bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative mapping of mRNA 3’ ends inPseudomonas aeruginosareveals a pervasive role for premature 3’ end formation in response to azithromycin
Authors: Konikkat Salini , Scribner Michelle R. , Eutsey Rory , Hiller N. Luisa , Cooper Vaughn S. , McManus C. Joel 
Published: June 2020

ABSTRACTPseudomonas aeruginosaproduces serious chronic infections in hospitalized patients and immunocompromised individuals, including patients with cystic fibrosis. The molecular mechanisms by whichP. aeruginosaresponds to antibiotics and other stresses to promote persistent infections may provide new avenues for therapeutic intervention. Azithromycin (AZM), an antibiotic frequently used in cystic fibrosis treatment, is thought to improve clinical outcomes through a number of mechanisms including impaired biofilm growth and quorum sensing (QS). The mechanisms underlying the transcriptional response to AZM remain unclear. Here, we interrogated theP. aeruginosatranscriptional response to AZM using a fast, cost-effective genome-wide approach to quantitate RNA 3’ ends (3pMap). We also identified hundreds ofP. aeruginosagenes with high incidence of premature 3’ end formation indicative of riboregulation in their transcript leaders using 3pMap. AZM treatment of planktonic and biofilm cultures alters the expression of hundreds of genes, including those involved in QS, biofilm formation, and virulence. Strikingly, most genes downregulated by AZM in biofilms had increased levels of intragenic 3’ ends indicating premature transcription termination, transcriptional pausing, or accumulation of stable intermediates resulting from the action of nucleases. Reciprocally, AZM reduced premature intragenic 3’ end termini in many upregulated genes. Most notably, reduced termination accompanied robust induction ofobgE, a GTPase involved in persister formation inP. aeruginosa. Our results support a model in which AZM-induced changes in 3’ end formation alter the expression of central regulators which in turn impairs the expression of QS, biofilm formation and stress response genes, while upregulating genes associated with persistence.
Genetic characterisation of a large antibiotic resistant environmental ST131E. coliplasmid using a long read hybrid assembly approach
Authors: James R.S. , Rangama S. , Clark V. , Wellington E.M.H. 
Published: June 2020

AbstractEscherichia coliStrain Type 131 are a globally disseminated environmentalE. colithat has been linked to the capture and spread of plasmid mediatedblaCTX-Mtype extended spectrum beta-lactamase (ESBLs). Accurately identifying such resistance genes in their wider genetic context provides a greater understanding of the mechanisms of selection and persistence in the environment. In this study we use a novel DNA extraction and enrichment method in combination with a custom long-read scaffold hybrid-assembly and polishing pipe line to identify the genetic context of the plasmid borneblaCTX-Mgene previously identified in an ST131 environmentalE. coliisolate. This has allowed us to discern the complete structure of a ~100kb environmental plasmid and further resolve theblaCTX-Mvariant to the group 9blaCTX-M-27gene. The upstream IS26 insertion element associated with the global capture and dissemination ofblaCTX-M-15was also identified in proximity to blaCTX-M-27. Furthermore, the lack of conjugative machinery identified on this plasmid, in combination with a toxin-antitoxin and plasmid partitioning system, indicates a mechanism of vertical transmission to maintain persistence in a population.
Difference in somatosensory event-related potentials in the blind subjects leads to better performance in tactile P300 BCI
Authors: Grigoryan Rafael , Goranskaya Dariya , Demchinsky Andrey , Ryabova Ksenia , Kuleshov Denis , Kaplan Alexander 
Published: June 2020

AbstractIn this study, we have created an 8-command P300 tactile BCI with two stimuli types, running on a minimally modified consumer Braille display and tested it on 10 blind subjects and 10 sighted controls. Blind subjects have demonstrated 27% higher median accuracy than sighted controls (p< 0.05), proving that the blind subjects are not only able to use tactile BCI but also can achieve superior results in comparison with sighted subjects. Median accuracy in the blind group with the best stimuli type has reached 95%. The difference in event-related potentials between groups is located in frontocentral sites before 300 ms post-stimulus and corresponds with early cognitive ERP components. The blind subjects have higher amplitude and lower latency of ERPs. This result is consistent through experimental conditions with different tactile stimuli. The classification performance for the blind subjects is correlated with Braille reading speed. This enables a discussion about mechanisms of plastic changes during sensory compensation after vision loss and its dependence on personal perceptual experience.Author summarySensory compensation following vision loss can be recognized as a unique model for neural plasticity. However, the magnitude of the effect and the specific tasks where it’s manifested is still a subject for debate. In this study, we have created a tactile brain-computer interface game to study how somatosensory processing is different between the blind and the sighted people. The participants were required to attend to tactile stimuli, and the correct stimulus was selected using realtime EEG classification. We have shown, for the first time, that the blind subjects are significantly better than the sighted in tactile brain-computer interface tasks. We have also found, that individual performance is correlated with Braille proficiency. This result links personal perceptual abilities in two different sensory tasks. EEG analysis revealed that differences in performance can be attributed to early cognitive processing steps. Along with practical considerations in brain-computer interface development, the results also add to the data on cognitive processing in the blind and enable the discussion on the importance of Braille education.
Cancer-specific associations of driver genes with immunotherapy outcome
Authors: Jun Tomi , Qing Tao , Dong Guanlan , Signaevski Maxim , Hopkins Julia F , Frampton Garrett M , Albacker Lee A , Cordon-Cardo Carlos , Samstein Robert , Pusztai Lajos , Huang Kuan-lin 
Published: June 2020

AbstractGenomic features such as microsatellite instability (MSI) and tumor mutation burden (TMB) are predictive of immune checkpoint inhibitor (ICI) response. However, they do not account for the functional effects of specific driver gene mutations, which may alter the immune microenvironment and influence immunotherapy outcomes. By analyzing a multi-cancer cohort of 1,525 ICI-treated patients, we identified 12 driver genes in 6 cancer types associated with treatment outcomes, including genes involved in oncogenic signaling pathways (NOTCH, WNT, FGFR) and chromatin remodeling. Mutations ofPIK3CA, PBRM1, SMARCA4, andKMT2Dwere associated with worse outcomes across multiple cancer types. In comparison, genes showing cancer-specific associations—such asKEAP1, BRAF, and RNF43—harbored distinct variant types and variants, some of which were individually associated with outcomes. In colorectal cancer, a commonRNF43indel was a putative neoantigen associated with higher immune infiltration and favorable ICI outcomes. Finally, we showed that selected mutations were associated with PD-L1 status and could further stratify patient outcomes beyond MSI or TMB, highlighting their potential as biomarkers for immunotherapy.
Keen relationship between COVID_19 and food supply suggest some animal origin foods as excellent vehicle of SARS-Cov-2
Authors: Saeedi Nazli , Rafat Seyed Abbas 
Published: June 2020

AbstractIn recent months, nearly all countries tried to decrease human-to-human contact as the principal mode of transmission of SARS-CoV-2. However, other modes of transmission also need to be clarified in more depth, especially, the foodborne transmission. We assessed the effect of animal origin foods consumption on the pandemic of COVID-19. For this purpose, we studied the relationship among 20 food supply as independent variables, and the parameter of Total Cases as dependent variable. Here we show a relationship between a group of animal origin foods and total cases. Regression, Bayes, and Lasso results showed that eggs and fresh water fish have positive coefficient. So, among the transmission ways of COVID_19, the role of foodborne transmission should be more significant than previously thought. The possibility of animal origin foodborne transmission should be taken into more consideration. The perspective is to expand the surveillance of SARS-Cov-2 during the food production chain. In conclusion, the results of the present study indicate that one important vehicle for SARS-Cov-2 may be some of animal origin foods. It is recommended that virologists examine the possibility of freshwater fish and chicken‘s eggs being as excellent vehicles/preservatives for SARS-Cov-2.
Determinants of capital structure: evidence from Malaysian firms
Authors: Saif-Alyousfi Abdulazeez Y.H. , Md-Rus Rohani , Taufil-Mohd Kamarun Nisham , Mohd Taib Hasniza , Shahar Hanita Kadir 
Published: June 2020

PurposeThe purpose of this paper is to examine the determinants of capital structure using a dataset of firms in Malaysia.Design/methodology/approachThis paper carries out a panel data analysis of 8,270 observations from 827 listed non-financial firms on the Malaysia stock market over the period 2008–2017. To estimate the model and analyse the data collected from the DataStream and World Bank databases, the authors use static panel estimation techniques as well as two-step difference and system dynamic GMM estimator.FindingsThe results show that profitability, growth opportunity, tax-shield, liquidity and cash flow volatility have a negative and significant impact on debt measures. However, the effects of collateral, non-debt tax and earnings volatility on measures of debt are positive and significant. In addition, firm size, firm age, inflation rate and interest rate are important determinants of the present value of debt. The results also show a significant inverse U-shaped relationship between the firm's age and its capital structure. In general, the results support the proposition advocated by the pecking order and trade-off theories.Practical implicationsThe results of this study necessitate formulation of various policy measures that can counter the effects of debt on firms.Originality/valueThe present study is among the earliest to use both the book and market value measures of capital structure. It also uses three proxies for each: total debt, long-term debt and short-term debt. It incorporates earning volatility and cash flow volatility as new independent variables in the model. These variables have not previously been used together with both book and market value measures of capital structure. The study also examines the non-monotonic relationship between firm's age and capital structure using a quadratic regression method. It applies both static panel techniques and dynamic GMM estimation techniques to analyse the data.
Capturing customer’s store loyalty through relationship benefits: moderating effect of retail innovation
Authors: Channa Nisar Ahmed , Bhutto Maqsood Hussain , Bhutto Musaira , Bhutto Niaz Ahmed , Tariq Beenish 
Published: June 2020

Purpose
Research suggests that innovation plays a key role in creating a competitive edge and business survival in highly competitive industries like retail. Despite the importance of innovation in retail establishments, very limited efforts have been made so far to study how innovation influences consumer behavior in retail establishments. This paper aims to identify the impact of relationship benefits (i.e. confidence, social and special treatment benefits) on consumer’s loyalty with the retail store and examine the moderating effect of retailer innovation in these relationships.

Design/methodology/approach
To conduct this study, a sample comprised of 400 consumers of four retail sectors (i.e. household, electronics, textile and food) was chosen. The data were analyzed through partial least squares structural equation modeling (PLS-SEM) technique.

Findings
The findings of this research suggest a significant positive influence of confidence and special treatment benefits on consumer loyalty and that retail innovation moderates the link between relationship benefits and consumer loyalty.

Originality/value
This research contributes to the existing literature in the domain of retail customer loyalty by empirically testing the under-studied phenomenon of retail innovation with the help of contingency theory.
Causative effects of motivation to transfer learning among relational dyads: the test of a model
Authors: Matthews Brian , Daigle Jamie , Cooper Joy 
Published: June 2020

PurposeThe purpose of this study is to validate multiplicative cycle that exists between the job readiness and satisfaction model explored by Matthewset al. (2018), the satisfaction and performance paradigmatic nuances analyzed by Judgeet al. (2001) and Gu and Chi (2009), in addition to the expectancy model theorized by Vroom (1964). The motivation to transfer learning serves as a conveyable variable transmitted within a learning continuum that sustains cyclical outputs.Design/methodology/approachAn archetype to explore the connection between the three hypothesized theories is created through a neural network program. Exploring this connection develops deeper understandings of the derivatives of employee motivation as it pertains to its effect on readiness, satisfaction, performance and achievement dyads. A detailed analysis of the literature leads to the hypothesis that the motivation to transfer learning creates a multiplicative effect among hypothesized relationships.FindingsThe neural network program scaffolds the proposed general belief that positive effects of transfer motives cause a cyclical effect that continues to perpetuate among hypothesized dyads. Conversely, if this motivation decreases or ceases among one or more dyads, the cyclical effect will retract and, eventually stop.Originality/valueBased on the neurologic outcome, one central theme emerged: managers must offer opportunities to acquire knowledge through assistive mechanisms (i.e. training) by providing external stability through controlled channels that activates the motivation to transfer learning into new opportunities. The transference of this knowledge produces reconstructive growth opportunities through continuous learning thus increasing performance.
Factors underlying the perceived importance of online student engagement strategies
Authors: Bolliger Doris U. , Martin Florence 
Published: June 2020

PurposeThe purpose of this research study is to validate an instrument that measures the importance instructors and students place on online student engagement strategies.Design/methodology/approachThe online student engagement strategies survey was completed by 160 faculty and 146 students. The data were analysed using descriptive statistics and an exploratory factor analysis. The factor structure was examined using a principal component analysis with an oblique rotation.FindingsResults show that the Online Engagement Strategies Questionnaire has a valid and reliable structure. Based on the exploratory factor analysis, four engagement constructs emerged including peer engagement, multimodal engagement, instructor engagement, and self-directed engagement. Results and discussion assist in identifying key engagement strategies within this online student engagement framework.Originality/valueThe validated instrument fills a gap in the literature, and it has value to practitioners, researchers, administrators and policy makers because it has practical applications.
Applying the MOA (motivation-opportunity-ability) model for the evaluation of residents' participation in built heritage rehabilitation: the case of Constantine
Authors: Benedjma Iqbal , Mahimoud Aissa 
Published: June 2020

PurposeIt has been widely recognised that the participation of residents is a significant issue in contemporary urban heritage conservation. However, studies confirm that the reasons behind residents' engagement are still difficult to assess, particularly in emerging countries. This paper aims to evaluate the factors that incite or prevent residents from participating in built heritage rehabilitation in the old city of Constantine, by applying the motivation-opportunity-ability (MOA) model.Design/methodology/approachA questionnaire-based survey was used to collect information from the residents. The collected data were then analysed using the structural equation model (SEM).FindingsThe findings show that the most significant factors affecting residents' participation were related to their motivations and abilities. Interestingly, factors related to the opportunities did not influence participation. Thus, autonomous rehabilitation according to the residents' motivation and abilities is more likely to be adopted.Research limitations/implicationsThese findings are limited to the selected sample, and some variables have been eliminated through the SEM analysis.Originality/valueHowever, as a first attempt to study residents' participation in built heritage rehabilitation in Constantine, the paper proposes a different perspective for assessing participation by considering its means and ends simultaneously. The paper also provides guidance to local decision-makers to improve the legal framework by implementing factors that encourage residents' involvement in sustainable heritage management.
New semi three-dimensional approach for simulation of Lamb wave clamp-on ultrasonic gas flowmeter
Authors: Mousavi Seyed Foad , Hashemabadi Seyed Hassan , Jamali Jalil 
Published: June 2020

Purpose
The purpose of this study is to numerically simulate the Lamb wave propagation through a clamp-on ultrasonic gas flowmeter (UGF) in contact mode, using a new semi three-dimensional approach. Moreover, experimental and analytical modeling results for transit time difference method have been used to confirm the simulation results at different gas flow velocities from 0.3 to 2.4 m/s.

Design/methodology/approach
The new semi three-dimensional approach involves the simulation of the flow field of the gas in a three-dimensional model and subsequently the simulation of wave generation, propagation and reception in a two-dimensional (2D) model. Moreover, the analytical model assumes that the wave transitions occur in a 2D mode.

Findings
The new approach is a semi three-dimensional approach used in this work, has better accuracy than a complete 2D simulation while maintaining the computing time and costs approximately constant. It is faster and less expensive than a complete 3D simulation and more accurate than a complete 2D simulation. It was concluded that the new approach could be extended to simulate all types of ultrasonic gas and non-gas flowmeters, even under harsh conditions.

Originality/value
In this work, a new approach for the numerical simulation of all types of ultrasonic flowmeters is introduced. It was used for simulation of a Lamb wave ultrasonic flow meter in contact mode.
Out‐of‐hospital Circulatory Measures to Identify Patients With Serious Injury: A Systematic Review
Authors: Newgard Craig D. , Cheney Tamara P. , Chou Roger , Fu Rongwei , Daya Mohamud R. , O'Neil Maya E. , Wasson Ngoc , Hart Erica L. , Totten Annette M. 
Published: June 2020

AbstractObjectiveThe objective was to systematically identify and summarize out‐of‐hospital measures of circulatory compromise as diagnostic predictors of serious injury, focusing on measures usable by emergency medical services to inform field triage decisions.MethodsWe searched Ovid MEDLINE, CINAHL, and the Cochrane databases from 1996 through August 2017 for published literature on individual circulatory measures in trauma. We reviewed reference lists of included articles for additional relevant citations. Measures of diagnostic accuracy included sensitivity, specificity, and area under the receiver operating characteristic curve (AUROC). Indicators of serious injury included resource need, serious anatomic injury, and mortality. We pooled estimates when data permitted.ResultsWe identified 114 articles, reporting results of 111 studies. Measures included systolic blood pressure (sBP), heart rate (HR), shock index (SI), lactate, base deficit, and HR variability. Pooled out‐of‐hospital sensitivity estimates were sBP < 90 mm Hg = 19% (95% confidence interval [CI] = 12% to 29%), HR ≥ 110 beats/min = 28% (95% CI = 20% to 37%), SI > 0.9 = 37% (95% CI = 22% to 56%), and lactate > 2.0 mmol/L = 74% (95% CI = 48% to 90%). Pooled specificity estimates were sBP < 90 mm Hg = 95% (95% CI = 91% to 97%), HR ≥ 110 beats/min = 85% (95% CI = 74% to 91%), SI > 0.9 = 85% (95% CI = 72% to 92%), and lactate > 2.0 mmol/L = 62% (95% CI = 51% to 72%). Pooled AUROCs included sBP = 0.67 (95% CI = 0.58 to 0.75), HR = 0.67 (95% CI = 0.56 to 0.79), SI = 0.72 (95% CI = 0.66 to 0.77), and lactate = 0.77 (95% CI = 0.67 to 0.82). Strength of evidence was low to moderate.ConclusionsOut‐of‐hospital circulatory measures are associated with poor to fair discrimination for identifying trauma patients with serious injuries. Many seriously injured patients have normal circulatory measures (low sensitivity), but when present, the measures are highly specific for identifying patients with serious injuries.
Helping Friends or Influencing Foes: Electoral and Policy Effects of Campaign Finance Contributions
Authors: Schnakenberg Keith E. , Turner Ian R. 
Published: June 2020

AbstractCampaign finance contributions may influence policy by affecting elections or influencing the choices of politicians once in office. To study the trade‐offs between these two paths to influence, we use a game in which contributions may affect electoral outcomes and signal policy‐relevant information to politicians. In the model, a campaign donor and two politicians each possess private information correlated with a policy‐relevant state of the world. The donor may allocate his or her budget to either an ally candidate who has relatively similar preferences or a moderate candidate whose preferences are relatively divergent from the donor's preferred policy. Contributions that increase the likelihood of the moderate being elected can signal good news about the donor's preferred policy and influence the moderate's policy choice. However, when the electoral effect of contributions is too small to demand sufficiently high costs to deter imitation by groups with negative information, this informational effect breaks down.