bluuebunny/crossref_metadata_2025_split huggingface dataset:
DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data
Authors: Ye Chengzhong , Speed Terence P , Salim Agus 
Published: June 2019

Abstract

Motivation
Dropout is a common phenomenon in single-cell RNA-seq (scRNA-seq) data, and when left unaddressed it affects the validity of the statistical analyses. Despite this, few current methods for differential expression (DE) analysis of scRNA-seq data explicitly model the process that gives rise to the dropout events. We develop DECENT, a method for DE analysis of scRNA-seq data that explicitly and accurately models the molecule capture process in scRNA-seq experiments.

Results
We show that DECENT demonstrates improved DE performance over existing DE methods that do not explicitly model dropout. This improvement is consistently observed across several public scRNA-seq datasets generated using different technological platforms. The gain in improvement is especially large when the capture process is overdispersed. DECENT maintains type I error well while achieving better sensitivity. Its performance without spike-ins is almost as good as when spike-ins are used to calibrate the capture model.

Availability and implementation
The method is implemented as a publicly available R package available from https://github.com/cz-ye/DECENT.

Supplementary information
Supplementary data are available at Bioinformatics online.
Toward Control? The Prospects and Challenges of Typhoid Conjugate Vaccine Introduction
Authors: Carey Megan E , Diaz Zoey I , Broadstock Martin , Bailey Roderick , Bentsi-Enchill Adwoa D , Larson Heidi J 
Published: June 2019

Abstract
With a newly World Health Organization (WHO)–prequalified typhoid conjugate vaccine (TCV), Gavi funding for eligible countries, and a WHO policy recommendation for TCV use, now is the time for countries to introduce TCVs as part of an integrated typhoid control program, particularly in light of the increasing burden of antimicrobial resistance. Continued vaccine development efforts will lead to secure supply of low-cost vaccines, and ongoing vaccine studies will provide critical vaccine performance data and inform optimal deployment strategies, in both routine use and in outbreak settings. TCV programs should include thoughtful communication planning and community engagement to counter vaccine hesitancy.
Increased wave action promotes muscle performance but increasing temperatures cause a tenacity–endurance trade-off in intertidal snails (Nerita atramentosa)
Authors: Clayman Samuel , Seebacher Frank 
Published: June 2019

AbstractConcurrent increases in wave action and sea surface temperatures increase the physical impact on intertidal organisms and affect their physiological capacity to respond to that impact. Our aim was to determine whether wave exposure altered muscle function in intertidal snails (Nerita atramentosa) and whether responses to wave action and temperature are plastic, leading to compensation for altered environmental conditions. We show that field snails from exposed shores had greater endurance and vertical tenacity than snails from matched protected shores (n = 5 pairs of shores). There were no differences in muscle metabolic capacities (strombine/lactate dehydrogenase, citrate synthase and cytochrome c oxidase activities) between shore types. Maximum stress (force/foot area) produced by isolated foot muscle did not differ between shore types, but foot muscle from snails on exposed shores had greater endurance. A laboratory experiment showed that vertical tenacity was greater in animals acclimated for 3 weeks to cool winter temperatures (15 C) compared to summer temperatures (25 C), but endurance was greater in snails acclimated to 25°C. Acclimation to water flow that mimicked wave action in the field increased vertical tenacity but decreased endurance. Our data show that increased wave action elicits a training effect on muscle, but that increasing sea surface temperature can cause a trade-off between tenacity and endurance. Ocean warming would negate the beneficial increase in tenacity that could render snails more resistant to acute impacts of wave action, while promoting longer term resistance to dislodgment by waves.
A human embryonic stem cell reporter line for monitoring chemical-induced cardiotoxicity
Authors: Tsai Su-Yi , Ghazizadeh Zaniar , Wang Hou-Jun , Amin Sadaf , Ortega Francis A , Badieyan Zohreh Sadat , Hsu Zi-Ting , Gordillo Miriam , Kumar Ritu , Christini David J , Evans Todd , Chen Shuibing 
Published: June 2019

Abstract

Aims
Human embryonic stem cells (hESCs) can be used to generate scalable numbers of cardiomyocytes (CMs) for studying cardiac biology, disease modelling, drug screens, and potentially for regenerative therapies. A fluorescence-based reporter line will significantly enhance our capacities to visualize the derivation, survival, and function of hESC-derived CMs. Our goal was to develop a reporter cell line for real-time monitoring of live hESC-derived CMs.

Methods and results
We used CRISPR/Cas9 to knock a mCherry reporter gene into the MYH6 locus of hESC lines, H1 and H9, enabling real-time monitoring of the generation of CMs. MYH6:mCherry+ cells express atrial or ventricular markers and display a range of cardiomyocyte action potential morphologies. At 20 days of differentiation, MYH6:mCherry+ cells show features characteristic of human CMs and can be used successfully to monitor drug-induced cardiotoxicity and oleic acid-induced cardiac arrhythmia.

Conclusion
We created two MYH6:mCherry hESC reporter lines and documented the application of these lines for disease modelling relevant to cardiomyocyte biology.
IL-12 and Mucosal CD14+ Monocyte-Like Cells Induce IL-8 in Colonic Memory CD4+ T Cells of Patients With Ulcerative Colitis but not Crohn’s Disease
Authors: Chapuy Laurence , Bsat Marwa , Rubio Manuel , Sarkizova Sisi , Therrien Amélie , Bouin Mickael , Orlicka Katarzina , Weber Audrey , Soucy Geneviève , Villani Alexandra-Chloé , Sarfati Marika 
Published: June 2019

Abstract

Background and Aims
CD14+ mononuclear phagocytes [MNPs] and T cells infiltrate colon in ulcerative colitis [UC]. Here we investigated how CD14+ MNPs and the cytokines they produce shape the colonic effector T cell profile.

Methods
Colonic or mesenteric lymph node [mLNs] CD4+ T cells isolated from UC or Crohn’s disease [CD] patients were stimulated with cytokines or autologous CD14+ MNPs. Cytokine expression was assessed by intracytoplasmic staining and multiplex ELISA. Unsupervised phenotypic multicolour analysis of colonic CD14+ MNPs was performed using the FlowSOM algorithm.

Results
Among CD14+CD64+HLA-DR+SIRPα + MNPs, only the pro-inflammatory cytokine-producing CD163− subpopulation accumulated in inflamed UC colon and promoted mucosal IL-1β-dependent Th17, Th17/Th1, Th17/Th22 but not Th1 responses. Unsupervised phenotypic analysis of CD14+CD64+ MNPs segregated CD163− monocyte-like cells and CD163+ macrophages. Unexpectedly, IL-12, IL-1β and CD163−, but not CD163+, cells induced IL-8 expression in colonic CD4+ T cells, which co-expressed IFN-γ and/or IL-17 in UC and not CD. The CD163− monocyte-like cells increased the frequency of IL-8+IL-17+/−IFN-γ +/− T cells through IL-1β and IL-12. Finally, colonic IL-8+ T cells co-expressing GM-CSF, TNF-α and IL-6 were detected ex vivo and, promoted by IL-12 in the mucosa and mLNs in UC only.

Conclusions
Our findings established a link between monocyte-like CD163− MNPs, IL-12, IL-1β and the detection of colonic memory IL-8-producing CD4+ T cells, which might all contribute to the pathogenesis of UC.
It is a medical emergency! Act fast: a case report of painless aortic dissection
Authors: Yanamadala Anusha , Kumar Sanjay , Lichtenberg Robert 
Published: June 2019

Abstract

Background
A painless presentation of aortic dissection is rare in about 5% of cases. A few case reports discussed about involvement of coronary arteries causing bradycardia. In our case, we are presenting a rare presentation of aortic dissection with initial presentation as bradycardia without involvement of coronary arteries and without cardiac symptoms.

Case summary
A 56-year-old man with history of hypertension presented with acute onset of altered mental status and right hand numbness. Initial vital signs were remarkable for bradycardia with heart rate 36/min. Physical exam was only significant for decreased sensation for light touch on right hand. Electrocardiogram showing marked sinus bradycardia. Initial computed tomography (CT) head did not show any acute abnormalities. On Day 2, patient complained of new weakness in left upper extremity. On exam, he had dysmetria, left upper extremity drift and cold to touch. Blood pressure was significantly different in both arms with 141/83 mmHg on right and 44/23 mmHg on left. He underwent immediate CT angiography chest showing Type 1 aortic dissection with extension into the brachiocephalic artery and right common carotid artery (RCCA) with thrombosis in RCCA. Patient was emergently taken for surgical repair of aortic dissection and resuspension of aortic valve.

Discussion
In our case, the initial presentation of aortic dissection included isolated sinus bradycardia without cardiac symptoms and no evidence for atrioventricular block. The mechanism may have been involvement in the arterial supply of the carotid body receptors. Patients with coexisting symptoms such as bradycardia and neurological deficits should be evaluated for aortic dissection.
Electrically vs. imaging-guided left ventricular lead placement in cardiac resynchronization therapy: a randomized controlled trial
Authors: Stephansen Charlotte , Sommer Anders , Kronborg Mads Brix , Jensen Jesper Møller , Nørgaard Bjarne Linde , Gerdes Christian , Kristensen Jens , Jensen Henrik Kjærulf , Fyenbo Daniel Benjamin , Bouchelouche Kirsten , Nielsen Jens Cosedis 
Published: June 2019

Abstract

Aims
To test in a double-blinded, randomized trial whether the combination of electrically guided left ventricular (LV) lead placement and post-implant interventricular pacing delay (VVd) optimization results in superior increase in LV ejection fraction (LVEF) in cardiac resynchronization therapy (CRT) recipients.

Methods and results
Stratified according to presence of ischaemic heart disease, 122 patients were randomized 1:1 to LV lead placement targeted towards the latest electrically activated segment identified by systematic mapping of the coronary sinus tributaries during CRT implantation combined with post-implant VVd optimization (intervention group) or imaging-guided LV lead implantation by cardiac computed tomography venography, 82Rubidium myocardial perfusion imaging and speckle tracking echocardiography targeting the LV lead towards the latest mechanically activated non-scarred myocardial segment (control group). Follow-up was 6 months. Primary endpoint was absolute increase in LVEF. Additional outcome measures were changes in New York Heart Association class, 6-minute walk test, and quality of life, LV reverse remodelling, and device related complications. Analysis was intention-to-treat. A larger increase in LVEF was observed in the intervention group (11 ± 10 vs. 7 ± 11%; 95% confidence interval 0.4–7.9%, P = 0.03); when adjusting for pre-specified baseline covariates this difference did not maintain statistical significance (P = 0.09). Clinical response, LV reverse remodelling, and complication rates did not differ between treatment groups.

Conclusion
Electrically guided CRT implantation appeared non-inferior to an imaging-guided strategy considering the outcomes of change in LVEF, LV reverse remodelling and clinical response. Larger long-term studies are warranted to investigate the effect of an electrically guided CRT strategy.
Development of de novo resistance in Salmonella Typhimurium treated with antibiotic combinations
Authors: Dawan Jirapat , Uddin Md Jalal , Ahn Juhee 
Published: June 2019

Abstract
This study was designed to evaluate the evolution of antibiotic resistance in Salmonella enterica serovar Typhimurium treated with the combination of antibiotics. The experimental evolution of antibiotic resistance of S. Typhimurium was evaluated either under single antibiotic (kanamycin, KAN; penicillin, PEN; erythromycin, ERY) or in combination of two antibiotics (KAN + PEN or KAN + ERY) as measured by fractional inhibitory concentrations (FICs), stepwise resistance selection, cross-resistance evaluation, resistance fitness and relative gene expression. KAN + PEN and KAN + ERY showed the synergistic effect against S. Typhimurium (FIC index &lt; 0.5). KAN + ERY delayed the induction of de novo mutations in S. Typhimurium. The cross-resistance of S. Typhimurium to all antibiotics except ERY and tetracycline was observed in KAN and PEN alone. The fitness cost was lower in single antibiotic treatments than combinations. The highest relative fitness was 0.91 in PEN, followed by KAN (0.84) and ERY (0.78), indicating the low fitness costs in single antibiotic treatments. The overexpression of efflux pump-related genes (acrA and acrB), outer membrane-related gene (ompC) and adherence-related gene (csgD) were observed in the single antibiotic treatments. Our results suggest that KAN + PEN and KAN + ERY could be used as a potential therapeutic treatment by decreasing the evolution of antibiotic resistance in S. Typhimurium and reusing conventional antibiotics.
Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling
Authors: Lozano-Fernandez Jesus , Giacomelli Mattia , Fleming James F , Chen Albert , Vinther Jakob , Thomsen Philip Francis , Glenner Henrik , Palero Ferran , Legg David A , Iliffe Thomas M , Pisani Davide , Olesen Jørgen 
Published: June 2019

AbstractThe relationships of crustaceans and hexapods (Pancrustacea) have been much discussed and partially elucidated following the emergence of phylogenomic data sets. However, major uncertainties still remain regarding the position of iconic taxa such as Branchiopoda, Copepoda, Remipedia, and Cephalocarida, and the sister group relationship of hexapods. We assembled the most taxon-rich phylogenomic pancrustacean data set to date and analyzed it using a variety of methodological approaches. We prioritized low levels of missing data and found that some clades were consistently recovered independently of the analytical approach used. These include, for example, Oligostraca and Altocrustacea. Substantial support was also found for Allotriocarida, with Remipedia as the sister of Hexapoda (i.e., Labiocarida), and Branchiopoda as the sister of Labiocarida, a clade that we name Athalassocarida (=”nonmarine shrimps”). Within Allotriocarida, Cephalocarida was found as the sister of Athalassocarida. Finally, moderate support was found for Hexanauplia (Copepoda as sister to Thecostraca) in alliance with Malacostraca. Mapping key crustacean tagmosis patterns and developmental characters across the revised phylogeny suggests that the ancestral pancrustacean was relatively short-bodied, with extreme body elongation and anamorphic development emerging later in pancrustacean evolution.
Wartime Rupture and Reconfiguration in French Family Life: Experience and Legacy
Authors: Dodd Lindsey 
Published: June 2019

Abstract
‘Wartime Rupture and Reconfiguration in French Family Life: Experience and Legacy’, by Lindsey Dodd Family separation is a widespread consequence of war, particularly war which targets civilian populations. This article draws on oral history narratives recorded by the author with French people who became child evacuees or refugees in France during the Second World War. All ended up in the département of the Creuse, in central France, hosted by people with whom they had no previous connection. Experiences of family rupture and reconfiguration have been considered by psychologists, but rarely by historians. As children live their lives mainly in the domestic sphere, close examination of their wartime worlds gives insight into the indirect effects of conflict on the youngest members of society. I argue that the experience of the Second World War must be understood as profound and lasting, even among those who did not experience combat, persecution or aggression directly. My case studies complicate understandings of family separation as a wholly negative experience for children in war, without compromising sensitivity to the nuances of individual difference. And I show the power of subjective retrospective sources to reveal the legacy of war inside commemorative actions situated well below national levels, which go unacknowledged in studies focused on the ‘collective’ or ‘cultural’ memory of the period.
Developmental and Evolutionary Allometry of the Mammalian Limb Skeleton
Authors: Cooper Kimberly L 
Published: June 2019

AbstractThe variety of limb skeletal proportions enables a remarkable diversity of behaviors that include powered flight in bats and flipper-propelled swimming in whales using extremes of a range of homologous limb architectures. Even within human limbs, bone lengths span more than an order of magnitude from the short finger and toe bones to the long arm and leg bones. Yet all of this diversity arises from embryonic skeletal elements that are each a very similar size at formation. In this review article, I survey what is and is not yet known of the development and evolution of skeletal proportion at multiple hierarchical levels of biological organization. These include the cellular parameters of skeletal elongation in the cartilage growth plate, genes associated with differential growth, and putative gene regulatory mechanisms that would allow both covariant and independent evolution of the forelimbs and hindlimbs and of individual limb segments. Although the genetic mechanisms that shape skeletal proportion are still largely unknown, and most of what is known is limited to mammals, it is becoming increasingly apparent that the diversity of bone lengths is an emergent property of a complex system that controls elongation of individual skeletal elements using a genetic toolkit shared by all.
The Road to Nonprofit Diversity and Inclusion
Authors: Walker Vernetta 
Published: June 2019

Abstract
Leadership at the board and executive levels across the nonprofit sector remains predominantly composed of white individuals, despite an increasingly diverse society. Research documents distinct benefits associated with diversity and inclusion, but efforts to move the dial have fallen short. This article explores how voluntary associations can prioritize racial/ethnic equity in their governance and provides specific steps for the examination of culture, practices, and processes required to operationalize change.
There are a variety of professional societies and associations, also known as business leagues, established under the Internal Revenue Code. To be exempt, these organizations must be devoted to improving an industry or profession, as distinguished from performing particular services for individuals, and when successful they serve to improve the economic and social well-being of the entire nation.
How People Judge the Usability of a Desktop Graphic User Interface at Different Time Points: Is there Evidence for Memory Decay, Recall Bias or Temporal Bias?
Authors: Boyd Kyle , Bond Raymond , Vertesi Attila , Dogan Huseyin , Magee Justin 
Published: June 2019

Abstract

The System Usability Scale (SuS) survey is a widely respected tool for measuring usability. Generally, a SuS score is administered directly after a usability test to assess the usability and user experience of digital products. However, some researchers have used SuS as a survey as part of longitudinal ‘in the wild’ trials where SuS is often completed some period after the trial. The aim of this research was to determine if a participant’s memory of a product’s usability would change if a SuS survey was administered at different times after a test. Hence, we sought to understand if recalling the usability of a digital technology was affected by temporal bias or memory decay. This paper includes results and findings from two studies, study 1 involved evaluating a web application and study 2 involved evaluating a virtual learning environment. Collectively the two studies had 212 participants (n = 212). The findings conclude that there is no significant change of the user’s recollection of the usability of digital product as evidenced by an analysis of users who completed multiple SuS surveys over a short term period of 3 weeks or over an extended period of time of 6 months.

RESEARCH HIGHLIGHTS
The system usability scale is used to test for memory decay and temporal bias in judging the user experience of technologies at different time points. 212 participants took part in two studies ranging from 3 weeks to 6 months. There is no evidence that there is a temporal bias or memory decay when users complete a SuS survey at the two different time points of 3 weeks and 6 months.
Cost-aware active learning for named entity recognition in clinical text
Authors: Wei Qiang , Chen Yukun , Salimi Mandana , Denny Joshua C , Mei Qiaozhu , Lasko Thomas A , Chen Qingxia , Wu Stephen , Franklin Amy , Cohen Trevor , Xu Hua 
Published: June 2019

Abstract

Objective
Active Learning (AL) attempts to reduce annotation cost (ie, time) by selecting the most informative examples for annotation. Most approaches tacitly (and unrealistically) assume that the cost for annotating each sample is identical. This study introduces a cost-aware AL method, which simultaneously models both the annotation cost and the informativeness of the samples and evaluates both via simulation and user studies.

Materials and Methods
We designed a novel, cost-aware AL algorithm (Cost-CAUSE) for annotating clinical named entities; we first utilized lexical and syntactic features to estimate annotation cost, then we incorporated this cost measure into an existing AL algorithm. Using the 2010 i2b2/VA data set, we then conducted a simulation study comparing Cost-CAUSE with noncost-aware AL methods, and a user study comparing Cost-CAUSE with passive learning.

Results
Our cost model fit empirical annotation data well, and Cost-CAUSE increased the simulation area under the learning curve (ALC) scores by up to 5.6% and 4.9%, compared with random sampling and alternate AL methods. Moreover, in a user annotation task, Cost-CAUSE outperformed passive learning on the ALC score and reduced annotation time by 20.5%–30.2%.

Discussion
Although AL has proven effective in simulations, our user study shows that a real-world environment is far more complex. Other factors have a noticeable effect on the AL method, such as the annotation accuracy of users, the tiredness of users, and even the physical and mental condition of users.

Conclusion
Cost-CAUSE saves significant annotation cost compared to random sampling.