bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding why racial/ethnic inequities along the HIV care continuum persist in the United States: a qualitative exploration of systemic barriers from the perspectives of African American/Black and Latino persons living with HIV
Authors: Filippone Prema , Serrano Samantha , Campos Stephanie , Freeman Robin , Cluesman Sabrina R. , Israel Khadija , Amos Brianna , Cleland Charles M. , Gwadz Marya 
Published: August 2023

Abstract
Background
Racial/ethnic inequities along the HIV care continuum persist in the United States despite substantial federal investment. Numerous studies highlight individual and social-level impediments in HIV, but fewer foreground systemic barriers. The present qualitative study sought to uncover and describe systemic barriers to the HIV care continuum from the perspectives of African American/Black and Latino persons living with HIV (PLWH) with unsuppressed HIV viral load, including how barriers operated and their effects.

Methods
Participants were African American/Black and Latino PLWH with unsuppressed HIV viral load (N = 41). They were purposively sampled for maximum variability on key indices from a larger study. They engaged in semi-structured in-depth interviews that were audio-recorded and professionally transcribed. Data were analyzed using directed content analysis.

Results
Participants were 49 years old, on average (SD = 9), 76% were assigned male sex at birth, 83% were African American/Black and 17% Latino, 34% were sexual minorities (i.e., non-heterosexual), and 22% were transgender/gender-nonbinary. All had indications of chronic poverty. Participants had been diagnosed with HIV 19 years prior to the study, on average (SD = 9). The majority (76%) had taken HIV medication in the six weeks before enrollment, but at levels insufficient to reach HIV viral suppression. Findings underscored a primary theme describing chronic poverty as a fundamental cause of poor engagement. Related subthemes were: negative aspects of congregate versus private housing settings (e.g., triggering substance use and social isolation); generally positive experiences with health care providers, although structural and cultural competency appeared insufficient and managing health care systems was difficult; pharmacies illegally purchased HIV medication from PLWH; and COVID-19 exacerbated barriers. Participants described mitigation strategies and evidenced resilience.

Conclusions
To reduce racial/ethnic inequities and end the HIV epidemic, it is necessary to understand African American/Black and Latino PLWH’s perspectives on the systemic impediments they experience throughout the HIV care continuum. This study uncovers and describes a number of salient barriers and how they operate, including unexpected findings regarding drug diversion and negative aspects of congregate housing. There is growing awareness that systemic racism is a core determinant of systemic barriers to HIV care continuum engagement. Findings are interpreted in this context.
BNIP3 as a potential biomarker for the identification of prognosis and diagnosis in solid tumours
Authors: Yu Qin , Fu Wenhao , Fu Yutang , Ye Wenjing , Yan Huiqiong , Yu Zecheng , Li Ruirui , Cai Yili , Chen Yuxin , Wang Lingyun , Wei Xianqiao , Chen Yangkun , Zhang Yuheng , Ying Huazhong , Tang Furong , Dai Fangwei , Han Wei 
Published: August 2023

Abstract
Background
Traditional radiotherapy and chemotherapy have been intensively studied for their role in the treatment of tumours. However, these therapies often cause side effects for patients, which calls for the development of novel treatment options for tumours. B-cell lymphoma-2 (Bcl-2)/adenovirus E1B 19 kDa-interacting protein 3 (BNIP3) reportedly apoptosis-inducing effects in tumour cells and is associated with the progression and treatment of multiple tumours. Nevertheless, little is known about its potential role in tumour diagnosis and targeted therapy.

Findings
The results of the study demonstrated that the interaction of BNIP3 with HDAC1 may affect the progression of breast invasive cancer (BRCA), sarcoma (SARC), kidney renal clear cell carcinoma (KIRC), and low-grade glioma (LGG). BNIP3 seemed to exert its effects in BRCA and SARC primarily through gene silencing and integrator complex, and in KIRC and LGG, mainly by affecting olfactory function, suggesting that targeted therapy can be developed based on the above signalling pathway and downstream molecules.

Interpretation
BNIP3 has emerged as a promising therapeutic and diagnostic target for BRCA, SARC, KIRC, and LGG, providing new insights into tumour molecular therapies in the clinic.
Health system governance assessment in protracted crisis settings: Northwest Syria
Authors: Alaref Maher , Al-Abdulla Orwa , Al Zoubi Zedoun , Al Khalil Munzer , Ekzayez Abdulkarim 
Published: August 2023

Abstract
Background
Since the withdrawal of government forces from Northwest Syria due to the conflict, several national initiatives have aimed to create alternative governance approaches to replace the central governmental system. One of the recent initiatives was the formulation of so-called ‘Central Bodies’ as institutional governance structures responsible for thematic planning and service provision; for example, the referral unit is responsible for planning and delivering medical referral services. However, the governance and administrative rules of procedures of these bodies could be immature or unsystematic. Assessing the governance of this approach cannot be condoned, especially with the urgent need for a methodical approach to strategic planning, achieving strategic humanitarian objectives, and efficiently utilizing available resources. Multiple governance assessment frameworks have been developed. However, none were created to be applied in protracted humanitarian settings. This research aims to assess the extent to which the existing health governance structure (central bodies) was capable of performing the governance functions in the absence of a legitimate government in Northwest Syria.

Methods and materials
A governance assessment framework was adopted after an extensive literature review and group discussions. Four principles for the governance assessment framework were identified; legitimacy, accountability and transparency, effectiveness and efficiency, and strategic vision. Focus Group Discussions were held to assess the levels of the selected principles on the governance thermometer scale. Qualitative and quantitative data were analyzed using NVivo 12 and SPSS 22 software programs, respectively.

Results
The level of the four principles on the governance thermometer scale was between the lowest and middle quintiles; ‘very poor or inactive’ and ‘fair and requires improvement’, respectively. The results indicate that the governance approach of Central Bodies in NWS is underdeveloped and summons comprehensive systematic development. The poor internal mechanisms, poor planning and coordination, and the absence of strategic vision were among the most frequent challenges to developing the approach.

Conclusion
Humanitarian actors and donors should pay more attention to health governance approaches and tools in protracted crises. The central bodies must improve coordination with the stakeholders and, most importantly, strategic planning. Establishing or utilizing an independent planning committee, with financial and administrative independence, is crucial to maintain and improving contextual governance mechanisms in Northwest Syria.
Quantitative proteomic and phosphoproteomic analysis reveal the relationship between mitochondrial dysfunction and cytoskeletal remodeling in hiPSC-CMs deficient in PINK1
Authors: Liu Huiwen , Wang Li , Xu Hao , Tan Bin , Yi Qin , Deng Hongrong , Chen Yunxia , He Bolin , Tian Jie , Zhu Jing 
Published: August 2023

Abstract
Background
Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are seed cells that can be used for alternative treatment of myocardial damage. However, their immaturity limits their clinical application. Mitochondrial development accompanies cardiomyocyte maturation, and PINK1 plays an important role in the regulation of mitochondrial quality. However, the role and mechanism of PINK1 in cardiomyocyte development remain unclear.

Methods
We used proteomic and phosphoproteomic to identify protein and phosphosite changes in hiPSC-CMs deficient in PINK1. Bioinformatics analysis was performed to identify the potential biological functions and regulatory mechanisms of these differentially expressed proteins and validate potential downstream mechanisms.

Results
Deletion of PINK1 resulted in mitochondrial structural breakdown and dysfunction, accompanied by disordered myofibrils arrangement. hiPSC-CMs deficient in PINK1 exhibited significantly decreased expression of mitochondrial ATP synthesis proteins and inhibition of the oxidative phosphorylation pathway. In contrast, the expression of proteins related to cardiac pathology was increased, and the phosphoproteins involved in cytoskeleton construction were significantly altered. Mechanistically, PINK1 deletion damaged the mitochondrial cristae of hiPSC-CMs and reduced the efficiency of mitochondrial respiratory chain assembly.

Conclusion
The significantly differentially expressed proteins identified in this study highlight the important role of PINK1 in regulating mitochondrial quality in hiPSC-CMs. PINK1-mediated mitochondrial respiratory chain assembly is the basis for mitochondrial function. Whereas the cytoskeleton may be adaptively altered in response to mitochondrial dysfunction caused by PINK1 deletion, inadequate energy supply hinders myocardial development. These findings facilitate the exploration of the mechanism of PINK1 in cardiomyocyte development and guide efforts to promote the maturation of hiPSC-CMs.
Gegen Qinlian decoction (GQD) inhibits ulcerative colitis by modulating ferroptosis-dependent pathway in mice and organoids
Authors: Wang Xue , Quan Jianye , Xiu Chengkui , Wang Jiali , Zhang Jiaqi 
Published: August 2023

Abstract
Background
Gegen Qinlian decoction (GQD) is a classic prescription for treating ulcerative colitis (UC) in traditional Chinese medicine. However, the therapeutic mechanism has not been fully clarified.

Purpose
In the present study, we aimed to evaluate the role of ferroptosis-mediated IEC death in UC treated mice with GQD by using DSS-induced a colitis mouse model and RSL3-induced ferroptosis in intestinal organoids.

Methods
The effects of GQD on DSS-treated colitis were examined via daily body weight, DAI, colon length, HE staining, PAS staining, ZO-1 and Occludin immunohistochemical staining. Ferroptosis was determined by analysis of iron load, MDA, GSH, mitochondrial morphology, and expression of ferroptosis-associated proteins (GPX4, SLC7A11 and ACSL4).

Results
In vivo, GQD administration reduced body weight loss and DAI scores, increased colon length, and improved intestinal histological characteristics and epithelial barrier dysfunction. GQD administration obviously improved the levels of ferroptosis markers (iron load, MDA, GSH, and mitochondrial morphology) and the expression of ferroptosis-associated proteins (GPX4, SLC7A11 and ACSL4). Consistent with in vivo results, GQD administration partially reversed the levels of mtROS, Fe2+ and MDA in intestinal organoids induced by RSL3, and notably improved morphological destruction, histological damage and epithelial barrier dysfunction in organoids.

Conclusions
In this study, we demonstrated that ferroptosis was triggered in DSS-induced experimental colitis and that GQD adiministration could protect against colonic damage and intestinal epithelial barrier dysfunction by inhibiting ferroptosis.
Evaluation of randomized controlled trials: a primer and tutorial for mental health researchers
Authors: Harrer Mathias , Cuijpers Pim , Schuurmans Lea K. J. , Kaiser Tim , Buntrock Claudia , van Straten Annemieke , Ebert David 
Published: August 2023

Abstract
Background
Considered one of the highest levels of evidence, results of randomized controlled trials (RCTs) remain an essential building block in mental health research. They are frequently used to confirm that an intervention “works” and to guide treatment decisions. Given their importance in the field, it is concerning that the quality of many RCT evaluations in mental health research remains poor. Common errors range from inadequate missing data handling and inappropriate analyses (e.g., baseline randomization tests or analyses of within-group changes) to unduly interpretations of trial results and insufficient reporting. These deficiencies pose a threat to the robustness of mental health research and its impact on patient care. Many of these issues may be avoided in the future if mental health researchers are provided with a better understanding of what constitutes a high-quality RCT evaluation.

Methods
In this primer article, we give an introduction to core concepts and caveats of clinical trial evaluations in mental health research. We also show how to implement current best practices using open-source statistical software.

Results
Drawing on Rubin’s potential outcome framework, we describe that RCTs put us in a privileged position to study causality by ensuring that the potential outcomes of the randomized groups become exchangeable. We discuss how missing data can threaten the validity of our results if dropouts systematically differ from non-dropouts, introduce trial estimands as a way to co-align analyses with the goals of the evaluation, and explain how to set up an appropriate analysis model to test the treatment effect at one or several assessment points. A novice-friendly tutorial is provided alongside this primer. It lays out concepts in greater detail and showcases how to implement techniques using the statistical software R, based on a real-world RCT dataset.

Discussion
Many problems of RCTs already arise at the design stage, and we examine some avoidable and unavoidable “weak spots” of this design in mental health research. For instance, we discuss how lack of prospective registration can give way to issues like outcome switching and selective reporting, how allegiance biases can inflate effect estimates, review recommendations and challenges in blinding patients in mental health RCTs, and describe problems arising from underpowered trials. Lastly, we discuss why not all randomized trials necessarily have a limited external validity and examine how RCTs relate to ongoing efforts to personalize mental health care.
Automating Rey Complex Figure Test scoring using a deep learning-based approach: a potential large-scale screening tool for cognitive decline
Authors: Park Jun Young , Seo Eun Hyun , Yoon Hyung-Jun , Won Sungho , Lee Kun Ho 
Published: August 2023

Abstract
Background
The Rey Complex Figure Test (RCFT) has been widely used to evaluate the neurocognitive functions in various clinical groups with a broad range of ages. However, despite its usefulness, the scoring method is as complex as the figure. Such a complicated scoring system can lead to the risk of reducing the extent of agreement among raters. Although several attempts have been made to use RCFT in clinical settings in a digitalized format, little attention has been given to develop direct automatic scoring that is comparable to experienced psychologists. Therefore, we aimed to develop an artificial intelligence (AI) scoring system for RCFT using a deep learning (DL) algorithm and confirmed its validity.

Methods
A total of 6680 subjects were enrolled in the Gwangju Alzheimer’s and Related Dementia cohort registry, Korea, from January 2015 to June 2021. We obtained 20,040 scanned images using three images per subject (copy, immediate recall, and delayed recall) and scores rated by 32 experienced psychologists. We trained the automated scoring system using the DenseNet architecture. To increase the model performance, we improved the quality of training data by re-examining some images with poor results (mean absolute error (MAE) $$\ge$$
≥
5 [points]) and re-trained our model. Finally, we conducted an external validation with 150 images scored by five experienced psychologists.

Results
For fivefold cross-validation, our first model obtained MAE = 1.24 [points] and R-squared ($${R}^{2}$$

R

2

) = 0.977. However, after evaluating and updating the model, the performance of the final model was improved (MAE = 0.95 [points], $${R}^{2}$$

R

2

= 0.986). Predicted scores among cognitively normal, mild cognitive impairment, and dementia were significantly different. For the 150 independent test sets, the MAE and $${R}^{2}$$

R

2

between AI and average scores by five human experts were 0.64 [points] and 0.994, respectively.

Conclusion
We concluded that there was no fundamental difference between the rating scores of experienced psychologists and those of our AI scoring system. We expect that our AI psychologist will be able to contribute to screen the early stages of Alzheimer’s disease pathology in medical checkup centers or large-scale community-based research institutes in a faster and cost-effective way.
Bilateral total hip arthroplasty in a case with fibrous dysplasia: a case report
Authors: Moharrami Alireza , Mirghaderi Peyman , Moazen-Jamshidi Mir Mansour , Hoseini Zare Nima , Sharifpour Sadula , Mortazavi S. M. Javad 
Published: August 2023

AbstractBackgroundFibrous dysplasia (FD) is a benign neoplasm with a broad spectrum of presentations. The treatment of FD in the hip region is controversial among orthopedic surgeons. Several treatment options exist, including curettage and grafting, valgus osteotomy, medial displacement osteotomy, and so on. Performing total hip arthroplasty (THA) on these patients and their subsequent outcome is still in infancy.Case presentationThe patient is a 32-year-old white female with bilateral proximal femur FD who underwent bilateral THA with long stem implants. A year following surgery, she had no complications and had satisfactory radiological, pain, and functional outcomes.ConclusionA bilateral THA with a long stem prosthesis showed promising results when performed following appropriate curettage of the proximal bone in an FD case. A cementless long stem could have enabled better diaphyseal fixation distal to the lesion site.
Similarity-based pairing improves efficiency of siamese neural networks for regression tasks and uncertainty quantification
Authors: Zhang Yumeng , Menke Janosch , He Jiazhen , Nittinger Eva , Tyrchan Christian , Koch Oliver , Zhao Hongtao 
Published: August 2023

AbstractSiamese networks, representing a novel class of neural networks, consist of two identical subnetworks sharing weights but receiving different inputs. Here we present a similarity-based pairing method for generating compound pairs to train Siamese neural networks for regression tasks. In comparison with the conventional exhaustive pairing, it reduces the algorithm complexity from O(n2) to O(n). It also results in a better prediction performance consistently on the three physicochemical datasets, using a multilayer perceptron with the circular fingerprint as a proof of concept. We further include into a Siamese neural network the transformer-based Chemformer, which extracts task-specific features from the simplified molecular-input line-entry system representation of compounds. Additionally, we propose a means to measure the prediction uncertainty by utilizing the variance in predictions from a set of reference compounds. Our results demonstrate that the high prediction accuracy correlates with the high confidence. Finally, we investigate implications of the similarity property principle in machine learning.
Graphical Abstract
Hepatocyte-specific Sox9 knockout ameliorates acute liver injury by suppressing SHP signaling and improving mitochondrial function
Authors: Qin Dan , Wang Rui , Ji Jinwei , Wang Duo , Lu Yuanyuan , Cao Shiyao , Chen Yaqing , Wang Liqiang , Chen Xiangmei , Zhang Lisheng 
Published: August 2023

Abstract
Background and Aims
Sex determining region Y related high-mobility group box protein 9 (Sox9) is expressed in a subset of hepatocytes, and it is important for chronic liver injury. However, the roles of Sox9+ hepatocytes in response to the acute liver injury and repair are poorly understood.

Methods
In this study, we developed the mature hepatocyte-specific Sox9 knockout mouse line and applied three acute liver injury models including PHx, CCl4 and hepatic ischemia reperfusion (IR). Huh-7 cells were subjected to treatment with hydrogen peroxide (H2O2) in order to induce cellular damage in an in vitro setting.

Results
We found the positive effect of Sox9 deletion on acute liver injury repair. Small heterodimer partner (SHP) expression was highly suppressed in hepatocyte-specific Sox9 deletion mouse liver, accompanied by less cell death and more cell proliferation. However, in mice with hepatocyte-specific Sox9 deletion and SHP overexpression, we observed an opposite phenotype. In addition, the overexpression of SOX9 in H2O2-treated Huh-7 cells resulted in an increase in cytoplasmic SHP accumulation, accompanied by a reduction of SHP in the nucleus. This led to impaired mitochondrial function and subsequent cell death. Notably, both the mitochondrial dysfunction and cell damage were reversed when SHP siRNA was employed, indicating the crucial role of SHP in mediating these effects. Furthermore, we found that Sox9, as a vital transcription factor, directly bound to SHP promoter to regulate SHP transcription.

Conclusions
Overall, our findings unravel the mechanism by which hepatocyte-specific Sox9 knockout ameliorates acute liver injury via suppressing SHP signaling and improving mitochondrial function. This study may provide a new treatment strategy for acute liver injury in future.

Graphical Abstract
Indigenous communities and influenza: protocol for a systematic review and meta-analysis
Authors: Alves D. E. , Rogeberg O. , Sattenspiel L. , Mamelund S. 
Published: August 2023

Abstract
Background
Several studies have documented that specific Indigenous groups have been disproportionately affected by previous pandemics. The objective of this paper is to describe the protocol to be used in a review and meta-analysis of the literature on Indigenous groups and influenza. Using this protocol as a guide, a future study will provide a comprehensive historical overview of pre-COVID impact of influenza on Indigenous groups by combining data from the last five influenza pandemics and seasonal influenza up to date.

Methods/principle findings
The review will include peer-reviewed original studies published in English, Spanish, Portuguese, Swedish, Danish, and Norwegian. Records will be identified through systematic literature search in eight databases: Embase, MEDLINE, CINAHL, Web of Science, Academic Search Ultimate, SocINDEX, ASSIA, and Google Scholar. Results will be summarized narratively and using meta-analytic strategies.

Discussion
To our knowledge, there is no systematic review combining historical data on the impact of both seasonal and pandemic influenza on Indigenous populations. By summarizing results within and across Indigenous groups, different countries, and historical periods, as well as research in six different languages, we aim to provide information on how strong the risk for influenza is among Indigenous groups and how consistent this risk is across groups, regions, time, and seasonal versus the specific pandemic influenza strains.

Systematic review registration
PROSPERO CRD42021246391