bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of salivary glue genes inDrosophilaspecies
Authors: Da Lage Jean-Luc , Thomas Gregg W. C. , Bonneau Magalie , Courtier-Orgogozo Virginie 
Published: June 2018

AbstractBackgroundAt the very end of the larval stage Drosophila expectorate a glue secreted by their salivary glands to attach themselves to a substrate while pupariating. The glue is a mixture of apparently unrelated proteins, some of which are highly glycosylated and possess internal repeats. Because species adhere to distinct substrates (i.e. leaves, wood, rotten fruits), glue genes are expected to evolve rapidly.ResultsWe used available genome sequences and PCR-sequencing of regions of interest to investigate the glue genes in 20Drosophilaspecies. We discovered a new gene in addition to the seven glue genes annotated inD. melanogaster.We also identified a phase 1 intron at a conserved position present in five of the eight glue genes ofD. melanogaster, suggesting a common origin for those glue genes. A slightly significant rate of gene turnover was inferred. Both the number of repeats and the repeat sequence were found to diverge rapidly, even between closely related species. We also detected high repeat number variation at the intrapopulation level inD. melanogaster.ConclusionMost conspicuous signs of accelerated evolution are found in the repeat regions of several glue genes.
Integration of accessibility data from structure probing into RNA-RNA interaction prediction
Authors: Miladi Milad , Montaseri Soheila , Backofen Rolf , Raden Martin 
Published: June 2018

AbstractSummaryExperimental structure probing data has been shown to improve thermodynamics-based RNA secondary structure prediction. To this end, chemical reactivity information (as provided e.g. by SHAPE) is incorporated, which encodes whether or not individual nucleotides are involved in intra-molecular structure. Since inter-molecular RNA-RNA interactions are often confined to unpaired RNA regions, SHAPE data is even more promising to improve interaction prediction. Here we show how such experimental data can be incorporated seamlessly into accessibility-based RNA-RNA interaction prediction approaches, as implemented in IntaRNA. This is possible via the computation and use of unpaired probabilities that incorporate the structure probing information. We show that experimental SHAPE data can significantly improve RNA-RNA interaction prediction. We evaluate our approach by investigating interactions of a spliceosomal U1 snRNA transcript with its target splice sites. When SHAPE data is incorporated, known target sites are predicted with increased precision and specificity.Availabilityhttps://github.com/BackofenLab/IntaRNA
OTUB1 non-catalytically regulates the stability of the E2 ubiquitin conjugating enzyme UBE2E1
Authors: Pasupala Nagesh , Morrow Marie E. , Que Lauren T. , Malynn Barbara A. , Ma Averil , Wolberger Cynthia 
Published: June 2018

AbstractOTUB1 is a deubiquitinating enzyme that cleaves K48-linked polyubiquitin chains and also regulates ubiquitin signaling through a unique, non-catalytic mechanism. OTUB1 binds to a subset of E2 ubiquitin conjugating enzymes and inhibits their activity by trapping the E2~ubiquitin thioester and preventing ubiquitin transfer. The same set of E2s stimulate the deubiquitinating activity of OTUB1 when the E2 is not charged with ubiquitin. Previous studies have shown that, in cells, OTUB1 binds to members of the UBE2D (UBCH5) and UBE2E families, as well as to UBC13 (UBE2N). Cellular roles have been identified for the interaction of OTUB1 with UBC13 and members of the UBE2D family, but not for UBE2E E2 enzymes. We report here a novel role for OTUB1-E2 interactions in modulating E2 protein ubiquitination. We find that depletion of OTUB1 dramatically destabilizes the E2 conjugating enzyme UBE2E1 (UBE2E1) in cells and that this effect is independent of the catalytic activity of OTUB1 but depends on the ability of OTUB1 to bind to UBE2E1. We show that OTUB1 suppresses UBE2E1 autoubiquitinationin vitroand in cells, thereby preventing UBE2E1 from being targeted to the proteasome for degradation. Taken together, we have found a new role for OTUB1 in rescuing specific E2s from degradationin vivo.
In situtranscriptome characteristics are lost following culture adaptation of adult cardiac stem cells
Authors: Kim Taeyong , Echeagaray Oscar H. , Wang Bingyan J , Casillas Alexandria , Broughton Kathleen M. , Kim Bong-Hyun , Sussman Mark A 
Published: June 2018

AbstractRegenerative therapeutic approaches for myocardial diseases often involve adoptive transfer of stem cells expandedex vivo. Prior studies indicate that cell culture conditions affect functional and phenotypic characteristics, but relationship(s) of cultured cells derived from freshly isolated populations and the heterogeneity of the cultured population remain poorly defined. Functional and phenotypic characteristics of adoptively donated cells will determine outcomes of interventional treatment for disease, necessitating characterization of the impact thatex vivoexpansion has upon isolated stem cell populations. Single-cell RNA-Seq profiling (scRNA-Seq) was performed to determine consequences of culture expansion upon adult cardiac progenitor cells (CPCs) as well as relationships with other cell populations. Bioinformatic analyses reveal loss of identity marker genes in cultured CPCs while simultaneously acquiring thousands of additional genes. Cultured CPCs exhibited decreased transcriptome variability within their population relative to their freshly isolated cells. Findings were validated by comparative analyses using scRNA-Seq datasets of various cell types generated by multiple scRNA-Seq technology. Increased transcriptome diversity and decreased population heterogeneity in the cultured cell population relative to freshly isolated cells may help account for reported outcomes associated with experimental and clinical use of CPCs for treatment of myocardial injury.
A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex
Authors: de Vries Saskia E. J. , Lecoq Jerome , Buice Michael A. , Groblewski Peter A. , Ocker Gabriel K. , Oliver Michael , Feng David , Cain Nicholas , Ledochowitsch Peter , Millman Daniel , Roll Kate , Garrett Marina , Keenan Tom , Kuan Leonard , Mihalas Stefan , Olsen Shawn , Thompson Carol , Wakeman Wayne , Waters Jack , Williams Derric , Barber Chris , Berbesque Nathan , Blanchard Brandon , Bowles Nicholas , Caldejon Shiella , Casal Linzy , Cho Andrew , Cross Sissy , Dang Chinh , Dolbeare Tim , Edwards Melise , Galbraith John , Gaudreault Nathalie , Griffin Fiona , Hargrave Perry , Howard Robert , Huang Lawrence , Jewell Sean , Keller Nika , Knoblich Ulf , Larkin Josh , Larsen Rachael , Lau Chris , Lee Eric , Lee Felix , Leon Arielle , Li Lu , Long Fuhui , Luviano Jennifer , Mace Kyla , Nguyen Thuyanh , Perkins Jed , Robertson Miranda , Seid Sam , Shea-Brown Eric , Shi Jianghong , Sjoquist Nathan , Slaughterbeck Cliff , Sullivan David , Valenza Ryan , White Casey , Williford Ali , Witten Daniela , Zhuang Jun , Zeng Hongkui , Farrell Colin , Ng Lydia , Bernard Amy , Phillips John W. , Reid R. Clay , Koch Christof 
Published: June 2018

SummaryTo understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of neural activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical activity from nearly 60,000 neurons collected from 6 visual areas, 4 layers, and 12 transgenic mouse lines from 221 adult mice, in response to a systematic set of visual stimuli. Using this dataset, we reveal functional differences across these dimensions and show that visual cortical responses are sparse but correlated. Surprisingly, responses to different stimuli are largely independent, e.g. whether a neuron responds to natural scenes provides no information about whether it responds to natural movies or to gratings. We show that these phenomena cannot be explained by standard local filter-based models, but are consistent with multi-layer hierarchical computation, as found in deeper layers of standard convolutional neural networks.
Low MSH2 protein levels identify muscle-invasive bladder cancer resistant to cisplatin
Authors: Goodspeed Andrew , Jean Annie , Costello James C. 
Published: June 2018

AbstractBackgroundThe response to first-line, platinum-based treatment of muscle-invasive bladder cancer has not improved in three decades.ObjectiveThe objective of this study is to identify genes that predict cisplatin resistance in bladder cancer.DesignWe performed a whole-genome, CRISPR-based screen in a bladder cancer cell line treated with cisplatin to identify genes that mediate response to cisplatin. Targeted validation was performed in vitro across two bladder cancer cell lines. The top gene candidate was validated in a publicly available bladder cancer dataset containing 340 bladder cancer patients with treatment, protein, and survival information.Results and limitationsThe cisplatin resistance screen suggested the mismatch repair pathway through the loss of MSH2 and MLH1 contribute to cisplatin resistance. Bladder cancer cells depleted of MSH2 are resistant to cisplatin in vitro, in part due to a reduction in apoptosis. These cells maintain sensitivity to the cisplatin-analog, oxaliplatin. Bladder tumors with low protein levels of MSH2 have poorer overall survival when treated with cisplatin- or carboplatin-based therapy.ConclusionsWe generated in vitro and clinical support that bladder cancer cell lines and tumors with low levels of MSH2 are more resistant to cisplatin-based therapy. Further studies are warranted to determine the ability of MSH2 protein levels to serve as a prospective biomarker of chemotherapy response in bladder cancer.Patient summaryWe report the first evidence that the protein level of MSH2 may contribute to chemotherapy resistance observed in bladder cancer. MSH2 levels has the potential to serve as a biomarker of treatment response.
Household consumption expenditure and inequality: evidence from Nigerian data
Authors: Nwosu Emmanuel O. , Ojonta Obed , Orji Anthony 
Published: June 2018

Purpose
Enhancing household consumption and reducing inequality are among the fundamental goals of many developing countries. The purpose of this study therefore is to disaggregate household consumption expenditure into food and non-food and, thus, decompose inequality into within- and between-groups.

Design/methodology/approach
The study adopts generalised entropy (GE) measures. Second, the study uses regression-based inequality decomposition to ascertain the determinants of inequality in food and non-food expenditure using household demographic and socioeconomic characteristics as covariates.

Findings
The results show that non-food expenditure is the major source of inequality in household consumption expenditure in both urban and rural areas with inequality coefficients of above 0.6 compared to about 0.4 for food expenditure. The decompositions also show that within-group inequalities for non-food and food expenditure are, respectively, 0.97 and 0.365 using the Theil index, while between-group inequalities for non-food and food are, respectively, 0.016 and 0.035. Furthermore, the regression-based inequality decompositions show that variables such as living in rural areas, household size, household dwelling and household dwelling characteristics account for the significant proportion of inequality in food and non-food expenditure.

Originality/value
The policy implication of the findings, among others, is that policies should focus on addressing inequality within rural and urban areas, especially with respect to non-food expenditure than in inequality existing between urban and rural areas. These non-food expenditures include expenditure in education, health, energy, accommodation, water and sanitation.
Congruence and celebrity endorser credibility in Japanese OTC drug advertising
Authors: Morimoto Mariko 
Published: June 2018

Purpose
Based on congruency theory, this study aims to examine the effects of celebrity endorsement on endorser credibility in Japanese over-the-counter (OTC) drug advertising using multiple celebrity categories. In particular, this research explored brand–endorser congruence and endorser–consumer congruence and their roles in attitude formation.

Design/methodology/approach
A 3 (endorser categories: actor/actress, athlete and talent/TV personality) × 2 (endorser’s gender) factorial experimental design with 480 Japanese consumers was used in the study.

Findings
In Japanese OTC drug advertising, actors/actresses and athletes were regarded as more credible than talents (TV personalities) by Japanese consumers. Endorser categories also had a significant influence on identification with the endorser through ideal self-congruency. Additionally, endorser credibility mediated the relationship between identification and advertising evaluations. However, it did not mediate the relationship between perceived similarity with the endorser and advertising responses.

Originality/value
Little is known about the effectiveness of celebrity endorsers in OTC drug advertising from a source credibility perspective. This study attempted to shed light on the role of endorser fit in the framework of source credibility in drug advertising that usually places an emphasis on informational cues rather than peripheral cues such as source effects.
Organizational knowledge management and sharing
Authors: Silva Fábio Ferreira , Odelius Catarina Cecilia 
Published: June 2018

Purpose
This paper aims to identify empirically the influence of learning mechanisms provided by organizations on knowledge sharing in the organizational environment.

Design/methodology/approach
A quantitative study was developed in which a sample of 268 individuals from civil and military organizations of the Federal Direct Administration was researched. The questionnaire used was composed of the Organizational Learning Mechanism Scale, which was adapted at the time of the present study, in addition to a scale on knowledge sharing, which was developed within the scope of this research. After performing the factorial analysis for both scales, a canonical correlation analysis was performed between the group of variables associated with the learning mechanisms (independent variables) and the group of variables on knowledge sharing (dependent variables).

Findings
The results found in the canonical correlation analysis indicate that the learning mechanisms are responsible for explaining 35 per cent of the variance (R² = 0.352) of the group of variables on knowledge sharing.

Practical implications
The findings of this research can help the researched organizations to increase the knowledge management actions, mainly in relation to the actions that favor social interaction among the individuals in the work environment, making possible the exchange of knowledge and experiences in the internal organizational context, and exploring in a positive way actions related to internal acquisition.

Social implications
The deeper knowledge about the relationship between organizational actions promoted by top management and knowledge support decision-making in the organizational environment regarding contextual factors that influence social interaction between individuals. In relation to the sharing of knowledge, a high correlation of knowledge absorption and reproduction aspects with the knowledge sharing phenomenon was perceived, so that the possibility of organizations thinking in ways that provide the individual with formal and informal environments can be foreseen.

Originality/value
The main contributions of this research are to measure the intensity of the relationship between learning mechanisms and knowledge sharing; and to test the predictive effect of learning mechanisms on knowledge sharing. Regarding the methodological aspects, it was opportune to approach the phenomenon through a little used lens in the context of administration research: the analysis of canonical correlation, which represents another look at the influence of the actions of the top management and the interaction of individuals. The discussions and the data analysis carried out in this research allow us to envisage significant contributions of this work to the analysis and theoretical refinement of the study of the variables treated.
Principals and teacher evaluation
Authors: Donaldson Morgaen , Mavrogordato Madeline 
Published: June 2018

Purpose
The purpose of this paper is to examine how school leaders use high-stakes teacher evaluation to improve and, if necessary, remove low-performing teachers in their schools. It explores how cognitive, relational and organizational factors play a role in shaping the way school leaders implement teacher evaluation.

Design/methodology/approach
Using a database of in-depth interviews with 17 principals and assistant principals, this study uses cross-case comparisons to examine one district’s efforts to improve the performance of low-performing teachers through evaluation.

Findings
School leaders’ framing of teacher performance and their efforts to improve instruction reveal the cognitive, relational and organizational aspects of working with low-performing teachers and, if necessary, pursuing removal. Notably, this study found that cognitive and relational factors were important in school leaders’ teacher improvement efforts, but organizational factors were most salient when attempting to remove teachers.

Research limitations/implications
Because evaluating and developing teachers has become such an important aspect of school leaders’ day to day work, this study suggests that school leaders could benefit from more assistance from district personnel and that preparation programs should build in opportunities for aspiring leaders to learn more about their role as evaluators.

Originality/value
The success or failure of teacher evaluation systems largely hinges on school leaders, yet there is scant research on how school leaders make decisions to develop and remove low-performing teachers. This study sheds light on the central role school leaders play in implementing high-stakes teacher evaluation.
A discourse analysis of financial inclusion: post-liberalization mapping in rural and urban India
Authors: Lenka Sanjaya Kumar , Barik Rajesh 
Published: June 2018

Purpose
The purpose of this study is to measure the availability, accessibility and usability of financial products and services in both rural and urban India from 1991 to 2014.

Design/methodology/approach
This paper uses principal component analysis (PCA) method to construct financial inclusion index that serves as a proxy variable for indicating the inclusiveness of financial products and services among the rural and urban people. To fulfill this objective, the study proposes separate indexes of financial inclusion for both rural and urban India from 1991 to 2014. The paper uses annual time series data from 1991 to 2014 to construct the rural-urban financial inclusion index. The used data have been collected from the basic statistical returns of Reserve Bank of India and Economic Political Weekly research foundation.

Findings
The study inferences that though there is a remarkable increase in financial inclusion in India from 1991 onwards, it does not result in sizeable growth of financial access to rural masses in comparison to urban masses. The rural India does not substantiate an equivalent growth to that of urban India, contrasting a perceptible increase in financial inclusion. The finding of this study will help the researchers and policymakers to understand the status of financial inclusion in the context of both rural and urban India. Furthermore, policymakers can take appropriate policy initiatives to fulfill the financial inclusion gap that exists between rural and urban people. Additionally, the proposed index is easy to compute and can be used to make comparison across countries for further studies.

Originality/value
The present paper attempts to include all possible dimensions (and indicators within a dimension) that have been considered so far by various authors. Therefore, the authors hope that this index will be more indicative and accurate than previous index. Again, the authors propose to use PCA for the first time to assign the weight of factors in the financial inclusion index for rural and urban India separately.
The persistent problem of integrated care in English NHS hospitals
Authors: Erskine Jonathan , Castelli Michele , Hunter David , Hungin Amritpal 
Published: June 2018

Purpose
The purpose of this paper is to determine whether some aspects of the distinctive Mayo Clinic care model could be translated into English National Health Service (NHS) hospital settings, to overcome the fragmented and episodic nature of non-emergency patient care.

Design/methodology/approach
The authors used a rapid review to assess the literature on integrated clinical care in hospital settings and critical analysis of links between Mayo Clinic’s care model and the organisation’s performance and associated patient outcomes.

Findings
The literature directly concerned with Mayo Clinic’s distinctive ethos and approach to patient care is limited in scope and largely confined to “grey” sources or to authors and institutions with links to Mayo Clinic. The authors found only two peer-reviewed articles which offer critical analysis of the contribution of the Mayo model to the performance of the organisation.

Research limitations/implications
Mayo Clinic is not the only organisation to practice integrated, in-hospital clinical care; however, it is widely regarded as an exemplar.

Practical implications
There are barriers to implementing a Mayo-style model in English NHS hospitals, but they are not insurmountable and could lead to much better coordination of care for some patients.

Social implications
The study shows that there is an appetite among NHS patients and staff for better coordinated, multi-specialty care within NHS hospitals.

Originality/value
In the English NHS integrated care generally aims to improve coordination between primary, community and secondary care, but problems remain of fragmented care for non-emergency hospital patients. Use of a Mayo-type care model, within hospital settings, could offer significant benefits to this patient group, particularly for multi-morbid patients.