bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tibanna: software for scalable execution of portable pipelines on the cloud
Authors: Lee Soohyun , Johnson Jeremy , Vitzthum Carl , Kırlı Koray , Alver Burak H , Park Peter J 
Published: April 2019

Abstract

Summary
We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network.

Availability and implementation
Source code is available on GitHub at https://github.com/4dn-dcic/tibanna.

Supplementary information
Supplementary data are available at Bioinformatics online.
The metastatic phenotype shift toward myofibroblast of adipose-derived mesenchymal stem cells promotes ovarian cancer progression
Authors: Tang Huijuan , Chu Yijing , Huang Zaiju , Cai Jing , Wang Zehua 
Published: April 2019

Abstract
Ovarian cancer metastasizes to organs in the abdominal cavity, such as the omentum that is a rich source of adipose-derived mesenchymal stem cells (ADSCs). In present, ADSCs have received more and more attention for their roles in the development of cancer. In this study, we examined α-smooth muscle actin (α-SMA) expression and carcinoma-associated fibroblast (CAF)-like differentiation capabilities in ADSCs from omentum of different patients. The effects of ADSCs on the proliferation and invasion of epithelial ovarian cancer cells (EOCCs) were also assessed in vitro and in vivo. Our results showed that ADSCs from omentum of ovarian cancer patients, no matter whether metastasis or not, expressed higher levels of α-SMA than ADSCs from patients with benign gynecologic disease. Using direct and indirect co-culture system, we found that EOCCs induced ADSCs to express CAF markers, including α-SMA and fibroblast activation protein, via the transforming growth factor beta 1 (TGF-β1) signaling pathway. Moreover, co-cultured ADSCs exhibited functional properties similar to those of CAFs, including the ability to promote EOCCs proliferation, progression and metastasis both in vitro and in vivo. Furthermore, blocking the TGF-β1 pathway can counteract the CAF-like differentiation and tumor promotion effect of ADSCs. Our results suggest that ADSCs are a source of CAFs and that they participate in the interaction between EOCCs and the omental microenvironment. EOCCs could induce ADSCs in the omentum to differentiate before ovarian cancer metastasis, which participate in the formation of omental metastatic niches and promote the proliferation and invasion of ovarian cancer.
Hippocampal Blood Flow Is Increased After 20 min of Moderate-Intensity Exercise
Authors: Steventon J J , Foster C , Furby H , Helme D , Wise R G , Murphy K 
Published: April 2019

Abstract
Long-term exercise interventions have been shown to be a potent trigger for both neurogenesis and vascular plasticity. However, little is known about the underlying temporal dynamics and specifically when exercise-induced vascular adaptations first occur, which is vital for therapeutic applications. In this study, we investigated whether a single session of moderate-intensity exercise was sufficient to induce changes in the cerebral vasculature. We employed arterial spin labeling magnetic resonance imaging to measure global and regional cerebral blood flow (CBF) before and after 20 min of cycling. The blood vessels’ ability to dilate, measured by cerebrovascular reactivity (CVR) to CO2 inhalation, was measured at baseline and 25-min postexercise. Our data showed that CBF was selectively increased by 10–12% in the hippocampus 15, 40, and 60 min after exercise cessation, whereas CVR to CO2 was unchanged in all regions. The absence of a corresponding change in hippocampal CVR suggests that the immediate and transient hippocampal adaptations observed after exercise are not driven by a mechanical vascular change and more likely represents an adaptive metabolic change, providing a framework for exploring the therapeutic potential of exercise-induced plasticity (neural, vascular, or both) in clinical and aged populations.
The Association Between Breast Milk Group B Streptococcal Capsular Antibody Levels and Late-onset Disease in Young Infants
Authors: Dangor Ziyaad , Khan Mahtaab , Kwatra Gaurav , Izu Alane , Nakwa Firdose , Ramdin Tanusha , Fredericks Joy , Lala Sanjay G , Madhi Shabir A 
Published: April 2019

Abstract

Background
Animal-model studies have demonstrated less group B streptococcal (GBS) invasive disease and gastrointestinal colonization after enteral administration of serotype-specific capsular antibodies. There is, however, a paucity of information on the association of breast milk GBS serotype-specific capsular antibodies and risks for invasive disease in infants. The aim of this study was to explore the association between natural secretory immunoglobulin A (sIgA) capsular antibodies in breast milk and the occurrence of late-onset disease (LOD) in young infants.

Methods
A matched case-control study was undertaken in infants &lt;3 months of age in Johannesburg, South Africa. Breast milk samples were collected on cases and controls matched for gestational age, maternal age, and human immunodeficiency virus status at time of enrollment. Capsular serotype Ia, Ib, III, and V sIgA antibody concentrations were measured using the fluorescence-based micro-bead immunosorbent assay.

Results
Breast milk samples were available for 31 LOD cases (8 serotype Ia and 23 serotype III), 21 recto-vaginally colonized matched controls (10 serotype Ia and 11 serotype III), and 84 serotype Ia and 105 serotype III noncolonized matched controls. Using a Bayesian model to estimate the probability of disease, there were 90% reductions in the risks of developing serotypes Ia and III LOD with sIgA concentrations ≥0.14 µg/mL and ≥2.52 µg/mL, respectively.

Conclusions
Breast milk sIgA capsular antibodies were associated with lower risks for LOD in young infants. The ability of GBS polysaccharide-protein conjugate vaccines currently under development to induce sIgA responses warrant investigation as potential mediators of protection against LOD.
Emergence of Attenuated Measles Illness Among IgG-positive/IgM-negative Measles Cases: Victoria, Australia, 2008–2017
Authors: Gibney Katherine B , Attwood Lucy O , Nicholson Suellen , Tran Thomas , Druce Julian , Healy Julia , Strachan Janet , Franklin Lucinda , Hall Robert , Cross Gail B 
Published: April 2019

Abstract

Background
Waning measles immunity among vaccinated individuals may result in an attenuated illness. This study compares the epidemiological, clinical, and laboratory profile of measles cases with waning immunity with other measles cases.

Methods
Polymerase chain reaction–positive (+) measles cases notified to Victoria’s Department of Health and Human Services from 2008 to 2017 with immunoglobulin (Ig) M and IgG tested at diagnosis were classified according to serology at diagnosis: IgG negative (−) (nonimmune), IgM+/IgG+ (indeterminate), or IgM−/IgG+ (waning immunity).

Results
Between 2008 and 2017, 297 measles cases were notified, of whom 190 (64%) were included; 151 of 190 (79%) were nonimmune at diagnosis, 26 (14%) were indeterminate, and 13 (7%) had waning immunity. Between 2008–2013 and 2014–2017, the proportion of cases with waning immunity increased from 0 of 87 (0%) to 13 of 103 (13%) (P &lt; .001) and the diagnostic sensitivity of initial IgM fell from 93% to 81% (P = .012), respectively. Seven (54%) waning immunity cases reported receiving measles-containing vaccines; 1 case had 2 documented doses. Compared with nonimmune and indeterminate cases, waning immunity cases were more likely to be male; less likely to report fever, coryza, and cough; and had lower burden of virus (higher cycle threshold values). Waning immunity cases had higher IgG titers than indeterminate cases (mean optical density values, 1.96 vs 0.71; P = .004). Onward transmission from 1 waning immunity case was documented.

Conclusions
Waning immunity among measles cases, associated with secondary vaccine failure and modified clinical illness, is emerging in Victoria with transmission potential.
Prolapse and regurgitation of the four heart valves in a patient with Ehlers–Danlos Syndrome: a case report
Authors: Chango Azanza Diego Xavier , Munín Martin Alejandro , Sánchez Gustavo Anibal , Spernanzoni Fernando 
Published: April 2019

Abstract

Background
The Ehlers–Danlos Syndrome (EDS) is part of a group of connective tissue diseases that affect the synthesis and processing of collagen leading to alterations in the structure of many tissues and organs.

Case summary
Herein, we reported a case of a patient with prolapse of the four cardiac valves. Non-significant regurgitation of the mitral, aortic, and tricuspid valves was observed. The pulmonary regurgitation (PR) was considered significant. Dilatation of the right ventricle with preserved systolic function was also noted. A cardiac magnetic resonance confirmed the findings of the echocardiogram and determined a severe PR (regurgitant fraction of 41%). The physical examination revealed hyperlaxity of the joints, skin hyperelasticity, defects in wound healing, and abdominal hernias suggesting EDS. The stress test did not develop any symptoms or complex arrhythmias. In this patient, the heart team initially decided medical treatment and evolutionary control. At the moment, he remains asymptomatic.

Discussion
Valvular involvement in EDS is an infrequent event and the compromise of the four cardiac valves is exceptional. The existence of severe PR with a marked increase in ventricular volumes, even in the absence of symptoms, in most cases requires an intervention on the valve. However, in patients with EDS, there are a high rate of complications and interventions should be avoided as much as possible.
Effectiveness of randomized controlled trial of a mobile app to promote healthy lifestyle in obese and overweight patients
Authors: Apiñaniz Antxon , Cobos-Campos Raquel , Sáez de Lafuente-Moríñigo Arantza , Parraza Naiara , Aizpuru Felipe , Pérez Iraida , Goicoechea Enara , Trápaga Nerea , García Laura 
Published: April 2019

AbstractBackgroundHealth advice is useful for establishing behavioural changes, but such changes tend not to last. It would therefore be good to identify mechanisms for reinforcing advice and one option is the use of information and communication technologies. Given the limited evidence on the effectiveness of such technologies, we decided to conduct a clinical trial to assess the efficacy of a mobile application (app) for supporting the provision health advice for weight loss.MethodsA randomized clinical trial with 110 obese and overweight patients from the Basque public health care network (Araba). Patients were randomly allocated to the control (health advice) or intervention (health advice + app) groups. Primary (weight) and secondary (blood cholesterol level, blood pressure, haemoglobin A1c (HbA1c) and adherence to dietary and exercise recommendations) outcome variables were assessed at 1, 3 and 6 months after the end of the intervention.ResultsThere were no significant differences in weight (0.357 kg; P = 0.7), blood cholesterol (2.6 mg/dl; P = 0.617), blood pressure (2.3 mmHg; P = 0.369) or adherence to recommendations on diet (84.6% in control and 92.9% the intervention group, P = 0.413) or physical activity (56% in controls and 75% the intervention group, P = 0.145). On the other hand, there were significant differences in HbA1c in favour of the control group (−0.095%; %; P = 0.046).DiscussionThe use of AKTIDIET® to support health advice for weight loss cannot be recommended. More high quality studies are needed, and patients should be involved in the design of apps to increase their efficacy and usability.Clinical trial registrationNCT02308176.
Improving employment opportunities of the unemployed by health and work ability promotion in Finland
Authors: Hult Marja , Pietilä Anna-Maija , Saaranen Terhi 
Published: April 2019

Abstract
The study explored the impact of self-rated health (SRH) and work ability on employment, and examined the effects of meaningfulness, social networks and physical activity on health and work ability with a population-based cross-sectional survey data (n = 12 729) of full-time employed and unemployed workers. SRH, perceived work ability and levels of perceived meaningfulness, social networks and physical activity were all significantly better among employed workers compared to unemployed people. The results showed that work ability mediated the effect of health on employment and predicted employment. Meaningfulness, social networks and physical activity had direct positive effects on health and work ability, and also on employment. The results indicated that good health is a substantial element of good work ability, which in turn is needed to maintain or to get a job. Our findings suggested that perceiving one’s life as meaningful, having a strong social network and being physically active are important predictors of good health as well as of good work ability. These could be contributing factors to re-employment among unemployed people.
On Twisted Gelfand Pairs Through Commutativity of a Hecke Algebra
Authors: Hendel Yotam I 
Published: April 2019

AbstractFor a locally compact, totally disconnected group $G$, a subgroup $H$, and a character $\chi :H \to \mathbb{C}^{\times }$ we define a Hecke algebra ${\mathcal{H}}_\chi$ and explore the connection between commutativity of ${\mathcal{H}}_\chi$ and the $\chi$-Gelfand property of $(G,H)$, that is, the property $\dim _{\mathbb{C}} (\rho ^*)^{(H,\chi ^{-1})} \leq 1$ for every $\rho \in \textrm{Irr}(G)$, the irreducible representations of $G$. We show that the conditions of the Gelfand–Kazhdan criterion imply commutativity of ${\mathcal{H}}_\chi$ and verify in several simple cases that commutativity of ${\mathcal{H}}_\chi$ is equivalent to the $\chi$-Gelfand property of $(G,H)$. We then show that if $G$ is a connected reductive group over a $p$-adic field $F$, and $G/H$ is $F$-spherical, then the cuspidal part of ${\mathcal{H}}_\chi$ is commutative if and only if $(G,H)$ satisfies the $\chi$-Gelfand property with respect to all cuspidal representations ${\rho \in \textrm{Irr}(G)}$. We conclude by showing that if $(G,H)$ satisfies the $\chi$-Gelfand property with respect to all irreducible $(H\backslash G,\chi ^{-1})$-tempered representations of $G$ then ${\mathcal{H}}_\chi$ is commutative.
Variety in Self-Expression Undermines Self-Continuity
Authors: Rifkin Jacqueline R , Etkin Jordan 
Published: April 2019

AbstractFrom dating profiles and social media accounts to online streaming services, consumers are often asked to express who they are by constructing an assortment. Apple Music, for example, asks new users to indicate “two or more” of their favorite types of music when they create an account. But while consumers might create such self-expressive assortments to communicate who they are, could the composition of these assortments also affect how people see themselves? Seven studies demonstrate that perceiving greater variety in a self-expressive assortment undermines self-continuity. This occurs because variety leads consumers to infer that their preferences are less stable, thereby decreasing the belief that their identity stays the same over time. Variety’s effect generalizes across multiple domains of self-expression (e.g., books, music, television) and has downstream consequences for service evaluation and even unrelated decision-making (e.g., intertemporal tradeoffs). The findings advance understanding of how choice shapes identity, the role of variety in consumers’ lives, and factors that affect self-continuity. The results also have implications for the marketers who encourage (and the consumers who construct) self-expressive assortments.
Extending the Boundaries of Sensory Marketing and Examining the Sixth Sensory System: Effects of Vestibular Sensations for Sitting versus Standing Postures on Food Taste Perception
Authors: Biswas Dipayan , Szocs Courtney , Abell Annika 
Published: April 2019

AbstractPrior research has examined the role of the traditional five sensory systems (visual, olfactory, haptic, auditory, and gustatory) and how they influence food evaluations. This research extends the boundaries of sensory marketing by examining the effects of the vestibular system, often referred to as the “sixth sensory system,” which is responsible for balance and posture. The results of six experiments show that vestibular sensations related to posture (i.e., sitting vs. standing) influence food taste perceptions. Specifically, standing (vs. sitting) postures induce greater physical stress on the body, which in turn decreases sensory sensitivity. As a result, when eating in a standing (vs. sitting) posture, consumers rate the taste of pleasant-tasting foods and beverages as less favorable, the temperature as less intense, and they consume smaller amounts. The effects of posture on taste perception are reversed for unpleasant-tasting foods. These findings have conceptual implications for broadening the frontiers of sensory marketing and for the effects of sensory systems on food taste perceptions. Given the increasing trend toward eating while standing, the findings also have practical implications for restaurant, retail, and other food-service environment designs.
Efficacy, Safety, and Immunogenicity of an Escherichia coli-Produced Bivalent Human Papillomavirus Vaccine: An Interim Analysis of a Randomized Clinical Trial
Authors: Qiao You-Lin , Wu Ting , Li Rong-Cheng , Hu Yue-Mei , Wei Li-Hui , Li Chang-Gui , Chen Wen , Huang Shou-Jie , Zhao Fang-Hui , Li Ming-Qiang , Pan Qin-Jing , Zhang Xun , Li Qing , Hong Ying , Zhao Chao , Zhang Wen-Hua , Li Yan-Ping , Chu Kai , Li Mei , Jiang Yun-Fei , Li Juan , Zhao Hui , Lin Zhi-Jie , Cui Xue-Lian , Liu Wen-Yu , Li Cai-Hong , Guo Dong-Ping , Ke Li-Dong , Wu Xin , Tang Jie , Gao Guo-Qi , Li Ba-Yi , Zhao Bin , Zheng Feng-Xian , Dai Cui-Hong , Guo Meng , Zhao Jun , Su Ying-Ying , Wang Jun-Zhi , Zhu Feng-Cai , Li Shao-Wei , Pan Hui-Rong , Li Yi-Min , Zhang Jun , Xia Ning-Shao 
Published: April 2019

Abstract

Background
The high cost and insufficient supply of human papillomavirus (HPV) vaccines have slowed the pace of controlling cervical cancer. A phase III clinical trial was conducted to evaluate the efficacy, safety, and immunogenicity of a novel Escherichia coli-produced bivalent HPV-16/18 vaccine.

Methods
A multicenter, randomized, double-blind trial started on November 22, 2012 in China. In total, 7372 eligible women aged 18–45 years were age-stratified and randomly assigned to receive three doses of the test or control (hepatitis E) vaccine at months 0, 1, and 6. Co-primary endpoints included high-grade genital lesions and persistent infection (over 6 months) associated with HPV-16/18. The primary analysis was performed on a per-protocol susceptible population of individuals who were negative for relevant HPV type-specific neutralizing antibodies (at day 0) and DNA (at day 0 through month 7) and who received three doses of the vaccine. This report presents data from a prespecified interim analysis used for regulatory submission.

Results
In the per-protocol cohort, the efficacies against high-grade genital lesions and persistent infection were 100.0% (95% confidence interval = 55.6% to 100.0%, 0 of 3306 in the vaccine group vs 10 of 3296 in the control group) and 97.8% (95% confidence interval = 87.1% to 99.9%, 1 of 3240 vs 45 of 3246), respectively. The side effects were mild. No vaccine-related serious adverse events were noted. Robust antibody responses for both types were induced and persisted for at least 42 months.

Conclusions
The E coli-produced HPV-16/18 vaccine is well tolerated and highly efficacious against HPV-16/18–associated high-grade genital lesions and persistent infection in women.
A Permutation Test on Complex Sample Data
Authors: Toth Daniell 
Published: April 2019

Abstract
Permutation tests are a distribution-free way of performing hypothesis tests. These tests rely on the condition that the observed data are exchangeable among the groups being tested under the null hypothesis. This assumption is easily satisfied for data obtained from a simple random sample or a controlled study after simple adjustments to the data, but there is no general method for adjusting survey data collected using a complex sample design to allow for permutation tests. In this article, we propose a general method for performing a pseudo-permutation test that accounts for the complex sample design. The proposed method is not a true permutation test in that the new values do not come from the set of observed values in general but of an expanded set of values satisfying a random-effects model on the clustered residuals of a design-consistent estimating equation. We provide a set of conditions under which this procedure leads to consistent test results. Tests using a simulated population and an application analyzing US Bureau of Labor Statistics consumer expenditure data comparing the performance of the proposed method to permutation tests that ignore the sample design demonstrate that it is necessary to account for the design features in order to obtain reasonable p value estimates.
CEP–CEPR1 signalling inhibits the sucrose-dependent enhancement of lateral root growth
Authors: Chapman Kelly , Taleski Michael , Ogilvie Huw A , Imin Nijat , Djordjevic Michael A 
Published: April 2019

AbstractLateral root (LR) proliferation is a major determinant of soil nutrient uptake. How resource allocation controls the extent of LR growth remains unresolved. We used genetic, physiological, transcriptomic, and grafting approaches to define a role for C-TERMINALLY ENCODED PEPTIDE RECEPTOR 1 (CEPR1) in controlling sucrose-dependent LR growth. CEPR1 inhibited LR growth in response to applied sucrose, other metabolizable sugars, and elevated light intensity. Pathways through CEPR1 restricted LR growth by reducing LR meristem size and the length of mature LR cells. RNA-sequencing of wild-type (WT) and cepr1-1 roots with or without sucrose treatment revealed an intersection of CEP–CEPR1 signalling with the sucrose transcriptional response. Sucrose up-regulated several CEP genes, supporting a specific role for CEP–CEPR1 in the response to sucrose. Moreover, genes with basally perturbed expression in cepr1-1 overlap with WT sucrose-responsive genes significantly. We found that exogenous CEP inhibited LR growth via CEPR1 by reducing LR meristem size and mature cell length. This result is consistent with CEP–CEPR1 acting to curtail the extent of sucrose-dependent LR growth. Reciprocal grafting indicates that LR growth inhibition requires CEPR1 in both the roots and shoots. Our results reveal a new role for CEP–CEPR1 signalling in controlling LR growth in response to sucrose.