bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Allogeneic Hematopoietic Stem Cell Transplantation on the HIV Reservoir and Immune Response in 3 HIV-Infected Individuals
Authors: Koelsch Kersten K. , Rasmussen Thomas A. , Hey-Nguyen William J. , Pearson Chester , Xu Yin , Bailey Michelle , Marks Katherine H. , Sasson Sarah C. , Taylor Mark S. , Tantau Robyn , Obeid Solange , Milner Brad , Morrissey Orla , Pinto Angie N. , Suzuki Kazuo , Busch Michael P. , Keating Sheila M. , Kaiser Philipp , Yukl Steven , Wong Joseph K. , Hiener Bonnie M. , Palmer Sarah , Zaunders John , Post Jeffrey J. , Chan Derek J. , Avery Sharon , Milliken Sam T. , Kelleher Anthony D. , Lewin Sharon R. , Cooper David A. 
Published: March 2017

Background:
Allogeneic hematopoietic stem cell transplantation (HSCT) can lead to significant changes to the HIV reservoir and HIV immune responses, indicating that further characterization of HIV-infected patients undergoing HSCT is warranted.

Methods:
We studied 3 patients who underwent HSCT after either reduced intensity conditioning or myeloablative conditioning regimen. We measured HIV antigens and antibodies (Ag/Ab), HIV-specific CD4+ T-cell responses, HIV RNA, and DNA in plasma, peripheral blood mononuclear cells, isolated CD4+ T cells from peripheral blood, and lymph node cells. The patients remained on antiretroviral therapy throughout the follow-up period.

Results:
All patients have been in continued remission for 4–6 years post-HSCT. Analyses of HIV RNA and DNA levels showed substantial reductions in HIV reservoir–related measurements in all 3 patients, changes in immune response varied with pronounced reductions in 2 patients and a less dramatic reduction in 1 patient. One patient experienced unexpected viral rebound 4 years after HSCT.

Conclusions:
These 3 cases highlight the substantial changes to the HIV reservoir and the HIV immune response in patients undergoing allogeneic HSCT. The viral rebound observed in 1 patient indicates that replication competent HIV can re-emerge several years after HSCT despite these marked changes.
Overall Splenectomy Rates Stable Despite Increasing Usage of Angiography in the Management of High-grade Blunt Splenic Injury
Authors: Dolejs Scott C. , Savage Stephanie A. , Hartwell Jennifer L. , Zarzaur Ben L. 
Published: March 2017

Objective:
The purpose of this study was to understand the contemporary trends of splenectomy in blunt splenic injury (BSI) and to determine if angiography and embolization (ANGIO) may be impacting the splenectomy rate.

Background:
The approach to BSI has shifted to increasing use of nonoperative management, with a greater reliance on ANGIO. However, the impact ANGIO has on splenic salvage remains unclear with little contemporary data.

Methods:
The National Trauma Data Bank was used to identify patients 18 years and older with high-grade BSI (Abbreviated Injury Scale >II) treated at Level I or II trauma centers between 2008 and 2014. Primary outcomes included yearly rates of splenectomy, which was defined as early if performed within 6 hours of ED admission and delayed if greater than 6 hours, ANGIO, and mortality. Trends were studied over time with hierarchical regression models.

Results:
There were 53,689 patients who had high-grade BSI over the study period. There was no significant difference in the adjusted rate of overall splenectomy over time (24.3% in 2008, 24.3% in 2014, P value = 0.20). The use of ANGIO rapidly increased from 5.3% in 2008 to 13.5% in 2014 (P value < 0.001). Mortality was similar overtime (8.7% in 2008, 9.0% in 2014, P value = 0.33).

Conclusion:
Over the last 7 years, the rate of angiography has been steadily rising while the overall rate of splenectomy has been stable. The lack of improved overall splenic salvage, despite increased ANGIO, calls into question the role of ANGIO in splenic salvage on high-grade BSI at a national level.
Imaging morphogenesis
Authors: Bell Donald M. 
Published: March 2017

The hostile environment of the microscope stage poses numerous challenges to successful imaging of morphogenesis in live tissues. This review aims to highlight some of the main practical considerations to take into account when embarking on a project to image cell behaviour in the context of cells' normal surroundings. Scrutiny of these activities is likely to be the most informative approach to understanding mechanical morphogenesis but is often confounded by the substantial technical difficulties involved in imaging samples over extended periods of time. Repeated observation of cells in live tissue requires that strategies be adopted to prioritize the stability of the sample, ensuring that it remains viable and develops normally while being held in a manner accessible to microscopic examination. Key considerations when creating reliable protocols for time-lapse imaging may be broken down into three main criteria; labelling, mounting and image acquisition. Choices and compromises made here, however, will directly influence image quality, and even small refinements can substantially improve what information may be extracted from images. Live imaging of tissue is difficult but paying close attention to the basics along with a little innovation is likely to be well rewarded.
This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’.
Vertex models: from cell mechanics to tissue morphogenesis
Authors: Alt Silvanus , Ganguly Poulami , Salbreux Guillaume 
Published: March 2017

Tissue morphogenesis requires the collective, coordinated motion and deformation of a large number of cells. Vertex model simulations for tissue mechanics have been developed to bridge the scales between force generation at the cellular level and tissue deformation and flows. We review here various formulations of vertex models that have been proposed for describing tissues in two and three dimensions. We discuss a generic formulation using a virtual work differential, and we review applications of vertex models to biological morphogenetic processes. We also highlight recent efforts to obtain continuum theories of tissue mechanics, which are effective, coarse-grained descriptions of vertex models.
This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’.
Cellular systems for epithelial invagination
Authors: Pearl Esther J. , Li Jingjing , Green Jeremy B. A. 
Published: March 2017

Epithelial invagination is a fundamental module of morphogenesis that iteratively occurs to generate the architecture of many parts of a developing organism. By changing the physical properties such as the shape and/or position of a population of cells, invagination drives processes ranging from reconfiguring the entire body axis during gastrulation, to forming the primordia of the eyes, ears and multiple ducts and glands, during organogenesis. The epithelial bending required for invagination is achieved through a variety of mechanisms involving systems of cells. Here we provide an overview of the different mechanisms, some of which can work in combination, and outline the circumstances in which they apply.This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’.
Parallel evolution of sperm hyper-activation Ca2+channels
Authors: Cooper Jacob C. , Phadnis Nitin 
Published: March 2017

AbstractSperm hyper-activation is a dramatic change in sperm behavior where mature sperm burst into a final sprint in the race to the egg. The mechanism of sperm hyper-activation in many metazoans, including humans, consists of a jolt of Ca2+into the sperm flagellum via CatSper ion channels. Surprisingly,CatSpergenes have been independently lost in several animal lineages. InDrosophila, sperm hyper-activation is performed through the co-option of the polycystic kidney disease 2 (Dpkd2) Ca2+channel. The parallels betweenCatSpersin primates andDpkd2inDrosophilaprovide a unique opportunity to examine the molecular evolution of the sperm hyper-activation machinery in two independent, nonhomologous calcium channels separated by more than 500 million years of divergence. Here, we use a comprehensive phylogenomic approach to investigate the selective pressures on these sperm hyper-activation channels. First, we find that the entireCatSpercomplex evolves rapidly under recurrent positive selection in primates. Second, we find thatpkd2has parallel patterns of adaptive evolution inDrosophila. Third, we show that this adaptive evolution ofpkd2is driven by its role in sperm hyper-activation. These patterns of selection suggest that the evolution of the sperm hyper-activation machinery is driven by sexual conflict with antagonistic ligands that modulate channel activity. Together, our results add sperm hyper-activation channels to the class of fast evolving reproductive proteins and provide insights into the mechanisms used by the sexes to manipulate sperm behavior.
ClusterEnG: An interactive educational web resource for clustering big data
Authors: Manjunath Mohith , Zhang Yi , Yeo Steve H. , Sobh Omar , Russell Nathan , Followell Christian , Bushell Colleen , Ravaioli Umberto , Song Jun S. 
Published: March 2017

AbstractSummaryClustering is one of the most common techniques used in data analysis to discover hidden structures by grouping together data points that are similar in some measure into clusters. Although there are many programs available for performing clustering, a single web resource that provides both state-of-the-art clustering methods and interactive visualizations is lacking. ClusterEnG (acronym for Clustering Engine for Genomics) provides an interface for clustering big data and interactive visualizations including 3D views, cluster selection and zoom features. ClusterEnG also aims at educating the user about the similarities and differences between various clustering algorithms and provides clustering tutorials that demonstrate potential pitfalls of each algorithm. The web resource will be particularly useful to scientists who are not conversant with computing but want to understand the structure of their data in an intuitive manner.AvailabilityClusterEnG is part of a bigger project called KnowEnG (Knowledge Engine for Genomics) and is available athttp://education.knoweng.org/clustereng.Contactsongi@illinois.edu
Primary souring: a novel bacteria-free method for sour beer production
Authors: Osburn Kara , Amaral Justin , Metcalf Sara R. , Nickens David M. , Rogers Cody M. , Sausen Christopher , Caputo Robert , Miller Justin , Li Hongde , Tennessen Jason M. , Bochman Matthew L. 
Published: March 2017

AbstractIn the beverage fermentation industry, especially at the craft or micro level, there is a movement to incorporate as many local ingredients as possible to both capture terroir and stimulate local economies. In the case of craft beer, this has traditionally only encompassed locally sourced barley, hops, and other agricultural adjuncts. The identification and use of novel yeasts in brewing lags behind. We sought to bridge this gap by bio-prospecting for wild yeasts, with a focus on the American Midwest. We isolated 284 different strains from 54 species of yeast and have begun to determine their fermentation characteristics. During this work, we found several isolates of five species that produce lactic acid and ethanol during wort fermentation:Hanseniaspora vineae,Lachancea fermentati,Lachancea thermotolerans,Schizosaccharomyces japonicus, andWickerhamomyces anomalus. Tested representatives of these species yielded excellent attenuation, lactic acid production, and sensory characteristics, positioning them as viable alternatives to lactic acid bacteria (LAB) for the production of sour beers. Indeed, we suggest a new LAB-free paradigm for sour beer production that we term “primary souring” because the lactic acid production and resultant pH decrease occurs during primary fermentation, as opposed to kettle souring or souring via mixed culture fermentation.Chemical compounds studied in this article:Lactic acid (PubChem CID: 612); Ethanol (PubChem CID: 702)Abbreviations:ABV, alcohol by volume; DIC, differential interference contrast; EtOH, ethanol; FG, final gravity; gDNA, genomic DNA; IBU, international bittering unit; LAB, lactic acid bacteria; LASSO, lactic acid specific soft-agar overlay; N-J, neighbor-joining; OG, original gravity; WLN, Wallerstein Laboratories nutrient; YPD, yeast extract, peptone, and dextrose
Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape
Authors: Swaminathan Anandh , Poole William , Pandey Ayush , Hsiao Victoria , Murray Richard M. 
Published: March 2017

AbstractIn systems and synthetic biology, it is common to build chemical reaction network (CRN) models of biochemical circuits and networks. Although automation and other high-throughput techniques have led to an abundance of data enabling data-driven quantitative modeling and parameter estimation, the intense amount of simulation needed for these methods still frequently results in a computational bottleneck. Here we present bioscrape (Bio-circuit Stochastic Single-cell Reaction Analysis and Parameter Estimation) - a Python package for fast and flexible modeling and simulation of highly customizable chemical reaction networks. Specifically, bioscrape supports deterministic and stochastic simulations, which can incorporate delay, cell growth, and cell division. All functionalities - reaction models, simulation algorithms, cell growth models, partioning models, and Bayesian inference - are implemented as interfaces in an easily extensible and modular object-oriented framework. Models can be constructed via Systems Biology Markup Language (SBML) or specified programmatically via a Python API. Simulation run times obtained with the package are comparable to those obtained using C code - this is particularly advantageous for computationally expensive applications such as Bayesian inference or simulation of cell lineages. We first show the package’s simulation capabilities on a variety of example simulations of stochastic gene expression. We then further demonstrate the package by using it to do parameter inference on a model of integrase enzyme-mediated DNA recombination dynamics with experimental data. The bioscrape package is publicly available online (https://github.com/biocircuits/bioscrape) along with more detailed documentation and examples.
Cycad coralloid roots contain bacterial communities including cyanobacteria andCaulobacterspp that encode niche-specific biosynthetic gene clusters
Authors: Gutiérrez-García Karina , Bustos-Díaz Edder D. , Corona-Gómez José Antonio , Ramos-Aboites Hilda E. , Sélem-Mojica Nelly , Cruz-Morales Pablo , Pérez-Farrera Miguel A. , Barona-Gómez Francisco , Cibrián-Jaramillo Angélica 
Published: March 2017

AbstractCycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species fromDioon(Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, includingBradyrhizobium, Burkholderia, Mesorhizobium, Nostoc, andRhizobiumspecies, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities and used for whole-genome inferences that suggest twoDioon-specific monophyletic groups and a level of specialization characteristic of co-evolved symbiotic relationships. In agreement with this, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with metabolite profiling using multiphoton excitation fluorescence microscopy, we also show thatCaulobacterspecies co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.
DNA-dependent protein synthesis exhibited by cancer shed particulates
Authors: Ulaganathan Vijay K. , Ullrich Axel 
Published: March 2017

AbstractGenetic heterogeneity in tumours is the bonafide hallmark applicable to all cancer types (Burrell et al, 2013). Furthermore, deregulated ribosome biogenesis and elevated protein biosynthesis have been consistently associated with multiple cancer types (Ruggero, 2012; Ruggero & Pandolfi, 2003). We observed that under cultivation conditions almost all cancer cell types actively shed significant amount of particulates as compared to non-malignant cell lines requiring frequent changing of cultivation media. We therefore asked if cancer cell shed particulates might still retain biological activity associated with protein biosynthesis. Here, we communicate our observations of DNA-dependent protein biosynthetic activity exhibited by the cell-free particulates shed by the cancer cell lines. Using pulsed isotope labelling approach we confirmed the cell-free protein translation activity exhibited by particulates shed by various cancer cell lines. Interestingly, the bioactivity was largely dependent on temperature, pH and on 3’-DNA elements. Our results demonstrate that cancer shed particulates are biologically active and may potentially drive expression of tissue non-specific promoters in distant organs.
Corrosion of copper exposed to Zhanjiang and Zhuhai atmospheric environments
Authors: Su Wei , Lv Wangyan , Liu Zhengchun , Zhang Zengguang 
Published: March 2017

Purpose
The aim of this paper was to study the initial corrosion behavior of copper in the substations of Zhanjiang and Zhuhai.

Design/methodology/approach
The copper exposed at the substation of Guangdong coastal region in southern China for up to 12 months. The rust layer formed on the copper has been examined by scanning electron microscopy, X-ray energy spectrum, X-ray diffraction and electrochemical polarization techniques.

Findings
The corrosion weight loss of copper at Zhanjiang exposure site is a little more serious than that at Zhuhai exposure site in every exposure period. The corrosion products of copper have different changes in color and composition at the two exposure sites. The tensile strength of copper has a slight decrease after one-year exposure.

Originality/value
The atmospheric exposure experiments of copper in the substations of Zhanjiang and Zhuhai have been adopted for the first time. The corrosion behavior of copper was investigated, and it can provide reference for material selection of the substation.
Performance of Ni–Cu–ZrO2nanocomposite coatings fabricated by electrodeposition technique
Authors: Abdel Hamid Z. , El-Etre A.Y. , Fareed M. 
Published: March 2017

PurposeThe purpose of this study is to investigate the effect of the incorporated zirconia (ZrO2) nanoparticles on the performance of the deposited layer Ni–Cu alloy on steel sheet.Design/methodology/approachThe aim was to produce Ni–Cu–ZrO2nanocomposite coatings by electrodeposition technique and estimate the influence of ZrO2 nanoparticles on the performance of Ni–Cu alloy. The surface morphologies and chemical compositions of the deposited layers were assessed using scanning electron microscopy and energy-dispersive X-ray analysis, respectively. Nanoindentation was used as a well-advanced technique for measuring microhardness and Young’s modulus values of different coatings. The corrosion resistance in 3.5 per cent NaCl solution of electrodeposited films has been investigated.FindingsThe main conclusion is that the surface morphologies of Ni–Cu–ZrO2 nanocomposite coatings were fine granular compared with Ni–Cu alloy. The corrosion behavior illustrated that the incorporation of ZrO2nanoparticles with Ni–Cu film improved the corrosion resistance. Significant improvement was also demonstrated in the hardness of nanocomposite coatings.Social implicationsThe optimized industrial use of steel-coated Ni–Cu alloy with super properties. Consequently, a social benefit can be associated with the reduction in the corrosion rate and increases the microhardness and Young’s modulus.Originality/valueThe results presented in this work are an insight into understanding the incorporation of ceramic reinforcement with metal or alloy films (matrix) on carbon steel using the electrodeposition technique. The development of corrosion resistance of Ni–Cu alloys has been considered as a promising behavior. In this work, a consistent assessment of the results achieved on laboratory scale has been conducted.
Mediating effects of students’ social bonds between self-esteem and customer citizenship behaviour in the context of international university branch campuses
Authors: Tan VieMing , Quoquab Farzana , Ahmad Fauziah Sh. , Mohammad Jihad 
Published: March 2017

PurposeThe purpose of this paper is to offer empirical evidence on the role of self-esteem and social bonding in explaining citizenship behaviour of students at international university branch campuses (IBCs).Design/methodology/approachA sample of 400 students from four IBCs in Malaysia was administered in a questionnaire. Data were analysed using SPSS and partial least squares 3.0.FindingsThis research demonstrates that students’ self-esteem and social bonds have positive direct effects on customer citizenship behaviour (CCB). Moreover, self-esteem has an indirect effect on CCB via intervening of attachment, commitment and involvement of social bonds.Research limitations/implicationsCCB of IBC students can be explained by self-consistency theory via mediation of social bonds from social bonding theory.Practical implicationsTo encourage CCB in IBCs, university management should target students who have high self-esteem, closely tied to parents and lecturers, committed to university, highly involved in co-curricular activities and comply with university regulations.Originality/valueGreater understanding of students’ citizenship behaviour may help transnational universities to improve relationship marketing strategy and enhance students’ campus experience.
Cosmopolitanism and ethnocentrism among young consumers in emerging Asia
Authors: Han C. Min 
Published: March 2017

Purpose
The purpose of this paper is to investigate how consumer cosmopolitanism (COS) and consumer ethnocentrism (CET) may affect young populations in China (an emerging country) and Korea (an advanced emerging country) on their evaluations of Japanese brands.

Design/methodology/approach
The author hypothesize that the levels and the effects of COS and CET will differ between China and Korea because of their differing levels of economic development and globalization. Surveys were conducted with 311 Chinese and Korean young individuals with comparable sample characteristics.

Findings
The research reveals a few interesting findings. First, the findings show that Chinese young consumers may be more ethnocentric and moderately less cosmopolitan than their Korean counterparts. Additionally, COS was found to have greater effects on evaluations of Japanese brands in China than in Korea. On the other hand, CET played a subdued role in brand evaluations for both countries.

Research limitations/implications
The findings suggest that COS and CET may have reduced influences on future consumers in emerging Asia and other emerging countries as they experience increasing globalization.

Originality/value
This study addresses an under-researched issue of how consumer values may change in emerging Asia experiencing rapid economic development and globalization.