bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and Severity of Depression and Anxiety in Patients With Systemic Sclerosis
Authors: Faezi Seyedeh Tahereh , Paragomi Pedram , Shahali Ashraf , Akhlaghkhah Maryam , Akbarian Mahmood , Akhlaghi Maassoomeh , Kheirandish Masoumeh , Gharibdoost Farhad 
Published: January 2017

Background
Systemic sclerosis (SSc) is a chronic multisystem connective tissue disorder with detrimental impact on quality of life. Patients with SSc face emotional distress and frequently meet criteria for a psychiatric disorder. However, the pattern of psychiatric manifestations may vary according to socioethnic background.

Objectives
We investigated the prevalence of depressive and anxiety symptoms and examined their association with sociodemographic and clinical factors in Iranian SSc patients.

Methods
Depressive and anxiety symptoms were evaluated by Beck Depression Inventory and Cattell questionnaire in 114 SSc patients. The associations between sociodemographic and clinical factors and depressive/anxiety symptoms were examined via multivariate analysis.

Results
The prevalence of depressive symptoms was 68.4%. There was a significant association between depressive symptoms and pulmonary and gastrointestinal manifestations. Also, diffuse SSc patients were more prone to depressive symptoms. Mean Rodnan scores were significantly higher in patients with depressive symptoms in comparison with subjects with no depressive symptoms. The prevalence of anxiety symptoms was 23.6%. Anxiety symptoms were not associated with demographic characteristics, SSc subtype, disease duration, Rodnan score, other clinical features, and previous history of depression in the patients or their family. The coincidence of anxiety and depression was 82.8%.

Conclusions
Depressive and anxiety symptoms are prevalent among Iranian SSc population. The depressive symptoms showed correlation with pulmonary and gastrointestinal involvement, as well as diffuse SSc subtype.
Metal Artifact Reduction in X-ray Computed Tomography Using Computer-Aided Design Data of Implants as Prior Information
Authors: Ruth Veikko , Kolditz Daniel , Steiding Christian , Kalender Willi A. 
Published: January 2017

Objectives
The performance of metal artifact reduction (MAR) methods in x-ray computed tomography (CT) suffers from incorrect identification of metallic implants in the artifact-affected volumetric images. The aim of this study was to investigate potential improvements of state-of-the-art MAR methods by using prior information on geometry and material of the implant.

Materials and Methods
The influence of a novel prior knowledge–based segmentation (PS) compared with threshold-based segmentation (TS) on 2 MAR methods (linear interpolation [LI] and normalized-MAR [NORMAR]) was investigated. The segmentation is the initial step of both MAR methods. Prior knowledge–based segmentation uses 3-dimensional registered computer-aided design (CAD) data as prior knowledge to estimate the correct position and orientation of the metallic objects. Threshold-based segmentation uses an adaptive threshold to identify metal. Subsequently, for LI and NORMAR, the selected voxels are projected into the raw data domain to mark metal areas. Attenuation values in these areas are replaced by different interpolation schemes followed by a second reconstruction. Finally, the previously selected metal voxels are replaced by the metal voxels determined by PS or TS in the initial reconstruction. First, we investigated in an elaborate phantom study if the knowledge of the exact implant shape extracted from the CAD data provided by the manufacturer of the implant can improve the MAR result. Second, the leg of a human cadaver was scanned using a clinical CT system before and after the implantation of an artificial knee joint. The results were compared regarding segmentation accuracy, CT number accuracy, and the restoration of distorted structures.

Results
The use of PS improved the efficacy of LI and NORMAR compared with TS. Artifacts caused by insufficient segmentation were reduced, and additional information was made available within the projection data. The estimation of the implant shape was more exact and not dependent on a threshold value. Consequently, the visibility of structures was improved when comparing the new approach to the standard method. This was further confirmed by improved CT value accuracy and reduced image noise.

Conclusions
The PS approach based on prior implant information provides image quality which is superior to TS-based MAR, especially when the shape of the metallic implant is complex. The new approach can be useful for improving MAR methods and dose calculations within radiation therapy based on the MAR corrected CT images.
Perspectives of Patients, Caregivers and Researchers on Research Priorities in Donation and Transplantation in Canada: A Pilot Workshop
Authors: Allard Julie , Durand Céline , Anthony Samantha J. , Dumez Vincent , Hartell David , Hébert Marie-Josée , West Lori J. , Wright Linda , Fortin Marie-Chantal 
Published: January 2017

Background
It is vitally important to seek input from key stakeholders to increase the quality and relevance of health-related research and accelerate its adoption into practice. Patients and caregivers have rarely been involved in setting research priorities in the transplantation and donation field. The objectives of this explorative study are: (i) to discuss research priorities within the Canadian National Transplant Research Program during a priority-setting exercise with patients, caregivers, organ donors and researchers and (ii) to compare the identified priorities with research published in 2 prestigious transplantation journals.

Methods
A pilot workshop attended by 10 patients and caregivers and 5 researchers was held in Montréal (Quebec, Canada) in August 2014 to identify research priorities. Priorities were identified using a thematic analysis of the workshop transcription conducted by multiple coders. These priorities were compared with the topics of research articles published in 2 major transplantation journals between 2012 and 2014.

Results
The themes of the 10 research priorities identified by study participants were related to different research domains: social, cultural, and environmental health factors (4); biomedical or clinical (4); and research about health systems and services (2). 26.7% of the research articles published were related to the identified priorities. Thirteen percent looked at ways to improve graft survival and 8.5% looked at the development of tolerance, 2 priorities identified by participants. Fewer than 5% examined the other 8 research priorities identified as important by workshop participants.

Conclusions
This is the first study reporting patients' and researchers' priorities in the field of transplantation and donation in Canada. There is a discrepancy between topics that key stakeholders find important and research published in 2 major transplantation journals. The research priorities identified during our initial workshop will be validated through a national survey and workshop.
5 Years Experience With Drug Eluting and Bare Metal Stents as Primary Intervention in Transplant Renal Artery Stenosis
Authors: Estrada Chelsea C. , Musani Muzammil , Darras Frank , Suh Heesuck , Abate Mersema T. , Mani Anil , Nord Edward P. 
Published: January 2017

Background
Transplant renal artery stenosis (TRAS) is a common vascular complication after kidney transplantation and is associated with refractory hypertension, volume overload, and graft injury or loss. This article describes 5-year outcomes of endovascular intervention for TRAS with bare metal and drug eluting stents (DES).

Methods
We investigated, as a prospective cohort study, patient and graft outcomes after the targeted use of DES for vessel diameter less than 5 mm and bare metal stents (BMS) for vessel diameter greater than 5 mm as the primary management for TRAS.

Results
From March 2008 to November 2014, 57 patients were stented for hemodynamically significant TRAS; 29 received DES, 26 received BMS, and 2 patients received both stent types. They were followed up for a mean of 35.1 ± 22.8 months; a subset of these patients who all received DES were followed up for 61.7 ± 17.5 months. Mean serum creatinine declined from 2.87 ± 1.5 mg/dL at the time of intervention to 1.98 ± 0.76 mg/dL (P < 0.001) at one month follow-up and was 1.96 ±0.92 mg/dL (P < 0.001) at 35.1 ± 22.8 months. Mean systolic blood pressure declined from 159.05 ± 19.68 mm Hg at time of intervention to 135.65 ± 15.10 mm Hg (P < 0.001) at most recent visit. Clinically driven restenosis requiring repeat revascularization occurred in 15.7% of patients.

Conclusions
Primary stenting with DES and BMS is both successful in the initial treatment of TRAS and also produced an immediate and long-term reduction in serum creatinine and systolic blood pressure.
Agrochemical synergism imposes higher risk to Neotropical bees than to honeybees
Authors: Tomé Hudson V. V. , Ramos Gabryele S. , Araújo Micaele F. , Santana Weyder C. , Santos Gil R. , Guedes Raul Narciso C. , Maciel Carlos D. , Newland Philip L. , Oliveira Eugênio E. 
Published: January 2017

Bees are key pollinators whose population numbers are declining, in part, owing to the effects of different stressors such as insecticides and fungicides. We have analysed the susceptibility of the Africanized honeybee,
Apis mellifera
, and the stingless bee,
Partamona helleri,
to commercial formulations of the insecticides deltamethrin and imidacloprid. The toxicity of fungicides based on thiophanate-methyl and chlorothalonil were investigated individually and in combination, and with the insecticides. Results showed that stingless bees were more susceptible to insecticides than honeybees. The commercial fungicides thiophanate-methyl or chlorothalonil caused low mortality, regardless of concentration; however, their combination was as toxic as imidacloprid to both species, and over 400-fold more toxic than deltamethrin for
A. mellifera
. There were highly synergistic effects on mortality caused by interactions in the mixture of imidacloprid and the fungicides thiophanate-methyl, chlorothalonil and the combined fungicide formulation in
A. mellifera,
and also to a lesser extent in
P. helleri
. By contrast, mixtures of the deltamethrin and the combined fungicide formulation induced high synergy in
P. helleri
, but had little effect on the mortality of
A. mellifera
. Differences in physiology and modes of action of agrochemicals are discussed as key factors underlying the differences in susceptibility to agrochemicals.
The onset of thermalization in finite-dimensional equations of hydrodynamics: insights from the Burgers equation
Authors: Venkataraman Divya , Sankar Ray Samriddhi 
Published: January 2017

Solutions to finite-dimensional (all spatial Fourier modes set to zero beyond a finite wavenumber

K

G

), inviscid equations of hydrodynamics at long times are known to be at variance with those obtained for the original infinite dimensional partial differential equations or their viscous counterparts. Surprisingly, the solutions to such Galerkin-truncated equations develop sharp localized structures, called
tygers
(Ray
et al.
2011
Phys. Rev. E
84
, 016301 (
doi:10.1103/PhysRevE.84.016301
)), which eventually lead to completely thermalized states associated with an equipartition energy spectrum. We now obtain, by using the analytically tractable Burgers equation, precise estimates, theoretically and via direct numerical simulations, of the time

τ

c

at which thermalization is triggered and show that

τ

c

∼

K

G

ξ

, with

ξ
=
−

4
9

. Our results have several implications, including for the analyticity strip method, to numerically obtain evidence for or against blow-ups of the three-dimensional incompressible Euler equations.
ARCS: Assembly Roundup by Chromium Scaffolding
Authors: Yeo Sarah , Coombe Lauren , Chu Justin , Warren René L , Birol Inanç 
Published: January 2017

AbstractSequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to lack of linkage information over long stretches of DNA – a shortcoming that is being addressed by new sequencing protocols, such as linked reads from 10X Genomics. Here we present ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H. sapiens genome assembly can be increased over six-fold using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad utility in harnessing the barcoding information contained in Chromium data for connecting high-quality sequences in genome assembly drafts. Availability: http://www.bcgsc.ca/platform/bioinfo/software/arcsSupplementary information available online.
Pebbles as Dry Ice Replacement for Snap Freezing of Rodents Brains
Authors: Bernard René , Mosch Larissa , Dirnagl Ulrich 
Published: January 2017

AbstractDry ice is commonly used as a cooling agent in the preclinical research environment. It permits rapid freezing of tissues and organs through liquid media. Laboratories depend on a constant supply of dry ice because it disintegrates in a matter of days. Here we tested whether commercially available pebble gravel could be used as dry ice replacement for snap freezing mouse brains in 2-methylbutane. We monitored 2-methylbutane temperature for one hour and tested different setups with the focus on creating a practical solution that can be used in every research laboratory. While gravel pebbles cannot replace dry ice in the laboratory entirely, they present a useful addition as readily available and reusable cooling agent.
Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens
Authors: Linck Ethan B. , Hanna Zach , Sellas Anna , Dumbacher John P. 
Published: January 2017

ABSTRACTLaboratory techniques for high-throughput sequencing have enhanced our ability to generate DNA sequence data from millions of natural history specimens collected prior to the molecular era, but remain poorly tested at shallower evolutionary time scales. Hybridization capture using restriction site associated DNA probes (hyRAD) is a recently developed method for population genomics with museum specimens (Suchan et al. 2016). The hyRAD method employs fragments produced in a restriction site associated double digestion as the basis for probes that capture orthologous loci in samples of interest. While promising in that it does not require a reference genome, hyRAD has yet to be applied across study systems in independent laboratories. Here we provide an independent assessment of the effectiveness of hyRAD on both fresh avian tissue and dried tissue from museum specimens up to 140 years old and investigate how variable quantities of input DNA affects sequencing, assembly, and population genetic inference. We present a modified bench protocol and bioinformatics pipeline, including three steps for detection and removal of microbial and mitochondrial DNA contaminants. We confirm that hyRAD is an effective tool for sampling thousands of orthologous SNPs from historic museum specimens to describe phylogeographic patterns. We find that modern DNA performs significantly better than historical DNA better during sequencing, but that assembly performance is largely equivalent. We also find that the quantity of input DNA predicts %GC content of assembled contiguous sequences, suggesting PCR bias. We caution against sampling schemes that include taxonomic or geographic autocorrelation across modern and historic samples.
Biochemical, serological and molecular confirmation ofSalmonellaisolates
Authors: Prasanna Kumar V. , Singh S. P. , Upadhyay A. K. , Kumar Deepak 
Published: January 2017

AbstractSalmonellosis is one of the most frequently reported food-borne diseases world-wide commonly caused bySalmonellaTyphimurium andSalmonellaEnteritidis serovars. The present study was undertaken to confirmSalmonellaisolates by various techniques. All the 94 isolates were confirmed to be S. Typhimurium through various morphological, biochemical, serological and molecular methods.
Emergence of localized patterns in globally coupled networks of relaxation oscillators with heterogeneous connectivity
Authors: Leiser Randolph J. , Rotstein Horacio G. 
Published: January 2017

AbstractRelaxation oscillators may exhibit small amplitude oscillations (SAOs) in addition to the typical large amplitude oscillations (LAOs) as well as abrupt transitions between them (canard phenomenon). Localized cluster patterns in networks of relaxation oscillators consist of one cluster oscillating in the LAO regime or exhibiting mixed-mode oscillations (LAOs interspersed with SAOs), while the other oscillates in the SAO regime. We investigate the mechanisms underlying the generation of localized patterns in globally coupled networks of piecewise-linear (PWL) relaxation oscillators where global feedback acting on the rate of change of the activator (fast variable) involves the inhibitor (slow variable). We also investigate of these patterns are affected by the presence of a diffusive type of coupling whose synchronizing effects compete with the symmetry breaking global feedback effects.
Stem cell differentiation is a stochastic process with memory
Authors: Stumpf Patrick S. , Smith Rosanna C. G. , Lenz Michael , Schuppert Andreas , Müller Franz-Josef , Babtie Ann , Chan Thalia E. , Stumpf Michael P. H. , Please Colin P. , Howison Sam D. , Arai Fumio , MacArthur Ben D. 
Published: January 2017

AbstractPluripotent stem cells are able to self-renew indefinitely in culture and differentiate into all somatic cell typesin vivo. While much is known about the molecular basis of pluripotency, the molecular mechanisms of lineage commitment are complex and only partially understood. Here, using a combination of single cell profiling and mathematical modeling, we examine the differentiation dynamics of individual mouse embryonic stem cells (ESCs) as they progress from the ground state of pluripotency along the neuronal lineage. In accordance with previous reports we find that cells do not transit directly from the pluripotent state to the neuronal state, but rather first stochastically permeate an intermediate primed pluripotent state, similar to that found in the maturing epiblast in development. However, analysis of rate at which individual cells enter and exit this intermediate metastable state using a hidden Markov model reveals that the observed ESC and epiblast-like ‘macrostates’ conceal a chain of unobserved cellular ‘microstates’, which individual cells transit through stochastically in sequence. These hidden microstates ensure that individual cells spend well-defined periods of time in each functional macrostate and encode a simple form of epigenetic ‘memory’ that allows individual cells to record their position on the differentiation trajectory. To examine the generality of this model we also consider the differentiation of mouse hematopoietic stem cells along the myeloid lineage and observe remarkably similar dynamics, suggesting a general underlying process. Based upon these results we suggest a statistical mechanics view of cellular identities that distinguishes between functionally-distinct macrostates and the many functionally-similar molecular microstates associated with each macrostate. Taken together these results indicate that differentiation is a discrete stochastic process amenable to analysis using the tools of statistical mechanics.
Demonstration of short-term plasticity in the dorsolateral prefrontal cortex with theta burst stimulation: A TMS-EEG study
Authors: Chung Sung Wook , Lewis Benjamin P. , Rogasch Nigel C. , Saeki Takashi , Thomson Richard H. , Hoy Kate E. , Bailey Neil W. , Fitzgerald Paul B. 
Published: January 2017

AbstractObjectivesTo examine the effects of intermittent TBS (iTBS) and continuous TBS (cTBS) on cortical reactivity in the dorsolateral prefrontal cortex.Methods10 healthy participants were stimulated with either iTBS, cTBS or sham at F3 electrode. Single- and paired-pulse TMS and concurrent electroencephalography (EEG) were used to assess change in cortical reactivity and long-interval intracortical inhibition (LICI) via TMS-evoked potentials (TEPs) and TMS-evoked oscillations.ResultsSignificant increases in N120 amplitudes (p < 0.01) were observed following iTBS over prefrontal cortex. Changes in TMS-evoked theta oscillations and LICI of theta oscillations were also observed following iTBS (increase) and cTBS (decrease). Change in LICI of theta oscillations correlated with change in N120 amplitude following TBS (r = −0.670, p = 0.001).ConclusionsThis study provides preliminary evidence that TBS produces direct changes in cortical reactivity in the prefrontal cortex. Combining TBS with TMS-EEG may be a useful approach to optimise stimulation paradigms prior to the conduct of clinical trials.SignificanceTBS is able to modulate cortical reactivity and cortical inhibition in the prefrontal cortex.HighlightsEffects of iTBS and cTBS were studied in the DLPFC using TMS-EEGiTBS increased N120 amplitude, theta power and LICI of thetacTBS decreased theta power alone
Cross-cultural management education rebooted
Authors: Dietz Joerg , Fitzsimmons Stacey R. , Aycan Zeynep , Francesco Anne Marie , Jonsen Karsten , Osland Joyce , Sackmann Sonja A. , Lee Hyun-Jung , Boyacigiller Nakiye A. 
Published: January 2017

PurposeGraduates of cross-cultural management (CCM) courses should be capable of both tackling international and cross-cultural situations and creating positive value from the diversity inherent in these situations. Such value creation is challenging because these situations are typically complex due to differences in cultural values, traditions, social practices, and institutions, such as legal rules, coupled with variation in, for example, wealth and civil rights among stakeholders. The paper aims to discuss these issues.Design/methodology/approachThe authors argue that a scientific mindfulness approach to teaching CCM can help students identify and leverage positive aspects of differences and thereby contribute to positive change in cross-cultural situations.FindingsScientific mindfulness combines mindfulness and scientific thinking with the explicit goal to drive positive change in the world.Originality/valueThe authors explain how the action principles of scientific mindfulness enable learners to build positive value from cultural diversity. The authors then describe how to enact these principles in the context of CCM education.