bluuebunny/crossref_metadata_2025_split huggingface dataset:
End-user research in support of long-acting systemic antiretroviral delivery systems: insights from qualitative research with providers and target users in South Africa
Authors: Brown Morgan S. , Hanif Homaira , Little Kristen M. , Clark Meredith R. , Thurman Andrea R. , Flomen Lola , Doncel Gustavo F. 
Published: December 2022

Abstract
Background
While oral pre-exposure prophylaxis (PrEP) has been shown to reduce the risk of HIV, challenges such as adhering to a daily-dosing regimen and persistence have emerged as barriers for at-risks populations in South Africa. This qualitative research sought to investigate perceptions of and preferences for a long-acting, biodegradable implantable PrEP product designed to address these barriers.

Methods
To identify and understand motivators, barriers, and preferences for the PrEP implant, we conducted qualitative in-depth interviews (IDIs) among health care providers (HCPs) and target end-users (young women, adolescent girls, and female sex workers) in urban and rural/peri-urban regions of Gauteng Province, South Africa. The IDIs focused on defining values, beliefs, habits, lifestyles, influencers, and information channels for potential PrEP implant end-users.

Results
We conducted 36 IDIs across health care providers and target end-user respondent segments. Respondents had generally positive reactions to the PrEP implant. Most end-users felt that some undesirable aspects of the implant (e.g., side effects, pain during insertion, potential scarring, and inability to remove implant) would be offset by having a highly effective, and long-lasting HIV prevention product. Although some HCPs believed the implantable PrEP would lead to increases in promiscuity and risky sexual behavior, most HCPs saw value in the PrEP implant’s long duration of protection, its biodegradability, and the likelihood of higher adherence relative to oral PrEP.

Conclusions
This study is a first step toward further research needed to demonstrate the demand for a biodegradable, long-acting implantable PrEP and suggests such a product would be accepted by end-users and HCPs in South Africa. This study indicates the need to develop more convenient, discreet, long-acting, and highly effective biomedical HIV prevention options for at-risk populations.
COVID-19 impact on index testing services and programmatic cost in 5 high HIV prevalence Indian districts
Authors: Pollard Rose , Enugu Ajay , Sriudomporn Salin , Bell Jade , Ghosh Subash Chandra , Arumugam Visvanathan , Mugundu Parthasarathy , Singh Aditya , McFall Allison M. , Mehta Shruti H. , Patenaude Bryan N. , Solomon Sunil S. 
Published: December 2022

AbstractBackgroundRestrictions to curb the first wave of COVID-19 in India resulted in a decline in facility-based HIV testing rates, likely contributing to increased HIV transmission and disease progression. The programmatic and economic impact of COVID-19 on index testing, a standardized contact tracing strategy, remains unknown.MethodsRetrospective programmatic and costing data were analyzed under a US government-supported program to assess the pandemic’s impact on the programmatic outcomes and cost of index testing implemented in two Indian states (Maharashtra and Andhra Pradesh). We compared index testing continuum outcomes during lockdown (April–June 2020) and post-lockdown (July–Sept 2020) relative to pre-lockdown (January–March 2020) by estimating adjusted rate ratios (aRRs) using negative binomial regression. Startup and recurrent programmatic costs were estimated across geographies using a micro-costing approach. Per unit costs were calculated for each index testing continuum outcome.ResultsPre-lockdown, 2431 index clients were offered services, 3858 contacts were elicited, 3191 contacts completed HIV testing, 858 contacts tested positive, and 695 contacts initiated ART. Compared to pre-lockdown, the number of contacts elicited decreased during lockdown (aRR = 0.13; 95% CI: 0.11–0.16) and post-lockdown (aRR = 0.49; 95% CI: 0.43–0.56); and the total contacts newly diagnosed with HIV also decreased during lockdown (aRR = 0.22; 95% CI: 0.18–0.26) and post-lockdown (aRR = 0.52; 95% CI: 0.45–0.59). HIV positivity increased from 27% pre-lockdown to 40% during lockdown and decreased to 26% post-lockdown. Further, ART initiation improved from 81% pre-lockdown to 88% during lockdown and post-lockdown. The overall cost to operate index testing was $193,457 pre-lockdown and decreased during lockdown to $132,177 (32%) and $126,155 (35%) post-lockdown. Post-lockdown unit cost of case identification rose in facility sites ($372) compared to pre-lockdown ($205), however it decreased in community-based sites from pre-lockdown ($277) to post-lockdown ($166).ConclusionsThere was a dramatic decline in the number of index testing clients in the wake of COVID-19 restrictions that resulted in higher unit costs to deliver services; yet, improved linkage to ART suggests that decongesting centres could improve efficiency. Training index testing staff to provide support across services including non-facility-based HIV testing mechanisms (i.e., telemedicine, HIV self-testing, community-based approaches) may help optimize resources during public health emergencies.
Patterns and prognostic predictive value of perineural invasion in esophageal squamous cell carcinoma
Authors: Ma Yu , Chen Jie , Yao Xi , Li Zhenzhen , Li Wensheng , Wang Hongtao , Zhu Jianfei 
Published: December 2022

Abstract
Background
The pathological phenotype of perineural invasion (PNI) in squamous cell carcinoma (ESCC) is prevalent but highly heterogeneous.

Methods
Postoperative specimens from all patients with ESCC at Shaanxi Provincial People’s Hospital were evaluated for PNI using haematoxylin and eosin (H&E) staining and S100 immunohistochemistry (IHC). We determined the correlation between PNI status and clinical outcomes.

Results
Among 349 ESCC cases, PNI was identified in 127 patients (36.3%), and four subtypes of PNI were identified in our study. Correlation analysis confirmed that PNI was related to tumour invasion depth (pT stage) and lymph node status (pN stage) (P < 0.05). Multivariate analysis showed that PNI (P = 0.001) was an independent factor affecting disease-free survival (DFS) in ESCC, and a similar result was found for overall survival (OS) (P = 0.017). Further analysis revealed that PNI status was a prognostic factor of DFS (P < 0.001) and OS (P = 0.003) exclusively in pN-negative patients. We also found that patients with the PNI-a subtype had better DFS (P = 0.002) and OS (P = 0.002) than patients with the other three subtypes (PNI-b, c, d).

Conclusion
The pathological phenotypes of PNI are diverse, and the identification of PNI subtypes has important clinical guiding value.
Complications of radical hysterectomy with pelvic lymph node dissection for cervical cancer: a 10-year single-centre clinical observational study
Authors: Jing Huang , Xiuhong Wu , Ying Yu , Xiyun Cheng , Deping Luo , Changmei Shen , Qi Wang , Tao Peng , Yiyun Pan 
Published: December 2022

Abstract
Background and purpose
The complications of radical surgery for cervical cancer can increase patient suffering and affect their quality of life. This retrospective study assessed the safety of radical hysterectomy (RH) with pelvic lymph node dissection (PLND) by observing the complications of patients with cervical cancer who underwent this procedure in a single centre over 10 years. Our findings may provide experience and evidence for preventing and reducing complications.

Methods
A total of 2226 cervical cancer patients who met the inclusion criteria were enrolled. All patients underwent RH + PLND. Intraoperative injury to adjacent tissues and short-term and long-term complications were recorded to analyze factors associated with the occurrence of complications.

Results
Postoperative complications occurred in 34.41% (766/2226) of patients, including 7.68% of patients with injury to adjacent tissues, 31.45% with short-term complications, and 2.96% with long-term complications. Age, tumor size, invasion depth, parametrial invasion, lymph vascular space invasion (LVSI), lymph node metastasis, International Federation of Gynaecology and Obstetrics (FIGO) stage, and surgical procedure were closely associated with the postoperative complications of RH + PLND (P < 0.05).

Conclusions
The results of this study showed that RH + PLND for cervical cancer is safe and practical. Patients aged 40–60 years, with tumors ≥ 4 cm, invasion depth ≥ 2/3, parametrial invasion, LVSI, lymph node metastasis, FIGO stage > IB2, and who underwent open surgery were more prone to complications.
Nomogram model predicts the risk of visual impairment in diabetic retinopathy: a retrospective study
Authors: Zhao Yuancheng , Yu Rentao , Sun Chao , Fan Wei , Zou Huan , Chen Xiaofan , Huang Yanming , Yuan Rongdi 
Published: December 2022

Abstract
Background
To develop a model for predicting the risk of visual impairment in diabetic retinopathy (DR) by a nomogram.

Methods
Patients with DR who underwent both optical coherence tomography angiography (OCTA) and fundus fluorescein angiography (FFA) were retrospectively enrolled. FFA was conducted for DR staging, swept-source optical coherence tomography (SS-OCT) of the macula and 3*3-mm blood flow imaging by OCTA to observe retinal structure and blood flow parameters. We defined a logarithm of the minimum angle of resolution visual acuity (LogMAR VA) ≥0.5 as visual impairment, and the characteristics correlated with VA were screened using binary logistic regression. The selected factors were then entered into a multivariate binary stepwise regression, and a nomogram was developed to predict visual impairment risk. Finally, the model was validated using the area under the receiver operating characteristic (ROC) curve (AUC), calibration plots, decision curve analysis (DCA), and clinical impact curve (CIC).

Results
A total of 29 parameters were included in the analysis, and 13 characteristics were used to develop a nomogram model. Finally, diabetic macular ischaemia (DMI) grading, disorganization of the retinal inner layers (DRIL), outer layer disruption, and the vessel density of choriocapillaris layer inferior (SubVD) were found to be statistically significant (P < 0.05). The model was found to have good accuracy based on the ROC (AUC = 0.931) and calibration curves (C-index = 0.930). The DCA showed that risk threshold probabilities in the (3–91%) interval models can be used to guide clinical practice, and the proportion of people at risk at each threshold probability is illustrated by the CIC.

Conclusion
The nomogram model for predicting visual impairment in DR patients demonstrated good accuracy and utility, and it can be used to guide clinical practice.

Trial registration
Chinese Clinical Trial Registry, ChiCTR2200059835. Registered 12 May 2022,
https://www.chictr.org.cn/edit.aspx?pid=169290&htm=4
Association between dietary theobromine with depression: a population-based study
Authors: Li Xin-yu , Liu Hui , Zhang Lu-yu , Yang Xi-tao 
Published: December 2022

Abstract
Objective
The purpose of this study is to investigate the possible link between dietary theobromine intake and symptoms of depression.

Materials and methods
These results are based on the responses of 3637 people who took part in the National Health and Nutrition Examination Survey in 2017–2018. Participants' daily theobromine intake was determined using a 24-h food questionnaire from the 2017–2018 cycle. Presence of depression was defined as a score of 5 or above on the Patient Health Questionnaire. Association between theobromine intake and depression was examined using a multivariate logistic regression adjusting for several relevant sociodemographic, lifestyle and health-related factors.

Results
A total of 6903 participants were included in the study. The results of multivariate logistic regression showed a correlation between depressive symptoms and theobromine intake (OR:1.17, 95%CI:1.02–1.34).

Conclusions
Our cross-sectional population based study suggests that increased theobromine intake is associated with increased risk for depression. Nevertheless, more investigations are needed to confirm our findings.
Social determinants and mental health needs of Palestine refugees and UNRWA responses in Gaza during the COVID-19 pandemic: a qualitative assessment
Authors: Jamal Zeina , ElKhatib Zoheir , AlBaik Shatha , Horino Masako , Waleed Mohammed , Fawaz Farah , Loffreda Giulia , Seita Akihiro , Witter Sophie , Diaconu Karin 
Published: December 2022

Abstract
Background
Due to pre-existing difficulties, refugees are especially susceptible to the negative effects of the pandemic; nonetheless, the pandemic’s effect on this group is still unclear. The purpose of this study was to determine the effects of the COVID-19 pandemic on the mental health of Palestine refugees in Gaza by identifying the role of social determinants. During the pandemic, the United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) enacted a number of policies and measures. The purpose of this research was to assess their efficacy and acceptability.

Methods
This qualitative study took place between August and November 2020. Twenty-nine key-informant interviews were conducted remotely with UNRWA Headquarters, field and clinical staff in Gaza and with community members, aged ≥18 years and residing in Rafah and Jabalia camps. We sought informed consent verbally or via email. Data was coded based on the framework for social determinants of mental health.

Results
Interview results indicated that the relationship might be unidirectional, with COVID-19 causing the degradation of living conditions and vice versa, with living conditions exacerbating the COVID-19 situation by facilitating virus transmission. In other instances, the association between mental health determinants and COVID-19 might be bidirectional. In terms of experiencing violence and anxieties, women, children, and daily-paid employees were significantly more disadvantaged than other groups in the community. UNRWA modified its service delivery techniques in order to continue providing essential services. In general, UNRWA’s strategies throughout the pandemic were deemed beneficial, but insufficient to meet the needs of Gazans.

Conclusion
The pandemic highlights the need to go beyond disease treatment and prevention to address social determinants to improve refugees’ health and reduce their susceptibility to future shocks. UNRWA has rapidly implemented telemedicine and mental telehealth services, making it imperative to assess the efficacy of these novel approaches to provide care at a distance. A long-term option may be to employ a hybrid strategy, which combines online and in-person therapy.
Intimate partner violence against women in Southern Punjab, Pakistan: A phenomenological study
Authors: Sattar Tehmina , Ahmad Saeed , Asim Muhammad 
Published: December 2022

Abstract
Background
Intimate Partner Violence (IPV) refers to behavior by an intimate partner that can cause physical, sexual, or psychological harm; is a common global public health issue requiring immediate attention. IPV is the most common form of violence in rural areas of Punjab, Pakistan.

Methods
This qualitative phenomenological study collected 46 in-depth interviews from married women who experienced IPV in the rural areas of South Punjab. A semi-structured interview guide was used for data collection. These women were selected through a snowball sampling technique from October 2018 to March 2019. Researchers accessed the study setting with the help of gatekeepers (Lady Health Workers and Village Heads). The interviews were audio-recorded in the local language (Saraiki) and were translated into English. The data were analyzed using the thematic inductive analysis technique.

Results
The study has presented multifaceted factors of IPV by using the socio-ecological framework in rural areas of South Punjab, Pakistan. The current study introduced culturally contextualized terminologies of "protection," "physical submissiveness," "mental delicacy," and "social security". For married women, culturally embedded terms became the primary cause of IPV. In addition, the study also highlighted some of the cultural terminologies (such as run-mureed, watta-satta, beghairat, izzat, etc.) that are ubiquitous in the local context that sometimes intensifies IPV in the family and community sphere. Furthermore, the study discussed how gender-based inequalities trigger a status quo that ultimately creates power discrimination between spouses, which perpetuates violence in the domestic context.

Conclusions
Gender-prejudiced roles and expectations imposed by orthodoxy, misinterpretations of Islamic teachings, and dominant patriarchy can be contested through awareness campaigns among the public, and gender sensitization drives among public institutions of police and judiciary. Education and employment-based can lead to women's empowerment and help to challenge the orthodox anti-feminist societal norms and the role of kinship-based networks in the family and community sphere.
Assessing the acceptability of dried blood spot testing for HIV and STBBI among Métis people in a community driven pilot project in Alberta, Canada
Authors: Landy Rachel , Atkinson Danielle , Ogilvie Kandace , St. Denys Raye , Lund Carrielynn , Worthington Catherine ,   on behalf of the DRUM & SASH team
Published: December 2022

AbstractBackgroundLittle literature exists on culturally grounded approaches for addressing human immunodeficiency virus (HIV) and sexually transmitted and blood-borne infections (STBBI) among Métis people. The goal of this mixed-methods research was to explore the experiences of Métis community members participating in a dried blood spot testing (DBST) for HIV/STBBI pilot for Métis communities in Alberta, Canada, with the aim of assessing the acceptability of this testing method.MethodsGrounded in community-based and Indigenous research approaches and working in partnership with a Métis community-based organization, data collection included a survey and four gathering circles with Métis DBST recipients at one of two community events, and semi-structured interviews with three DBST providers.ResultsTwenty-six of the 30 DBST recipients completed surveys, and 19 DBST recipients participated in gathering circles. Survey results suggest DBST is a highly acceptable STBBI testing method to Métis community members. Thematic analysis of gathering circle and interview transcripts revealed four broad themes related to the participants’ experiences with DBST related to its acceptability (i. ease of DBST process, ii. overcoming logistical challenges associated with existing STBBI testing, iii. Reducing stigma through health role models and event-based, and iv. Métis-specific services).ConclusionsThese findings illustrate the potential for DBST to be part of a culturally grounded, Métis-specific response to HIV and STBBI.
De novo emergence, existence, and demise of a protein-coding gene in murids
Authors: Petrzilek Jan , Pasulka Josef , Malik Radek , Horvat Filip , Kataruka Shubhangini , Fulka Helena , Svoboda Petr 
Published: December 2022

Abstract
Background
Genes, principal units of genetic information, vary in complexity and evolutionary history. Less-complex genes (e.g., long non-coding RNA (lncRNA) expressing genes) readily emerge de novo from non-genic sequences and have high evolutionary turnover. Genesis of a gene may be facilitated by adoption of functional genic sequences from retrotransposon insertions. However, protein-coding sequences in extant genomes rarely lack any connection to an ancestral protein-coding sequence.

Results
We describe remarkable evolution of the murine gene D6Ertd527e and its orthologs in the rodent Muroidea superfamily. The D6Ertd527e emerged in a common ancestor of mice and hamsters most likely as a lncRNA-expressing gene. A major contributing factor was a long terminal repeat (LTR) retrotransposon insertion carrying an oocyte-specific promoter and a 5′ terminal exon of the gene. The gene survived as an oocyte-specific lncRNA in several extant rodents while in some others the gene or its expression were lost. In the ancestral lineage of Mus musculus, the gene acquired protein-coding capacity where the bulk of the coding sequence formed through CAG (AGC) trinucleotide repeat expansion and duplications. These events generated a cytoplasmic serine-rich maternal protein. Knock-out of D6Ertd527e in mice has a small but detectable effect on fertility and the maternal transcriptome.

Conclusions
While this evolving gene is not showing a clear function in laboratory mice, its documented evolutionary history in Muroidea during the last ~ 40 million years provides a textbook example of how a several common mutation events can support de novo gene formation, evolution of protein-coding capacity, as well as gene’s demise.
Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips
Authors: Feng Dan , Liang Zhe , Wang Yifan , Yao Jiaying , Yuan Zan , Hu Guihua , Qu Ruihong , Xie Shang , Li Dongwei , Yang Liwen , Zhao Xinai , Ma Yanfei , Lohmann Jan U. , Gu Xiaofeng 
Published: December 2022

Abstract
Background
Root development and function have central roles in plant adaptation to the environment. The modification of root traits has additionally been a major driver of crop performance since the green revolution; however, the molecular underpinnings and the regulatory programmes defining root development and response to environmental stress remain largely unknown. Single-cell reconstruction of gene regulatory programmes provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes associated with cell type-specific gene expression remain largely unexplored.

Results
To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq (scATAC-seq) to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell type-specific accessibility variance across most of the major cell types and allowed us to identify sets of transcription factors which associate with accessible chromatin regions (ACRs). Using root hair differentiation as a model, we demonstrate that chromatin and gene expression dynamics during cell type differentiation correlate in pseudotime analyses. In addition to developmental trajectories, we describe chromatin responses to heat and identify cell type-specific accessibility changes to this key environmental stimulus.

Conclusions
We report chromatin landscapes during rice root development at single-cell resolution. Our work provides a framework for the integrative analysis of regulatory dynamics in this important crop organ at single-cell resolution.