bluuebunny/crossref_metadata_2025_split huggingface dataset:
ACValidator: a novel assembly-based approach for in silico validation of circular RNAs
Authors: Sekar Shobana , Geiger Philipp , Adkins Jonathan , Serrano Geidy , Beach Thomas G. , Liang Winnie S. 
Published: February 2019

AbstractCircular RNAs (circRNAs) are evolutionarily conserved RNA species that are formed when exons ‘back-splice’ to each other. Current computational algorithms to detect these back-splicing junctions produce divergent results, and hence there is a need for a method to distinguish true positive circRNAs. To this end, we developed ACValidator (Assembly based CircRNA Validator) for in silico validation of circRNAs. ACValidator extracts reads from a user-defined window on either side of the circRNA junction and assembles them to generate contigs. These contigs are aligned against the circRNA sequence to find contigs spanning the backspliced junction. When evaluated on simulated datasets, ACValidator achieved over 80% sensitivity and specificity on datasets with an average of 10 circRNA-supporting reads and with read lengths of at least 100 bp. In experimental datasets, ACValidator produced higher validation percentages for samples treated with ribonuclease R compared to non-treated samples. Our workflow is applicable to non-polyA-selected RNAseq datasets and can also be used as a candidate selection strategy for experimental validations. All workflow scripts are freely accessible on our github page https://github.com/tgen/ACValidator along with detailed instructions to set up and run ACValidator.Author summaryCircular RNAs (circRNAs) are a recent addition to the class of non-coding RNAs and are produced when exons ‘back-splice’ and form closed circular loops. Although several computational algorithms have been developed to detect circRNAs from RNA sequencing (RNAseq) data, they produce divergent results. We hence developed the software Assembly based Circular RNA Validator (ACValidator) as an orthogonal strategy to separately validate predicted circRNAs in silico. ACValidator takes as input a sequence alignment mapping (SAM) file and the circRNA coordinate(s) to be validated. Reads surrounding the circRNA junction are extracted from the SAM file and assembled to generate contigs. These contigs are then aligned against the circRNA sequence to identify contigs that span the back-spliced junction. We evaluated our workflow on simulated as well as experimental datasets to demonstrate the utility of our approach. ACValidator is implemented in python and is highly computationally efficient, with a run time of less than 2 minutes for an 8 GB SAM file. This workflow is applicable to non-polyA-selected RNAseq datasets and can also be used as a candidate selection strategy for experimental validations.
New factors for protein transport identified by a genome-wide CRISPRi screen in mammalian cells
Authors: Bassaganyas Laia , Popa Stephanie J. , Horlbeck Max , Ashok Anupama , Stewart Sarah E. , Butnaru Cristian M. , Brouwers Nathalie , Heydari Kartoosh , Ripoche Jean , Weissman Jonathan , Schekman Randy , Malhotra Vivek , Moreau Kevin , Villeneuve Julien 
Published: February 2019

AbstractProtein and membrane trafficking pathways are critical for cell and tissue homeostasis. Traditional genetic and biochemical approaches have shed light on basic principles underlying these processes. However, the list of factors required for secretory pathways function remains incomplete, and mechanisms involved in their adaptation poorly understood. Here, we present a powerful strategy based on a pooled genome-wide CRISPRi screen that allowed the identification of new factors involved in protein transport. Two newly identified factors, TTC17 and CCDC157, localized along the secretory pathway and were found to interact with resident proteins of ER-Golgi membranes. In addition, we uncovered that upon TTC17 knockdown, the polarized organization of Golgi cisternae was altered, creating glycosylation defects, and that CCDC157 is an important factor for the fusion of transport carriers to the Golgi complex. In conclusion, our work identified and characterized new actors in the mechanisms of protein transport and secretion, and opens stimulating perspectives for the use of our platform in physiological and pathological contexts.
Using machine learning-based lesion behavior mapping to identify anatomical networks of cognitive dysfunction: spatial neglect and attention
Authors: Wiesen Daniel , Sperber Christoph , Yourganov Grigori , Rorden Christopher , Karnath Hans-Otto 
Published: February 2019

AbstractPrevious lesion behavior studies primarily used univariate lesion behavior mapping techniques to map the anatomical basis of spatial neglect after right brain damage. These studies led to inconsistent results and lively controversies. Given these inconsistencies, the idea of a widespread network that might underlie spatial orientation and neglect has been pushed forward. In such case, univariate lesion behavior mapping methods might have been inherently limited in uncover the presumed network in a single study due to limited statistical power. By using multivariate lesion-mapping based on support vector regression, we aimed to validate the network hypothesis directly in a large sample of 203 newly recruited right brain damaged patients. In a single analysis, this method identified a network of parietal, temporal, frontal, and subcortical regions, which also included white matter tracts connecting these regions. The results were compared to univariate analyses of the same patient sample using different combinations of lesion volume correction and statistical thresholding. The comparison revealed clear benefits of multivariate lesion behavior mapping in identifying brain networks.
Bacterial defiance as a form of prodrug failure
Authors: Holt Brandon Alexander , Kwong Gabriel A. 
Published: February 2019

ABSTRACTClassifying the mechanisms of antibiotic failure has led to the development of new treatment strategies for killing bacteria. Among the currently described mechanisms, which include resistance, persistence and tolerance, we propose bacterial defiance as a form of antibiotic failure specific to prodrugs. As a prototypic model of a bacteria-activated prodrug, we construct cationic antimicrobial peptides (AMP), which are charge neutralized until activated by a bacterial protease. This construct successfully eliminated the vast majority of bacteria populations, while localizing activity to bacterial membranes and maintaining low active drug concentration. However, we observed defiant bacteria populations, which survive in the presence of identical drug concentration and exposure time. Using a multi-rate kinetic feedback model, we show that bacteria switch between susceptibility and defiance under clinically relevant environmental (e.g., hyperthermia) and genetic (e.g., downregulated protease expression) conditions. From this model, we derive a dimensionless quantity (Bacterial Advantage Heuristic, BAH) – representing the balance between bacterial proliferation and prodrug activation – that perfectly classifies bacteria as defiant or susceptible across a broad range of conditions. To apply this concept to other classes of prodrugs, we expand this model to include both linear and nonlinear terms and use general pharmacokinetic parameters (e.g., half-life, EC50, etc.). Taken together, this model reveals an analogous dimensionless quantity (General Advantage Key, GAK), which can applied to prodrugs with different activation mechanisms. We envision that these studies will enable the development of more effective prodrugs to combat antibiotic resistance.
Identification and development of talent in surgery
Authors: Dall Jensen Rune , Ravn Sissel , Krogh Christensen Mette 
Published: February 2019

Purpose
Education of the surgeon and development of surgical expertise have been debated for centuries. Today, research in surgical education applies terms and methods from other performance domains such as sport and music. However, there still seems to be a lack of consensus as to how talent may be brought into the discourse about surgical education. Especially, when it comes to identifying and developing trainees who in the future will perform better than the average surgeon.

Design/methodology/approach
This five-step scoping study aims to map existing literature about talent identification, talent development and development of expertise in the domains of surgery, sport and music in the period of 1985-2014.

Findings
A total of 242 studies, divided in the four domains of surgery (69 studies), sport (115 studies), music (34 studies) and cross-disciplinary studies (24 studies) published in the period 1985-2014 were included.

Originality/value
Informed by the performance domains of sports and music and their inclusion of a holistic, ecological approach to research, this study suggests that research in surgical education may benefit from broadening its view on talent by including psychosocial variables and environmental, demographic and structural influencers when considering how surgical talent may be identified and developed.
Performance modeling and assessment of maintenance priorities for steam generation unit of a sugar plant
Authors: Sharma Gaurav , Tewari Puran Chandra 
Published: February 2019

Purpose
The purpose of this paper is to deal with the performance modeling and assessment of maintenance priorities for steam generation unit of a sugar plant.

Design/methodology/approach
The unit comprises of four subsystems, i.e., Bagasse elevator, Bagasse carrier, boiler and feed pump. The Chapman–Kolmogorov equations are generated on the basis of transition diagram and further solved recursively to obtain the performance modeling with the help of normalizing condition using the Markov approach.

Findings
Decision matrices are formed with the help of different combinations of failure and repair rates of all subsystems. The performance of steam generation unit is evaluated in terms of availability levels depicted in decision matrices and plots of failure rates and repair rates of various subsystems. The maintenance priorities of various subsystems of steam generation unit are decided on the basis of effect of failure and repair rates of subsystems on the availability of steam generation unit. The key finding is that the boiler subsystem is the most critical subsystem and hence should be kept on top maintenance priority for performance enhancement of the steam generation unit.

Originality/value
The acceptance of both performance modeling and maintenance priorities decision by the management of sugar plant will result in the enhancement of unit availability and reduction of maintenance cost.
Exploring intersectionality and the employment of school leaders
Authors: Fuller Edward , Hollingworth Liz , An Brian P. 
Published: February 2019

Purpose
There is growing recognition of the importance of educator diversity. The purpose of this paper is to examine the production, placement and employment of school leaders as assistant principals, principals and school leaders in Texas by the intersection of race/ethnicity and gender over 23 years.

Design/methodology/approach
This is a quantitative study that employs multilevel logistic regression analysis to examine using 25 years of educator employment data from Texas.

Findings
The authors find descriptive evidence of an increase in diversity of school leaders driven by a decreasing percentage of white men educators and an increasing percentage of Latina educators. Important differences, however, emerge when examining assistant principal vs principal positions, particularly with respect to the odds of being hired. The authors find black male and Latino educators are more likely than white male educators to be hired as an assistant principal but are less likely than white male educators to be hired as a principal. Women educators, regardless of race/ethnicity were less likely to be hired as assistant principals or principals relative to white male educators. Women of color had the lowest odds of being hired in any position relative to white male educators. With respect to school leader preparation program accountability, the authors find few program characteristics associated with placement and differences between programs explained very little of the variation in placement rates, bringing into question efforts to hold programs accountable for such outcomes.

Originality/value
A longitudinal examination of racial/ethnic and gender intersectionality over 25 years is a unique contribution to the study of inequitable access to school leadership positions.
Reputation management in cyberspace: evidence from Jordan’s luxury hotel market
Authors: Alrawadieh Zaid , Dincer Mithat Zeki 
Published: February 2019

PurposeDrawing on a sample of 520 negative reviews posted on TripAdvisor against all five-star hotels operating in Petra, Jordan, the purpose of this paper is to evaluate the response of luxury hotels to negative online reviews by considering the Response Rate (RR), the Response Time (RT) and the Response Content (RC).Design/methodology/approachA deductive content analysis was used on hotels’ managerial responses. Based on the literature review, a four-construct scheme was identified to guide the analysis including Appreciation; Apology; Explanation; and Incentive. The managerial responses were carefully read and manually coded based on the four-construct scheme. The time between the review posting date and the date of the managerial response was also recorded. Luxury hotel managers were also surveyed to obtain insights into their perceptions and practices with respect to online reputation management.FindingsThe findings call into question luxury hotels’ awareness of the harmful impact of negative online reviews. Specifically, the findings suggest that less than half of the negative reviews received a managerial response, and that more than half of these were standardized and did not refer to the issues raised in the reviews. The low response rate coupled with the hotel managers’ consensus on the importance of answering all online reviews indicates inconsistency between hotel managers’ perceptions and practices with regard to online reputation management.Originality/valueThe paper adds to the ongoing debate on reputation management in the hospitality industry by considering the managerial response to negative online reviews. The paper discusses several managerial implications for hotel managers as well as avenues for future research.
Measuring the burden of multimorbidity among Medicare beneficiaries via condition counts and cumulative duration
Authors: Maciejewski Matthew L. , Hammill Bradley G. 
Published: February 2019

ObjectiveThe study's purpose was to describe the cumulative duration of 19 chronic conditions among Medicare fee‐for‐service (FFS) beneficiaries and examine variation in total expenditures explained by cumulative duration and condition counts.Design, Setting, Study Design, and Data ExtractionIn a retrospective cohort of FFS beneficiaries age ≥68, 2015 Medicare enrollment and claims data (N = 20 124 230) were used to identify the presence or absence of 19 diagnosed chronic conditions, and to construct MCC categories (0‐1, 2‐3, 4‐5, 6+) and cumulative duration of each of 19 conditions from the date of first possible occurrence in claims (1/1/1999) to the end of follow‐up (date of death or 12/31/2015). Total Medicare expenditures were estimated using linear models adjusted for demographic characteristics.Principal FindingsMultimorbidity was common (71.7 percent with 2+ conditions). The mean cumulative duration of all 19 conditions was 23.6 person‐years, which varied greatly by age and number of conditions. Condition counts were more predictive of Medicare expenditures than cumulative duration (R‐squared for continuous measures = 0.461 vs 0.272; R‐squared for quartiles = 0.408 vs 0.266).ConclusionsThe cumulative duration of chronic conditions varied widely for Medicare beneficiaries, especially for those with 6+ conditions, but was less predictive of total expenditures than condition counts.
Forensic Gait Analysis and Recognition: Standards of Evidence Admissibility
Authors: Macoveciuc Ioana , Rando Carolyn J. , Borrion Hervé 
Published: February 2019

AbstractGait is one biological characteristic which has attracted strong research interest due to its potential use in human identification. Although almost two decades have passed since a forensic gait expert has testified to the identity of a perpetrator in court, the methods remain insufficiently robust, considering the recent paradigm shift witnessed in the forensic science community regarding quality of evidence. In contrast, technological advancements have taken the lead, and research into automated gait recognition has greatly surpassed forensic gait analysis in terms of the size of acquired datasets and demographic variability of participants, tested variables, and statistical evaluation of results. Despite these advantages, gait recognition presents with different problems which are yet to be resolved. Therefore, courts should treat gait evidence with caution, as they should any other form of evidence originating from disciplines without fully established codes of practice, error rates, and demonstrable applications in forensic scenarios.
Endothelial toll‐like receptor 4 maintains lung integrity via epigenetic suppression of p16INK4a
Authors: Kim So‐Jin , Shan Peiying , Hwangbo Cheol , Zhang Yi , Min Jin‐Na , Zhang Xuchen , Ardito Taylor , Li Alfred , Peng Tien , Sauler Maor , Lee Patty J. 
Published: February 2019

AbstractWe previously reported that the canonical innate immune receptor toll‐like receptor 4 (TLR4) is critical in maintaining lung integrity. However, the molecular mechanisms via which TLR4 mediates its effect remained unclear. In the present study, we identified distinct contributions of lung endothelial cells (Ec) and epithelial cells TLR4 to pulmonary homeostasis using genetic‐specific, lung‐ and cell‐targeted in vivo methods. Emphysema was significantly prevented via the reconstituting of human TLR4 expression in the lung Ec of TLR4−/− mice. Lung Ec‐silencing of TLR4 in wild‐type mice induced emphysema, highlighting the specific and distinct role of Ec‐expressed TLR4 in maintaining lung integrity. We also identified a previously unrecognized role of TLR4 in preventing expression of p16INK4a, a senescence‐associated gene. Lung Ec‐p16INK4a‐silencing prevented TLR4−/− induced emphysema, revealing a new functional role for p16INK4ain lungs. TLR4 suppressed endogenous p16INK4a expression via HDAC2‐mediated deacetylation of histone H4. These findings suggest a novel role for TLR4 in maintaining of lung homeostasis via epigenetic regulation of senescence‐related gene expression.
Caloric restriction controls stationary phase survival through Protein Kinase A (PKA) and cytosolic pH
Authors: Dolz‐Edo Laura , van der Deen Margaretha , Brul Stanley , Smits Gertien Jacoba 
Published: February 2019

AbstractCalorie restriction is the only physiological intervention that extends lifespan throughout all kingdoms of life. In the budding yeast Saccharomyces cerevisiae, cytosolic pH (pHc) controls growth and responds to nutrient availability, decreasing upon glucose depletion. We investigated the interactions between glucose availability, pHc and the central nutrient signalling cAMP‐Protein Kinase A (PKA) pathway. Glucose abundance during the growth phase enhanced acidification upon glucose depletion, via modulation of PKA activity. This actively controlled reduction in starvation pHc correlated with reduced stationary phase survival. Whereas changes in PKA activity affected both acidification and survival, targeted manipulation of starvation pHc showed that cytosolic acidification was downstream of PKA and the causal agent of the reduced chronological lifespan. Thus, caloric restriction controls stationary phase survival through PKA and cytosolic pH.
Cryptocurrency, confirmatory bias and news readability – evidence from the largest Chinese cryptocurrency exchange
Authors: Zhang Shuyu , Zhou Xuanyu , Pan Huifeng , Jia Junyi 
Published: February 2019

AbstractWe investigate whether Chinese cryptocurrency investors show confirmatory bias when processing authority‐related news. Authority‐related news is defined as news that is related to government authority (including central bank) policies or talk. By using data from the largest cryptocurrency exchange in China, we find that investors’ response to authority‐related news is negative and significant in general. Moreover, we find that the abnormal trading volume and standard deviation of abnormal trading volume are significantly higher for authority‐related news with higher readability, suggesting investors respond to the more readable authority‐related news with more trading behaviour.
Parenting style associations with sensory threshold and behaviour: a prospective cohort study in term/preterm infants
Authors: Neel Mary Lauren , Slaughter James C. , Stark Ann R. , Maitre Nathalie L. 
Published: February 2019

AbstractAimEarly‐life atypical sensory functioning and behavioural profiles are often associated with long‐term developmental problems, especially in former preterm infants. We tested whether parenting style is associated with atypical sensory threshold or behavioural outcomes in preterm and term infants assessed during early childhood.MethodsWe prospectively evaluated parenting style for a cohort of term and preterm infants who had previous assessments of sensory development and behaviour. We used standardised tools to evaluate parenting style, sensory neurological threshold at one year, and internalising and externalising behavioural tendencies at two years. Covariates included gestational age, sex and maternal education.ResultsFor the entire cohort (n = 82), children of more permissive parents were 2.7 times more likely to demonstrate abnormal sensory neurological thresholds compared to children of parents with less permissive styles (CI: 1.4–4.9). More permissive parenting scores were also associated with 2.4 times increased internalising (CI: 1.3–4.2) and 3.0 times increased externalising (CI: 1.6–5.6) tendencies. In the preterm group only, higher authoritative parenting scores were associated with fewer behavioural problems.ConclusionPermissive parenting is associated with worse infant sensory and behavioural outcomes. Authoritative parenting is associated with fewer behavioural problems in preterm children. Modification of parenting style may improve sensory development and behavioural outcomes.
Constructing Transnational Solidarity: The Role of Campaign Governance
Authors: Sarkar Santanu , Kuruvilla Sarosh 
Published: February 2019

AbstractOur inductive study of two transnational labour solidarity efforts focuses on the role of campaign governance. Specifically, we study contrasting campaign strategies, tactics and coalition structures in campaigns by two global union federations, UNI Global Union and the IUF, contextualized in terms of how these campaigns unfolded in India. Our contribution consists of two arguments. The first is that a degree of internal consistency amongst different campaign elements is important for success, and the second is that a mode of articulation that allows for local concerns in affiliate countries to find voice in global campaigns is more likely to result in concrete gains at the local level.