bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human T‐cell receptor V gene segment of alpha and beta families: A revised primer design strategy
Authors: Ch'ng Angela Chiew Wen , Chan Soo Khim , Ignatius Joshua , Lim Theam Soon 
Published: March 2019

AbstractThe application of human TCR in cancer immunotherapy has gained momentum with developments in tumor killing strategies using endogenous adaptive immune responses. The successful coverage of a diverse TCR repertoire is mainly attributed to the primer design of the human TCR V genes. Here, we present a refined primer design strategy of the human TCR V gene by clustering V gene sequence homolog for degenerate primer design based on the data from IMGT. The primers designed were analyzed and the PCR efficiency of each primer set was optimized. A total of 112 alpha and 160 beta sequences were aligned and clustered using a phylogram yielding 32 and 27 V gene primers for the alpha and beta family. The new primer set was able to provide 93.75% and 95.63% coverage for the alpha and beta family, respectively. A semi‐qualitative approach using the designed primer set was able to provide a relative view of the TCR V gene diversity in different populations. Taken together, the new primers provide a more comprehensive coverage of the TCR gene diversity for improved TCR library generation and TCR V gene analysis studies.
Analysis of Sublethal Toxicity in Developing Zebrafish Embryos Exposed to a Range of Petroleum Substances
Authors: Hedgpeth Bryan M. , Redman Aaron D. , Alyea Rebecca A. , Letinski Daniel J. , Connelly Martin J. , Butler Josh D. , Zhou Heping , Lampi Mark A. 
Published: March 2019

Abstract
The Organisation for Economic Co-operation and Development (OECD) test guideline 236 (fish embryo acute toxicity test; 2013) relies on 4 endpoints to describe exposure-related effects (coagulation, lack of somite formation, tail-bud detachment from the yolk sac, and the presence of a heartbeat). Danio rerio (zebrafish) embryos were used to investigate these endpoints along with a number of additional sublethal effects (cardiac dysfunction, pericardial edema, yolk sac edema, tail curvature, hatch success, pericardial edema area, craniofacial malformation, swim bladder development, fin development, and heart rate) following 5-d exposures to 7 petroleum substances. The substances investigated included 2 crude oils, 3 gas oils, a diluted bitumen, and a petrochemical containing a mixture of branched alcohols. Biomimetic extraction–solid-phase microextraction (BE–SPME) was used to quantify freely dissolved concentrations of test substances as the exposure metric. The results indicated that the most prevalent effects observed were pericardial and yolk sac edema, tail curvature, and lack of embryo viability. A BE–SPME threshold was determined to characterize sublethal morphological alterations that preceded embryo mortality. Our results aid in the understanding of aquatic hazards of petroleum substances to developing zebrafish beyond traditional OECD test guideline 236 endpoints and show the applicability of BE–SPME as a simple analytical tool that can be used to predict sublethal embryo toxicity. Environ Toxicol Chem 2019;38:1302–1312. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
Optimization of textural characteristics of restructured pimiento strips by response surface methodology
Authors: Mousavi Seyyed Mohammad Reza , Rafe Ali , Yeganehzad Samira 
Published: March 2019

AbstractIn this study, the effect of guar gum (0.5%–1% w/w), sodium alginate (1%–2% w/w), and calcium chloride (2%–8% w/w) on textural properties of restructuring pimiento strips (RPS) was investigated. The gums were added to the pimiento strip formula, and different quality attributes including rupture force, energy to fracture, hardness, adhesiveness, cohesiveness, springiness, and chewiness were determined. Based on the textural properties of RPS, it was optimized by response surface methodology. All the textural properties of RPS were found to be significantly affected by alteration in guar gum, sodium alginate, and calcium chloride. The regression models for product’s response like rupture force and energy to fracture were highly significant. Results showed that restructured pimiento strip formula containing guar gum 1% w/w along with sodium alginate 2% w/w and 8% calcium chloride improved the textural and tensile properties. According to the RSM results on the textural properties of RPS, it is feasible to achieve the high elasticity and rigidity of pimiento strips as well as obtain the ability to tolerate thermal and mechanical stresses with appreciable textural integrity during processing such as pasteurization that would be investigated in another work.
Subset testing and analysis of multiple phenotypes
Authors: Derkach Andriy , Pfeiffer Ruth M. 
Published: March 2019

AbstractMeta‐analysis of multiple genome‐wide association studies (GWAS) is effective for detecting single‐ or multimarker associations with complex traits. We develop a flexible procedure (subset testing and analysis of multiple phenotypes [STAMP]) based on mixture models to perform a region‐based meta‐analysis of different phenotypes using data from different GWAS and identify subsets of associated phenotypes. Our model framework helps distinguish true associations from between‐study heterogeneity. As a measure of association, we compute for each phenotype the posterior probability that the genetic region under investigation is truly associated. Extensive simulations show that STAMP is more powerful than standard approaches for meta‐analyses when the proportion of truly associated outcomes is between 25% and 50%. For other settings, the power of STAMP is similar to that of existing methods. We illustrate our method on two examples, the association of a region on chromosome 9p21 with the risk of 14 cancers, and the associations of expression of quantitative trait loci from two genetic regions with their cis‐single‐nucleotide polymorphisms measured in 17 tissue types using data from The Cancer Genome Atlas.
Engaging Australian men in masculinity and suicide – A concept test of social media materials and a website
Authors: Schlichthorst Marisa , King Kylie , Turnure Jackie , Phelps Andrea , Pirkis Jane 
Published: March 2019

AbstractIssue addressedMen dominate the suicide statistics and are less likely than women to seek help for emotional problems, and this has been linked to aspects of stoic masculinity. Promoting help‐seeking and challenging stoic thinking may help to address this problem, but it is unclear what works in engaging men in these topics.MethodsWe developed a multimedia intervention called Man Up – including a documentary and digital campaign. We tested promotional materials and the website by interviewing 17 men from different ages and backgrounds about their perceptions, and asked them whether the materials generated interest in the topics of the documentary.ResultsParticipants preferred visual materials that were relatable to them and included active and direct language. This helped them to understand and identify with the messages being imparted. Participants had mixed views on talking about masculinity and the use of the term “man up,” with some expressing interest and others being deterred by it. Sharing content about mental health and suicide was seen by some as a risk to personal reputation and their relationships with others.ConclusionsOur findings informed the design of targeted materials for the national Man Up campaign and website which were then used in a multilevel national health promotion intervention in Australia.So what?Our study provided valuable insights beyond Man Up for those seeking to design and deliver health promotion interventions targeting Australian men and engage in sensitive and stigmatised male health issues. Using active and empowering language was especially important when addressing men which contrasts with many promotional materials currently available.
Unsteady MHD chemically reactive double‐diffusive Casson fluid past a flat plate in porous medium with heat and mass transfer
Authors: Das M. , Mahanta G. , Shaw S. , Parida S.B. 
Published: March 2019

AbstractIn this paper, an attempt has been made to analyze the effects of various parameters, such as Soret and Dufour effects, chemical reaction, magnetic field, porosity on the fluid flow, and heat and mass transfer of an unsteady Casson fluid flow past a flat plate. Convective boundary conditions in heat and mass transfer and slip constant on velocity have been taken into account for analysis. The governing equations of the model have been solved numerically using the MATLAB program bvp4c. The impact of various parameters of the model on the velocity, temperature, and concentration profiles has been analyzed through different graphs. To get an insight into the physical quantities of engineering interest, viz, skin friction, Sherwood number, and Nusselt number, their numerical values have been computed for various parameters. The range of the parameters used in numerical computations are , , , , , , and . It has been noticed from the tabulated values that the skin friction gets enhanced with the increase in the thermal and solutal Grashof number, whereas its reverse effects have been observed with an increase in the Biot number. In limiting case, the present study is also compared with the available results in the literature.
Estimating minimum streamflow from measurements at ungauged sites in regions with streamflow‐gauging networks
Authors: Konrad Christopher , Rumsey Christine 
Published: March 2019

AbstractEstimation of low flows in rivers continues to be a vexing problem despite advances in statistical and process‐based hydrological models. We develop a method to estimate minimum streamflow at seasonal to annual timescales from measured streamflow based on regional similarity in the deviations of daily streamflow from minimum streamflow for a period of interest. The method is applied to 1,019 gauged sites in the Western United States for June to December 2015. The gauges were clustered into six regions with distinct timing and magnitude of low flows. A gamma distribution was fit each day to the deviations in specific discharge (daily streamflow divided by drainage area) from minimum specific discharge for gauges in each region. The Kolmogorov–Smirnov test identified days when the gamma distribution was adequate to represent the distribution of deviations in a region. The performance of the gamma distribution was evaluated at gauges by comparing daily estimates of minimum streamflow with estimates from area‐based regression relations for minimum streamflow. Each region had at least 8 days during the period when streamflow measurements would provide better estimates than the regional regression equation, but the number of such days varied by region depending on aridity and homogeneity of streamflow within the region. Synoptic streamflow measurements at ungauged sites have value for estimating minimum streamflow and improving the spatial resolution of hydrological model in regions with streamflow‐gauging networks.
The Life Science Toolbox Provided by Chemical Biology
Authors: Schultz Carsten 
Published: March 2019

AbstractThis perspective covers a fraction of the diverse engineering branches of chemical biology. Long before the term chemical biology was created, there was the desire to use chemistry for unraveling the endlessly complex world of biology. The impact of this work has been tremendous, as we are now able to follow and switch biological processes at will and in realtime. In fact, without these tools it will be very difficult to address the complexity of biology in the future.
Parenting self‐efficacy in the context of poverty and HIV in Eastern Uganda: A qualitative study
Authors: Augustinavicius Jura L. , Familiar‐Lopez Itziar , Winch Peter J. , Murray Sarah M. , Ojuka Caesar , Boivin Michael J. , Bass Judith K. 
Published: March 2019

ABSTRACTWe sought to understand social representations of effective parenting and parenting self‐efficacy among female HIV‐affected caregivers in rural Eastern Uganda. We conducted in‐depth interviews (n = 21) to describe parenting experiences and caregivers’ perceptions of their own parenting abilities and to create vignettes for use in directed focus groups. We carried out open focus groups (n = 2) to gain social perspectives on parenting, and directed focus groups (n = 2) concentrated on parenting self‐efficacy. Analysis involved memoing and inductive and deductive coding of transcripts. Caregivers’ perceptions of their own parenting were grounded in parenting values such as providing children with basic needs, having well‐behaved children, and having good relationships with children. Caregivers’ perceptions were influenced by challenges, including single parenthood, living with HIV, limited family resources, and mental health problems. When facing challenges, caregivers relied on social support and faith as well as their own parenting confidence. Caregivers’ perceptions of their parenting abilities were influenced by how they felt others perceived them, their satisfaction in the parenting role, their perseverance despite challenges, and the extent to which they had a vision for their family. Our findings contextualize parenting self‐efficacy within parenting values, challenges, and social perceptions among HIV‐affected caregivers in rural Uganda.
Preparation and properties of dopamine‐modified alginate/chitosan–hydroxyapatite scaffolds with gradient structure for bone tissue engineering
Authors: Shi Dongjian , Shen Jiali , Zhang Zhuying , Shi Chang , Chen Mingqing , Gu Yanglin , Liu Yang 
Published: March 2019

AbstractThree‐dimensional (3D) homogenous scaffolds composed of natural biopolymers have been reported as superior candidates for bone tissue engineering. There are still remaining challenges in fabricating the functional scaffolds with gradient structures to similar with natural bone tissues, as well as high mechanical properties and excellent affinity to surround tissues. Herein, inspired by the natural bone structure, a gradient‐structural scaffold composed of functional biopolymers was designed to provide an optimized 3D environment for promoting cell growth. To increase the interactions among the scaffolds, dopamine (DA) was employed to modify alginate (Alg) and needle‐like nano‐hydroxyapatite (HA) was prepared with quaternized chitosan as template. The obtained dopamine‐modified alginate (Alg‐DA) and quaternized chitosan‐templated hydroxyapatite (QCHA) were then used to fabricate the porous gradient scaffold by “iterative layering” freeze‐drying technique with further crosslinking by calcium ions (Ca2+). The as‐prepared Alg‐DA/QCHA gradient scaffolds were possessed seamlessly integrated layer structures and high levels of porosity at around 77.5%. Moreover, the scaffolds showed higher compression modules (1.7 MPa) than many other biopolyermic scaffolds. The gradient scaffolds showed appropriate degradation rate to satisfy with the time of the bone regeneration. Both human chondrocytes and fibroblasts could adhesive and growth well on the scaffolds in vitro. Furthermore, an excellent osteogenetic activity of the gradient scaffold can effectively promote the regeneration of the bone tissue and accelerate the repair of the bone defects in vivo, compared with that of the scaffold with the homogenous structure. The novel multilayered scaffold with gradient structure provided an interesting option for bone tissue engineering. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 1615–1627, 2019.
Novel ultrafine‐grained β‐type Ti–28Nb–2Zr–8Sn alloy for biomedical applications
Authors: Zhang Yidi , Guo Tianqi , Li Qiushi , Qin Jie , Ding Xinxin , Ye Shan , Zhao Jinghui , Zhou Yanmin 
Published: March 2019

AbstractTitanium alloys are widely accepted as orthopedic or dental implant materials in the medical field. It is important to evaluate the biocompatibility of an implant material prior to use. A new β‐type ultrafine‐grained Ti–28Nb–2Zr–8Sn (TNZS) alloy with low Young's modulus of 31.6 GPa was fabricated. This study aims to evaluate the biocompatibility of TNZS alloy. In this study, we examined the microstructure, chemical composition and surface wettability of the TNZS alloy. The mouse embryonic osteoblast MC3T3‐E1 cells and human umbilical vein endothelial cells (HUVECs) were cultured to study the cytocompatibility of TNZS alloy. Also, we evaluated the proinflammatory response of TNZS alloy in vitro and in vivo. The results show that the TNZS did not cause cytotoxicity, genotoxicity to MC3T3‐E1 cells and HUVECs. Whereas, the TNZS alloy could significantly promote the cell proliferation, cell spreading and cell adhesion of MC3T3‐E1 cells and HUVECs, as well as facilitate the osteogenic differentiation of MC3T3‐E1 cells. Moreover, the TNZS alloy did not induce any remarkable proinflammatory response in vitro and in vivo. Thus, the novel TNZS alloy with an elasticity closer to that of human bone is biologically safe and could be a potential candidate for biomedical implant application. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 1628–1639, 2019.
Multimodal porogen platforms for calcium phosphate cement degradation
Authors: Lodoso‐Torrecilla Irene , Grosfeld Eline‐Claire , Marra Abe , Smith Brandon T , Mikos Antonios G , Ulrich Dietmar JO , Jansen John A , van den Beucken Jeroen JJP 
Published: March 2019

AbstractCalcium phosphate cements (CPCs) represent excellent bone substitute materials due to their biocompatibility and injectability. However, their poor degradability and lack of macroporosity limits bone regeneration. The addition of poly(d,l‐lactic‐co‐glycolic acid) (PLGA) particles improves macroporosity and therefore late stage material degradation. CPC degradation and hence, bone formation at an early stage remains challenging, due to the delayed onset of PLGA degradation (i.e., after 2–3 weeks). Consequently, we here explored multimodal porogen platforms based on sucrose porogens (for early pore formation) and PLGA porogens (for late pore formation) to enhance CPC degradation and analyzed mechanical properties, dynamic in vitro degradation and in vivo performance in a rat femoral bone defect model. Porogen addition to CPC showed to decrease compressive strength of all CPC formulations; transition of the crystal phase upon in vitro incubation increased compressive strength. Although dynamic in vitro degradation showed rapid sucrose dissolution within 1 week, no additional effects on CPC degradation or bone formation were observed upon in vivo implantation. © 2019 The Authors. journal Of Biomedical Materials Research Part A Published By Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 1713–1722, 2019.
Mechanical Competence and Bone Quality Develop During Skeletal Growth
Authors: Zimmermann Elizabeth A , Riedel Christoph , Schmidt Felix N , Stockhausen Kilian E , Chushkin Yuriy , Schaible Eric , Gludovatz Bernd , Vettorazzi Eik , Zontone Federico , Püschel Klaus , Amling Michael , Ritchie Robert O , Busse Björn 
Published: March 2019

ABSTRACT
Bone fracture risk is influenced by bone quality, which encompasses bone's composition as well as its multiscale organization and architecture. Aging and disease deteriorate bone quality, leading to reduced mechanical properties and higher fracture incidence. Largely unexplored is how bone quality and mechanical competence progress during longitudinal bone growth. Human femoral cortical bone was acquired from fetal (n = 1), infantile (n = 3), and 2- to 14-year-old cases (n = 4) at the mid-diaphysis. Bone quality was assessed in terms of bone structure, osteocyte characteristics, mineralization, and collagen orientation. The mechanical properties were investigated by measuring tensile deformation at multiple length scales via synchrotron X-ray diffraction. We find dramatic differences in mechanical resistance with age. Specifically, cortical bone in 2- to 14-year-old cases exhibits a 160% greater stiffness and 83% higher strength than fetal/infantile cases. The higher mechanical resistance of the 2- to 14-year-old cases is associated with advantageous bone quality, specifically higher bone volume fraction, better micronscale organization (woven versus lamellar), and higher mean mineralization compared with fetal/infantile cases. Our study reveals that bone quality is superior after remodeling/modeling processes convert the primary woven bone structure to lamellar bone. In this cohort of female children, the microstructural differences at the femoral diaphysis were apparent between the 1- to 2-year-old cases. Indeed, the lamellar bone in 2- to 14-year-old cases had a superior structural organization (collagen and osteocyte characteristics) and composition for resisting deformation and fracture than fetal/infantile bone. Mechanistically, the changes in bone quality during longitudinal bone growth lead to higher fracture resistance because collagen fibrils are better aligned to resist tensile forces, while elevated mean mineralization reinforces the collagen scaffold. Thus, our results reveal inherent weaknesses of the fetal/infantile skeleton signifying its inferior bone quality. These results have implications for pediatric fracture risk, as bone produced at ossification centers during children's longitudinal bone growth could display similarly weak points. © 2019 American Society for Bone and Mineral Research.
Caveolin‐1 regulates human trabecular meshwork cell adhesion, endocytosis, and autophagy
Authors: Wu Zhenggen , Huang Chukai , Xu Ciyan , Xie Lijing , Liang Jia‐Jian , Liu Lifang , Pang Chi Pui , Ng Tsz Kin , Zhang Mingzhi 
Published: March 2019

AbstractImpaired trabecular meshwork (TM) outflow is implicated in the pathogenesis of primary open‐angle glaucoma (POAG). We previously identified the association of a caveolin‐1 (CAV1) variant with POAG by genome‐wide association study. Here we report a study of
CAV1 knockout (KO) effect on human TM cell properties. We generated human
CAV1‐KO TM cells by CRISPR/Cas9 technology, and we found that the
CAV1‐KO TM cells less adhered to the surface coating than the wildtype TM cells by 69.34% (
P < 0.05), but showed no difference in apoptosis. Higher endocytosis ability of dextran and transferrin was also observed in the
CAV1‐KO TM cells (4.37 and 1.89‐fold respectively,
P < 0.001), compared to the wildtype TM cells. Moreover, the
CAV1‐KO TM cells had higher expression of extracellular matrix‐degrading enzyme genes (
ADMTS13 and
MMP14) as well as autophagy‐related genes (
ATG7 and
BECN1) and protein (LC3B‐II) than the wildtype TM cells. In summary, results from this study showed that the
CAV1‐KO TM cells have reduced adhesion with higher extracellular matrix‐degrading enzyme expression, but increased endocytosis and autophagy activities, indicating that
CAV1 could be involved in the regulation of adhesion, endocytosis, and autophagy in human TM cells.