bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agreement and Reproducibility of Proton Density Fat Fraction Measurements Using Commercial MR Sequences Across Different Platforms
Authors: Jang Jong Keon , Lee Seung Soo , Kim Bohyun , Cho Eun-Suk , Kim Yeong Jae , Byun Jae Ho , Park Beom Jin , Kim So Yeon , Kim Jin Hee 
Published: March 2019

Objectives
The aim of this study was to evaluate the agreement and reproducibility of proton density fat fraction (PDFF) measurements using commercial magnetic resonance (MR) sequences across different imagers, vendors, and field strengths via a phantom experiment.

Materials and Methods
Eleven fat-water emulsion phantoms of varying fat proportions (ie, 0–50 weight%) were constructed. Phantom PDFFs were estimated using commercial chemical shift–based MR imaging sequences with Siemens 1.5 T and 3.0 T, Philips 3.0 T, and GE 1.5 T and 3.0 T imagers, and MR spectroscopic sequences (HISTO) with Siemens 1.5 T and 3.0 T imagers. Agreement among the estimated PDFF values between commercial sequences was evaluated using Bland-Altman analysis. Reproducibility of the PDFF measurements across commercial sequences was evaluated using the reproducibility coefficient. The test-retest repeatability of the PDFF measurements was evaluated using the repeatability coefficient.

Results
The repeatability coefficient of the PDFF measurements was 0.31% to 1.58% for the absolute PDFF value for commercial sequences. Statistically significant biases in the estimated PDFF were noted in 19 of 21 pairwise comparisons of commercial sequences (range of mean biases, −4.48% to 8.15% for the absolute PDFF value). The reproducibility coefficient of PDFF measurements was 9.0% for the absolute PDFF value over all commercial sequences and 10.6% for the absolute PDFF value over all chemical shift–based MR imaging sequences.

Conclusions
The measurement of the PDFF is highly repeatable with commercial MR sequences but is not reproducible across different sequences, imager vendors, and field strengths. The use of the same sequence and imager is therefore recommended for the longitudinal follow-up of hepatic steatosis using commercial MR sequences for PDFF measurements.
Familial Cavernous Hemangioma
Authors: Torres Guadalupe , Kini Ashwini T. , Al Othman Bayan , Lee Andrew G. 
Published: March 2019

Abstract:
A 30-year-old woman presented with diplopia after resection of an intracranial cavernous malformation. Fundus examination showed an asymptomatic intraocular cavernous hemangioma of the retina. Clinicians should be aware of the potential coexistence of intraocular and intracranial cavernous malformations; the presence of both should suggest familial etiology. As with other intracranial and intraocular vascular lesions (e.g., arteriovenous malformation in Wyburn-Mason syndrome, retinal hemangioblastoma in von Hippel Lindau disease, and choroidal hemangioma in Sturge–Weber syndrome), the presence of a vascular lesion in either location should prompt evaluation for additional pathology.
The Dementias Platform UK (DPUK) Data Portal
Authors: Bauermeister S , Orton C , Thompson S , Barker R A , Bauermeister J R , Ben-Shlomo Y , Brayne C , Burn D , Campbell A , Calvin C , Chandran S , Chaturvedi N , Chene G , Chessell I P , Corbett A , Davis D H J , Denis M , Dufouil C , Elliott P , Fox N , Hill D , Hofer SM , Hu M T , Jindra C , Kee F , Kim C H , Kim C , Kivimaki M , Koychev I , Lawson R A , Linden G J , Lyons R A , Mackay C , Matthews P M , McGuiness B , Middleton L , Moody C , Moore K , Na D L , O’Brien J T , Ourselin S , Paranjothy S , Park K S , Porteous D J , Richards M , Ritchie C W , Rohrer J D , Rossor M N , Rowe J B , Scahill R , Schnier C , Schott J M , Seo S W , South M , Steptoe A , Tabrizi S J , Tales A , Tillin T , Timpson N J , Toga A W , Visser PJ , Wade-Martins R , Wilkinson T , Williams J , Wong A , Gallacher J E 
Published: March 2019

AbstractThe Dementias Platform UK (DPUK) Data Portal is a data repository facilitating access to data for 3 370 929 individuals in 42 cohorts. The Data Portal is an end-to-end data management solution providing a secure, fully auditable, remote access environment for the analysis of cohort data. All projects utilising the data are by default collaborations with the cohort research teams generating the data.The Data Portal uses UK Secure eResearch Platform (UKSeRP) infrastructure to provide three core utilities: data discovery, access, and analysis. These are delivered using a 7 layered architecture comprising: data ingestion, data curation, platform interoperability, data discovery, access brokerage, data analysis and knowledge preservation. Automated, streamlined, and standardised procedures reduce the administrative burden for all stakeholders, particularly for requests involving multiple independent datasets, where a single request may be forwarded to multiple data controllers. Researchers are provided with their own secure ‘lab’ using VMware which is accessed using two factor authentication.Over the last 2 years, 160 project proposals involving 579 individual cohort data access requests were received. These were received from 268 applicants spanning 72 institutions (56 academic, 13 commercial, 3 government) in 16 countries with 84 requests involving multiple cohorts. Project are varied including multi-modal, machine learning, and Mendelian randomisation analyses. Data access is usually free at point of use although a small number of cohorts require a data access fee.
Distribution of iridescent colours in hummingbird communities results from the interplay between selection for camouflage and communication
Authors: Gruson Hugo , Elias Marianne , Parra Juan L. , Andraud Christine , Berthier Serge , Doutrelant Claire , Gomez Doris 
Published: March 2019

AbstractIdentification errors between closely related, co-occurring, species may lead to misdirected social interactions such as costly interbreeding or misdirected aggression. This selects for divergence in traits involved in species identification among co-occurring species, resulting from character displacement. On the other hand, predation may select for crypsis, potentially leading co-occurring species that share the same environment and predators to have a similar appearance. However, few studies have explored how these antagonistic processes influence colour at the community level. Here, we assess colour clustering and overdispersion in 189 hummingbird communities, tallying 112 species, across Ecuador and suggest possible evolutionary mechanisms at stake by controlling for species phylogenetic relatedness. In hummingbirds, most colours are iridescent structural colours, defined as colours that change with the illumination or observation angle. Because small variations in the underlying structures can have dramatic effects on the resulting colours and because iridescent structures can produce virtually any hue and brightness, we expect iridescent colours to respond finely to selective pressures. Moreover, we predict that hue angular dependence – a specific aspect of iridescent colours – may be used as an additional channel for species recognition. In our hummingbird assemblages in Ecuador, we find support for colour overdispersion in ventral and facial patches at the community level even after controlling for the phylogeny, especially on iridescence-related traits, suggesting character displacement among co-occurring species. We also find colour clustering at the community level on dorsal patches, suspected to be involved in camouflage, suggesting that the same cryptic colours are selected among co-occurring species.This article has been peer-reviewed and recommended byPeer Community In Evolutionary Biology
Application of Volumetric Absorptive Micro Sampling to Measure Multidimensional Anti-Influenza Hemagglutinin Igg Antibodies by MPlex-Flu Assay
Authors: Wang Jiong , Li Dongme , Wiltse Alexander , Emo Jason , Hilchey Shannon P. , Zand Martin S. 
Published: March 2019

AbstractRecently, volumetric absorptive microsampling (VAMS) has been used for peripheral blood sampling and analyses in several fields. VAMS ensures accurate sampling by collecting a fixed blood volume (10 or 20µL) on a volumetric swab in blood spot format, and allows for long-term sample storage. The mPlex-Flu assay is a novel, multidimensional assay that measures the concentration of antibodies against multiple influenza virus hemagglutinins simultaneously strains with a small volume of serum (less than 5µL). Here we describe combining these two methods to measure multidimensional influenza antibody activity using a finger-stick and VAMS. In this study, we compared influenza antibody profiles measured from capillary blood obtained with a finger-stick, and venous whole blood collected by traditional phlebotomy from 20 subjects using the mPlex-Flu assay. We found that results with the two sampling methods were virtually identical across all influenza strains within the same subject (mean ofR2=0.9470), and that antibodies remained stable over three weeks when VAMS samples were stored at room temperature and transported using a variety of shipping methods. Additionally, VAMS sampling is an easy and highly reproducible process; when volunteers performed finger stick VAMS at home by themselves, the results of anti-HA antibody concentrations showed that they are highly consistent with sampling performed by study personnel on-site (R2=0.9496). This novel approach provides advantages for clinical influenza vaccine studies, including ease of sampling, low cost, and high accuracy. We conclude that these methods could provide an accurate and low-cost means for monitoring the influenza virus antibody responses in large population studies.
Direction of gait asymmetry following stroke determines acute response to locomotor task
Authors: Little Virginia L , Perry Lindsay A , Mercado Mae WV , Kautz Steven A , Patten Carolynn 
Published: March 2019

AbstractBackgroundGiven the prevalence of gait dysfunction following stroke, walking recovery is a primary goal of rehabilitation. However, current gait rehabilitation approaches fail to demonstrate consistent benefits. Furthermore, asymmetry is a prominent feature of gait dysfunction following stroke. Differential patterns of gait asymmetry may respond differently to gait training parameters.ObjectiveThe purpose of this study was to determine whether differential responses to locomotor task condition occur on the basis of direction of step length asymmetry (Symmetrical, NPshort, Pshort) observed during overground walking.MethodsParticipants first walked overground at their self-selected walking speed. Overground data were compared against three task conditions all tested during treadmill walking: self-selected speed with 0% body weight support (TM); self-selected speed with 30% body weight support (BWS); and fastest comfortable speed with 30% body weight support and nonparetic leg guidance (GuidanceNP). Our primary outcomes were: step length, single limb support duration, and stride length.ResultsWe identified differences in the response to locomotor task conditions for each step length asymmetry subgroup. GuidanceNPinduced an acute spatial symmetry only in the NPshortgroup and temporal symmetry in the Symmetrical group.ConclusionsTask conditions consistent with locomotor training do not produce uniform effects across subpatterns of gait asymmetry. We identified differential responses to locomotor task conditions between groups with distinct asymmetry patterns, suggesting these subgroups may require unique intervention strategies. Despite group differences in asymmetry characteristics, improvements in symmetry noted in the Symmetrical and NPshortgroups were driven by changes in both the paretic and nonparetic limbs.
Genomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia
Authors: Li Yan , Pulford Caisey V. , Díaz Paula , Perez-Sepulveda Blanca M. , Duarte Carolina , Predeus Alexander V. , Wiesner Magdalena , Heavens Darren , Low Ross , Schudoma Christian , Lipscombe James , Montaño Angeline , Hall Neil , Moreno Jaime , Hinton Jay C. D. 
Published: March 2019

AbstractSalmonellosis is an endemic human infection, associated with both sporadic cases and outbreaks throughout Colombia. Typhimurium is the most common Colombian serovar ofSalmonella enterica, responsible for 32.5% of theSalmonellainfections. Whole genome sequencing (WGS) is being used increasingly in Europe and the USA to study the epidemiology ofSalmonella, but there has not yet been a WGS-based analysis ofSalmonellaassociated with bloodstream infection in Colombia. Here, we analysed 209 genome sequences of ColombianS. Typhimurium and monophasicS. 4,[5],12:i:-isolates from Colombia from 1999 to 2017. We used a core genome-based maximum likelihood tree to define seven distinct clusters which were predominantly Sequence Type (ST) 19 isolates. We also identified the first ST313 and monophasic ST34 isolates to be reported in Colombia. The history of each cluster was reconstructed with a Bayesian tree to reveal a timeline of evolution. Cluster 7 was closely related to European multidrug-resistant (MDR) DT104. Cluster 4 became the dominant variant ofSalmonellain 2016, and resistance to nalidixic acid was associated with a plasmid-encodedqnrB19gene. Our findings suggest multiple transfers ofS. Typhimurium between Europe and Colombia.Author summaryThe large-scale genome sequencing ofSalmonellaTyphimurium and monophasicSalmonella4,[5],12:i:-involved bloodstream isolates from Colombia. The two serovars were responsible for about 1/3 ofSalmonellainfections in Colombia in the past 20 years. To identify the population structure we used Whole Genome Sequencing, performedin silicosequence typing, obtained phylogenetic trees, inferred the evolutionary history, detected the plasmids and prophages, and associated the antibiotic resistance (AMR) genotype with phenotype. Different clusters showed temporal replacement. The Colombian sequence type 313 was distinct from African lineages due to the absence of a key virulence-related gene,bstA. One of the Colombian clusters is likely to belong to the global epidemic of DT104, according to the evolutionary history and the AMR profile. The most common cluster in recent years was resistant to nalidixic acid and carried a plasmid-mediated antibiotic resistant geneqnrB19. Our findings will inform the ongoing efforts to combat Salmonellosis by Colombian public health departments.
Hybrid decay: a transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize
Authors: Xue Wei , Anderson Sarah N. , Wang Xufeng , Yang Liyan , Crisp Peter A. , Li Qing , Noshay Jaclyn , Albert Patrice S. , Birchler James A. , Bilinski Paul , Stitzer Michelle C. , Ross-Ibarra Jeffrey , Flint-Garcia Sherry , Chen Xuemei , Springer Nathan M. , Doebley John F. 
Published: March 2019

ABSTRACTIn the course of generating populations of maize with teosinte chromosomal introgressions, an unusual sickly plant phenotype was noted in individuals from crosses with two teosinte accessions collected near Valle de Bravo, Mexico. The plants of these Bravo teosinte accessions appear phenotypically normal themselves and the F1plants appear similar to typical maize x teosinte F1s. However, upon backcrossing to maize, the BC1and subsequent generations display a number of detrimental characteristics including shorter stature, reduced seed set and abnormal floral structures. This phenomenon is observed in all BC individuals and there is no chromosomal segment linked to the sickly plant phenotype in advanced backcross generations. Once the sickly phenotype appears in a lineage, normal plants are never again recovered by continued backcrossing to the normal maize parent. Whole-genome shotgun sequencing reveals a small number of genomic sequences, some with homology to transposable elements, that have increased in copy number in the backcross populations. Transcriptome analysis of seedlings, which do not have striking phenotypic abnormalities, identified segments of 18 maize genes that exhibit increased expression in sickly plants. Ade novoassembly of transcripts present in plants exhibiting the sickly phenotype identified a set of 59 up-regulated novel transcripts. These transcripts include some examples with sequence similarity to transposable elements and other sequences present in the recurrent maize parent (W22) genome as well as novel sequences not present in the W22 genome. Genome-wide profiles of gene expression, DNA methylation and sRNAs are similar between sickly plants and normal controls, although a few up-regulated transcripts and transposable elements are associated with altered sRNA or methylation profiles. This study documents hybrid incompatibility and genome instability triggered by the backcrossing of Bravo teosinte with maize. We name this phenomenon “hybrid decay” and present ideas on the mechanism that may underlie it.
Direct visualization of native CRISPR target search in live bacteria reveals Cascade DNA surveillance mechanism
Authors: Vink Jochem N.A. , Martens Koen J.A. , Vlot Marnix , McKenzie Rebecca E. , Almendros Cristóbal , Bonilla Boris Estrada , Brocken Daan J.W. , Hohlbein Johannes , Brouns Stan J.J. 
Published: March 2019

AbstractCRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here we visualized individual Cascade complexes in a native type I CRISPR-Cas system. We uncovered an exponential relationship between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and impact CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.One sentence summaryThe results from in vivo tracking of single CRISPR RNA-surveillance complexes in the native host cell explain their ability to rapidly recognize invader sequences.
PamgeneAnalyzeR open and reproducible pipeline for kinase profiling
Authors: Bekkar Amel , Nasrallah Anita , Guex Nicolas , Fajas Lluis , Xenarios Ioannis , Lopez-Mejia Isabel C. 
Published: March 2019

AbstractProtein phosphorylation - catalyzed by protein kinases - is the most common post-translational modification. It increases the functional diversity of the proteome and influences various aspects of normal physiology and can be altered in disease states. High throughput profiling of kinases is becoming an essential experimental approach to investigate their activity and this can be achieved using technologies such as PamChip® arrays provided by PamGene for kinase activity measurement. Here we present “pamgeneAnalyzeR”, an R package developed as an alternative to the manual steps necessary to extract the data from PamChip® peptide microarrays images in a reproducible and robust manner. The extracted data can be directly used for downstream analysis.Availability and implementationPamgeneAnalyzeR is implemented in R and can be obtained from https://github.com/amelbek/pamgeneAnalyzeR.
Neural correlates of object and action naming practice
Authors: Delikishkina Ekaterina , Lingnau Angelika , Miceli Gabriele 
Published: March 2019

AbstractWord retrieval deficits are a common problem in patients with stroke-induced brain damage. While complete recovery of language in chronic aphasia is rare, patients’ naming ability can be significantly improved by speech therapy. A growing number of neuroimaging studies have tried to pinpoint the neural changes associated with successful outcome of naming treatment. However, the mechanisms supporting naming practice in the healthy brain have received little attention. Yet, understanding these mechanisms is crucial for teasing them apart from functional reorganization following brain damage. To address this issue, we trained a group of healthy monolingual Italian speakers on naming pictured objects and actions for ten consecutive days and scanned them before and after training. Although activity during object vs. action naming dissociated in several regions (lateral occipitotemporal, parietal and left inferior frontal cortices), training effects for the two word classes were similar and included activation decreases in classical language regions of the left hemisphere (posterior inferior frontal gyrus, anterior insula), potentially due to decreased lexical selection demands. Additionally, MVPA revealed training-related activation changes in the left parietal and temporal cortices associated with the retrieval of knowledge from episodic memory (precuneus, angular gyrus) and facilitated access to phonological word forms (posterior superior temporal sulcus).
University student engagement in learning
Authors: Lau Patricia Yin Yin , Lee Christina Kwai Choi , Ho ChyeKok 
Published: March 2019

PurposeThe purpose of this paper is to explore how university fieldtrips progressively deepen student engagement, and explain that stage-by-stage using the organismic integration theory.Design/methodology/approachUsing reflective logs, follow-up focus groups after two years and facilitator observations, this Malaysian qualitative study followed 12 business students across two three-day rainforest fieldtrips.FindingsStudents progressed toward greater – and enduring – engagement, and transferable socio-cognitive skills, via three thematic stages. Voice and self-reflection – motivated by protecting group harmony – were key, enabled by facilitator and peer encouragement.Research limitations/implicationsThis exploratory study invites research in specified education cultures. Further, a longitudinal, quantitative study could be designed to examine the conceptual framework developed in Figure 1.Practical implicationsUniversity curricula, especially in collectivist high power distance cultures, should include fieldtrips as a particularly powerful form of experiential learning. Benefits of deeper engagement extend beyond present to future courses and the workplace. Higher student attraction/retention and employability may follow. Intrinsic motivation grows through the student–instructor interaction, watching theoretical principles in action, and having eureka moments through reflection, expression and exchange of ideas.Originality/valueThe research fills a gap by mapping student engagement progressively from extrinsic to intrinsic motivation along with socio-cognitive competencies. The authors reveal the centrality of voice and reflection to promote group harmony, explain the roles of facilitators and peers and show long-lasting transferable benefits to learning. Novelly, the authors provide empirical support for existing conceptual frameworks but also extend these.