bluuebunny/crossref_metadata_2025 huggingface dataset:
Macroevolution of protective coloration across caterpillars reflects relationships with host plants
Authors: Robinson Moria L. , Weber Marjorie G. , Freedman Micah G. , Jordan Evan , Ashlock Sarah R. , Yonenaga Jenna , Strauss Sharon Y.
Published: January 2023

A critical function of animal coloration is avoiding attack, either by warning predators or reducing detectability. Evolution of these divergent strategies may depend on prey palatability and apparency to predators: conspicuous coloration may be favoured if species are distasteful, or habitats make hiding difficult; by contrast, camouflage may be effective if prey lack defences or environments are visually complex. For insect herbivores, host plants provide both chemical defence and the background against which they are detected or obscured; thus, plant traits may be key to coloration in these foundational terrestrial organisms. We use 1808 species of larval Lepidoptera to explore macroevolution of protective coloration strategy. We find that colour and pattern evolve jointly in caterpillars, similar to an array of species across the animal kingdom, while individual elements of coloration evolve closely with diet ecology. Consistent with key tenets of plant defence and plant–herbivore coevolutionary theory, conspicuous colours are associated with herbaceous host plants—thought to be defended by toxins—while camouflage colours and patterns are associated with woody plants and grasses. Contrary to theory, dietary specialization is not associated with conspicuous coloration. Our results add valuable insights into the evolutionary forces shaping colour and pattern in nature.
Phenotypic characterization of Eimeria tenella-specific chicken T-cells responding to in vitro parasite antigen re-stimulation
Authors: Wattrang Eva , Lundén Anna , Ibrahim Osama , Dalgaard Tina Sørensen
Published: January 2023

Introduction. Coccidiosis, caused by protozoan parasites of genus Eimeria, is a disease with large impact on poultry production worldwide. It is well known that Eimeria immunity is dependent on Th1-type responses.

Gap Statement.
In vitro assessment of Eimeria-specific T-cell activity would therefore be a valuable research tool but has so far proven difficult to establish.

Aim. The present study aimed to evaluate in vitro induced blast transformation and CD25 expression in defined chicken T-cell populations as a measure of Eimeria immunity.

Methodology. Three E. tenella infection experiments were performed and PBMC and/or spleen cells were collected between 6 and 16 days after infection of chickens. Cells were stimulated in vitro with E. tenella antigens and T-cell activation was assessed by immunofluorescence labelling and flow cytometry.

Results. The results consistently showed statistically significant E. tenella specific activation of TCRα/β+T cells within a ‘window’ from 8 to 14 days after infection for both spleen cells and PBMC. Responding T-cells were identified as CD4+CD8-, CD4+CD8αα+ and CD4-CD8αβ+ where the CD4+CD8αα+ cells generally showed the highest responses. All three of these TCRα/βT-cell subsets showed significant E. tenella induced blast transformation and/or CD25 expression albeit not always in concert on the same days after infection indicating complex kinetics of T-cell responses. In general, responses were higher for spleen cells compared to PBMC for all responding T-cell populations.

Conclusions. This methodology shows promise to study Eimeria-specific T-cells, e.g. to evaluate vaccine responses. Results indicated that a Th1-type response was induced and suggested a role for CD4+CD8αα+ cells in Eimeria immunity.
Pre-exposure Prophylaxis Uptake Concerns in the Democratic Republic of the Congo: Key Population and Healthcare Workers Perspectives
Authors: Shen Yanhan , Franks Julie , Reidy William , Olsen Halli , Wang Chunhui , Mushimbele Nadine , Mazala Richted Tenda , Tchissambou Tania , Malele Faustin , Kilundu Apolinaire , Bingham Trista , Djomand Gaston , Mukinda Elie , Ewetola Raimi , Abrams Elaine J. , Teasdale Chloe A.
Published: January 2023

Key populations (KP) in the Democratic Republic of the Congo (DRC), including female sex workers (FSW), are disproportionally affected by HIV. Quantitative feedback surveys were conducted at seven health facilities in DRC with 70 KP clients enrolled in services to measure pre-exposure prophylaxis (PrEP) benefits and concerns. The surveys also assessed satisfaction with PrEP services and experiences of stigma at the health facilities. Thirty healthcare workers (HCW) were surveyed to measure attitudes, beliefs, and acceptability of providing services to KP. KP client survey participants were primarily female SW. KP clients reported that the primary concern about taking PrEP was fear of side effects. HCW concurred with clients that experienced and anticipated side effects were a primary PrEP uptake concern, along with costs of clinic visits.
Determinants of protection against SARS-CoV-2 Omicron BA.1 and Delta infections in fully vaccinated outpatients
Authors: Roy Alvaro , Saade Carla , Josset Laurence , Clément Bénédicte , Morfin Florence , Destras Grégory , Valette Martine , Icard Vinca , Oblette Antoine , Debombourg Marion , Garrigou Christine , Brengel-Pesce Karen , Generenaz Laurence , Saker Kahina , Hernu Romain , Pozzetto Bruno , Lina Bruno , Trabaud Mary-Anne , Trouillet-Assant Sophie , Bal Antonin
Published: January 2023

Objectives

We aimed to evaluate the association between the humoral and cellular immune responses and symptomatic SARS-CoV-2 infection with Delta or Omicron BA.1 variants in fully vaccinated outpatients.

Methods

Anti-RBD IgG levels and IFN-γ release were evaluated at PCR-diagnosis of SARS-CoV-2 in 636 samples from negative and positive patients during Delta and Omicron BA.1 periods.

Results

Median levels of anti-RBD IgG in positive patients were significantly lower than in negative patients for both variants (p< 0.05). The risk of Delta infection was inversely correlated with anti-RBD IgG titres (aOR = 0.63, 95% CI [0.41; 0.95],p= 0.03) and it was lower in the hybrid immunity group compared to the homologous vaccination group (aOR = 0.22, 95% CI [0.05; 0.62],p= 0.01). In contrast, neither the vaccination scheme nor anti-RBD IgG titers were associated with the risk of BA.1 infection in multivariable analysis. IFN-γ release post-SARS-CoV-2 peptide stimulation was not different between samples from patients infected (either with Delta or Omicron BA.1 variant) or not (p= 0.77).

Conclusions

Our results show that high circulating levels of anti-RBD IgG and hybrid immunity were independently associated with a lower risk of symptomatic SARS-CoV-2 infection in outpatients with differences according to the infecting variant.
WITHDRAWN: Body dysmorphic-induced Androgenic Anabolic Steroids usage and its association with mental health outcomes
Authors: Gawash Ahmed , Zia Hasan , Lo David F.
Published: January 2023

Withdrawal statement

The authors have withdrawn this manuscript because of significant methodological errors: Upon further review, we identified significant errors in our methodology that could impact the validity of our findings. Specifically, we realized that some of the analyses were conducted incorrectly, which may have led to misleading conclusions. We believe these errors could compromise the integrity of the results and misinform readers about the implications of our work. We are committed to ensuring the highest standards in our research, and correcting these issues will require substantial revisions and additional analyses. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Does blood viscosity affect cerebral blood flow? A study in a population living in a high-altitude city
Authors: Huamaní Charles , Bayona-Pancorbo William , Sarmiento William , Córdova-Heredia Golda , Cruz-Huanca Luz , Damián-Saavedra Paulina , Requena Nathalie , Oré-Montalvo Víctor , Pérez-Alviz Carlos , Acuña-Mamani Juan C.
Published: January 2023

Background

Viscosity affects flows by increasing resistance to movement; therefore, variations in blood viscosity (BV) levels could modify the cerebral blood flow.

Objective

This study aimed to determine the level of correlation between BV and cerebral blood flow in people acclimated to chronic hypoxia who have high BV levels.

Methods

Prospective observational study was conducted among clinically healthy young adults living in the city of Cusco (3,399 m above sea level). All participants were examined at low and high shear rates (75 and 300 sec−1) to simulate the dynamic component of BV. A transcranial Doppler study of the middle cerebral artery was performed to measure systolic, diastolic, and mean flow velocities (FVs) and resistance and pulsatility indices (PIs).

Results

A total of 131 participants were included. The median viscosity levels were 5.01cP [interquartile range (IQR): 4.45–5.73cP] at 300 sec−1and 6.16 cP [IQR: 5.58-7.20 cP] at 75 sec−1, the mean FV was 57 m/s [IQR: 50–65 m/s5], and the PI was 0.91 [0.86–1.02]. BV was negatively correlated with mean FV (r: −0.17, p=0.007), while it showed no correlation with other values of blood flow, resistance, or PI.

Conclusions

Changes in BV levels have a minimal impact on the mean FV but not on other parameters. This finding suggests that in young and clinically healthy individuals, there are autoregulation mechanisms that compensate for BV variations, although they are not completely understood.
Extensive SARS-CoV-2 testing reveals BA.1/BA.2 asymptomatic rates and underreporting in school children
Authors: Martignoni Maria M. , Mohammadi Zahra , Loredo-Osti JC , Hurford Amy
Published: January 2023

Case underreporting during the COVID-19 pandemic has been a major challenge to the planning and evaluation of public health responses. Inconsistent underreporting can undermine effective risk assessment due to high uncertainty in predicted future scenarios. Underreporting rates have been particularly high among children and youth, given that asymptomatic school children were often considered a less vulnerable population. In January 2022, the Canadian province of Newfoundland and Labrador (NL) was experiencing an Omicron variant outbreak (BA.1/BA.2 subvariants) and public health officials recommended that all students returning to elementary, junior high, and high schools (∼59,452 students) complete two rapid antigen tests (RATs) to be performed three days apart. To estimate the prevalence of SARS-CoV-2, we asked parents and guardians to report the results of the RATs completed by K-12 students using an online survey, and to specify the students’ school level and if students with positive RAT results had symptoms. When comparing the survey responses with the number of cases and tests reported by the NL testing system, we found that 1 out of every 4.3 (3.1-5.3) positive households were captured by provincial case count, with 5.1% positivity estimated from the RAT results, and 1.2% positivity reported by the provincial testing system. The survey data indicate that a higher percentage of SARS-CoV-2 cases were found in elementary schools, with 62.9% of positive cases (95% CI: 44.3%, 83.0%) reported from elementary school students, and the remaining 37.1% (95% CI: 22.7%, 52.9%) reported from junior high and high school students. Asymptomatic infections were 59.8% of the positive cases, with no significant difference between asymptomatic rates in elementary schools (60.8%) or in junior high and high schools (58.1%). Given the low survey participation rate (3.5%), our results may suffer from sample selection biases, and should be interpreted with caution. Nonetheless, our estimate of the underreporting ratio is consistent with ratios calculated from serology data, and our study provides insights into infection prevalence and asymptomatic infections in school children, a currently understudied population.

We declare that

This manuscript is original and is not a violation or infringement of any existing copyright or license

The manuscript is not under consideration elsewhere

All authors meet the definition of authorship as set out by the International Committee of Medical Journal Editors (ICMJE)

Permission has been obtained from the copyright holder(s) if indicated, for the use of any third-party textual, graphic, artistic or other material
SARS-CoV-2 Envelope protein triggers depression and dysosmia via TLR2 mediated neuroinflammation
Authors: Su Wenliang , Ju Jiahang , Gu Minghui , Wang Xinrui , Liu Shaozhuang , Yu Jiawen , Mu Dongliang
Published: January 2023

Background

Depression and dysosmia have been regarded as the main neurological symptoms in COVID-19 patients, the mechanism of which remains unclear. Current studies have demonstrated that SARS-CoV-2 envelope protein served as a pro-inflammatory factor as sensed by Toll like receptor 2 (TLR2), suggesting the viral infection independent pathological feature of E protein. In this study, we aim to determine the role of E protein in depression, dysosmia and associated neuroinflammation in central nervous system (CNS).

Methods

Depression and olfactory function were observed in both female and male mice as receiving intracisternal injection of envelope protein. Immunohistochemistry was applied in conjunction with RT-PCR to assess the glial activation, blood-brain barrier status and mediators synthesis in cortex, hippocampus and olfactory bulb. TLR2 was pharmacologically blocked to determine its role in E protein related depression and dysosmia.

Results

Intracisternal injection of envelope protein evoked depression and dysosmia in both female and male mice. Immunohistochemistry suggested that envelope protein upregulated IBA1 and GFAP in cortex, hippocampus and olfactory bulb, while ZO-1 was downregulated. Moreover, IL-1β, TNF-α, IL-6, CCL2, MMP2 and CSF1 were upregulated in both cortex and hippocampus, whereas IL-1β, IL-6 and CCL2 were upregulated in olfactory bulb. Furtherly, inhibiting microglia, but not astrocyte, alleviated depression and dysosmia induced by envelope protein. Finally, RT-PCR and immunohistochemistry suggested that TLR2 was upregulated in cortex, hippocampus and olfactory bulb, the blocking of which mitigated depression and dysosmia induced by envelope protein.

Conclusions

Our study demonstrates that envelope protein could directly induce depression and dysosmia together with obvious neuroinflammation in CNS. TLR2 mediated depression and dysosmia induced by envelope protein, which could serve as a promising therapeutic target for neurological manifestation in COVID-19 patients.
Terrestrial laser scan metrics predict surface vegetation biomass and consumption in a frequently burned southeastern U.S. ecosystem
Authors: Loudermilk E. Louise , Pokswinski Scott , Hawley Christie M. , Maxwell Aaron , Gallagher Michael , Skowronski Nicholas , Hudak Andrew T. , Hoffman Chad , Hiers J. Kevin
Published: January 2023

Fire-prone landscapes found throughout the world are increasingly managed with prescribed fire for a variety of objectives. These frequent low-intensity fires directly impact lower forest strata, and thus estimating surface fuels or understory vegetation is essential for planning, evaluating, and monitoring management strategies and studying fire behavior and effects. Traditional fuel estimation methods have applications for stand-level and canopy fuel loading; however, local-scale understory biomass remains challenging because of complex within-stand heterogeneity and fast recovery post-fire. Previous studies have demonstrated how single location terrestrial laser scanning (TLS) can be used to estimate plot-level vegetation characteristics and impacts from prescribed fire. To build upon this methodology, co-located single TLS scans and physical biomass measurements were used to generate linear models for predicting understory vegetation and fuel biomass as well as consumption by fire in a southeastern U.S. pineland. A variable selection method was used to select the six most important TLS-derived structural metrics for each linear model, where model fit ranged in R2from 0.61 to 0.74. This study highlights a prospect for efficiently estimating vegetation and fuel characteristics relevant to prescribed burning via the integration of a single-scan TLS method adaptable by managers and relevant for coupled fire-atmosphere models.
Tricycle surveillance in Antananarivo, Madagascar: circulation of both extended-spectrum beta-lactamase producingEscherichia colistrains and plasmids among humans, chickens and the environment
Authors: Milenkov Milen , Proux Caroline , Rasolofoarison Tiavina Lalaina , Rakotomalala Fetra Angelot , Rasoanandrasana Saida , Rahajamanana Lalaina Vonintsoa , Rafalimanana Christian , Ravaoarisaina Zakasoa , Ramahatafandry Ilo Tsimok’Haja , Westeel Emilie , Petitjean Marie , Marin Julie , Mullaert Jimmy , Han Lien , Clermont Olivier , Raskine Laurent , Endtz Hubert , Andremont Antoine , Denamur Erick , Komurian-Pradel Florence , Hervé Samison Luc , Armand-Lefevre Laurence
Published: January 2023

Background

Antimicrobial resistance is a major public health threat, affecting not only humans but also animals and the environment. Although the “One Health” dimension of resistance is well recognized, data are lacking on the circulation of resistance, particularly in low-income countries. The World Health Organization has proposed a protocol called Tricycle, focusing on extended-spectrum beta-lactamase (ESBL)-Escherichia colisurveillance in the three sectors. We implemented Tricycle in Madagascar to assess ESBL-E. coliprevalence and describe intra- and inter-sector circulation of ESBL-E. coliand plasmids.

Methods

289 pregnant women, 246 farm chickens and 28 surface waters were sampled in Antananarivo (the capital city) area and tested for ESBL-E. coli. Isolates were sequenced by short-(Illumina) and long-(Nanopore) read methods.

Findings

ESBL-E. coliprevalence was 29·8%, 56·9% and 100% in pregnant women, chickens, and the environment, respectively. The wet season was associated with higher rates of carriage in humans (OR=3·1, 95%CI 1·8-5·3) and animals (OR=2·8 95%CI 1·7-4·8). Sequencing of 277 non-duplicated isolates (82, 118 and 77 from each sector, respectively) showed high genetic diversity (90 STs identified) with differences between sectors. Single nucleotide polymorphism (SNP) analysis revealed 169/277 (61%) isolates grouped into 44 clusters (≥2 isolates) of closely related isolates (<40 SNPs), of which 24 contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were allblaCTX-M(77.6%blaCTX-M-15), chromosomally integrated in 57·4% (159/277) of isolates, and plasmidic in 40·8% (113/277). The 114 ESBL-carrying plasmids were mainly IncF (55·2%, n=63) and IncY (36·8%, n=42). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) subtypes, and all IncY plasmids, highly conserved, were observed in isolates of differing genetic backgrounds from all sectors.

Interpretation

Despite varying strain population structures in the three sectors, both ESBL-E. colistrains and plasmids are circulating among humans, chickens and the environment in the capital of Madagascar.

Funding

Fondation Mérieux, INSERM, Université Paris Cité
BURNOUT: A PREDICTOR OF ORAL HEALTH IMPACT PROFILE AMONG NIGERIAN EARLY CAREER DOCTORS
Authors: Ogunsuji OO , Adebayo OM , Kanmodi KK , Fagbule OF , Adeniyi MA , James NT , Yahya AI , Salihu MO , Babarinde TO , Olaopa OI , Selowo TT , Enebeli UU , Ishaya DG
Published: January 2023

Introduction

There have been reported association of oral health disorders with burnout, stress, and mental health. Arguably, with these reported associations, and the current prevalence of burnout amongst Nigerian doctors, exploring the role of burnout on oral health amongst Nigerian doctors is timely. This study aims to determine the relationship between burnout and oral health-related quality of life amongst Early Career Doctors (ECDs) in Nigeria, while also identifying the role other possible predictors plays in this relationship.

Methods

This was a cross-sectional study conducted amongst Nigerian ECDs as part of Challenges of Residency Training in Nigeria (CHARTING) II project. A total of 632 ECDs were recruited across thirty-one tertiary hospitals in the 6 geopolitical zones of the country using a multistage cluster sampling technique. A self-administered paper-based semi-structured questionnaire was given to each participant that consented. The tools used to assess burnout and Oral health-related quality of life (OHRQoL) were Copenhagen Burnout Inventory (CBI) and Oral Health Impact Profile (OHIP-14) respectively. Independent samples T-test, ANOVA and Multiple linear regression were used to draw inferences from the data collected.

Results

Overall mean OHIP-14 score of all participants was 11.12 (±9.23). The scores for the 3 dimensions of burnout were below 50% with CBI-Personal Burnout having the highest score of 49.96 (±19.15). Significant positive correlations (p < 0.001) were found between OHIP-14 and all the dimensions of burnout, as the burnout scores were increasing, there was a corresponding increase in the OHIP scores thus poorer OHRQoL. The regression model shows that the predictors of OHIP were CBI-PB (p = 0.003), use of fluoride paste (p = 0.039), use of tobacco (p = 0.005) and being a denture user (p = 0.047).

Conclusion

This study shows a positive correlation between burnout and OHIP of ECDs. We found that as burnout was increasing, OHIP increased thus implying poorer oral health related quality of life amongst ECDs. The use of fluoride toothpaste, tobacco and denture are other factors we found that could affect the OHIP of ECDs.
Determinants of Covid-19 vaccine uptake among the elderly aged 58 years and above in Kericho County, Kenya: Institution based cross sectional survey
Authors: Anino Calvince Otieno , Wandera Immaculate , Ondicho Zachary Masimba , Kirui Collins Kipruto , Makero Carjetine Syallow , Omari Phanice Kerubo , Sanga Philip
Published: January 2023

Background

Hesitancy to Covid-19 vaccine is a global challenge despite the compelling evidence of the value of vaccine in preventing disease and saving lives. It is suggested that context-specific strategies can enhance acceptability and decrease hesitancy to Covid-19 vaccine. Hence, the study determined uptake and determinants of Covid-19 vaccine following a sustained voluntary vaccination drive by Kenyan government.

Method

We conducted institution based cross-sectional survey of 1244 elderly persons aged 58 to 98 years in the months of January, February and March, 2022. A multinomial logistic regression analysis was used to investigate determinants of Covid 19 vaccine uptake. The predictor variables included socioeconomic and demographic characteristics, convenience and ease of access of the vaccine, collective responsibility, complacency and the three dimensions of confidence; trust in safety, trust in decision makers and delivery system. The findings are reported as the adjusted odd ratio (AOR) at 95% confidence interval (CI). Significant level was considered at p <0.05.

Result

The results from the multinomial logistic regression analysis indicated that advanced age and presence of chronic disease were associated with increased odds of doubt on Covid 19 vaccine, while long distance from vaccination centers was associated with increased odds of delay in vaccination.

Conclusion

Overall, the findings of this study have provided valuable insights into the factors influencing vaccine hesitancy among the elderly population in Kenya and will inform the development of targeted interventions to increase vaccine acceptance and uptake in this population.
COVID-19 INDUCES SENESCENCE AND EXHAUSTION OF T CELLS IN PATIENTS WITH MILD/MODERATE AND SEVERE DISEASE DURING A SEVEN-DAY INTERVAL
Authors: Pedroso Rodrigo Balsinha , Araújo Ventura Lucas Haniel , Torres Lícia , Camatta Giovanna Caliman , Caixeta Felipe , Nascimento Leandro Souza , Mota Catarina , Mendes Ana Catarina , Ribeiro Filipa , Guimarães Henrique Cerqueira , Calvão Barbuto Rafael , Silveira-Nunes Gabriela , Teixeira-Carvalho Andrea , Graça Luis , Caetano Faria Ana Maria
Published: January 2023

Risk factors for the development of severe COVID-19 include several comorbidities, but age was the most striking one since elderly people were disproportionately affected by SARS-Cov-2. Major drivers that can explain this markedly unfavourable response in the elderly are inflammaging and immunosenescence. Recent reports have shown that the relationship between immunosenescence and COVID-19 can be bidirectional, since hospitalized patients with severe COVID-19 have an accumulation of senescent T cells suggesting that immunosenescence can be also exacerbated by SARS-CoV-2 infection. Therefore, the present work was designed to examine the emergence of immunosenescence in a longitudinal study in two distinct cohorts of COVID-19 patients, and to determine whether the senescence alterations were restricted to severe cases of the disease. Our data, with patients from Portugal and Brazil, identified their distinctive inflammatory profile and provided evidence of increased frequencies of senescent and exhausted T cells within a seven-day period in patients with mild to severe COVID-19. These results support the view that SARS-CoV2 infection can accelerate immunosenescence in both CD4 and CD8 T cell compartments in a short period of time.
Long term follow-up of colorectal cancer screening attendees identifies differences inPhascolarctobacterium spp. using 16S rRNA and metagenome sequencing
Authors: Bucher-Johannessen C. , Birkeland E. , Vinberg E. , Bemanian V. , Hoff G. , Berstad P. , Rounge TB.
Published: January 2023

Background

The microbiome has been implicated in the initiation and progression of colorectal cancer (CRC) in cross sectional studies. However, there is a lack of studies using prospectively collected samples.

Methods

We analysed 144 archived faecal samples from participants in the NORwegian Colorectal CAncer Prevention (NORCCAP) trial diagnosed with CRC or high-risk adenomas (HRA) at screening, or who remained cancer-free during 17 years of follow-up. We performed 16S rRNA sequencing of all samples, and metagenome sequencing on a subset of 47 samples. Differences in taxonomy and gene content between outcome groups were assessed for alpha and beta diversity, and differential abundance.

Results

Diversity and composition analyses showed no significant differences between CRC, HRA, and healthy controls.Phascolarctobacterium succinatutenswas more abundant in CRC compared to healthy controls in both the 16S and metagenome data. The abundance ofBifidobacteriumandLachnospiraceae spp. were associated with time to CRC diagnosis.

Conclusion

Using a longitudinal study design, we identified three taxa as being potentially associated with CRC. These should be the focus of further studies of microbial changes occurring prior to CRC diagnosis.
Simulating Ultrasound images from CT Scans
Authors: Nasser Sahar Almahfouz , Sethi Amit
Published: January 2023

Anatomical information in ultrasound (US) imaging has not been exploited fully because its wave interference pattern (WIP) has been viewed as speckle noise. We tested the idea that more information can be retrieved by disentangling the WIP rather than discarding it as noise. We numerically solved the forward model of generating US images from computed tomography (CT) images by solving wave-equations using the Stride library. By doing so, we have paved the way for using deep neural networks to be trained on the data generated by the forward model to simulate the solution of the inverse problem, which is generating the CT-style and CT-quality images from a real US image. We demonstrate qualitative features of the generated images that are rich in anatomical details and realism.
Self-assessment of problem-solving skills and Clinical Reasoning among sixth-year medical students University of Baghdad / College of medicine
Authors: Hasan Ahmed M. , Abbas Ibrahim N. , Abdulrazak Ahmed A. , Almothaffar Ali
Published: January 2023

Objectives

To assess the level of problem solving skills of Sixth grade medical students of College of Medicine/ University of Baghdad using self-assessment tool.

Materials and Methods

A cross-sectional study to assess Problem Solving Disposition in Sixth year Medical Students in College of Medicine/ University of Baghdad. A printed survey of the questionnaire was distributed to sixth year medical students in august 2022. A sample of 151 students participated in the study by filling of the printed questionnaire which was validated by a previous study in a medical school in Mexico.

Results

The number of sixth Grade medical students in University of Baghdad/ College of medicine that participated in the study was 151 of whom 70 (46.35 %) were males and 81 (53.65 %) were females.

The mean score of the “knowledge of discipline” was 2.973± 0.999, as for the “pattern recognition” component the mean was 2.198 ±0.559, and the mean for the “application of general strategies” component was 2.158± 0.492.

The independent sample T-test results for the “Knowledge of discipline” category showed a mean score for females of 3.137 and a mean score for males of 2.778 with a p value >0.05.

For correlations between the categories one of the items of the “Pattern Recognition” category had a positive correlation with a statistical significance with 2 items from “Application of general strategies for problem solving” category.

Conclusion

Sixth year medical students in University of Baghdad/ college of medicine are better self-perceived in the pattern recognition and application of general strategies for problem-solving categories than the knowledge of discipline, males assess themselves in remembering concepts as better than their female counterparts.
Sex-specific impact of body weight on atherosclerotic cardiovascular disease incidence in individuals with and without ideal cardiovascular health
Authors: Paulin Audrey , Manikpurage Hasanga D. , Després Jean-Pierre , Thériault Sébastien , Arsenault Benoit J.
Published: January 2023

Background

The impact of an elevated body mass index (BMI) on atherosclerotic cardiovascular diseases (ASCVD) risk in individuals who are “metabolically healthy” is debated. Our objective was to investigate the respective contributions of BMI as well as lifestyle and cardiometabolic risk factors combined to ASCVD incidence in 319,866 UK Biobank participants.

Methods

We developed a cardiovascular health score (CVHS) based on four lifestyle and six cardiometabolic parameters. The impact of the CVHS on incident ASCVD (15,699 events) alone and in BMI and waist-to-hip ratio categories was assessed using Cox proportional hazards in women and men separately.

Results

In participants with a high CVHS (8-10), those with a BMI ≥ 35.0 kg/m2had a nonsignificant higher ASCVD risk (HR=1.20 [95% CI, 0.84-1.70], p=0.32) compared to those with a BMI of 18.5-24.9 kg/m2. In participants with a BMI 18.5-24.9 kg/m2, those with a lower CVHS (0-2) had a higher ASCVD risk (HR=4.06 [95% CI, 3.23-5.10], p<0.001) compared to those with a higher CVHS (8-10). When we used the waist-to-hip ratio instead of the BMI, a dose-response relationship between the WHR and ASCVD risk was obtained in healthier participants. Results were similar in women compared to men.

Conclusions

In participants of the UK Biobank, the relationship between the BMI and ASCVD incidence in healthy individuals was inconsistent whereas cardiovascular risk factors strongly predicted ASCVD incidence in all BMI categories. Weight inclusive interventions targeting lifestyle-related and metabolic risk factors are likely to prevent cardiovascular outcomes, regardless of their impact on body weight.
Enhanced transmissibility, infectivity and immune resistance of the SARS-CoV-2 Omicron XBB.1.5 variant
Authors: Uriu Keiya , Ito Jumpei , Zahradnik Jiri , Fujita Shigeru , Kosugi Yusuke , Schreiber Gideon ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Sato Kei
Published: January 2023

In 2022, we have elucidated the characteristics of a variety of newly emerging SARS-CoV-2 Omicron subvariants. At the end of 2022, the XBB.1.5 variant, an descendant of XBB.1 that acquired the S:F486P substitution, emerged and is rapidly spreading in the USA and is the latest variant of concern. Although the features of XBB.1.5 was already reported by another group as a preprint, we think multiple and independent evaluations important, and these reports are crucial for sustained global health. In this study, our epidemic dynamics analysis revealed that the relative effective reproduction number (Re) of XBB.1.5 is more than 1.2-fold greater than that of the parental XBB.1, and XBB.1.5 is outcompeting BQ.1.1, the predominant lineage in the USA as of December 2022. Our data suggest that XBB.1.5 will rapidly spread worldwide in the near future. Yeast surface display assay and pseudovirus assay respectively showed that the ACE2 binding affinity and infectivity of XBB.1.5 is 4.3-fold and 3.3-fold higher than those of XBB.1, respectively. Moreover, neutralization assay revealed that XBB.1.5 is robustly resistant to BA.2 breakthrough infection sera (41-fold versus B.1.1, 20-fold versus BA.2) and BA.5 breakthrough infection sera (32-fold versus B.1.1, 9.5-fold versus BA.5), respectively. Because the immune resistance of XBB.1.5 is comparable to that of XBB.1, our results suggest that XBB.1.5 is the most successful XBB lineage as of January 2023 by acquiring the S:F486P substitution to augment ACE2 binding affinity without losing remarkable immune resistance, which leads to greater transmissibility.
Bioregional boundaries and genomically-delineated stocks in snapper (Chrysophrys auratus) from southeastern Australia
Authors: Bertram Andrea , Bell Justin , Brauer Chris , Fowler Anthony , Hamer Paul , Sandoval-Castillo Jonathan , Stewart John , Wellenreuther Maren , Beheregaray Luciano B.
Published: January 2023

Marine species often exhibit genetic discontinuities concordant with biogeographic boundaries, frequently occurring due to changes in ocean circulation, bathymetry, coastline topography and temperature. Here we used 10,916 single nucleotide polymorphisms (SNPs) to assess the concordance between population genomic differentiation and coastal biogeography in the fishery important snapper (Chrysophrys auratus) across southeastern Australia. Additionally, we investigated whether spatial scales of assessment and management of snapper align with evidence from population genomics. Across 488 snapper samples from 11 localities between the west coast of South Australia and the south coast of New South Wales, we detected genomic structure concordant with the region’s three biogeographic provinces. We also detected fine-scale genetic structuring relating to spatial variation in spawning and recruitment dynamics, as well as temporal stability in the genomic signal associated with two important spawning grounds. The current management boundaries in the region coincided with either the genetic breaks at bioregional boundaries or with localscale variation. Our study highlights the value of population genomic surveys in species with high dispersal potential for uncovering stock boundaries and demographic variation related to spawning and recruitment. It also illustrates the importance of marine biogeography in shaping population structure in commercial species with high dispersal potential.
WITHDRAWN: Infratentorial Morphometry and Deep Brain Stimulation Outcome in Cervical Dystonia
Authors: Andrews Luke , Keller Simon S. , Osman-Farah Jibril , Bhojak Maneesh , Macerollo Antonella
Published: January 2023

Withdrawal statement

The corresponding author (LA) has withdrawn their manuscript owing to inaccuracies in the data analysis and subsequent conclusions. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Specimen sharing for epidemic preparedness: building a local-to-global virtual biorepository framework
Authors: Giri Judith , Pezzi Laura , Cachay Rodrigo , Gèlvez Ramirez Rosa Margarita , Tami Adirana , Bethencourt Sarah , Lozano Anylea , Poje Julia , Jaenisch Thomas , Chu May
Published: January 2023

We present a framework for a federated, virtual biorepository system (VBS) with locally collected and maintained specimens, based on a ‘global goods’ model and principles of equitable access and benefit sharing. The VBS is intended to facilitate timely access to biological specimens and associated data for outbreak-prone infectious diseases to accelerate the development and evaluation of diagnostics, assess vaccine efficacy, and to support surveillance and research needs. The VBS is aimed to be aligned with the WHO BioHub and other specimen sharing efforts as a force multiplier to meet the needs of strengthening global tools for countering epidemics. The purpose of our research is to lay the basis of the collaboration, management and principles of equitable sharing focused on low- and middle-income country partners. Here we report on surveys and interviews undertaken with biorepository-interested parties to better understand needs and barriers for specimen access and share examples from the ZIKAlliance partnership on the governance and operations of locally organized biorepositories.
Detecting and Adjusting for Hidden Biases due to Phenotype Misclassification in Genome-Wide Association Studies
Authors: Burstein David , Hoffman Gabriel , Mathur Deepika , Venkatesh Sanan , Therrien Karen , Fanous Ayman H. , Bigdeli Tim B. , Harvey Philip D. , Roussos Panos , Voloudakis Georgios
Published: January 2023

With the advent of healthcare-based genotyped biobanks, genome-wide association studies (GWAS) leverage larger sample sizes, incorporate patients with diverse ancestries and introduce noisier phenotypic definitions. Yet the extent and impact of phenotypic misclassification on large-scale datasets is not currently well understood due to a lack of statistical methods to estimate relevant parameters from empirical data. Here, we develop a statistical method and scalable software, PheMED,PhenotypicMeasurement ofEffectiveDilution, to quantify phenotypic misclassification across GWAS using only summary statistics. We illustrate how the parameters estimated by PheMED relate to the negative and positive predictive value of the labeled phenotype, compared to ground truth, and how misclassification of the phenotype yields diluted effect-sizes of variant-phenotype associations. Furthermore, we apply our methodology to detect multiple instances of statistically significant dilution in real-world data. We demonstrate how effective dilution biases downstream GWAS replication and heritability analyses despite utilizing current best practices, and provide a dilution-aware meta-analysis approach that outperforms existing methods. Consequently, we anticipate that PheMED will be a valuable tool for researchers to address phenotypic data quality issues both within and across cohorts.
Trans-ethnic Polygenic Risk Scores for Body Mass Index: An International Hundred K+ Cohorts Consortium Study
Authors: Qu Huiqi , Connolly John J , Kraft Peter , Long Jirong , Pereira Alexandre , Flatley Christopher , Turman Constance , Prins Bram , Mentch Frank , Lotufo Paulo A , Magnus Per , Stampfer Meir J , Tamimi Rulla , Eliassen A Heather , Zheng Wei , Knudsen Gun Peggy Stromstad , Helgeland Oyvind , Butterworth Adam S. , Hakonarson Hakon , Sleiman Patrick M.
Published: January 2023

Background

While polygenic risk scores hold significant promise in estimating an individual’s risk of developing a complex trait such as obesity, their application in the clinic has, to date, been limited by a lack of data from non-European populations. As a collaboration model of the International Hundred K+ Cohorts Consortium (IHCC), we endeavored to develop a globally applicable trans-ethnic PRS for body mass index (BMI) through this relatively new international effort.

Methods

The PRS model was developed trained and tested at the Center for Applied Genomics (CAG) of The Children’s Hospital of Philadelphia (CHOP) based on a BMI meta-analysis from the GIANT consortium. The validated PRS models were subsequently disseminated to the participating sites. Scores were generated by each site locally on their cohorts and summary statistics returned to CAG for final analysis.

Results

We show that in the absence of a well powered trans-ethnic GWAS from which to derive SNPs and effect estimates, trans-ethnic scores can be generated from European ancestry GWAS using Bayesian approaches such as LDpred to adjust the summary statistics using trans-ethnic linkage disequilibrium reference panels. The ported trans-ethnic scores outperform population specific-PRS across all non-European ancestry populations investigated including East Asians and three-way admixed Brazilian cohort.

Conclusions

Widespread use of PRS in the clinic is hampered by a lack of genotyping data in individuals of non-European ancestry for the vast majority of traits. Here we show that for a truly polygenic trait such as BMI adjusting the summary statistics of a well powered European ancestry study using trans-ethnic LD reference results in a score that is predictive across a range of ancestries including East Asians and three-way admixed Brazilians.
Transdiagnostic MRI Markers of Psychopathology following Traumatic Brain Injury: A Systematic Review and Meta-Analysis Protocol
Authors: Samiotis Alexia , Hicks Amelia J , Ponsford Jennie , Spitz Gershon
Published: January 2023

Introduction

Psychopathology following traumatic brain injury (TBI) is a common and debilitating consequence that is often associated with reduced functional and psychosocial outcomes. There is a lack of evidence regarding the neural underpinnings of psychopathology following TBI, and whether there may be transdiagnostic neural markers that are shared across traditional psychiatric diagnoses. The aim of this systematic review and meta-analysis is to examine the association of MRI-derived markers of brain structure and function with both transdiagnostic and specific psychopathology following moderate-severe TBI.

Methods and analysis

A systematic literature search of Embase (1974–2022), Ovid MEDLINE (1946–2022) and PsycINFO (1806–2022) will be conducted. Publications in English that investigate MRI correlates of psychopathology characterised by formal diagnoses or symptoms of psychopathology in closed moderate-severe TBI populations over 16 years of age will be included. Publications will be excluded that: a) evaluate non-MRI neuroimaging techniques (CT, PET, MEG, EEG); b) comprise primarily a paediatric cohort; c) comprise primarily penetrating TBI. Eligible studies will be assessed against a modified Joanna Briggs Institute Critical Appraisal Instrument and data will be extracted by two independent reviewers. A descriptive analysis of MRI findings will be provided based on qualitative synthesis of data extracted. Quantitative analyses will include a meta-analysis and a network meta-analysis where there is sufficient data available.

Ethics and dissemination

Ethics approval is not required for the present study as there will be no original data collected. We intend to disseminate the results through publication to a high-quality peer-reviewed journal and conference presentations on completion.

PROSPERO registration number

CRD42022358358

Article Summary

Strengths and limitations of this study:

This is a comprehensive review of MRI markers of psychopathology among adults with moderate – severe traumatic brain injuries.

We will investigate neural correlates across the spectrum of psychopathology rather than focusing on specific diagnoses, allowing for transdiagnostic investigations of brain structure and function alterations after TBI with comorbid psychopathology.

We will be restricting eligible studies to English language.

We will capture pre-injury psychopathology where data are available and analyse the associations with post-injury psychopathology and neural correlates.
Light and temperature regulate m6A-RNA modification to regulate growth in plants
Authors: Artz Oliver , Ackermann Amanda , Taylor Laura , Koo Peter K. , Pedmale Ullas V.
Published: January 2023

N6-methyladenosine is a highly dynamic, abundant mRNA modification which is an excellent potential mechanism for fine tuning gene expression. Plants adapt to their surrounding light and temperature environment using complex gene regulatory networks. The role of m6A in controlling gene expression in response to variable environmental conditions has so far been unexplored. Here, we map the transcriptome-wide m6A landscape under various light and temperature environments. Identified m6A-modifications show a highly specific spatial distribution along transcripts with enrichment occurring in 5’UTR regions and around transcriptional end sites. We show that the position of m6A modifications on transcripts might influence cellular transcript localization and the presence of m6A-modifications is associated with alternative polyadenylation, a process which results in multiple RNA isoforms with varying 3’UTR lengths. RNA with m6A-modifications exhibit a higher preference for shorter 3’UTRs. These shorter 3’UTR regions might directly influence transcript abundance and localization by including or excluding cis-regulatory elements. We propose that environmental stimuli might change the m6A landscape of plants as one possible way of fine tuning gene regulation through alternative polyadenylation and transcript localization.
Reduced glycolysis links resting zone chondrocyte proliferation in the growth plate
Authors: Kobayashi Tatsuya , Young Cameron , Zhou Wen , Rhee Eugene P.
Published: January 2023

A gain-of-function mutation of the chondrocyte-specific microRNA, miR-140-5p, encoded by the MIR140 gene, causes spondyloepiphyseal dysplasia, Nishimura type (SEDN, also known as SED, MIR140 type; MIM, 611894). We reported that a mouse model for SEDN showed a unique growth plate phenotype that is characterized by an expansion of the resting zone of the growth plate and an increase in resting chondrocytes, of which the mechanism of regulation is poorly understood. We found that the miR-140 mutant chondrocytes showed a significant reduction of Hif1a, the master transcription factor that regulates energy metabolism in response to hypoxia. Based on this finding, we hypothesized that energy metabolism plays a regulatory role in resting chondrocyte proliferation and growth plate development. In this study, we show that suppression of glycolysis via LDH ablation causes an expansion of the resting zone and skeletal developmental defects. We have also found that reduced glycolysis results in reduced histone acetylation in the miR-140 mutant as well as LDH-deficient chondrocytes likely due to the reduction in acetyl-CoA generated from mitochondria-derived citrate. Reduction in acetyl-CoA conversion from citrate by deleting Acly caused an expansion of the resting zone and a similar gross phenotype to LDH-deficient bones without inducing energy deficiency, suggesting that the reduced acetyl-CoA, but not the ATP synthesis deficit, is responsible for the increase in resting zone chondrocytes. Comparison of the transcriptome between LDH-deficient and Acly-deficient chondrocytes also showed overlapping changes including upregulation in Fgfr3. We also confirmed that overexpression of an activation mutation of Ffgr3 causes an expansion of resting zone chondrocytes. These data demonstrate the association between reduced glycolysis and an expansion of the resting zone and suggest that it is caused by acetyl-CoA deficiency, but not energy deficiency, possibly through epigenetic upregulation of FGFR3 signaling.