bluuebunny/crossref_metadata_2025 huggingface dataset:
Knowledge and attitudes about HIV pre-exposure prophylaxis: Evidence from in-depth interviews and focus group discussions with policy makers, healthcare providers, and end-users in Lesotho
Authors: Geldsetzer Pascal , Chebet Joy J. , Tarumbiswa Tapiwa , Phate-Lesihla Rosina , Maponga Chivimbiso , Mandara Esther , Bärnighausen Till , McMahon Shannon A.
Published: June 2022

Studies on PrEP knowledge and attitudes have mostly focused on key populations in North America and Europe. To inform Lesotho’s national rollout of PrEP to the general population, this research aimed to characterize knowledge and attitudes towards PrEP among policy makers, implementing partners, healthcare providers, and PrEP end-users in Lesotho. Respondents were purposively selected to participate based on personal experience in the development and implementation of Lesotho’s PrEP program, or the personal use of PrEP. We conducted 106 in-depth interviews with policy makers (n=5), implementing partners (n=4), and end-users (current PrEP users = 55; former PrEP users = 36; and PrEP “decliners” = 6). In addition, we held 11 focus group discussions (FGDs) with a total of 105 healthcare providers. Interview and FGD transcripts were analyzed following the tenets of Grounded Theory. Respondents expressed positive attitudes towards PrEP, owing to experienced and perceived personal, familial, and societal benefits. PrEP was viewed as i) an opportunity for serodiscordant couples to remain together, ii) a means of conceiving children with minimized risk of HIV infection, iii) providing a sense of agency and control, and iv) an avenue for addressing the HIV epidemic in Lesotho. Respondents demonstrated understanding of PrEP’s intended use, eligibility requirements, and modality of use. However, they also reported that several important misconceptions of PrEP were common among adults in Lesotho, including the belief that PrEP protects against sexually transmitted infections other than HIV, promotes promiscuity, prevents pregnancy, causes seroconversion, and provides lifelong protection from taking the pill just once. In addition to building on the perceived advantages of PrEP to shape a positive message, Lesotho’s national rollout of PrEP will likely benefit from a communication strategy that specifically addresses the common misconceptions of PrEP identified in this study.
A Multi-Institutional Study Benchmarking Cycle Threshold Values for Major Clinical SARS-CoV-2 RT-PCR Assays
Authors: Kirby J.E. , Cheng A. , Cleveland M.H. , Degli-Angeli E. , DeMarco C.T. , Faron M. , Gallagher T. , Garlick R.K. , Goecker E. , Coombs R.W. , Huang C. , Louzao R. , Denny T.N. , Morreale E. , Oakley G. , Reymann G. , Schade A. , Scianna S. , Tsongalis G.J. , Vallone P.M. , Huggett J. , Ledeboer N.A. , Lefferts J.A.
Published: June 2022

Real-time, reverse transcriptase PCR assays are a pervasive technology used for diagnosis of SARS-CoV-2 infection. These assays produce a cycle threshold value (Ct) corresponding to the first amplification cycle in which reliable amplification is detected. (1)Such Ct values have been used by clinicians and in public health settings to guide treatment, monitor disease progression, assess prognosis, and inform isolation practices. To understanding the risk of reporting out uncalibrated Ct values and potential for instead reporting out calibrated viral load values, we performed a multi-institutional study to benchmark major clinical platforms against a calibrated standard. We found that for any given Ct value, corresponding viral loads varied up to 1000-fold among the different tests. In contrast, when these different assays were calibrated against a common standard and then used to test unknown de-identified specimens at several dilutions, viral load values showed high precision between methods (standard deviation and range of 0.36 and 1.1 log10 genome copies) and high accuracy compared with droplet digital PCR (ddPCR) determinations (difference between mean CDC N2 and Sarbeco E ddPCR determinations and mean determinations by calibrated RT-PCR assays examined in our study of 0.044 log10 genome copies). We, therefore, find strong support for calibration of SARS-CoV-2 RT-PCR tests to allow conversion of cycle thresholds to accurate and precise viral load values that are reproducible across major clinical systems. Implementation of calibrated assays will provide more reliable information for clinical decision making and allow more rigorous interpretation of SARS-CoV-2 laboratory data in clinical and laboratory investigation.
Mathematical modelling of COVID-19 with periodic transmission: The case of South Africa
Authors: Assan Belthasara , Nyabadza Farai
Published: June 2022

The data on SARS-CoV-2 (COVID-19) in South Africa shows seasonal transmission patterns to date, with the peaks having occurred in winter and summer since the out-breaks began. The transmission dynamics have mainly been driven by variations in environmental factors and virus evolution, and the two are at the center of driving the different waves of the disease. It is thus important to understand the role of seasonality in the transmission dynamics of COVID-19. In this paper a compartmental model with a time dependent transmission rate is formulated and the stabilities of the steady states analysed. We note that if R0 < 1, the disease-free equilibrium is globally asymptotically stable, and the disease completely dies out and when R0 > 1, the system admits a positive periodic solution, and the disease is uniformly or periodically persistent. The model is fitted to data on new cases in South Africa for the first four waves. The model results clearly indicate the need to consider seasonality in the transmission dynamics of COVID-19 and its importance in modelling fluctuations in the data for new cases. The potential impact of seasonality in the transmission patterns of COVID-19 and the public health implications are discussed.
A stop-gain variant inBTNL9is associated with atherogenic lipid profiles
Authors: Carlson Jenna C. , Krishnan Mohanraj , Rosenthal Samantha L. , Russell Emily M. , Zhang Jerry Z. , Hawley Nicola L. , Moors Jaye , Cheng Hong , Dalbeth Nicola , de Zoysa Janak R. , Watson Huti , Qasim Muhammad , Murphy Rinki , Naseri Take , Reupena Muagututi’a Sefuiva , Viali Satupa‘itea , Stamp Lisa K. , Tuitele John , Kershaw Erin E. , Deka Ranjan , McGarvey Stephen T. , Merriman Tony R. , Weeks Daniel E. , Minster. Ryan L.
Published: June 2022

Current understanding of lipid genetics has come mainly from studies in European-ancestry populations; limited effort has focused on Polynesian populations, whose unique population history and high prevalence of dyslipidemia may provide insight into the biological foundations of variation in lipid levels. Here we performed an association study to fine map a suggestive association on 5q35 with high-density lipoprotein cholesterol (HDL-C) seen in Micronesian and Polynesian populations. Fine-mapping analyses in a cohort of 2,851 Samoan adults highlighted an association between a stop-gain variant (rs200884524; c.652C>T, p.R218*; posterior probability = 0.9987) inBTNL9and both lower HDL-C and greater triglycerides (TG). Meta-analysis across this and several other cohorts of Polynesian ancestry from Samoa, American Samoa, and Aotearoa New Zealand confirmed the presence of this association (βHDL-C= -1.60 mg/dL,pHDL-C= 7.63 × 10−10; βTG= 12.00 mg/dL,pTG= 3.82 × 10−7). While this variant appears to be Polynesian-specific, there is also evidence of association from other multi-ancestry analyses in this region. This work provides evidence of a previously unexplored contributor to the genetic architecture of lipid levels and underscores the importance of genetic analyses in understudied populations.
Upscaling health worker training on sepsis in South Eastern Nigeria using innovative digital strategies: an interventional study
Authors: Otu Akaninyene , Onwusaka Obiageli , Otokpa Daniel E. , Edadi Ukam , Udoh Ubong , Yougha Peter , Oduche Chinelo , Okuzu Okey , Jacob Shevin T , Rylance Jamie , Effa Emmanuel
Published: June 2022

Introduction

Sepsis is a leading cause of morbidity and mortality worldwide. In low- to middle-income countries (LMICs) such as Nigeria, the disproportionately high mortality rate is linked to lack of awareness, poor recognition, and late implementation of sepsis care bundles among health workers. Training of health workers using digital platforms may improve knowledge and skills and lead to better patient outcomes.

Methods

This Cross-sectional study involved developing and deploying a sepsis module through an innovative application (FHIND/ARCS Sepsis tutorial app) to doctors in Calabar, Nigeria. We assessed quantitative pre- and post-intervention knowledge scores for those completing the electronic training module on sepsis between both assessments. A user satisfaction survey evaluated the content of the tutorial and the usability of the app.

Results

One hundred and two doctors completed the course. There were more males than females (58.8% versus 41.2%). Over half (52%) were junior doctors, a minority were general practitioners and house officers (3% and 5%, respectively) and 72.6% had practiced for periods ranging from one to 15 years post qualification. Gender and age appeared to have no statistically significant association with pre- and post-test scores. The oldest age group (61-70) had the lowest mean pre- and post-test scores while general practitioners had higher mean pre- and post-test scores than other cadres.

The majority (95%) of participants recorded higher post-test than pre-test scores demonstrated by a statistically significant overall increase in mean scores (25.5% ±14.7, P<0.0001).

Participants were satisfied with the content and multimodal delivery of the material and found the app useable.

Conclusion

Digital training in sub-Saharan Africa is feasible and can sustainably close the critical knowledge gap required to respond more effectively to medical emergencies such as sepsis in LMIC settings.
Genomic analysis of Rad26 and Rad1–Rad10 reveals differences in their dependence on Mediator and RNA polymerase II
Authors: Gopaul Diyavarshini , Denby Wilkes Cyril , Goldar Arach , Giordanengo Aiach Nathalie , Barrault Marie-Bénédicte , Novikova Elizaveta , Soutourina Julie
Published: June 2022

Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/ERCC5(XPG) endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/ERCC6(CSB) and Rad1–Rad10/ERCC4(XPF)-ERCC1, addressing the question of a potential link of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae. Our genomic analyses reveal that Rad1–Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially at highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we show that Rad1–Rad10 and Rad26 colocalize with Mediator at intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we found that Mediator stabilization on core promoters leads to an increase in Rad1–Rad10 chromatin binding, whereas Rad26 occupancy follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results show the relationships between Rad1–Rad10, Rad26, Mediator, and Pol II, modulated by the changes in binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1–Rad10 and Rad26 NER proteins and reveal important differences in their dependence on Mediator and Pol II. Rad2 is the most dependent on Mediator, followed by Rad1–Rad10, whereas Rad26 is the most closely related to Pol II. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair machineries, which are relevant for human diseases including cancer and XP/CS syndromes.
Coordination in a not-for-profit organisation during the COVID-19 pandemic: organisational sensemaking during planning meetings
Authors: Kober Ralph , Thambar Paul J.
Published: June 2022

Purpose

The authors examine how a not-for-profit organisation (NPO) coordinates NPO's actions during the coronavirus disease 2019 (COVID-19) global pandemic to remain focussed on strategic and operational goals.

Design/methodology/approach

The authors conducted a live case study of an NPO as the crises caused by the COVID-19 pandemic unfolded. Drawing on a sensemaking perspective that incorporates sensegiving, the authors develop a framework of five types of organisational sensemaking. The authors analyse weekly planning meetings during which managers discussed past performance, forecast performance and the forecast duration of current cash reserves.

Findings

The authors show how three of the five types of organisational sensemaking helped to coordinate actions. The authors highlight how accounting information triggers organisational sensemaking processes; but depending on the type of organisational sensemaking, accounting information has little further role. The authors also show that the stability of decisions depends on the types of organisational sensemaking.

Practical implications

The authors show how coordination as a management control practice is enabled by organisational sensemaking within an NPO during a crisis. Organisational sensemaking enabled the agreement of actions, which enabled coordination. Accounting practices provided trigger mechanisms to facilitate organisational sensemaking.

Originality/value

Since this study is the first to examine sensemaking processes and accounting practices in coordination in an NPO in a pandemic, the authors contribute to the limited research on NPOs during crises and on the management control practice of coordination. The authors extend the accounting literature on sensemaking by showing that, whilst accounting triggers organisational sensemaking, accounting is only implicated in one type of organisational sensemaking and by revealing the different outcomes of the different types of organisational sensemaking.
Conceptualising language archives through legacy materials
Authors: Weber Tobias
Published: June 2022

Purpose

The purpose of this paper is to discuss the role of linguistic legacy materials within archives and databases. These data of past documentation projects are currently playing a minor role in the design of modern language archives. This is due to various challenges that legacy materials pose – ethical considerations, difficulties with formats, unclear or deficient metadata. Tackling these challenges can highlight general issues in language documentation and the use of language data. These insights can be used to inform the design of tools and infrastructures for data in this field, both recent and legacy materials.

Design/methodology/approach

This paper is conceptual and theorises digital language archives through their oldest deposits. It is informed by the author’s experiences in working with linguistic legacy materials of the South Estonian Kraasna dialect. The discussion makes references to relevant discourses in linguistics, archiving and computer science, encouraging transdisciplinary efforts in the design of language archives.

Findings

A digital archive created around linguistic legacy materials has the potential to respond to challenges posed by current data.

Originality/value

This paper discusses digital language archives from the perspective of documentary linguistics. It introduces the challenges and necessary steps in curating legacy materials. Several suggestions for the design of digital archives arise from this discussion. These ideas can inspire creators of digital language archives and provide a view from researchers using legacy materials.
End-to-end digital transformation for document flow at a professional council in South Africa
Authors: Chauke Tshepo Arnold , Ngoepe Mpho
Published: June 2022

Purpose

Many organisations, including professional councils, operate manually to ensure document flow to clients and stakeholders. This results in the loss of valuable documentation such as certificates and the incurring of costs due to the returning of post to the sender. The purpose of this study was to explore digital transformation of document flow at the South African Council for Social Science Professionals.

Design/methodology/approach

The methodological approach involved qualitative data collected through interviews, observation and document analysis in response to research questions. The study was a participatory action research project that involved collaboration between researchers and study participants in defining and solving the problem through needs assessment exercise. All three phases of participatory action research were followed, namely, the “look phase”: getting to know stakeholders so that the problem is defined on their terms and the problem definition is reflective of the community context; the “think phase”: interpretation and analysis of what was learned in the “look phase” and the “act phase”: planning, implementing, and evaluating, based on information collected and interpreted in the first two phases.

Findings

The study identified various issues relating to poor data quality, high rate of registered postal returns and non-delivery electronic messages that cannot reach all the intended recipients and accumulation of data for decades. In this regard, the study proposes a framework that can be used by SACSSP to update and verify their details on the portal, as well as digital certificates for membership.

Research limitations/implications

Although the proposed framework is tailor-made for the professional council, it is not depended on prescribed technologies due to usage of open standards that can be used by industry and researchers. Therefore, it can be applied in other context where institutions such as universities communicate with many clients via postal or courier services.

Originality/value

The study used participatory action research involving the researchers and the organisation to solve the problem. The study presented a workflow that the council can use to ensure that the documents reach intended recipients. Furthermore, digital transformation of the process will ensure that the registered professionals are able to access their certificates online and can print them when necessary.
The stakeholder's roles in risk management related to food supply chain recalls: a systematic literature review
Authors: Oliveira Lucas Lima de , da Silva Andrea Lago , Pereira Carla Roberta , Chaudhuri Atanu
Published: June 2022

Purpose

Food supply chains (FSCs) are becoming increasingly complex and vulnerable to recall risks due to quality failures. Measures for supply chain risk management can minimize these recall risks. However, this responsibility must be shared by all stakeholders in the chain. This study aims to analyze the roles of different stakeholders in managing risks in the events of food recalls.

Design/methodology/approach

A systematic literature review was carried out, and 110 articles were explored to identify risk management actions and to link them to the role of stakeholders involved in FSC recall.

Findings

The study found that nine stakeholders were responsible for 25 hazard management actions related to food safety and traceability systems, regulatory and preventive measures, and control and response mechanisms for food recalls in the FSC.

Originality/value

This article contributes to the literature by proposing an explanatory map associating risk management actions to different stakeholders in food recall. The actions were grouped according to whether they were prevention actions to avoid a food recall or contention actions to limit the negative economic effects and maintain the health of the population.
Students' experiences of academic coaching in Norway: a pilot study
Authors: Brevik Saethern Beate , Glømmen Anne Margrethe , Lugo Ricardo , Ellingsen Pål
Published: June 2022

Purpose

The purpose of this study was to identify and describe how students experience academic coaching in higher education in Norway.

Design/methodology/approach

The study employed a descriptive and exploratory qualitative design where semi-structured interviews formed the basis for data collection. Thematic analysis was used as an analytic strategy to identify, organise and find patterns or themes that emerged from the data.

Findings

The findings showed that academic coaching positively influenced the respondents' ability to identify the necessary and efficient cognitive processes and metacognitive skills needed to cope with everyday scholastic challenges. Academic coaching affected the respondents' metacognitive skills and cognitive processes in terms of evolving their self-efficacy, self-awareness, self-regulation, motivation, stress identification, goal identification, goal setting and development of new strategies.

Research limitations/implications

The findings in this study reflect the respondents' subjective opinions and further research is needed to validate these findings.

Originality/value

This article addresses a gap in the field of research by offering a descriptive pilot study and thematic analysis of students' experiences with academic coaching in Norway.
Robust market timing tests of Canadian hybrid mutual funds
Authors: Ayadi Mohamed A. , Chaibi Anis , Kryzanowski Lawrence
Published: June 2022

Purpose

Prior research has documented inconclusive and/or mixed empirical evidence on the timing performance of hybrid funds. Their performance inferences generally do not efficiently control for fixed-income exposure, conditioning information, and cross-correlations in fund returns. This study examines the stock and bond timing performances of hybrid funds while controlling and accounting for these important issues. It also discusses the inferential implications of using alternative bootstrap resampling approaches.

Design/methodology/approach

We examine the stock and bond timing performances of hybrid funds using (un)conditional multi-factor benchmark models with robust estimation inferences. We also rely on the block bootstrap method to account for cross-correlations in fund returns and to separate the effects of luck or sampling variation from manager skill.

Findings

We find that the timing performance of portfolios of funds is neutral and sensitive to controlling for fixed-income exposures and choice of the timing measurement model. The block-bootstrap analyses of funds in the tails of the distributions of stock timing performances suggest that sampling variation explains the underperformance of extreme left tail funds and confirms the good and bad luck in the bond timing management of tail funds. We report inference changes based on whether the Kosowski et al. or the Fama and French bootstrap approach is used.

Originality/value

This study provides extensive and robust evidence on the stock and bond timing performances of hybrid funds and their sensitivity based on (un)conditional linear multi-factor benchmark models. It examines the timing performances in the extreme tails funds using the block bootstrap method to efficiently identify (un)skilled fund managers. It also highlights the sensitivity of inferences to the choice of testing methodology.
Managerial perspectives on green-lean-six sigma adoption in the flexible packaging industry: empirical evidence from an emerging economy
Authors: Farrukh Amna , Mathrani Sanjay , Sajjad Aymen
Published: June 2022

Purpose

This paper attempts to explore the green-lean-six sigma (GLSS) practices in the continuous process industry particularly in the flexible packaging (FP) industry in an emerging economy for addressing environmental sustainability issues.

Design/methodology/approach

The authors have employed a qualitative multiple-case approach to examine managerial perspectives on GLSS adoption in the flexible packaging industry. Semi-structured interviews with senior corporate managers in two large FP organizations in Pakistan were conducted as the primary source of data collection.

Findings

Drawing on the natural resource-based view (NRBV), the analysis revealed that organizations are implementing key GLSS practices such as environmental management system (ISO 14001), cause–effect analysis, renewable energy sources, total productive maintenance, and statistical process control to effectively manage waste, conserve resources, control air emissions, and improve environmental and workplace safety.

Originality/value

The authors argue that this is one of the first research studies that has utilized NRBV to investigate the application of the GLSS approach in the process industry, specifically in the FP industry in an emerging economy.
Keep calm—this is a judgment-free zone: teacher perceptions about classroom intervisitations
Authors: Cascio González Elizabeth
Published: June 2022

Purpose

This article aims to consider teacher's views about intervisitations regarding its application and its usefulness as a community-enhancer. Many educators venture into the world of teaching because they love learning and value learning from their peers (rather than merely from text or administrators); however, teacher reservations or hesitations towards the practice of engaging in intervisitations do exist and can serve as an obstacle.

Design/methodology/approach

The findings reported in this study resulted from the analysis of two teacher's perspectives towards classroom intervisitations. The subset of data presented in this study resulted from the surveys and semi-structured interviews that were conducted. Qualitative methodology was used to address the research question as it allows for a greater exploration, description and ideally the emotions of participants/teachers. The coding process consisted of open coding, which then led to axial coding and the elevation of codes to themes.

Findings

In this study, teacher buy-in would be enhanced through the protocol feeling more personalized, less-dictated and more flexible in its execution, especially through the support of administrators and district leaders. In addition, teacher mindsets and perceptions also need some reshifting and should be part of the professional development process involving intervisitation roll-outs as any hesitations/limitations/and lack of willingness need to be honed in on and prioritized. Lastly, limiting teachers from an appropriate amount of time to complete such work may also encourage shallow collaboration among teachers instead of in-depth reflexive practice. By prioritizing intervisitations and/or inter-teacher collaboration in the building and allowing teachers to embark on professional development sessions with each other as a means of growing as a teacher and community, all will flourish.

Originality/value

Through examining the narratives of two educators, it was found that teacher willingness to partake in intervisitations is dependent on the school climate, particularly with regards to trust and a yearn-to-learn among inter-school peers and administrators. In addition, providing ample time and educating teachers on the benefits of such practices enhances one's wanting to independently venture into such work.
Changes in eating behaviours due to crises, disasters and pandemics: a scoping review
Authors: Hunter Lauren , Gerritsen Sarah , Egli Victoria
Published: June 2022

Purpose

This literature scoping review aims to investigate if, how and why eating behaviours change after a crisis event such as a natural disaster, financial crisis or pandemic in high-income countries.

Design/methodology/approach

The COVID-19 pandemic and resulting “lockdowns” and social distancing measures have changed access to food, the types of food consumed and usual eating behaviours. Early research on the effect of the COVID-19 pandemic is compared with existing literature on other high-impact crises in high-income countries around the world, such as Hurricane Katrina and the Global Financial Crisis. A search of four electronic databases in August 2020 of literature from 2000 to 2020 yielded 50 relevant publications that were included in the qualitative thematic analysis.

Findings

The analysis found that crisis events made accessing food more difficult and led to increased food insecurity. Home cooking, sharing food and eating together (within households during the pandemic) all increased during and after a crisis. Resources often reduced and needed to be pooled. Crises had a multi-directional impact on dietary patterns, and the motivators for dietary pattern change differ between populations and crises.

Originality/value

In conclusion, eating behaviours impacted by crises because of the disruption of food systems, increased food insecurity and changes in daily routines. Community networks were a strong protective factor against adverse outcomes from food insecurity.
Characterization of Haemaphysalis longicornis microbiome collected from different regions of Korean peninsula
Authors: Sang Min Kyu , Park Jie eun , Song Dae Kwon , Jeong Jun Yang , Hwang Hee Ju , Kim Hyun woo , Kim Tae Yun , Park So Young , Kang Se Won , Patnaik Bharat Bhusan , Cha Sung‐Jae , Han Yeon Soo , Lee Hee Il , Lee Yong Seok
Published: June 2022

Ticks are vectors that cause disease by transmitting bacteria, viruses, and protozoa to humans or animals. The Asian longhorned tick Haemaphysalis longicornis, a vector of medical and veterinary importance, is widely distributed in the Korean peninsula and can transmit various pathogens including Rickettsia spp., Borrelia spp., Francisella spp., Coxiella spp., and severe fever with thrombocytopenia syndrome virus (SFTS virus). Despite the abundance and importance, studies on the microbiome of H. longicornis in Korea are limiting. Here we first report the microbiome diversity of H. longicornis in terms of region, stage, and sex. H. longicornis used in this study were collected from 16 different regions. The V3‐V4 region was amplified and sequenced by MiSeq platform. The microbial diversity analysis was performed using Qiime2. A total of 1,754,418 non‐chimeric reads were obtained from a total of 46 samples, and an average of 126 operational taxonomic units (OTUs) and a total of 1,398 OTUs were identified. Our results were used for H. longicornis microbial community database construction for each region that enables to identify singularities in each region.
Population structure of 3907 worldwide pigs and the introgression of Chinese indigenous pigs by European pigs
Authors: Tang Hongbo , Ouyang Jing , Liu Siyu , Xiong Yanpeng , Wu Yongfei , Wang Luping , Wang Cong , Yan Xueming , Shen Yangyang , Chen Hao
Published: June 2022

With the improvement in sequencing technology and the decrease in sequencing cost, increasing amounts of genomic data for pigs have been uploaded to public databases. However, no researchers have to date integrated all currently available data to uncover the global genetic status of pigs. Meanwhile, little is known about the introgression from European to Chinese pigs and its underlying influences. Therefore, we integrated the effective genotype data of 3907 pigs from 193 populations worldwide using population genetic analysis, gene flow analysis and a sharing‐IBD study. These findings illustrate not only the population structure of 59 Chinese native breeds and others but also the amounts of gene flow and introgression that have occurred between Western and Chinese pigs. In addition, we demonstrate the presence of introgressed European haplotypes in Chinese indigenous breeds and identify relevant introgressed regions that contain genes associated with growth and feed efficiency. Moreover, we compare the introgression patterns of Western and Chinese pigs and further discuss possible explanations for why the level of introgression differs between Chinese pig breeds and Western modern breeds. Collectively, this study provides a fine global population structure analysis of pigs and presents evidence of European pigs being interbred with local breeds in China.
Isolation of Leydig cells from adult rat testes by magnetic‐activated cell sorting protocol based on prolactin receptor expression
Authors: Ji Minpeng , Chen Dan , Zhao Xingyi , Huang Fu , Guan Xiaoju , Wen Xin , Wang Jiexia , Shao Jingjing , Xie Jiajia , Shan Dan , Cao Shuyan , Chen Congde , Chen Haolin
Published: June 2022

Background

The primary function of testicular Leydig cells (LCs) is to produce testosterone (T). In vitro culture of the cells represents a very important approach to study androgen production and its regulations. Various methods have been developed for the enrichment of the cells from the testes. However, getting cells in large numbers with high purity and viability is still challenging. Here, we describe a new way to isolate LCs from rat testes in large quantity with high purity and viability.

Methods

Enzymatic digested testicular cells from adult rats were labelled with prolactin receptor (PRLR) antibody. The positive cells were isolated by magnetic‐activated cell sorting (MACS) protocol. Purified LCs were tested in vitro for their steroidogenic (T production) and non‐steroidogenic (25‐OH‐vitamin D production and Insl3 and Cyp2r1expressions) functions in the presence of Luteinizing Hormone (LH) for up to 24 h.

Results

Reanalysis of scRNA‐seq data indicates that Prlr expression is highly specific in LCs of adult rat testis. MACS procedure based on PRLR expression was able to isolate LCs with very high yield (about 106 cells/testis), high purity (about 95%) and viability (> 93%). Purified LCs retained high steroidogenic and non‐steroidogenic functions in responding to maximal LH stimulations, with more than 10‐fold increases in T production in 3 h and 42% and 103% increases in Insl3 and Cyp2r1 expressions in 24 h.

Discussion and conclusion

We have established an excellent way to purify high quality LCs from adult rat testis that can serve as a useful tool to study the physiology, pharmacology and toxicology of the cells in vitro.
Refusing Colonial Forms of Solidarity on O’odham Lands/theUS–Mexico Borderlands
Authors: Kartal Rebekah
Published: June 2022

In the US–Mexico borderlands, coalitions have formed to successfully thwart attempted amplification of militarisation in the region. However, in the borderlands, where migrants are criminalised and the colonisation of Indigenous lands and life is ongoing, coalition building is complicated due to the distinct positionalities of anti‐militarisation activists. This paper analyses solidarity from the perspective of anti‐militarisation organisations and activists in Southern Arizona/on occupied O’odham lands. I contend that desires for solidarity built around the worker, despite the recognition of unique struggles, reveal certain tendencies in activism remain bound to settler colonial ways of relating and understanding. Nonetheless, I argue that ongoing resistance to settler colonial terms of condition may motivate moves to refuse colonial forms of solidarity by reimagining coalition building as transpiring through reciprocal exchange of (hi)stories between differently positioned activists, rather than seeking a struggle that is common to all.
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Authors: Lee Jung‐Seok , Park Jin‐Young , Chung Hye‐Min , Song Young Woo , Strauss Franz‐Josef
Published: June 2022

The cover image is based on the Research Article Vertical ridge augmentation feasibility using unfixed collagen membranes and particulate bone substitutes: A 1‐ to 7‐year retrospective single‐cohort observational study by Jung‐Seok Lee et al., https://doi.org/10.1111/cid.13084.

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Musical Garden Paths: Evidence for Syntactic Revision Beyond the Linguistic Domain
Authors: Cecchetti Gabriele , Herff Steffen A. , Rohrmeier Martin A.
Published: June 2022

While theoretical and empirical insights suggest that the capacity to represent and process complex syntax is crucial in language as well as other domains, it is still unclear whether specific parsing mechanisms are also shared across domains. Focusing on the musical domain, we developed a novel behavioral paradigm to investigate whether a phenomenon of syntactic revision occurs in the processing of tonal melodies under analogous conditions as in language. We present the first proof‐of‐existence for syntactic revision in a set of tonally ambiguous melodies, supporting the relevance of syntactic representations and parsing with language‐like characteristics in a nonlinguistic domain. Furthermore, we find no evidence for a modulatory effect of musical training, suggesting that a general cognitive capacity, rather than explicit knowledge and strategies, may underlie the observed phenomenon in music.
Simplicity as a Cue to Probability: Multiple Roles for Simplicity in Evaluating Explanations
Authors: Vrantsidis Thalia H. , Lombrozo Tania
Published: June 2022

People often face the challenge of evaluating competing explanations. One approach is to assess the explanations’ relative probabilities–for example, applying Bayesian inference to compute their posterior probabilities. Another approach is to consider an explanation's qualities or “virtues,” such as its relative simplicity (i.e., the number of unexplained causes it invokes). The current work investigates how these two approaches are related. Study 1 found that simplicity is used to infer the inputs to Bayesian inference (explanations’ priors and likelihoods). Studies 1 and 2 found that simplicity is also used as a direct cue to the outputs of Bayesian inference (the posterior probability of an explanation), such that simplicity affects estimates of posterior probability even after controlling for elicited (Study 1) or provided (Study 2) priors and likelihoods, with simplicity having a larger effect in Study 1, where posteriors are more uncertain and difficult to compute. Comparing Studies 1 and 2 also suggested that simplicity plays additional roles unrelated to approximating probabilities, as reflected in simplicity's effect on how “satisfying” (vs. probable) an explanation is, which remained largely unaffected by the difficulty of computing posteriors. Together, these results suggest that the virtue of simplicity is used in multiple ways to approximate probabilities (i.e., serving as a cue to priors, likelihoods, and posteriors) when these probabilities are otherwise uncertain or difficult to compute, but that the influence of simplicity also goes beyond these roles.
Postdiction in Visual Awareness and Intrinsic Religiosity
Authors: Kéri Szabolcs
Published: June 2022

The mistiming and fusion of predictive thought and actual perception result in postdiction in awareness, a critical factor in the emergence of nonrational beliefs. Individuals with delusive thinking tend to experience a temporal reversal of prediction (“I guess the rain will fall.”) and real perception (“I feel the rain falling.”), incorrectly showing conviction that their predictions are correct. It is unknown how postdiction is related to religious cognition with a particular reference to intrinsic religiosity when religious beliefs and values are master motives and fundamental frameworks of life. Using a temporal decision‐making task, we investigated a group of religiously committed individuals, atheists, and people from the general community. Results revealed higher postdiction at short thought‐precept time intervals in the intrinsic religious group relative to the atheists. Intrinsic religiosity, but not delusive thinking, was predicted by postdiction in both religious individuals and the general population. These results indicate that people who display pronounced thought‐percept reversal and fusion feel that they are close to a higher power and the sacred.
Elephants are Gray: Linguistic Sensitivity and the Use of Generic Utterances in Pedagogical and Nonpedagogical Contexts
Authors: Markwalder Ursina , Saalbach Henrik , Schalk Lennart
Published: June 2022

Prior research indicates that humans adapt their language depending on context. This linguistic sensitivity has been suggested to indicate a natural pedagogy shared by all humans. This sensitivity has, however, only been demonstrated with English‐speaking samples thus far. In two studies, we followed the experimental procedure of the original study to replicate their findings with German‐speaking samples. With Study 2 conducted in the diglossic environment of the German‐speaking part of Switzerland, we were additionally able to provide a first test for whether this sensitivity is restricted to the language spoken in formal educational settings or occurs also in everyday language. Across both studies, we found a more frequent use of generic utterances in the pedagogical context than in the nonpedagogical context, both in Germany (Study 1) and in Switzerland (Study 2). These results and the strong effect sizes provide clear support for a natural pedagogy.
N6‐methyladenosine‐modified circRNA RERE modulates osteoarthritis by regulating β‐catenin ubiquitination and degradation
Authors: Liu Yuxi , Yang Yunhan , Lin Yucheng , Wei Bing , Hu Xinyue , Xu Li , Zhang Weituo , Lu Jun
Published: June 2022

Objectives

N6‐methyladenosine (m6A) is one of the most abundant internal RNA modifications. We investigated the role of m6A‐modified circRERE in osteoarthritis (OA) and its mechanism.

Materials and Methods

CircRERE and IRF2BPL were screened by microarrays. The role of m6A‐modification in circRERE was examined by methylated RNA precipitation and morpholino oligo (MOs) treatment. The axis of circRERE/miR‐195‐5p/IRF2BPL/β‐catenin was determined using flow cytometry, western blotting and immunofluorescence in human chondrocytes (HCs) and corroborated using a mouse model of destabilization of medial meniscus (DMM) with intra‐articular (IA) injection of adeno‐associated viruses (AAV).

Results

CircRERE was decreased in OA cartilage and chondrocytes compared with control. CircRERE downregulation was likely attributed to its increased m6A modification prone to endoribonucleolytic cleavage by YTHDF2‐HRSP12‐RNase P/MRP in OA chondrocytes. MOs transfection targeting HRSP12 binding motifs in circRERE partially reversed decreased circRERE expression and increased apoptosis in HCs treated with IL‐1β for 6 h. CircRERE exerted chondroprotective effects by targeting miR‐195‐5p/IRF2BPL, thus regulating the ubiquitination and degradation of β‐catenin. CircRere (mouse homologue) overexpression by IA‐injection of AAV‐circRere into mice attenuated the severity of DMM‐induced OA, whereas AAV‐miR‐195a‐5p or AAV‐sh‐Irf2bpl reduced the protective effects. The detrimental effects of AAV‐sh‐Irf2bpl on DMM‐induced OA were substantially counteracted by ICG‐001, an inhibitor of β‐catenin.

Conclusions

Our study is a proof‐of‐concept demonstration for targeting m6A‐modified circRERE and its target miR‐195‐5p/IRF2BPL/β‐catenin as potential therapeutic strategies for OA treatment.
Amyloid deposition with a granulomatous reaction in a resection specimen: A clue for a pre‐existing Merkel cell carcinoma
Authors: Rothrock Aimi T. , Truong Luan D. , Shehabeldin Ahmed , Wong Michael K. K. , Cho Woo Cheal , Nagarajan Priyadharsini , Vanderbeck Kaitlin , Curry Jonathan L. , Torres‐Cabala Carlos A. , Prieto Victor G. , Aung Phyu P.
Published: June 2022

Merkel cell carcinoma (MCC) is an aggressive, highly metastatic, cutaneous neuroendocrine malignancy with poor prognosis. Here, we describe a MCC excision specimen with a rare case of tumor‐associated amyloid deposition in the absence of residual tumor cells. A 72‐year‐old man presented with a lesion of 5–6 months' duration on his left elbow, clinically thought to be a ganglion cyst. The biopsy specimen revealed a Stage IIA MCC with classic histomorphologic and immunophenotypic findings, with tumor extending to the tissue edges. The patient underwent wide local excision with negative margins and a negative sentinel lymph node biopsy. Although the patient did not receive any presurgical chemotherapy, immunotherapy, or targeted therapy, the re‐excision specimen showed only amphophilic, feathery deposits that were salmon‐pink with Congo red stain and further confirmed as amyloid by electron microscopy; there were no residual carcinoma cells. Amyloid deposition in MCC has been described in rare case reports. Our case was extraordinary in that there was only amyloid deposition and an associated granulomatous reaction, without identifiable MCC cells. This case demonstrates that amyloid deposition may be evidence of a prior MCC at the site of a prior procedure and may warrant careful evaluation for residual MCC.
Finding what you don’t know: Testing SDM methods for poorly known species
Authors: Radomski Tom , Beamer David , Babineau Alan , Wilson Christa , Pechmann Joseph , Kozak Kenneth H.
Published: June 2022

Aim

A limitation of species distribution models (SDMs) is that species with low sample sizes are difficult to model. Yet, it is often important to know the habitat associations of poorly known species to guide conservation efforts. Techniques have been proposed for modelling species’ distributions from a few records, but their performance relative to one another has not been compared. Because these models are built and evaluated with small data sets, sampling error could cause severely biased sampling in environmental space. As a result, SDMs are likely to underpredict geographic distributions given small sample sizes. We perform the first comparison of methods explicitly promoted or developed for predicting the geographic ranges of species with very low sample sizes.

Location

North Carolina, USA.

Taxon

South Mountains Grey‐cheeked Salamander (Plethodon meridianus).

Methods

Using the sparse, existing georeferenced records ofP. meridianus, we built SDMs using a range of methods that previous researchers have argued should work for low sample sizes. We then tested each SDM’s ability to accurately predict independent survey data that were not georeferenced prior to our study. We compared SDMs using omission error and AUC.

Results

Roughly half of the models successfully predicted survey records in the range centre, and all models had high omission error rates in the range exterior. In the range of interior or exterior, the ‘ensemble of small models’ technique produced SDMs with high omission error rates. Spatial filtering had a negligible impact on model performance. Most, but not all, models outperformed predictions using distance from known populations. Using one of the best‐performing methods, we developed an improved range map ofP. meridianus.

Main Conclusions

Geographically peripheral populations were difficult to predict for all SDMs, though some methods were clearly inferior for our data set. We recommend that when sample sizes are low, researchers use Maxent with species‐specific model settings.