bluuebunny/crossref_metadata_2025_split huggingface dataset:
A reproducible and generalizable software workflow for analysis of large-scale neuroimaging data collections using BIDS Apps
Authors: Zhao Chenying , Jarecka Dorota , Covitz Sydney , Chen Yibei , Eickhoff Simon B. , Fair Damien A. , Franco Alexandre R. , Halchenko Yaroslav O. , Hendrickson Timothy J. , Hoffstaedter Felix , Houghton Audrey , Kiar Gregory , Macdonald Austin , Mehta Kahini , Milham Michael P. , Salo Taylor , Hanke Michael , Ghosh Satrajit S. , Cieslak Matthew , Satterthwaite Theodore D. 
Published: January 2024

Abstract
Neuroimaging research faces a crisis of reproducibility. With massive sample sizes and greater data complexity, this problem becomes more acute. Software that operates on imaging data defined using the Brain Imaging Data Structure (BIDS)—the BIDS App—has provided a substantial advance. However, even using BIDS Apps, a full audit trail of data processing is a necessary prerequisite for fully reproducible research. Obtaining a faithful record of the audit trail is challenging—especially for large datasets. Recently, the FAIRly big framework was introduced as a way to facilitate reproducible processing of large-scale data by leveraging DataLad—a version control system for data management. However, the current implementation of this framework was more of a proof of concept, and could not be immediately reused by other investigators for different use cases. Here, we introduce the BIDS App Bootstrap (BABS), a user-friendly and generalizable Python package for reproducible image processing at scale. BABS facilitates the reproducible application of BIDS Apps to large-scale datasets. Leveraging DataLad and the FAIRly big framework, BABS tracks the full audit trail of data processing in a scalable way by automatically preparing all scripts necessary for data processing and version tracking on high performance computing (HPC) systems. Currently, BABS supports jobs submissions and audits on Sun Grid Engine (SGE) and Slurm HPCs with a parsimonious set of programs. To demonstrate its scalability, we applied BABS to data from the Healthy Brain Network (HBN; n = 2,565). Taken together, BABS allows reproducible and scalable image processing and is broadly extensible via an open-source development model.
Communication and coordination of care for people living with HIV: a qualitative study of the patient perspective
Authors: Warner Sherridan , Cheung Daniel , Condon Ashleigh , Cunningham Juliet , Bailie Jodie , Minc Ariane , Herbert Simone , Edmiston Natalie 
Published: January 2024

Abstract
Background
There is growing consensus that primary health care (PHC) providers have an important role in providing holistic, preventative care for people living with human immunodeficiency virus (PLHIV). In regional Australia, HIV care is primarily delivered through specialist services, thus adequate coordination and communication between specialist and PHC professionals is crucial. This study aimed to explore patient experiences of the coordination of care and health care professional communication for PLHIV in regional Australia.

Methods
Semi-structured interviews with PLHIV in a regional area of Australia were conducted in March to April 2022. Interviews were conducted via video conferencing, face-to-face, or via telephone call. Interviews were audio-recorded and manually transcribed. Transcripts were coded inductively and thematic analysis was conducted to explore perspectives on communication and coordination.

Results
Thirteen participants were interviewed. Most participants were male, aged 50–70, were diagnosed with HIV more than ten years ago, and had been living in regional Australia long-term. Through qualitative analysis, themes emerged in the following areas: (1) Patient perception of care coordination; (2) Patient understanding of modality of communication; (3) Positive attitudes towards communication between healthcare professionals; and (4) Concerns for information sharing between healthcare professionals. Many participants highlighted lack of clarity around care coordination as a key issue in their healthcare, with some citing themselves as the primary care coordinator. Participants identified that coordination and communication between PHC professionals and specialist services are essential in the delivery of their health care, but some were hesitant for this to occur. Hesitancy was entrenched in some patients’ distrust of healthcare due to previous experiences of confidentiality breaches and stigma.

Conclusion
This study identifies the need for clarity in coordination between health care professionals to deliver safe and effective HIV care, which may occur through care plans. Patient support for communication between healthcare providers may be strengthened by ensuring trust in the people and systems involved. Eliminating stigma in healthcare as well as building more trustworthy electronic-based communication technologies are essential components to trust-building between PLHIV and healthcare systems.
Association between suicide attempts and anemia in late-life depression inpatients
Authors: Li Jie , Wang Lan , Wang Ziyi , Zhao Fengxue , Sun Yadi , Lu Ying , Yang Lei 
Published: January 2024

Abstract
Background
Anemia is strongly associated with late-life depression (LLD), however, few studies have investigated the relationship between anemia and suicide attempts in LLD patients. It is still challenging to predict suicide risk in patients with depression. Therefore, there is growing interest in potential biomarkers of depressive disorders and suicidal behavior, which may play a significant role in the early diagnosis and treatment of depression. This study aimed to compare serum ferritin, folate, vitamin B12, and erythrocyte parameter levels in patients with LLD with those in healthy older adults, and the relationship between serum ferritin, folate, vitamin B12, and suicide attempts in patients.

Methods
Serum ferritin, folate, vitamin B12, and erythrocyte parameter levels were measured in 66 hospitalized LLD patients (30 without suicide attempt, 36 with suicide attempt) and 47 healthy individuals. All participants were surveyed for basic conditions and suicide attempts, and depression was assessed in LLD patients.

Results
Serum ferritin, folate, vitamin B12, red blood cell count, hemoglobin, hematocrit, mean platelet volume and plateletcrit levels were significantly lower in LLD patients compared with healthy older adults (P < 0.05). Further analysis of the relationship between serum ferritin, folate, and vitamin B12 levels and LLD patients’ suicide attempts and showed a significant negative association between serum folate and vitamin B12 and suicide attempts (P < 0.05).

Conclusions
Serum ferritin, folate, vitamin B12, red blood cell count, hemoglobin, hematocrit, mean platelet volume and plateletcrit levels were significantly lower in LLD patients than in healthy older adults. In addition, reduced serum folate and vitamin B12 levels in patients may have some effect on suicide attempts. More mechanistic studies are needed to further explain this association.
T1 mapping as a quantitative imaging biomarker for diagnosing cervical cancer: a comparison with diffusion kurtosis imaging
Authors: Zhang Zanxia , Liu Jie , Zhang Yong , Qu Feifei , Grimm Robert , Cheng Jingliang , Wang Weijian , Zhu Jinxia , Li Shujian 
Published: January 2024

Abstract
Background
T1 mapping can potentially quantitatively assess the intrinsic properties of tumors. This study was conducted to explore the ability of T1 mapping in distinguishing cervical cancer type, grade, and stage and compare the diagnostic performance of T1 mapping with diffusion kurtosis imaging (DKI).

Methods
One hundred fifty-seven patients with pathologically confirmed cervical cancer were enrolled in this prospectively study. T1 mapping and DKI were performed. The native T1, difference between native and postcontrast T1 (T1diff), mean kurtosis (MK), mean diffusivity (MD), and apparent diffusion coefficient (ADC) were calculated. Cervical squamous cell carcinoma (CSCC) and adenocarcinoma (CAC), low- and high-grade carcinomas, and early- and advanced-stage groups were compared using area under the receiver operating characteristic (AUROC) curves.

Results
The native T1 and MK were higher, and the MD and ADC were lower for CSCC than for CAC (all p < 0.05). Compared with low-grade CSCC, high-grade CSCC had decreased T1diff, MD, ADC, and increased MK (p < 0.05). Compared with low-grade CAC, high-grade CAC had decreased T1diff and increased MK (p < 0.05). Native T1 was significantly higher in the advanced-stage group than in the early-stage group (p < 0.05). The AUROC curves of native T1, MK, ADC and MD were 0,772, 0.731, 0.715, and 0.627, respectively, for distinguishing CSCC from CAC. The AUROC values were 0.762 between high- and low-grade CSCC and 0.835 between high- and low-grade CAC, with T1diff and MK showing the best discriminative values, respectively. For distinguishing between advanced-stage and early-stage cervical cancer, only the AUROC of native T1 was statistically significant (AUROC = 0.651, p = 0.002).

Conclusions
Compared with DKI-derived parameters, native T1 exhibits better efficacy for identifying cervical cancer subtype and stage, and T1diff exhibits comparable discriminative value for cervical cancer grade.
Respectful maternity care in Israel during the Covid-19 pandemic: a cross-sectional study of associations between childbirth care practices and women’s perceptions of care
Authors: Palgi-Hacker Hagar , Sacks Emma , Landry Megan 
Published: January 2024

Abstract
Background
Respectful maternity care is a crucial part of quality care and is associated with better health outcomes. Early in the Covid-19 pandemic, reports from across the world indicated that infection containment measures were often implemented in ways that resulted in disrespectful care of women during facility-based childbirths in violation of evidence-based practices. This study aimed to explore the associations between childbirth care practices and perceptions of care as satisfactory and respectful among women who delivered in Israeli hospitals during the first six months of the Covid-19 pandemic.

Methods
A cross-sectional self-administered online survey was conducted to explore women’s perceptions of maternity care using an adapted version of the WHO Community Survey Tool for measuring how women are treated during facility-based childbirth. Multivariate logistic regression models evaluated the associations between sociodemographic characteristics, obstetric information, and measurements of childbirth experiences and women’s perceptions of receiving respectful and satisfactory care.

Results
The responses of 981 women were included in the analysis. While the majority of women perceived the care they received as both respectful (86.54%) and satisfactory (80.22%), almost 3 in 4 women (72.68%) reported experiencing at least one type of disrespectful care. Positive communication with the medical staff and respect for autonomy were associated with a more positive birth experience for women. Women were more likely to perceive their care as respectful if they did not feel ignored (AOR = 40.11;22.87–70.34). Perception of satisfactory care was more likely among women who had the opportunity to discuss preferences with the medical staff (AOR = 10.15; 6.93–14.86). Having Covid-19 procedures explained increased the likelihood of reporting respectful and satisfactory care (AOR = 2.89;1.91–4.36; AOR = 2.83;2.01–4).

Conclusion
Understanding which care practices are associated with women’s perceptions of care at facility-based births is critical to ensuring quality care. The findings of this study can inform future work and research aimed at enhancing respectful maternity care during times of crisis and beyond.
Evaluating the effect of recombinant human growth hormone treatment on sleep-related breathing disorders in toddlers with Prader–Willi syndrome: a one-year retrospective cohort study
Authors: Guo Haiyan , Fu Jinrong , Zhou Yufeng , Luo Feihong , Cheng Ruoqian 
Published: January 2024

Abstract
Background
Recombinant human growth hormone (rhGH) therapy is beneficial for children with Prader–Willi syndrome (PWS) in improving short stature and metabolism, but the effect of early rhGH treatment on respiratory and sleep parameters for PWS children under three years old remains elusive. Thus, this study aimed to investigate the impact of rhGH treatment on sleep-related breathing disorders (SRBDs) for toddlers with PWS.

Methods
A total of 17 age-matched PWS patients receiving rhGH treatment (rhGH group) and 17 control individuals not receiving rhGH treatment (non-rhGH group) were recruited for this study between October 2018 and January 2023. Data related to polysomnography-polygraphy (PSG) and serum levels of insulin-like growth factor (IGF-1) and insulin-like growth factor binding protein 3 (IGFBP-3) were collected.

Results
The mean age in the rhGH group was 20.76 ± 9.22 months, which was comparable to that of the non-rhGH group (25.23 ± 13.81 months). The demographic and anthropometric parameters were similar across the two groups after 52 weeks of treatment. Administration of rhGH to toddlers did not exert adverse effects on the obstructive apnea–hypopnea index (OAHI), central apnea index (CAI), oxygen desaturation index (ODI), mean percutaneous oxygen saturation (SpO2), lowest SpO2, duration when SpO2 is lower than 90%, or proportion of the patients with SpO2 lower than 90%. Furthermore, the increased IGF-1 z-score and IGFBP-3 level did not worsen SRBDs.

Conclusion
Treatment with rhGH for 52 weeks on young toddlers with PWS showed no deleterious effects on SRBDs. This shed more light on the importance of initiating rhGH therapy early in PWS patients.
Risperidone plasma level, and its correlation with CYP2D6 gene polymorphism, clinical response and side effects in chronic schizophrenia patients
Authors: Wang Xiaoyi , Huang Jing , Lu Jianjun , Li Xuemei , Tang Hui , Shao Ping 
Published: January 2024

Abstract
Background
To explore the influence of CYP2D6 genetic polymorphism on risperidone metabolism, thereby affecting risperidone’s effects and safeties in patients with chronic schizophrenia.

Methods
Sixty-nine subjects with chronic schizophrenia treated with risperidone were recruited. CYP2D6 genotypes was determined using targeted sequencing and translated into phenotype using activity system. Risperidone plasma concentrations were measured using HPLC. Positive and Negative Symptom Scale (PANSS) and Brief Psychiatric Rating Scale (BPRS) were used to evaluate the existence and severity of psychiatric symptoms, Barnes Akathisia Scale (BAS) and Extrapyramidal Symptom Rating Scale (ESRS) for neurological side effects. Metabolic and endocrine status assess were also included.

Results
The plasma drug concentrations varied hugely among individuals. Intermediate metabolizer (IM) group had higher plasma levels of RIP and dose corrected RIP concentration, RIP/9-OH-RIP ratio and C/D ratio than normal metabolizer (NM) group (p < 0.01). There was no statistic difference between responders and non-responders in dose-adjusted plasma concentrations and ratios of RIP/9-OH-RIP and C/D. The occurrence of EPS was related to active moiety levels in 4th week (p < 0.05). The prolactin (PRL) levels in two follow-ups were both significantly higher than baseline (p < 0.01). PRL change from baseline to week 4 and week 8 were both positively associated with active moiety concentration detected in week 4 (p < 0.05).

Conclusions
The risperidone plasma levels have great inter- and intraindividual variations, and are associated with the CYP2D6 phenotypes, as well as the changes in serum prolactin in patients diagnosed with chronic schizophrenia.
The mediating effect of dysmorphic concern in the association between avoidant restrictive food intake disorder and suicidal ideation in adults
Authors: Salameh Gaelle , El Khoury Nour , Hallit Rabih , Malaeb Diana , Sakr Fouad , Dabbous Mariam , Fekih-Romdhane Feten , Obeid Sahar , Hallit Souheil 
Published: January 2024

Abstract
Background
Reflecting on the existing literature on suicidal ideation and Avoidant/Restrictive Food Intake Disorder (ARFID), this article investigates the complex relationship between them, hypothesizing about the possibility of dysmorphic concerns, being a mediator linking ARFID to suicidal ideation.

Methods
Using a snowball sampling approach, a survey was created on Google Forms and circulated across messaging applications and social media networks (WhatsApp, Instagram, Messenger). The sample involved 515 participants recruited between February and March 2023. The questionnaire included the following scales: Nine-items Avoidant/Restrictive Food Intake Disorder screen (NIAS), Dysmorphic Concern Questionnaire (DCQ), and Columbia-Suicide Severity Rating Scale (C-SSRS). When filling the questionnaire, respondents were warned that they can experience distress when answering certain questions and received information about mental health services. Five hundred fifteen adults participated in this study, with a mean age of 27.55 ± 10.92 years and 60.1% females.

Results
After adjusting over potential confounders (i.e., age, education, marital status, and household crowding index), analyses showed that dysmorphic concerns fully mediated the association between avoidant restrictive eating and suicidal ideation. Higher avoidant restrictive eating was significantly associated with more dysmorphic concerns, and higher dysmorphic concerns were significantly associated with the presence of suicidal ideation. Finally, avoidant restrictive eating was not significantly associated with suicidal ideation.

Conclusion
This study highlights the potential indirect link between ARFID and suicidal ideation mediated by dysmorphic concerns. While no direct connection was observed between ARFID and suicidal ideation, the presence of dysmorphic concerns appeared to be a crucial factor in amplifying the risk of suicidal ideation in individuals with ARFID. This emphasizes the importance of addressing dysmorphic concerns alongside ARFID treatment to enhance mental health interventions and outcomes.
Psychometric properties of the Chinese version of the Exercise Self-Efficacy Scale for the Transtheoretical Model: a confirmatory analysis among Chinese children and adolescents
Authors: Yao Liying , Zhou Ke , Zhou Yanli , Kueh Yee Cheng , Liu Hongyou , Liu Zhongbiao , Pan Mingzhu , Kuan Garry 
Published: January 2024

Abstract
Background
Self-efficacy has been recognized as a critical component in people’s participation and maintenance of physical activity. This study aims to validate the Chinese version of the Exercise Self-Efficacy Scale (ESE) among Chinese children and adolescents using confirmatory factor analysis (CFA).

Methods
A cross-sectional study was conducted on two primary and two secondary schools in central China. The ESE scale was translated into Chinese (ESE-C) using the standard forward-backward translation method. Data were analyzed using Mplus 8 for the CFA.

Results
The final model showed a satisfactory level of goodness-of-fit (CFI = 0.918; TLI = 0.905; SRMR = 0.043; RMSEA = 0.066), indicating a good construct validity of the ESE-C for children and adolescents in mainland China. Furthermore, the final ESE-C model achieved composite reliability values of 0.963 and average variance extraction values of 0.597, indicating sufficient convergent and discriminant validity. Besides, the Cronbach’s alpha value was 0.964, demonstrating excellent internal consistency of the ESE-C scale.

Conclusion
The ESE-C scale is a valid instrument for assessing exercise self-efficacy among children and adolescents in mainland China.
Possible prognostic impact of PKCι genetic variants in prostate cancer
Authors: Hafeez Amna , Shabbir Maria , Khan Khushbukhat , Trembley Janeen H. , Badshah Yasmin , Zafar Sameen , Shahid Kanza , Shah Hania , Ashraf Naeem Mahmood , Hamid Arslan , Afsar Tayyaba , Almajwal Ali , Marium Afifa , Razak Suhail 
Published: January 2024

Abstract
Background
Single nucleotide polymorphisms (SNPs) have been linked with prostate cancer (PCa) and have shown potential as prognostic markers for advanced stages. Loss of function mutations in PKCι have been linked with increased risk of malignancy by enhancing tumor cell motility and invasion. We have evaluated the impact of two coding region SNPs on the PKCι gene (PRKCI) and their prognostic potential.

Methods
Genotypic association of non-synonymous PKCι SNPs rs1197750201 and rs1199520604 with PCa was determined through tetra-ARMS PCR. PKCι was docked with interacting partner Par-6 to determine the effect of these variants on PKCι binding capabilities. Molecular dynamic simulations of PKCι docked with Par-6 were performed to determine variant effects on PKCι protein interactions. The possible impact of changes in PKCι protein interactions on epithelial cell polarity was hypothesized.

Results
PKCι rs1199520604 mutant genotype TT showed association with PCa (p = 0.0055), while rs1197750201 mutant genotype AA also showed significant association with PCa (P = 0.0006). The binding interaction of PKCι with Par-6 was altered for both variants, with changes in Van der Waals energy and electrostatic energy of docked structures.

Conclusion
Genotypic analysis of two non-synonymous PKCι variants in association with PCa prognosis was performed. Both variants in the PB1 domain showed potential as a prognostic marker for PCa. In silico analysis of the effect of the variants on PKCι protein interactions indicated they may be involved in PCa progression through aberration of epithelial cell polarity pathways.
Acute caval thrombosis leading to obstructive shock in the early post insertion period of an inferior vena cava filter: a case report and literature review
Authors: Gao ShuTing , Chen YunFei , Huang YaTing , Dang YiPing , Li YiQing 
Published: January 2024

Abstract
Background
Obstructive shock is extremely rare in clinical practice and is caused by acute blood flow obstruction in the central vessels of either the systemic or pulmonary circulation. Utilizing inferior vena cava filters (IVCFs) to prevent pulmonary embolism (PE) is associated with some potential complications, such as inferior vena cava thrombosis (IVCT). Shock as a direct result of IVCT is rare. We present a case of obstructive shock secondary to extensive IVCT caused by inadequate anticoagulant therapy after the placement of an IVCF.

Case presentation
A 63-year-old male patient with a traffic accident injury presented orthopaedic trauma and lower limb deep vein thrombosis (DVT). He experienced sudden and severe abdominal pain with hypotension, tachycardia, tachypnea, oliguria and peripheral oedema 5 days after IVCF placement and 3 days after cessation of anticoagulant therapy. Considering that empirical anti-shock treatment lasted for a while and the curative effect was poor, we finally recognized the affected vessels and focused on the reason for obstructive shock through imaging findings—inferior vena cava thrombosis and occlusion. The shock state immediately resolved after thrombus aspiration. The same type of shock occurred again 6 days later during transfer from the ICU to general wards and the same treatment was administered. The patient recovered smoothly in the later stage, and the postoperative follow-up at 1, 3, and 12 months showed good results.

Conclusion
This case alerts clinicians that it is crucial to ensure adequate anticoagulation therapy after IVCF placement, and when a patient presents with symptoms such as hypotension, tachycardia, and lower limb and scrotal oedema postoperatively, immediate consideration should be given to the possibility of obstructive shock, and prompt intervention should be based on the underlying cause.