bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of an HIV/STI and partner violence health promotion intervention for abused US Virgin Islands women
Authors: Alexander Kamila A , Sharps Phyllis , Addison Helena , Bertrand Desiree , Bauman Aletha , Braithwaite-Hall Marilyn , Yarandi Hossein N , Callwood Gloria , Jemmott Loretta S , Campbell Jacquelyn C 
Published: July 2023

Abstract
Women in the US Virgin Islands (USVI) experience intimate partner violence (IPV) and human immunodeficiency virus (HIV) at disproportionate rates compared to women on the US mainland. Women in violent relationships report experiencing controlling behaviours that decrease their ability to negotiate for sex using condoms or to prevent unwanted pregnancies. Though several evidence-based interventions exist to prevent either IPV or HIV, few address them through an integrated health promotion approach or attend to particular USVI cultural mores. This article describes the systematic development of a theory based, culturally tailored, integrated health promotion intervention that addresses IPV and HIV among USVI women experiencing abuse. The process included: (i) identifying and integrating evidence-based health promotion interventions, (ii) conducting formative research using focus groups, (iii) synthesizing focus group data to inform intervention development and (iv) developing a culturally and linguistically appropriate intervention specific to the needs and concerns of USVI women. The Empowered Sisters Project: Making Choices Reducing Risks (ESP) was developed through this research. ESP is a three-session health promotion curriculum focussed on enhancing sexual health and safety among women experiencing abuse. The ESP intervention components included promoting condom use, increasing IPV and HIV knowledge and developing a personalized safety plan. Health professionals facilitated individual intervention sessions using culturally tailored visual media and scripts. This program focussed on experiences of women living in the USVI and has implications for utility across the Caribbean diaspora.
Determinants of cervical cancer screening among women living with HIV in Zimbabwe
Authors: Antabe Roger , Luginaah Nasong A , Kangmennaang Joseph , Mkandawire Paul 
Published: July 2023

Abstract
In sub-Saharan Africa (SSA), cervical cancer (CC) is the second leading cause of cancer-related deaths, with human immunodeficiency virus (HIV) seropositive women being particularly vulnerable. Despite the benefits of early CC screening in reducing HIV-related CC deaths, CC screening uptake remains limited, with wide disparities in access across SSA. As part of a larger study, this paper examines the determinants of CC screening among HIV-seropositive women of reproductive age (15–49 years) in Zimbabwe. Using the 2015 Zimbabwe Demographic and Health Survey, we conducted multilevel analyses of CC screening among 1490 HIV-seropositive women, nested in 400 clusters. Our findings revealed that, even though 74% of HIV-seropositive women knew about CC, only 17.6% of them reported ever screening for it. Women who held misconceptions about HIV (OR = 0.47, p = 0.01) were less likely to screen for CC compared to those with accurate knowledge about HIV and CC. HIV-seropositive women with secondary or higher education were more likely to screen (OR = 1.39, p = 0.04) for CC compared to those with a primary or lower level of education. Age was positively associated with screening for CC. Furthermore, locational factors, including province and rural–urban residence, were associated with CC screening. Based on these findings, we call for integrated care and management of HIV and non-communicable diseases in Southern Africa, specifically, Zimbabwe due to the legacy of HIV in the region.
Novel pathological variants of NHP2 affect N-terminal domain flexibility, protein stability, H/ACA Ribonucleoprotein (RNP) complex formation and telomerase activity
Authors: Maliński Bartosz , Vertemara Jacopo , Faustini Elena , Ladenvall Claes , Norberg Anna , Zhang Yuming , von Castelmur Eleonore , Baliakas Panagiotis , Tisi Renata , Cammenga Jörg , Lottersberger Francisca 
Published: July 2023

Abstract
Telomere biology disorders (TBDs) are characterized by short telomeres, premature aging, bone marrow failure and cancer predisposition. Germline mutations in NHP2, encoding for one component of the telomerase cofactor H/ACA RNA binding complex together with Dyskerin, NOP10 and GAR1, have been previously reported in rare cases of TBDs. Here, we report two novel NHP2 variants (NHP2-A39T and NHP2-T44M) identified in a compound heterozygous patient affected by premature aging, bone marrow failure/myelodysplastic syndrome and gastric cancer. Although still able to support cell viability, both variants reduce the levels of hTR, the telomerase RNA component, and telomerase activity, expanding the panel of NHP2 pathological variants. Furthermore, both variants fail to be incorporated in the H/ACA RNA binding complex when in competition with wild-type endogenous NHP2, and the lack of incorporation causes their drastic proteasomal degradation. By RoseTTAFold prediction followed by molecular dynamics simulations, we reveal a dramatic distortion of residues 33–41, which normally position on top of the NHP2 core, as the main defect of NHP2-A39T, and high flexibility and the misplacement of the N-terminal region (residues 1–24) in NHP2-T44M and, to a lower degree, in NHP2-A39T. Because deletion of amino acids 2–24 causes a reduction in NHP2 levels only in the presence of wild-type NHP2, while deletion of amino acids 2–38 completely disrupts NHP2 stability, we propose that the two variants are mis-incorporated into the H/ACA binding complex due to the altered dynamics of the first 23 amino acids and/or the distortion of the residues 25–41 loop.
Influence of microbial fermentation on the antioxidant activity of phenolic substances in Saccharomyces cerevisiae
Authors: Prudêncio de Souza Edlene Ribeiro , Braz Marcos Vinicius da Conceição , Castro Rosane Nora , Pereira Marcos Dias , Riger Cristiano Jorge 
Published: July 2023

Abstract

Aim
Using in vitro assay and eukaryotic cell model of Saccharomyces cerevisiae, we investigated the impact of microbial fermentation on the antioxidant activity of phenolic substances.

Methods and Results
Caffeic acid phenethyl ester (CAPE) and mangiferin were fermented by lactic acid bacteria (LAB), and the antioxidant activity of the fermented products was compared to that of the pure substances. This comparison was assessed using high-performance liquid chromatography (HPLC), in vitro by 2,2-Diphenyl-1-picrylhydrazyl (DPPH), and in vivo in yeast cells. The wild-type strain (BY4741) and its isogenic mutants in glutathione (Δgsh1), catalase (Δctt1), and superoxide dismutase (Δsod1) were treated with CAPE and mangiferin, fermented or not, and exposed to hydrogen peroxide (H2O2)-induced stress. The antioxidant activity was evaluated by cellular viability, intracellular oxidation, and lipid peroxidation. We expected that fermentation would change the antioxidant activity of phenolic substances. While HPLC analysis revealed changes in the composition of fermented products, significant alterations in antioxidant activity were only observed when using mutant strains. The fermentation of mangiferin increased dependency on GSH compared to the respective pure phenolic substance to resolve H2O2-induced stress. Additionally, CAPE appeared to act as a preconditioning agent, enhancing antioxidant responses, and promoting increased tolerance to H2O2 stress, and this mechanism was maintained after fermentation.

Conclusions
This study highlights that fermentation impacts the enzymatic mechanism of oxidative stress resolution, even though differences could not be observed in in vitro assays or in the wild-type strain.
Studying Nonlinear Change in Music Therapy Applying Dynamic Systems Theory
Authors: Antichi Lorenzo , Giannini Marco , Edwards Jane 
Published: July 2023

Abstract
Change in music therapy is often modeled linearly. In linear analysis, change is represented as the difference between the scores recorded before and after treatment, where changes in the input are proportional to the output. However, changes in complex systems are often not linear and depend on time. We propose Dynamic Systems Theory (DST) as a means to overcome the shortcomings of linear analysis and enrich the study of change in music therapy. This article aims to introduce and critically discuss the applications of DST in music therapy, focusing on its theoretical and methodological aspects. DST offers a meta-framework to model nonlinear change in music therapy, considering time as continuous. The application of DST can further enhance the understanding of how music therapy works, the shape of the change, and how the relevant therapeutic processes within music therapy support therapeutic change. An introduction to DST theory is provided along with its history, implications, assessment methods, statistical analyses, mathematical modeling, and implementation examples in music therapy research.
The DeCAMFounder: nonlinear causal discovery in the presence of hidden variables
Authors: Agrawal Raj , Squires Chandler , Prasad Neha , Uhler Caroline 
Published: July 2023

Abstract
Many real-world decision-making tasks require learning causal relationships between a set of variables. Traditional causal discovery methods, however, require that all variables are observed, which is often not feasible in practical scenarios. Without additional assumptions about the unobserved variables, it is not possible to recover any causal relationships from observational data. Fortunately, in many applied settings, additional structure among the confounders can be expected. In particular, pervasive confounding is commonly encountered and has been utilised for consistent causal estimation in linear causal models. In this article, we present a provably consistent method to estimate causal relationships in the nonlinear, pervasive confounding setting. The core of our procedure relies on the ability to estimate the confounding variation through a simple spectral decomposition of the observed data matrix. We derive a DAG score function based on this insight, prove its consistency in recovering a correct ordering of the DAG, and empirically compare it to previous approaches. We demonstrate improved performance on both simulated and real datasets by explicitly accounting for both confounders and nonlinear effects.
Automated calibration for stability selection in penalised regression and graphical models
Authors: Bodinier Barbara , Filippi Sarah , Nøst Therese Haugdahl , Chiquet Julien , Chadeau-Hyam Marc 
Published: July 2023

Abstract
Stability selection represents an attractive approach to identify sparse sets of features jointly associated with an outcome in high-dimensional contexts. We introduce an automated calibration procedure via maximisation of an in-house stability score and accommodating a priori-known block structure (e.g. multi-OMIC) data. It applies to [Least Absolute Shrinkage Selection Operator (LASSO)] penalised regression and graphical models. Simulations show our approach outperforms non-stability-based and stability selection approaches using the original calibration. Application to multi-block graphical LASSO on real (epigenetic and transcriptomic) data from the Norwegian Women and Cancer study reveals a central/credible and novel cross-OMIC role of LRRN3 in the biological response to smoking. Proposed approaches were implemented in the R package sharp.
A Falciformispora senegalensis grain model in Galleria mellonella larvae
Authors: Ma Jingyi , Konings Mickey , Verbon Annelies , van de Sande Wendy W J 
Published: July 2023

Abstract
Eumycetoma is a subcutaneous implantation mycosis often found in the foot. One of the hallmarks of eumycetoma is the formation of grains. These grains are either black or white, and the consistency and morphology differs per causative agent. The two most common causative agents of black-grain eumycetoma are Madurella mycetomatis and Falciformispora senegalensis. Since grains cannot be formed in vitro, in vivo models are needed to study grain formation. Here, we used the invertebrate Galleria mellonella to establish an in vivo grain model for F. senegalensis. Three different F. senegalensis strains were selected, and four different inocula were used to infect G. mellonella larvae, ranging from 0.04 mg/larvae to 10 mg/larvae. Larval survival was monitored for 10 days. Grain formation was studied macroscopically and histologically. The efficacy of antifungal therapy was determined for itraconazole, amphotericin B, and terbinafine. A concentration of 10 mg F. senegalensis per larva was lethal for the majority of the larvae within 10 days. At this inoculum, grains were formed within 24 h after infection. The grains produced in the larvae resembled those formed in human patients. Amphotericin B given at 1 mg/kg 4 h, 28 h, and 52 h after infection prolonged larval survival. No enhanced survival was noted for itraconazole or terbinafine. In conclusion, we developed a F. senegalensis grain model in G. mellonella larvae in which grains were formed that were similar to those formed in patients. This model can be used to monitor grain formation over time and study antifungal efficacy.
mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability
Authors: Vijjamarri Anil Kumar , Gupta Neha , Onu Chisom , Niu Xiao , Zhang Fan , Kumar Rakesh , Lin Zhenguo , Greenberg Miriam L , Hinnebusch Alan G 
Published: July 2023

Abstract
We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors. Although the Environmental Stress Response (ESR) is activated in dhh1Δ and pat1Δ mutants, hundreds of non-ESR transcripts are elevated in a manner indicating cumulative repression by Pat1 and Dhh1 in wild-type cells. These mRNAs show both reduced decapping and diminished transcription in the mutants, indicating that impaired mRNA turnover drives transcript derepression in cells lacking Dhh1 or Pat1. mRNA degradation stimulated by Dhh1/Pat1 is not dictated by poor translation nor enrichment for suboptimal codons. Pat1 and Dhh1 also collaborate to reduce translation and protein production from many mRNAs. Transcripts showing concerted translational repression by Pat1/Dhh1 include mRNAs involved in cell adhesion or utilization of the poor nitrogen source allantoin. Pat1/Dhh1 also repress numerous transcripts involved in respiration, catabolism of non-preferred carbon or nitrogen sources, or autophagy; and we obtained evidence for elevated respiration and autophagy in the mutants. Thus, Pat1 and Dhh1 function as post-transcriptional repressors of multiple pathways normally activated only during nutrient limitation.
The FLIP-FIGNL1 complex regulates the dissociation of RAD51/DMC1 in homologous recombination and replication fork restart
Authors: Zhang Qianting , Fan Jiayi , Xu Wei , Cao Huiwen , Qiu Cheng , Xiong Yi , Zhao Huacun , Wang Yong , Huang Jun , Yu Chao 
Published: July 2023

Abstract
Recruitment of RAD51 and/or DMC1 recombinases to single-strand DNA is indispensable for homology search and strand invasion in homologous recombination (HR) and for protection of nascent DNA strands at stalled replication forks. Thereafter RAD51/DMC1 dissociate, actively or passively, from these joint molecules upon DNA repair or releasing from replication stress. However, the mechanism that regulates RAD51/DMC1 dissociation and its physiological importance remain elusive. Here, we show that a FLIP-FIGNL1 complex regulates RAD51 and DMC1 dissociation to promote meiotic recombination and replication fork restart in mammals. Mice lacking FLIP are embryonic lethal, while germline-specific deletion of FLIP leads to infertility in both males and females. FLIP-null meiocytes are arrested at a zygotene-like stage with massive RAD51 and DMC1 foci, which frequently co-localize with SHOC1 and TEX11. Furthermore, FLIP interacts with FIGNL1. Depletion of FLIP or FIGNL1 in cell lines destabilizes each other and impairs RAD51 dissociation. Thus, the active dissociation of RAD51/DMC1 by the FLIP-FIGNL1 complex is a crucial step required for HR and replication fork restart, and represents a conserved mechanism in somatic cells and germ cells.
Toward the confirmation of atmospheric neutrino oscillations
Authors: Oyama Yuichi 
Published: July 2023

Abstract
The atmospheric muon neutrino deficit, which was possible evidence of νμ↔ντ oscillation, was reported by the Kamiokande experiment from 1988. Many experimental efforts were made to examine the Kamiokande results. Experiments which contributed to the confirmation of νμ↔ντ oscillation are reviewed. Especially, long-baseline neutrino-oscillation experiments are described in detail.
A call for obesity prevention interventions for young children with intellectual and developmental disabilities
Authors: Schenkelberg Michaela A , Clarke Emily C , Wasser Heather , Ward Dianne S , Essenmacher Mikayla M , Thompson Kelsey L , Willis Erik A 
Published: July 2023

Lay Summary
Health disparities among children with intellectual and developmental disabilities (IDD) are present in early childhood. Yet, this population is underrepresented in health behavior research. In this commentary the authors highlight the need for multi-level physical activity and nutrition research for obesity prevention with a specific focus on young children with Down syndrome, a population at greater risk of developing overweight and obesity compared to typically developing peers. This commentary describes the comorbidities and developmental challenges faced by many children with Down syndrome which may influence weight-related physical activity and nutrition behaviors. Additionally, the authors advocate for involving a multidisciplinary team of experts to inform the adaptation or development of multi-level, theory-driven behavioral interventions to prevent obesity among children with Down syndrome.
Longitudinal anellome dynamics in the upper respiratory tract of children with acute respiratory tract infections
Authors: Cao Le , Ma Yingying , Wan Zhenzhou , Li Bing , Tian Weimin , Zhang Chiyu , Li Yanpeng 
Published: July 2023

Abstract
Anelloviruses (AVs) are ubiquitous in humans and are the most abundant components of the commensal virome. Previous studies on the diversity, transmission, and persistence of AVs mainly focused on the blood or transplanted tissues from adults; however, the profile of the anellome in the respiratory tract in children are barely known. We investigated the anellome profile and their dynamics in the upper respiratory tract from a cohort of children with acute respiratory tract infections (ARTIs). Different to that in adult, betatorquevirus is the most abundant genus, followed by alphatorquevirus. We found that the relative abundance of betatorquevirus was higher in earlier time points, and in contrast, the abundance of alphatorquevirus was higher in later time points; these results might suggest that betatorquevirus decreased with age and alphatorquevirus increased with age in childhood. No difference regarding the diversity and abundance of anellome was found between single and multiple ARTIs, consistent with the idea that AV is not associated with certain disease. Most AVs are transient, and a small proportion (8 per cent) of them were found to be possibly persistent, with persistence time ranging from 1 month to as long as 56 months. Furthermore, the individual respiratory anellome appeared to be unique and dynamic, and the replacement of existing AVs with new ones are common over different time points. These findings demonstrate that betatorquevirus may be the early colonizer in children, and the individual respiratory anellome is unique, which are featured by both chronic infections and AV community replacement.
Interpretation of the Patient Health Questionnaire 9 in High-impact Chronic Pain
Authors: Aagaard Andrea , Ravn Sophie Lykkegaard , Andersen Tonny Elmose , Vaegter Henrik Bjarke 
Published: July 2023

Objectives:
Depression is prevalent among patients with chronic pain and may impact pain management. Accurate assessment is, however, complicated by overlapping symptoms. This study investigated how patients with high-impact chronic pain interpreted and responded to the Patient Health Questionnaire 9 (PHQ-9) to identify problematic items and causes hereof.

Methods:
Cognitive interviews using the Three-Step Test-Interview procedure were conducted during completion of the PHQ-9 in 33 patients with high-impact chronic pain referred to interdisciplinary treatment. Responses were analyzed using four coding categories: i) “congruent” (response consistent with intention); ii) “incongruent” (response not consistent intention); iii) “ambiguous” (response both congruent and incongruent or insufficient to evaluate congruency); and iv) “confused” (response with confused or misunderstood statements). Next, content of responses problematic items was analyzed to identify causes for non-congruency and encountered response difficulties were identified across all items.

Results:
Three items (item 2, 6, and 9) performed as intended (>97% congruent responses), while seven items (item 1, 3, 4, 5, 7, 8, and 10) were identified as problematic (<50% congruent responses). Problematic items had one or more issues: Responses were based on i) pain related issues or ii) other (non-pain) factors unrelated to depression, or item structure caused response difficulties due to wordings, reversion, or having two questions in one.

Discussion:
Problematic items limit the construct validity of the PHQ-9, leaving increased risk of inflated depression scores in high-impact chronic pain. Identified problems should guide future revisions to enhance validity and screening accuracy for the benefit of both research and clinical practice.