bluuebunny/crossref_metadata_2025_split huggingface dataset:
PIV measurement of internal flow in mini centrifugal pump
Authors: Shigemitsu T , Ogawa Y , Nakaishi E 
Published: March 2019

Abstract
The diameter of the ventricular assist pump and cooling pump for electrical devices like servers is about a dozen millimetres and these kinds of pumps belong to the mini pump. The internal flow condition of the mini centrifugal pump has to be clarified because there are so many types of mini pumps according to special specifications and shapes. Therefore, in this research, an open impeller was adopted as a mini centrifugal pump with 55mm impeller diameter in consideration of reduction in impeller manufacturing cost and its internal flow was investigated. Since the outlet angle of the test impeller is large, the maximum efficiency flow rate moves to a large flow rate and the relatively high head and efficiency were obtained in large flow rate region. In the present paper, the velocity and vorticity distribution near the volute tongue are shown and the internal flow in the mini centrifugal pump is clarified based on the PIV measurement results.
Pinetree: a step-wise gene expression simulator with codon-specific translation rates
Authors: Jack Benjamin R , Wilke Claus O 
Published: March 2019

Abstract

Motivation
Stochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programing interfaces, which limit their utility.

Results
We present Pinetree, a step-wise gene expression simulator with codon-specific translation rates. Pinetree models both transcription and translation in a stochastic framework with individual polymerase and ribosome-level detail. Written in C++ with a Python front-end, any user familiar with Python can specify a genome and simulate gene expression. Pinetree was designed to be efficient and scale to simulate large plasmids or viral genomes.

Availability and implementation
Pinetree is available on GitHub (https://github.com/benjaminjack/pinetree) and the Python Package Index (https://pypi.org/project/pinetree/).
Determining parameters for non-linear models of multi-loop free energy change
Authors: Ward Max , Sun Hongying , Datta Amitava , Wise Michael , Mathews David H 
Published: March 2019

AbstractMotivationPredicting the secondary structure of RNA is a fundamental task in bioinformatics. Algorithms that predict secondary structure given only the primary sequence, and a model to evaluate the quality of a structure, are an integral part of this. These algorithms have been updated as our model of RNA thermodynamics changed and expanded. An exception to this has been the treatment of multi-loops. Although more advanced models of multi-loop free energy change have been suggested, a simple, linear model has been used since the 1980s. However, recently, new dynamic programing algorithms for secondary structure prediction that could incorporate these models were presented. Unfortunately, these models appear to have lower accuracy for secondary structure prediction.ResultsWe apply linear regression and a new parameter optimization algorithm to find better parameters for the existing linear model and advanced non-linear multi-loop models. These include the Jacobson-Stockmayer and Aalberts & Nandagopal models. We find that the current linear model parameters may be near optimal for the linear model, and that no advanced model performs better than the existing linear model parameters even after parameter optimization.Availability and implementationSource code and data is available at https://github.com/maxhwardg/advanced_multiloops.Supplementary informationSupplementary data are available at Bioinformatics online.
RTNsurvival: an R/Bioconductor package for regulatory network survival analysis
Authors: Groeneveld Clarice S , Chagas Vinicius S , Jones Steven J M , Robertson A Gordon , Ponder Bruce A J , Meyer Kerstin B , Castro Mauro A A 
Published: March 2019

Abstract

Motivation
Transcriptional networks are models that allow the biological state of cells or tumours to be described. Such networks consist of connected regulatory units known as regulons, each comprised of a regulator and its targets. Inferring a transcriptional network can be a helpful initial step in characterizing the different phenotypes within a cohort. While the network itself provides no information on molecular differences between samples, the per-sample state of each regulon, i.e. the regulon activity, can be used for describing subtypes in a cohort. Integrating regulon activities with clinical data and outcomes would extend this characterization of differences between subtypes.

Results
We describe RTNsurvival, an R/Bioconductor package that calculates regulon activity profiles using transcriptional networks reconstructed by the RTN package, gene expression data, and a two-tailed Gene Set Enrichment Analysis. Given regulon activity profiles across a cohort, RTNsurvival can perform Kaplan-Meier analyses and Cox Proportional Hazards regressions, while also considering confounding variables. The Supplementary Information provides two case studies that use data from breast and liver cancer cohorts and features uni- and multivariate regulon survival analysis.

Availability and implementation
RTNsurvival is written in the R language, and is available from the Bioconductor project at http://bioconductor.org/packages/RTNsurvival/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Molecular profiling demonstrates modulation of immune cell function and matrix remodeling during luteal rescue†
Authors: Hughes Camilla K , Maalouf Samar W , Liu Wan-Sheng , Pate Joy L 
Published: March 2019

Abstract
The corpus luteum (CL) is essential for maintenance of pregnancy in all mammals and luteal rescue, which occurs around day 16–19 in the cow, is necessary to maintain luteal progesterone production. Transcriptomic and proteomic profiling were performed to compare the day 17 bovine CL of the estrous cycle and pregnancy. Among mRNA and proteins measured, 140 differentially abundant mRNA and 24 differentially abundant proteins were identified. Pathway analysis was performed using four programs. Modulated pathways included T cell receptor signaling, vascular stability, cytokine signaling, and extracellular matrix remodeling. Two mRNA that were less in pregnancy were regulated by prostaglandin F2A in culture, while two mRNA that were greater in pregnancy were regulated by interferon tau. To identify mRNA that could be critical regulators of luteal fate, the mRNA that were differentially abundant during early pregnancy were compared to mRNA that were differentially abundant during luteal regression. Eight mRNA were common to both datasets, including mRNA related to regulation of steroidogenesis and gene transcription. A subset of differentially abundant mRNA and proteins, including those associated with extracellular matrix functions, were predicted targets of differentially abundant microRNA (miRNA). Integration of miRNA and protein data, using miRPath, revealed pathways such as extracellular matrix–receptor interactions, abundance of glutathione, and cellular metabolism and energy balance. Overall, this study has provided a comprehensive profile of molecular changes in the corpus luteum during maternal recognition of pregnancy and has indicated that some of these functions may be miRNA-regulated.
MiR-664-2 impacts pubertal development in a precocious-puberty rat model through targeting the NMDA receptor-1†
Authors: Ju Minda , Yang Liu , Zhu Jing , Chen Zhejun , Zhang Mizhen , Yu Jin , Tian Zhanzhuang 
Published: March 2019

Abstract
Precocious puberty (PP) commonly results from premature activation of the hypothalamic–pituitary–gonadal axis (HPGA). Gonadotropin-releasing hormone (GnRH) is the initial trigger for HPGA activation and plays an important role in puberty onset. N-methyl-D-aspartate (NMDA) can promote pulsatile GnRH secretion and accelerates puberty onset. However, the mechanism of N-methyl-D-aspartate receptors (NMDARs) in PP pathogenesis remains obscure. We found that serum GnRH, luteinizing hormone (LH), follicle-stimulating hormone (FSH), estrogen (E2) levels, hypothalamic NMDAR1, and GnRH mRNA expression peaked at the vaginal opening (VO) day. Next, the hypothalamic NMDAR1 mRNA and protein levels in rats treated with danazol, a chemical commonly effecting on the reproductive system, were significantly increased at the VO day (postnatal day 24) compared to controls, accompanied by enhanced serum GnRH, LH, FSH, and E2 levels. Further, microRNA-664-2 (miR-664-2) was selected after bioinformatics analysis and approved in primary hypothalamic neurons, which binds to the 3′-untranslated regions of NMDAR1. Consistently, the miR-664-2 expression in hypothalamus of the Danazol group was decreased compared to Vehicle. Our results suggested that attenuated miR-664-2 might participate in PP pathogenesis through enhancing the NMDAR1 signaling.
Comparison of different algorithms for the assessment of cardiovascular risk after kidney transplantation by the time of entering waiting list
Authors: Herzog Anna Laura , Kalogirou Charis , Wanner Christoph , Lopau Kai 
Published: March 2019

AbstractBackgroundThe prevalence of cardiovascular disease is high among patients with chronic kidney disease and cardiovascular events (CVE) remain the leading cause of death after kidney transplantation (KT). We performed a retrospective analysis of 389 KT recipients to assess if the European Society of Cardiology Score (ESC-Score), Framingham Heart Study Score (FRAMINGHAM), Prospective Cardiovascular Munster Study Score (PROCAM-Score) or Assessing cardiovascular risk using Scottish Intercollegiate Guidelines Network Score (ASSIGN-Score) algorithms can predict cardiovascular risk after KT at the time of entering the waiting list.Methods389 KT candidates were scored by the time of entering the waiting list. Pearsons chi-square test, cox regression analysis and survival estimates were performed to evaluate the reliability of the cardiovascular scoring models after successful KT.ResultsDuring a follow-up of 8 ± 5.8 years, 96 patients (30%) died due to cardiovascular problems, whereas 13.9% suffered non-fatal CVE. Graft loss occurred in 84 patients (21.6%). Predictors of CVE, survival and graft loss were age and the length of end-stage kidney disease. All scores performed well in assessing the risk for CVE (P &lt; 0.01). Receiver-operating characteristic analysis using the ESC-SCORE, as an example, suggested a cut-off for risk stratification and clinical decisions.ConclusionsWe found all tested scores were reliable for cardiovascular assessment. We suggest using cardiac scores for risk assessment before KT and then taking further steps according to current guidelines.
Propensity-matched comparison of the long-term outcome of the Nunn and two-patch techniques for the repair of complete atrioventricular septal defects
Authors: Bell Douglas , Thakeria Priyanka , Betts Kim , Justo Robert , Jalali Homayoun , Wijesekera Vishva , Venugopal Prem , Karl Tom , Alphonso Nelson 
Published: March 2019

Abstract

OBJECTIVES
To compare the long-term performance of the Nunn and 2-patch techniques for the repair of complete atrioventricular septal defects.

METHODS
Between January 1995 and December 2015, a total of 188 patients (Nunn n = 41; 2-patch n = 147) were identified from hospital databases. Univariable Cox regression was performed to calculate the risk of reintervention in each group. Propensity score matching was used to balance the Nunn group and the 2-patch group.

RESULTS
Baseline characteristics including age at surgery, weight, trisomy 21, other cardiac anomalies, previous operations and preoperative atrioventricular valve regurgitation did not differ between the 2 groups. Overall, there was no difference in mortality between the 2 groups (P = 0.43). Duration of cardiopulmonary bypass (CPB) and myocardial ischaemia time were 29 min (P &lt; 0.001) and 28 min (P &lt; 0.001) longer, respectively, in the 2-patch group. Median follow-up was 10.8 years (2–21 years). Unadjusted Cox regression did not reveal a significant difference in the risk of reoperation for either group 9 years after initial surgery [hazard ratio (HR) (Nunn) 0.512, 95% confidence interval 0.176–1.49; Nunn 89%; 2-patch 82%]. This finding was reiterated from Cox regression performed on the propensity-matched sample (31 pairs). The probability of freedom from moderate or worse left atrioventricular valve regurgitation or left ventricular outflow obstruction was similar in the 2 groups.

CONCLUSIONS
The Nunn and 2-patch techniques are comparable in terms of the long-term mortality and probability of freedom from reoperation, moderate or severe left atrioventricular valve regurgitation and left ventricular outflow obstruction. However, the duration of CPB and myocardial ischaemia is longer in the 2-patch group.
Income Mobility and Moving to a Better Neighbourhood: An Enquiry into Ethnic Differences in Finland
Authors: Vaalavuo Maria , van Ham Maarten , Kauppinen Timo M 
Published: March 2019

Abstract
The spatial concentration of immigrants in disadvantaged neighbourhoods may hinder their opportunities for social and economic integration. It is therefore important that immigrants can translate their available economic resources into mobility to less disadvantaged neighbourhoods. This study adds to existing research on the relationship between socioeconomic and spatial integration by focusing on the effects of income mobility on residential mobility. We analyse intra-urban residential mobility from low-income neighbourhoods into non-low-income neighbourhoods among immigrants and native-born residents in three urban regions in Finland. We use longitudinal register data for the 2004–2014 period for the full population, allowing a dynamic analysis of changes in income and neighbourhood of residence. Based on fixed-effects multinomial logit modelling of residential outcomes, we found that upward income mobility is connected to exit from low-income areas, but the effect is stronger among the native-born Finns than among those with an immigrant background. This stronger effect for natives is in contrast to findings of previous European studies, suggesting that these might have been influenced by unobserved individual-level heterogeneity. Our findings imply that both policies improving labour market opportunities of immigrants and policies reducing constraints for spatial integration are needed if the aim is to decrease ethnic residential segregation.
Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome
Authors: Bergman Alexandra , Vitay Dóra , Hellgren John , Chen Yun , Nielsen Jens , Siewers Verena 
Published: March 2019

ABSTRACT
Microbial conversion of biomass to fatty acids (FA) and products derived thereof is an attractive alternative to the traditional oleochemical production route from animal and plant lipids. This study examined if NADPH-costly FA biosynthesis could be enhanced by overexpressing the transcription factor Stb5 in Saccharomyces cerevisiae. Stb5 activates expression of multiple genes encoding enzymes within the pentose phosphate pathway (PPP) and other NADPH-producing reactions. Overexpression of STB5 led to a decreased growth rate and an increased free fatty acid (FFA) production during growth on glucose. The improved FFA synthetic ability in the glucose phase was shown to be independent of flux through the oxidative PPP. RNAseq analysis revealed that STB5 overexpression had wide-ranging effects on the transcriptome in the batch phase, and appeared to cause a counterintuitive phenotype with reduced flux through the oxidative PPP. During glucose limitation, when an increased NADPH supply is likely less harmful, an overall induction of the proposed target genes of Stb5 (eg. GND1/2, TAL1, ALD6, YEF1) was observed. Taken together, the strategy of utilizing STB5 overexpression to increase NADPH supply for reductive biosynthesis is suggested to have potential in strains engineered to have strong ability to consume excess NADPH, alleviating a potential redox imbalance.
The dynamics of dissent: when actions are louder than words
Authors: Stimmer Anette , Wisken Lea 
Published: March 2019

Abstract
A profusion of international norms influences state behaviour. Ambiguities and tensions in the normative framework can give rise to contestation. While research on norm contestation has focused on open debates about norms, we identify a second type of norm contestation where norms are contested through particular forms of implementation. We therefore distinguish between contestation through words and actions, that is, discursive and behavioural contestation. Discursive contestation involves debates about the meaning and/or (relative) importance of norms. Behavioural contestation, by contrast, eschews such debates. Instead, different norm understandings become apparent in the different ways in which actors shape the implementation of norms. Despite being a potentially powerful mechanism of challenging and changing norms, behavioural contestation has fallen outside the purview of the literature in part because it frequently remains below the radar. The two forms of contestation overlap when the practices of behavioural contestation are brought to the attention of and discussed by the international community. Thus, discursive and behavioural contestation are not mutually exclusive but can happen at the same time, sequentially or independently of each other. This introduction to a special section of the May 2019 issue of International Affairs, on ‘The dynamics of dissent’, develops the concept of behavioural contestation and outlines triggers and effects of this hitherto under-researched expression of dissent.
The Inflammatory Bowel Disease Symptom Inventory: A Patient-report Scale for Research and Clinical Application
Authors: Sexton Kathryn A , Walker John R , Targownik Laura E , Graff Lesley A , Haviva Clove , Beatie Brooke E , Petty Sarah K , Bernstein Matthew T , Singh Harminder , Miller Norine , Bernstein Charles N 
Published: March 2019

Abstract

Objectives
Existing measures of inflammatory bowel disease (IBD) symptoms are not well suited to self-report, inadequate in measurement properties, insufficiently specific, or burdensome for brief or repeated administration. We aimed to develop a patient-reported outcome measure to assess a broader range of IBD symptoms.

Methods
The IBD Symptoms Inventory (IBDSI) was developed by adapting symptom items from existing clinician-rated or diary-format inventories; after factor analysis, 38 items were retained on 5 subscales: bowel symptoms, abdominal discomfort, fatigue, bowel complications, and systemic complications. Participants completed the IBDSI and other self-report measures during a clinic visit. A nurse administered the Harvey Bradshaw Index (HBI) for Crohn’s disease (CD) or the Powell-Tuck Index (PTI) for ulcerative colitis (UC), and a gastroenterologist completed a global assessment of disease severity (PGA).

Results
The 267 participants with CD (n = 142) or UC (n = 125), ages 18 to 81 (M = 43.4, SD = 14.6) were 58.1% female, with a mean disease duration of 13.9 (SD = 10.5) years. Confirmatory factor analysis supported the 5 subscales. The total scale and subscales showed good reliability and significant correlations with self-report symptom and IBD quality of life measures, the HBI, PTI, and PGA.

Conclusions
The IBDSI showed strong measurement properties: a supported factor structure, very good internal consistency, convergent validity, and excellent sensitivity and specificity to clinician-rated active disease. Self-report HBI and PTI items, when extracted from this measure, produced scores comparable to clinician-administered versions. The 38-item IBDSI, or 26-item short form, can be used as a brief survey of common IBD symptoms in clinic or research settings.
Microbiota Metabolite Butyrate Differentially Regulates Th1 and Th17 Cells’ Differentiation and Function in Induction of Colitis
Authors: Chen Liang , Sun Mingming , Wu Wei , Yang Wenjing , Huang Xiangsheng , Xiao Yi , Ma Chunyan , Xu Leiqi , Yao Suxia , Liu Zhanju , Cong Yingzi 
Published: March 2019

Abstract

Background
How the gut microbiota regulates intestinal homeostasis is not completely clear. Gut microbiota metabolite short-chain fatty acids (SCFAs) have been reported to regulate T-cell differentiation. However, the mechanisms underlying SCFA regulation of T-cell differentiation and function remain to be investigated.

Methods
CBir1, an immunodominant microbiota antigen, transgenic T cells were treated with butyrate under various T-cell polarization conditions to investigate butyrate regulation of T-cell differentiation and the mechanism involved. Transfer of butyrate-treated CBir T cells into Rag1-/- mice was performed to study the in vivo role of such T cells in inducing colitis.

Results
Although butyrate promoted Th1 cell development by promoting IFN-γ and T-bet expression, it inhibited Th17 cell development by suppressing IL-17, Rorα, and Rorγt expression. Interestingly, butyrate upregulated IL-10 production in T cells both under Th1 and Th17 cell conditions. Furthermore, butyrate induced T-cell B-lymphocyte-induced maturation protein 1 (Blimp1) expression, and deficiency of Blimp1 in T cells impaired the butyrate upregulation of IL-10 production, indicating that butyrate promotes T-cell IL-10 production at least partially through Blimp1. Rag1-/- mice transferred with butyrate-treated T cells demonstrated less severe colitis, compared with transfer of untreated T cells, and administration of anti-IL-10R antibody exacerbated colitis development in Rag-/- mice that had received butyrate-treated T cells. Mechanistically, the effects of butyrate on the development of Th1 cells was through inhibition of histone deacetylase but was independent of GPR43.

Conclusions
These data indicate that butyrate controls the capacity of T cells in the induction of colitis by differentially regulating Th1 and Th17 cell differentiation and promoting IL-10 production, providing insights into butyrate as a potential therapeutic for the treatment of inflammatory bowel disease.
Mortality After First Hospital Admission for Inflammatory Bowel Disease: A Nationwide Registry Linkage Study
Authors: Opstelten Jorrit L , Vaartjes Ilonca , Bots Michiel L , Oldenburg Bas 
Published: March 2019

Abstract

Background
The goal of this study was to determine long-term mortality and causes of death in patients after hospitalization for inflammatory bowel disease (IBD).

Methods
A cohort of patients admitted to the hospital because of IBD for the first time between 1998 and 2010 was identified by linkage of nationwide Dutch registries. Mortality risks and causes of death in Crohn’s disease (CD) and ulcerative colitis (UC) patients were compared with a large random sample of individuals from the general population. Multivariable Cox regression models were used to calculate hazard ratios (HRs) with 95% confidence intervals (CIs).

Results
In total, 23,003 patients (56.1% women; mean age, 44.8 years) were hospitalized for IBD. Patients admitted for IBD had a higher risk of death than those from the general population. Adjusted HRs for 5-year all-cause mortality were 2.42 (95% CI, 1.15–5.12) and 1.45 (95% CI, 1.26–1.66) in men and women hospitalized for CD, respectively. Corresponding HRs for UC were 1.59 (95% CI, 1.39–1.83) and 1.13 (95% CI, 0.98–1.31). Mortality among patients after hospitalization for IBD decreased between 1998–2004 and 2005–2010. Patients admitted for UC had a higher risk of all-cause mortality than those admitted for CD. Inflammatory bowel disease patients died more often from (colorectal) cancer and gastrointestinal disease and less often from cardiovascular disease relative to the general population.

Conclusions
Mortality of patients after hospitalization for IBD has decreased over time. Causes of death in CD and UC patients differ from those in the general population.