bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the ScreenFire and Xpert HPV assays for the detection of human papillomavirus and cervical precancer among women living with HIV in Malawi
Authors: Mungo Chemtai , Guliam Anagha , Chinula Lameck , Inturrisi Federica , Msowoya Lizzie , Mkochi Tawonga , Jawadu Siniya , de Sanjosé Silvia , Schiffman Mark , Tang Jennifer H. , Smith Jennifer S. 
Published: May 2024

Abstract
Background
The World Health Organization recommends human papillomavirus (HPV) testing for primary cervical cancer screening, including among women living with HIV (WLWH). Low-and-middle-income countries account for 85% of the cervical cancer burden globally, yet have limited access to HPV-based screening, largely due to cost. This study aims to compare the performance of a rapid, isothermal amplification HPV assay (ScreenFire) to that of the Xpert HPV assay for the detection of HPV and cervical precancer among WLWH in Malawi.

Methods
We utilized stored self- and provider-collected specimens from a prospective cohort study of WLWH in Malawi from July 2020 to February 2022. Specimens were tested with both Xpert and ScreenFire HPV assays. The overall and within-channel non-hierarchical agreement between ScreenFire and Xpert was determined for both self- and provider-collected specimens. Hierarchical ScreenFire HPV positivity by channel was compared to Xpert for each histological diagnosis—cervical intraepithelial neoplasia grade 2 or worse (CIN2+) compared to <CIN2.

Results
315 matched self- and provider-collected specimens had valid results from both Xpert and ScreenFire testing and were included in analyses, of which 279 and 36 were HPV positive and HPV negative, respectively, on Xpert self-collection. Of the 315, 245 (78%) had normal pathology, 21 CIN1 (7%), 14 CIN2 (4%), and 35 CIN3 (11%). Of the 245 with normal pathology, 213 (87%) and 188 (77%) were HPV-positive on Xpert and ScreenFire self-collected specimens, respectively. Among provider-collected specimens, the assays had 80% agreement on overall HPV positivity (unweighted kappa 0.59, 95% 0.50–0.69). ScreenFire was HPV-positive in 90% of self-collected specimens that were HPV-positive on Xpert. Channel agreement between the assays was high for both self- and provider-collected specimens, but slightly lower for HPV18/45. In hierarchical analysis, ScreenFire demonstrated high concordance with Xpert testing for detecting CIN2+ cases in all channels, missing no HPV 16 or HPV 18/45 positive CIN2+ case that was positive on Xpert, in both self- and provider-collected specimens.

Conclusion
In this study of stored specimens, the ScreenFire HPV assay performed well in the detection of HPV and CIN2+ among WLWH compared to the Xpert HPV assay. If supported by larger validation studies, ScreenFire could be an affordable alternative point-of-care HPV assay for use in LMICs.
Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci
Authors: D’haene Eva , López-Soriano Víctor , Martínez-García Pedro Manuel , Kalayanamontri Soraya , Rey Alfredo Dueñas , Sousa-Ortega Ana , Naranjo Silvia , Van de Sompele Stijn , Vantomme Lies , Mahieu Quinten , Vergult Sarah , Neto Ana , Gómez-Skarmeta José Luis , Martínez-Morales Juan Ramón , Bauwens Miriam , Tena Juan Jesús , De Baere Elfride 
Published: May 2024

Abstract
Background
Vision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space.

Results
To understand the role of differential chromatin architecture in establishing tissue-specific expression at inherited retinal disease loci, we mapped genome-wide chromatin interactions using in situ Hi-C and H3K4me3 HiChIP on neural retina and RPE/choroid from human adult donor eyes. We observed chromatin looping between active promoters and 32,425 and 8060 candidate CREs in the neural retina and RPE/choroid, respectively. A comparative 3D genome analysis between these two retinal tissues revealed that 56% of 290 known inherited retinal disease genes were marked by differential chromatin interactions. One of these was ABCA4, which is implicated in the most common autosomal recessive inherited retinal disease. We zoomed in on retina- and RPE-specific cis-regulatory interactions at the ABCA4 locus using high-resolution UMI-4C. Integration with bulk and single-cell epigenomic datasets and in vivo enhancer assays in zebrafish revealed tissue-specific CREs interacting with ABCA4.

Conclusions
Through comparative 3D genome mapping, based on genome-wide, promoter-centric, and locus-specific assays of human neural retina and RPE, we have shown that gene regulation at key inherited retinal disease loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes at retinal disease loci, but also delineate the search space for non-coding genomic variation underlying unsolved inherited retinal diseases.

Graphical Abstract
Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection
Authors: Barry Timothy , Mason Kaishu , Roeder Kathryn , Katsevich Eugene 
Published: May 2024

AbstractSingle-cell CRISPR screens (perturb-seq) link genetic perturbations to phenotypic changes in individual cells. The most fundamental task in perturb-seq analysis is to test for association between a perturbation and a count outcome, such as gene expression. We conduct the first-ever comprehensive benchmarking study of association testing methods for low multiplicity-of-infection (MOI) perturb-seq data, finding that existing methods produce excess false positives. We conduct an extensive empirical investigation of the data, identifying three core analysis challenges: sparsity, confounding, and model misspecification. Finally, we develop an association testing method — SCEPTRE low-MOI — that resolves these analysis challenges and demonstrates improved calibration and power.
RECOVER-NEURO: study protocol for a multi-center, multi-arm, phase 2, randomized, active comparator trial evaluating three interventions for cognitive dysfunction in post-acute sequelae of SARS-CoV-2 infection (PASC)
Authors: Knopman David S. , Laskowitz Daniel T. , Koltai Deborah C. , Charvet Leigh E. , Becker Jacqueline H. , Federman Alex D. , Wisnivesky Juan , Mahncke Henry , Van Vleet Thomas M. , Bateman Lucinda , Kim Dong-Yun , O’Steen Ashley , James Melissa , Silverstein Adam , Lokhnygina Yuliya , Rich Jennifer , Feger Bryan J. , Zimmerman Kanecia O. 
Published: May 2024

Abstract
Background
Post-acute sequelae of SARS-CoV-2 infection (PASC) symptoms have broad impact, and may affect individuals regardless of COVID-19 severity, socioeconomic status, race, ethnicity, or age. A prominent PASC symptom is cognitive dysfunction, colloquially referred to as “brain fog” and characterized by declines in short-term memory, attention, and concentration. Cognitive dysfunction can severely impair quality of life by impairing daily functional skills and preventing timely return to work.

Methods
RECOVER-NEURO is a prospective, multi-center, multi-arm, phase 2, randomized, active-comparator design investigating 3 interventions: (1) BrainHQ is an interactive, online cognitive training program; (2) PASC-Cognitive Recovery is a cognitive rehabilitation program specifically designed to target frequently reported challenges among individuals with brain fog; (3) transcranial direct current stimulation (tDCS) is a noninvasive form of mild electrical brain stimulation.
The interventions will be combined to establish 5 arms: (1) BrainHQ; (2) BrainHQ + PASC-Cognitive Recovery; (3) BrainHQ + tDCS-active; (4) BrainHQ + tDCS-sham; and (5) Active Comparator. The interventions will occur for 10 weeks. Assessments will be completed at baseline and at the end of intervention and will include cognitive testing and patient-reported surveys. All study activities can be delivered in Spanish and English.

Discussion
This study is designed to test whether cognitive dysfunction symptoms can be alleviated by the use of pragmatic and established interventions with different mechanisms of action and with prior evidence of improving cognitive function in patients with neurocognitive disorder. If successful, results will provide beneficial treatments for PASC-related cognitive dysfunction.

Trial registration
ClinicalTrials.gov NCT05965739. Registered on July 25, 2023.
Superiority trial for the development of an ideal method for the closure of midline abdominal wall incisions to reduce the incidence of wound complications after elective gastroenterological surgery: study protocol for a randomized controlled trial
Authors: Fukai Shota , Mizusawa Yuki , Noda Hiroshi , Tsujinaka Shingo , Maeda Yukihisa , Hasebe Ryuji , Eguchi Yusuke , Kanemitsu Rina , Matsuzawa Natsumi , Abe Iku , Endo Yuhei , Fukui Taro , Takayama Yuji , Ichida Kosuke , Inoue Koetsu , Muto Yuta , Watanabe Fumiaki , Futsuhara Kazushige , Miyakura Yasuyuki , Rikiyama Toshiki 
Published: May 2024

Abstract
Background
The recent guidelines from the European and American Hernia Societies recommend a continuous small-bite suturing technique with slowly absorbable sutures for fascial closure of midline abdominal wall incisions to reduce the incidence of wound complications, especially for incisional hernia. However, this is based on low-certainty evidence. We could not find any recommendations for skin closure. The wound closure technique is an important determinant of the risk of wound complications, and a comprehensive approach to prevent wound complications should be developed.

Methods
We propose a single-institute, prospective, randomized, blinded-endpoint trial to assess the superiority of the combination of continuous suturing of the fascia without peritoneal closure and continuous suturing of the subcuticular tissue (study group) over that of interrupted suturing of the fascia together with the peritoneum and interrupted suturing of the subcuticular tissue (control group) for reducing the incidence of midline abdominal wall incision wound complications after elective gastroenterological surgery with a clean-contaminated wound. Permuted-block randomization with an allocation ratio of 1:1 and blocking will be used. We hypothesize that the study group will show a 50% reduction in the incidence of wound complications. The target number of cases is set at 284. The primary outcome is the incidence of wound complications, including incisional surgical site infection, hemorrhage, seroma, wound dehiscence within 30 days after surgery, and incisional hernia at approximately 1 year after surgery.

Discussion
This trial will provide initial evidence on the ideal combination of fascial and skin closure for midline abdominal wall incision to reduce the incidence of overall postoperative wound complications after gastroenterological surgery with a clean-contaminated wound. This trial is expected to generate high-quality evidence that supports the current guidelines for the closure of abdominal wall incisions from the European and American Hernia Societies and to contribute to their next updates.

Trial registration
UMIN-CTR UMIN000048442. Registered on 1 August 2022. https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000055205
Establishment and partial characterisation of a new cell line derived from adult tissues of the tsetse fly Glossina morsitans morsitans
Authors: Bell-Sakyi Lesley , Haines Lee R. , Petrucci Giovanni , Beliavskaia Alexandra , Hartley Catherine , Khoo Jing Jing , Makepeace Benjamin L. , Abd-Alla Adly M. M. , Darby Alistair C. 
Published: May 2024

Abstract
Background
Insect cell lines play a vital role in many aspects of research on disease vectors and agricultural pests. The tsetse fly Glossina morsitans morsitans is an important vector of salivarian trypanosomes in sub-Saharan Africa and, as such, is a major constraint on human health and agricultural development in the region.

Methods
Here, we report establishment and partial characterisation of a cell line, GMA/LULS61, derived from tissues of adult female G. m. morsitans. GMA/LULS61 cells, grown at 28 °C in L-15 (Leibovitz) medium supplemented with foetal bovine serum and tryptose phosphate broth, have been taken through 23 passages to date and can be split 1:1 at 2-week intervals. Karyotyping at passage 17 revealed a predominantly haploid chromosome complement. Species origin and absence of contaminating bacteria were confirmed by PCR amplification and sequencing of fragments of the COI gene and pan-bacterial 16S rRNA gene respectively. However, PCR screening of RNA extracted from GMA/LULS61 cells confirmed presence of the recently described Glossina morsitans morsitans iflavirus and Glossina morsitans morsitans negevirus, but absence of Glossina pallipides salivary gland hypertrophy virus. GMA/LULS61 cells supported infection and growth of 6/7 different insect-derived strains of the intracellular bacterial symbiont Wolbachia.

Conclusions
The GMA/LULS61 cell line has potential for application in a variety of studies investigating the biology of G. m. morsitans and its associated pathogenic and symbiotic microorganisms.

Graphical Abstract
Response to semaglutide of non-drinker subjects with type 2 diabetes
Authors: Petralli Giovanni , Raggi Francesco , Zoppo Alice Del , Rovera Chiara , Salvati Antonio , Brunetto Maurizia Rossana , Solini Anna 
Published: May 2024

Abstract
Background
Metabolic dysfunction-associated Steatotic Liver Disease (MASLD) displays a worse prognosis in subjects with type 2 diabetes (T2D); effective treatments are, so far, scanty. Semaglutide showed efficacy in improving steatohepatitis. We longitudinally observed a MASLD cohort of T2D subjects starting semaglutide, to detect an improvement of non-invasive surrogates of steatosis and fibro-inflammatory liver involvement, evaluating the role of mild alcohol consumption.

Patients and methods
In 62 overweight/obese T2D subjects with MASLD (36 non-drinker and 26 mild alcohol consumers), anthropometric, bio-humoral and transient elastography (TE) data were collected before (T0) and after an average time of 6.4 month (T1) from injective semaglutide prescription. Circulating levels of hormones (GIP, GLP-1, glucagon, insulin) and inflammatory markers (TNFα, MCP-1, IL-18, IL-10) were measured. Steatotic and necro-inflammatory liver involvement was evaluated with FibroScan controlled attenuation parameter (CAP) and liver stiffness (LS), respectively.

Results
Significant (p < 0.006) T0-T1 reductions of BMI, waist circumference, fasting glucose, and HbA1c were observed. AST (-10 ± 3 IU/L), ALT (-18 ± 5 IU/L), GGT (-33 ± 15 IU/L), CAP (-25 ± 8 dB/m) and LS (-0.8 ± 0.4 kPa) were reduced, too. GLP-1 increased (+ 95.9 pM, p < 0.0001) and IL-18 was reduced (-46.6 pg/ml, p = 0.0002). After adjustment for confounders, CAP improving was only related to GLP-1 increase (ß=-0.437, p = 0.0122). Mild alcohol intake did not influence these relations.

Conclusion
Use of semaglutide in subjects with T2D and MASLD is associated with a significant decline of liver steatosis and necroinflammation proxies; mild alcohol assumption did not exert any influence. An independent effect of GLP-1 raise was observed on reduction of steatosis, irrespective of alcohol consumption.
Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium
Authors: Laue Hannah E. , Bonham Kevin S. , Coker Modupe O. , Moroishi Yuka , Pathmasiri Wimal , McRitchie Susan , Sumner Susan , Hoen Anne G. , Karagas Margaret R. , Klepac-Ceraj Vanja , Madan Juliette C. ,   program collaborators for Environmental influences on Child Health Outcomes, Smith P. B. , Newby K. L. , Jacobson L. P. , Catellier D. J. , Gershon R. , Cella D. , Koinis Mitchell D. , Deoni S. , D’Sa V. 
Published: May 2024

Abstract
Background
Identifying modifiable risk factors of autism spectrum disorders (ASDs) may inform interventions to reduce financial burden. The infant/toddler gut microbiome is one such feature that has been associated with social behaviors, but results vary between cohorts. We aimed to identify consistent overall and sex-specific associations between the early-life gut microbiome and autism-related behaviors.

Methods
Utilizing the Environmental influences on Children Health Outcomes (ECHO) consortium of United States (U.S.) pediatric cohorts, we gathered data on 304 participants with fecal metagenomic sequencing between 6-weeks to 2-years postpartum (481 samples). ASD-related social development was assessed with the Social Responsiveness Scale (SRS-2). Linear regression, PERMANOVA, and Microbiome Multivariable Association with Linear Models (MaAsLin2) were adjusted for sociodemographic factors. Stratified models estimated sex-specific effects.

Results
Genes encoding pathways for synthesis of short-chain fatty acids were associated with higher SRS-2 scores, indicative of ASDs. Fecal concentrations of butyrate were also positively associated with ASD-related SRS-2 scores, some of which may be explained by formula use.

Limitations
The distribution of age at outcome assessment differed in the cohorts included, potentially limiting comparability between cohorts. Stool sample collection methods also differed between cohorts. Our study population reflects the general U.S. population, and thus includes few participants who met the criteria for being at high risk of developing ASD.

Conclusions
Our study is among the first multicenter studies in the U.S. to describe prospective microbiome development from infancy in relation to neurodevelopment associated with ASDs. Our work contributes to clarifying which microbial features associate with subsequent diagnosis of neuropsychiatric outcomes. This will allow for future interventional research targeting the microbiome to change neurodevelopmental trajectories.
Factors associated with timely initiation of antenatal care among reproductive age women in The Gambia: a multilevel fixed effects analysis
Authors: Daniels-Donkor Silas Selorm , Afaya Agani , Daliri Dennis Bomansang , Laari Timothy Tienbia , Salia Solomon Mohammed , Avane Mabel Apaanye , Afaya Richard Adongo , Yakong Vida Nyagre , Ayanore Martin Amogre , Alhassan Robert Kaba 
Published: May 2024

Abstract
Background
A significant factor impacting the incidence of maternal and neonatal fatalities is the timely initiation of antenatal care (ANC) services in healthcare facilities. Despite the recommendations by the World Health Organization and the numerous benefits of timely initiation of ANC, studies have revealed that the overall prevalence of timely ANC initiation in 36 sub-Saharan African countries remains low and women in The Gambia also initiate ANC late. However, no known study in The Gambia has focused on assessing the factors associated with timely initiation of ANC at the time of writing this paper. Thus, this study aimed to assess the prevalence and factors associated with the timely initiation of ANC among reproductive-age women in The Gambia.

Methods
A cross-sectional survey design was used in this study and conducted among 5,734 reproductive-age women using data from the 2019–2020 Gambia Demographic and Health Survey (GDHS). Using STATA version 14.0, we conducted the analysis using descriptive and inferential statistics. Multilevel logistic regression models were fitted to determine the factors associated with timely ANC utilization and adjusted odds ratios were used to present the results with statistical significance set at p < 0.05.

Results
The overall prevalence of timely initiation of ANC services among reproductive-age women in The Gambia was 43.0%. We found that women aged 30–34 [aOR = 1.79, 95% CI = 1.30–2.47], those who were married [aOR = 2.69, 95% CI = 1.85–3.90] as well as women from the richest households [aOR = 1.63, 95% CI = 1.20, 2.20] had higher odds of seeking timely ANC services as compared to their counterparts. Also, those who had given birth to two children [aOR = 0.74, 95% CI = 0.6 -0.91] had lower odds of initiating timely ANC as compared to those who had given birth only once. Women who reside in rural areas [aOR = 1.72, 95%CI = 1.34, 2.20] also had higher odds of seeking timely ANC services than those residing in urban areas.

Conclusion
Individual-level factors such as maternal age, marital status, parity, wealth status, place of residence, and religion were associated with the timely initiation of ANC services among reproductive-age women. These factors ought to be considered in efforts to increase the timely initiation of ANC among reproductive-age women in The Gambia.
Remote family education and support program for parents of patients with adolescent and early adulthood eating disorders based on interpersonal psychotherapy: study protocol for a pilot randomized controlled trial
Authors: Katsuki Fujika , Watanabe Norio , Kondo Masaki , Sawada Hanayo , Yamada Atsurou 
Published: May 2024

Abstract
Background
In cases of adolescent and early adulthood eating disorders, despite the importance of the patients’ relationship with their parents, conflict and confusion frequently occur among them. Interpersonal psychotherapy (IPT) is a present-focused psychotherapy that emphasizes the interpersonal context of symptoms. We developed a remote family education and support program exclusively for parents of patients with eating disorders, based on the principle of IPT. The use of IPT is expected to reduce conflicts in the patient-parent relationship. Consequently, parents will be better able to listen to patients, and patients will be better able to express their thoughts and desires. In this study, we describe the protocol for a randomized controlled trial designed to examine the effectiveness of this program in promoting effective communication in their home based on active listening skills of parents of patients with adolescent and early adulthood eating disorders.

Methods
Participants will be parents of patients aged 12–29 years with adolescent and early adulthood eating disorders. Individually randomized, parallel-group trial design will be employed. Seventy participants will be allocated to one of two treatment conditions: (1) remote family education and support program (four, 150 min weekly group sessions) for parents plus treatment-as-usual for patients (consultation by physicians or no treatment), or (2) waiting for the control condition (parents will wait to start the program for 8 weeks) plus treatment-as-usual for patients. The primary outcome measure will be parents’ active listening ability as measured by the Active Listening Attitude Scale at 8 weeks after randomization. Additionally, perception of social support (Social Provision Scale-10 item), loneliness (UCLA Loneliness Scale), mental health status (K6), family function (Family Assessment Device), and parent-evaluated eating disorder symptoms (Anorectic Behavior Observation Scale) will be assessed. Data from the intention-to-treat sample will be analyzed 8 weeks after randomization.

Discussion
This is the first study to evaluate the effectiveness of a family education and support program for parents of patients with adolescent and early adulthood eating disorders based on IPT. If this type of intervention is effective, although indirect, it could be a new support method for this patient population.
Trial registration: Clinical Trials. gov ID NCT05840614.