bluuebunny/crossref_metadata_2025 huggingface dataset:
Expected values for the accuracy of predicted breeding values accounting for genetic differences between reference and target populations
Authors: Cuyabano Beatriz C. D. , Boichard Didier , Gondro Cedric
Published: February 2024

Background

Genetic merit, or breeding values as referred to in livestock and crop breeding programs, is one of the keys to the successful selection of animals in commercial farming systems. The developments in statistical methods during the twentieth century and single nucleotide polymorphism (SNP) chip technologies in the twenty-first century have revolutionized agricultural production, by allowing highly accurate predictions of breeding values for selection candidates at a very early age. Nonetheless, for many breeding populations, realized accuracies of predicted breeding values (PBV) remain below the theoretical maximum, even when the reference population is sufficiently large, and SNPs included in the model are in sufficient linkage disequilibrium (LD) with the quantitative trait locus (QTL). This is particularly noticeable over generations, as we observe the so-called erosion of the effects of SNPs due to recombinations, accompanied by the erosion of the accuracy of prediction. While accurately quantifying the erosion at the individual SNP level is a difficult and unresolved task, quantifying the erosion of the accuracy of prediction is a more tractable problem. In this paper, we describe a method that uses the relationship between reference and target populations to calculate expected values for the accuracies of predicted breeding values for non-phenotyped individuals accounting for erosion. The accuracy of the expected values was evaluated through simulations, and a further evaluation was performed on real data.

Results

Using simulations, we empirically confirmed that our expected values for the accuracy of PBV accounting for erosion were able to correctly determine the prediction accuracy of breeding values for non-phenotyped individuals. When comparing the expected to the realized accuracies of PBV with real data, only one out of the four traits evaluated presented accuracies that were significantly higher than the expected, approaching $$\sqrt{{{\text{h}}}^{2}}$$

h

2

.

Conclusions

We defined an index of genetic correlation between reference and target populations, which summarizes the expected overall erosion due to differences in allele frequencies and LD patterns between populations. We used this correlation along with a trait’s heritability to derive expected values for the accuracy ($${\text{R}}$$
R
) of PBV accounting for the erosion, and demonstrated that our derived $${\text{E}}\left[{\text{R}}|{\text{erosion}}\right]$$

E

R
|
erosion

is a reliable metric.
An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome
Authors: Chai Hua , Lin Siyin , Lin Junqi , He Minfan , Yang Yuedong , OuYang Yongzhong , Zhao Huiying
Published: February 2024

Background

Predicting outcome of breast cancer is important for selecting appropriate treatments and prolonging the survival periods of patients. Recently, different deep learning-based methods have been carefully designed for cancer outcome prediction. However, the application of these methods is still challenged by interpretability. In this study, we proposed a novel multitask deep neural network called UISNet to predict the outcome of breast cancer. The UISNet is able to interpret the importance of features for the prediction model via an uncertainty-based integrated gradients algorithm. UISNet improved the prediction by introducing prior biological pathway knowledge and utilizing patient heterogeneity information.

Results

The model was tested in seven public datasets of breast cancer, and showed better performance (average C-index = 0.691) than the state-of-the-art methods (average C-index = 0.650, ranged from 0.619 to 0.677). Importantly, the UISNet identified 20 genes as associated with breast cancer, among which 11 have been proven to be associated with breast cancer by previous studies, and others are novel findings of this study.

Conclusions

Our proposed method is accurate and robust in predicting breast cancer outcomes, and it is an effective way to identify breast cancer-associated genes. The method codes are available at: https://github.com/chh171/UISNet.
Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing
Authors: Young Benjamin D. , Williamson Olivia M. , Kron Nicholas S. , Andrade Rodriguez Natalia , Isma Lys M. , MacKnight Nicholas J. , Muller Erinn M. , Rosales Stephanie M. , Sirotzke Stephanie M. , Traylor-Knowles Nikki , Williams Sara D. , Studivan Michael S.
Published: February 2024

Long-read sequencing is revolutionizingde-novogenome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-readde-novogenome assemblies now starting to be publicly available, opening the door for a wide array of ‘omics-based research. Here we present a newde-novogenome assembly for the endangered Caribbean star coral,Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our newde-novoassembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additionalO. faveolatafragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affectingO. faveolata, as well as itsincreasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other ‘omics analyses to aid in the conservation of this species.
Fine-scale geographic difference of the endangered Big-headed Turtle (Platysternon megacephalum) fecal microbiota, and comparison with the syntopic Beale’s Eyed Turtle (Sacalia bealei)
Authors: Fong Jonathan J. , Sung Yik-Hei , Ding Li
Published: February 2024

Background

Studies have elucidated the importance of gut microbiota for an organism, but we are still learning about the important influencing factors. Several factors have been identified in helping shape the microbiome of a host, and in this study we focus on two factors—geography and host. We characterize the fecal microbiota of the Big-headed Turtle (Platysternon megacephalum) and compare across a relatively fine geographic scale (three populations within an 8-km radius) and between two syntopic hosts (P. megacephalum and Sacalia bealei). Both species are endangered, which limits the number of samples we include in the study. Despite this limitation, these data serve as baseline data for healthy, wild fecal microbiotas of two endangered turtle species to aid in conservation management.

Results

For geography, the beta diversity of fecal microbiota differed between the most distant sites. The genus Citrobacter significantly differs between sites, which may indicate a difference in food availability, environmental microbiota, or both. Also, we identify the common core microbiome for Platysternon across Hong Kong as the shared taxa across the three sites. Additionally, beta diversity differs between host species. Since the two species are from the same site and encounter the same environmental microbiota, we infer that there is a host effect on the fecal microbiota, such as diet or the recruitment of host-adapted bacteria. Lastly, functional analyses found metabolism pathways (KEGG level 1) to be the most common, and pathways (KEGG level 3) to be statistically significant between sites, but statistically indistinguishable between species at the same site.

Conclusions

We find that fecal microbiota can significantly differ at a fine geographic scale and between syntopic hosts. Also, the function of fecal microbiota seems to be strongly affected by geographic site, rather than species. This study characterizes the identity and function of the fecal microbiota of two endangered turtle species, from what is likely their last remaining wild populations. These data of healthy, wild fecal microbiota will serve as a baseline for comparison and contribute to the conservation of these two endangered species.
Current state of neuroprotective therapy using antibiotics in human traumatic brain injury and animal models
Authors: Ritter Katharina , Somnuke Pawit , Hu Lingjiao , Griemert Eva-Verena , Schäfer Michael K.E.
Published: February 2024

TBI is a leading cause of death and disability in young people and older adults worldwide. There is no gold standard treatment for TBI besides surgical interventions and symptomatic relief. Post-injury infections, such as lower respiratory tract and surgical site infections or meningitis are frequent complications following TBI. Whether the use of preventive and/or symptomatic antibiotic therapy improves patient mortality and outcome is an ongoing matter of debate. In contrast, results from animal models of TBI suggest translational perspectives and support the hypothesis that antibiotics, independent of their anti-microbial activity, alleviate secondary injury and improve neurological outcomes. These beneficial effects were largely attributed to the inhibition of neuroinflammation and neuronal cell death. In this review, we briefly outline current treatment options, including antibiotic therapy, for patients with TBI. We then summarize the therapeutic effects of the most commonly tested antibiotics in TBI animal models, highlight studies identifying molecular targets of antibiotics, and discuss similarities and differences in their mechanistic modes of action.
Clinical nomogram prediction model to assess the risk of prolonged ICU length of stay in patients with diabetic ketoacidosis: a retrospective analysis based on the MIMIC-IV database
Authors: Shi Jincun , Chen Fujin , Zheng Kaihui , Su Tong , Wang Xiaobo , Wu Jianhua , Ni Bukao , Pan Yujie
Published: February 2024

Background

The duration of hospitalization, especially in the intensive care unit (ICU), for patients with diabetic ketoacidosis (DKA) is influenced by patient prognosis and treatment costs. Reducing ICU length of stay (LOS) in patients with DKA is crucial for optimising healthcare resources utilization. This study aimed to establish a nomogram prediction model to identify the risk factors influencing prolonged LOS in ICU-managed patients with DKA, which will serve as a basis for clinical treatment, healthcare safety, and quality management research.

Methods

In this single-centre retrospective cohort study, we performed a retrospective analysis using relevant data extracted from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database. Clinical data from 669 patients with DKA requiring ICU treatment were included. Variables were selected using the Least Absolute Shrinkage and Selection Operator (LASSO) binary logistic regression model. Subsequently, the selected variables were subjected to a multifactorial logistic regression analysis to determine independent risk factors for prolonged ICU LOS in patients with DKA. A nomogram prediction model was constructed based on the identified predictors. The multivariate variables included in this nomogram prediction model were the Oxford acute severity of illness score (OASIS), Glasgow coma scale (GCS), acute kidney injury (AKI) stage, vasoactive agents, and myocardial infarction.

Results

The prediction model had a high predictive efficacy, with an area under the curve value of 0.870 (95% confidence interval [CI], 0.831–0.908) in the training cohort and 0.858 (95% CI, 0.799–0.916) in the validation cohort. A highly accurate predictive model was depicted in both cohorts using the Hosmer–Lemeshow (H-L) test and calibration plots.

Conclusion

The nomogram prediction model proposed in this study has a high clinical application value for predicting prolonged ICU LOS in patients with DKA. This model can help clinicians identify patients with DKA at risk of prolonged ICU LOS, thereby enhancing prompt intervention and improving prognosis.
Effect of neutrophil to lymphocyte ratio on prognosis of elderly patients with severe sepsis combined with diabetes mellitus
Authors: Jin Shan , Yin Jun-bin , Li Wei , Zang Li-li
Published: February 2024

Background

To investigate the predictive value of neutrophil-to-lymphocyte ratio (NLR) in the short-term prognosis of elderly patients with severe sepsis combined with diabetes mellitus (DM).

Methods

The clinical data of 162 elderly patients with severe sepsis combined with DM from January 2018 to December 2022 were retrospectively collected. These patients were divided into a survival group (n = 104) and a death group (n = 58) according to 90-day prognosis. The number of neutrophils, lymphocytes, and NLR were compared. The optimal cut-off value for NLR to predict 90-day prognosis in elderly patients with severe sepsis combined with DM was determined using Receiver Operator Characteristic (ROC) curves, and the patients were divided into high and low NLR groups depending on the optimal cut-off value. The Kaplan-Meier method was used to plot the survival curves of the high and low NLR groups. Risk factors for the 90-day death in elderly patients with severe sepsis combined with DM were analyzed by a multivariate cox regression model.

Results

There were no significant differences in gender, age, history of hypertension and hyperlipidemia, intensive care unit (ICU) stay, duration of mechanical ventilation, and oxygenation index between the survival group and death group (p > 0.05). However, acute physiological and chronic health evaluation II (APACHE II) scores, and sepsis-related organ failure assessment (SOFA) scores were significantly lower in the survival group compared with the death group (p < 0.05). In the survival group, neutrophils counts and NLR were much lower than those in the death group, while lymphocytes counts were much higher (p < 0.05). ROC curves showed that the optimal cut-off value for NLR to predict 90-day mortality in elderly patients with severe sepsis combined with DM was 3.482. Patients were divided into high NLR and low NLR groups based on whether NLR was ≥ 3.482. In terms of the log-rank test results, patients in the low NLR group had a significantly higher 90-day survival rate than those in the high NLR group (Logrank χ2 = 8.635, p = 0.003). The multivariate cox regression model showed that the length of ICU stay longer than 15 days and NLR ≥ 3.482 were independent risk factors for 90-day prognosis in elderly patients with severe sepsis combined with DM.

Conclusion

NLR ≥ 3.482 can be used to predict whether poor prognosis occurs in the short term after illness in elderly patients with severe sepsis combined with DM, and has good assessment value.
Low physical activity is a risk factor for sarcopenia: a cross-sectional analysis of two exercise trials on community-dwelling older adults
Authors: Hämäläinen Onni , Tirkkonen Anna , Savikangas Tiina , Alén Markku , Sipilä Sarianna , Hautala Arto
Published: February 2024

Background

Physical inactivity is an important factor in the development of sarcopenia. This cross-sectional study explores the prevalence of sarcopenia and associations of physical activity (PA) with sarcopenia in two exercise trial populations. These study groups are clinically meaningful community-dwelling populations at increased risk for sarcopenia: older adults not meeting the PA guidelines and those with a recent hip fracture (HF).

Methods

Data from 313 older adults who did not meet the PA guidelines (60% women; age 74.5 ± 3.8, body mass index 27.9 ± 4.7) and 77 individuals with HF diagnosed on average 70 ± 28 days earlier (75% women; age 79.3 ± 7.1, body mass index 25.3 ± 3.6) were included in this study. Grip strength and muscle mass (Dual-energy X-ray absorptiometry [DXA] in older adults not meeting the PA guidelines and bioimpedance analysis in participants with HF) were used to assess sarcopenia according to the European Working Group in Older People 2019 (EWGSOP2) criteria. The current level of PA was self-reported using a question with seven response options in both study groups and was measured with a hip-worn accelerometer for seven consecutive days in older adults not meeting the PA guidelines.

Results

The prevalence of sarcopenia and probable sarcopenia was 3% (n = 8) and 13% (n = 41) in the older adults not meeting the PA guidelines and 3% (n = 2) and 40% (n = 31) in the HF group, respectively. In the age- and sex-adjusted logistic regression model, the lowest levels of self-reported PA were associated with increased probable sarcopenia and sarcopenia risk in older adults not meeting the PA guidelines (OR 2.8, 95% CI, 1.3–6.1, p = 0.009) and in the HF group (OR 3.9, 95% CI, 1.4–11.3, p = 0.012). No significant associations between accelerometer-measured PA and probable sarcopenia or sarcopenia were found.

Conclusions

Probable sarcopenia is common among community-dwelling older adults not meeting the PA guidelines and very common among individuals recovering from HF who are able to be involved in exercise interventions. In addition, since low PA is associated with higher probable sarcopenia and sarcopenia risk, it is recommended to screen for sarcopenia and promote regular physical activity to prevent sarcopenia in these populations.
Comorbidity and household income as mediators of gender inequalities in dementia risk: a real-world data population study
Authors: Zubiagirre Uxue , Ibarrondo Oliver , Larrañaga Igor , Soto-Gordoa Myriam , Mar-Barrutia Lorea , Mar Javier
Published: February 2024

Background

Low household income (HI), comorbidities and female sex are associated with an increased risk of dementia. The aim of this study was to measure the mediating effect of comorbidity and HI on the excess risk due to gender in relation to the incidence and prevalence of dementia in the general population.

Methods

A retrospective and observational study using real-world data analysed all people over 60 who were registered with the Basque Health Service in Gipuzkoa. The study measured HI level, the Charlson comorbidity index (CCI), age and sex. The prevalence and incidence of dementia were analysed using logistic regression and Poisson regression models, respectively, adjusted by HI, sex, comorbidity and age. We estimated the combined mediation effect of HI and comorbidity on the prevalence of dementia associated with gender.

Results

Of the 221,777 individuals, 3.85% (8,549) had a diagnosis of dementia as of 31 December 2021. Classification by the CCI showed a gradient with 2.90% in CCI 0–1, 10.60% in CCI 2–3 and 18.01% in CCI > 3. Both low HI and gender were associated with a higher crude prevalence of dementia. However, in the CCI-adjusted model, women had an increased risk of dementia, while HI was no longer statistically significant. The incidence analysis produced similar results, although HI was not significant in any model. The CCI was significantly higher for men and for people with low HI. The mediation was statistically significant, and the CCI and HI explained 79% of the gender effect.

Conclusions

Comorbidity and low HI act as mediators in the increased risk of dementia associated with female sex. Given the difference in the prevalence of comorbidities by HI, individual interventions to control comorbidities could not only prevent dementia but also reduce inequalities, as the risk is greater in the most disadvantaged population.
Risk factors associated with functional decline in older hospital survivors with acute lower respiratory tract infections: a prospective cohort study
Authors: Weng Bingxuan , Jin Jin , Huang Lixue , Tong Xunliang , Jiao Wenshu , Wang Yuanqi , Fang Chuangsen , Wang Mengyuan , Li Yanming
Published: February 2024

Objective

To evaluate the dynamics of basic activity of daily living (BADL) in older patients with acute lower respiratory tract infections (LRTIs) during acute phase and to investigate risk factors associated with decreased physical function at discharge.

Methods

We conducted a prospective cohort study of patients aged 65 years and older who were hospitalized for acute LRTIs between April 15, 2020 and January 15, 2023. All patients received geriatric assessment at admission, including emotion, cognition, frailty, physical function status and so on. The BADL was also evaluated by the Barthel Index (BI) at two weeks before admission by recall (baseline status), at admission and at discharge. Based on the BI grades at baseline and at discharge, patients were classified into two groups: ADL decline and no ADL decline. Multivariable adjusted logistic regression models were used to evaluate the risk factors of decreased physical function.

Results

A total of 364 older survivors with LRTIs were included in the analysis. The median age was 74 years (IQR 61.0–82.0), 231 (62.6%) were male, the median length of stay was 10 days. In the geriatric assessment, 139 patients (38.2%) were classified as frailty, 137 patients (37.6%) experienced insomnia, 60 patients (16.5%) exhibited cognitive impairments, and 37 patients (10.2%) were defined as malnutrition. Additionally, 30 patients (8.2%) dealt with emotional disorders. On average, patients were taking 3 medications, and Charlson Comorbidity Index score was 4. 72 patients (19.8%) had function decline at discharge. In the multivariable analysis, frailty status had an odds ratio of 4.25 (95% CI 1.31–19.26) for decreased physical function and cognitive impairment had an odds ratio of 2.58 (95% CI 1.27–5.19).

Conclusions

About 20% older patients with LRTIs experienced functional decline at discharge. Compared to age, severity of diseases and length of stay, frailty and cognitive impairment performed better at predicting the function decline. The apply of geriatric assessment may contribute to enhance the quality of management and treatment for patients with the older with LRTIs.
Costs of distributing HIV self-testing kits in Eswatini through community and workplace models
Authors: McGee Kathleen , d’Elbée Marc , Dekova Ralitza , Sande Linda A. , Dube Lenhle , Masuku Sanele , Dlamini Makhosazana , Mangenah Collin , Mwenge Lawrence , Johnson Cheryl , Hatzold Karin , Neuman Melissa , Meyer-Rath Gesine , Terris-Prestholt Fern
Published: February 2024

Background

This study evaluates the implementation and running costs of an HIV self-testing (HIVST) distribution program in Eswatini. HIVST kits were delivered through community-based and workplace models using primary and secondary distribution. Primary clients could self-test onsite or offsite. This study presents total running economic costs of kit distribution per model between April 2019 and March 2020, and estimates average cost per HIVST kit distributed, per client self-tested, per client self-tested reactive, per client confirmed positive, and per client initiating antiretroviral therapy (ART).

Methods

Distribution data and follow-up phone interviews were analysed to estimate implementation outcomes. Results were presented for each step of the care cascade using best-case and worst-case scenarios. A top-down incremental cost-analysis was conducted from the provider perspective using project expenditures. Sensitivity and scenario analyses explored effects of economic and epidemiological parameters on average costs.

Results

Nineteen thousand one hundred fifty-five HIVST kits were distributed to 13,031 individuals over a 12-month period, averaging 1.5 kits per recipient. 83% and 17% of kits were distributed via the community and workplace models, respectively. Clients reached via the workplace model were less likely to opt for onsite testing than clients in the community model (8% vs 29%). 6% of onsite workplace testers tested reactive compared to 2% of onsite community testers. Best-case scenario estimated 17,458 (91%) clients self-tested, 633 (4%) received reactive-test results, 606 (96%) linked to confirmatory testing, and 505 (83%) initiated ART.

Personnel and HIVST kits represented 60% and 32% of total costs, respectively. Average costs were: per kit distributed US$17.23, per client tested US$18.91, per client with a reactive test US$521.54, per client confirmed positive US$550.83, and per client initiating ART US$708.60. Lower rates for testing, reactivity, and linkage to care in the worst-case scenario resulted in higher average costs along the treatment cascade.

Conclusion

This study fills a significant evidence gap regarding costs of HIVST provision along the client care cascade in Eswatini. Workplace and community-based distribution of HIVST accompanied with effective linkage to care strategies can support countries to reach cascade objectives.
A clinical utility evaluation of dual HIV/Syphilis point-of-care tests in non-clinical settings for screening for HIV and syphilis in men who have sex with men
Authors: Fernàndez-López Laura , Reyes-Urueña Juliana , Egea Laia , Chernyshev Andrii , Upmace Inga , Ćosić Mitja , Mejías William , González Victoria , Blondeel Karel , Thwin Soe Soe , Gios Lorenzo , Mirandola Massimo , Peeling Rosanna , Kiarie James , Casabona Jordi , Toskin Igor ,   ProSPeRo group
Published: February 2024

Background

Dual point-of-care tests (POCTs) for the simultaneous detection of antibodies to HIV and syphilis have been developed. Since community-based organisations (CBO) are effective providers of HIV and syphilis testing among men who have sex with men (MSM), evaluation of the utility of these dual tests at CBO testing services is a high priority. The aim of this study is to determine the feasibility of performing dual HIV-syphilis POCT testing among both users and providers at these non-clinical sites.

Methods

This evaluation assessed the utility of two lateral flow immunochromatographic antibody technologies for dual screening for HIV/syphilis among MSM seeking testing in four CBO testing services in Spain, Slovenia, Latvia, and Ukraine. The study’s conceptual framework divides the concept of feasibility into two inter-related domains, acceptability, and usability and further breaks it down into six subdomains: learnability, willingness, suitability, satisfaction, efficacy, and effectiveness. The feasibility analysis was performed by calculating the median score in 3 stages (for individual questions, subdomains, and domains), using a summated scores method.

Results

The final sample included 844 participants, 60 of which were found to be HIV test positive (7.1%) and 61 (7.2%) positive on testing for syphilis. There was a small difference (1.1%) when comparing the results of the two dual POCTs under evaluation to the tests routinely used at each site. The inter-rater agreement showed a high concordance between two independent readings. The analysis of the feasibility for the users of the services indicated good satisfaction, suitability, and willingness. In addition, among 18 providers the total mean score showed good acceptability and usability, good willingness, easy learnability, high suitability, and good efficacy, but lower satisfaction and effectiveness. The operational characteristics of both dual study POCTs were well evaluated by providers.

Conclusions

The introduction of dual HIV and syphilis  POCTs in CBO testing services for screening of MSM is feasible, with a high acceptability and usability both for users and providers. Implementation of dual POCTs for HIV and syphilis in CBO testing services is an opportunity for scaling up integrated HIV/syphilis testing for MSM.
Independent clinic-based evaluation of dual POCTs for screening for HIV and syphilis in men who have sex with men in Italy, Malta, Peru, and the United Kingdom
Authors: Sherriff Nigel , Mirandola Massimo , Silva Ronaldo , Cordioli Maddalena , Sawyer Alexandra , Gios Lorenzo , Zorzi Antonella , Huber Jorg , Vera Jaime , Richardson Daniel , Hassan-Ibrahim Mohammed , Wlazly Dominika , Padovese Valeska , Barbara Christopher , Darmanin Anabel , Schembri Aaron , Caceres Carlos , Vargas Silver , Blondeel Karel , Kiarie James , Kurbonov Firdavs , Peeling Rosanna W. , Thwin Soe Soe , Toskin Igor ,   other Editorial Board Members of the ProSPeRo Network, Hançali Amina , Oumzi Hicham , Mwima Simon , Kyambadde Peter , Ssewanyana Isaac
Published: February 2024

Introduction

Globally, the incidence of HIV and syphilis can be reduced by the use of validated point of care tests (POCTs). As part of the WHO PRoSPeRo Network, we aimed to evaluate the performance, acceptability, and operational characteristics of two dual HIV/syphilis POCTs (Bioline HIV/Syphilis Duo (Abbott) and DPP® HIV-Syphilis assay (Chembio) for the screening of HIV and syphilis amongst men who have sex with men (MSM).

Method and analyses

A cross sectional study of 2,577 MSM in Italy, Malta, Peru, and the United Kingdom (UK) presenting to seven clinic sites, were enrolled. Finger prick blood was collected to perform POCTs and results compared with standard laboratory investigations on venepuncture blood. Acceptability and operational characteristics were assessed using questionnaires. Diagnostic meta-analysis was used to combine data from the evaluation sites.

Results

Based on laboratory tests, 23.46% (n = 598/2549) of participants were confirmed HIV positive, and 35.88% of participants (n = 901/2511) were positive on treponemal reference testing. Of all participants showing evidence of antibodies to Treponema pallidum, 50.56% (n = 455/900) were Rapid Plasma Reagin (RPR) test reactive. Of HIV positive individuals, 60.62% (n = 354/584) had evidence of antibodies to T. pallidum, and of these 60.45% (n = 214/354) exhibited reactive RPR tests indicating probable (co)infection. For Bioline POCT, pooled sensitivities and specificities for HIV were 98.95% and 99.89% respectively, and for syphilis were 73.79% and 99.57%. For Chembio pooled sensitivities and specificities for HIV were 98.66% and 99.55%, and for syphilis were 78.60% and 99.48%. Both tests can detect greater than 90% of probable active syphilis cases, as defined by reactive RPR and treponemal test results. These dual POCTs were preferred by 74.77% (n = 1,926) of participants, due to their convenience, and the operational characteristics made them acceptable to health care providers (HCPs).

Conclusions

Both the Bioline and the Chembio dual POCT for syphilis and HIV had acceptable performance, acceptability and operational characteristics amongst MSM in the PRoSPeRo network. These dual POCTs could serve as a strategic, more cost effective, patient and healthcare provider (HCP) friendly alternative to conventional testing; in clinical and other field settings, especially those in resource-limited settings.
External quality assessment to support the WHO ProSPeRo study for the evaluation of two dual HIV/syphilis point-of-care tests in seven countries
Authors: Cao Weiping , Fakile Yetunde F. , Shukla Mayur R. , Pettus Kevin , Lupoli Kathryn , Hong Jaeyoung , Pillay Allan , Kularatne Ranmini , Oumzil Hicham , Padovese Valeska , Sherriff Nigel , SSewanyana Isaac , Vargas Silver K. , Zorzi Antonella , Blondeel Karel , Toskin Igor , Kersh Ellen N.
Published: February 2024

Background

Sexually transmitted infections (STIs) such as syphilis and HIV remain to be a significant public health issue worldwide. Dual rapid point-of-care tests (POCTs) have shown promise for detecting antibodies to HIV and syphilis but have not been fully evaluated in the field. Our study supported the WHO ProSPeRo study on Sexually Transmitted Infection Point-of-Care Testing (STI POCT) by providing external quality assessment (EQA) for HIV and syphilis testing in reference laboratories and their associated clinical sites in seven countries.

Methods

HIV/syphilis serum liquid and dried tube specimen (DTS) panels were prepared by CDC. Liquid panels were distributed to the reference laboratories for three rounds of testing using commercially and locally available laboratory-based serological tests. DTS panels were sent to the clinical testing sites for 8 rounds of POC testing using the Abbott SD BIOLINE HIV/Syphilis Duo test (hereafter referred to as SD BIOLINE) and the Chembio Dual Path Platform (DPP) HIV-Syphilis assay. EQA panels were tested at CDC using the Rapid Plasma Reagin (RPR) test and the Treponema pallidum Particle Agglutination assay (TP-PA) for syphilis antibodies. Genetic Systems HIV-1/HIV-2 Plus O EIA, Geenius HIV Supplemental Assay and the Oraquick Advance HIV test were used to detect HIV antibodies in the EQA panels. Results from the reference laboratories and POCT sites were compared to those obtained at the CDC and a percentage agreement was calculated.

Results

Qualitative RPR and TP-PA performed at the reference laboratories demonstrated 95.4–100% agreement with CDC results while quantitative RPR and TP-PA tests demonstrated 87.7% and 89.2% agreement, respectively. A 93.8% concordance rate was observed for qualitative HIV testing in laboratories. EQA testing at clinical sites using dual tests showed 98.7% and 99.1% agreement for detection of HIV antibodies and eight out of 10 sites had > 95.8% agreement for syphilis testing. However, two clinical sites showed only 65.0–66.7% agreement for SD BIOLINE and 84.0–86.7% for DPP, respectively, for syphilis testing.

Conclusions

Overall, laboratories demonstrated high EQA performance in this study. Both HIV/syphilis POCTs gave expected results in the clinic-based evaluations using DTS. However, testing errors were identified in a few testing sites suggesting the necessity for continuous training and monitoring the quality of POC testing.
Individualized estimation of arterial carbon dioxide partial pressure using machine learning in children receiving mechanical ventilation
Authors: Han Hye-Ji , Lee Bongjin , Park June Dong
Published: February 2024

Background

Measuring arterial partial pressure of carbon dioxide (PaCO2) is crucial for proper mechanical ventilation, but the current sampling method is invasive. End-tidal carbon dioxide (EtCO2) has been used as a surrogate, which can be measured non-invasively, but its limited accuracy is due to ventilation-perfusion mismatch. This study aimed to develop a non-invasive PaCO2 estimation model using machine learning.

Methods

This retrospective observational study included pediatric patients (< 18 years) admitted to the pediatric intensive care unit of a tertiary children’s hospital and received mechanical ventilation between January 2021 and June 2022. Clinical information, including mechanical ventilation parameters and laboratory test results, was used for machine learning. Linear regression, multilayer perceptron, and extreme gradient boosting were implemented. The dataset was divided into 7:3 ratios for training and testing. Model performance was assessed using the R2 value.

Results

We analyzed total 2,427 measurements from 32 patients. The median (interquartile range) age was 16 (12−19.5) months, and 74.1% were female. The PaCO2 and EtCO2 were 63 (50−83) mmHg and 43 (35−54) mmHg, respectively. A significant discrepancy of 19 (12–31) mmHg existed between EtCO2 and the measured PaCO2. The R2 coefficient of determination for the developed models was 0.799 for the linear regression model, 0.851 for the multilayer perceptron model, and 0.877 for the extreme gradient boosting model. The correlations with PaCO2 were higher in all three models compared to EtCO2.

Conclusions

We developed machine learning models to non-invasively estimate PaCO2 in pediatric patients receiving mechanical ventilation, demonstrating acceptable performance. Further research is needed to improve reliability and external validation.
Wording the trajectory of the three-year COVID-19 epidemic in a general population – Belgium
Authors: Vanderpas Jean , Dramaix Michèle , Coppieters Yves
Published: February 2024

The trajectory of COVID-19 epidemic waves in the general population of Belgium was analysed by defining quantitative criteria for epidemic waves from March 2020 to early 2023. Peaks and starting/ending times characterised nine waves numerated I to IX based on the daily reported incidence number (symbol INCID) and three “endemic” interval periods between the first four waves. The SIR compartmental model was applied to the first epidemic wave by fitting the daily prevalence pool (symbol I) calculated as the sum of the daily incidence rate and estimated number of subjects still infectious from the previous days. The basic reproductive number R0 was calculated based on the exponential growth rate during the early phase and on medical literature knowledge of the time of generation of SARS-CoV-2 infection. The first COVID-19 wave was well fitted by an open SIR model. According to this approach, dampened recurrent epidemic waves evolving through an endemic state would have been expected. This was not the case with the subsequent epidemic waves being characterised by new variants of concern (VOC). Evidence-based observations: 1) each epidemic wave affected less than a fifth of the general population; 2) the Vth epidemic wave (VOC Omicron) presented the greatest amplitude. The lack of recurrence of the same VOC during successive epidemic waves strongly suggests that a VOC has a limited persistence, disappearing from the population well before the expected proportion of the theoretical susceptible cohort being maximally infected. Fitting the theoretical SIR model, a limited persistence of VOCs in a population could explain that new VOCs replace old ones, even if the new VOC has a lower transmission rate than the preceding one. In conclusion, acquisition of potential defective mutations in VOC during an epidemic wave is a potential factor explaining the absence of resurgence of a same VOC during successive waves. Such an hypothesis is open to discussion and to rebuttal. A modified SIR model with epidemic waves of variable amplitude related not only to R0 and public health measures but also to acquisition of defective fitting in virus within a population should be tested.
Factors related to increased alcohol misuse by students compared to non-students during the first Covid-19 lockdown in France: the Confins study
Authors: Kinouani Shérazade , Macalli Mélissa , Arsandaux Julie , Montagni Ilaria , Texier Nathalie , Schück Stéphane , Tzourio Christophe
Published: February 2024

Background

The closure of bars and lockdowns related to the Covid-19 pandemic changed alcohol use levels in France during the spring of 2020. We wondered whether this sudden cessation of social interactions impacted students more than non-students and what factors specific to students would explain the increase in alcohol misuse. The aims of this study were to compare self-reported changes in alcohol misuse (alcohol intake and binge-drinking frequency) during the first Covid-19 lockdown from March 17 to May 10, 2020, between French students and non-students and describe factors associated with this alcohol misuse in each subgroup.

Methods

Data collected in the Confins study from April 8 to May 10, 2020, were used in cross-sectional analyses stratified by student status. Multiple logistic regression was performed to estimate the association between self-reported increase in alcohol intake or binge-drinking frequency (at least six drinks of alcohol on one occasion) and demographic, socioeconomic, and clinical factors, as well as conditions associated with the Covid-19 pandemic. The population-attributable fraction was then used to estimate the contribution of identified risk factors to increased alcohol misuse in students and non-students.

Results

Among both students and non-students, a self-reported decrease or no change in alcohol intake or binge-drinking was more common than an increase. However, the risk factors explaining an increase in alcohol intake differed among students (≥ 25 years old, not working or studying in the health field, and having suicidal ideation during the last 7 days) and non-students (having a medical diagnosis of mental disorders). The risk factors explaining an increase in binge-drinking frequency were similar in the two subgroups (being a tobacco smoker before lockdown and not practicing any physical activity during the last 7 days), except suicidal thoughts, which was a risk factor for alcohol misuse specific to students.

Conclusions

These results highlight the vulnerability of certain French students to alcohol misuse and the necessity of combining both mental health and substance use-related screening in the student population.
Comparison of microbial abundance and diversity in uterine and peritoneal fluid in infertile patients with or without endometriosis
Authors: Zhu Jue , Chen Yichen , Chen Huan , Sun Yuhui , Yan Lifeng , Zhu Miaohua , chen Liang , Wang Qiming , Zhang Jing
Published: February 2024

Introduction

Endometriosis (EM) is a multifactorial disease that affects 10 − 15% of women of reproductive age. Additionally, 30–50% of women with EM suffer from infertility. The mechanism of infertility caused by EM has not yet been consistently explained. In recent years, studies have shown a link between infertility associated with EM and changes in the reproductive tract microbiota.

Methods

In this study, we involved 26 EM patients (8 cases of stage I-II and 18 cases of stage III-IV) and 31 control subjects who were tubal obstruction-related infertility (TORI). The samples from peritoneal fluid (PF) and uterine fluid (UF) were collected and sequenced by 16 S rRNA amplicon.

Results

In the comparison of microbial diversity, we found no significant differences in the microbial diversity of PF and UF between patients with stage I-II EM and those with TORI. However, there was a significant difference in microbial diversity among patients with stage III-IV EM compared to the previous two groups. Lactobacillus decreased in PF of EM compared to the control group, while it increased in UF. In PF, the abundance of Pseudomonas, Enterococcus, Dubosiella and Klebsiella was significantly higher in patients with stage III-IV compared to TORI patients. And in UF, the main differences existed between stage I-II EM compared to the other two groups. The abundance of pontibacter, aquabacterium, Rikenellaceae and so on at the genus level was significantly enriched in the EM patients with stage I-II. In the analysis based on KEGG database, EM may affect the receptivity related pathways of the endometrium by influencing changes in the uterine microbiota.

Conclusion

Our results indicated that as EM progresses, the microorganisms in UF and PF keep changing. These changes in the microbiota, as well as the resulting alternations in gene functional classification, may play an important role in the infertility associated with EM.
Healthcare providers’ experience of identifying and caring for women subjected to sex trafficking: a qualitative study
Authors: Andersson Mikaela , Örmon Karin
Published: February 2024

Background

Men’s violence against women, including human trafficking for sexual exploitation, is a severe threat to global health. Healthcare providers are uniquely positioned to identify and care for women subjected to human trafficking for sexual exploitation. They are among the few professionals the women interact with while being exposed to human trafficking for sexual exploitation. This study aims to describe healthcare workers’ experience of identifying and caring for women subjected to human trafficking for sexual exploitation seeking women’s healthcare.

Method

A qualitative design was chosen and nine qualitative interviews with healthcare providers were conducted and analyzed using the content analysis method.

Results

Three main categories were revealed: (1) the importance of being attentive, (2) the importance of providing safety, and (3) the importance of collaborating, followed by a number of subcategories: behavioral and physical signs, limited time to interact, security measures, value of confidence building, organizational collaboration, essential external network, and information transmission.

Conclusions

As the women subjected to sex trafficking have limited time in healthcare, it is important for healthcare providers to be attentive and act immediately if suspecting human trafficking for sexual exploitation. It may be the only possibility for the healthcare providers to care for these women and reach them. They must endeavor to provide the women with safety due to their vulnerable position at the hospital. However, these women may leave the healthcare setting unidentified and unaided, which highlights the importance of collaboration on multiple levels.
Specific dairy foods and risk of frailty in older women: a prospective cohort study
Authors: Struijk Ellen A. , Fung Teresa T. , Rodriguez-Artalejo Fernando , Bischoff-Ferrari Heike A. , Willett Walter C. , Lopez-Garcia Esther
Published: February 2024

Background

Dairy contains a complex mixture of lipids, proteins, and micronutrients. Whether habitual dairy consumption is associated with health benefits is not well established. Since dairy is high in nutrients that are potentially protective against frailty, the association between dairy products and the risk of frailty is of interest.

Methods

We analyzed data from 85,280 women aged ≥ 60 years participating in the Nurses’ Health Study. Consumption of milk, yogurt, and cheese was obtained from repeated food frequency questionnaires administered between 1980 and 2010. Frailty was defined as having at least three of the following five criteria from the FRAIL scale: fatigue, low strength, reduced aerobic capacity, having ≥ 5 chronic illnesses, and a weight loss of ≥ 5%. The occurrence of frailty was assessed every four years from 1992 to 2018. Cox proportional hazard models were used to examine the association between the intake of dairy foods and frailty.

Results

During follow-up we identified 15,912 incident cases of frailty. Consumption of milk or yogurt was not associated with the risk of frailty after adjustment for lifestyle factors, medication use, and overall diet quality. Cheese consumption was positively associated with risk of frailty [relative risk (95% confidence interval) for one serving/day increment in consumption: 1.10 (1.05, 1.16)]. Replacing one serving/day of milk, yogurt, or cheese with one serving/day of whole grains, nuts, or legumes was associated with a significant lower risk of frailty, while replacing milk, yogurt, or cheese with red meat or eggs was associated with an increased risk. When milk was replaced with a sugar-sweetened or artificially sweetened beverage, a greater risk of frailty was observed, while replacing milk with orange juice was associated with a lower risk of frailty.

Conclusions

The results suggest that the association between milk, yogurt, and cheese and frailty partly depends on the replacement product. Habitual consumption of milk or yogurt was not associated with risk of frailty, whereas cheese consumption may be associated with an increased risk.