bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Cobalamin (Vitamin B12) on Gentamicin Induced Nephrotoxicity in Rat
Authors: Hajihashemi Saeed , Hamidizad Zeinab , Rahbari Ali , Ghanbari Fatemeh , Motealeghi Zohre 
Published: September 2017

Abstract
Background The main side effect of gentamicin is nephrotoxicity. The effect of cobalamin (Cob) was investigated on gentamicin nephrotoxicity in rats.
Methods Renal injury induced by i.p. injection of gentamicin (100 mg/kg) for 8 consecutive days. Cobalamin (6 mg/kg/day, i.p) treatment was done for 8 consecutive days as co-treatment and post-treatment protocol.
Results Cobalamin significantly increased creatinine clearance levels and renal blood flow which were reduced by gentamicin. Also, cobalamin significantly improved serum electrolytes (sodium and potassium) levels which were disturbed by gentamicin. Cobalamin significantly compensated deficits in the antioxidant defense mechanisms, suppressed lipid per oxidation and ameliorated renal tissue damage mediated by gentamicin.
Conclusion The results of the current study indicated that cobalamin effectively protected the kidney tissue against gentamicin induced acute nephrotoxicity in rats. The antioxidant and anti-inflammatory activities can be supposed the main factors responsible for the nephroprotective effect of cobalamin.
Influence of High-Dose Folic Acid on Methotrexate Efficacies and Safety in Japanese Rheumatoid Arthritis Patients
Authors: Kameyama Shun , Kase Yuko , Kurihara Saori , Yoshida Fumiko , Noda Masamitu , Iiduka Toshimi , Horiguchi Masami , Sugiyama Kentaro , Hirano Toshihiko 
Published: September 2017

Abstract
Backgrounds Folic acid dose at ≦5 mg/week has been recommended for rheumatoid arthritis (RA) patients to decrease risk of methotrexate adverse effects. However, higher doses of folic acid is used in some cases. We examined the influence of high-dose folic acid on methotrexate efficacies and safety in Japanese RA patients.
Methods 502 RA patients of four hospitals prescribed methotrexate and folic acid were included. These patients were divided into two subgroups according to the threshold of folic acid dose by 5 mg/week. Basic patient characteristics, methotrexate doses, and the efficacies or adverse effects of methotrexate were retrospectively compared between the two patient subgroups.
Results The frequency of folic acid use at doses higher than 5 mg/week was significantly different between the four hospitals (P<0.001). The prevalence of methotrexate adverse effects was not significantly different between the patients taking folic acid less and more than 5 mg/week. However, in the lower dose methotrexate subgroup (≦8 mg/week), the prevalence of patients exhibiting abnormal serum ALT concentrations in the patients using higher (>5 mg/week) dose of folic acid was significantly higher than that in the lower (≦5 mg/week) folic acid-treated subgroup (P=0.029). Folic acid dose between patients taking methotrexate less and more than 8 mg/week was not significantly different.
Major conclusion Folic acid dose was dependent on the hospitals, while efficacies and hepatotoxicity of methotrexate was not basically different between patients taking less and more than 5 mg/week of folic acid.
Taguchi Experimental Design for Optimization of Recombinant Human Growth Hormone Production in CHO Cell Lines and Comparing its Biological Activity with Prokaryotic Growth Hormone
Authors: Aghili Zahra , Zarkesh-Esfahani Sayyed 
Published: September 2017

AbstractGrowth hormone deficiency results in growth retardation in children and the GH deficiency syndrome in adults and they need to receive recombinant-GH in order to rectify the GH deficiency symptoms. Mammalian cells have become the favorite system for production of recombinant proteins for clinical application compared to prokaryotic systems because of their capability for appropriate protein folding, assembly, post-translational modification and proper signal. However, production level in mammalian cells is generally low compared to prokaryotic hosts. Taguchi has established orthogonal arrays to describe a large number of experimental situations mainly to reduce experimental errors and to enhance the efficiency and reproducibility of laboratory experiments.In the present study, rhGH was produced in CHO cells and production of rhGH was assessed using Dot blotting, western blotting and Elisa assay. For optimization of rhGH production in CHO cells using Taguchi method An M16 orthogonal experimental design was used to investigate four different culture components. The biological activity of rhGH was assessed using LHRE-TK-Luciferase reporter gene system in HEK-293 and compared to the biological activity of prokaryotic rhGH.A maximal productivity of rhGH was reached in the conditions of 1%DMSO, 1%glycerol, 25 µM ZnSO4 and 0 mM NaBu. Our findings indicate that control of culture conditions such as the addition of chemical components helps to develop an efficient large-scale and industrial process for the production of rhGH in CHO cells. Results of bioassay indicated that rhGH produced by CHO cells is able to induce GH-mediated intracellular cell signaling and showed higher bioactivity when compared to prokaryotic GH at the same concentrations.
CD1d-Restricted pathways in hepatocytes control local natural killer T cell homeostasis and hepatic inflammation
Authors: Zeissig Sebastian , Peuker Kenneth , Iyer Shankar , Gensollen Thomas , Dougan Stephanie K. , Olszak Torsten , Kaser Arthur , Blumberg Richard S. 
Published: September 2017

SignificanceInvariant natural killer T (iNKT) cells recognize lipid antigens in the context of CD1d and have potent effects on immunity. Control of iNKT cells is critical to prevent inflammation, but the mechanisms that maintain homeostasis of iNKT cells in peripheral tissues are incompletely understood. Here we demonstrate that hepatocytes promote the apoptosis of local, liver-resident iNKT cells in a manner dependent on CD1d. In the absence of hepatocyte CD1d or microsomal triglyceride transfer protein, a protein responsible for lipid transfer onto CD1d, hepatic iNKT cell numbers are increased, which is associated with susceptibility to iNKT cell-dependent hepatitis. This work thus reveals a pathway of peripheral induction of immune tolerance, which limits susceptibility to iNKT cell-dependent inflammation in the liver.
Waiting can be an optimal conservation strategy, even in a crisis discipline
Authors: Iacona Gwenllian D. , Possingham Hugh P. , Bode Michael 
Published: September 2017

Significance
Every year, more species are driven to extinction by the combined pressures of habitat destruction, invasive species, and climate change. These ongoing losses have created a “crisis culture” in conservation, where project funds are spent as soon as they are received. We challenge this orthodoxy and demonstrate how strategic delays can improve efficiency. Waiting can allow agencies to leverage additional benefits from their funds, through investment, capacity building, or monitoring and research. With the right amount of delay, limited conservation resources can protect more species. Surprisingly, they can even do so in less time. Our results suggest that, in addition to their current focus on where to target resources, conservation managers should carefully choose when to spend these funds.
Arresting dissolution by interfacial rheology design
Authors: Beltramo Peter J. , Gupta Manish , Alicke Alexandra , Liascukiene Irma , Gunes Deniz Z. , Baroud Charles N. , Vermant Jan 
Published: September 2017

Significance
The challenge of creating foams and emulsions with well-controlled size distribution and properties is encountered in many structured materials, such as food formulations and consumer care products. These products, like ice cream for example, must remain stable over long shelf lifetimes while their microstructure dictates product performance and consumer satisfaction. Despite the common use of particles to stabilize bubbles and emulsions, the cause of such stabilization is unknown. Here, we provide the link between the particles’ ability to impart a resistance, or “armor,” against bubble dissolution and their interfacial rheological properties. We propose a design strategy based on controlling interfacial particle interactions to arrest dissolution of small bubbles to create foam and emulsion materials with stable microstructures and controllable textures.
Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation
Authors: Brady Jacob P. , Farber Patrick J. , Sekhar Ashok , Lin Yi-Hsuan , Huang Rui , Bah Alaji , Nott Timothy J. , Chan Hue Sun , Baldwin Andrew J. , Forman-Kay Julie D. , Kay Lewis E. 
Published: September 2017

Significance
The cell is divided into compartments where specific biochemical functions are performed. These compartments can be delineated by membranes or through phase separation of proteins or protein and nucleic acids to form membraneless organelles. The latter situation occurs with an intrinsically disordered region of Ddx4, a major constituent of germ granules. The nature of the interior of membraneless organelles is poorly understood. Here, we use NMR to show that the intrinsically disordered Ddx4 region remains disordered and highly dynamic in the phase-separated state, while diffusing as slowly as a particle the size of a bacterial cell. Ddx4 molecules form a network of interactions on phase separation, providing an alternative environment to that found in membrane-encapsulated organelles.
Nanoswitch-linked immunosorbent assay (NLISA) for fast, sensitive, and specific protein detection
Authors: Hansen Clinton H. , Yang Darren , Koussa Mounir A. , Wong Wesley P. 
Published: September 2017

Significance
Basic research and medical diagnostics rely on the ability to detect and quantify specific proteins in biological fluids. While numerous current detection techniques exist, these are often limited by trade-offs between ease of use, sensitivity, and cost. Here, we present the nanoswitch-linked immunosorbent assay (NLISA), an accessible, sensitive, and low-cost detection platform that is based upon nanoscale devices that change confirmation upon binding a target protein. NLISA is surface-free and includes a kinetic-proofreading purification step, enabling both enhanced sensitivity and the ability to accurately distinguish between similar proteins from different strains of the same virus or that differ by only a single mutation. Our method is also readily transferable to point-of-care devices due to an easy readout and few hands-on steps.
Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses
Authors: Chen Zhenguo , Sun Lei , Zhang Zhihong , Fokine Andrei , Padilla-Sanchez Victor , Hanein Dorit , Jiang Wen , Rossmann Michael G. , Rao Venigalla B. 
Published: September 2017

Significance
The WT bacteriophage T4 head is prolate with icosahedral T=13 ends closing the central cylindrical section. The structure of a T=13 icosahedral head assembly, in which the major capsid protein of T4 phage had a single mutation at a residue in the interface between neighboring subunits, has been determined to 3.3-Å resolution. The structure shows the extensive network of interactions between the major capsid proteins gp23 and the vertex proteins gp24 and the stabilizing Soc proteins. We show that the angle between hexameric and pentameric capsomers helps to determine the triangulation number (T number) and suggests how other viruses assemble consistently with a predetermined T number.
RABIF/MSS4 is a Rab-stabilizing holdase chaperone required for GLUT4 exocytosis
Authors: Gulbranson Daniel R. , Davis Eric M. , Demmitt Brittany A. , Ouyang Yan , Ye Yihong , Yu Haijia , Shen Jingshi 
Published: September 2017

Significance
Rab GTPases are central regulators of vesicle-mediated cargo transport. They are switched from the GDP-bound inactive conformation to the GTP-bound active state by guanine nucleotide exchange factors (GEFs). Rab-interacting factor (RABIF)/mammalian suppressor of Sec4 (MSS4) and its yeast homolog DSS4 are the first putative GEFs isolated for Rabs, but their biological function and molecular mechanism remained unclear. In this work, we demonstrate that RABIF plays a crucial role in exocytosis. Unexpectedly, we discovered that RABIF does not function as a GEF, as previously assumed. Instead, RABIF is a Rab-stabilizing holdase chaperone, a previously unrecognized mode of Rab regulation independent of its GDP-releasing activity. We suggest that a requirement for holdase chaperones is likely a general feature of Rab GTPases.
Screening, Brief Intervention, and Referral to Treatment (SBIRT) Curriculum Integration and Sustainability: Social Work and Nursing Faculty Perspectives
Authors: Belfiore M. Nicole , Blinka Marcela D. , BrintzenhofeSzoc Karlynn , Shields Joseph 
Published: September 2017

Background The Substance Abuse and Mental Health Services Administration (SAMHSA) has funded grants to universities to provide training and conduct research on the dissemination of Screening, Brief Intervention, and Referral to Treatment (SBIRT) to health care professionals. However, when it comes to integrating SBIRT content into an existing curriculum, difficulties can arise. When there is so much content already in the curriculum, adding more can be challenging. Additionally, some faculty believe that course curricula should be driven by the expertise and knowledge of faculty, not by opportunities afforded because of grant funding. Methods Using qualitative semi-structured faculty interviews and thematic data analysis, this study explored the process and content issues surrounding the integration of SBIRT content into the Masters of Social Work (MSW) and Masters of Science in Nursing (MSN) curricula at one university. Results Guidelines for the successful integration of SBIRT content into MSW and MSN curricula fall into two thematic areas: 1. Encourage buy-in and ownership of SBIRT curriculum development by current faculty. 2. Use a scaffolded approach. SBIRT includes several unique content areas which should be integrated per competencies addressed in each course. SBIRT content areas lend themselves to integration into a range of courses, employing an array of learning techniques and teaching materials. Scaffolding content requires creativity, which serves as the basis of the six subthemes that guide a scaffolded SBIRT integration approach. Conclusions SBIRT offers an evidence based intervention that uses a public health approach to reduce harm from substance use. As such, professional nursing and social work education programs should teach SBIRT to their master's level practitioners. This paper proposes guidelines for integrating that content into existing curricula.
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing
Authors: Äijö Tarmo , Müller Christian L , Bonneau Richard 
Published: September 2017

AbstractMotivationThe number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis.ResultsTo address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling approaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence and environmental noise models.Availability and implementationA Stan implementation of the proposed method is available under MIT license at https://github.com/tare/GPMicrobiome.Supplementary informationSupplementary data are available at Bioinformatics online.
High dimensional classification with combined adaptive sparse PLS and logistic regression
Authors: Durif Ghislain , Modolo Laurent , Michaelsson Jakob , Mold Jeff E , Lambert-Lacroix Sophie , Picard Franck 
Published: September 2017

AbstractMotivationThe high dimensionality of genomic data calls for the development of specific classification methodologies, especially to prevent over-optimistic predictions. This challenge can be tackled by compression and variable selection, which combined constitute a powerful framework for classification, as well as data visualization and interpretation. However, current proposed combinations lead to unstable and non convergent methods due to inappropriate computational frameworks. We hereby propose a computationally stable and convergent approach for classification in high dimensional based on sparse Partial Least Squares (sparse PLS).ResultsWe start by proposing a new solution for the sparse PLS problem that is based on proximal operators for the case of univariate responses. Then we develop an adaptive version of the sparse PLS for classification, called logit-SPLS, which combines iterative optimization of logistic regression and sparse PLS to ensure computational convergence and stability. Our results are confirmed on synthetic and experimental data. In particular, we show how crucial convergence and stability can be when cross-validation is involved for calibration purposes. Using gene expression data, we explore the prediction of breast cancer relapse. We also propose a multicategorial version of our method, used to predict cell-types based on single-cell expression data.Availability and implementationOur approach is implemented in the plsgenomics R-package.Supplementary informationSupplementary data are available at Bioinformatics online.
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm
Authors: Xie Zhengwei , Zhang Tianyu , Ouyang Qi 
Published: September 2017

Abstract

Motivation
One of the long-expected goals of genome-scale metabolic modelling is to evaluate the influence of the perturbed enzymes on flux distribution. Both ordinary differential equation (ODE) models and constraint-based models, like Flux balance analysis (FBA), lack the capacity to perform metabolic control analysis (MCA) for large-scale networks.

Results
In this study, we developed a hyper-cube shrink algorithm (HCSA) to incorporate the enzymatic properties into the FBA model by introducing a pseudo reaction V constrained by enzymatic parameters. Our algorithm uses the enzymatic information quantitatively rather than qualitatively. We first demonstrate the concept by applying HCSA to a simple three-node network, whereby we obtained a good correlation between flux and enzyme abundance. We then validate its prediction by comparison with ODE and with a synthetic network producing voilacein and analogues in Saccharomyces cerevisiae. We show that HCSA can mimic the state-state results of ODE. Finally, we show its capability of predicting the flux distribution in genome-scale networks by applying it to sporulation in yeast. We show the ability of HCSA to operate without biomass flux and perform MCA to determine rate-limiting reactions.

Availability and implementation
Algorithm was implemented by Matlab and C ++. The code is available at https://github.com/kekegg/HCSA.

Supplementary information
Supplementary data are available at Bioinformatics online.
LinkageMapView—rendering high-resolution linkage and QTL maps
Authors: Ouellette Lisa A , Reid Robert W , Blanchard Steven G , Brouwer Cory R 
Published: September 2017

Abstract

Motivation
Linkage and quantitative trait loci (QTL) maps are critical tools for the study of the genetic basis of complex traits. With the advances in sequencing technology over the past decade, linkage map densities have been increasing dramatically, while the visualization tools have not kept pace. LinkageMapView is a free add-on package written in R that produces high resolution, publication-ready visualizations of linkage and QTL maps. While there is software available to generate linkage map graphics, none are freely available, produce publication quality figures, are open source and can run on all platforms. LinkageMapView can be integrated into map building pipelines as it seamlessly incorporates output from R/qtl and also accepts simple text or comma delimited files. There are numerous options within the package to build highly customizable maps, allow for linkage group comparisons, and annotate QTL regions.

Availability and implementation
https://cran.r-project.org/web/packages/LinkageMapView/
Disablement in Context: Neighborhood Characteristics and Their Association With Frailty Onset Among Older Adults
Authors: Caldwell Julia T , Lee Haena , Cagney Kathleen A 
Published: September 2017

AbstractObjectivesFrailty, an aggregate expression of risk resulting from age- or disease-associated physiologic accumulation, is responsible for large economic and societal costs. Little is known about how the context in which older adult’s live may contribute to differences in frailty. This study clarifies the role of neighborhood structural characteristics and social processes for understanding declines in health status.MethodData from two waves of the National Social Life, Health and Aging Project were linked to tract-level information from the 2000 Census (n = 1,925). Frailty was measured with in-home assessments and self-report. Ordered logistic regressions were employed to estimate the role of tract-level structural and social process indicators at baseline on frailty at follow-up.ResultsLiving in a neighborhood characterized with a higher density of African Americans and with more residential instability was associated with higher odds of frailty. Adults in neighborhoods with increasing levels of physical disorder had higher odds of frailty (adjusted odds ratio [AOR]: 1.20, 95% confidence interval [CI]: 1.03, 1.39), while those exposed to more social cohesion had lower odds (AOR: 0.87, CI: 0.78, 0.97).DiscussionFor older adults, both neighborhood structural and social process characteristics appear to be independently associated with frailty.