bluuebunny/crossref_metadata_2025_split huggingface dataset:
The OASES project: exploring the outer Solar System through stellar occultation with amateur-class telescopes
Authors: Arimatsu K. 
Published: February 2025

The exploration of kilometre-sized trans-Neptunian objects (TNOs) is one of the ultimate goals in the search for the origin and evolution of the Solar System. However, such exploration is challenging because these small bodies are too faint to be directly detected. One potential avenue for detecting and investigating small and faint TNOs is the monitoring of stellar occultation events. This paper reviews the concept and methodology of monitoring observations of stellar occultations by small, unidentified TNOs, focusing on our observational programme, Organized Autotelescopes for Serendipitous Event Survey (OASES). OASES aims to detect and investigate stellar occultations by unidentified TNOs using multiple amateur-sized telescopes equipped with commercial complementary metal-oxide-semiconductor (CMOS) cameras. Through the monitoring observations conducted so far, OASES has found one possible occultation event by a kilometre-sized TNO. The paper also discusses future developments of the OASES project and deliberates on the potential of movie observations in expanding the frontiers of outer Solar System research.
This article is part of the theme issue ‘Major advances in planetary sciences thanks to stellar occultations’.
The avian embryo as a time-honoured animal model in developmental, biomedical and agricultural research
Authors: Burggren Warren , Dzialowski Edward , Tzschentke Barbara 
Published: February 2025

Avian embryos have been at the core of embryological, morphological, physiological and biochemical/molecular research, especially involving research in three primary areas: developmental, biomedical and agricultural research. As developmental models, the avian embryo—especially that of the chicken—has been the single most used embryo model, perhaps in part from the combination of large size, ease of access and prior knowledge base. Developmental research with avian embryos has included organ system studies of the heart, vasculature, lungs, kidneys, nervous system, etc., as well as integrated physiological processes including gas-exchange, acid–base and ion/water regulation. In terms of translational research, avian embryos have modelled vascular development, based on the easily accessible chorioallantoic membrane under the eggshell. This same respiratory organ has enabled toxicological studies of how pollutants affect vertebrate development. Investigation of the transition to pulmonary breathing and the associated emergence of respiratory control has also relied heavily upon the avian embryo. In addition to developmental and biomedical investigations, the avian embryo has been studied intensively due to the huge importance of domesticated birds as a food source. Consequently, the effects of environment (including temperature, humidity, noise levels and photoperiod) during incubation on subsequent post-hatch phenotype are being actively investigated.
This article is part of the theme issue ‘The biology of the avian respiratory system’.
The avian respiratory system: implications for anaesthesia
Authors: Ludders John 
Published: February 2025

Anaesthesia is not a natural state for any animal, including birds. The unique anatomic and physiological attributes of the class Aves that have made it possible for birds to inhabit every continent on this planet and to live in a variety of environments, some considered challenging if not inhospitable to mammals, pose challenges to their anaesthetic management. Indeed, it is more challenging than the anaesthetic management of mammals, a reality substantiated by the fact that the risk of anaesthesia-related death of birds is up to 20 times higher than for dogs and cats. This article highlights those anatomic (respiratory system, renal–portal system), physiological (gas exchange, respiratory control mechanisms in respiratory brainstem and peripheral chemoreceptor areas, including intrapulmonary chemoreceptors) and pharmacological attributes (pharmacokinetics and pharmacodynamics) that make anaesthetic management, both inhalant and injectable anaesthesia, of birds challenging, and how those challenges are managed.
This article is part of the theme issue ‘The biology of the avian respiratory system’.
A multi-center study on the percentage of relative abundance, of Klebsiella pneumoniae and Klebsiella oxytoca ,socio-demographic profile and clinical parameters of oral squamous carcinoma tissues of a group of Sri Lankan male patients
Authors: Perera Manosha Lakmali , Perera Irosha 
Published: February 2025

Background: Emergence of carbapenemase producing Klebsiella pneumoniae and asymptomatic oral colonization within human populations has become a public health threat Enrichment of oral Klebsiella species in neoplastic remain unclear.
Aim: To find out the percentage of relative abundance, of Klebsiella pneumoniae and Klebsiella oxytoca,socio-demographic profile and clinical parameters of oral squamous carcinoma tissues of a group of Sri Lankan male patients in multi-centers.
Method: A group of male patients comprising 25 OSCC cases visiting 9 OMF units in 6 Provinces in Sri Lanka represented the vast majority of OSCC patients. DNA extracted from fresh biopsies was sequenced for the V1 to V3 region with Illumina’s 2 × 300–bp chemistry. High-quality nonchimeric merged reads were classified to the species level with a prioritized BLASTN-based algorithm and identified upto species level. Downstream compositional analysis was performed with QIIME (Quantitative Insights into Microbial Ecology)
Results: K. pneumoniae was presented an average relative abundance of 1.45%, significantly higher than K. oxytoca, which has a relative abundance of 0.03%.
Conclusion: K. pneumoniae over growth was seen compared to K. oxytoca in OSCC cases. This possess an emerging threat of transmitting this pathogen in the community and heath care associated environments as the oral and nasal cavities act as ideal niche for nourishment and flourishment of this opportunistic pathogen, notorious for nosocomial infections and multi drug resistance.
A truncated SARS-CoV-2 nucleocapsid protein enhances virus fitness by evading antiviral responses
Authors: Mulloy Rory P. , Evseev Danyel , Bui-Marinos Maxwell P. , Sharlin Noga , Corcoran Jennifer A. 
Published: February 2025

ABSTRACTViruses face a selective pressure to evade cellular antiviral responses to control the outcome of an infection. However, due to their limited genome size, viruses must adopt unique strategies to confront cellular sensors. Since emerging in humans, SARS-CoV-2 has accrued multiple mutations throughout its genome, some of which enhanced virus replication and led to the rise of viral variants. However, the biological consequences of many of these changes remain to be discovered. Here, we show that SARS-CoV-2 produces a truncated form of the nucleocapsid protein, called N*M210. Due to the acquisition of a viral transcription regulatory sequence (TRS) in the N gene, certain variants, such as Omicron, produce a new viral mRNA that markedly increases N*M210expression. We show that N*M210is a dsRNA binding protein, which inhibits multiple arms of the cellular antiviral response, including blocking interferon induction and inhibiting stress granule formation. We created a panel of recombinant SARS-CoV-2 viruses (rSARS-2) with mutations in the N gene that increased or decreased N*M210production. We show that N*M210production increases virus fitness, as viruses that produce more N*M210outcompeted wild-type rSARS-2. We demonstrate that the fitness advantage provided by N*M210is partly due to its ability to potently block stress granules. We propose a model where, to evade the cellular antiviral response, SARS-CoV-2 has evolved a mechanism to increase the production of a truncated form of the N protein, which broadly limits the activation of dsRNA-induced antiviral responses, tipping the balance in favour of the virus in the battle for control of the cell.HighlightsSARS-CoV-2 variants evolved to upregulate truncated N (N*) synthesis to increase virus fitnessN*M210is a potent dsRNA-binding protein that blocks cellular dsRNA sensingN*M210inhibits stress granule formation independent of G3BP1 binding
A framework for evaluating predicted sperm trajectories in crowded microscopy videos
Authors: Hart David , Cashwell Kylie , Bhandari Anita , Schmidt Cameron 
Published: February 2025

AbstractFor many years, sperm trajectory analysis for microscopy videos has determined categories of sperm motility. These categories are dependent on kinematic parameters such as Curvilinear Velocity and Beat Frequency. These outputs, however, ultimately rely on the quality of the tracking for each individual sperm in the microscopy video. Previous approaches have relied on calculating these values on short time scales or for isolated sperm to avoid the tracking errors that occur in crowded (high cell-density) microscopy videos, but improving fertility analysis will require accurately tracking trajectories at physiologically-relevant time scales and cell densities. In this work, we identify a framework for accurately assessing the quality of sperm trajectory tracking independent of motility outputs. We utilize common cell tracking metrics and propose modifications based on conditions unique to sperm microscopy. Additionally, we provide a dataset of three fully-labeled microscopy videos to allow for future comparisons and developments.Author summaryThis report develops a computer vision framework to track individual sperm cells in crowded (high cell-density) microscopy videos, with the goal of improving automated analysis of sperm motility patterns. The task of accurately analyzing sperm movement is deceptively challenging due to the high rate of cell crossovers, an issue that has long impeded long-term tracking of sperm trajectories. Here, we introduce new evaluation metrics and provide a labeled dataset to serve as a baseline for future improvements.
Disease tolerant mice shelter a pathogenic intestinal microbiota able to trigger lethal disease in low tolerant hosts
Authors: Vidal Vinícius M. , Ferreira Letícia M. , Yilmaz Bahtiyar , Montes-Cobos Elena , Gama Andreza M.S. , Kitoko Jamil Z. , Rosa Samara G. , Teixeira Gabriel A. , Farias José N. D. , Raghavan Varsha , Littman Dan , de Souza Heitor S.P. , Canto Fábio B. , Bozza Marcelo T. 
Published: February 2025

AbstractDisease tolerance is a defensive strategy that limits tissue damage during infection. Macrophage migration inhibitory factor (MIF)-deficient mice (Mif-/-) are protected in different models of infection and intestinal inflammation due to unclear disease tolerance mechanisms, whereas low disease-tolerantIl10-/-mice develop microbiota-dependent spontaneous gut inflammation. Here, we examined whether IL-10 is required for the phenotype seen inMif-/-mice and, conversely, the contribution of MIF during IL-10 deficiency. While breeding for double-deficientMif-/-Il10-/-mice, we unexpectedly observed thatIl10-/-individuals died within days after co-housing withMif-/-mice. We found that healthyMif-/-hosts endure a highly diverse, unique and dysbiotic-like microbiota composition, including antibiotic-resistantEnterobacteriaceaespecies, which were sufficient to cause acute and lethal Th1-driven colitis inIl10-/-recipients. The disease was characterized by increased frequencies of IFNγ+cells and neutrophils within colonic lamina propria.Mif-/-Il10-/-mice died prematurely, and survivors developed communicable disease, - indicating that lack of IL-10 is a dominant trait. These findings suggest that tolerant individuals harbor a gut microbiota enriched in pathogens/pathobionts, which can trigger disease in susceptible hosts.
A simplified co-culture reveals altered cardiotoxic responses to doxorubicin in hPSC-derived cardiomyocytes in the presence of endothelial cells
Authors: Brescia Marcella , Chatrian Andrea , Keselman Paul , Gallant James , Paulsson Elsa Sörman , Mol Mervyn P.H. , Sjögren Rickard , Raymond Karine , Orlova Valeria , Barnes Kalpana , Wales Richard , Austerjost Jonas , Olszowy Michael W. , Mummery Christine L. , van Meer Berend J. , Davis Richard P. 
Published: February 2025

AbstractCardiotoxicity is a significant challenge in cancer therapies, particularly with doxorubicin, a widely used anthracycline known for its broad anti-cancer spectrum but life-threatening cardiac side effects. There is a critical need for more predictivein vitromodels to understand doxorubicin-induced cardiotoxicity and patient-specific drug responses. In this study, we used human pluripotent stem cell (hPSC)-derived cardiomyocytes (hPSC-CMs), cardiac fibroblasts (hPSC-cFBs) and endothelial cells (hPSC-ECs) to investigate the cardiotoxic effects of doxorubicin in two-dimensional mono-and multi-cell type cultures. By mimicking the cumulative dose effect seen in patients through repeated doxorubicin treatments and using a machine learning-basedin silicoimage analysis tool, we could precisely quantify caspase 3/7 activity as an early toxicity marker and identify hPSC-CMs in multi-cell type cultures. This innovative approach allowed continuous monitoring of apoptosis from phase-contrast images, revealing that hPSC-ECs showed higher sensitivity to doxorubicin than isogenic hPSC-CMs or hPSC-cFBs and significantly enhanced cardiomyocyte toxicity in co-culture. In contrast, dermal fibroblasts differentiated from the same hPSC line showed no toxic response under the same treatment regimen. These results challenge the conventional focus on cardiomyocytes as the target of drug-induced cardiac damage. Our findings not only highlight the complex interplay among different cardiac cell types in mediating the toxic effects of doxorubicin, but also demonstrate the potential of AI-enabled tools to advance personalized drug screening and safety assessments.
Polarization-Sensitive Optical Coherence Tomography Imaging of Posterior Staphyloma Edges in Eyes with High Myopia
Authors: Wu Yijin , Lu Hongshuang , Chen Changyu , Xiong Jianping , Yamanari Masahiro , Takahashi Hiroyuki , Sugisawa Keigo , Okamoto Michiaki , Wang Yining , Wang Ziye , Takahashi Tomonari , Kamoi Koju , Ohno-Matsui Kyoko 
Published: February 2025

AbstractPurposeTo investigate the arrangement and orientation of the collagen fibers in the inner and outer scleral layers at the edges of posterior staphylomas using polarization-sensitive optical coherence tomography (PS-OCT).Methods195 eyes of 105 highly myopic patients who underwent PS-OCT examinations between August 2023 and May 2024 at Institute of Science Tokyo were studied. The PS-OCT images were analyzed to assess the orientation and birefringence of scleral collagen fibers at the staphyloma edges, covering macular and inferior staphylomas.ResultsEighty-eight eyes of 60 highly myopic patients whose posterior staphylomas were confirmed in the ultra-widefield optical coherence tomography images underwent PS-OCT image processing. Thirty-six eyes from 27 patients were selected for further analysis. The optic axis images showed that 25 (18 upper and 7 lower) of 30 (83.3%) macular staphyloma edges had an aggregation of the inner scleral fibers, characterized by an arc-like gathering of the horizontal fibers along the edge. All eight upper edges from 8 eyes with an inferior staphyloma had an aggregation of the inner scleral fibers with relatively linear horizontal fibers across the macula. The birefringence images of the upper and lower edges of the macular and inferior staphylomas had different patterns, including a mixture of low and high, and relatively high birefringence.ConclusionsAn uneven aggregation of inner scleral fibers at the staphyloma edges in highly myopic eyes offers a more nuanced understanding of the pathogenesis of staphylomas. This finding also has pivotal implications for developing the targeted interventions to prevent the progression of staphylomas in eyes with high myopia.
Effects of an early water, sanitation, hygiene, and nutritional intervention on child development at school age: a 7-year follow-up of a cluster-randomized trial in rural Bangladesh
Authors: Tofail Fahmida , Pitchik Helen O. , Islam Mahfuza , Khan Rizwana , Shoab Abul K. , Akter Fahmida , Aktar Shirina , Huda Tarique M.N. , Rahman Mahbubur , Winch Peter J. , Luby Stephen P. , Fernald Lia C.H. 
Published: February 2025

AbstractBackgroundA previous cluster-randomized controlled trial in Bangladesh found that individual or combined water, handwashing, sanitation, and nutrition interventions during pregnancy and after birth improved developmental outcomes of children at 1 and 2 years of age. We aimed to determine if these intervention effects were sustained at school-age.Methods and FindingsPregnant women were enrolled between May 2012 and July 2013 and randomized into chlorinated drinking water (W); improved sanitation (S); handwashing with soap (H); combined WSH; nutrition counselling and provision of lipid-based supplements (N); combined WSH+N, or a passive control arm (C) (N=5,551). We followed-up enrolled mothers and children 5 years after intervention completion. Primary outcomes were child cognition, fine motor abilities, behaviour, school achievement, and executive function; secondary outcomes were maternal mental health and the home environment. We conducted intention to treat analyses using generalized linear models to determine unadjusted and adjusted comparisons between each arm and the control, accounting for pair-matching and block level clustering.Between September 2019 and February 2021, we re-enrolled 3,832 children. Children in the WSH+N, N, and S arms had improved cognitive scores on one or more domains compared to the control arm, with adjusted effect sizes between 0.10 (95%CI: 0.00, 0.20) and 0.15 (0.03, 0.27). Children in all arms except S had improved prosocial behaviour, with effect sizes between 0.21 (0.07, 0.34) and 0.33 (0.17, 0.49). No intervention effects were observed for fine motor, difficult behaviours, executive functioning, or school achievement. Maternal depressive symptoms were improved in the WSH+N, H, and N arms, and the stimulating home environment was improved in all intervention arms. Data collection for this study was interrupted by a 6-month pause at the start of the COVID-19 pandemic.ConclusionsAt 7 years of age, we found small, sustained impacts of early water, sanitation, hygiene, and nutrition interventions on child cognitive and social-emotional outcomes, the stimulating home environment, and maternal mental health. Future work to determine the mechanisms underlying these intervention effects will further inform the design of early interventions to improve child health and development.Trial registrationFollow-up trial:ClinicalTrials.gov,NCT04443855Original WASH-Benefits Bangladesh (WASH-B):ClinicalTrials.gov,NCT01590095
Life Course Sleep Duration Trajectories and Risk and Age at Onset of Parkinson’s Disease
Authors: Fang Yi , Hardy Rebecca , Yaffe Kristine , Little Simon J. , Tanner Caroline M. , Leng Yue 
Published: February 2025

AbstractImportanceInvestigating associations between life course sleep duration and Parkinson’s disease (PD) may help clarify the role of sleep in early detection and/or prevention of PD.ObjectiveTo characterize life course sleep duration trajectories and their associations with PD risk and age at onset (AAO).DesignTwo ongoing online cohorts: Parkinson’s Progression Markers Initiative (PPMI)-Online (discovery; started in 2021) and Fox Insight (FI; validation; started in 2018).SettingParticipants reported sleep duration across life stages, with PD-related follow-ups every three months.ParticipantsA convenience sample of 5,660 individuals with PD and 10,245 without PD from PPMI-Online, and 1,929 participants with PD from FI.ExposuresSelf-reported sleep duration from ages 18 to 80+ in PPMI-Online and 12 to 66+ in FI. Latent class growth analysis (LCGA) identified sleep trajectories.Main Outcomes and MeasuresPD risk and AAO were assessed using logistic and linear regression, adjusting for demographics, lifestyle, comorbidities.ResultsThe combined sample included 17,834 participants [age at sleep report 67.2±7.83 years; 9,735 (54.6%) female]. LCGA identified nine sleep trajectories in PPMI-Online, stable in early adulthood but diverging in midlife (stable, increasing, decreasing). Midlife sleep reductions (6-7 to ≤5-6 hours/day: OR = 1.90, 95% CI 1.61-2.24,P< .001; 7-8 to ≤6-7 hours/day: OR = 1.64, 95% CI 1.40-1.91,P< .001) and consistent short sleep (<=6 hours/day throughout adulthood: OR = 1.41, 95% CI 1.19-1.67, P < .001) demonstrated increased PD risk. Short sleep in early adulthood or midlife also had earlier AAO. The strongest effects were seen in those with ≤6 hours/day throughout adulthood (PPMI-Online: β = −2.45 years, 95% CI −3.33 to −1.56, P <.001) and those with a continuous decrease since adolescence (FI: β = −4.23 years, 95% CI −5.52 to −2.93, P < .001). These effects were independent of rapid eye movement sleep behavior disorders.Conclusions and RelevanceSelf-reported short sleep in early adulthood and midlife sleep reductions are associated with increased PD risk and earlier AAO. Self-perceived midlife sleep reduction may be a marker for future PD. Persons with chronic short sleep may be candidates for preventive intervention.Key PointsQuestion:What is the relationship between life course sleep duration trajectories and the risk and age at onset of Parkinson’s disease (PD)?Findings:In this cohort study including 7,589 participants with PD and 10,245 without PD, short sleep duration in early adulthood or decreasing sleep duration after age 50 were associated with an increased risk and earlier age at onset of PD.Meaning:Short sleep duration over the life course, even in early adulthood (< 40 years), may contribute to risk of late-life PD; declining sleep duration after age 50 is a potential prodromal sign of PD.