bluuebunny/crossref_metadata_2025_split huggingface dataset:
Marigold: a machine learning-based web app for zebrafish pose tracking
Authors: Teicher Gregory , Riffe R. Madison , Barnaby Wayne , Martin Gabrielle , Clayton Benjamin E. , Trapani Josef G. , Downes Gerald B. 
Published: January 2025

Abstract

Background
High-throughput behavioral analysis is important for drug discovery, toxicological studies, and the modeling of neurological disorders such as autism and epilepsy. Zebrafish embryos and larvae are ideal for such applications because they are spawned in large clutches, develop rapidly, feature a relatively simple nervous system, and have orthologs to many human disease genes. However, existing software for video-based behavioral analysis can be incompatible with recordings that contain dynamic backgrounds or foreign objects, lack support for multiwell formats, require expensive hardware, and/or demand considerable programming expertise. Here, we introduce Marigold, a free and open source web app for high-throughput behavioral analysis of embryonic and larval zebrafish.

Results
Marigold features an intuitive graphical user interface, tracks up to 10 user-defined keypoints, supports both single- and multiwell formats, and exports a range of kinematic parameters in addition to publication-quality data visualizations. By leveraging a highly efficient, custom-designed neural network architecture, Marigold achieves reasonable training and inference speeds even on modestly powered computers lacking a discrete graphics processing unit. Notably, as a web app, Marigold does not require any installation and runs within popular web browsers on ChromeOS, Linux, macOS, and Windows. To demonstrate Marigold’s utility, we used two sets of biological experiments. First, we examined novel aspects of the touch-evoked escape response in techno trousers (tnt) mutant embryos, which contain a previously described loss-of-function mutation in the gene encoding Eaat2b, a glial glutamate transporter. We identified differences and interactions between touch location (head vs. tail) and genotype. Second, we investigated the effects of feeding on larval visuomotor behavior at 5 and 7 days post-fertilization (dpf). We found differences in the number and vigor of swimming bouts between fed and unfed fish at both time points, as well as interactions between developmental stage and feeding regimen.

Conclusions
In both biological experiments presented here, the use of Marigold facilitated novel behavioral findings. Marigold’s ease of use, robust pose tracking, amenability to diverse experimental paradigms, and flexibility regarding hardware requirements make it a powerful tool for analyzing zebrafish behavior, especially in low-resource settings such as course-based undergraduate research experiences. Marigold is available at: https://downeslab.github.io/marigold/.
Impact of kidney volume on incidence of in-hospital kidney-related adverse outcomes in patients with acute heart failure
Authors: Saito Akira , Asano Taku , Komiyama Nobuyuki , Ohde Sachiko 
Published: January 2025

Abstract

Background
Recent studies revealed an association between small kidney volume and progression of kidney dysfunction in particular settings such as kidney transplantation and transcatheter aortic valve implantation. We hypothesized that kidney volume was associated with the incidence of kidney-related adverse outcomes such as worsening renal function (WRF) in patients with acute heart failure (AHF).

Methods
This study was a single-center retrospective cohort study. It included patients admitted for AHF treatment between 2011 and 2021 and who underwent computed tomography (CT) that included images of the kidneys on the date of admission. We measured the volume of the right and left kidneys using dedicated volume analyzing software for 3D-CT (SYNAPSE VINCENT, Fuji Film, Tokyo, Japan) and determined the total kidney volume by adding the volumes of the left and right kidneys. We defined the composite of death from any cause, initiating renal replacement therapy, and WRF during hospitalization as major adverse kidney events (MAKE). We conducted multivariate logistic regression analysis to evaluate the impact of MAKE and each component of MAKE adjusted for age, sex, body surface area, estimated Glomerular Filtration Rate (eGFR) on admission date and the factors that were significantly associated with the incidence of MAKE by bivariate analysis.

Results
In the 229 patients enrolled in the analysis, death from any cause, initiating RRT, and WRF occurred in 30 (13.1%), 10 (4.4%), and 85 (37.3%) patients, respectively. It was found that small kidney volume (≤ 250 ml) was independently associated with the increased incidence of MAKE (odds ratio 3.92, 95% confidence interval [1.18–13.08], p = 0.026) and WRF (odds ratio 6.58, 95%confidence interval [1.85–23.42] p = 0.004). The area under the receiver operating characteristic curve for multivariate logistic regression analysis of MAKE was 0.71.

Conclusions
Kidney volume on admission was independently associated with the increased incidence of kidney-related adverse outcomes during hospitalization in patients with AHF.
Identification of patient demographic, clinical, and SARS-CoV-2 genomic factors associated with severe COVID-19 using supervised machine learning: a retrospective multicenter study
Authors: Nirmalarajah Kuganya , Aftanas Patryk , Barati Shiva , Chien Emily , Crowl Gloria , Faheem Amna , Farooqi Lubna , Jamal Alainna J. , Khan Saman , Kotwa Jonathon D. , Li Angel X. , Mozafarihashjin Mohammad , Nasir Jalees A. , Shigayeva Altynay , Yim Winfield , Yip Lily , Zhong Xi Zoe , Katz Kevin , Kozak Robert , McArthur Andrew G. , Daneman Nick , Maguire Finlay , McGeer Allison J. , Duvvuri Venkata R. , Mubareka Samira 
Published: January 2025

Abstract

Background
Drivers of COVID-19 severity are multifactorial and include multidimensional and potentially interacting factors encompassing viral determinants and host-related factors (i.e., demographics, pre-existing conditions and/or genetics), thus complicating the prediction of clinical outcomes for different severe acute respiratory syndrome coronavirus (SARS-CoV-2) variants. Although millions of SARS-CoV-2 genomes have been publicly shared in global databases, linkages with detailed clinical data are scarce. Therefore, we aimed to establish a COVID-19 patient dataset with linked clinical and viral genomic data to then examine associations between SARS-CoV-2 genomic signatures and clinical disease phenotypes.

Methods
A cohort of adult patients with laboratory confirmed SARS-CoV-2 from 11 participating healthcare institutions in the Greater Toronto Area (GTA) were recruited from March 2020 to April 2022. Supervised machine learning (ML) models were developed to predict hospitalization using SARS-CoV-2 lineage-specific genomic signatures, patient demographics, symptoms, and pre-existing comorbidities. The relative importance of these features was then evaluated.

Results
Complete clinical data and viral whole genome level information were obtained from 617 patients, 50.4% of whom were hospitalized. Notably, inpatients were older with a mean age of 66.67 years (SD ± 17.64 years), whereas outpatients had a mean age of 44.89 years (SD ± 16.00 years). SHapley Additive exPlanations (SHAP) analyses revealed that underlying vascular disease, underlying pulmonary disease, and fever were the most significant clinical features associated with hospitalization. In models built on the amino acid sequences of functional regions including spike, nucleocapsid, ORF3a, and ORF8 proteins, variants preceding the emergence of variants of concern (VOCs) or pre-VOC variants, were associated with hospitalization.

Conclusions
Viral genomic features have limited utility in predicting hospitalization across SARS-CoV-2 diversity. Combining clinical and viral genomic datasets provides perspective on patient specific and virus-related factors that impact COVID-19 disease severity. Overall, clinical features had greater discriminatory power than viral genomic features in predicting hospitalization.
Addressing racial and ethnic disparities in premature exits from permanent supportive housing among residents with substance use disorders
Authors: Panadero Talia J. , Gabrielian Sonya , Seamans Marissa J. , Gelberg Lillian , Tsai Jack , Harris Taylor 
Published: January 2025

Abstract

Background
Permanent supportive housing (PSH) is an evidence-based practice for reducing homelessness that subsidizes permanent, independent housing and provides case management—including linkages to health services. Substance use disorders (SUDs) are common contributing factors towards premature, unwanted (“negative”) PSH exits; little is known about racial/ethnic differences in negative PSH exits among residents with SUDs. Within the nation’s largest PSH program at the Department of Veterans Affairs (VA), we examined relationships among SUDs and negative PSH exits (for up to five years post-PSH move-in) across racial/ethnic subgroups.

Methods
We used VA administrative data to identify a cohort of homeless-experienced Veterans (HEVs) (n = 2,712) who were housed through VA Greater Los Angeles’ PSH program from 2016–2019. We analyzed negative PSH exits by HEVs with and without SUDs across racial/ethnic subgroups (i.e., African American/Black, Non-Hispanic White, Hispanic/Latino, and Other/Mixed [Asian, American Indian or Alaskan Native, and Native Hawaiian or Other Pacific Islander, and mixed race/ethnicity]) in controlled models and accounting for competing risk of death.

Results
In competing risk models, HEVs with at least one SUD had 1.3 times the hazard of negative PSH exits compared to those without SUDs (95% CI: 1.00, 1.61). When stratifying by race/ethnicity, Other/Mixed race residents with at least one SUD had 6.4 times the hazard of negative PSH exits compared to their peers without SUDs (95% CI: 1.61–25.50). Hispanic/Latino residents with at least one SUD had 1.9 times the hazard compared to those without SUDs; however, this association was not statistically significant (95% CI: 0.85–4.37). African American/Black residents with at least one SUD had 1.2 times the hazard compared to those without SUDs (95% CI: 0.85–1.64), indicating no evidence of an association with negative PSH exits. Non-Hispanic White residents with at least one SUD had 1.1 times the hazard compared to those without SUDs (95% CI: 0.75–1.66), similarly indicating no evidence to suggest an association with negative PSH exits.

Conclusions
These findings suggest relationships between SUDs and negative PSH exits differ between racial/ethnic groups and suggest there may be value in culturally specific tailoring and implementation of SUD services for these subgroups.
Experiences, perceptions and ethical considerations of the malaria infection study in Thailand
Authors: Naemiratch Bhensri , Kulpijit Natinee , Ruangkajorn Supanat , Day Nicholas P. J. , Prachumsri Jetsumon , Cheah Phaik Yeong 
Published: January 2025

Abstract

Background
Thailand has made significant progress in malaria control efforts in the past decade, with a decline in the number of reported cases. However, due to cross-border movements over the past 5 years, reported malaria cases in Thailand have risen. The Malaria Infection Study in Thailand (MIST) involves deliberate infection of healthy volunteers with Plasmodium vivax malaria parasites, and the assessment of the efficacy of potential vaccine and drug candidates in order to understand acquired protection against malaria parasites.

Methods
This paper drew from ethics and social science qualitative study called MIST-ETHICS embedded within the MIST studies. MIST-ETHICS aimed to describe and understand the experiences, perceptions and ethical considerations of the MIST studies. Data were obtained from semi-structured interviews and a focus group discussion. A total of 46 participants participated in MIST-ETHICS .

Results
Three major themes emerged: experiences and perceptions of MIST, reasons for joining MIST, and ethical considerations. We found that although compensation was a motivation for participation, this was secondary to it being beneficial to self (health checks; link to health networks; building merit) and others (medical research contribution; altruism). Participants expressed varied opinions regarding the requirement of a university degree as one of the inclusion criteria for MIST.

Conclusions
Our study revealed widespread concerns about long-term health effects and safety. Ethical considerations, including obtaining valid informed consent and ensuring participant inclusivitiy, were deem essential. Despite some debate regarding eligibility criteria, most participants agreed that the informed consent process was robust, accompanied by a strong sense of responsibility to contribute to the greater good. We emphasize the importance of continuously gathering participants’ feedback for quality control, such as improving information materials to clarify the purpose of initial phases, their contributing to later phases, and the rationale behind each selection criterion.

Trial registration
This manuscript is part of the clinical trials registered under ClinicalTrials.gov IDs NCT04083508 (MIST1) registered on 5 Sep 2019 and NCT05071079 (MIST2) registered on 28 July 2021. However, the manuscript pertains to a qualitative study that does not require trial registration.
Knowledge and attitude of nosocomial infection prevention and control precautions among healthcare personnel at Kiruddu Referral Hospital in Kampala, Uganda
Authors: Ekakoro Newton , Nakayinga Ritah , Kaddumukasa Martha A. , Mbatudde Maria 
Published: January 2025

Abstract

Background
A key concern for global public health is nosocomial infections. Essential to the fight against nosocomial infection, is healthcare professionals’ knowledge and attitudes. Therefore, this study investigated healthcare professionals’ knowledge and attitudes toward nosocomial infection at the Kiruddu Referral Hospital, Kampala, Uganda.

Methods
A facility-based cross-sectional study was carried out at Kiruddu Referral Hospital in Kampala, Uganda. We selected the participants using simple random sampling. Data were collected from a total of 78 healthcare personnel using pretested, structured, self-administered questionnaires. We used SPSS version 20.0 for data analysis and applied descriptive statistics to present the frequencies and percentages. Pearson’s Chi-square test was used to evaluate the association between independent factors and knowledge and attitude (KA) ratings on hospital-acquired infection (HAI) prevention. P-values less than 0.05 were regarded as statistically significant.

Results
Among the different categories of health workers, doctors exhibited the highest level of knowledge. There was a significant association between knowledge scores and occupation (χ2LR = 25.610; P = 0.000). The mean knowledge scores across different infection prevention aspects were as follows: hand hygiene (82.2 ± 18.9), PPE use (71.8 ± 23.1), sharp disposal and sharp injuries (59.2 ± 25.7), and waste management (57.4 ± 29.9). Notably, 20.5% of participants did not change PPE between patients, and 44.9% indicated that their workload negatively impacted their ability to follow infection prevention standards.

Conclusion
The study highlighted gaps in healthcare personnel’s knowledge and attitudes toward infection prevention. It is therefore important to provide regular targeted training programs emphasizing underrepresented areas, PPE availability, strengthen policy enforcement, and integrate infection prevention education into medical and nursing curricula.
Inhibition of NLRP3 enhances pro-apoptotic effects of FLT3 inhibition in AML
Authors: Sieberer Helene , Luciano Michela , Amend Diana , Blöchl Constantin , Eglseer Anna , Steinkellner Alina , Rieser Sebastian , Andosch Ancuela , Steiner Philip , Hummer Laura , Krenn Peter W. , Dang Hieu-Hoa , Huber Christian G. , Aberger Fritz , Neuper Theresa , Horejs-Hoeck Jutta 
Published: January 2025

Abstract
FLT3 mutations occur in approximately 25% of all acute myeloid leukemia (AML) patients. While several FLT3 inhibitors have received FDA approval, their use is currently limited to combination therapies with chemotherapy, as resistance occurs, and efficacy decreases when the inhibitors are used alone. Given the highly heterogeneous nature of AML, there is an urgent need for novel targeted therapies that address the disease from multiple angles. Recent research has identified the NLRP3 inflammasome as a potential new driver in AML. Here, we investigated the efficacy of different NLRP3 inhibitors in targeting AML cells in vitro. Our findings reveal that NLRP3 inhibition induces cell cycle arrest as well as signs of senescence in multiple AML cell lines. In contrast, NLRP3 inhibition selectively induced apoptosis in FLT3 mutant AML cell lines, but not in FLT3 wild-type AML cells. Moreover, we show that NLRP3 inhibition impairs FLT3 signaling by reducing both FLT3 expression as well as downstream signaling in FLT3 mutant cells. A database analysis revealed a strong positive correlation between FLT3 and NLRP3 in cancer, which was particularly evident in AML patients. Strikingly, the simultaneous inhibition of NLRP3 and FLT3 markedly enhanced apoptosis in FLT3-ITD mutant AML cells, but not in FLT3 wild-type cells. In summary, this study reveals a promising combined therapeutic strategy specifically targeting NLRP3/FLT3-ITD positive AML blasts in vitro, highlighting a potential new avenue for AML treatment.
Gastrointestinal complications of hepatic glycogen storage disease: a national survey questionnaire study in China
Authors: Zhang Xiaoyan , Su Zexiong , Wu Jiaxing , Zeng Hanshi , Jiang Xun , Wang Ying , Shen Huiqing , Xie Xiaoli , Xiao Yuan , Tang Qing , Luo Xiaoping , Zhong Xuemei , Chen Huan , Lan Jiaoli , Chen Yongxin , Zeng Xiaolu , Zhang Huiqiong , Li Zhiling , Zhang Yuxin , Yang Min 
Published: January 2025

Abstract

Background
Hepatic glycogen storage diseases (GSD) are inborn errors of metabolism with abnormal storage or utilization of glycogen, a complex disease with significant genetic heterogeneity and similar clinical manifestations. This study aimed to describe the gastrointestinal symptoms and endoscopic features of hepatic GSD, including types Ia, Ib, III, VI, and IX, to provide evidence for etiology and treatment.

Methods
A national cohort survey questionnaire was distributed to patients diagnosed with GSD type Ia, Ib, III, VI, and IX through genetic testing or their parents in mainland China in May 2022. Expert gastroendoscopists performed endoscopic examinations and evaluations in 10 hospitals. Descriptive statistics were used for analysis.

Results
A total of 315 patients with hepatic GSD were included in the study, including 191 males and 124 females, the median age at diagnosis was 1.42 years (range = 0.08–36.08 years), with a median age of 5.42 years at the time of investigation (range = 0.58–38.08 years). 95% of patients relied on uncooked corn starch (UCCS) for blood glucose maintenance, and the median age of initiation was 18.5 months (range = 4-360 months). The common characteristics of these GSDs were hypoglycemia, lactic acidosis, anemia, liver enlargement, hyperlipidemia, hyperuricemia, and weakness. More than 60% of patients reported gastrointestinal symptom including anorexia, nausea/vomiting, abdominal pain, abdominal bloating, diarrhea, and mucus or bloody stool. The incidence of gastrointestinal symptoms in patients with GSD type Ia, Ib, III, VI and IX were 68%, 68%, 48%, 59% and 48%, respectively. A total of 48 GSD patients underwent gastroenteroscopy, 54% (26/48, 24 patients with type Ib, 1 patient with type Ia and 1 with III) were diagnosed with GSD-associated inflammatory bowel disease (IBD), the endoscopic images showed mucosal edema, erythema, erosions, single or scattered multiple large, deep, round ulcers and strictures, without linear ulcers and cobblestone mucosal lesions.

Conclusion
Patients with GSD type Ia, Ib, III, VI and IX had different degrees of gastrointestinal complications, among which patients with type Ia, Ib and III were the most prominent, and the proportion of GSD-Ib patients had a higher proportion of GSD-associated IBD.
Evaluating Computerised Assessment of Motor Imitation (CAMI) for identifying autism-specific difficulties not observed for attention-deficit hyperactivity disorder or neurotypical development
Authors: Santra Romila , Pacheco Carolina , Crocetti Deana , Vidal René , Mostofsky Stewart H. , Tunçgenç Bahar 
Published: January 2025

Background
Reliable and specific biomarkers that can distinguish autism spectrum disorders (ASDs) from commonly co-occurring attention-deficit/hyperactivity disorder (ADHD) are lacking, causing misses and delays in diagnosis, and reducing access to interventions and quality of life.

Aims
To examine whether an innovative, brief (1-min), videogame method called Computerised Assessment of Motor Imitation (CAMI), can identify ASD-specific imitation differences compared with neurotypical children and children with ADHD.

Method
This cross-sectional study used CAMI alongside standardised parent-report (Social Responsiveness Scale, Second Edition) and observational measures of autism (Autism Diagnostic Observation Schedule-Second Edition; ADOS-2), ADHD (Conners) and motor ability (Physical and Neurological Examination for Soft Signs). The sample comprised 183 children aged 7–13 years, with ADHD (without ASD), with ASD (with and without ADHD) and who were neurotypical.

Results
Regardless of co-occurring ADHD, children with ASD showed poorer CAMI performance than neurotypical children (P < 0.0001; adjusted R2 = 0.28), whereas children with ADHD and neurotypical children showed similar CAMI performance. Receiver operating curve and support vector machine analyses showed that CAMI distinguishes ASD from both neurotypical children (80% true positive rate) and children with ADHD (70% true positive rate), with a high success rate significantly above chance. Among children with ASD, poor CAMI performance was associated with increased autism traits, particularly ADOS-2 measures of social affect and restricted and repetitive behaviours (adjusted R2 = 0.23), but not with ADHD traits or motor ability.

Conclusions
Four levels of analyses confirm that poor imitation measured by the low-cost and scalable CAMI method specifically distinguishes ASD not only from neurotypical development, but also from commonly co-occurring ADHD.