bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revealing a Cleft in the Community: A Systematic Review of Sociodemographic Disparities Affecting the Care of Patients With Cleft Lip
Authors: Obinero Chioma G. , Boyd Alexandra , Barrera Jose , Valenti Alyssa , Munabi Naikhoba , Imahiyerobo Thomas , Greives Matthew R. 
Published: January 2024

Introduction: Comprehensive management of cleft lip with or without cleft palate (CL/P) often begins prenatally, continues into adulthood, and involves multidisciplinary collaboration. This study aims to review the current literature and summarize sociodemographic disparities that impact access to care, management, and postoperative outcomes in patients with CL/P. Methods: A systematic review was conducted using Pubmed, Embase, and Medline databases. Studies discussing sociodemographic disparities regarding access to care, management, and treatment outcomes for patients with CL/P were included. Studies performed outside the US and published before the year 2000 were excluded. Results: Of 3782 studies initially identified, 26 met the inclusion criteria. Disparities discussed included access to care (n = 11), missed appointments (n = 2), use of nasoalveolar molding [NAM] (n = 3), surgical timing (n = 8), and surgical outcomes (n = 8). Minority race or ethnicity, particularly black, Hispanic, Asian, and Native-American, as well as public insurance were associated with impaired access to care. Other factors causing impaired access to care were non-English primary language and high cost. Predictors for missed appointments were black race and Medicaid insurance. Decreased use of or success with NAM was associated with Asian race, public insurance, and long travel distance to a cleft care center. Factors associated with delayed CL surgery were Asian or black race, Hispanic ethnicity, public insurance, and non-English primary language. Surgical outcomes were assessed using various esthetic, speech, and quality of life measures; factors linked to worse outcomes included black or latin race and public insurance. Conclusion: Patients with CL/P from minority racial or ethnic groups, particularly black, Asian, and Hispanic, as well as those with public insurance are disproportionately impacted by health disparities. Disparities related to age, geographic location, and primary language have also been reported, among others. Statewide or institutional social programs may help address these disparities.
A Systematic Review of State Office-Based Buprenorphine Treatment Laws Effective During 2022: Counseling, Dosage, and Visit Frequency Requirements
Authors: Andraka-Christou Barbara , Golan Olivia K. , Williams Michelle , Buksbaum Scott , Gordon Adam J. , Stein Bradley D. 
Published: January 2024

Background: Buprenorphine is among the most effective treatments for opioid use disorder. Even though the federal government recently eliminated the waiver requirement and patient limits applicable to office-based buprenorphine treatment (OBBT), among other settings, some states may still have policies imposing requirements on OBBT providers not required by federal law. Methods: We collected statutes and regulations from 50 US states and the District of Columbia (ie, 51 jurisdictions) between August 11 and November 30, 2022 using the Nexis Uni legal database and search terms related to OBBT counseling, dosage, and/or frequency of visits. We then used template analysis, a mixed deductive-inductive qualitative method, to analyze legal content. Results: Ten jurisdictions (20%) in 2022 had an OBBT counseling, dosage, and/or visit frequency requirement. Four jurisdictions had at least one law in each OBBT policy category examined. One-fifth of jurisdictions have OBBT policies not required under federal law. Five of these jurisdictions are among those with the highest overdose death rates per capita, according to publicly available data from 2021. Some OBBT requirements could potentially limit clinician interest in offering buprenorphine treatment or result in inadequate care (eg, if dosage limitations are too low.) Conclusions: Even though a federal waiver is no longer required for OBBT, our results suggests that at least some jurisdictions have other OBBT requirements, such as counseling, dosage, and/or frequency requirements. Given the severity of the ongoing opioid overdose crisis, policymakers should carefully consider the extent to which OBBT requirements are evidence based.
Congenital fibrinogen disorders: a retrospective clinical and genetic analysis of the Prospective Rare Bleeding Disorders Database
Authors: Mohsenian Samin , Palla Roberta , Menegatti Marzia , Cairo Andrea , Lecchi Anna , Casini Alessandro , Neerman-Arbez Marguerite , Asselta Rosanna , Scardo Sara , Siboni Simona Maria , Blatny Jan , Zapletal Ondrej , Schved Jean-Francois , Giansily-Blaizot Muriel , Halimeh Susan , Daoud Mohamad Ayman , Platokouki Helen , Pergantou Helen , Schutgens Roger E. G. , Van Haaften-Spoor Monique , Brons Paul , Laros-van Gorkom Britta , Van Pinxten Elise , Borhany Munira , Fatima Naveena , Mikovic Danijela , Saracevic Marko , Özdemir Gül Nihal , Ay Yılmaz , Makris Michael , Lockley Caryl , Mumford Andrew , Harvey Andrew , Austin Steve , Shapiro Amy , Williamson Adrianna , McGuinn Catherine , Goldberg Ilene , De Moerloose Philippe , Peyvandi Flora 
Published: January 2024

Abstract
Congenital fibrinogen deficiency (CFD) is a rare bleeding disorder caused by mutations in FGA, FGB, and FGG. We sought to comprehensively characterize patients with CFD using PRO-RBDD (Prospective Rare Bleeding Disorders Database). Clinical phenotypes, laboratory, and genetic features were investigated using retrospective data from the PRO-RBDD. Patients were classified from asymptomatic to grade 3 based on their bleeding severity. In addition, FGA, FGB, and FGG were sequenced to find causative variants. A total of 166 CFD cases from 16 countries were included, of whom 123 (30 afibrinogenemia, 33 hypofibrinogenemia, 55 dysfibrinogenemia, and 5 hypodysfibrinogenemia) were well characterized. Considering the previously established factor activity and antigen level thresholds, bleeding severity was correctly identified in 58% of the cases. The rates of thrombotic events among afibrinogenemic and hypofibrinogenemic patients were relatively similar (11% and 10%, respectively) and surprisingly higher than in dysfibrinogenemic cases. The rate of spontaneous abortions among 68 pregnancies was 31%, including 86% in dysfibrinogenemic women and 14% with hypofibrinogenemia. Eighty-six patients received treatment (69 on-demand and/or 17 on prophylaxis), with fibrinogen concentrates being the most frequently used product. Genetic analysis was available for 91 cases and 41 distinct variants were identified. Hotspot variants (FGG, p.Arg301Cys/His and FGA, p.Arg35Cys/His) were present in 51% of dysfibrinogenemia. Obstetric complications were commonly observed in dysfibrinogenemia. This large multicenter study provided a comprehensive insight into the clinical, laboratory, and genetic history of patients with CFDs. We conclude that bleeding severity grades were in agreement with the established factor activity threshold in nearly half of the cases with quantitative defects.
Frozen tissue coring and layered histological analysis improves cell type-specific proteogenomic characterization of pancreatic adenocarcinoma
Authors: Savage Sara R. , Wang Yuefan , Chen Lijun , Jewell Scott , Newton Chelsea , Dou Yongchao , Li Qing Kay , Bathe Oliver F. , Robles Ana I. , Omenn Gilbert S. , Thiagarajan Mathangi , Zhang Hui , Hostetter Galen , Zhang Bing 
Published: January 2024

Abstract
Background
Omics characterization of pancreatic adenocarcinoma tissue is complicated by the highly heterogeneous and mixed populations of cells. We evaluate the feasibility and potential benefit of using a coring method to enrich specific regions from bulk tissue and then perform proteogenomic analyses.

Methods
We used the Biopsy Trifecta Extraction (BioTExt) technique to isolate cores of epithelial-enriched and stroma-enriched tissue from pancreatic tumor and adjacent tissue blocks. Histology was assessed at multiple depths throughout each core. DNA sequencing, RNA sequencing, and proteomics were performed on the cored and bulk tissue samples. Supervised and unsupervised analyses were performed based on integrated molecular and histology data.

Results
Tissue cores had mixed cell composition at varying depths throughout. Average cell type percentages assessed by histology throughout the core were better associated with KRAS variant allele frequencies than standard histology assessment of the cut surface. Clustering based on serial histology data separated the cores into three groups with enrichment of neoplastic epithelium, stroma, and acinar cells, respectively. Using this classification, tumor overexpressed proteins identified in bulk tissue analysis were assigned into epithelial- or stroma-specific categories, which revealed novel epithelial-specific tumor overexpressed proteins.

Conclusions
Our study demonstrates the feasibility of multi-omics data generation from tissue cores, the necessity of interval H&E stains in serial histology sections, and the utility of coring to improve analysis over bulk tissue data.
PoMeLo: a systematic computational approach to predicting metabolic loss in pathogen genomes
Authors: Glascock Abigail , Waltari Eric , Dudas Gytis , Wong Joan , Ahyong Vida 
Published: January 2024

Abstract
Background
Genome streamlining, the process by which genomes become smaller and encode fewer genes over time, is a common phenomenon among pathogenic bacteria. This reduction is driven by selection for minimized energy expenditure in a nutrient-rich environment. As pathogens evolve to become more reliant on the host, metabolic genes and resulting capabilities are lost in favor of siphoning metabolites from the host. Characterizing genome streamlining, gene loss, and metabolic pathway degradation can be useful in assessing pathogen dependency on host metabolism and identifying potential targets for host-directed therapeutics.

Results
PoMeLo (Predictor of Metabolic Loss) is a novel evolutionary genomics-guided computational approach for identifying metabolic gaps in the genomes of pathogenic bacteria. PoMeLo leverages a centralized public database of high-quality genomes and annotations and allows the user to compare an unlimited number of genomes across individual genes and pathways. PoMeLo runs locally using user-friendly prompts in a matter of minutes and generates tabular and visual outputs for users to compare predicted metabolic capacity between groups of bacteria and individual species. Each pathway is assigned a Predicted Metabolic Loss (PML) score to assess the magnitude of genome streamlining. Optionally, PoMeLo places the results in an evolutionary context by including phylogenetic relationships in visual outputs. It can also initially compute phylogenetically-weighted mean genome sizes to identify genome streamlining events. Here, we describe PoMeLo and demonstrate its use in identifying metabolic gaps in genomes of pathogenic Treponema species.

Conclusions
PoMeLo represents an advance over existing methods for identifying metabolic gaps in genomic data, allowing comparison across large numbers of genomes and placing the resulting data in a phylogenetic context. PoMeLo is freely available for academic and non-academic use at https://github.com/czbiohub-sf/pomelo.
Evaluation of soluble suppression of tumorigenicity 2 (sST2) as serum marker for liver fibrosis
Authors: Hildenbrand Florian F. , Illi Barbara , von Felten Stefanie , Bachofner Jacqueline , Gawinecka Joanna , von Eckardstein Arnold , Müllhaupt Beat , Mertens Joachim C. , Blümel Sena 
Published: January 2024

Abstract
Background & aims
With the increase in patients at risk of advanced liver disease due to the obesity epidemic, there will be a need for simple screening tools for advanced liver fibrosis. Soluble suppression of tumorigenicity 2 (sST2) is a serum biomarker for fibrotic processes. The aim of this study was to evaluate sST2 as marker for liver fibrosis in patients successfully treated for chronic hepatitis C.

Methods
424 patients from the Swiss Hepatitis C Cohort Study were screened for inclusion in this post-hoc cohort study. Inclusion criteria were sustained virological response (SVR), available elastography (VCTE) and serum samples for biomarker analysis before and after treatment. For the validation of sST2, values were compared to VCTE, FIB-4 and APRI using Spearman’s correlation and AUROC analyses.

Results
Data of 164 subjects were finally analyzed. Median sST2 values slightly increased with VCTE-derived fibrosis stages and remained stable after reaching SVR within the respective fibrosis stage, suggesting that sST2 is not influenced by liver inflammation. However, correlation of sST2 pre- and post-treatment with VCTE was fair (Spearman’s rho = 0.39 and rho = 0.36). The area under the curve (AUROC) for sST2 in detecting VCTE-defined F4 fibrosis (vs. F0-F3) before therapy was 0.74 (95%CI 0.65–0.83), and 0.67(95%CI 0.56–0.78) for the discrimination of F3/F4 fibrosis vs. F0-F2. Adding sST2 to either APRI or FIB-4, respectively, increased diagnostic performance of both tests.

Conclusions
sST2 can potentially identify patients with advanced fibrosis as a single serum marker and in combination with APRI and FIB-4.
Tuakana-teina peer education programme to help Māori elders enhance wellbeing and social connectedness
Authors: Oetzel John G. , Simpson Mary , Meha Pare , Cameron Michael P. , Zhang Yingsha , Nock Sophie , Reddy Rangimahora , Adams Hariata , Akapita Ngapera , Akariri Ngareo , Anderson Justina , Clark Marama , Ngaia Kawarau , Hokowhitu Brendan 
Published: January 2024

Abstract
Background
There are significant inequities between Māori (Indigenous people) and non-Māori in ageing outcomes. This study used a strengths-based approach based on the key cultural concept of mana motuhake (autonomy and self-actualisation) to develop a tuakana-teina (literally older sibling-younger sibling) peer education programme to assist kaumātua (elders) in addressing health and social needs. The purpose of this study was to test the impact on those receiving the programme. Three aims identify the impact on outcomes, resources received and the cost effectiveness of the programme.

Methods
Five Kaupapa Māori (research and services guided by Māori worldviews) iwi (tribe) and community providers implemented the project using a partnership approach. Tuakana (peer educators) had up to six conversations each with up to six teina (peer learners) and shared information related to social and health services. A pre- and post-test, clustered staggered design was the research design. Participants completed a baseline and post-programme assessment of health and mana motuhake measures consistent with Māori worldviews. Open-ended questions on the assessments, five focus groups, and four individual interviews were used for qualitative evaluation.

Findings
A total of 113 kaumātua were recruited, and 86 completed the programme. The analysis revealed improvements in health-related quality of life, needing more help with daily tasks, life satisfaction, paying bills and housing problems. Qualitative results supported impacts of the programme on mana motuhake and hauora (holistic health) through providing intangible and tangible resources. Cost-effectiveness analysis showed that the intervention is cost effective, with a cost per QALY of less than the conventional threshold of three times GDP per capita.

Conclusions
A culturally-resonant, strengths-based programme developed through a participatory approach can significantly improve health and social outcomes in a cost-effective way.

Trial Registry
Clinical trial registry: Trial registration: (ACTRN12620000316909). Prospectively registered 06/03/2020, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=379302&isClinicalTrial=False.
Factors associated with an unsuppressed viral load among HIV-positive individuals attending STI services in South Africa, 2019
Authors: Mapiye Marceline , Ravhuhali Khuliso , de Voux Alex , Kufa Tendesayi 
Published: January 2024

Abstract
Background
Sexually transmitted infections (STIs), particularly in the absence of viral suppression, increase the risk of HIV transmission to uninfected partners. We determined factors associated with having an unsuppressed VL among HIV-positive individuals attending STI services in South Africa (SA).

Methods
We analysed secondary cross-sectional data collected on HIV-positive individuals presenting with STI symptoms s at sentinel sites in Western Cape and Gauteng provinces between January–December 2019 in SA. We compared demographic characteristics of individuals on ART or not on ART, and a Poisson regression model to identify factors associated with having an unsuppressed VL (≥ 50 copies/ml) was used.

Results
Among 93 HIV-positive individuals attending STI services with VL data, the median age was 32 years (IQR 27–37). Thirty-two (34.41%) individuals were on ART compared to 61 (65.59%) not on ART. Most of those on ART (56.25%) had an unsuppressed VL, while 86.89% of those not on ART had an unsuppressed VL. ART use was associated with a 33% lower prevalence of having unsuppressed VL. In a model adjusting for age, age at first sex and oral sex, none of the factors were significant. Among those on ART, individuals < 25 years were more likely to have an unsuppressed VL (aPRR = 1.94: 95% CI = 1.27–2.97) compared to those ≥ 25 years.

Conclusion
ART use among HIV-positive individuals was low and VL suppression among those on ART was sub-optimal. Intensified ART initiation and adherence support to HIV-positive individuals seeking STI services could improve VL suppression.
Radiographic characteristics of rifampicin-resistant tuberculosis in the STREAM stage 1 trial and their influence on time to culture conversion in the short regimen
Authors: Chiang Chen-Yuan , Bern Henry , Goodall Ruth , Chien Shun-Tien , Rusen I. D. , Nunn Andrew ,   on behalf of the STREAM Sub-study Collaborators, Ali Oumer , Teferi Mekonnen , Ndlovu Muziwandile , Ngubane Nosipho , Bennet Rachel , Fabiane Stella , Meredith Sarah , Nyamda Naranbat , Tsogt Bazarragchaa , Dat Phan-Thuong , Howell Pauline , Hailu Meseret , Meressa Daniel , Aucock Samantha , Moodliar Ronelle 
Published: January 2024

Abstract
Background
Stage 1 of the STREAM trial demonstrated that the 9 month (Short) regimen developed in Bangladesh was non-inferior to the 20 month (Long) 2011 World Health Organization recommended regimen. We assess the association between HIV infection and radiographic manifestations of tuberculosis and factors associated with time to culture conversion in Stage 1 of the STREAM trial.

Methods
Reading of chest radiographs was undertaken independently by two clinicians, and films with discordant reading were read by a third reader. Recording of abnormal opacity of the lung parenchyma included location (right upper, right lower, left upper, and left lower) and extent of disease (minimal, moderately-advanced, and far advanced). Time to culture conversion was defined as the number of days from initiation of treatment to the first of two consecutive negative culture results, and compared using the log-rank test, stratified by country. Cox proportional hazards models, stratified by country and adjusted for HIV status, were used to identify factors associated with culture conversion.

Results
Of the 364 participants, all but one had an abnormal chest X-ray: 347 (95%) had opacities over upper lung fields, 318 (87%) had opacities over lower lung fields, 124 (34%) had far advanced pulmonary involvement, and 281 (77%) had cavitation. There was no significant association between HIV and locations of lung parenchymal opacities, extent of opacities, the presence of cavitation, and location of cavitation. Participants infected with HIV were significantly less likely to have the highest positivity grade (3+) of sputum culture (p = 0.035) as compared to participants not infected with HIV. Cavitation was significantly associated with high smear positivity grades (p < 0.001) and high culture positivity grades (p = 0.004) among all participants. Co-infection with HIV was associated with a shorter time to culture conversion (hazard ratio 1.59, 95% CI 1.05–2.40).

Conclusions
Radiographic manifestations of tuberculosis among the HIV-infected in the era of anti-retroviral therapy may not differ from that among those who were not infected with HIV. Radiographic manifestations were not consistently associated with time to culture conversion, perhaps indicating that the Short regimen is sufficiently powerful in achieving sputum conversion across the spectrum of radiographic pulmonary involvements.

Trial registration
ISRCTN ISRCTN78372190. Registered 14/10/2010. The date of first registration 10/02/2016.
The mediating effects of motivation on the relations between occupational stress and physical activity among underresourced afterschool program staff
Authors: Deng Anqi , Zarrett Nicole , Sweeney Allison M. 
Published: January 2024

Abstract
Objective
Guided by Self-Determination Theory, this study aimed to examine the potential mediating effects of autonomous and controlled motivations on physical activity (PA) experiences of afterschool program (ASP) staff with occupational stress.

Method
A total of 58 ASP staff provided full data. Staff occupational stress and self-determination motivations for PA were assessed. Participants’ daily moderate-to-vigorous physical activity (MVPA) was measured using accelerometer wear. A path analysis was used to address the research purpose.

Results
Occupational stress negatively and indirectly predicted daily MVPA which was mediated by controlled motivation (β = − 4.15, p <.05). Autonomous motivation directly and positively predicted daily MVPA across all types and levels of ASP staff occupational stress (β = 9.93, p =.01).

Conclusions
Autonomous motivation is a powerful predictor of staff PA levels despite the degree to which they experience stress. In contrast, controlled motivations are more vulnerable to occupational stress, and can lead to lower MVPA.

Trial registration
Connect Through PLAY: A Staff-based Physical Activity Intervention for Middle School Youth (Connect). https://clinicaltrials.gov/ct2/show/NCT03732144. Registered 11/06/2018. Registration number: NCT03732144.