bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adverse pregnancy outcomes associated with antiretroviral therapy initiated before pregnancy and during pregnancy: a retrospective study in Hubei province, China
Authors: Tan Yuting , Wu Songjie , Yan Yajun , Zou Shi , Feng Ling , Guo Wei , Wu Mengmeng , Luo Mingqi , Liang Ke 
Published: May 2023

BackgroundAntiretroviral therapy (ART) initiation before pregnancy was reported to have an increased risk of adverse pregnancy outcomes (APOs) than ART initiation during pregnancy. However, the risks of APOs associated with different ART regimens initiated before or during pregnancy remain unknown.MethodsPregnant women living with HIV (PWLHIV) from Hubei Province, China, were retrospectively enrolled between January 1, 2004, and December 31, 2021. The trends of ART initiation time and application of different ART regimens were evaluated over time, separately. Using no ART exposure before and during pregnancy as control, the risks of APOs associated with protease inhibitor (PI) based regimens and non-nucleoside reverse transcriptase inhibitors (NNRTIs) based regimens initiated before pregnancy were analyzed; and the risks of APOs associated with PI-based regimens, NNRTIs based regimens and zidovudine (AZT) monotherapy initiated during pregnancy were analyzed. APOs, including low birthweight (LBW), stillbirth, preterm birth (PTB) and early miscarriage, were reviewed.ResultsAmong 781 PWLHIV including 1,010 pregnancies, 522 pregnancies (51.7%) were exposed to ART before or during pregnancy. Of them, the proportion of ART initiation before pregnancy per year increased from around 20% in the early period to more than 60% after 2019. Efavirenz (EFV)-nucleoside reverse transcriptase inhibitors (NRTIs) (32.2%), LPV/r-NRTIs (31.2%), and nevirapine (NVP)-NRTIs (27.4%) were the most commonly used regimens, and the proportion of LPV/r-NRTIs used per year has increased to around 50.0% in recent years. LPV/r-NRTIs was associated with higher risks of LBW whether initiated before pregnancy [adjusted OR (aOR) = 2.59, 95%CI 1.04–6.45, p = 0.041] or during pregnancy (aOR = 2.19, 95%CI 1.03–4.67, p = 0.041), compared with no exposure to ART before and during pregnancy. However, no matter initiated before or during pregnancy, LPV/r-NRTIs had no significantly increased risks of stillbirth, PTB and early miscarriage, and EFV /NVP-NRTIs and AZT monotherapy had no significantly increased risks of LBW, stillbirth, PTB and early miscarriage when compared with no exposure to ART before and during pregnancy.ConclusionOur data suggests that LPV/r-NRTIs has been widely used among PWLHIV in recent years. However, the potential risk of LBW should be continuously monitored among PWLHIV whether LPV/r-NRTIs is initiated before or during pregnancy.
Deep learning-based classification system of bacterial keratitis and fungal keratitis using anterior segment images
Authors: Won Yeo Kyoung , Lee Hyebin , Kim Youngjun , Han Gyule , Chung Tae-Young , Ro Yong Man , Lim Dong Hui 
Published: May 2023

IntroductionInfectious keratitis is a vision threatening disease. Bacterial and fungal keratitis are often confused in the early stages, so right diagnosis and optimized treatment for causative organisms is crucial. Antibacterial and antifungal medications are completely different, and the prognosis for fungal keratitis is even much worse. Since the identification of microorganisms takes a long time, empirical treatment must be started according to the appearance of the lesion before an accurate diagnosis. Thus, we developed an automated deep learning (DL) based diagnostic system of bacterial and fungal keratitis based on the anterior segment photographs using two proposed modules, Lesion Guiding Module (LGM) and Mask Adjusting Module (MAM).MethodsWe used 684 anterior segment photographs from 107 patients confirmed as bacterial or fungal keratitis by corneal scraping culture. Both broad- and slit-beam images were included in the analysis. We set baseline classifier as ResNet-50. The LGM was designed to learn the location information of lesions annotated by ophthalmologists and the slit-beam MAM was applied to extract the correct feature points from two different images (broad- and slit-beam) during the training phase. Our algorithm was then externally validated using 98 images from Google image search and ophthalmology textbooks.ResultsA total of 594 images from 88 patients were used for training, and 90 images from 19 patients were used for test. Compared to the diagnostic accuracy of baseline network ResNet-50, the proposed method with LGM and MAM showed significantly higher accuracy (81.1 vs. 87.8%). We further observed that the model achieved significant improvement on diagnostic performance using open-source dataset (64.2 vs. 71.4%). LGM and MAM module showed positive effect on an ablation study.DiscussionThis study demonstrated that the potential of a novel DL based diagnostic algorithm for bacterial and fungal keratitis using two types of anterior segment photographs. The proposed network containing LGM and slit-beam MAM is robust in improving the diagnostic accuracy and overcoming the limitations of small training data and multi type of images.
Explainable ensemble machine learning model for prediction of 28-day mortality risk in patients with sepsis-associated acute kidney injury
Authors: Yang Jijun , Peng Hongbing , Luo Youhong , Zhu Tao , Xie Li 
Published: May 2023

BackgroundSepsis-associated acute kidney injury (S-AKI) is a major contributor to mortality in intensive care units (ICU). Early prediction of mortality risk is crucial to enhance prognosis and optimize clinical decisions. This study aims to develop a 28-day mortality risk prediction model for S-AKI utilizing an explainable ensemble machine learning (ML) algorithm.MethodsThis study utilized data from the Medical Information Mart for Intensive Care IV (MIMIC-IV 2.0) database to gather information on patients with S-AKI. Univariate regression, correlation analysis and Boruta were combined for feature selection. To construct the four ML models, hyperparameters were tuned via random search and five-fold cross-validation. To evaluate the performance of all models, ROC, K-S, and LIFT curves were used. The discrimination of ML models and traditional scoring systems was compared using area under the receiver operating characteristic curve (AUC). Additionally, the SHapley Additive exPlanation (SHAP) was utilized to interpret the ML model and identify essential variables. To investigate the relationship between the top nine continuous variables and the risk of 28-day mortality. COX regression-restricted cubic splines were utilized while controlling for age and comorbidities.ResultsThe study analyzed data from 9,158 patients with S-AKI, dividing them into a 28-day mortality group of 1,940 and a survival group of 7,578. The results showed that XGBoost was the best performing model of the four ML models with AUC of 0.873. All models outperformed APS-III 0.713 and SAPS-II 0.681. The K-S and LIFT curves indicated XGBoost as the most effective predictor for 28-day mortality risk. The model’s performance was evaluated using ROCpr curves, calibration curves, accuracy, precision, and F1 scores. SHAP force plots were utilized to interpret and visualize the personalized predictive power of the 28-day mortality risk model. Additionally, COX regression restricted cubic splines revealed an interesting non-linear relationship between the top nine variables and 28-day mortality.ConclusionThe use of ensemble ML models has shown to be more effective than the LR model and conventional scoring systems in predicting 28-day mortality risk in S-AKI patients. By visualizing the XGBoost model with the best predictive performance, clinicians are able to identify high-risk patients early on and improve prognosis.
The pregnancy outcomes in patients with epididymal obstructive azoospermia after microsurgical vasoepididymostomy: a systematic review and meta-analysis
Authors: Wang Zilong , Wang Xinkun , Song Changze , Lu Fuding , Zhai Jiawen , Li Naifa , Jiang Baohong , Tan Senbao , Xuan Xujun 
Published: May 2023

PurposePregnancy outcomes (overall patency rate, overall pregnancy rate, natural pregnancy rate, and the ratio of patients with pregnancy by assisted reproductive technology) after microsurgical vasoepididymostomy (MVE) in patients with epididymal obstructive azoospermia (EOA) were assessed through meta-analysis.MethodWe searched PubMed, Embase, Web of Science, and the Cochrane Library databases up to 28 September 2022 for published literature related to retrospective or prospective clinical studies of obstructive azoospermia after apparent microsurgical vasoepididymostomy. Our search terms included obstructive azoospermia, epididymis obstruction, epididymal obstruction and vasoepididymostomy, and epididymovasostomy. Two researchers independently performed the literature search and assessed the eligibility of selected studies according to established inclusion criteria. The meta-analysis was performed using RevMan 5.4 software.ResultA total of 504 patients with EOA were included in 10 studies (including 2 prospective clinical studies and 8 retrospective clinical studies). The mean patency rate after MVE was 72% (95% CI 68–76%). The overall pregnancy rate was 34% (95% CI 30–38%). The natural pregnancy rate is 21% (95% CI 17–24%). The ratio of patients with pregnancy by assisted reproductive technology (ART) was 34.9%. For the factors affecting pregnancy outcomes after MVE, the overall pregnancy rates in patients receiving bilateral MVE were significantly higher than those receiving unilateral MVE (75.4 vs. 24.6%). The mean best sperm count and sperm motility in patients with overall pregnancy were significantly higher than those with failing pregnancies. For the subgroup meta-analysis of microsurgical vasoepididymostomy, there were no statistically significant differences in the overall patency rate (68 vs. 70%), the overall pregnancy rate (33 vs. 37%), the natural pregnancy rate (20 vs. 23%), the ratio of ART (30 vs. 28%) in end-to-side or end-to-end anastomosis, and longitudinal or triangular intussusception MVE.ConclusionVasectomy patency rates are higher, but natural pregnancy rates are lower in EOA male infertility patients after MVE. Altering the MVE procedures alone does not significantly improve pregnancy outcomes, but ART after MVE could improve the chance of pregnancy regardless of sperm parameters. We recommended that human sperms from EOA male infertility patients should be cryopreserved during intraoperative MVE for application in the subsequent ICSI treatment procedure.
Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex
Authors: Himmelstrand Kajsa , Brandström Durling Mikael , Karlsson Magnus , Stenlid Jan , Olson Åke 
Published: May 2023

IntroductionMitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species.MethodsIn this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers.Results and DiscussionCompared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.
Etiology of recurrent cystitis in postmenopausal women based on vaginal microbiota and the role of Lactobacillus vaginal suppository
Authors: Sekito Takanori , Wada Koichiro , Ishii Ayano , Iwata Takehiro , Matsubara Takehiro , Tomida Shuta , Watanabe Masami , Araki Motoo , Sadahira Takuya 
Published: May 2023

BackgroundThe vaginal microbiota can be altered by uropathogenic bacteria associated with recurrent cystitis (RC), and the vaginal administration of Lactobacillus have suggested certain effects to prevent RC. The relationship between vaginal microbiota and the development of RC has not been elucidated. We aimed to clarify the etiology of RC from vaginal microbiota and importance of vaginal Lactobacillus.MethodsVaginal samples obtained from 39 postmenopausal women were classified into four groups: healthy controls; uncomplicated cystitis; RC; and prevention (prevented RC by Lactobacillus crispatus-containing vaginal suppositories). Principal coordinate analysis and beta-diversity analysis was used to assess 16S rRNA gene sequencing data from the vaginal microbiome.ResultsCluster analysis divided the vaginal bacterial communities among 129 vaginal samples into three clusters (A, B, and C). Fourteen of 14 (100%) samples from the RC group and 51 of 53 (96%) samples from the prevention group were in clusters B and C, while 29 of 38 (76%) samples from the healthy group and 14 of 24 (58%) samples from the uncomplicated cystitis group were in cluster A. The principal coordinate analysis showed that plots in the uncomplicated cystitis group were similar to the healthy group, indicating a large separation between the RC group and the uncomplicated cystitis group. On beta-diversity analysis, there were significant differences between the healthy group and the uncomplicated cystitis group (p = 0.045), and between the RC group and the uncomplicated cystitis group or the healthy group (p = 0.001, p = 0.001, respectively). There were no significant differences between the RC group and the prevention group (p = 0.446). The top six taxa were as follows: Prevotella, Lactobacillus, Streptococcus, Enterobacteriaceae, Anaerococcus, and Bifidobacterium. Among patients with RC, Lactobacillus was undetectable before administration of suppositories, while the median relative abundance of Lactobacillus was 19% during administration of suppositories (p = 0.0211), reducing the average cystitis episodes per year (6.3 vs. 2.4, p = 0.0015).ConclusionThe vaginal microbiota of postmenopausal women with RC is differed from healthy controls and uncomplicated cystitis in terms of lack of Lactobacillus and relatively dominant of Enterobacteriaceae. Vaginal administration of Lactobacillus-containing suppositories can prevent RC by stabilizing vaginal dysbiosis and causing a loss of pathogenic bacteria virulence.
Genome sequencing with comprehensive variant calling identifies structural variants and repeat expansions in a large fraction of individuals with ataxia and/or neuromuscular disorders
Authors: Ek Marlene , Nilsson Daniel , Engvall Martin , Malmgren Helena , Thonberg Håkan , Pettersson Maria , Anderlid Britt-Marie , Hammarsjö Anna , Helgadottir Hafdis T. , Arnardottir Snjolaug , Naess Karin , Nennesmo Inger , Paucar Martin , Hjartarson Helgi Thor , Press Rayomand , Solders Göran , Sejersen Thomas , Lindstrand Anna , Kvarnung Malin 
Published: May 2023

IntroductionNeuromuscular disorders (NMDs) have a heterogeneous etiology. A genetic diagnosis is key to personalized healthcare and access to targeted treatment for the affected individuals.MethodsIn this study, 861 patients with NMDs were analyzed with genome sequencing and comprehensive variant calling including single nucleotide variants, small insertions/deletions (SNVs/INDELs), and structural variants (SVs) in a panel of 895 NMD genes, as well as short tandem repeat expansions (STRs) at 28 loci. In addition, for unsolved cases with an unspecific clinical presentation, the analysis of a panel with OMIM disease genes was added.ResultsIn the cohort, 27% (232/861) of the patients harbored pathogenic variants, of which STRs and SVs accounted for one-third of the patients (71/232). The variants were found in 107 different NMD genes. Furthermore, 18 pediatric patients harbored pathogenic variants in non-NMD genes.DiscussionOur results highlight that for children with unspecific hypotonia, a genome-wide analysis rather than a disease-based gene panel should be considered as a diagnostic approach. More importantly, our results clearly show that it is crucial to include STR- and SV-analyses in the diagnostics of patients with neuromuscular disorders.
The incidence of vestibular neuritis in Italy
Authors: Mandalà Marco , Salerni Lorenzo , Ferretti Fabio , Bindi Ilaria , Gualtieri Giacomo , Corallo Giulia , Viberti Francesca , Gusinu Roberto , Fantino Claudio , Ponzo Silvia , Astore Serena , Boccuzzi Simone , Nuti Daniele 
Published: May 2023

ObjectiveThis study aims to estimate the incidence of Vestibular neuritis (VN) in three different districts in Italy, its epidemiological features, and the prevalence of comorbidities associated with it.MethodsAn observational prospective study of 198 patients referred to ENT departments in Siena, Grosseto, and Cuneo was carried out over a 2-year period. Each patient underwent a complete otoneurologic examination in the first 48 h from the onset of symptoms and a brain MRI in the early stages of the disease. The follow-up lasted for 1 year.ResultsThe total VN incidence rate of the three municipalities was 48.497 (95% CI: 48.395–48.598) and its standardized value was 53.564 (95% CI: 53.463–53.666). The total VN incidence rate for the whole sample (municipality and district of the three centers) was 18.218 (95% CI: 18.164–18.272), and its standardized value was 20.185 (95% CI: 20.129–20.241). A significant difference was highlighted between patients living in the city compared to those living in the surrounding area (p &lt; 0.000), this may be due to the ease of reaching the otoneurological referral center.ConclusionThe total incidence rate for the three municipalities was 48.497. This result is higher than previously reported studies.
Increased selenium and decreased iron levels in relation to risk of coronary artery disease in patients with diabetes
Authors: Tian Mengyun , Hu Teng , Ying Jiajun , Cui Hanbin , Huangfu Ning 
Published: May 2023

BackgroundObservational studies have reported inconsistent associations between micronutrient levels and the risk of coronary artery disease (CAD) in diabetic patients. We aim to explore the causal association between genetically predicted concentrations of micronutrients (phosphorus, magnesium, selenium, iron, zinc, and copper) and CAD in patients with diabetes.MethodsSingle nucleotide polymorphisms (SNPs) connected to serum micronutrient levels were extracted from the corresponding published genome-wide association studies (GWASs). Summary-level statistics for CAD in diabetic patients were obtained from a GWAS of 15,666 patients with diabetes. The primary analysis was carried out with the inverse variance weighted approach, and sensitivity analyses using other statistical methods were further employed to assess the robustness of the results.ResultsGenetically predicted selenium level was causally associated with a higher risk of CAD in diabetic patients (odds ratio [OR]: 1.25; 95% confidence interval [CI]: 1.10–1.42; p = 5.01 × 10−4). While, genetically predicted iron concentrations in patients with diabetes were inversely associated with the risk of CAD (OR: 0.82; 95% CI: 0.75–0.90; p = 2.16 × 10−5). The association pattern kept robust in most sensitivity analyses. Nominally significant associations were observed for magnesium and copper with the risk of CAD in patients with diabetes. No consistent evidence was found for the causal associations between phosphorus and zinc levels, and the risk of CAD in patients with diabetes.ConclusionWe provide consistent evidence for the causal effect of increased selenium and decreased iron levels on CAD in patients with diabetes, highlighting the necessity of micronutrient monitoring and application in these patients.
Effects of early introduction of solid foods on nutrient intake in preterm infants during their 1st year of life: a secondary outcome analysis of a prospective, randomized intervention study
Authors: Gsoellpointner Melanie , Eibensteiner Fabian , Thanhaeuser Margarita , Ristl Robin , Jilma Bernd , Berger Angelika , Haiden Nadja 
Published: May 2023

Very low birth weight (VLBW) infants have higher nutritional needs even after hospital discharge. However, data concerning current nutrient intakes at different time points after the introduction of solid foods and whether dietary reference values are being met are scarce. To adress this issue, this secondary analysis of a prospective, two-arm interventional study in 177 VLBW infants 21 investigates dietary intake comparing early and late (early: 10–12 weeks corrected for gestational age, late: 16–18 weeks corrected for gestational age) introduction of standardized complementary food during the first year of life. Nutritional intake was assessed using self-reported monthly 3-day dietary records from 3 until 12 months, corrected for gestational age. The time point of the introduction of solid foods did not influence nutrient intake, but the early introduction of solids tended toward a higher proportional intake of protein and carbohydrates and a lower intake of fat as a percentage of total energy) during the 1st year of life, corrected for gestational age. The results of this study indicate that this standardized feeding concept was sufficient for zinc, calcium, and phosphorus intake. However, dietary iron and vitamin D intakes did not meet the recommendations. Thus, prolonged iron supplementation should be considered beyond the introduction of meat and vitamin D supplementation at least until 12 months, corrected for gestational age.Trial registration numberClinicalTrials.gov: NCT01809548.