-seq for large datasets quickly. ViewBS can generate publication-quality figures, such as meta-plots, heat maps and violin-boxplots, which can help users to answer biological questions. We illustrate its application using BS-seq data from Arabidopsis thaliana.

Availability
ViewBS is freely available at: https://github.com/xie186/ViewBS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data
Authors: Piccolo Brian D , Wankhade Umesh D , Chintapalli Sree V , Bhattacharyya Sudeepa , Chunqiao Luo , Shankar Kartik 
Published: October 2017

Abstract

Summary
Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive.

Availability and implementation
DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed.
MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks
Authors: Hollander Markus , Hamed Mohamed , Helms Volkhard , Neininger Kerstin 
Published: October 2017

Abstract

Summary
Mutations in genomic key elements can influence gene expression and function in various ways, and hence greatly contribute to the phenotype. We developed MutaNET to score the impact of individual mutations on gene regulation and function of a given genome. MutaNET performs statistical analyses of mutations in different genomic regions. The tool also incorporates the mutations in a provided gene regulatory network to estimate their global impact. The integration of a next-generation sequencing pipeline enables calling mutations prior to the analyses. As application example, we used MutaNET to analyze the impact of mutations in antibiotic resistance (AR) genes and their potential effect on AR of bacterial strains.

Availability and implementation
MutaNET is freely available at https://sourceforge.net/projects/mutanet/. It is implemented in Python and supported on Mac OS X, Linux and MS Windows. Step-by-step instructions are available at http://service.bioinformatik.uni-saarland.de/mutanet/.

Supplementary information
Supplementary data are available at Bioinformatics online.
An analytical framework for the study of epidemic models on activity driven networks
Authors: Zino Lorenzo , Rizzo Alessandro , Porfiri Maurizio 
Published: October 2017

AbstractNetwork theory has greatly contributed to an improved understanding of epidemic processes, offering an empowering framework for the analysis of real-world data, prediction of disease outbreaks, and formulation of containment strategies. However, the current state of knowledge largely relies on time-invariant networks, which are not adequate to capture several key features of a number of infectious diseases. Activity driven networks (ADNs) constitute a promising modelling framework to describe epidemic spreading over time varying networks, but a number of technical and theoretical gaps remain open. Here, we lay the foundations for a novel theory to model general epidemic spreading processes over time-varying, ADNs. Our theory derives a continuous-time model, based on ordinary differential equations (ODEs), which can reproduce the dynamics of any discrete-time epidemic model evolving over an ADN. A rigorous, formal framework is developed, so that a general epidemic process can be systematically mapped, at first, on a Markov jump process, and then, in the thermodynamic limit, on a system of ODEs. The obtained ODEs can be integrated to simulate the system dynamics, instead of using computationally intensive Monte Carlo simulations. An array of mathematical tools for the analysis of the proposed model is offered, together with techniques to approximate and predict the dynamics of the epidemic spreading, from its inception to the endemic equilibrium. The theoretical framework is illustrated step-by-step through the analysis of a susceptible–infected–susceptible process. Once the framework is established, applications to more complex epidemic models are presented, along with numerical results that corroborate the validity of our approach. Our framework is expected to find application in the study of a number of critical phenomena, including behavioural changes due to the infection, unconscious spread of the disease by exposed individuals, or the removal of nodes from the network of contacts.
Anchored Hybrid Enrichment-Based Phylogenomics of Leafhoppers and Treehoppers (Hemiptera: Cicadomorpha: Membracoidea)
Authors: Dietrich Christopher H , Allen Julie M , Lemmon Alan R , Lemmon Emily Moriarty , Takiya Daniela M , Evangelista Olivia , Walden Kimberly K O , Grady Patrick G S , Johnson Kevin P 
Published: October 2017

AbstractA data set comprising DNA sequences from 388 loci and &gt;99,000 aligned nucleotide positions, generated using anchored hybrid enrichment, was used to estimate relationships among 138 leafhoppers and treehoppers representative of all major lineages of Membracoidea, the most diverse superfamily of hemipteran insects. Phylogenetic analysis of the concatenated nucleotide sequence data set using maximum likelihood produced a tree with most branches receiving high support. A separate coalescent gene tree analysis of the same data generally recovered the same strongly supported clades but was less well resolved overall. Several nodes pertaining to relationships among leafhopper subfamilies currently recognized based on morphological criteria were separated by short internodes and received low support. Although various higher taxa were corroborated with improved branch support, relationships among some major lineages of Membracoidea are only somewhat more resolved than previously published phylogenies based on single gene regions or morphology. In agreement with previous studies, the present results indicate that leafhoppers (Cicadellidae) are paraphyletic with respect to the three recognized families of treehoppers (Aetalionidae, Melizoderidae, and Membracidae). Divergence time estimates indicate that most of the poorly resolved divergence events among major leafhopper lineages occurred during the lower to middle Cretaceous and that most modern leafhopper subfamilies, as well as the lineage comprising the three recognized families of treehoppers, also arose during the Cretaceous.
Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins
Authors: Bohn Jennifer A , Van Etten Jamie L , Schagat Trista L , Bowman Brittany M , McEachin Richard C , Freddolino Lydia , Goldstrohm Aaron C 
Published: October 2017

Abstract
Human Pumilio proteins, PUM1 and PUM2, are sequence specific RNA-binding proteins that regulate protein expression. We used RNA-seq, rigorous statistical testing and an experimentally derived fold change cut-off to identify nearly 1000 target RNAs—including mRNAs and non-coding RNAs—that are functionally regulated by PUMs. Bioinformatic analysis defined a PUM Response Element (PRE) that was significantly enriched in transcripts that increased in abundance and matches the PUM RNA-binding consensus. We created a computational model that incorporates PRE position and frequency within an RNA relative to the magnitude of regulation. The model reveals significant correlation of PUM regulation with PREs in 3′ untranslated regions (UTRs), coding sequences and non-coding RNAs, but not 5′ UTRs. To define direct, high confidence PUM targets, we cross-referenced PUM-regulated RNAs with all PRE-containing RNAs and experimentally defined PUM-bound RNAs. The results define nearly 300 direct targets that include both PUM-repressed and, surprisingly, PUM-activated target RNAs. Annotation enrichment analysis reveal that PUMs regulate genes from multiple signaling pathways and developmental and neurological processes. Moreover, PUM target mRNAs impinge on human disease genes linked to cancer, neurological disorders and cardiovascular disease. These discoveries pave the way for determining how the PUM-dependent regulatory network impacts biological functions and disease states.
Theoretical modeling of Comptonized X-ray spectra of super-Eddington accretion flow: Origin of hard excess in ultraluminous X-ray sources
Authors: Kitaki Takaaki , Mineshige Shin , Ohsuga Ken , Kawashima Tomohisa 
Published: October 2017

Abstract
X-ray continuum spectra of super-Eddington accretion flow are studied by means of Monte Carlo radiative transfer simulations based on the radiation hydrodynamic simulation data, in which both thermal- and bulk-Compton scatterings are taken into account. We compare the calculated spectra of accretion flow around black holes with masses of MBH = 10, 102, 103, and 104 M⊙ for a fixed mass injection rate (from the computational boundary at 103 rs) of 103 LEdd/c2 (with rs, LEdd, and c being the Schwarzschild radius, the Eddington luminosity, and the speed of light, respectively). The soft X-ray spectra exhibit mass dependence in accordance with the standard-disk relation; the maximum surface temperature is scaled as $T \propto M_{\,\rm BH}^{\,-1/4}$. The spectra in the hard X-ray band, by contrast with soft X-ray, look to be quite similar among different models, if we normalize the radiation luminosity by MBH. This reflects that the hard component is created by thermal- and bulk-Compton scatterings of soft photons originating from an accretion flow in the overheated and/or funnel regions, the temperatures of which have no dependence on mass. The hard X-ray spectra can be reproduced by a Wien spectrum with the temperature of T ∼ 3 keV accompanied by a hard excess at photon energy above several keV. The excess spectrum can be fitted well with a power law with a photon index of Γ ∼ 3. This feature is in good agreement with that of the recent NuSTAR observations of ULXs (ultra-luminous X-ray sources).
Quantitative and Qualitative Analysis of the Impact of Adoption of a Mobile Application for the Assessment of Professionalism in Medical Trainees
Authors: Cendán Juan C. , Castiglioni Analia , Johnson Teresa R. , Eakins Mike , Verduin Marcia L. , Asmar Abdo , Metcalf David , Hernandez Caridad 
Published: October 2017

Purpose
Capturing either lapses or excellence in behaviors related to medical professionalism is difficult. The authors report a mixed-methods analysis of a novel mobile platform for assessing medical professionalism in a training environment.

Method
A mobile Web-based platform to facilitate professionalism assessment in a situated clinical setting (Professional Mobile Monitoring of Behaviors [PROMOBES]) was developed. A professionalism framework consisting of six domains (reliability, adaptability, peer relationships, upholding principles, team relationships, and scholarship) encompassing 25 subelements underpins the reporting structure. This pilot study involved 26 faculty supervising 93 medical trainees at two sites from January 12 to August 8, 2016. Notable professionalism behaviors were linked to the framework domains and elements; narrative details about incidences were captured on mobile devices. Surveys gauged the technological functionality and impact of PROMOBES on faculty assessment of professionalism. Qualitative focus groups were employed to elucidate user experience.

Results
Although users anticipated PROMOBES’s utility would be for reporting lapses in professionalism, 94.7% of reports were for commendation. Comfort assessing professionalism (P = .04) and recognition of the reporting procedures for professionalism-related concerns (P = .01) improved. PROMOBES attained high acceptance ratings. Focus group analysis revealed that the explicit connection to the professionalism framework was powerful; similarly, the near real-time reporting capability, multiple observer inputs, and positive feedback facilitation were strengths.

Conclusions
Making the professionalism framework visible and accessible via a mobile platform significantly strengthens faculty knowledge and behaviors regarding assessment. The strong desire to capture positive behaviors was an unexpected finding.
Personalized Video Feedback and Repeated Task Practice Improve Laparoscopic Knot-Tying Skills: Two Controlled Trials
Authors: Abbott Eduardo F. , Thompson Whitney , Pandian T.K. , Zendejas Benjamin , Farley David R. , Cook David A. 
Published: October 2017

Purpose
Compare the effect of personalized feedback (PF) vs. task demonstration (TD), both delivered via video, on laparoscopic knot-tying skills and perceived workload; and evaluate the effect of repeated practice.

Method
General surgery interns and research fellows completed four repetitions of a simulated laparoscopic knot-tying task at one-month intervals. Midway between repetitions, participants received via e-mail either a TD video (demonstration by an expert) or a PF video (video of their own performance with voiceover from a blinded senior surgeon). Each participant received at least one video per format, with sequence randomly assigned. Outcomes included performance scores and NASA Task Load Index (NASA-TLX) scores. To evaluate the effectiveness of repeated practice, scores from these trainees on a separate delayed retention test were compared against historical controls who did not have scheduled repetitions.

Results
Twenty-one trainees completed the randomized study. Mean change in performance scores was significantly greater for those receiving PF (difference = 23.1 of 150 [95% confidence interval (CI): 0, 46.2], P = .05). Perceived workload was also significantly reduced (difference = −3.0 of 20 [95% CI: −5.8, −0.3], P = .04). Compared with historical controls (N = 93), the 21 with scheduled repeated practice had higher scores on the laparoscopic knot-tying assessment two weeks after the final repetition (difference = 1.5 of 10 [95% CI: 0.2, 2.8], P = .02).

Conclusions
Personalized video feedback improves trainees’ procedural performance and perceived workload compared with a task demonstration video. Brief monthly practice sessions support skill acquisition and retention.
Using the Readiness for Clerkship and Residency Surveys to Evaluate the Effectiveness of Four MD Programs: A Cross-Institutional Generalizability Study
Authors: Peterson Linda N. , Rusticus Shayna A. , Eva Kevin W. , Wilson Derek A. , Pittini Richard J. , Schreiber Martin , Pinchin Sheila E. , Moffatt Susan L. , Sargeant Joan M. , Warren Andrew E. , Alexiadis-Brown Peggy 
Published: October 2017

Purpose
The importance of confidence for learning and performance makes learners’ perceptions of readiness for the next level of training valuable indicators of curricular success. The “Readiness for Clerkship” (RfC) and “Readiness for Residency” (RfR) surveys have been shown to provide reliable ratings of the relative effectiveness of various aspects of training. This study examines the generalizability of those results.

Method
Surveys were administered at four medical schools approximately four months after the start of clerkship and eight months after the start of residency during 2013–2015. Collected data were anonymized. A total of 647 medical students and 483 residents participated.

Results
Reliabilities of G = 0.8 could be obtained with only 6 to 12 medical students and 8 to 15 residents. Within MD programs, no meaningful differences in item ratings were observed across cohorts. Residents in each school consistently rated themselves higher than clerks on the majority of Medical Expert and Communicator competencies common to both surveys. Similar strengths and weaknesses were identified across programs, but differences were observed on five clerkship items and one residency item.

Conclusions
Across four MD programs, the RfC and RfR surveys provided reliable ratings of the relative effectiveness of aspects of training with small numbers of respondents. The capacity of these surveys to efficiently identify perceived strengths and weaknesses held by cohorts of learners may, thereby, facilitate program improvement.
Health Care Organizations and Policy Leadership: Perspectives on Nonsmoker-Only Hiring Policies
Authors: McDaniel Patricia A. , Malone Ruth E. 
Published: October 2017

Purpose
To explore employers’ decisions to base hiring policies on tobacco or nicotine use and community perspectives on such policies, and analyze the implications for organizational identity, community engagement, and health promotion.

Method
From 2013 to 2016, 11 executives from six health care organizations and one non-health-care organization with nonsmoker-only hiring policies were interviewed about why and how their policies were created and implemented, concerns about the policies, and perceptions of employee and public reactions. Focus groups were conducted with community members (n = 51) who lived in or near cities where participating employers were based, exploring participants’ opinions about why an employer would stop hiring smokers and their support (or not) for such a policy.

Results
Most employers excluded from employment those using all forms of nicotine. Several explained their adoption of the policy as a natural extension of a smoke-free campus and as consistent with their identity as health care organizations. They regarded the policy as promoting health. No employer mentioned engaging in a community dialogue before adopting the policy or reported efforts to track the policy’s impact on rejected applicants. Community members understood the cost-saving appeal of such policies, but most opposed them. They made few exceptions for health care organizations.

Conclusions
Policy decisions undertaken by health care organizations have influence beyond their immediate setting and may establish precedents that others follow. Nonsmoker-only hiring policies may fit with a health care organization’s institutional identity but may not be congruent with community values or promote public health.
Simulation-Based Mastery Learning for Thoracentesis Skills Improves Patient Outcomes: A Randomized Trial
Authors: Barsuk Jeffrey H. , Cohen Elaine R. , Williams Mark V. , Scher Jordan , Jones Sasha F. , Feinglass Joe , McGaghie William C. , O’Hara Kelly , Wayne Diane B. 
Published: October 2017

Purpose
Physicians-in-training often perform bedside thoracenteses in academic medical centers, and complications are more common among less experienced clinicians. Simulation-based mastery learning (SBML) is one potential solution to this problem. This study evaluated the effects of a randomized trial of thoracentesis SBML on patient complications: iatrogenic pneumothorax (IP), hemothorax, and reexpansion pulmonary edema (REPE).

Method
The authors randomized internal medicine residents to undergo thoracentesis SBML at a tertiary care academic center from December 2012 to May 2016. They subsequently compared thoracentesis complications from procedures performed by SBML-trained residents, traditionally trained residents (no simulation training), and those referred to pulmonary medicine or interventional radiology (IR).

Results
During the study period, 917 thoracenteses were performed on 709 patients. IP occurred in 60 (6.5%) procedures, of which 7 (11.6%) were clinically meaningful. SBML-trained residents performed procedures with a trend toward lower combined clinically meaningful complications (IP, hemothorax, REPE) compared with traditionally trained residents (7.9% vs. 0%; P = .06). SBML-trained residents caused fewer clinically meaningful IPs compared with traditionally trained residents, pulmonary, and IR referrals (P = .02). Hemothorax occurred after 4 (0.4%) thoracenteses, and SBML-trained residents had a trend toward lower hemothorax (0) compared with other groups (P = .07). REPE occurred after 3 (0.3%) procedures, with no differences between groups. SBML-trained residents performed procedures with lower combined clinically meaningful complications compared with other groups (P = .008).

Conclusions
Residents randomized to an SBML intervention performed thoracenteses with low rates of clinically meaningful complications. Rigorous education represents a successful quality improvement strategy.
A review of current management of vasculo-Behcet's
Authors: Merashli Mira , Eid Rozana El , Uthman Imad 
Published: October 2017

Purpose of review
To give an overview of recently published articles about the management of vasculo-Behcet's with particular emphasis on anticoagulation.

Recent findings
Biologic agents are emerging as a potential therapeutic option in refractory vasculo-Behcet with a good safety profile. Evidence further shows that following nonpulmonary aneurysm repair, there is a reduced risk of recurrent aneurysmal formation at the operative site in patients treated with immunosuppressants in addition to their surgery, than those undergoing surgical intervention alone.

Summary
Behcet disease patients are at risk of developing multiple vascular complications including thrombosis and aneurysms. Treatment should focus on reducing inflammation; and the role of anticoagulation is still debatable.