bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Prevalence of Sexually Transmitted Infections and Poor Sensitivity and Specificity of Screening Algorithms for Chlamydia and Gonorrhea Among Female Sex Workers in Zimbabwe: Analysis of Respondent-Driven Sampling Surveys in 3 Communities
Authors: Chabata Sungai T. , Fearon Elizabeth , Musemburi Sithembile , Machingura Fortunate , Machiha Anna , Hargreaves James R. , Ndowa Francis J. , Mugurungi Owen , Cowan Frances M. , Steen Richard 
Published: November 2024

Background
Effective strategies to reduce sexually transmitted infection burden and transmission among female sex workers (FSWs) and their networks are needed. We report sexually transmitted infection prevalence among FSWs in Zimbabwe and investigate the performance of screening algorithms.

Methods
Respondent-driven sampling (RDS) surveys, including blood sampling for syphilis serology, were conducted among FSWs in 3 communities in Zimbabwe in 2017. In addition, a random sample of one-third of participants were offered genital examination and sexually transmitted infection (STI) testing. Data on symptoms and clinical signs were analyzed to determine the proportion of asymptomatic and clinically inapparent STIs by HIV status, and the sensitivity, specificity, and predictive values of syndromic, clinical, and hybrid screening algorithms for chlamydia and gonorrhea. Analyses were RDS-II weighted.

Results
Overall, 2507 women were included in the RDS surveys, and 661 of 836 (79.1%) of those randomly offered genital examination and STI testing accepted. The prevalence of STI by site ranged from 15.7% to 20.0% for syphilis (rapid plasma reagin + Treponema pallidum hemagglutination assay), 6.8% to 14.3% for gonorrhea, 8.4% to 10.1% for chlamydia, 26.6% to 35.5% for trichomonas, and 37.0% to 47.6% for any high-risk human papilloma virus. A high proportion of infections were both asymptomatic and clinically undetectable (gonorrhea: 41.2%, chlamydia: 51.7%, trichomonas: 62.8%). Screening algorithms performed poorly whether based on symptoms only (sensitivity: 53.3% gonorrhea, 43.3% chlamydia) or either symptoms or clinical signs (sensitivity: 58.7% gonorrhea, 48.3% chlamydia).

Conclusions
Sexually transmitted infection burden is high among FSWs in Zimbabwe. The low sensitivity and specificity of screening algorithms used to guide syndromic management mean that more effective approaches are required to strengthen STI control. As access to HIV-specific prevention methods like preexposure prophylaxis increases, support for consistent condom use needs to be strengthened.
Increasing STI and HIV preventive behaviors and addressing community-prioritized social determinants of health among young GBQMSM and transgender women of color: Piloting a bilingual multilevel intervention
Authors: Rhodes Scott D. , Mann-Jackson Lilli , Alonzo Jorge , Song Eunyoung Y. , Garcia Manuel , Robles Arvizu José A. , Bell Jonathan , Trent Scott , Aguilar-Palma Sandy , Aviles Lucero Refugio , Smart Benjamin D. 
Published: November 2024

Abstract

Background
Sexually transmitted infections (STIs) and HIV disproportionately affect young people; gay, bisexual, queer, and other men who have sex with men (GBQMSM); transgender women; and persons of color. Our community-based participatory research partnership developed and implemented Impact Triad, a bilingual multilevel intervention harnessing peer navigation and mHealth to increase STI/HIV preventive behaviors and address four community-prioritized social determinants of health -- education, employment, social support, and discrimination -- among young African American/Black and Latine GBQMSM and transgender women.

Methods
Fifteen community-based peer navigators were trained to work within their social networks for 12 months. Each navigator engaged five social network members who completed baseline and immediate post-intervention assessments (retention rate = 97.3%). Regression modeling was used to assess changes in outcomes between baseline and follow-up.

Results
Among 74 enrolled social network members, the average age was 27.8; 61% identified as African American/Black, 31% as Latine, and 8% as multiracial/multiethnic. The majority self-identified as cisgender men and 8% as transgender women; 78% identified as gay. About half reported monthly income below $1,000.
Compared to baseline, at follow-up, social network members increased: STI screening (P = .001), HIV testing (P = .001), condom use (P = .03), and PrEP use (P = .02). Knowledge of PrEP (P < .0001) and of community-based educational (P = .047), job-training (P = .002), and job-finding resources (P = .02) also increased. Social support increased (P < .0001) and perceived discrimination decreased (P < .01).

Conclusions
Pilot findings suggest that Impact Triad is promising in increasing STI/HIV protective behaviors and addressing social determinants of health among young GBQMSM and transgender women of color; further testing is warranted.
Comparison of Patient-Specific Plates and Pre-Bent Plates for Preserving Condylar Position in Mandible Reconstruction
Authors: Le Phuc H. , Kim Hyounmin , Son Moo H. , Cha In-Ho , Kim Hyung J. , Nam Woong , Kim Dongwook 
Published: November 2024

Objectives:
To compare the efficacy of patient-specific 3-dimensional (3D)-printed plates (PSP) and pre-bent universal reconstruction plates (PBP) in preserving the 3D position of the mandibular condyle and total operation time during mandibular reconstruction with a fibula-free flap.

Materials and Methods:
This retrospective study included 18 patients who underwent mandibular reconstruction using fibular free flaps. Both groups utilized virtual surgical planning (VSP) and 3D-printed surgical guides. Nine patients received PSP, and 9 received PBP. Postoperative and computed tomography (CT) scans were analyzed to assess 3D deviations of the mandibular condyles and operation times.

Results:
PSP demonstrated superior accuracy in medial-lateral condylar displacement (2.5 ± 1.42 versus 4.92 ± 2.42 mm, P = 0.02) and better angular accuracy in the coronal (1.46 ± 1.16 deg versus 5.45 ± 2.75 deg, P = 0.001) and transverse planes (3.55 ± 2.82 deg versus 8.99 ± 5.56 deg, P = 0.023). There was no significant difference in total operation time between PSP and PBP groups (487.7 ± 90.1 versus 547.3 ± 110.1 min, P = 0.226), despite all PSP patients having additional immediate implant placement and prosthesis delivery.

Conclusions:
PSP offers better condylar accuracy and allows immediate implant placement without increasing surgical time compared with PBP.
A Mortise and Tenon Framework Composed of Costal Cartilage and Expanded Polytetrafluoroethylene in Rhinoplasty for Asians: Application Ⅱ of Dai Exogenous Extension Stent Concept
Authors: Yu Bao-Fu , Wei Jiao , Dai Chuan-Chang 
Published: November 2024

Background:
The septum is often underdeveloped in East Asian populations, and traditional endogenous extension stents may not adequately fulfill the requirements for rhinoplasty. Herein, we present an innovative exogenous extension framework featuring a mortise and tenon structure specifically designed for East Asians.

Methods:
This framework comprises a mushroom-shaped rib cartilage component and a lancet-shaped expanded polytetrafluoroethylene (ePTFE) element, which are interconnected through a mortise and tenon design. The costal cartilage serves as a strut to support the nasal column and elevate the nasal tip. The ePTFE is utilized to augment the nasal dorsum and root, enhancing overall shape while being securely attached to the rib cartilage via the mortise and tenon structure. This configuration establishes a stable exogenous extension framework that also facilitates nose elongation. The safety and efficacy have been validated through over 10 years of clinical practice.

Results:
Over the past decade, we have performed this procedure in more than 500 cases without any complications, such as necrosis of the nasal column, ischemia of the nasal tip, or adverse graft appearances. Notable improvements in nasal morphology were observed across all patients. In addition, no postoperative restrictions on nasal ventilation were reported by any patient. Overall, patient satisfaction regarding surgical outcomes was exceptionally high.

Conclusions:
This framework represents an advanced implementation of exogenous extension stent concept, which is particularly effective for East Asians since it does not require a well-developed nasal septum to provide support. In addition, it does not increase the risk of restricted nasal ventilation.

Level of Evidence:
Level IV.
Revealing reassortment in influenza A viruses with TreeSort
Authors: Markin Alexey , Macken Catherine A. , Baker Amy L. , Anderson Tavis K. 
Published: November 2024

AbstractReassortment among influenza A viruses (IAV) facilitates genomic evolution and has been associated with interspecies transmission and pandemics. We introduce a novel tool called TreeSort that accurately identifies recent and ancestral reassortment events on datasets with thousands of IAV whole genomes. The algorithm has immediate relevance to modern large-scale surveillance studies that generate thousands of whole genomes. TreeSort uses the phylogeny of a selected IAV segment as a reference and finds the branches on the phylogeny where reassortment has occurred with high probability by incorporating information from other gene segments. The tool reports the particular gene segments that were involved in reassortment and how different they are from prior gene pairings. Using TreeSort, we studied reassortment patterns of different IAV subtypes isolated in avian, swine, and human hosts. Avian IAV demonstrated more reassortment than human and swine IAV, with the avian H7 subtype displaying the most frequent reassortment. Reassortment in the swine and human H3 subtypes was more frequent than in the swine and human H1 subtypes, respectively. The highly pathogenic avian influenza H5N1 clade 2.3.4.4b had elevated reassortment rates in the 2020-2023 period; however, the surface protein-encoding genes (HA, NA, and MP) co-evolved together with almost no reassortment among these genes. We observed similar co-evolutionary patterns with very low rates of reassortment among the surface proteins for the human H1 and H3 lineages, suggesting that strong co-evolution and preferential pairings among surface proteins are a consequence of high viral fitness. Our algorithm enables real-time tracking of IAV reassortment within and across different hosts, can be applied to determine how specific genes evolve in response to reassortment events, and can identify novel viruses for pandemic risk assessment. TreeSort is available athttps://github.com/flu-crew/TreeSort.
Contributions to the force of infection of SARS-CoV-2 in Dutch long-term care facilities
Authors: de Wit Mariken M. , van Zelst Marino , Boere Tjarda M. , van Gaalen Rolina D. , de Jong Mart C. M. , van Hoek Albert Jan , ten Bosch Quirine 
Published: November 2024

AbstractBackgroundResidents of long-term care facilities (LTCFs) have been disproportionately affected during the COVID-19 pandemic. To inform decision-making around interventions, we quantified the SARS-CoV-2 infection risk for residents and the relative contribution of different infection sources. We estimated the force of infection (FOI) experienced by Dutch LTCF residents over time and quantified the contribution of residents, LTCF healthcare workers (HCWs), and the general population.Methods & findingsCase data were obtained by Municipal Health Services as part of the Dutch national surveillance program. During the study period (1 October 2020 to 10 November 2021), testing policies included symptom-based testing, exposure-based testing, and facility-wide serial testing. We used a data augmentation approach to include uncertainty in the timing of infection, while taking account of different testing policies. We constructed a Bayesian generalized linear model to estimate group-specific transmission rate parameters and contributions to the FOI experienced by residents.During the study period 36,877 cases were registered among residents and 19,676 among HCWs. The total daily FOI towards residents was highest in December 2020 (1.7*10−3, 95% CI: 1.5*10−3– 1.9*10−3) and lowest in June 2021 (1.1*10−595%CI: 7.6*10−6– 1.7*10−5). Resident-directed type-reproduction numbers and FOI declined as COVID-19 vaccination rollout started in residents, HCWs, and the older general population (February-May 2021). Most resident infections in spring and summer 2021 were attributable to infections in the general population. The relative contribution of the general population to the FOI decreased in summer 2021 when vaccination was available population-wide. In October-November 2021, type-reproduction numbers and FOI increased again. We observed an increase in residents’ susceptibility to infection in this period, which was only partially explained by the emergence of the Delta variant. Sensitivity analyses showed that the temporal trends in relative contributions to the FOI were not impacted by assumptions about immunity build-up among residents, nor by underreporting of infections.ConclusionsCOVID-19 vaccination appears to have been effective in reducing SARS-CoV-2 transmission towards residents, although other factors such as seasonality or non-pharmaceutical interventions may also have contributed to this. This effect seemed to have decreased by autumn 2021, which could be due to waning of immunity or changes in control practices. Our estimates of temporal trends in relative contributions to the FOI in LTCF residents can help target intervention efforts.
Pushing the Boundaries for Centrally Located Breast Tumors in Oncoplastic Breast Surgery: A Single Centre Audit
Authors: Koppiker C.B , Noor Aijaz Ul , Joshi Sneha , Mishra Rupa , Sivadasan Priya , Sheikh Shama , Vartak Anushree , Athavle Namrata , Sharma Purva , Pai Mugdha , Deshmukh Chetan , Dhar Upendra , Busheri Laleh , Munshi Manasi 
Published: November 2024

AbstractBackgroundBreast Conservative Surgery (BCS) was considered a contraindication for centrally located breast tumor (CLBT), with mastectomy being the preferred treatment. However, advances in oncoplastic techniques now offer promising alternatives by facilitating wider surgical margins and enhancing cosmetic outcomes. This study aims to evaluate surgical, oncological, aesthetic outcome and quality of life (QoL) of oncoplastic breast surgery (OBS) for CLBT.Material and MethodsIn this study, 136 patients with CLBT were treated with various oncoplastic techniques including Level I (Grisotti Flap), Level II (Therapeutic Mammoplasty), and Level III (Perforator Flap) techniques. Surgical approach selection was guided by breast-size and degree of ptosis. Oncological and cosmetic outcomes were evaluated by surgeons post-operatively.ResultsThe mean age of the patient was 52.7 years (range: 22-79). The Level I oncoplasty technique was utilised in 7 patients (11.7%); Level II (Therapeutic Mammoplasty) oncoplasty in 57 patients (41.9%) and Level 3 (Perforator Flaps) in 52 patients (38.2%). 13.9% of post-operative complications were observed. Cosmetic score revealed good to excellent outcomes regarding the patients’ satisfaction toward the surgical procedure. The study observed low rate of local recurrence (4.4%), distant recurrence (5.8%) and metastasis (5.8%). Mortality was 3.6% while all survival (OS) and disease-free survival (DFS) were high at 93.82% and 90.6%, respectively demonstrate the effectiveness of the surgical and adjuvant therapy employed.DiscussionOBS offer viable and effective approach for managing CLBT. These procedures not only achieve satisfactory aesthetic results, but also ensure oncological safety, making them a promising alternate to mastectomy for CLBT.
Early Prediction of Hypertensive Disorders of Pregnancy Using Machine Learning and Medical Records from the First and Second Trimesters
Authors: Mousavi Seyedeh Somayyeh , Tierney Kim , Robichaux Chad , Boulet Sheree Lynn , Franklin Cheryl , Chandrasekaran Suchitra , Sameni Reza , Clifford Gari D. , Katebi Nasim 
Published: November 2024

AbstractHypertensive disorders of pregnancy (HDPs) remain a major challenge in maternal health. Early prediction of HDPs is crucial for timely intervention. Most existing predictive machine learning (ML) models rely on costly methods like blood, urine, genetic tests, and ultrasound, often extracting features from data gathered throughout pregnancy, delaying intervention.This study developed an ML model to identify HDP risk before clinical onset using affordable methods. Features were extracted from blood pressure (BP) measurements, body mass index values (BMI) recorded during the first and second trimesters, and maternal demographic information.We employed a random forest classification model for its robustness and ability to handle complex datasets. Our dataset, gathered from large academic medical centers in Atlanta, Georgia, United States (2010-2022), comprised 1,190 patients with 1,216 records collected during the first and second trimesters. Despite the limited number of features, the model’s performance demonstrated a strong ability to accurately predict HDPs. The model achieved an F1- score, accuracy, positive predictive value, and area under the receiver-operating characteristic curve of 0.76, 0.72, 0.75, and 0.78, respectively.In conclusion, the model was shown to be effective in capturing the relevant patterns in the feature set necessary for predicting HDPs. Moreover, it can be implemented using simple devices, such as BP monitors and weight scales, providing a practical solution for early HDPs prediction in low-resource settings with proper testing and validation. By improving the early detection of HDPs, this approach can potentially help with the management of adverse pregnancy outcomes.
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks
Authors: Paton Victor , Türei Denes , Ivanova Olga , Müller-Dott Sophia , Rodriguez-Mier Pablo , Venafra Veronica , Perfetto Livia , Garrido-Rodriguez Martin , Saez-Rodriguez Julio 
Published: November 2024

AbstractSummaryWe present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrastructure for the network biology community that supports the development of better methods and benchmarks, by enhancing interoperability and integration.Availability and ImplementationNetworkCommons is implemented in Python and offers programmatic access to multiple omics datasets, network inference methods, and benchmarking setups. It is a free software, available athttps://github.com/saezlab/networkcommons.Contactsaezlab@ebi.ac.uk,martin.garrido@embl.deSupplementary DataContribution guidelines, additional figures, and descriptions for data, knowledge, methods, evaluation strategies and their implementation are available in the Supplementary Data and in the NetworkCommons documentation athttps://networkcommons.readthedocs.io/.
UPR deficiency in budding yeast reveals a trade-off between ER folding capacity and maintenance of euploidy
Authors: Bartolutti Constantine , Kim Allison J , Brar Gloria A 
Published: November 2024

AbstractThe Unfolded Protein Response (UPR) was discovered in budding yeast as a mechanism that allows cells to adapt to ER stress. While the Ire1 branch of this pathway is highly conserved, it is not thought to be important for cellular homeostasis in the absence of stress. Surprisingly, we found that removal of UPR activity led to pervasive aneuploidy in budding yeast cells, suggesting selective pressure resulting from UPR-deficiency. Aneuploid UPR-deficient cells grew better than euploid cells, but exhibited heightened general proteostatic stress, a hallmark of aneuploidy in wild-type cells. Modulation of key genes involved in ER proteostasis that were encoded on aneuploid chromosomes, could phenocopy the effects of aneuploidy, indicating that the reason cells require UPR activity to maintain euploidy is to counteract protein folding stress in the ER. In support of this model, aneuploidy in UPR-deficient cells can be prevented by expression of a UPR-independent general ER chaperone. Overall, our results indicate an unexpected role for the UPR in basal cell growth that is sufficiently important for cells to accept the costly trade-off of aneuploidy in the absence of UPR activity.
The Association Between Prevotella copri and Advanced Fibrosis in the Progression of Metabolic Dysfunction-Associated Steatotic Liver Disease
Authors: Leitman Madelaine , Zhang David , Pawar Shrey , Shera Simer , Hernandez Laura , Jacobs Jonathan P. , Dong Tien S. 
Published: November 2024

AbstractMetabolic dysfunction-associated steatotic liver disease (MASLD), driven by obesity and metabolic syndrome, is increasingly prevalent and a significant contributor to liver fibrosis, cirrhosis, and liver-related mortality. Emerging research implicates the gut microbiome as a critical player in MASLD progression, yet specific microbial drivers remain poorly understood. Here, we explore the role ofPrevotella copri(P. copri) in MASLD progression through both human patient cohorts and a mouse model of diet-induced obesity. Using 16S rRNA sequencing, we identified elevatedP. copriabundance in MASLD patients with advanced fibrosis, linked with significant shifts in microbial diversity and bacterial network connectivity. To investigate causality, experimental colonization ofP. copriin mice on a high-fat diet worsened MASLD progression, withP. copri-colonized mice showing significant increases in hepatic steatosis, liver triglyceride accumulation, and body weight, independent of caloric intake. At the molecular level,P. copricolonization downregulated key lipid metabolism genes, such as Carnitine Palmitoyltransferase 1, Diacylglycerol Acyltransferase, and Adipose Triglyceride Lipase, and impaired tight intestinal junction integrity through the downregulation of cluadins, occludin, and zonula occludens-1. Collectively, our findings positionP. coprias a possible driver of MASLD progression by promoting hepatic steatosis through lipid and triglyceride accumulation and fibrosis through decreased tight junction integrity. These insights suggest a promising therapeutic avenue to target specific microbial signatures likeP. coprito curb MASLD progression and mitigate the associated risk of advanced fibrosis.
A motif preferred adenine base editor with minimal bystander and off-targets editing
Authors: Shang Mengyu , Li Yinuo , Cao Qiuyu , Ren Jingxuan , Zeng Yuqiang , Wang Jinxin , Ge Xiyu , Zhang Xiaohui 
Published: November 2024

Abstract48% of hereditary disease are caused by single C-to-T base conversion, which makes efficient A-to-G base editing tools (ABEs) have great potential in the treatment of these diseases. However, the existing efficient ABE, while catalyzing A-to-G conversion, will bring more A and C bystander editing and off-target events, which poses safety concerns for their clinical application. Here, we developed ABE10 (ABE8e with TadA-8e A48E) for efficient and accurate editing of As in YA motifs with YAY>YAR (Y=T or C, R=A or G) hierarchy through structure-oriented rational design. Compared with ABE3.1, currently the only motif (YAC) preference ABE version, ABE10 exhibited A-to-G editing efficiency improvement with an average up to 3.1-fold in indicated YA motif while maintaining reduced bystander Cs editing and minimized DNA or RNA off-targets. Also, we showed ABE10 corrected pathogenic mutation with high efficiency and precision in human cells. Moreover, by ABE10, we efficiently and precisely generated hypocholes-terolemia and tail-loss mouse models mimicking human associated disease and mousePCSK9base editing in vivo for hypercholesterolemia gene therapy, indicating their great potential in broad applications for and disease modeling and gene therapy.