bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population
Authors: Bonifazi Renzo , Calus Mario P. L. , ten Napel Jan , Veerkamp Roel F. , Biffani Stefano , Cassandro Martino , Savoia Simone , Vandenplas Jérémie 
Published: June 2023

Abstract
Background
International evaluations combine data from different countries allowing breeders to have access to larger panels of elite bulls and to increase the accuracy of estimated breeding values (EBV). However, international and national evaluations can use different sources of information to compute EBV (EBVINT and EBVNAT, respectively), leading to differences between them. Choosing one of these EBV results in losing the information that is contained only in the discarded EBV. Our objectives were to define and validate a procedure to integrate publishable sires’ EBVINT and their associated reliabilities computed from pedigree-based or single-step international beef cattle evaluations into national evaluations to obtain “blended” EBV. The Italian (ITA) pedigree-based national evaluation was used as a case study to validate the integration procedure.

Methods
Publishable sires’ international information, i.e. EBVINT and their associated reliabilities, was included in the national evaluation as pseudo-records. Data were available for 444,199 individual age-adjusted weaning weights of Limousin cattle from eight countries and 17,607 genotypes from four countries (ITA excluded). To mimic differences between international and national evaluations, international evaluations included phenotypes (and genotypes) of animals born prior to January 2019, while national evaluations included ITA phenotypes of animals born until April 2019. International evaluations using all available information were considered as reference scenarios. Publishable sires were divided into three groups: sires with ≥ 15, < 15 and no recorded offspring in ITA.

Results
Overall, for these three groups, integrating either pedigree-based or single-step international information into national pedigree-based evaluations improved the similarity of the blended EBV with the reference EBV compared to national evaluations without integration. For instance, the correlation with the reference EBV for direct (maternal) EBV went from 0.61 (0.79) for a national evaluation without integration to 0.97 (0.88) when integrating single-step international information, on average across all groups of publishable sires.

Conclusions
Our proposed one-animal-at-a-time integration procedure yields blended EBV that are in close agreement with full international EBV for all groups of animals analysed. The procedure can be directly applied by countries since it does not rely on specific software and is computationally inexpensive, allowing straightforward integration of publishable sires’ EBVINT from pedigree-based or single-step based international beef cattle evaluations into national evaluations.
Integrin alpha 6 homozygous splice-site mutation causes a new form of junctional epidermolysis bullosa in Charolais cattle
Authors: Boussaha Mekki , Boulling Arnaud , Wolgust Valérie , Bourgeois-Brunel Lorraine , Michot Pauline , Grohs Cécile , Gaiani Nicolas , Grivaud Pierre-Yves , Leclerc Hélène , Danchin-Burge Coralie , Vilotte Marthe , Rivière Julie , Boichard Didier , Gourreau Jean-Marie , Capitan Aurélien 
Published: June 2023

Abstract
Background
Inherited epidermolysis bullosa (EB) is a group of painful and life-threatening genetic disorders that are characterized by mechanically induced blistering of the skin and mucous membranes. Congenital skin fragility resembling EB was recently reported in three Charolais calves born in two distinct herds from unaffected parents. Phenotypic and genetic analyses were carried out to describe this condition and its molecular etiology.

Results
Genealogical, pathological and histological investigations confirmed the diagnosis of recessive EB. However, the affected calves showed milder clinical signs compared to another form of EB, which was previously reported in the same breed and is caused by a homozygous deletion of the ITGB4 gene. Homozygosity mapping followed by analysis of the whole-genome sequences of two cases and 5031 control individuals enabled us to prioritize a splice donor site of ITGA6 (c.2160 + 1G > T; Chr2 g.24112740C > A) as the most compelling candidate variant. This substitution showed a perfect genotype–phenotype correlation in the two affected pedigrees and was found to segregate only in Charolais, and at a very low frequency (f = 1.6 × 10−4) after genotyping 186,154 animals from 15 breeds. Finally, RT-PCR analyses revealed increased retention of introns 14 and 15 of the ITGA6 gene in a heterozygous mutant cow compared with a matched control. The mutant mRNA is predicted to cause a frameshift (ITGA6 p.I657Mfs1) that affects the assembly of the integrin α6β4 dimer and its correct anchoring to the cell membrane. This dimer is a key component of the hemidesmosome anchoring complex, which ensures the attachment of basal epithelial cells to the basal membrane. Based on these elements, we arrived at a diagnosis of junctional EB.

Conclusions
We report a rare example of partial phenocopies observed in the same breed and due to mutations that affect two members of the same protein dimer, and provide the first evidence of an ITGA6 mutation that causes EB in livestock species.
Transcriptional profile of Trichomonas vaginalis in response to metronidazole
Authors: Xie Yiting , Zhong Ping , Guan Wei , Zhao Yanqing , Yang Shuguo , Shao Yan , Li Jian 
Published: June 2023

Abstract
Background
Trichomoniasis caused by Trichomonas vaginalis, combined with its complications, has long frequently damaged millions of human health. Metronidazole (MTZ) is the first choice for therapy. Therefore, a better understanding of its trichomonacidal process to ultimately reveal the global mechanism of action is indispensable. To take a step toward this goal, electron microscopy and RNA sequencing were performed to fully reveal the early changes in T. vaginalis at the cellular and transcriptome levels after treatment with MTZ in vitro.

Results
The results showed that the morphology and subcellular structures of T. vaginalis underwent prominent alterations, characterized by a rough surface with bubbly protrusions, broken holes and deformed nuclei with decreased nuclear membranes, chromatin and organelles. The RNA-seq data revealed a total of 10,937 differentially expressed genes (DEGs), consisting of 4,978 upregulated and 5,959 downregulated genes. Most DEGs for the known MTZ activators, such as pyruvate:ferredoxin oxidoreductase (PFOR) and iron-sulfur binding domain, were significantly downregulated. However, genes for other possible alternative MTZ activators such as thioredoxin reductase, nitroreductase family proteins and flavodoxin-like fold family proteins, were dramatically stimulated. GO and KEGG analyses revealed that genes for basic vital activities, proteostasis, replication and repair were stimulated under MTZ stress, but those for DNA synthesis, more complicated life activities such as the cell cycle, motility, signaling and even virulence were significantly inhibited in T. vaginalis. Meanwhile, increased single nucleotide polymorphism (SNP) and insertions - deletions (indels) were stimulated by MTZ.

Conclusions
The current study reveals evident nuclear and cytomembrane damage and multiple variations in T. vaginalis at the transcriptional level. These data will offer a meaningful foundation for a deeper understanding of the MTZ trichomonacidal process and the transcriptional response of T. vaginalis to MTZ-induced stress or even cell death.
HealthyRHearts - reducing cholesterol in rural adults via telehealth-based medical nutrition therapy: protocol for a cluster randomised controlled trial
Authors: Schumacher Tracy L. , Herbert Jaimee , May Jennifer , Ramanathan Shanthi , Brown Leanne J. , Guppy Michelle , Williams Annabelle , Rollo Megan E. , Attia John , Collins Clare E. 
Published: June 2023

Abstract
Background
Few randomised controlled trials specifically focus on prevention in rural populations. Cardiovascular disease (CVD) contributes to approximately one quarter of deaths in Australia. Nutrition is a key component affecting many risk factors associated with CVD, including hypercholesterolaemia. However, access to medical nutrition therapy (MNT) is limited for people living in rural areas, potentially exacerbating inequities related to health outcomes. Telehealth services present an opportunity to improve MNT access and address healthcare disparities for rural populations. The present study aims to evaluate feasibility, acceptability, and cost-effectiveness of a telehealth MNT CVD intervention program in lowering CVD risk over 12-months in regional and rural primary health care settings.

Methods/design
A cluster randomised controlled trial set in rural and regional general practices in NSW, Australia, and their consenting patients (n = 300 participants). Practices will be randomised to either control (usual care from their General Practitioner (GP) + low level individualised dietetic feedback) or intervention groups (usual care from their GP + low level individualised dietetic feedback + telehealth MNT intervention). Telehealth consultations will be delivered by an Accredited Practising Dietitian (APD), with each intervention participant scheduled to receive five consultations over a 6-month period. System-generated generic personalised nutrition feedback reports are provided based on completion of the Australian Eating Survey – Heart version (AES-Heart), a food frequency questionnaire. Eligible participants must be assessed by their GP as at moderate (≥ 10%) to high (> 15%) risk of a CVD event within the next five years using the CVD Check calculator and reside in a regional or rural area within the Hunter New England Central Coast Primary Health Network (HNECC PHN) to be eligible for inclusion. Outcome measures are assessed at baseline, 3, 6 and 12 months. The primary outcome is reduction in total serum cholesterol. Evaluation of the intervention feasibility, acceptability and cost-effective will incorporate quantitative, economic and qualitative methodologies.

Discussion
Research outcomes will provide knowledge on effectiveness of MNT provision in reducing serum cholesterol, and feasibility, acceptability, and cost-effectiveness of delivering MNT via telehealth to address CVD risk in rural regions. Results will inform translation to health policy and practice for improving access to clinical care in rural Australia.

Trial registration
This trial is registered at anzctr.org.au under the acronym HealthyRHearts (Healthy Rural Hearts), registration number ACTRN12621001495819.
Incidence and risk factors of fasting hyperglycaemia following first-attack acute pancreatitis before discharge: a retrospective study
Authors: Liu Chengsi , Shi Qiao , Zhang Xiaoyi , Xue Enfu , Li Hanjun , Wang Weixing 
Published: June 2023

Abstract
Background
Pancreatic endocrine insufficiency is more likely to occur after acute pancreatitis (AP), but the risk factors affecting pancreatic endocrine function remain controversial. Therefore, exploring the incidence and risk factors of fasting hyperglycaemia following first-attack AP is important.

Methods
Data were collected from 311 individuals with first-attack AP without previous diabetes mellitus (DM) or impaired fasting glucose (IFG) history treated in the Renmin Hospital of Wuhan University. Relevant statistical tests were performed. A two-sided p-value < 0.05 was considered statistically significant.

Results
The incidence of fasting hyperglycaemia in individuals with first-attack AP was 45.3%. Univariate analysis showed that age (χ2 = 6.27, P = 0.012), aetiology (χ2 = 11.184, P = 0.004), serum total cholesterol (TC) (χ2 = 14.622, P < 0.001), and serum triglyceride (TG) (χ2 = 15.006, P < 0.001) were significantly different between the hyperglycaemia and non-hyperglycaemia groups (P < 0.05). The serum calcium concentration (Z=-2.480, P = 0.013) was significantly different between the two groups (P < 0.05). Multiple logistic regression analysis showed that age- ≥60 years (P < 0.001, OR = 2.631, 95%Cl = 1.529–4.527) and TG ≥ 5.65 mmol/L (P < 0.001, OR = 3.964, 95%Cl = 1.990–7.895) were independent risk factors for fasting hyperglycaemia in individuals with first-attack AP (P < 0.05).

Conclusions
Old age, serum triglycerides, serum total cholesterol, hypocalcaemia, and aetiology are associated with fasting hyperglycaemia following first-attack AP. Age ≥ 60 years and TG ≥ 5.65 mmol/L are independent risk factors for fasting hyperglycaemia following first-attack AP.
Incidence rate and predictors of COVID-19 in the two largest cities of Burkina Faso - prospective cohort study in 2021 (ANRS-COV13)
Authors: Kaboré Nongodo Firmin , Ouédraogo Samiratou , Mamguem Ariane Kamga , Traoré Isidore Tiandiogo , Kania Dramane , Badolo Hermann , Sanou Guillaume , Koné Amariane , Yara Mimbouré , Kagoné Thérèse , Ouédraogo Esperance , Konaté Blahima , Médah Rachel , de Rekeneire Nathalie , Poda Armel , Diendéré Arnaud Eric , Ouédraogo Boukary , Billa Oumar , Paradis Gilles , Dabakuyo-Yonli Tienhan Sandrine , Tinto Halidou 
Published: June 2023

Abstract
Background
Early data on COVID-19 (based primarily on PCR testing) indicated a low burden in Sub-Saharan Africa. To better understand this, this study aimed to estimate the incidence rate and identify predictors of SARS-CoV-2 seroconversion in the two largest cities of Burkina Faso. This study is part of the EmulCOVID-19 project (ANRS-COV13).

Methods
Our study utilized the WHO Unity protocol for cohort sero-epidemiological studies of COVID-19 in general population. We conducted random sampling stratified by age group and sex. Individuals aged 10 years and older in the cities of Ouagadougou and Bobo-Dioulasso, Burkina Faso were included and surveyed at 4 time points, each 21 days apart, from March 3 to May 15, 2021. WANTAI SARS-CoV-2 Ab ELISA serological tests were used to detect total antibodies (IgM, IgG) in serum. Predictors were investigated using Cox proportional hazards regression.

Results
We analyzed the data from 1399 participants (1051 in Ouagadougou, 348 in Bobo-Dioulasso) who were SARS-CoV-2 seronegative at baseline and had at least one follow-up visit. The incidence rate of SARS-CoV-2 seroconversion was 14.3 cases [95%CI 13.3–15.4] per 100 person-weeks. The incidence rate was almost three times higher in Ouagadougou than in Bobo-Dioulasso (Incidence rate ratio: IRR = 2.7 [2.2–3.2], p < 0.001). The highest incidence rate was reported among women aged 19–59 years in Ouagadougou (22.8 cases [19.6–26.4] per 100 person-weeks) and the lowest among participants aged 60 years and over in Bobo-Dioulasso, 6.3 cases [4.6–8.6] per 100 person-weeks. Multivariable analysis showed that participants aged 19 years and older were almost twice as likely to seroconvert during the study period compared with those aged 10 to 18 years (Hazard ratio: HR = 1.7 [1.3–2.3], p < 0.001). Those aged 10–18 years exhibited more asymptomatic forms than those aged 19 years and older, among those who achieved seroconversion (72.9% vs. 40.4%, p < 0.001).

Conclusion
The spread of COVID-19 is more rapid in adults and in large cities. Strategies to control this pandemic in Burkina Faso, must take this into account. Adults living in large cities should be the priority targets for vaccination efforts against COVID-19.
Memory B-cells are enriched in the blood of patients with acute Buruli ulcer disease: a prospective observational study
Authors: Adjei Jonathan Kofi , Aniagyei Wilfred , Adankwah Ernest , Seyfarth Julia , Mayatepek Ertan , Berko Daniel Antwi , Ackam Nancy , Annani-Akollor Max Efui , Sakyi Samuel Asamoah , Amoako Yaw Ampem , Owusu Dorcas , Jacobsen Marc , Phillips Richard Odame 
Published: June 2023

Abstract
Background
Buruli ulcer disease (BUD) caused by Mycobacterium (M.) ulcerans is characterized by necrotic skin lesions. As for other mycobacterial infections, e.g., tuberculosis, the immune response is important for host protection. B-cells may play a role in antimycobacterial immunity but studies characterizing the B-cell repertoire and memory generation in BUD and during the course of treatment are scarce.

Methods
We investigated the adaptive immune cell repertoire in children with BUD and healthy matched controls by flow cytometry. Analyses prior to treatment, also in a study group of patients with tuberculosis, as well as three time points during BUD treatment (i.e., week 8, 16, and 32) were performed. In addition, BUD disease severity as well as treatment response were analysed for association with B-cell repertoire differences.

Results
Children with BUD had comparable total B- and T-cell proportions but differed largely in B-cell subsets. Memory B-cell (B mem) proportions were higher in children with BUD whereas regulatory B-cell (B reg) proportions were lower as compared to healthy controls and tuberculosis patients. Lower naïve (B naïve) and higher transitional B-cell (B trans) proportions characterized children with BUD in comparison with tuberculosis patients. Under treatment, B mem proportions decreased significantly whereas proportions of B reg and B naive increased concomitantly in children with BUD. Also, we found significant correlation between lesion size and B mem as well as B reg. However, we did not detect associations between treatment efficacy and B-cell proportions.

Conclusions
These results suggest a role of B-cell subsets in the immune response against M. ulcerans. Furthermore, changes in B-cell subset proportions may be used as markers for treatment monitoring in BUD.
Comparison of endotracheal aspirate and bronchoalveolar lavage fluid metagenomic next-generation sequencing in severe pneumonia: a nested, matched case–control study
Authors: Bao Renren , Mei Qing , Yang Tianjun , Zhang Lei , Zhu Chunyan , Fan Xiaoqin , Wang Yinzhong , Tong Fei , He Yuxi , Fang Xiaowei , Geng Shike , Yang Yu , Sheng Ximei , Pan Aijun 
Published: June 2023

Abstract
Objectives
To compare clinical outcomes in patients with severe pneumonia according to the diagnostic strategy used.

Methods
In this retrospective, nested, case–control study, patients with severe pneumonia who had undergone endotracheal aspirate (ETA) metagenomic next-generation sequencing of (mNGS) testing (n = 53) were matched at a ratio of 1 to 2 (n = 106) by sex, age, underlying diseases, immune status, disease severity scores, and type of pneumonia with patients who had undergone bronchoalveolar lavage fluid (BALF) mNGS. The microbiological characteristics and patient’s prognosis of the two groups were compared.

Results
An overall comparison between the two groups showed no significant differences in bacterial, fungal, viral, or mixed infections. However, subgroup analysis of 18 patients who received paired ETA and BALF mNGS showed a complete agreement rate for the two specimens of 33.3%. There were more cases for whom targeted treatment was initiated (36.79% vs. 22.64%; P = 0.043) and fewer cases who received no clinical benefit after mNGS (5.66% vs. 15.09%; P = 0.048) in the BALF group. The pneumonia improvement rate in the BALF group was significantly higher than in the ETA group (73.58% vs. 87.74%, P = 0.024). However, there were no significant differences in ICU mortality or 28-day mortality.

Conclusions
We do not recommend using ETA mNGS as the first-choice method for analyzing airway pathogenic specimens from severe pneumonia patients.
Leishmania species and clinical characteristics of Pacific and Amazon cutaneous leishmaniasis in Ecuador and determinants of health-seeking delay: a cross-sectional study
Authors: Bezemer Jacob M. , Freire-Paspuel Byron P. , Schallig Henk D. F. H. , de Vries Henry J.C. , Calvopiña Manuel 
Published: June 2023

AbstractBackgroundCutaneous Leishmaniasis (CL) affects up to 5.000 people in Ecuador each year.L. guyanensisandL. braziliensisare the most common of the eight CL-causingLeishmaniaspecies. Earlier CL research concentrated on the easily accessible Pacific region. This study aims to describe theLeishmaniaspecies in Pacific and Amazon ecoregions, to analyze regional differences in CL patient clinical presentation, and to identify determinants of health-seeking delay.MethodsAll cases in this cross-sectional study were diagnosed using smear slide microscopy, PCR, or both. Cytochrome B gene sequencing was used to identify the causativeLeishmaniaspecies in qPCR-positive samples.ResultsThis study included 245 patients, with 154 (63%) infected in the Pacific region and 91 (37%) infected in the Amazon. CausativeLeishmaniaspecies were identified in 135 patients (73% of qPCR positives).L. guyanensiswas identified in 76% (102/135) of the samples andL. braziliensisin 19% (26/135). The Pacific region had a low prevalence of 6% (5/89) ofL. braziliensis. For the first time, we reportL. guyanensisfrom the central Amazon,L. braziliensisfrom the northern Pacific, andL. lainsonifrom both the central Amazon and northern Pacific. Amazon cases had a longer median health-seeking delay in months (2.0, IQR 3.0) than Pacific cases (1.0, IQR 1.5). Prolonged health-seeking delay was associated with older age, Amerindian ethnicity, infection at lower altitudes, non-ulcerative lesions, and lesions on the lower limbs.ConclusionsIn the Pacific region, health-seeking delay is relatively short andL. braziliensisprevalence remains low. Limited access to health care and stigma might explain the prolonged health-seeking delay in the Amazon. We recommend larger studies on the distribution ofLeishmaniaspecies in Amazon CL cases and additional regional research into diagnostic test accuracy. Furthermore, the determinants of health-seeking delay in Ecuador should be investigated further.
Digital panoramic radiography and CBCT as auxiliary tools for detection of low bone mineral density in post-menopausal women: a cross-sectional study
Authors: Abdinian Mehrdad , Milaei Mina , Soltani Parisa 
Published: June 2023

Abstract
Background
Osteoporosis is a chronic, multifactorial skeletal disease that occurs especially in women following a decrease in estrogen levels and decrease in bone mineral density. The aim of this study was to evaluate the relationship between qualitative and quantitative indexes in panoramic radiographs and quantitative indexes in CBCT images with femoral and vertebral BMD in postmenopausal women.

Methods
This comparative cross-sectional study was performed on postmenopausal women aging 40 to 80 years attending for obtaining either panoramic radiograph or mandibular CBCT scan. Dual energy X-ray absorptiometry (DEXA) was performed from the femur and lumbar vertebra. Quantitative parameters of mental index (MI), panoramic mandibular index (PMI), antegonial index (AI) as well as qualitative parameters of mandibular cortical index (MCI) and trabecular bone pattern (TP) were evaluated in panoramic radiographs. Quantitative parameters computed tomography mandibular index (CTMI), computed tomography index (inferior) [CTI(I)] and computed tomography index (superior) [CTI(S)] were analyzed in CBCT images. Kolmogorov-Smirnov tests and Pearson correlation coefficient were used (α = 0.05).

Results
In individuals with panoramic radiography, statistically significant correlations were observed between MI with vertebral and femoral T-score, AI with vertebral and femoral T-score (except for the right AI with femoral T-score), and TP with vertebral and femoral T-score (p < 0.05). In the group with CBCT scans, the correlations between CTMI with vertebral and femoral T-score, CTI(I) with vertebral and femoral T-score, and CTI(S) with vertebral and femoral T-score were statistically significant (p < 0.05).

Conclusions
in CBCT images, quantitative indexes of CTMI, CTI(I), and CTI(S), and in panoramic images, quantitative indexes of MI and AI and qualitative index of TP can be used to predict the possibility of osteoporosis in postmenopausal women.