bluuebunny/crossref_metadata_2025 huggingface dataset:
Ratatosk – Hybrid error correction of long reads enables accurate variant calling and assembly
Authors: Holley Guillaume , Beyter Doruk , Ingimundardottir Helga , Kristmundsdottir Snædis , Eggertsson Hannes P. , Halldorsson Bjarni V.
Published: July 2020

Motivation

Long Read Sequencing (LRS) technologies are becoming essential to complement Short Read Sequencing (SRS) technologies for routine whole genome sequencing. LRS platforms produce DNA fragment reads, from 103to 106bases, allowing the resolution of numerous uncertainties left by SRS reads for genome reconstruction and analysis. In particular, LRS characterizes long and complex structural variants undetected by SRS due to short read length. Furthermore, assemblies produced with LRS reads are considerably more contiguous than with SRS while spanning previously inaccessible telomeric and centromeric regions. However, a major challenge to LRS reads adoption is their much higher error rate than SRS of up to 15%, introducing obstacles in downstream analysis pipelines.

Results

We present Ratatosk, a new error correction method for erroneous long reads based on a compacted and colored de Bruijn graph built from accurate short reads. Short and long reads color paths in the graph while vertices are annotated with candidate Single Nucleotide Polymorphisms. Long reads are subsequently anchored to the graph using exact and inexact fc-mer matches to find paths corresponding to corrected sequences. We demonstrate that Ratatosk can reduce the raw error rate of Oxford Nanopore reads 6-fold on average with a median error rate as low as 0.28%. Ratatosk corrected data maintain nearly 99% accurate SNP calls and increase indel call accuracy by up to about 40% compared to the raw data. An assembly of the Ashkenazi individual HG002 created from Ratatosk corrected Oxford Nanopore reads yields a contig N50 of 43.22 Mbp and less misassemblies than an assembly created from PacBio HiFi reads.

Availability

https://github.com/DecodeGenetics/Ratatosk

Contact

guillaume.holley@decode.is
Mode of Targeting to the Proteasome Determines GFP Fate
Authors: Bragança Christopher E. , Kraut Daniel A.
Published: July 2020

The Ubiquitin-proteasome system (UPS) is the canonical pathway for protein degradation in eukaryotic cells. Green fluorescent protein (GFP) is frequently used as a reporter in proteasomal degradation assays. However, there are multiple variants of GFP in use, and these variants have different stabilities. We previously found that the proteasome’s ability to unfold and degrade substrates is enhanced by polyubiquitin chains on the substrate, and that proteasomal ubiquitin receptors mediate this activation. Herein we investigate how the fate of GFP variants of differing stabilities is determined by the mode of targeting to the proteasome. We compared two targeting systems: linear Ub4degrons and the UBL domain from yeast Rad23, both of which are commonly used in degradation experiments. Surprisingly, the UBL degron allows for degradation of the most stable sGFP-containing substrates, while the Ub4degron does not. Destabilizing the GFP by circular permutation allows degradation with either targeting signal, indicating that domain stability and mode of targeting combine to determine substrate fate. Finally, we show that the ubiquitin receptor Rpn13 is primarily responsible for the enhanced ability of the proteasome to degrade stable UBL-tagged substrates.
Estimating the burden of COVID-19 on mortality, life expectancy and lifespan inequality in England and Wales: A population-level analysis
Authors: Aburto José Manuel , Kashyap Ridhi , Schöley Jonas , Angus Colin , Ermisch John , Mills Melinda C. , Dowd Jennifer Beam
Published: July 2020

Objective

To determine the impact of the COVID-19 pandemic on mortality, life expectancy and lifespan inequality in the first half of 2020 (from week 1 to week 26 starting June 22) in England and Wales.

Design

Demographic analysis of all-cause mortality from week 1 through week 26 of 2020 using publicly available death registration data from the Office for National Statistics.

Setting and population

England and Wales population by age and sex in 2020.

Main outcome measure

Age and sex-specific excess mortality risk and deaths above a baseline adjusted for seasonality in the first half of 2020. We additionally provide estimates of life expectancy at birth and lifespan inequality defined as the standard deviation in age at death.

Results

We estimate that there have been 53,937 (95% Prediction Interval: 53,092, 54,746) excess deaths in the first half of 2020, 54% of which occurred in men. Excess deaths increased sharply with age and men experienced elevated risks of death in all age groups. Life expectancy at birth dropped 1.7 and 1.9 years for females and males relative to the 2019 levels, respectively. Lifespan inequality also fell over the same period.

Conclusions

Quantifying excess deaths and their impact on life expectancy at birth provides a more comprehensive picture of the full COVID-19 burden on mortality. Whether mortality will return to - or even fall below - the baseline level remains to be seen as the pandemic continues to unfold and diverse interventions are put in place.

Summary boxes

What is already known on this topic

COVID-19 related deaths may be misclassified as other causes of death thereby underestimating the full impact of the pandemic on mortality. Excess mortality, the difference between observed deaths and what would have been expected in the absence of the pandemic, is a useful metric to quantify the overall impact of the pandemic on mortality and population health. Life expectancy at birth and lifespan inequality assess the cumulative impact of the pandemic on population health.

What this study adds

We examine death registration data from the Office for National Statistics from 2015 to week 26 (mid-year) in 2020 to quantify the impact of the COVID-19 pandemic on mortality in England and Wales thus far. We estimate excess mortality risk by age and sex, and quantify the impact of excess mortality risk on excess deaths, life expectancy and lifespan inequality. During weeks 10 through 26 of 2020, elevated mortality rates resulted in 53,937 additional deaths compared with baseline mortality. Life expectancy at birth for males and females in the first half of 2020 was 78 and 81.8 years, which represent a decline of 1.9 and 1.7 years of life lost relative to the year 2019. Lifespan inequality, a measure of the spread or variation in ages at death, declined due to the increase of mortality at older ages.
A three-dimensional musculoskeletal model of the dog
Authors: Stark Heiko , Fischer Martin S. , Hunt Alexander , Young Fletcher , Quinn Roger , Andrada Emanuel
Published: July 2020

Dogs are an interesting object of investigation because of the wide range of body size, body mass, and physique. In the last several years, the number of clinical and biomechanical studies on dog locomotion has increased. However, the relationship between body structure and joint load during locomotion, as well as between joint load and degenerative diseases of the locomotor system (e.g. dysplasia), are not sufficiently understood. In vivo measurements/records of joint forces and loads or deep/small muscles are complex, invasive, and sometimes ethically questionable. The use of detailed musculoskeletal models may help in filling that knowledge gap. We describe here the methods we used to create a detailed musculoskeletal model with 84 degrees of freedom and 134 muscles. Our model has three key-features: Three-dimensionality, scalability, and modularity. We tested the validity of the model by identifying forelimb muscle synergies of a beagle at walk. We used inverse dynamics and static optimization to estimate muscle activations based on experimental data. We identified three muscle synergy groups by using hierarchical clustering. Predicted activation patterns exhibited good agreement with experimental data for most of the forelimb muscles. We expect that our model will speed up the analysis of how body size, physique, agility, and disease influence joint neuronal control and loading in dog locomotion.
Influence of governance regime on controller roles – supervisory board members’ perspectives on business unit controller roles and role conflict
Authors: Steens Bert , de Bont Anouk , Roozen Frans
Published: July 2020

Purpose

The plethora of changes in the corporate governance landscape over the past two decades has the potential to tighten governance regimes and influence the preference of supervisory board members vis-à-vis the involved decision-making role of business unit (BU) controllers and their independent fiduciary role. Stricter financial reporting and compliance requirements may lead organizations to prioritize the latter role. However, recent studies support the need to balance these roles, inducing the potential for role conflict. The purpose of this study is to shed light on the influence of a tight and loose governance regime on this balance as preferred by supervisory board members.

Design/methodology/approach

This study uses a unique data set from an experiment among 73 supervisory board members. The authors take their perspective because compliance with governance codes and corporate policies are relevant topics for their function.

Findings

The authors find evidence for the preference of supervisory board members for “all-round” BU controllers who, irrespective of the governance regime, demonstrate substantial levels of fiduciary and decision-making qualities and deal with the resulting role conflict.

Originality/value

The outcomes of the experiment among supervisory board members provide evidence for their preferences concerning the balance of the two primary controller roles and for the potential of role conflict. The authors have not found studies that provide such empirical evidence.
Can academic leadership competencies have effect on students' cognitive, skill and affective learning outcomes? Higher education perspective
Authors: Radwan Omaymah , Ghavifekr Simin , Abdul Razak Ahmad Zabidi
Published: July 2020

Purpose

The main purpose is to analyse the effect of academic leadership competencies (LCs) on student learning outcomes (SLOs) in terms of cognitive, skill and affective aspects.

Design/methodology/approach

The study utilised quantitative research that focussed on correlation design by randomly distributing questionnaires containing 53 items to a total of 496 faculty members in Saudi Arabia public higher education institutions (HEIs). The data was analysed using SPSS (V.24) and SEM-AMOS.

Findings

Results show a direct and significant effect of academic LC on students' cognitive, skill and affective learning outcomes in public HEIs.

Research limitations/implications

The main limitation was that the participants of public HEIs were from Saudi Arabia. However, the findings have provided valuable understandings and a comprehensive conclusion about the impact of academic LC on SLOs in terms of cognitive, skill and affective aspects. The study recommended that different LC should be further developed. Future studies proposed to investigate the factors that support academic leaders to affect SLOs directly in HEIs.

Originality/value

The findings contribute to the body of knowledge regarding the significant and direct effect of academic LC on SLOs in HEIs. The findings have the potential to reflect positively on the academic leaders in public HEIs. The findings act as a guide for HEIs in terms of the importance of academic LC for having desirable SLOs. This study is crucial for educational policymakers and practitioners of academic leadership as the academic leaders' effort will greatly contribute to the HEIs as well as the nation's development in general.
How to improve teachers’ instructional practices: the role of professional learning activities, classroom observation and leadership content knowledge in Turkey
Authors: Özdemir Nedim
Published: July 2020

Purpose

This study focused on the impact of principals' leadership content knowledge, evaluation practices and teachers' professional learning activities on classroom instruction.

Design/methodology/approach

Data were collected from 425 teachers who worked in 46 elementary and lower secondary public schools within two provinces in Turkey. Teachers were asked to fill out a questionnaire on principals’ leadership content knowledge, evaluation feedback, professional learning activities and changed instructional practices. This study employed multilevel structural equation modeling (MSEM) by using the Bayesian estimation method to analyze the research hypotheses.

Findings

Findings indicate that if teachers perceive the evaluation progress as more useful, then they will participate in more professional learning activities, and they will be more effective in their classroom practices. This study also indicates that teachers' professional learning activities stimulate their instructional practices.

Research limitations/implications

Although the number of schools and teachers allows using multilevel analysis, it limits the findings generalized beyond the sample. To compensate for this limitation, the author confirmed that the sample was representative of the larger population by examining the size of students and teachers, SES and teachers' job experience. The author also conducted a Bayesian estimator to strengthen the test of significance of effects.

Practical implications

This study underlines the critical role of leadership content knowledge in evaluating practices and providing useful feedback perceived by teachers in elementary and secondary schools. Principals should lead to instruction by knowing how to address a lack of teachers' pedagogical content knowledge and classroom practices. The Ministry of Education should support principals in becoming effective instructional leaders to observe teachers and provide them meaningful feedback on teaching.

Originality/value

Despite increased interest in this construct, research on principals' and teachers' responses to adapt the recent form of teachers’ performance evaluation systems is scant, especially in developing countries’ context. Moreover, little is known about the paths through which principals can enhance classroom practices by providing useful feedback. Given these trends in policy and practice context, this study provides empirical evidence that principals can enact the teachers' performance evaluation that affects classroom instruction.
Examining the interrelatedness among human resources management practices, entrepreneurial traits and corporate entrepreneurship in emerging markets: an evidence from Egypt
Authors: Shehata Gamal Mohamed , Montash Mohammed Abdel-Hakim , Areda Mohamed Raafat
Published: July 2020

Purpose

The main purpose of this paper is to investigate the relationships among a set of human resources management (HRM) practices, entrepreneurial traits (ET) and corporate entrepreneurship (CE) in an emerging market such as the Egyptian one.

Design/methodology/approach

This research is explanatory in nature where it explains the causal relationships between the variables. Data was collected from 230 human resources (HR) managers and professional serving in top Egyptian financial institutions. Data was analyzed using structural equation modeling with relevant goodness-of-fit statistics.

Findings

The results of this study indicate that HRM practices have significant impact on the development of ET of personnel currently operating in the Egyptian financial institutions. Besides, the results confirm the effect of HRM practices on ET, which in turn have significant impact on CE.

Practical implications

This research provides an appropriate direction for HR managers on how to best design HR programs directed toward the development of strong CE orientation. It also highlights the core ET needed to enhance CE in emerging economies. The validated hypothetical relationships of this model serve as the baseline for those managers to plan, execute and measure the consequences of those HRM programs.

Originality/value

Although HRM is widely considered as a critical driving force for CE, there is a remarkable scarcity of empirical research examining the role of ET. The conceptual model tested in this research typically deepens both HRM scholars and managers’ understanding of how they can best connect HRM practices to ET and CE in emerging economies. The findings of this study open the door for a new venue of research in the HRM area of study, particularly in emerging markets that search for a fast-growing rate of economic prosperity. The findings of this study lend support for HRM as an antecedent to CE rather than vice versa.
The effect of halal supply chain management on halal integrity assurance for the food industry in Malaysia
Authors: Mohamed Yusaini Hisham , Abdul Rahim Abdul Rahman , Ma'aram Azanizawati
Published: July 2020

Purpose

The purpose of this study is to outline the results of the empirical testing in the field of halal food supply chain and halal integrity assurance (HIA), as well as to provide a research framework of their relationships.

Design/methodology/approach

This study is based on the exploratory research paper using quantitative data collection to empirically experimented with concepts and provide practical solutions for halal industry players to optimize their halal food supply chain integrity assurance.

Findings

The findings show the halal supply chain of the food and beverage industry has a significant effect on HIA. The results also suggest the halal industry with a high focus on supply chain business processes and supply chain network structure are expected to have better HIA.

Research limitations/implications

As this study only focuses on the halal industry in Malaysia specifically on food and beverages, its findings cannot be generalized to other categories. Issues of applicability of this study to other countries also need to be considered.

Practical implications

This study addresses the assurance of halal integrity is a crucial element in managing a halal food supply chain in the halal industry. It has empirically identified the important elements to strengthen halal food supply chain integrity assurance in the halal industry.

Social implications

It is important to manage knowledge, commitment and trust in any halal organization as a catalyst for HIA. This study presents a better understanding of the halal concept application in society.

Originality/value

There is a lack of empirical study on halal food supply chain integrity assurance even though the issue of HIA is widely discussed in the halal industry. Thus, this study has used an industry survey to empirically experimented with concepts and provide practical contributions to enhance halal food supply chain integrity assurance.
Exploring the best policy scenario plan for the dairy supply chain: a DEMATEL approach
Authors: Susanty Aries , Puspitasari Nia Budi , Prastawa Heru , Renaldi Stellya Veronica
Published: July 2020

Purpose

This research primarily aims to find and analyse the interaction among success factors for improving the performance of Indonesia’s dairy milk supply chain. Further, this research aims to formulate the right policies for improving the performance of the chain based on the success factor that belongs to cause groups.

Design/methodology/approach

The paper analyses 10 success factors for improving the performance of the Indonesian dairy supply chain with the decision-making trial and evaluation laboratory (DEMATEL) method and analyses the Delphi method to formulate the right policies for improving performance.

Findings

There are four important influencing factors that directly impact the overall system, i.e. the number of dairy cattle import, national milk demand, the total number of dairy farmers and the number of dairy cattle ownership or herd size. Several alternative policies have been designed by several experts according to the influencing factors, i.e. the government assists in the procurement of imported cattle, provides financial assistance to farmers in the form of low-interest financing, improves the partnership system between farmers and dairy cooperatives, provides a reward system for the farmers and increases the level of formality of contract between the farmers and cooperatives.

Research limitations/implications

Interrelationships of each success factor and the most important influencing success factors could not be generally determined because it depends on the point of view of the experts. Future research can apply the success factors proposed by this research to the different dairy milk supply chain. Then, this research used only nine experts for formulating alternative policies. Future research may repeat this method using multiple experts to justify the validity of the research. Moreover, this research only explored 21 success factors of the increase in the performance of the Indonesian dairy supply chain. Future research should consider not only the supply side and number of dairy cattle but also several success factors from the causal relationship diagram in the broader dairy milk supply chain.

Practical implications

This research provides essential insights for policymakers, as they have to understand and evaluate the success factors before formulating several alternative policies.

Social implications

The research has revealed that the right alternative policies can be designed, as the causal factor has been known.

Originality/value

This research contributes to applying a combination of causal relationship diagram of System Dynamic and DEMATEL method as a qualitative and quantitative method in one integrated way through performance dairy supply chain analysis. As a result, this research draws a policy for the dairy supply chain referring to the success factor as a cause for the low performance of the Indonesian dairy supply chain.
The effect of workplace ostracism on knowledge sharing: the mediating role of organization-based self-esteem and organizational silence
Authors: Takhsha Mina , Barahimi Negar , Adelpanah Arash , Salehzadeh Reza
Published: July 2020

Purpose

This study aims to evaluate the effect of workplace ostracism on organization-based self-esteem (OBSE), organizational silence and knowledge sharing.

Design/methodology/approach

The statistical population of this research includes the employees of University of Isfahan in Iran. The structural equation modeling method is used to analyze the data and the conceptual model using 130 participants.

Findings

The empirical results suggest that ostracism and organizational silence influence knowledge sharing, negatively. Ostracism influences organizational silence, positively; and ostracism influences OBSE, negatively. Furthermore, organization-based self-esteem influences knowledge sharing, positively. In addition, the indirect relationship from ostracism to knowledge sharing through organizational silence was confirmed; however, the mediating role of OBSE in the relationship between workplace ostracism and knowledge sharing was not confirmed.

Originality/value

This research is among the first to evaluate the relationship between workplace ostracism, knowledge sharing, organizational silence and OBSE simultaneously.
Alliance justice and relational performance: the mediating role of boundary spanners' citizenship behaviors
Authors: Bai Xuan , Li Julie Juan
Published: July 2020

Purpose

The purpose of this paper is to examine the types of justice that affect knowledge acquisition and opportunism in strategic alliances and how these justice mechanisms function.

Design/methodology/approach

Data were collected from both top-level and operating-level boundary spanners in 295 strategic alliances in China (a total of 590 boundary spanners). A structural equation model (SEM) with bias-corrected bootstrap method was used to test the hypotheses.

Findings

The results show that although both procedural justice and distributive justice are important in deterring opportunism, procedural justice is more effective at enhancing knowledge acquisition than distributive justice is. The results also demonstrate that boundary spanners' helping behaviors are more effective at fostering knowledge acquisition, whereas boundary spanners' voice behaviors have more impact on mitigating opportunism. In addition, boundary spanners' citizenship behaviors partially mediate the relationship between justice and interfirm-level performance.

Originality/value

This study adds a boundary-spanning lens to justice literature by uncovering the missing link between justice and alliance outcomes.
The limits to employee involvement? Employee participation without HRM in a small not-for-profit organisation
Authors: Philip Karen , Arrowsmith Jim
Published: July 2020

Purpose

The strategic human resource management (HRM) literature emphasises the importance of employee involvement and participation for outcomes such as job satisfaction, employee retention and organisational performance. Situational factors identified as conducive to employee participation in decision-making include small size, via less hierarchical, proximate and informal workplace relations. Ownership and mission are also important, with not-for-profit (NFP) organisations generally having more collectivist, commitment-based cultures that support open decision-making. However, such organisations often have weak HRM policies and practices. This paper examines the process and outcomes of employee participation in a small NFP through in-depth case study research.

Design/methodology/approach

Single case study utilising longitudinal participant observation, interviews, reflective diary, documentary analysis.

Findings

Operating as a collective, the organisation was bound by time and capacity limitations in its ability to plan strategically or even to make routine decisions. Basic HR policies and practices in areas such as staff recruitment and performance management were sub-standard or unobserved. Consequences included poor management, inconsistent training, staff burnout, high labour turnover and sub-optimal performance. The results suggest that weak managerial coordination and the absence of a dedicated HR function subvert effective people management. In such circumstances, strong forms of employee participation fail to deliver anticipated equity and efficiency outcomes.

Research limitations/implications

Single case study.

Practical implications

Small organisations need HR policies and dedicated support to ensure that employee involvement and participation are effective.

Originality/value

The findings demonstrate how employee involvement and participation can be subverted by inadequate HR processes, adding qualitative evidence to support theories of HR “bundling” in high-involvement work practices. The research also contributes to the neglected area of HRM in small NFPs.
Annual report readability and trade credit
Authors: Xu Hongkang , Pham Trung H. , Dao Mai
Published: July 2020

Purpose

The purpose of this study is to examine the influence of the readability of annual reports on firms’ ability to obtain trade credit from suppliers. Particularly, the authors conjecture that annual report readability helps firms obtain more trade credit from suppliers.

Design/methodology/approach

The authors use the Gunning Fog Index as the primary measure of annual report readability and the ratio of accounts payable to the book value of total assets as the measure of trade credit.

Findings

Results from the study of 4,754 firms during the 2004–2016 period indicate that suppliers extend more trade credit to firms with more readable financial reports. The authors’ results are robust to alternative measures of trade credit and annual report readability. The authors’ results remain robust when we control for firm fixed effects and potential endogeneity problems using the instrumental variable approach. A further test shows that the level of trade credit is higher for firms in business service industries, and that this relation is weakened when firms disclose less readable 10-K filings.

Originality/value

The authors’ findings provide new insight into the role of financial report readability in firms’ ability to obtain trade financing from suppliers. The authors’ results are also in line with the SEC’s encouragement that firms use plain English and easy language in financial reporting.
Education, health and care plans: What do we know so far?
Authors: Cochrane Hannah , Soni Anita
Published: July 2020

The Children and Families Act, 2014 and the new Special Educational Needs and Disability SEND Code of Practice (DfE and DoH, 2014) has led to reforms in how children and young people with special educational needs and disabilities are supported in England. Now, five years on, research has begun to emerge exploring the implementation of the new statutory assessment process, the Education, Health and Care (EHC) plans and the outcomes of the process in England. This article seeks to review current research about the introduction of EHC needs assessment process and plans. It highlights three key themes: experiences of the process, reflections on the EHC plans and the outcomes of the process. Whilst parental involvement has improved, and there is some evidence of multiagency work, the views of children and young people continue to be marginalised, and EHC Plans are highly variable in quality, indicating that person‐centred approaches are not yet fully implemented. This indicates a need for further research on how to effectively involve CYP with SEND in statutory processes and support.
The Role of the Common Agricultural Policy in Enhancing Farm Income: A Dynamic Panel Analysis Accounting for Farm Size in Italy
Authors: Biagini Luigi , Antonioli Federico , Severini Simone
Published: July 2020

As a multi‐objective policy, the EU Common Agricultural Policy continues to secure significant income support for farmers as one of the nine specific objectives. We estimate the income transfer efficiency of a broad set of pivotal policy measures, focusing on the effects of farm structure on income transfer efficiency. We use dynamic modelling, based on a micro‐data panel of Italian farms for the period 2008–2014, allowing for endogeneity, simultaneity bias, and omitted variables. In line with previous studies and economic expectations, we find that decoupled direct payments provide the highest contribution to agricultural incomes, followed by agri‐environmental payments and on‐farm investment subsidies. Coupled payments have no significant impacts on farmers’ income. Generally, for all analysed Common Agricultural Policy measures, large farms benefit from greater transfer efficiency levels compared with medium and small farms. These differences among instruments and across farms suggest that policy‐participation costs may play a pivotal role, together with the economic structure of farms, in determining the income transfer efficiency of CAP policies.
Antibiotic resistance and biofilm formation ability of Salmonella serotypes isolated from beef, mutton, and meat contact surfaces at retail
Authors: Manafi Leila , Aliakbarlu Javad , Dastmalchi Saei Habib
Published: July 2020

In this study, Salmonella isolates recovered from meat (beef and mutton) and meat contact surfaces at retail were investigated to determine their serotype, antibiotic resistance, and biofilm formation ability. Salmonella was found in 29 (24.17%) samples out of 120 samples including 14/50 (28%) of beef, 10/40 (25%) of mutton, and 5/30 (16.67%) of meat contact surfaces. Seven isolates were identified as S. Enteritidis, three as S. Typhimurium, and two as S. Typhi, while the rest of the isolates were considered as other Salmonella spp. All of the isolates were resistant to at least one antimicrobial agent and 48.27% of them were identified as multidrug‐resistant (MDR) Salmonella. All (100%) of meat contact surfaces isolates, 42.8% of beef isolates, and 30% of mutton isolates were found to be MDR Salmonella. Resistance to nalidixic acid (100%), tetracycline (79.3%), and sulphamethoxazole/trimethoprim (44.8%) were observed. The gyrA gene was detected in 19 of 29 isolates, but tetA was found in one isolate. All of the serotypes were able to form biofilm (75.86 % moderate and 24.14 % strong) and S. Enteritidis was the strongest biofilm producer. The findings indicated that the majority of Salmonella isolates in this study were MDR and biofilm producer. Then, safety measures such as cleaning and disinfection must be taken to control Salmonella and promote public health.

Practical Application

The present study provides useful information on the prevalence of Salmonella serotypes in meat and meat contact surfaces and their antibiotic resistance patterns as well as biofilm formation capacities. Improving hygiene practices in livestock, slaughterhouses, and at retails may reduce the risk of meat contamination to Salmonella. Meanwhile, high levels of antibiotic resistance in Salmonella isolates emphasized on the improper use of antibiotics.
Association of circulating galectin‐3 with gestational diabetes mellitus, progesterone, and insulin resistance
Authors: Zhang Zeqing , Kang Xuehui , Guo Yaming , Zhang Jianhua , Xie Junhui , Shao Shiying , Xiang Ying , Chen Gang , Yu Xuefeng
Published: July 2020

Background/Objective

Because galectin‐3 has been proposed to regulate obesity and insulin resistance in mice, we hypothesized that circulating galectin‐3 levels are associated with presence of gestational diabetes mellitus (GDM), progesterone, and insulin resistance.

Methods

Circulating galectin‐3 levels were measured using an enzyme‐linked immunosorbent assay (ELISA) in women with GDM (n = 137) and their controls (n = 81). Associations of galectin‐3 and progesterone with GDM and insulin resistance were evaluated using regression models.

Results

Circulating galectin‐3 levels were increased in the individuals with GDM (P < .001) and associated significantly with progesterone (r = 0.42,P < .001), gestational age at sampling (r = 0.23,P < .001), current body mass index (BMI; r = 0.17,P= .02), estrogen (r = 0.15,P < .03), fasting glucose (r = 0.41,P < .001), fasting insulin (r = 0.39,P < .001), and homeostasis model assessment of insulin resistance (HOMA‐IR; r = 0.44,P < .001). After adjustment for potential confounders, including current BMI, subjects in the highest tertile of galectin‐3 levels were more likely to have GDM (odds ratio 4.71, 95% confidence interval 2.01‐11.06) as compared with the lowest tertile. The association between circulating galectin‐3 levels and GDM remained significant after adjusting for progesterone, but significantly attenuated after adjustment with HOMA‐IR. Furthermore, the multiple linear regression analyses after adjustment for confounders showed an independent association between galectin‐3 levels and HOMA‐IR (β = .41,P < .001), suggesting that association of circulating gelactin‐3 levels with GDM might be mediated via insulin resistance. Progesterone demonstrated the expected associations with galectin‐3, GDM, and HOMA‐IR.

Conclusions

Circulating galectin‐3 levels are associated with GDM possibly through increased insulin resistance. The association of galectin‐3 with progesterone highlights a potential role of progesterone in its interaction with galectin‐3.
The Infant Scalp Score: A Validated Tool to Stratify Risk of Traumatic Brain Injury in Infants With Isolated Scalp Hematoma
Authors: Schutzman Sara A. , Nigrovic Lise E. , Mannix Rebekah
Published: July 2020

Objectives

The objective was to validate the previously derived Infant Scalp Score (ISS) that uses clinical signs in infants with isolated scalp hematoma (ISH) after head trauma to stratify risk for clinically important traumatic brain injury (ciTBI) or TBI on computed tomography (CT).

Methods

Using the publicly available Pediatric Emergency Care Applied Research Network TBI data set, we selected infants ≤ 1 year with GCS 14 to 15 who had ISH (defined as hematoma without other signs/symptoms of TBI). CT scans were obtained at the treating physician’s discretion. We calculated ISS based on age, hematoma size, and location (range = 0–8) for each patient and calculated the sensitivity and specificity of the score for ciTBI and TBI on CT across a range of ISS cut‐points.

Results

We included 1,289 infants ≤ 1 year of whom 462 (36%) had CT performed. Twelve had ciTBI and 59 had TBI on CT. An ISS cutoff ≥ 4 had sensitivity of 100% for ciTBI (95% confidence interval [CI] = 0.74 to 1.0) and TBI with specificity of 0.49 (95% CI = 0.46 to 0.51). An ISS cutoff of ≥5 had a sensitivity of 100% for ciTBI (95% CI = 0.74 to 1.0) and specificity of 0.68 (95% CI = 0.66 to 0.71), but missed three infants with TBI on CT (none of whom required intervention). The receiver operating characteristic curves for clinical score to detect ciTBI and TBI had areas under the curve of 0.916 and 0.807, respectively.

Conclusions

The ISS accurately stratified risk for ciTBI and TBI on CT in infants with ISH and is a useful tool to help guide clinical decision making.
Detecting changes in task length due to task‐switching in the presence of repeated length‐biased sampling
Authors: Walter Scott R. , Brown Bruce M. , Dunsmuir William T.M.
Published: July 2020

Clinical work is characterised by frequent interjection of external prompts causing clinicians to switch from a primary task to deal with an incoming secondary task, a phenomenon associated with negative effects in experimental studies. This is an important yet underexplored aspect of work in safety critical settings in general, since an increase in task length due to task‐switching implies reduced efficiency, while decreased length suggests hastening to compensate for the increased workload brought by the unexpected secondary tasks, which is a potential safety issue. In such observational settings, longer tasks are naturally more likely to have one or more task‐switching events: a form of length bias. To assess the effect of task‐switching on task completion time, it is necessary to estimate counterfactual task lengths had they not experienced any task‐switching, while also accounting for length bias. This is a problem that appears simple at first, but has several counterintuitive considerations resulting in a uniquely constrained solution space. We review the only existing method based on an assumption that task‐switches occur according to a homogeneous Poisson process. We propose significant extensions to flexibly incorporate heterogeneity that is more representative of task‐switching in real‐world contexts. The techniques are applied to observations of emergency physicians’ workflow in two hospital settings.
Approximate Bayesian inference for case‐crossover models
Authors: Stringer Alex , Brown Patrick , Stafford Jamie
Published: July 2020

A case‐crossover analysis is used as a simple but powerful tool for estimating the effect of short‐term environmental factors such as extreme temperatures or poor air quality on mortality. The environment on the day of each death is compared to the one or more “control days” in previous weeks, and higher levels of exposure on death days than control days provide evidence of an effect. Current state‐of‐the‐art methodology and software (integrated nested Laplace approximation [INLA]) cannot be used to fit the most flexible case‐crossover models to large datasets, because the likelihood for case‐crossover models cannot be expressed in a manner compatible with this methodology. In this paper, we develop a flexible and scalable modeling framework for case‐crossover models with linear and semiparametric effects which retains the flexibility and computational advantages of INLA. We apply our method to quantify nonlinear associations between mortality and extreme temperatures in India. An R package implementing our methods is publicly available.
Who uses ride‐hailing? Policy implications and evidence from the Greater Toronto and Hamilton Area
Authors: Shi Hong Yun (Eva) , Sweet Matthias N.
Published: July 2020

While many are eager to guide policy decisions on ride‐hailing, understanding the broader social and travel implications hinges on local contexts. Towards providing policy guidance in the Canadian context, this paper explores how mobility sub‐markets are related to ride‐hailing use in the Greater Toronto and Hamilton Area. Using data from a 2018 travel survey, cluster analysis is used to identify four traveller sub‐markets which are compared with ride‐hailing use. The first comprises “multi‐modalists,” who are younger, mobile, educated, and represent the largest group of ride‐hailing users. Second are users in two auto‐oriented markets—“private modalists” and “auto dependents”—who are older and least likely to engage in ride‐hailing. Finally, “low‐mobility travellers” are the most socio‐economically vulnerable and have lower household incomes, lower education attainment, lower likelihoods of being employed, fewer cars per household, and the highest reliance on public transportation among users in the traveller sub‐markets. Nevertheless, this group represents the second largest market for ride‐hailing, which fills a mobility gap in the absence of auto access. Understanding the social and travel behaviour implications from ride‐hailing is important towards crafting context‐appropriate public policy. Results from this study suggest that ride‐hailing is primarily used by those who are already highly mobile (multi‐modalists) and those who are most vulnerable (low‐mobility travellers).
The understated turn: Emerging interests and themes in Canadian posthumanist geography
Authors: Asker Chloe , Andrews Gavin J.
Published: July 2020

Posthumanist geography is a broad tradition incorporating a range of intersecting theoretical approaches including assemblage theory, actor‐network theory, new materialisms, affect theory, neo‐vitalism, political ecology, post‐phenomenology, and non‐representational theory—as well as contributions from a number of theoretically progressive subject fields such as new mobilities, relational thinking, sensory and performance studies, biosocial and biopolitics studies, and science and technology studies. The specificities of and differences between these traditions and fields aside, common to posthumanism is a scepticism of human exceptionalism. Here, the sovereign human subject is decentred, and in doing so, posthumanist work acknowledges the agencies of a full array of human and non‐human actors and forces. Recognizing that there are important “geographies to (the discipline of) geography,” this paper identifies and reviews some of the key posthumanist interests and themes that have emerged over recent years quietly and organically in Canadian geography, namely posthumanist (i) Indigenous geographies; (ii) animal and natures geographies; (iii) health, wellbeing, and disability geographies; (iv) affective and atmospheric geographies; and (v) non‐representational and creative methodologies. The paper concludes with some thoughts on the nature and strengths of Canadian posthumanist geography, and on some possibilities for future advancement.
COVID-19 vaccine-readiness for anti-CD20-depleting therapy in autoimmune diseases
Authors: Baker D , Roberts C A K , Pryce G , Kang A S , Marta M , Reyes S , Schmierer K , Giovannoni G , Amor S
Published: July 2020

Although most autoimmune diseases are considered to be CD4 T cell- or antibody-mediated, many respond to CD20-depleting antibodies that have limited influence on CD4 and plasma cells. This includes rituximab, oblinutuzumab and ofatumumab that are used in cancer, rheumatoid arthritis and off-label in a large number of other autoimmunities and ocrelizumab in multiple sclerosis. Recently, the COVID-19 pandemic created concerns about immunosuppression in autoimmunity, leading to cessation or a delay in immunotherapy treatments. However, based on the known and emerging biology of autoimmunity and COVID-19, it was hypothesised that while B cell depletion should not necessarily expose people to severe SARS-CoV-2-related issues, it may inhibit protective immunity following infection and vaccination. As such, drug-induced B cell subset inhibition, that controls at least some autoimmunities, would not influence innate and CD8 T cell responses, which are central to SARS-CoV-2 elimination, nor the hypercoagulation and innate inflammation causing severe morbidity. This is supported clinically, as the majority of SARS-CoV-2-infected, CD20-depleted people with autoimmunity have recovered. However, protective neutralizing antibody and vaccination responses are predicted to be blunted until naive B cells repopulate, based on B cell repopulation kinetics and vaccination responses, from published rituximab and unpublished ocrelizumab (NCT00676715, NCT02545868) trial data, shown here. This suggests that it may be possible to undertake dose interruption to maintain inflammatory disease control, while allowing effective vaccination against SARS-CoV-29, if and when an effective vaccine is available.
The cytological features of sclerosing mucoepidermoid carcinoma with eosinophilia of the thyroid gland: A case report
Authors: Nam Jong‐Hee , Han Chang‐Woo , Kim Nah Ihm , Kim Sung‐Sun , Choi Yoo‐Duk
Published: July 2020

Sclerosing mucoepidermoid carcinoma with eosinophilia (SMECE) is very rare in the thyroid gland. Cytopathologists should carefully examine squamoid cluster and eosinophils in Hashimoto's thyroiditis to raise suspicion of SMECE.
Extracellular matrix remodeling with stress and depression: Studies in human, rodent and zebrafish models
Authors: Blanco Ismary , Conant Katherine
Published: July 2020

Emerging evidence suggests that extracellular matrix (ECM) alterations occur with stress. Specifically, increases in perineuronal net (PNN) deposition have been observed in rodents exposed to chronic corticosterone or persistent social defeat stress. The PNN is a specific form of ECM that is predominantly localized to parvalbumin (PV)‐expressing inhibitory interneurons where it modulates neuronal excitability and brain oscillations that are influenced by the same. Consistent with a role for ECM changes in contributing to the depressive phenotype, recent studies have demonstrated that monoamine reuptake inhibitor type antidepressants can reduce PNN deposition, improve behavior and stimulate changes in gamma oscillatory power that may be important to mood and memory. The present review will highlight studies in humans, rodents and zebrafish that have examined stress, PNN deposition and/or gamma oscillations with a focus on potential cellular and molecular underpinnings.
A process‐based metacommunity framework linking local and regional scale community ecology
Authors: Thompson Patrick L. , Guzman Laura Melissa , De Meester Luc , Horváth Zsófia , Ptacnik Robert , Vanschoenwinkel Bram , Viana Duarte S. , Chase Jonathan M.
Published: July 2020

The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: (1) density‐independent responses to abiotic conditions, (2) density‐dependent biotic interactions and (3) dispersal. Stochasticity is incorporated in the demographic realisation of each of these processes. We formalise this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning and stability within metacommunities.