bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of thermal comfort and adaptation among the residents of cold climate in the lower Himalayan region of eastern India
Authors: Thapa Samar
Published: January 2022

Thermal comfort standards are required for overall indoor satisfaction and energy conservation. Even though the lower Himalayan region of Darjeeling has seen rapid growth in population due to its temperate type of climate, and thus resulting in manifold construction of concrete buildings, very few research on the built environment are reported from the region. In this paper, the author has discussed the yearlong thermal comfort study conducted in a naturally ventilated 3-storey un-insulated concrete building located at lower Himalayan region of Darjeeling, India. The mean indoor operative temperature were 16.7°C, 19.0°C and 22.3°C, the clothing insulation were 0.94 clo, 0.78 clo and 0.57 clo and the mean Griffiths’ comfort temperature were 18.1°C, 19.6°C and 22.4°C during the cool, moderate and warm seasons, respectively. Seasonal and gender-wise differences are reported in the paper. A logistic regression is presented to show the variation of single and multiple layers of clothing used by subjects to adapt with the plummeting temperature. A modification in the comfort standards for the region with lower and upper limits as 16.2°C and 23.3°C is also proposed.
The impact of the COVID-19 lockdown on services for substance use in Denmark: Implications for meeting users’ needs and recommendations for the future
Authors: del Palacio-Gonzalez Adriana , Thylstrup Birgitte , Houborg Esben
Published: January 2022

Background: The aim of this study was to document employees’ experiences of changes in service provision for substance use disorders (SUDs) during the first COVID-19 lockdown in Denmark (spring 2020), as well as to examine their relation to challenges in meeting the service users’ needs. Methods: Employees ( N = 373) working in SUD treatment and harm reduction services completed an online survey soon after the first national lockdown. The survey included questions about changes in service provision during the lockdown, perceived concerns of the service users, and challenges in meeting the users’ emerging needs. Results: Employees reported some positive changes in service provisions, such as increased flexibility in appointments, administering medication-assisted treatment (MAT), and use of telehealth. Negative changes were related to reduced contact with practitioners and harm reduction facilities. Approximately one third of employees reported significant challenges in meeting the users’ emerging needs. This was particularly so when users’ concerns were about physical and mental well-being, and substance use. In regression models, negative changes in the access to practitioners and MAT administration (but not other changes) predicted difficulties meeting the users’ needs. Conclusion: Employees in SUD treatment and harm reduction services in Denmark experienced both positive and negative changes as a result of the first lockdown. However, not all the provision changes were linked to challenges in meeting the users’ needs. We discuss practical and research implications of our findings with a focus on the users’ physical and mental health, use of telehealth, MAT, and overall service reorganisation.
Policy windows for drug consumption rooms in Finland
Authors: Unlu Ali , Tammi Tuukka , Hakkarainen Pekka
Published: January 2022

Background: Use of drug consumption rooms is a novel harm reduction approach to reach marginalised and isolated people who used drugs, under the high risk of overdose deaths and infectious diseases. The aim of this article was to evaluate the policy opportunities and barriers of the Helsinki City initiative for establishing the first drug consumption room (DCR) in Finland from the multiple streams framework. Method: A qualitative interview research method is used to evaluate the perspectives of stakeholders. By including 23 participants, we analysed the political, social and policy level advantages and disadvantages of the current initiative. Findings: Our results show that the cost of DCRs, the COVID-19 burdens on public resources, the requirement of legislative change, public unawareness, potential policy failure of DCRs, and its impacts on electoral votes constitute the main policy barriers. On the other hand, an increase in drug-related deaths, economic benefits of DCR for society, its effects on street safety and public order, being a local initiative, prospectus change in national drug strategy plans and motivation to catch up with EU standards were underlined as policy opportunities. Four issues, leadership, moral perspective, social change and generational differences, act as mediating factors, which are fluctuated according to public opinions and political environment. Conclusion: By applying the multiple streams framework, our results show that experts’ DCR problematisation is still beyond the public and political interest, which needs additional effort around problem identification and prioritisation. Besides public unawareness, the COVID-19 situation seems to be postponing policy progress since the primary attention and available funds have already been dedicated to public health. Already having a local initiative and an upcoming drug strategy plan might be good formal leverage, but unexpected events might also trigger discussions.
Dynamic analysis of soil-structure interaction shear model for beams on transversely isotropic viscoelastic soil
Authors: Li Zele , Noori Mohammad , Basu Dipanjan , Taciroglu E , Wu Zhishen , Altabey Wael A
Published: January 2022

Dynamic response problem of the Timoshenko shear beam resting on the transversely isotropic viscoelastic foundation and subjected to a moving load is investigated. The extended Hamilton's principle is used to obtain the dynamic response equations of the beam-soil system. The corresponding partial differential equations are derived using variational principle. Using the analytical solutions, finite-element method, and central difference method, these differential equations are solved and mutually verified. The Newmark-β iterative algorithm is employed to decouple the dynamic equations of the beam-soil system. A modified two-parameter spring foundation model is used to simulate the dynamic characteristics of soil medium. Finite-element analysis demonstrates that the developed shear model of beam-soil is effective and accurate. Other numerical examples are carried out to analyze the effect of the shear beam, the load speed, and transverse isotropy of the dynamic medium model.
Integrationism, practice-dependence and global justice
Authors: McLaughlin Alex
Published: January 2022

An increasingly popular approach to global justice claims we should be ‘integrationist,’ where integrationism represents an attempt to unify our theorising between different domains of global politics. These political theorists have argued that we cannot identify plausible principles in one domain, such as climate justice, which are not sensitive to general moral concerns. This paper argues we ought to reject the concept of integrationism. It shows that integrationism is either trivial, or it obscures relevant disagreement by ignoring the distinctive methodological and substantive commitments held by its opponents. The paper then argues that the relevant disagreement is actually about the role of practices for political philosophy and, as such, should be framed in terms of the distinction between practice-dependent and practice-independent theory. Finally, I provide my own account of that distinction, identifying a practice-dependent claim that those concerned about the narrowness of prominent accounts of global justice should target.
Investigation on off-axial tensile properties of 3D braided composites considering void defects
Authors: Zhang Chao , Li Ang , Gu Yuefeng , Mao Chunjian , Xu Xiwu
Published: January 2022

3D braided composites have been increasingly applied in the aerospace, automotive, and other high-tech industries as primary load-bearing structures due to their excellent integrated performance. Evaluation on the failure behavior of 3D braided composites subjected to off-axial loading still remains a challenging topic. We present in this paper a meso-scale finite element (FE) model containing void defects for investigating the off-axial tensile behavior of 3D braided composites. The FE model is verified and the effects of porosity are discussed in on-axial tensile conditions, and then it is executed to predict the mechanical response in general off-axial tensile cases. The strength properties of 3D braided composites, and more importantly the progressive damage behavior under typical off-axial loadings, are analyzed in detail. It is found that the off-axial tensile strength and corresponding failure mode of 3D braided composites are mainly affected by the braiding angle of specimen. The proposed FE modeling provides an appropriate reference for the numerical study of void defects and off-axis load problems in other textile composites.
Analysis of Mechanoreceptors and Free Nerve Endings of the Transverse Carpal Ligament
Authors: de Lima Lana L. , Ariel de Lima Diego , Freire Thiago H. B. , Almeida Francisco A. A. , Leite José A. D. , Cavalcante Maria L. C.
Published: January 2022

Background: The treatment of carpal tunnel syndrome (CTS) by sectioning the transverse carpal ligament (TCL) is not exempt from complications. Some nerve branches may be damaged by the incision. The aim of this study is to identify and map the TCL nerve endings, serving as a guide for sectioning this structure in a zone with less nerve ending density. Methods: Ten TCLs were obtained from fresh frozen cadavers. The TCLs were measured, divided into 3 equal bands (radial, central, and ulnar), and submitted to cryostat sectioning. The sections were subjected to immunofluorescence with the protein gene product (PGP) 9.5 and confocal microscopy analysis. Results: All the specimens contained type I and type IV mechanoreceptors. Neural elements occupied 0.695 ± 0.056% of the ligament area. The density of the neural elements was greater in the radial, followed by the ulnar and central bands, with 0.730 ± 0.083%, 0.686 ± 0.009%, and 0.669 ± 0.031%, respectively. Conclusion: The present findings suggest that the region with the least potential for neural element injury during TCL release is the central third near the transition with the ulnar third. When performed distally to proximally with a slight inclination from the radial to the ulnar, this release compromises the lowest nerve element density. Topographically, the proximal limit of the release is the distal wrist crease, while the distal limit is the intersection of Kaplan cardinal line and the axis of the third webspace.
Why Does Polly Dance? Caste and the Function of Dance in the Victorian Theatre
Authors: Hodgson Amanda
Published: January 2022

What is the effect of the dance scene in Tom Robertson's play Caste? Little emphasis has been placed on the contribution of dance to Victorian theatre practice. Yet dance was ubiquitous, featuring prominently in such genres as melodrama and extravaganza, and providing the source material for burlesque. Dance was employed as a component of the mise-en-scène, as a marker of transformation, and to express what could not otherwise be expressed in a censored theatrical environment. In Caste these functions serve to provide a counterweight to, and enable a critique of, the play's prevailing naturalism.
Perspectives from Journalism Professionals on the Application and Benefits of Constructive Reporting for Addressing Misinformation
Authors: van Antwerpen Natasha , Turnbull Deborah , Searston Rachel A.
Published: January 2022

The proliferation of misinformation in contemporary information environments contributes to increasing polarization and decreasing trust in institutions and experts, both of which encourage further proliferation of misinformation. Increasing attention has been brought to the role of news media in the spread and uptake of misinformation, and to the role of journalists and news organizations in combatting this spread. Constructive journalism is a relatively new approach to reporting which, among other aims, looks to increase audience engagement, reduce polarization, and provide a more accurate view of events. In early 2020, we interviewed 16 journalism professionals from Europe (UK inclusive), Australia, Africa, and North America across a range formats to explore their perceptions of the use ‘constructive’ reporting strategies to address the spread of misinformation. We used thematic analysis to produce three themes and six subthemes in journalists’ responses, ‘apathy against the machine’, with subthemes ‘journalism as a moderator’, and ‘news and mental health’; ‘standards as shared reality’, with subthemes, ‘pluralism not postmodernism’, and ‘this means information war’; and ‘truth, trust, and the turn to transparency’, with subthemes, ‘facts necessary but not sufficient’, and ‘principles not particulars’. Constructive journalism was thought to address misinformation by increasing engagement with news and institutions, reducing polarization, providing a sense of shared reality amidst increasingly diverse perspectives, increasing trust, and reducing misperceptions encouraged by selection and reporting strategies. Constructive journalism may be a promising approach to addressing the spread and consequences of misinformation, however, empirical work is needed to evaluate the efficacy of the approach.
More Than Skin Deep: Dermatologic Conditions in Athletes
Authors: Pujalte George G.A. , Costa Lorena M.C. , Clapp Adrianna D. , Presutti R. John , Sluzevich Jason C.
Published: January 2022

Context:

Athletes are a unique group of patients whose activities, particularly in high-contact sports such as wrestling and football, place them at high risk of developing skin conditions. The correct diagnosis of sports dermatoses requires familiarity with their clinical characteristics. It is critical that primary care physicians recognize the most common skin disorders to provide prompt treatment and prevent transmission.

Evidence Acquisition:

The Mayo Clinic library obtained articles from 2012 onward related to dermatologic conditions in athletes.

Study Design:

Review article.

Level of Evidence:

Level 3.

Results:

Dermatologic diseases in athletes are often infectious and contagious due to close-contact sports environments. Sports-related dermatoses include bacterial infections, such as impetigo, ecthyma, folliculitis, abscesses, furuncles, carbuncles, erysipelas, and cellulitis; fungal infections, such as tinea and intertrigo; viral infections, such as herpes, verrucae, and molluscum contagiosum; and noninfectious conditions, such as acne, blisters, and contact dermatitis.

Conclusion:

This article aims to address the manifestations of the most common cutaneous diseases in athletes on the first primary care visit. It discusses the appropriate tests and most recent evidence-based treatments for each ailment. It also addresses return-to-play recommendations related to the guidelines and regulations of selected sports organizations in the United States.

Strength of Recommendation Taxonomy (SORT):

C.
Injury History and Perceived Knee Function as Risk Factors for Knee Injury in Youth Team-Sports Athletes
Authors: Hietamo Jussi , Rantala Anni , Parkkari Jari , Leppänen Mari , Rossi Marko , Heinonen Ari , Steffen Kathrin , Kannus Pekka , Mattila Ville , Pasanen Kati
Published: January 2022

Background:

The identification of risk factors for sports injuries is essential before injury prevention strategies can be planned.

Hypothesis:

Previous acute knee injury and lower perceived knee function measured by Knee injury and Osteoarthritis Outcome Score (KOOS) will increase the risk of acute knee injury in youth team-sports athletes.

Study Design:

Prospective cohort study.

Level of Evidence:

Level 3.

Methods:

At baseline, youth (≤21 years old) male and female basketball and floorball athletes completed a questionnaire on previous acute knee injuries and perceived knee function (KOOS). A total of 211 male and 183 female athletes were followed for an acute knee injury up to 3 years. Unadjusted and adjusted Cox regression models were used in risk factor analyses.

Results:

In male athletes, previous acute knee injury and lower KOOS Pain, Activities of Daily Living, Sport and Recreation, and knee-related Quality of Life subscale scores increased the risk of acute knee injury in the unadjusted analyses. Adjusted analyses for male injuries were not performed because of low number of acute knee injuries (n = 18). In female athletes, previous acute knee injury increased the risk of acute knee injury when adjusted for athletes’ age and body mass index (hazard ratio, 2.6 [95% CI, 1.3-5.2]). In female athletes, none of the KOOS subscale scores were associated with the increased risk of acute knee injury in the adjusted analyses.

Conclusion:

Previous acute knee injury was associated with the risk of new acute knee injury in youth male and female athletes. In youth male athletes, additionally, lower perceived knee function in 4 out of 5 KOOS subscale scores were associated with the increased risk of new acute knee injury.

Clinical Relevance:

The treatment and rehabilitation of the present acute knee injury and secondary prevention of reinjury should be emphasized in youth team-sports athletes.
Quarantine and Mental Health Challenges for Occupational Medicine: The Case Report of a Nurse Infected With SARS-CoV-2
Authors: Buselli R. , Corsi M. , Veltri A. , Baldanzi S. , Chiumiento M. , Del Lupo E. , Marino R. , Necciari G. , Caldi F. , Perretta S. , Foddis R. , Guglielmi G. , Cristaudo A.
Published: January 2022

This case study draws attention to the psychosocial difficulties that emerged in the context of the coronavirus disease 2019 (COVID-19) outbreak in relation to the remote management of subjects with psychiatric vulnerabilities following exposure to prolonged quarantine. The case involves a 56-year-old hospital nurse, followed by the Occupational Health Department of a major university hospital in central Italy for mood instability in the context of a cyclothymic temperament. She was quarantined for occupationally acquired COVID-19 and remained positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via swab test for more than 2 months between March and May 2020. In this case study, we discuss the challenges presented by the risk of a prolonged quarantine in a psychologically vulnerable employee, the need for occupational medicine to provide adequate health surveillance of all health care workers during the COVID-19 pandemic, the effectiveness of telepsychiatry, and the difficulties in formulating a proper treatment strategy.
Metatarsal Bone Marrow Edema on Magnetic Resonance Imaging and Its Correlation to Bone Stress Injuries in Male Collegiate Basketball Players
Authors: Tenforde Adam S. , Outerleys Jereme , Bouxsein Mary L. , Buckless Colleen G. , Besier Thor , Davis Irene S. , Bredella Miriam A.
Published: January 2022

Background:

The presence of bone marrow edema (BME) on magnetic resonance imaging (MRI) has been used to evaluate for bone stress injuries in athletes.

Purpose:

To examine the prevalence of MRI findings, including BME, in a single male collegiate basketball team before and after a single season and to assess its association with clinically symptomatic metatarsal bone stress injuries.

Study Design:

Cohort Study; Level of evidence, 3.

Methods:

A total of 16 men on a single collegiate basketball team (mean age, 20.0 ± 1.8 years) underwent 1.5-T MRI focused on both midfeet during the preseason, and 13 underwent repeat MRI during the postseason. MRI findings included the presence of BME and the radiographic classification of the bone stress injury (grades 1-4). Injury surveillance performed by athletic trainers was used to identify metatarsal bone stress injuries over the course of the season.

Results:

Preseason MRI demonstrated metatarsal BME in 5 of the 16 participants, and postseason MRI demonstrated metatarsal BME in 4 of the 13 participants. All 4 of the participants with postseason BME had MRI findings of BME in the same metatarsals. Compared to those without BME, participants with metatarsal BME had a shorter history of basketball exposure (preseason: 10.4 ± 4.1 vs 14.2 ± 1.9 years, respectively [ P = .023]; postseason: 9.6 ± 4.1 vs 14.0 ± 2.1 years, respectively [ P = .024]), and those with postseason BME had started playing at an older age (9.8 ± 4.3 vs 6.2 ± 1.6 years, respectively; P = .050). The preseason MRI classification for metatarsals included grade 1 (n = 3), followed by grades 2 and 3 (n = 2 each). In the 4 participants with postseason MRI findings, the grade increased from 1 to 4 in 1 participant and was stable in the other 3. No participants were diagnosed clinically with a metatarsal bone stress injury during the season. BME of the sesamoids was identified in 6 participants, who trended toward being older (21.0 ± 2.2 vs 19.4 ± 1.3 years, respectively; P < .10), with the abnormalities persisting on postseason MRI in all players.

Conclusion:

Collegiate male basketball players may have a high prevalence of BME, often without associated symptoms. The absence of foot pain or a corresponding diagnosis of a metatarsal bone stress injury in this study suggests that MRI findings of BME in asymptomatic athletes should be interpreted with caution.
Red Flags of Dating Violence Among College Students: From the Perspective of Campus Service Providers in Costa Rica
Authors: Munoz-Rojas Derby , Ching-Alvarez Cristobal , Gonzalez-Pons Kwynn M.
Published: January 2022

Dating violence has negative consequences on the well-being of college students. Thus, it is imperative that providers of student-oriented services can detect and respond to dating violence. Although many universities worldwide have implemented dating violence screenings protocols, they are not yet common practice in Costa Rica. As a result, there is inadequate recognition of this problem, so it remains unaddressed. Therefore, this qualitative descriptive study explored the perceptions of professionals working in student-oriented services in Costa Rica about dating violence warning signs exhibited by college students. 29 providers from four public universities were interviewed, and three main areas were identified from a content analysis: the process that providers follow to identify dating violence, the visible signs that victims display, and the self-protective strategies that victims employ to hide their abuse. These findings are important for researchers and practitioners wanting to improve dating violence screening instruments for the Central American context.
Meta-regression Analysis of Study Heterogeneity for Systemic Outcomes after Periodontal Therapy
Authors: Oates T.W. , Guy V. , Ni K. , Ji C. , Saito H. , Shiau H. , Shah R. , Williams M.A. , Blasi G. , Goloubeva O.
Published: January 2022

Introduction:

The contribution of periodontal disease to adverse systemic consequences remains controversial. This analysis examined 2 well-investigated conditions independently and combined—adverse pregnancy outcomes and glycemic control for patients with diabetes—based on shared pathogenic mechanisms of periodontal infection and inflammation. It was proposed that inconsistencies in study design significantly contribute to outcome discrepancies found between periodontal intervention studies undergoing meta-analysis.

Methods:

Meta-analyses evaluating periodontal interventions on the rate of preterm birth and changes in glycated hemoglobin A1c in type 2 diabetes populations were conducted based on a systematic review of randomized controlled trials. Meta-regression covariates for exploring heterogeneity included sample size, level of medical management, and bias risk as moderator variables in a random-effects meta-regression.

Results:

Systematic review identified 17 studies of diabetes and 13 of pregnancy outcomes. Analyses of these studies identified 0.50% reduction in HbA1c and 0.78 odds ratio for preterm births. The heterogeneity associated with the models was high (I2 = 92.4 and I2 = 62.7%, respectively). The adjusted models evaluating each systemic condition separately accounted for 52.2% of the effect for diabetes and 81.4% for pregnancy outcome effects independently, and 63.5% collectively, across interventional studies.

Conclusion:

This systematic review with meta-regression analysis of heterogeneity demonstrates that disparate results seen in randomized controlled trials of periodontal therapy affecting systemic outcomes may be explained in large part by study design, specifically stringency in consideration of medical management and sample size. The potential for confounding factors to influence outcomes remains a concern in understanding the implications of oral health on systemic conditions.

Knowledge Transfer Statement:

The findings of this study demonstrate that much of the benefits seen from periodontal therapy on adverse systemic outcomes for diabetes and pregnancy are due to limitations in study design.
Contextuality of Entrepreneurial Orientation and Business Performance: The Case of Women Entrepreneurs in Bangladesh
Authors: Mozumdar Lavlu , Materia Valentina C. , Hagelaar Geoffrey , Islam Mohammad Amirul , Velde Gerben van der , Omta S. W. F. (Onno)
Published: January 2022

The present study intends to contribute to the debate on whether and how the entrepreneurial orientation (EO) theory explains business performance by exploring its efficacy when applied to a constrained context such as a developing country. This debate revolves around the understanding of the nature of EO within a specific context and the degree to which EO, as compared to environmental characteristics, contributes to business performance. In particular, it analyses the influence of EO on the business performance of women entrepreneurs engaged in the handicraft business in Bangladesh, focussing on the effect the business and social environments exert on this relation. The results obtained from hierarchical multiple regression analyses suggest that the EO construct requires flexibility in its conceptualisation and that the implications EO has on performance need to be understood in the light of the context in which the theory is adopted. Concerning the nature of EO, we find that, first, a combination of EO dimensions (rather than them individually taken as per the original theory) explains business performance in a constrained context. In particular, women who show characteristics of innovativeness and pro-activeness (as one construct) seem to report high performances, as well as those showing behaviours more prone to taking risks. However, while barriers posed by the social environment (e.g., socio-cultural norms and customs) tend to impact performance negatively, barriers in the business environment positively relate to business performance. This suggests that further research is needed to investigate how the local constrained context mediates EO’s impact on performance. Our findings contribute to the research efforts directed to understanding the dimensionality of the EO construct when applied to a constrained context and pave the way to the quest for what role the external factors (namely, the social and business environment) play in explaining performance in such a context.
From information to public preparedness in the Cascadia Subduction Zone: Examining risk communication outcomes in Metropolitan Portland, OR
Authors: MacPherson-Krutsky Carson C , Brand Brittany D , Lindell Michael K
Published: January 2022

A Cascadia Subduction Zone (CSZ) earthquake will cause widespread damage along the Pacific Northwest (PNW) coast of the United States. It is, therefore, crucial to understand how to reduce future impacts across this region and assess current levels of household preparedness. Here, we examine whether decades of risk and preparedness campaigns have established protective knowledge and promoted hazard adjustments for residents of the Portland, Oregon metropolitan (PDX) region, an area where risk and preparedness campaigns have been increasing over the last decade. We also explore how PDX preparedness levels compare to those in other PNW regions using analogous data from multiple surveys over a 20-year time interval and assess PDX respondent’s perceptions of risk information sources. We find that 63% of PDX residents do not intend to “Drop, Cover, and Hold On” (DCHO) when earthquake shaking starts and that, although residents are generally aware of earthquake hazards in the area, they are less aware of the specific risks for their homes. Furthermore, PDX residents’ preparedness levels seem to be comparable to those recently surveyed in Washington, but somewhat less than those surveyed two decades ago in California, though more comprehensive data are needed to verify these results. We also find that people rate risk information provided by emergency managers and their websites as more accurate, understandable, relevant, and new than other sources. Our results suggest that significant gaps remain in translating broad awareness of the CSZ earthquake into personal knowledge and preparedness. This work provides guidance to PDX emergency educators for more targeted messaging and provides methods to measure preparedness variables in other regions for future comparisons. By paying close attention to preparedness gaps, local officials can use their limited resources more effectively to develop strategies to inform their communities and improve preparedness before a major earthquake strikes.
scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data
Authors: Nguyen Vy , Griss Johannes
Published: January 2022

Background

Automatic cell type identification is essential to alleviate a key bottleneck in scRNA-seq data analysis. While most existing classification tools show good sensitivity and specificity, they often fail to adequately not-classify cells that are missing in the used reference. Additionally, many tools do not scale to the continuously increasing size of current scRNA-seq datasets. Therefore, additional tools are needed to solve these challenges.

Results

scAnnotatR is a novel R package that provides a complete framework to classify cells in scRNA-seq datasets using pre-trained classifiers. It supports both Seurat and Bioconductor’s SingleCellExperiment and is thereby compatible with the vast majority of R-based analysis workflows. scAnnotatR uses hierarchically organised SVMs to distinguish a specific cell type versus all others. It shows comparable or even superior accuracy, sensitivity and specificity compared to existing tools while being able to not-classify unknown cell types. Moreover, scAnnotatR is the only of the best performing tools able to process datasets containing more than 600,000 cells.

Conclusions

scAnnotatR is freely available on GitHub (https://github.com/grisslab/scAnnotatR) and through Bioconductor (from version 3.14). It is consistently among the best performing tools in terms of classification accuracy while scaling to the largest datasets.
An integrative analysis of DNA methylation and transcriptome showed the dysfunction of MAPK pathway was involved in the damage of human chondrocyte induced by T-2 toxin
Authors: Yang Xuena , Xiao Xue , Zhang Lu , Wang Bo , Li Ping , Cheng Bolun , Liang Chujun , Ma Mei , Guo Xiong , Zhang Feng , Wen Yan
Published: January 2022

Background

T-2 toxin is thought to induce the growth plate and articular cartilage damage of Kashin-Beck disease (KBD), an endemic osteochondropathy in China. This study aims to explore the potential underlying mechanism of such toxic effects by integrating DNA methylation and gene expression profiles.

Methods

In this study, C28/I2 chondrocytes were treated with T-2 toxin (5 ng/mL) for 24 h and 72 h. Global DNA methylation level of chondrocyte was tested by Enzyme-Linked Immuno Sorbent Assay. Genome-wide DNA methylation and expression profiles were detected using Illumina Infinium HumanMethylation850 BeadChip and RNA-seq technique, respectively. Differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified mainly for two stages including 24 h group versus Control group and 72 h group versus 24 h group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed by Metascape. DMGs and DEGs were further validated by Sequenom MassARRAY system and quantitative real-time polymerase chain reaction.

Results

The global DNA methylation levels of chondrocytes exposed to T-2 toxin were significantly increased (P < 0.05). For 24 h group versus Control group (24 VS C), 189 DEGs and 590 DMGs were identified, and 4 of them were overlapping. For 72 h group versus 24 h group (72 VS 24), 1671 DEGs and 637 DMGs were identified, and 45 of them were overlapping. The enrichment analysis results of DMGs and DEGs both showed that MAPK was the one of the mainly involved signaling pathways in the regulation of chondrocytes after T-2 toxin exposure (DEGs: P24VSc = 1.62 × 10− 7; P72VS24 = 1.20 × 10− 7; DMGs: P24VSc = 0.0056; P72VS24 = 3.80 × 10− 5).

Conclusions

The findings depicted a landscape of genomic methylation and transcriptome changes of chondrocytes after T-2 toxin exposure and suggested that dysfunction of MAPK pathway may play important roles in the chondrocytes damage induced by T-2 toxin, which could provide new clues for understanding the potential biological mechanism of KBD cartilage damage induced by T-2 toxin.