bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond autoantibodies: Biological roles of human autoreactive B cells in rheumatoid arthritis revealed by whole transcriptome profiling
Authors: Mahendra Ankit , Yang Xingyu , Abnouf Shaza , Park Daechan , Soomro Sanam , Adolacion Jay RT , Roszik Jason , Coarfa Cristian , Romain Gabrielle , Wanzeck Keith , Bridges S. Louis , Aggarwal Amita , Qiu Peng , Agarwal Sandeep Krishna , Mohan Chandra , Varadarajan Navin 
Published: June 2017

AbstractAlthough the contribution of B-cell derived autoreactive antibodies to rheumatoid arthritis (RA) has been studied extensively, the autoantibody-independent roles of B cells in the progression of the disease is not well-defined. Here we present the first comprehensive transcriptome profile of human autoreactive B cells in an autoimmune disease by performing RNA-sequencing of citrulline-specific B cells from RA patients. In order to facilitate a comprehensive understanding of the profile of these citrulline-specific (RA-CCPPOS) B cells, we performed comparative analyses to both citrulline-negative (RA-CCPNEG) B cells from the same donors, and identified 431 differentially expressed genes (DEGs); and hemagglutinin-specific (HA) B cells from healthy individuals and identified 1658 DEGs. Three-way comparisons of these B cell populations demonstrated that RA-CCPPOSB cells, in comparison to the RA-CCPNEGB cells, demonstrate a potential role in protein citrullination and inflammation; RA-CCPPOSB cells in comparison to HA-specific B cells demonstrate RA-specific signatures like the expression of pro-inflammatory cytokines, chemokines, costimulatory molecules and B-cell activation cascades; and all B cells from RA patients demonstrated a significant impact of the multitude of TNF signaling pathways. Furthermore, transcription factor profiling suggested that cyclic AMP (cAMP) related pathways and downstream signaling molecules are selectively enriched in RA-CCPPOScells in comparison to the other two B cell subsets. We advanced the understanding of the citrulline reactive B cells in RA pathophysiology by documenting and validating two novel observations in independent cohorts of patients: (1) the expression of IL15Rα is restricted to citrulline-specific cells within RA patients and the concentration of soluble IL15Rα is elevated in the sera of RA patients, (2) B cells from RA patients are capable of producing epidermal growth factor ligand, amphiregulin (AREG) which in turn has a direct impact on the mechanistic effectors of RA, osteoclasts and fibroblastlike synoviocytes (FLS). Overall, our comprehensive dataset identifies several existing FDA-approved drugs that can potentially be repurposed for RA and can serve as a foundation for studying the multi-faceted roles of B cells in other autoimmune diseases.
Contextual Tumor Suppressor Function of T Cell Death-Associated Gene 8 (TDAG8) in Hematological Malignancies
Authors: Justus Calvin R. , Sanderlin Edward J. , Dong Lixue , Sun Alice , Chi Jen-Tsan , Lertpiriyapong Kvin , Yang Li V. 
Published: June 2017

Key points1. TDAG8 (GPR65) gene expression is down-regulated in hematological malignancies.2. Restoration of TDAG8 gene expression in blood cancer cells suppresses tumor growth and metastasis.AbstractExtracellular acidosis is a condition found within the tumor microenvironment due to inadequate blood perfusion, hypoxia, and altered tumor cell metabolism. Acidosis has pleiotropic effects on malignant progression; therefore it is essential to understand how acidosis exerts its diverse effects. In this study a bioinformatics analysis revealed the expression of the proton sensing G-protein-coupled receptor TDAG8 is significantly reduced in human blood cancers in comparison to normal blood cells. To understand how TDAG8 functions in hematological malignancies, TDAG8 expression was restored in U937 acute myeloid leukemia cells and other blood cancer cells. It was discovered that severe acidosis, pH 6.4, inhibited U937 cell proliferation while mild acidosis, pH 6.9, stimulated cell proliferation. However, restoring TDAG8 gene expression modulated the U937 cell response to mild extracellular acidosis and physiological pH by reducing cell proliferation. Tumor xenograft experiments further revealed that restoring TDAG8 expression in U937 and Ramos cancer cells reduced tumor growth. It was also shown U937 cells with restored TDAG8 expression attached less to Matrigel, migrated slower toward a chemoattractant, and metastasized less in severe combined immunodeficient mice. These effects correlated with a reduction in c-myc oncogene expression. The mechanistic investigation indicated that Gα13/RhoA signaling arbitrated the TDAG8-mediated c-myc oncogene repression in response to acidosis. Overall, this study provides compelling data to support the concept that TDAG8 functions as a contextual tumor suppressor in hematological malignancies and sensitizes blood cancer cells to acidotic stress.
Reproducible Bioconductor Workflows Using Browser-based Interactive Notebooks and Containers
Authors: Almugbel Reem , Hung Ling-Hong , Hu Jiaming , Almutairy Abeer , Ortogero Nicole , Tamta Yashaswi , Yeung Ka Yee 
Published: June 2017

ABSTRACTObjectiveBioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, to allow users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server.Materials and methodsWe present three different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets and process RNA-seq data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need for installation of any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder.ResultsBiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods.ConclusionGiven the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as ubiquitous and necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols.
Structural propensity database of proteins
Authors: Tamiola Kamil , Heberling Matthew M , Domanski Jan 
Published: June 2017

AbstractAn overwhelming amount of experimental evidence suggests that elucidations of protein function, interactions, and pathology are incomplete without inclusion of intrinsic protein disorder and structural dynamics. Thus, to expand our understanding of intrinsic protein disorder, we have created a database of secondary structure (SS) propensities for proteins (dSPP) as a reference resource for experimental research and computational biophysics. The dSPP comprises SS propensities of 7,094 unrelated proteins, as gauged from NMR chemical shift measurements in solution and solid state. Here, we explain the concept of SS propensity and analyze dSPP entries of therapeutic relevance,α-synuclein, MOAG-4, and the ZIKA NS2B-NS3 complex to show: (1) how propensity mapping generates novel structural insights into intrinsically disordered regions of pathologically relevant proteins, (2) how computational biophysics tools can benefit from propensity mapping, and (3) how the residual disorder estimation based on NMR chemical shifts compares with sequence-based disorder predictors. This work demonstrates the benefit of propensity estimation as a method that reports both on protein structure, lability, and disorder.
Social responsibility in a troubled world
Authors: Anderson Verl , Ndalamba Ken Kalala , Caldwell Cam 
Published: June 2017

Purpose
Social responsibility (SR) in accepting the obligation to resolve the many troubling problems facing tomorrow’s generations is essential if those problems are to be effectively addressed. The purpose of this paper is to identify the nature of SR for business, academic institutions, government, religious institutions, and individuals.

Design/methodology/approach
This paper is a conceptual paper which relies heavily on the current literature about social obligations for five major organizations: business, academic institutions, government, religious institutions, and individuals.

Findings
The paper provides the standard of the virtuous continuum and the Hosmer decision-making model to explain why leaders, organizations, and individuals must be more responsible to be perceived as virtuous leaders, complete with 50 examples of action to be taken.

Research limitations/implications
As this paper is not an empirical study, it does not present research information.

Practical implications
This paper suggests that organizations can be more effective if they come to understand the responsibilities and stewardship of social responsibilities entrusted to them.

Originality/value
The paper expands on Hosmer’s research and incorporates a virtuous continuum in examining the responsibilities of leaders, organizations, and individuals. More importantly, this paper is among the first to identify specific steps organizations and individuals can take in addressing the challenges and problems facing the world of in key aspects of society.
Exploring the gap between policy and practice in private branding strategy management in an emerging market
Authors: Herstein Ram , Drori Netanel , Berger Ron , Barnes Bradley R. 
Published: June 2017

PurposePrivate-label goods are now available in more than 55 countries worldwide and their total sales value is estimated to be in excess of one trillion US dollars. The prevalence of such goods, however, drastically differs across countries. Whilst market share in some developed economies exceeds 50 percent, penetration appears much lower in emerging economies. The purpose of this paper is to investigate marketing issues surrounding such low-penetration levels in emerging markets.Design/methodology/approachIn-depth interviews were conducted with: 36 store managers and the marketing director of a large emerging market retail chain.FindingsEight factors were found to impede the retail chain’s vision regarding implementation of the private branding strategy.Practical implicationsSeveral implications are extracted from the study, mainly in the context of emerging markets that managers should consider in order to improve their private branding strategies.Originality/valueAlthough some research has aimed to shed light concerning the significance of private brands from retailers’ perspectives, such research has not tended to address the issue of how to implement private brand strategies in emerging markets. To bridge the gap, this study investigates these issues from a retail chain management perspective in order to potentially leverage performance advantages associated with the nurturing of private-label branded goods.
Do luxury brands successfully entice consumers? The role of bandwagon effect
Authors: Shaikh Shayan , Malik Aneela , Akram M.S. , Chakrabarti Ronika 
Published: June 2017

Purpose
The purpose of this paper is to explore the underlying motivations for bandwagon luxury brand consumption among consumers of an emergent market by empirically investigating the effects of consumers’ interdependent and independent orientations on their personality traits, such as conformity, need for uniqueness and status consumption, which in turn affect their bandwagon luxury brand consumption.

Design/methodology/approach
A paper-based survey method is used to collect data from more than 400 Pakistani consumers indulging in bandwagon luxury brand consumption. The model is estimated through structural equation modeling.

Findings
The results show that individuals’ personality traits significantly affect their bandwagon luxury brand consumption. Further, the results suggest that the relationship between individuals’ interdependent/independent orientation and bandwagon luxury brand consumption is partially/fully mediated by their personality traits.

Research limitations/implications
These findings offer insights into consumers’ perceptions about bandwagon luxury brand consumption and provide useful managerial implications for the managers/marketers to build reputable luxury brands.

Originality/value
This research contributes to the literature by investigating the mediating role of consumers’ personality traits in the relationship between their interdependent/independent orientation and bandwagon luxury brand consumption behavior. There is scant literature on bandwagon luxury brand consumption, especially in the context of collectivistic society where the proposed framework has been empirically tested.
Finding beneficiaries: trade adjustment assistance system in South Korea
Authors: Song Joon-heon 
Published: June 2017

Purpose
The purpose of this study is to explore the essential cause for the policy failure of Trade Adjustment Assistance (TAA) in South Korea.

Design/methodology/approach
To substantiate the claims made for the failure of the policy, this paper focuses on the differences in policy preferences among the government ministries and agencies involved in TAA.

Findings
The failure in the TAA policy, according to this study, was attributed to the conflicts and miscoordination arising from the differences in policy preferences among government ministries and agencies. To rectify this failure, the South Korean government had to revise its laws and regulations several times over a short period.

Originality/value
Drawing on the analytical framework of the literature on policy failure, this paper examines the causal relationships between outcomes of TAA policy and the conflicts or miscoordination among government bodies at each stage: initiatives and planning, implementation and operation of the policy.
Anti-persistence and long-memory behaviour of SAREITs
Authors: Ijasan Kolawole , Tweneboah George , Mensah Jones Odei 
Published: June 2017

PurposeThe purpose of this paper is to provide empirical evidence on the long-memory behaviour of South African real estate investment trusts (SAREITs).Design/methodology/approachThe study employs a battery of advanced techniques to examine the behaviour of returns of 29 SAREIT equities listed on the Johannesburg Stock Exchange. The authors analysed daily closing prices covering different periods up to 21 May 2016. The results provide support for long memory in majority of SAREIT returns.FindingsThe finding of negative fractional integration parameters provides evidence of anti-persistence in SAREIT returns.Practical implicationsIt is recommended that the regulatory authorities adopt technologies that allow a more effective, faster means to disseminate information, and improve the electronic trading mechanism that facilitates quicker price adjustment to news entering the market.Originality/valueThe paper determines the fractional differencing (long-memory) parameter for SAREITs and adds value to the existing body of knowledge.
Conversion of cis‐2‐carboxycyclohexylacetyl‐CoA in the downstream pathway of anaerobic naphthalene degradation
Authors: Weyrauch Philip , Zaytsev Andrey V. , Stephan Susanne , Kocks Lena , Schmitz Oliver J. , Golding Bernard T. , Meckenstock Rainer U. 
Published: June 2017

SummaryThe cyclohexane derivative cis‐2‐(carboxymethyl)cyclohexane‐1‐carboxylic acid [(1R,2R)‐/(1S,2S)‐2‐(carboxymethyl)cyclohexane‐1‐carboxylic acid] has previously been identified as metabolite in the pathway of anaerobic degradation of naphthalene by sulfate‐reducing bacteria. We tested the corresponding CoA esters of isomers and analogues of this compound for conversion in cell free extracts of the anaerobic naphthalene degraders Desulfobacterium strain N47 and Deltaproteobacterium strain NaphS2. Conversion was only observed for the cis‐isomer, verifying that this is a true intermediate and not a dead‐end product. Mass‐spectrometric analyses confirmed that conversion is performed by an acyl‐CoA dehydrogenase and a subsequent hydratase yielding an intermediate with a tertiary hydroxyl‐group. We propose that a novel kind of ring‐opening lyase is involved in the further catabolic pathway proceeding via pimeloyl‐CoA. In contrast to degradation pathways of monocyclic aromatic compounds where ring‐cleavage is achieved via hydratases, this lyase might represent a new ring‐opening strategy for the degradation of polycyclic compounds. Conversion of the potential downstream metabolites pimeloyl‐CoA and glutaryl‐CoA was proved in cell free extracts, yielding 2,3‐dehydropimeloyl‐CoA, 3‐hydroxypimeloyl‐CoA, 3‐oxopimeloyl‐CoA, glutaconyl‐CoA, crotonyl‐CoA, 3‐hydroxybutyryl‐CoA and acetyl‐CoA as observable intermediates. This indicates a link to central metabolism via β‐oxidation, a non‐decarboxylating glutaryl‐CoA dehydrogenase and a subsequent glutaconyl‐CoA decarboxylase.
Advantages of the modified double ring areolar incision over the traditional areolar incision in multicentric breast fibroadenoma surgery
Authors: Zhang Mingliang , Shen Gongjin , Zhang Song , Cui Zhen , Qian Jun 
Published: June 2017

BackgroundThis study was conducted to investigate the clinical advantages of modified double ring areola incision (MDRAI) compared to ordinary areola incision (OAI) in multicentric breast fibroadenoma in women.MethodsSixty cases of multicentric benign breast tumor were recruited from the First Affiliated Hospital of Bengbu Medical College from January to December 2016. The cases were divided into two groups according to surgical approach: MDRAI (n = 20) and OAI (n = 40). The operation duration, intraoperative blood loss, drainage time, and postoperative recurrence rate in the first six months were compared.ResultsThe mean age and tumor locations were not statistically different between the groups (P > 0.05). However, more lesions and larger tumor diameter were found in the MDRAI group than in the OAI group, with statistical difference (P < 0.05). The operation duration and drainage time of the two groups were not statistically different for unilateral or bilateral lesions (P > 0.05). However, the intraoperative blood loss was statistically different between the two groups (P < 0.05). All 60 cases received six months of follow‐up. Eight recurrent cases were found in the OAI group, but none in the MDRAI group. The recurrence rate was significantly different (χ2 = 4.62, P < 0.05).ConclusionCompared with OAI, MDRAI offers greater advantages in the aspects of blood loss and recurrence for the treatment of breast benign tumor, especially for multicentric larger lesions.
Estradiol inhibits hepatic stellate cell area and collagen synthesis in the chicken liver
Authors: Nishimura Shotaro , Teshima Akifumi , Kawabata Fuminori , Tabata Shoji 
Published: June 2017

AbstractHepatic stellate cells (HSCs) are the main collagen‐producing cells in the liver. The HSC area and amount of collagen fibers are different between male and female chickens. This study was performed to confirm the effect of estradiol on collagen synthesis in the growing chicken liver. Blood estradiol levels in chicks were compared at 4 and 8 weeks of age, and the collagen fibril network in liver tissue was observed at 8 weeks by scanning electron microscopy. Intraperitoneal administrations of estradiol and tamoxifen to male and female chicks, respectively, were performed daily from 5 to 8 weeks of age. The areas of HSCs and collagen contents were measured in the liver tissue. The blood estradiol level was higher in females than in males, and the collagen fibril network was denser in males than in females at 8 weeks of age. Estradiol administration in males induced decreases in the HSC area and collagen content of the liver. Conversely, tamoxifen administration in females induced an increase in the HSC area but did not facilitate collagen synthesis. Based on these results, estradiol inhibits the area and collagen synthesis of HSCs in the growing chicken liver under normal physiological conditions.
Hindered Care: Institutional Obstructions to Carework and Professionalism in Czech Nursing
Authors: Bludau Heidi 
Published: June 2017

AbstractOver its history, while nursing responsibilities have shifted from primarily hygienic tasks (vocational work) to more medically centered duties (professional work), the work of care remains at the core of the nursing profession. Nurses judge themselves and each other as professionals based on how well they are able to care for the patients in their charge. A professional nurse's ability to care centers on the institutional environment in which she works. Using an ethnographic case study of Czech nurses as migrants, this article explores how the discourse of care work enables nurses to examine their professional identities in different institutional contexts, that of their native Czech Republic and in foreign workplaces. At its foundation, I explore what happens when the institutional setting in which caring is supposed to take place hinders the production of caring practices.
Breastfeeding Support: From Informal Care Work to Professional Health‐Care Work
Authors: Eden Aimee R. 
Published: June 2017

AbstractBreastfeeding care work performed informally in the “private” domain by female kin and community largely disappeared in the United States after the emergence of artificial infant formula as a safe breast‐milk substitute at the turn of the nineteenth century. Infant formula feeding became the cultural norm, accompanied by the loss of experiential breastfeeding knowledge. Breastfeeding care work was transformed in the 1950s by volunteer mother‐to‐mother support groups formalized by La Leche League (LLL). In the 1980s, LLL drove the creation of a new allied health‐care professional: the International Board Certified Lactation Consultant (IBCLC). Drawing on interviews with 17 founders of the profession and 30 practicing IBCLCs, as well as on clinical observations of three IBCLCs working in different institutional settings and a content analysis of the professional journal, this ethnohistorical study explores the construction of expert knowledge and the implications of the professionalization of breastfeeding care work on IBCLC practice.