bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of Binding Interaction between Pif80 Protein Fragment and Aragonite
Authors: Du Yuan-Peng , Chang Hsun-Hui , Yang Sheng-Yu , Huang Shing-Jong , Tsai Yu-Ju , Huang Joseph Jen-Tse , Chan Jerry Chun Chung 
Published: August 2016

AbstractPif is a crucial protein for the formation of the nacreous layer inPinctada fucata. Three non-acidic peptide fragments of the aragonite-binding domain (Pif80) are selected, which contain multiple copies of the repeat sequence DDRK, to study the interaction between non-acidic peptides and aragonite. The polypeptides DDRKDDRKGGK (Pif80-11) and DDRKDDRKGGKDDRKDDRKGGK (Pif80-22) have similar binding affinity to aragonite. Solid-state NMR data indicate that the backbones of Pif80-11 and Pif80-22 peptides bound on aragonite adopt a random-coil conformation. Pif80-11 is a lot more effective than Pif80-22 in promoting the nucleation of aragonite on the substrate of β-chitin. Our results suggest that the structural arrangement at a protein-mineral interface depends on the surface structure of the mineral substrate and the protein sequence. The side chains of the basic residues, which function as anchors to the aragonite surface, have uniform structures. The role of basic residues as anchors in protein-mineral interaction may play an important role in biomineralization.
Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma
Authors: Zhong Zhenyu , Lv Mengxin , Chen Junxia 
Published: August 2016

AbstractCircular RNAs (circRNAs), a kind of non-coding RNAs, have shown large capabilities in gene regulation. However, the mechanisms underlying circRNAs remain largely unknown so far. Recent studies demonstrated that circRNAs play miRNA sponge effects and regulate gene expression by microRNA response elements. Here, we screened circRNA expression profiles of bladder carcinoma using microarray assay. A total of 469 dysregulated circular transcripts are found in bladder cancer compared with normal tissues, among which 285 were up-regulated and 184 were down-regulated. Six circRNAs were identified to have significant differences by qRT-PCR. We speculated that circRNAs might involve in cancer-related pathways via interactions with miRNA by multiple bioinformatical approaches. Therefore, we further predicted that circTCF25 could sequester miR-103a-3p/miR-107, which potentially lead to the up-regulation of thirteen targets related to cell proliferation, migration and invasion. Subsequently, we demonstrated that over-expression of circTCF25 could down-regulate miR-103a-3p and miR-107, increase CDK6 expression and promote proliferation and migration in vitro and vivo. This is the first study to exploit circRNA profiling and circRNA/miRNA interactions in bladder cancer. Our work laid the foundation to investigate the functions of circRNAs in cancers. The data also suggest that circTCF25 might be a new promising marker for bladder cancer.
Agglutinating mouse IgG3 compares favourably with IgMs in typing of the blood group B antigen: Functionality and stability studies
Authors: Klaus Tomasz , Bzowska Monika , Kulesza Małgorzata , Kabat Agnieszka Martyna , Jemioła-Rzemińska Małgorzata , Czaplicki Dominik , Makuch Krzysztof , Jucha Jarosław , Karabasz Alicja , Bereta Joanna 
Published: August 2016

AbstractMouse immunoglobulins M (IgMs) that recognize human blood group antigens induce haemagglutination and are used worldwide for diagnostic blood typing. Contrary to the current belief that IgGs are too small to simultaneously bind antigens on two different erythrocytes, we obtained agglutinating mouse IgG3 that recognized antigen B of the human ABO blood group system. Mouse IgG3 is an intriguing isotype that has the ability to form Fc-dependent oligomers. However, F(ab′)2 fragments of the IgG3 were sufficient to agglutinate type B red blood cells; therefore, IgG3-triggered agglutination did not require oligomerization. Molecular modelling indicated that mouse IgG3 has a larger range of Fab arms than other mouse IgG subclasses and that the unique properties of mouse IgG3 are likely due to the structure of its hinge region. With a focus on applications in diagnostics, we compared the stability of IgG3 and two IgMs in formulated blood typing reagents using an accelerated storage approach and differential scanning calorimetry. IgG3 was much more stable than IgMs. Interestingly, the rapid decrease in IgM activity was caused by aggregation of the molecules and a previously unknown posttranslational proteolytic processing of the μ heavy chain. Our data point to mouse IgG3 as a potent diagnostic tool.
Design and characterization of a polyamine derivative inhibiting the expression of type III secretion system in Pseudomonas aeruginosa
Authors: Wang Chao , Liu Xiaoling , Wang Jing , Zhou Jianuan , Cui Zining , Zhang Lian-Hui 
Published: August 2016

AbstractThe type III secretion system (TTSS) of Pseudomonas aeruginosa is a key virulence determinant for infection of eukaryotic hosts. Based on the findings that spermidine-mediated host-pathogen signalling is important for activation of type III secretion systems (TTSS), in this study, we designed, synthesized and evaluated a series of polyamine derivatives for their potentials in inhibiting the expression TTSS in P. aeruginosa. In vitro assay of 15 compounds synthesized in this study unveiled stringent structural requirements for TTSS-inhibitory activity. Among them, R101SPM, a conjugate between rhodamine 101 and spermine, showed a potent activity in inhibition of the TTSS gene expression and in attenuation of the TTSS-mediated cytotoxicity on human cells. In vivo analysis demonstrated that R101SPM could rescue mice from the lethal infection by P. aeruginosa. Moreover, genetic analysis showed that the full TTSS-inhibitory activity of R101SPM required a functional spermidine transporter. Taken together, our results present a new class of lead molecules for developing anti-virulence drugs and demonstrate that the spermidine transporter SpuDEGHF of P. aeruginosa is a promising drug target.
Bacterial IgA protease-mediated degradation of agIgA1 and agIgA1 immune complexes as a potential therapy for IgA Nephropathy
Authors: Wang Li , Li Xueying , Shen Hongchun , Mao Nan , Wang Honglian , Cui Luke , Cheng Yuan , Fan Junming 
Published: August 2016

AbstractMesangial deposition of aberrantly glycosylated IgA1 (agIgA1) and its immune complexes is a key pathogenic mechanism of IgA nephropathy (IgAN). However, treatment of IgAN remains ineffective. We report here that bacteria-derived IgA proteases are capable of degrading these pathogenic agIgA1 and derived immune complexes in vitro and in vivo. By screening 14 different bacterial strains (6 species), we found that 4 bacterial IgA proteases from H. influenzae, N. gonorrhoeae and N. meningitidis exhibited high cleaving activities on serum agIgA1 and artificial galactose-depleted IgA1 in vitro and the deposited agIgA1-containing immune complexes in the mesangium of renal biopsy from IgAN patients and in a passive mouse model of IgAN in vitro. In the modified mouse model of passive IgAN with abundant in situ mesangial deposition of the agIgA-IgG immune complexes, a single intravenous delivery of IgA protease from H. influenzae was able to effectively degrade the deposited agIgA-IgG immune complexes within the glomerulus, demonstrating a therapeutic potential for IgAN. In conclusion, the bacteria-derived IgA proteases are biologically active enzymes capable of cleaving the circulating agIgA and the deposited agIgA-IgG immune complexes within the kidney of IgAN. Thus, the use of such IgA proteases may represent a novel therapy for IgAN.
Tumor Growth Suppression Induced by Biomimetic Silk Fibroin Hydrogels
Authors: Yan Le-Ping , Silva-Correia Joana , Ribeiro Viviana P. , Miranda-Gonçalves Vera , Correia Cristina , da Silva Morais Alain , Sousa Rui A. , Reis Rui M. , Oliveira Ana L. , Oliveira Joaquim M. , Reis Rui L. 
Published: August 2016

AbstractProtein-based hydrogels with distinct conformations which enable encapsulation or differentiation of cells are of great interest in 3D cancer research models. Conformational changes may cause macroscopic shifts in the hydrogels, allowing for its use as biosensors and drug carriers. In depth knowledge on how 3D conformational changes in proteins may affect cell fate and tumor formation is required. Thus, this study reports an enzymatically crosslinked silk fibroin (SF) hydrogel system that can undergo intrinsic conformation changes from random coil to β-sheet conformation. In random coil status, the SF hydrogels are transparent, elastic, and present ionic strength and pH stimuli-responses. The random coil hydrogels become β-sheet conformation after 10 days in vitro incubation and 14 days in vivo subcutaneous implantation in rat. When encapsulated with ATDC-5 cells, the random coil SF hydrogel promotes cell survival up to 7 days, whereas the subsequent β-sheet transition induces cell apoptosis in vitro. HeLa cells are further incorporated in SF hydrogels and the constructs are investigated in vitro and in an in vivo chick chorioallantoic membrane model for tumor formation. In vivo, Angiogenesis and tumor formation are suppressed in SF hydrogels. Therefore, these hydrogels provide new insights for cancer research and uses of biomaterials.
Visual Outcome and Related Factors in Bilateral Total Congenital Cataract Patients: A Prospective Cohort Study
Authors: Zhang Li , Wu Xiaohang , Lin Duoru , Long Erping , Liu Zhenzhen , Cao Qianzhong , Chen Jingjing , Li Xiaoyan , Lin Zhuoling , Luo Lixia , Chen Hui , Xiang Wu , Liu Jinchao , Tan Xuhua , Qu Bo , Lin Haotian , Chen Weirong , Liu Yizhi 
Published: August 2016

AbstractThis study is to evaluate the visual outcome and identify its crucial related factors in children undergoing cataract surgery for bilateral total congenital cataract (CC). This prospective study included consecutive bilateral total cataract patients undergoing primary surgery at Zhongshan Ophthalmic Center (ZOC), Guangzhou, China from Jan 2010 to May 2014. Visual outcome was estimated by best-corrected visual acuity (BCVA) at last follow-up. Potential related factors, including gender, age at last follow-up, age at primary surgery, surgical procedure, postoperative complications (PCs), frequency of follow-up and changes in spectacles were evaluated. Eighty-eight children (176 eyes) were included in the cohort. The mean post-operative BCVA (logMAR) was 1.07 ± 0.53 at the mean follow-up duration 31.07 ± 19.36 months. Multivariable generalized estimating equations (GEEs) showed BCVA was significantly associated with PCs, age at last follow-up and age at primary surgery. Partial correlation analysis indicated age at primary surgery was positively correlated with BCVA controlling for the other factors, both for the whole age range (R = 0.415, P < 0.001) and age >6 months (R = 0.867, P < 0.001). Better visual acuity was related to early primary surgery and low PC occurrence in children with bilateral total CC. Timely surgical intervention and strict control of PCs would be potential steps to achieving better visual outcome.
Stress and Humoral Innate Immune Response of Gilthead Seabream Sparus aurata Cultured in Sea Cages
Authors: Salati Fulvio , Roncarati Alessandra , Angelucci Giulia , Fenza Alessandra , Meluzzi Adele 
Published: August 2016

Abstract
Innate and acquired immune responses of Gilthead Seabream Sparus aurata was studied under normal culture and short-term stressful conditions for 18 months in offshore sea cages in Alghero Bay, Italy. Every 45 d, 50 fish were sampled and divided into two groups: fish in the first group (normal culture conditions) were bled after harvesting; fish in the second group were put into a tank under stressful conditions (crowding and confinement) and bled after 2 h. Innate humoral immunity, such as complement-like, hemagglutination, and lysozyme activities, was determined in the sera of both groups. Pathogen challenge was not performed, but the specific humoral immune response was assessed against the most common pathogens affecting cultured fish in Sardinia. Stressed fish, compared with the control, showed a lower lysozyme activity against Vibrio (Listonella) anguillarum, which was not clearly correlated with temperatures. Complement-like activity differed between the first and second half of the study and, at the end of the trial, a slightly higher activity was recorded in the controls than in the stressed fish. Hemagglutination activity was mainly higher in the stressed fish than in control fish. Confinement, crowding, and cold water temperature caused decreased lysozyme activity in short-term stressed Gilthead Seabream compared with those reared normally. The specific humoral immune response, against V. anguillarum, Tenacibaculum mesophilum, Enterococcus Seriolicida, and Aeromonas sobria, fluctuated during the rearing period, particularly during the first year of culture.
Received October 12, 2015; accepted March 24, 2016 Published online August 2, 2016
MetaCoMET: a web platform for discovery and visualization of the core microbiome
Authors: Wang Yi , Xu Ling , Gu Yong Q. , Coleman-Derr Devin 
Published: August 2016

Motivation: A key component of the analysis of microbiome datasets is the identification of OTUs shared between multiple experimental conditions, commonly referred to as the core microbiome.
Results: We present a web platform named MetaCoMET that enables the discovery and visualization of the core microbiome and provides a comparison of the relative abundance and diversity patterns between subsets of samples within a microbiome dataset. MetaCoMET provides an efficient and interactive graphical interface for analyzing each subset defined by the union or disjunction of groups within the Venn diagram, and includes a graphical taxonomy summary, alpha diversity metrics, Principal Coordinate analysis, abundance-based heatmaps, and a chart indicating the geographic distribution of each sample.
Availability and Implementation: MetaCoMET is a user-friendly and efficient web platform freely accessible at http://probes.pw.usda.gov/MetaCoMET or http://aegilops.wheat.ucdavis.edu/MetaCoMET.
Contact: devin.coleman-derr@ars.usda.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Predicting G protein-coupled receptor downstream signaling by tissue expression
Authors: Hao Yun , Tatonetti Nicholas P. 
Published: August 2016

Motivation
G protein-coupled receptors (GPCRs) are central to how cells respond to their environment and a major class of pharmacological targets. However, comprehensive knowledge of which pathways are activated and deactivated by these essential sensors is largely unknown. To better understand the mechanism of GPCR signaling system, we integrated five independent genome-wide expression datasets, representing 275 human tissues and cell lines, with protein-protein interactions and functional pathway data.

Results
We found that tissue-specificity plays a crucial part in the function of GPCR signaling system. Only a few GPCRs are expressed in each tissue, which are coupled by different combinations of G-proteins or β-arrestins to trigger specific downstream pathways. Based on this finding, we predicted the downstream pathways of GPCR in human tissues and validated our results with L1000 knockdown data. In total, we identified 154,988 connections between 294 GPCRs and 690 pathways in 240 tissues and cell types.

Availability and Implementation
The source code and results supporting the conclusions of this article are available at http://tatonettilab.org/resources/GOTE/source_code/.

Contact
nick.tatonetti@columbia.edu

Supplementary information
Supplementary data are available at Bioinformatics online.
Knowledge, knowledge dynamics, and innovation
Authors: Scaringella Laurent 
Published: August 2016

Purpose– Knowledge is a strategic resource for firms and it can enable them to achieve competitive advantage. Large companies engaged in internationalization pay particular attention to knowledge as a source of innovation. The purpose of this paper is to investigate current debates in the field: the first is about cumulative vs composite knowledge; the second concerns the degree of diversity and redundancy in knowledge-based dynamics; and the third debate is about incremental vs radical innovation.Design/methodology/approach– The authors have used an inductive approach to perform a longitudinal case study of multinational corporation-semiconductor (MNC-SC). Total of 13 interviews were conducted over a four-year period. The MNC-SC case study has given the opportunity to analyse knowledge resources, knowledge, and innovation processes in a context of internationalization.Findings– The findings indicate that in order to achieve technological innovation in a context of internationalization, the company builds knowledge in a cumulative fashion, which can create a path dependency problem. To ensure complementarity between cross-functional teams located long distances from one another, and maximize the utilization of resources, MNC-SC must establish common standards. To maximize returns from composite knowledge, in a context of internationalization, knowledge diversity is preferable over redundancy. However, true knowledge transfer, sharing, and learning are limited. Combinatorial and incremental innovation through internationalization is a process based on trial and error; it maximizes technological performance and enables the company to fulfil needs without diverging from the technological trajectory of the SC industry.Originality/value– The internationalization process revealed limitations: limited understanding of the content of each knowledge module, competency traps, limited innovativeness, and therefore limited wealth creation.
Coping with strategic uncertainty: framework development and scenario derivation for a JV decision in the Russian truck industry
Authors: Winkler Jens , Moser Roger 
Published: August 2016

PurposeAcross country and regional borders firms are faced with the question whether to address individual markets on a stand-alone basis or cooperatively. In order to support such strategic decisions, this paper aims to develop a decision framework accounting for the most relevant market dynamics affecting joint venture (JV) decisions, particularly in the truck industry. Moreover, the authors apply the framework to an expert Delphi and scenario approach to back a Western original equipment manufacturers (OEM’s) JV decision in the truck industry in Russia. Based on country-specific projections structured along the globally applicable decision framework, the authors serve executives’ individual information demand in an institutionally unique emerging market environment.Design/methodology/approachOnline real-time expert Delphi study; scenario analysis; and expert workshops were used in this study.FindingsAmong other insights, the results predict hard times for Russian OEMs as they will likely face strong foreign competition, leading to decreased sales volumes and market shares. Although some experts doubt the survival of several Russian truck manufacturers, the Delphi sheds light on possible strategic responses, including consolidation, cooperation or focusing on new markets. Based on the Delphi results and an additional expert workshop, we draw multiple scenarios addressing, particularly, uncertain aspects of the industry’s development and their likely impact on the key stakeholder groups.Originality/valueAlthough there are some studies following a similar methodological approach as that in this study (von der Gracht and Darkow, 2010; Gnatzy and Moser, 2012), the authors break new ground in developing a JV-dedicated decision framework and applying it to a special emerging market industry setup.
The development of local private primary and secondary schooling in Hong Kong, 1841-2012
Authors: Cheung Alan C.K. , Randall E. Vance , Tam Man Kwan 
Published: August 2016

Purpose
– This paper is a historical review of the development of private primary and secondary education in Hong Kong from 1841-2012. The purpose of this paper is to examine the evolving relationship between the state and private schools in Hong Kong.

Design/methodology/approach
– This paper utilizes sources from published official documents, public data available on government websites, archival documents and newspapers. The authors also carried out a few individual interviews with legislators, government officials and principals who were familiar with the history of private education in Hong Kong.

Findings
– The colonial Hong Kong Government adopted laissez-faire policy in greater part of its rule until 1970s. The year 1978 marked the period of “state control” until the 1990s when privatization and deregulation emerged as a world trend in the governance of education. The role of government changed to that of “supervision” instead of “control.” Further, it is shown that the change of sovereignty did not avert the trend of decentralization, deregulation and privatization in education which is entrenched in the management of public affairs in human societies.

Originality/value
– The findings provides an illuminating look into the development of a society and how it grapples with the fundamental questions of the degree of social control and proper use of political power in a colonial setting.
Risks and older adults with atrial fibrillation in rural communities: an integration lens
Authors: Rush Kathy L , Oelke Nelly D , Reid R. Colin , Laberge Carol , Halperin Frank , Kjorven Mary 
Published: August 2016

Purpose
– Older adults with atrial fibrillation (AF) have put growing demands on a poorly integrated healthcare system. This is of particular concern in rural communities with rapid population aging and few healthcare resources elevating risk of stroke and mortality. The purpose of this paper is to explore healthcare delivery risks for rural older adults with AF.

Design/methodology/approach
– This qualitative study collected data from AF patients, healthcare providers and decision makers. Ten patients participated in six-month care journeys involving interviews, logs, photos, and chart reviews. In total, 13 different patients and ten healthcare providers participated in focus groups and two decision makers participated in interviews.

Findings
– Three key health service risks emerged: lack of patient-focussed access and self-management; unplanned care coordination and follow-up across the continuum of care; and ineffective teamwork with variable perspectives among patients, providers, and decision makers.

Originality/value
– This study extends the understanding of risks to the health system level. Results provide important information for further research aimed at interventions to improve health service delivery and policy change to mitigate risks for this population.