bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondria-targeting siRNA screening identifies mitochondrial calcium uniporter as a factor involved in nucleoid morphology
Authors: Kanon Hirotaka , Ishihara Takaya , Ban-Ishihara Reiko , Ota Azusa , Yasuda Tatsuki , Ichikawa Aoi , Ueyama Ruo , Baba Taiki , Takeda Kohsuke , Ogasawara Emi , Ishihara Naotada 
Published: February 2025

Abstract
Mitochondria are believed to have originated from the endosymbiosis of bacteria and they still contain their own genome, which is called mitochondrial DNA (mtDNA). Under fluorescence microscopy of cultured mammalian cells, mtDNA is observed as numerous tiny dot-like structures called mitochondrial nucleoids. In live-imaging, the morphology and distribution of nucleoids are change dynamically, but the molecular details remain poorly understood. In this study, we constructed a custom siRNA library targeting 1,164 human mitochondria-related genes, and from live-imaging-based screening of HeLa cells, we identified that mitochondria calcium uniporter (MCU), a pore-forming subunit of the mitochondrial Ca2+ channel, is involved in nucleoid morphology. We found that suppression of MCU by RNAi induced the formation of highly enlarged nucleoids as well as respiratory dysfunction and that the re-introduction of MCU or treatment with Ca2+ ionophore recovered the enlarged nucleoid morphology. These results suggest that mitochondrial Ca2+ uptake via MCU is associated with nucleoid morphology. The constructed siRNA library might be widely applied to analyze the roles of mitochondrial proteins in various cellular events, making it useful to understand the multifaceted functions of mitochondria in human cells.
Insight into the bacterial communities in the sediment–water interface across different salinities of Pacific White shrimp, Penaeus vannamei, by metabarcoding
Authors: Lalitha Natarajan , Katneni Vinaya Kumar , Jangam Ashok Kumar , Suganya Panjan Nathamuni , Sukumaran Suvana , Muralidhar Moturi 
Published: February 2025

Abstract
Microbes play an important role in the food chain by metabolizing organic matter, cycling nutrients, and maintaining a dynamic equilibrium among organisms in water and sediment. The objective is to study the fluctuating taxonomic microbial diversity profile in the sediment–water interface at different days of culture (DOC) of Penaeus vannamei in varying salinities using the Illumina MiSeq platform. Sediment samples were collected in Tamil Nadu, India, from low-saline, brackish water, and high-saline ponds at 30, 60, and 90 DOC. Bacterial richness and diversity in species were high in low-saline ponds. Beta-diversity variation indicated more differences in bacterial composition in high- and low-saline ponds. The predominant phyla observed were Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, and Cyanobacteria. High-saline ponds accounted for more nitrification bacterial communities, sulfur-reducing bacterial communities, sulfur-oxidizing bacterial communities, and high redox potential, whereas denitrification bacterial communities were high in brackish water ponds.
Learn from AI: The pursuit of objectivity
Authors: Wang Fengyi , Marouli Angeliki , Charoenwongwatthana Pisit , Chang Chien-Yi 
Published: February 2025

Abstract
Humans continuously face threats from emerging novel pathogens and antimicrobial resistant bacteria or fungi, which requires urgently and efficient solutions. Alternatively, microbes also produce compounds or chemicals highly valuable to humans of which require continuous refinement and improvement of yields. Artificial intelligence (AI) is a promising tool to search for solutions combatting against diseases and facilitating productivity underpinned by robust research providing accurate information. However, the extent of AI credibility is yet to be fully understood. In terms of human bias, AI could arguably act as a means of ensuring scientific objectivity to increase accuracy and precision, however, whether this is possible or not has not been fully discussed. Human bias and error can be introduced at any step of the research process including conducting experiments and data processing, through to influencing clinical applications. Despite AI's contribution to advance knowledge, the question remains, is AI able to achieve objectivity in microbiological research? Here, the benefits, drawbacks and responsibilities of AI utilization in microbiological research and clinical applications were discussed.
A possible trail of dust from a young, highly extincted brown dwarf in the outskirts of the Trapezium Cluster
Authors: Haworth Thomas J , McCaughrean Mark J , Pearson Samuel G , Booth Richard A 
Published: February 2025

ABSTRACT
We present the JWST discovery of a highly extincted ($A_V\sim 52$) candidate brown dwarf (${\sim} 0.018$ M$_\odot$) in the outskirts of the Trapezium Cluster that appears to be coincident with the end of a ${\sim} 1700$ au long, remarkably uniformly wide, dark trail that broadens only slightly at the end opposite the point source. We examine whether a dusty trail associated with a highly extincted brown dwarf could plausibly be detected with JWST and explore possible origins. We show that a dusty trail associated with the brown dwarf could be observable if dust within it is larger than that in the ambient molecular cloud. For example, if the ambient cloud has a standard ${\sim} 0.25$ $\mu$m maximum grain size and the trail contains micron-sized grains, then the trail will have a scattering opacity over an order of magnitude larger compared to the surroundings in NIRCam short-wavelength filters. We use a simple model to show that a change in maximum grain size can reproduce the high $A_V$ and the multifilter NIRCam contrast seen between the trail and its surroundings. We propose and explore two possible mechanisms that could be responsible for the trail: (i) a weak far ultraviolet radiation-driven wind from the circum-brown dwarf disc due to the O stars in the region and (ii) a Bondi–Hoyle–Lyttleton accretion wake. The former would be the most distant known case of the Trapezium stars’ radiation driving winds from a disc, and the latter would be the first known example of ‘late’ infall from the interstellar medium on to a low-mass object in a high-mass star-forming region.
Telemedicine as an alternative to in-person care in the field of rheumatic diseases: A systematic scoping review
Authors: Sada Ken-ei , Iwata Shigeru , Inoue Yuzaburo , Tanaka Eiichi , Nishida Keiichiro , Kawahito Yutaka , Abe Asami , Kawakami Atsushi , Miyamae Takako 
Published: February 2025

ABSTRACT

Objective
The COVID-19 pandemic prompted the widespread adoption of telemedicine as an alternative to in-person care. This systematic scoping review evaluated the effectiveness, cost-efficiency, and challenges of telemedicine for patients with rheumatic diseases.

Methods
A comprehensive search of the MEDLINE database was conducted using specific terms related to rheumatoid or juvenile arthritis, and telemedicine. The literature search included studies published up to March, 2024. In this review, we only considered studies assessing telemedicine as an alternative to in-person care.

Results
The search, conducted on 15 March 2024, generated 258 references. Eight reports from three randomized controlled trials and three observational studies were included. Randomized controlled trials have shown that the outcomes of telemedicine intervention are comparable to those of in-person care in terms of disease activity, functional status, and quality of life, while enabling fewer outpatient visits and cost-effectiveness. However, the high dropout rates highlight the importance of patient preferences and comprehensive education. Observational studies revealed similar findings but were limited by a high confounding bias.

Conclusion
Telemedicine offers economic advantages and maintains clinical outcomes comparable to those of in-person care. Its success depends on structured patient education and alignment with patient preferences. Further research is required, particularly in the context of healthcare in Japan.
Endometrial zinc transporter Slc39a10/Zip10 is indispensable for progesterone responsiveness and successful pregnancy in mice
Authors: Kawata Yui , Terakawa Jumpei , Takeshita Ayuu , Namiki Takafumi , Kageyama Atsuko , Noguchi Michiko , Murakami Hironobu , Fukada Toshiyuki , Ito Junya , Kashiwazaki Naomi 
Published: February 2025

Abstract
Zinc is a critical trace element that is important for various biological functions including male and female reproductive systems, but the molecular mechanisms that underlie fertility have been unclear. We show here that zinc signaling in the endometrial tissue is indispensable for successful pregnancy in mice. We observed that a uterine-specific genetic deletion of Slc39a10/Zip10, which encodes one of the zinc transporters to elevate the cytoplasmic level of zinc, results in female infertility due to failure of embryo invasion into the endometrium and subsequent embryonic loss. Zip10 mRNA is expressed in uterine tissues, especially in the decidualizing stromal cells during embryo implantation. The absence of ZIP10 leads to attenuation of progesterone–progesterone receptor (PGR) signals between the epithelium and the stroma, including abnormal expression of the PGR and its target molecules in both the epithelium and stroma in vivo. We found that depletion of intracytoplasmic zinc ions due to loss of ZIP10 disrupts the change in nuclear-to-cytoplasmic localization of GLI1, which is critical for PGR signaling in the decidualizing stromal cells in vitro not only in mice but also in humans. Our findings (i) highlight a biological relevance of ZIP10-mediated zinc homeostatic regulation in the establishment of a successful pregnancy and (ii) will help to prevent infertility in humans.
Effect of Vitamin D Deficiency on Development of Slipped Capital Femoral Epiphysis
Authors: Torres-Izquierdo Beltran , Galan-Olleros Maria , Momtaz David , Mittal Mehul M. , Gonuguntla Rishi , Tippabhatla Abhishek , Hosseinzadeh Pooya 
Published: February 2025

Objective:
Slipped capital femoral epiphysis (SCFE) is one of the most common hip disorders in adolescents, often linked to obesity. However, other factors, such as vitamin D deficiency, may also contribute to SCFE development. This study investigates the impact of vitamin D deficiency on SCFE development in a large cohort.

Methods:
We utilized the TriNetX national database to query pediatric patients with documented calcidiol levels. Patients with a recorded visit below the age of 9 and subsequent documented calcidiol levels were followed until SCFE occurrence or age 18. Patients were categorized into vitamin D adequate (≥ 30 ng/mL) and deficient (< 30 ng/mL) groups. Propensity score matching was performed using a multivariable logistic regression model to adjust for baseline characteristics, including age, sex, race, and body mass index percentile. Significance testing was conducted using the Fisher exact test and χ2 tests to compare SCFE risk between the cohorts, with a significance level set at P <0.05.

Results:
On preliminary analysis, 98,045 patients met the inclusion criteria. After matching, 34,552 individuals in both vitamin D deficient and adequate groups were included, with an average age of 8.4 years at the time of their first visit and 50% females. SCFE occurred in 136 (0.39%) and 48 (0.14%) patients in the vitamin D deficient and adequate groups, respectively (P < 0.0001). Vitamin D deficiency significantly increased SCFE risk, with a relative risk of 2.8 (95% CI: 2-3.9; P < 0.0001) and a hazard ratio of 1.6 (95% CI: 1.1-2.2; P < 0.0001).

Conclusion:
This study, one of the largest to date, establishes a significant association between vitamin D deficiency and SCFE development. After controlling for potential confounding variables, including body mass index, individuals with vitamin D deficiency were ∼2.83 times more likely to develop SCFE. The study findings highlight the need for further research to evaluate whether supplementation could mitigate this risk of developing SCFE.

Level of Evidence:
Level III.
Effect of Rectal Cancer Treatment Timing Standardization on Patient Outcomes
Authors: Sun James , Fredette Jordan D. , Hasler Jill S. , Vu Joceline V. , Philp Matthew , Poggio Juan L. , Porpiglia Andrea S. , Greco Stephanie H. , Reddy Sanjay S. , Farma Jeffrey M. , Villano Anthony M. 
Published: February 2025

Objectives:
The National Accreditation Program for Rectal Cancer (NAPRC) was established in 2017 to decrease rectal cancer treatment variation and improve oncologic outcomes. Initiating curative intent treatment <60 days of first evaluation is one NAPRC standard. We evaluated whether oncologic outcomes improved with timely treatment and factors associated with its receipt.

Methods:
Using the NCDB, we identified stage I to III rectal cancer patients treated from 2004 to 2020 treated with curative-intent surgery. Patients were stratified into 2 cohorts (timely [<60 d], delayed [≥60 d]) for survival analysis and exploration of variables associated with timely treatment.

Results:
We included 117,459 patients with a median age of 61 years (interquartile range: 52 to 70 y). Most patients were male (61.1%), White (86.2%), Charlson 0 (77.1%) with stage II (33.5%) or III (44.3%) cancer treated with chemoradiation (58.1%), or surgery (27.0%) first. Timely treatment was associated with improved overall survival (OS; median OS: 153.26 vs. 128.59 m). Patients in the highest income bracket (odds ratio [OR] 1.30) with stage II (OR: 1.27) or III (OR: 1.50) cancer receiving neoadjuvant chemotherapy (OR: 2.24) or chemoradiation (OR: 1.73) as the first treatment received more timely treatment. Patients with Charlson ≥2 (OR: 0.83) of Black (OR: 0.56) or Hispanic (OR: 0.73) race received more delayed treatment (all P<0.01).

Conclusions:
Timely rectal cancer treatment is associated with improved survival. Socioeconomic disparities limit timely treatment with attendant worse survival, supporting national homogenization of care. As multimodal care for rectal cancer becomes increasingly complex, timely treatment remains paramount.
Racial residential segregation is associated with ambient air pollution exposure after adjustment for multilevel sociodemographic factors: Evidence from eight US-based cohorts
Authors: Zewdie Hiwot Y. , Fahey Carolyn A. , Harrington Anna L. , Hart Jaime E. , Biggs Mary L. , McClure Leslie A. , Whitsel Eric A. , Kaufman Joel D. , Hajat Anjum 
Published: February 2025

Objective:
We examined if racial residential segregation (RRS) – a fundamental cause of disease – is independently associated with air pollution after accounting for other neighborhood and individual-level sociodemographic factors, to better understand its potential role as a confounder of air pollution-health studies.

Methods:
We compiled data from eight large cohorts, restricting to non-Hispanic Black and White urban-residing participants observed at least once between 1999 and 2005. We used 2000 decennial census data to derive a spatial RRS measure (divergence index) and neighborhood socioeconomic status (NSES) index for participants’ residing Census tracts, in addition to participant baseline data, to examine associations between RRS and sociodemographic factors (NSES, education, race) and residential exposure to spatiotemporal model-predicted PM2.5 and NO2 levels. We fit random-effects meta-analysis models to pool estimates across adjusted cohort-specific multilevel models.

Results:
Analytic sample included eligible participants in CHS (N = 3,605), MESA (4,785), REGARDS (22,649), NHS (90,415), NHSII (91,654), HPFS (32,625), WHI-OS (77,680), and WHI-CT (56,639). In adjusted univariate models, a quartile higher RRS was associated with 3.73% higher PM2.5 exposure (95% CI: 2.14%, 5.32%), and an 11.53% higher (95% CI: 10.83%, 12.22%) NO2 exposure on average. In fully adjusted models, higher RRS was associated with 3.25% higher PM2.5 exposure (95% CI: 1.45%, 5.05%; P < 0.05) and 10.22% higher NO2 exposure (95% CI: 6.69%, 13.74%; P < 0.001) on average.

Conclusions:
Our findings indicate that RRS is associated with the differential distribution of poor air quality independent of NSES or individual race, suggesting it may be a relevant confounder to be considered in future air pollution epidemiology studies.
Thromboelastometry and two activated clotting tests in detecting residual heparin after protamine in cardiac surgical patients
Authors: Moilanen Janne , Pada Marika , Ohtonen Pasi , Kaakinen Timo , Taskinen Panu , Savolainen Eeva-Riitta , Erkinaro Tiina 
Published: February 2025

BACKGROUND
After cardiac surgery, complete heparin reversal with protamine is essential. Accordingly, there is a need for an accurate and precise point-of-care device to detect possible residual heparin after protamine administration.

OBJECTIVES
To compare two different activated clotting time (ACT) tests and thromboelastometry in detecting postprotamine heparin activity after cardiac surgery.

DESIGN
A single-centre prospective, observational study.

SETTING
University Hospital from September 2021 to February 2023.

PARTICIPANTS
Fifty-five adult, elective cardiac surgical patients.

INTERVENTIONS
The ACT-LR and ACT+ tests of Hemochron Signature Elite device, and the coagulation time (CT) ratio from INTEM and HEPTEM tests of ROTEM Sigma device, were analysed after protamine administration and compared to baseline values.

MAIN OUTCOME MEASURES
Based on postprotamine antifactor Xa (anti-fXa) activity, the patients were divided into heparin (anti-fXa ≥0.2 IU ml−1) and no heparin (anti-fXa ≤0.1 IU ml−1) groups.

RESULTS
There was a mean bias of 44 [95% confidence interval (CI) 40 to 47] celite seconds between ACT-LR and ACT+ measurements. The absolute changes in ACT-LR, ACT+ and INTEM:HEPTEM CT ratio were variable and did not differ between the groups. The mean ± SD percentage changes between postprotamine and baseline ACT-LR and ACT+ values were 5.9 ± 17.5 and 5.9 ± 16.9% in the no residual heparin group, compared to 1.4 ± 8.4 and 9.9 ± 12.5% in the residual heparin group. Receiver operator characteristic curves for postprotamine INTEM:HEPTEM CT ratio and for percentage changes in ACT-LR and ACT+ to detect an anti-fXa at least 0.2 IU ml−1 had areas under the curve of 0.496 (95% CI, 0.329 to 0.663), 0.425 (95% CI, 0.260 to 0.591) and 0.583 (95% CI, 0.417 to 0.749), respectively.

CONCLUSION
Both the ACT-LR and ACT+ tests of Hemochron Signature Elite device and the INTEM:HEPTEM CT ratio of ROTEM Sigma device have poor ability to detect residual heparin shortly after protamine administration.
Enhancing Acute Reconstructive Skills in Burn Surgery Through Virtual Simulation
Authors: Warner-Levy John , Sheikh Zeeshan , Dheansa Baljit , Walsh Karl 
Published: February 2025

Summary:
Medical simulation has progressed to using sophisticated computerized systems such as virtual and augmented reality. Despite its widespread adoption across various specialties, its adoption in burn surgery remains limited. Consequently, we wish to report on the “Excision of an Unhealed Burn Wound” module on the Touch Surgery mobile application that simulates the tangential excision and reconstruction of a burn wound with a split-thickness skin graft. To ascertain their knowledge of the surgical management of an unhealed burn wound, 38 regional senior house officer trainees currently on a plastic surgery placement completed a multiple-choice test. The trainees then viewed a full demonstration of the “Excision of an Unhealed Burn Wound” burn surgery module, before repeating the multiple-choice test after 1 hour. The self-assessed knowledge of participants regarding the excision of a burn and skin graft procedure improved in 90% of cases. Similarly, knowledge of the different types of equipment used for burn surgery saw an improvement in 89.5% of cases. Additionally, 84.3% of participants reported improvement in their understanding of the principles of preparing and applying a split-thickness skin graft. All but one participant agreed that simulation is beneficial in teaching surgical procedures, with the lone participant providing no rationale. Despite the relative inability to provide trainees with hands-on experience using surgical instruments and the risk of constraining the user to a single, preferred operating technique, we feel that digital simulation offers a novel tool for educating trainees in burn surgery.
Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes
Authors: Franco-Enzástiga Úrzula , Inturi Nikhil N. , Natarajan Keerthana , Mwirigi Juliet M. , Mazhar Khadijah , Schlachetzki Johannes C. M. , Schumacher Mark , Price Theodore J. 
Published: February 2025

Abstract
Cell states are influenced by the regulation of gene expression orchestrated by transcription factors capable of binding to accessible DNA regions. To uncover if sex differences exist in chromatin accessibility in the human dorsal root ganglion (hDRG), where nociceptive neurons innervating the body are found, we performed bulk and spatial assays for transposase-accessible chromatin technology followed by sequencing (ATAC-seq) from organ donors without a history of chronic pain. Using bulk ATAC-seq, we detected abundant sex differences in the hDRG. In women, differentially accessible regions (DARs) mapped mostly to the X chromosome, whereas in men, they mapped to autosomal genes. Hormone-responsive transcription factor binding motifs such as EGR1/3 were abundant within DARs in women, while JUN, FOS, and other activating protein 1 factor motifs were enriched in men, suggesting a higher activation state of cells compared with women. These observations were consistent with spatial ATAC-seq data. Furthermore, we validated that EGR1 expression is biased to female hDRG using RNAscope. In neurons, spatial ATAC-seq revealed higher chromatin accessibility in GABAergic, glutamatergic, and interferon-related genes in women and in Ca2+-signaling-related genes in men. Strikingly, XIST, responsible for inactivating 1 X chromosome by compacting it and maintaining at the periphery of the nucleus, was found to be highly dispersed in female neuronal nuclei. This is likely related to the higher chromatin accessibility in X in female hDRG neurons observed using both ATAC-seq approaches. We have documented baseline epigenomic sex differences in the hDRG which provide important descriptive information to test future hypotheses.