bluuebunny/crossref_metadata_2025_split huggingface dataset:
Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values
Authors: Misra Rohan , Ferrena Alexander , Zheng Deyou 
Published: February 2024

AbstractThe identity of a cell type can be revealed by its transcriptome and epigenome profiles, both of which can be in flux temporally and spatially, leading to distinct cell states or subtypes. The popular and standard workflow for single cell RNA-seq (scRNA-seq) data analysis applies feature selection, dimensional reduction, and clustering on the gene expression values quantified by read counts, but alternative approaches using a simple classification of a gene to “on” and “off” (i.e., binarization of the gene expression) has been proposed for classifying cells and other downstream analyses. Here, we demonstrate that a direct concatenation of the binarized scRNA-seq data and the standard single cell ATAC-seq data is sufficient and effective for integrated clustering analysis, after applying term-frequency-inverse document frequency (TF-IDF) and single value decomposition (also called latent semantic indexing, LSI) algorithms to the combined data, when the two modalities of omic data are collected using paired multiomic technology. This proposed approach avoids the need for converting scATAC-seq data to gene activity scores for combined analysis and furthermore enables a direct investigation into the contribution of each data type to resolving cell type identity.
Prevalence of Depression and Associated Socio-economic Outcomes during Violent Conflict: A Matched Analysis for Palestine Using Nationally Representative Survey and Conflict Event Data
Authors: Ronzani Piero , Stojetz Wolfgang , Stammel Nadine , Boettche Maria , Zardetto Diego , Fenzl Sarah , Salhab Maen , Anderson Jessica M. , Finn Arden , Aghajanian Alia , Brück Tilman 
Published: February 2024

SummaryBackgroundMental health risks are high in conflict settings, but mental health research mostly focuses on non-conflict settings. Survey data from active conflict settings often suffer from low response rates, unrepresentative samples, and a lack of detailed information on the roots and implications of poor mental health. We overcome these challenges by analyzing nationally representative evidence on the prevalence, sources, and socio-economic correlates of depression, a highly disabling and costly public health issue, in an active conflict setting.MethodsWe analyze nationally and sub-nationally representative geocoded survey data from the Palestinians’ Psychological Conditions Survey, collected from 5,877 Palestinian individuals in West Bank and Gaza in 2022. We calculate representative depression statistics, disaggregate by sub-areas and across socio-demographic groups, and estimate the associations with geocoded violent conflict event data as well as survey-based trauma exposure across conflict types and socio-economic outcomes.Findings58 percent (SE=2·21) of adults in Palestine exhibit depressive symptoms. Prevalence is highest in Gaza (71 percent, SE=2·70), increases with exposure to violent conflict and traumatic events, and is associated with worse socio-economic outcomes. The associated losses for 2022 are equivalent to 732,555 Years Lost in Disability, representing 8·9 percent of Palestine’s GDP.InterpretationThose exposed to violence and traumatic events are disproportionately affected by depression in conflict settings, which may fuel poverty and instability. Scalable investments in mental health in conflict settings promise to not only support well-being but also strengthen productivity and social cohesion for a given level of violence.FundingThe study received funding by the World Bank’s State and Peace Building Trust Fund.
MICROCOSM FABRICATION PLATFORM FOR LIVE MICROSCOPY OF PLANT-SOIL SYSTEMS
Authors: Liu Yangminghao , Patko Daniel , de le Mata Alberto Llora , Dong Xingshui , Peral Emma Gomez , He Xinhua , Ameduri Bruno , Ladmiral Vincent , MacDonald Michael P , Dupuy Lionel X 
Published: February 2024

AbstractBiological processes in soil pores are critical to crop nutrition and productivity, but live observations of these processes at that scale have been difficult to accomplish. To address this challenge, we have developed new techniques for the fabrication of microcosms dedicated to live imaging of the rhizosphere which incorporate the ability to control water content in transparent soil. Chambers were assembled using poly(dimethyl siloxane) (PDMS) parts fabricated by injection moulding and subsequently joined to glass slides. The control of liquid fluxes in the microcosm was achieved by syringes passing through the PDMS parts or through custom made PDMS sponges. We then tested various low refractive index materials for the fabrication of transparent soils and carried out live microscopy using Fluorescence Light Sheet microscopy. The proposed fabrication techniques are modular and enabled the construction of a wide range of experimental systems, including split chamber systems for the control of water content in soil, heterogeneous distribution of water content, monitoring of dye tracers, and live observation of plant roots. Using the techniques, we show how plant roots increase water infiltration through increased permeability of dry soil layers. This study therefore establishes that material property control and microfabrication in model rhizosphere systems can greatly enhance our understanding of plant-soil interactions.
Regulation of host metabolism and defense strategies to survive neonatal infection
Authors: Wu Ziyuan , Tien Nguyen Tran Nam , Bæk Ole , Zhong Jingren , Klabunde Björn , Nguyen Tinh Thu , Yen Nguyen Thi Hai , Long Nguyen Phuoc , Nguyen Duc Ninh 
Published: February 2024

AbstractTwo distinct defense strategies, resistance and tolerance, enable a host to survive infectious diseases. Newborns, constrained by limited energy reserves, predominantly rely on tolerance to cope with infection. However, this approach may fail as pathogen levels surpass a critical threshold, prompting a shift to resistance that can lead to dysregulated immune responses and sepsis. The mechanisms governing the interplay between tolerance and resistance in newborns remain poorly understood. Here, we compare metabolic traits and defense strategies between survivors and non- survivors inStaphylococcus epidermidis(S. epidermidis)-infected preterm piglets, mimicking infection in preterm infants. Relative to non-survivors, survivors displayed elevated resistance during the early phase of infection, followed by stronger tolerance in later stages. Conversely, animals succumbing to sepsis showed clear signs of respiratory and metabolic acidosis, together with exaggerated inflammation and organ dysfunctions. Hepatic transcriptomics revealed a strong association between the tolerance phenotype and heightened oxidative phosphorylation in survivors, coupled with suppressed glycolysis and immune signaling. Plasma metabolomics supported the finding of enhanced mitochondrial metabolism in survivors. Our findings suggest a link between mitochondrial metabolism, disease tolerance, and ultimately improved survival during infections in newborns. Metabolic regulations related to tolerance may be exploited to discover novel therapeutics for neonatal infection.Conflict-of-interest statementThe authors have declared that no conflict of interest exists.
In-Vivo and In-Vitro Toxicity Evaluation of 2,3-Dimethylquinoxaline: an Antimicrobial Found in a Traditional Herbal Medicine
Authors: Alfadil Abdelbagi , Alsamhan Hamoud , Ali Ahmed , Alkreathy Huda , Alrabia Mohammad , fatani Asif , A Ibrahem Karem 
Published: February 2024

ABSTRACT2,3-dimethylquinoxaline (DMQ) is a broad-spectrum antimicrobial phytochemical. This study aims to assess its toxicological profile.In vitrostudies conducted in appropriate cell cultures, included assessment of cardiotoxicity, nephrotoxicity, and hepatotoxicity.An in vivostudy was conducted in mice to determine acute oral toxicity (AOT), and subacute oral toxicity (SAOT). Acute dermal toxicity (ADT) was conducted in rats. Allin-vitrotoxicity studies of DMQ had negative results at concentrations ≤100 µM except for a non-significant reduction in the ATP in human hepatocellular carcinoma cell culture. The median lethal dose of DMQ was higher than 2000 mg/kg. All animals survived the scheduled necropsy and none showed any alteration in clinical signs. Biochemistry analysis revealed a significant difference between the satellite and control groups, showing an increase in platelet counts and white blood cell counts by 99.8% and 188.8%, respectively. Histology revealed enlargement of renal corpuscles; hyperplasia of testosterone-secreting cells; and dilatation of coronaries and capillaries. The present data suggests an acceptable safety profile of DMQ in rodents except for thrombocytosis, leukocytosis, and histological changes in high doses that need further investigation.
Changes in the analgesic mechanism of oxytocin can contribute to hyperalgesia in Parkinson’s disease model rats
Authors: Usami Nayuka , Maegawa Hiroharu , Niwa Hitoshi 
Published: February 2024

AbstractPain is a major non-motor symptom of Parkinson’s disease (PD). The alterations in the descending pain inhibitory system (DPIS) have been reported to trigger hyperalgesia in PD patients. However, the underlying mechanisms remain unclear. In the current study, dopaminergic nigrostriatal lesions were induced in rats by injecting 6-hydroxydopamine (6-OHDA) into their medial forebrain bundle. The neural mechanisms underlying changes in nociception in the orofacial region of 6-OHDA-lesioned rats was examined by injecting formalin into the vibrissa pad. The 6-OHDA-lesioned rats were seen to exhibit increased frequency of face-rubbing and more c-Fos immunoreactive (c-Fos-IR) cells in the trigeminal spinal subnucleus caudalis (Vc), confirming hyperalgesia. Examination of the number of c-Fos-IR cells in the DPIS nuclei [including the midbrain ventrolateral periaqueductal gray, the locus coeruleus, the nucleus raphe magnus, and paraventricular nucleus (PVN)] showed that 6-OHDA-lesioned rats exhibited a significantly lower number of c-Fos-IR cells in the magnocellular division of the PVN (mPVN) after formalin injection compared to sham-operated rats. Moreover, the 6-OHDA-lesioned rats also exhibited significantly lower plasma oxytocin (OT) concentration and percentage of oxytocin-immunoreactive (OT-IR) neurons expressing c-Fos protein in the mPVN and dorsal parvocellular division of the PVN (dpPVN), which secrete the analgesic hormone OT upon activation by nociceptive stimuli, when compared to the sham-operated rats. The effect of OT on hyperalgesia in 6-OHDA-lesioned rats was examined by injecting formalin into the vibrissa pad after intracisternal administration of OT, and the findings showed a decrease in the frequency of face rubbing and the number of c-Fos-IR cells in the Vc. In conclusion, these findings confirm presence of hyperalgesia in PD patients, potentially due to suppression of the analgesic effects of OT originating from the PVN.
Woman the Hunter? Female foragers sometimes hunt, yet gendered divisions of labor are real
Authors: Venkataraman Vivek , Hoffman Jordie , Hames Raymond B. , Stibbard-Hawkes Duncan N.E. , Kramer Karen , Kelly Robert , Farquharson Kyle , Hagen Edward H. , Hewlett Barry S. , Davis Helen Elizabeth , Glowacki Luke , Jang Haneul , Syme Kristen , Starkweather Katie , Lew-Levy Sheina 
Published: February 2024

AbstractGendered divisions of labor are a feature of every known contemporary hunter-gatherer (forager) society. While gender roles are certainly flexible, and prominent and well-studied cases of female hunting do exist, it is more often men who hunt. A new study (Anderson et al., 2023) surveyed ethnographically known foragers and found that women hunt in 79% of foraging societies, with big-game hunting occurring in 33%. Based on this single type of labor, which is one among dozens performed in foraging societies, the authors question the existence of gendered division of labor altogether. As a diverse group of hunter-gatherer experts, we find that claims that foraging societies lack or have weak gendered divisions of labor are contradicted by empirical evidence. We conducted an in-depth examination of Anderson et al. (2023) data and methods, finding evidence of sample selection bias and numerous coding errors undermining the paper’s conclusions. Anderson et al. (2023) have started a useful dialogue to ameliorate the popular misconception that women never hunt. However, their analysis does not contradict the wide body of empirical evidence for gendered divisions of labor in foraging societies. Furthermore, a myopic focus on hunting diminishes the value of contributions that take different forms and downplays the trade-offs foragers of both sexes routinely face. We caution against ethnographic revisionism that projects Westernized conceptions of labor and its value onto foraging societies.
High sensitivity cameras can lower spatial resolution in high-resolution optical microscopy
Authors: Ortkrass Henning , Müller Marcel , Engdahl Anders Kokkvoll , Holst Gerhard , Huser Thomas 
Published: February 2024

AbstractHigh-resolution optical fluorescence microscopies and, in particular, super-resolution fluorescence microscopy, are rapidly adopting highly sensitive cameras as their referred photodetectors. Camera-based parallel detection facilitates high-speed live cell imaging with the highest spatial resolution. Here, we show that the drive to use ever more sensitive, photon-counting image sensors in cameras can, however, have detrimental effects on spatial resolution that many researchers are not aware of. Typical parameters which influence the selection of image sensors are pixel size, quantum efficiency, signal-to-noise performance, dynamic range, and frame rate of the sensor. A parameter that is, however, often overlooked, is the sensor’s modulation transfer function (MTF). We have determined the wavelength-specific MTF of front- and back-illuminated image sensors and evaluated how it affects the spatial resolution that can be achieved in high fluorescence microscopy modalities. We find significant differences in image sensor performance for sensors that cause the resulting spatial resolution to vary with up to 28%. This result shows that the choice of image sensor has significant impact on the imaging performance of all camera-based optical microscopy modalities.
Reliably Measuring Learning-Dependent Distractor Suppression with Eye Tracking
Authors: Kim Andy J. , Grégoire Laurent , Anderson Brian A. 
Published: February 2024

AbstractIn the field of psychological science, behavioral performance in computer-based cognitive tasks often exhibits poor reliability. The absence of reliable measures of cognitive processes contributes to non-reproducibility in the field and impedes investigation of individual differences. Specifically in visual search paradigms, response time-based measures have shown poor test-retest reliability and internal consistency across attention capture and distractor suppression, but one study has demonstrated the potential for oculomotor measures to exhibit superior reliability. Therefore, in this study, we investigated three datasets to compare the reliability of learning-dependent distractor suppression measured via distractor fixations (oculomotor capture) and latency to fixate the target (fixation times). Our findings reveal superior split-half reliability of oculomotor capture compared to that of fixation times regardless of the critical distractor comparison, with the reliability of oculomotor capture in most cases falling within the range that is acceptable for the investigation of individual differences. We additionally find that older adults have superior oculomotor reliability compared with young adults, potentially addressing a significant limitation in the aging literature of high variability in response time measures due to slower responses. Our findings highlight the utility of measuring eye movements in the pursuit of reliable indicators of distractor processing and the need to further test and develop additional measures in other sensory domains to maximize statistical power, reliability, and reproducibility.
Meningioma transcriptomic landscape demonstrates novel subtypes with regional associated biology and patient outcome
Authors: Thirimanne H. Nayanga , Bonnin Damian Almiron , Nuechterlein Nicholas , Arora Sonali , Jensen Matt , Parada Carolina A. , Qiu Chengxiang , Szulzewsky Frank , English Collin W , Chen William C , Sievers Philipp , Nassiri Farshad , Wang Justin Z. , Klisch Tiemo J , Aldape Kenneth D , Patel Akash J , Cimino Patrick J , Zadeh Gelareh , Sahm Felix , Raleigh David R. , Shendure Jay , Ferreira Manuel , Holland Eric C 
Published: February 2024

SummaryMeningiomas, the most common intracranial tumor, though mostly benign can be recurrent and fatal. WHO grading does not always identify high risk meningioma and better characterizations of their aggressive biology is needed. To approach this problem, we combined 13 bulk RNA-Seq datasets to create a dimension-reduced reference landscape of 1298 meningiomas. Clinical and genomic metadata effectively correlated with landscape regions which led to the identification of meningioma subtypes with specific biological signatures. Time to recurrence also correlated with the map location. Further, we developed an algorithm that maps new patients onto this landscape where nearest neighbors predict outcome. This study highlights the utility of combining bulk transcriptomic datasets to visualize the complexity of tumor populations. Further, we provide an interactive tool for understanding the disease and predicting patient outcome. This resource is accessible via the online tool Oncoscape, where the scientific community can explore the meningioma landscape.
A circadian behavioral analysis suite for real-time classification of daily rhythms in complex behaviors
Authors: Perry Logan J. , Perez Blanca E. , Wahba Larissa Rays , Nikhil KL , Lenzen William C. , Jones Jeff R. 
Published: February 2024

AbstractMeasuring animal behavior over long timescales has been traditionally limited to behaviors that are easily measurable with real-time sensors. More complex behaviors have been measured over time, but these approaches are considerably more challenging due to the intensive manual effort required for scoring behaviors. Recent advances in machine learning have introduced automated behavior analysis methods, but these often overlook long-term behavioral patterns and struggle with classification in varying environmental conditions. To address this, we developed a pipeline that enables continuous, parallel recording and acquisition of animal behavior for an indefinite duration. As part of this pipeline, we applied a recent breakthrough self-supervised computer vision model to reduce training bias and overfitting and to ensure classification robustness. Our system automatically classifies animal behaviors with a performance approaching that of expert-level human labelers. Critically, classification occurs continuously, across multiple animals, and in real time. As a proof-of-concept, we used our system to record behavior from 97 mice over two weeks to test the hypothesis that sex and estrogen influence circadian rhythms in nine distinct home cage behaviors. We discovered novel sex- and estrogen-dependent differences in circadian properties of several behaviors including digging and nesting rhythms. We present a generalized version of our pipeline and novel classification model, the “circadian behavioral analysis suite,” (CBAS) as a user-friendly, open-source software package that allows researchers to automatically acquire and analyze behavioral rhythms with a throughput that rivals sensor-based methods, allowing for the temporal and circadian analysis of behaviors that were previously difficult or impossible to observe.
Short periods of decreased water flow may modulate long-term ocean acidification in reef-building corals
Authors: Martins Catarina P.P. , Simancas-Giraldo Susana M. , Schubert Patrick , Wall Marlene , Wild Christian , Wilke Thomas , Ziegler Maren 
Published: February 2024

ABSTRACTOcean acidification (OA) poses a major threat to reef-building corals. Although water flow variability is common in coral reefs and modulates coral physiology, the interactive effects of flow and OA on corals remain poorly understood. Therefore, we performed a three-month OA experiment investigating the effect of changes in flow on coral physiology. We exposed the reef-building coralsAcropora cytherea,Pocillopora verrucosa, andPorites cylindricato control (pH 8.0) and OA (pH 7.8) conditions at moderate flow (6 cm s-1) and monitored OA effects on growth. Throughout the experiment, we intermittently exposed all corals to low flow (2 cm s-1) for 1.5 h and measured their photosynthesis:photosynthesis (P:R) ratio under low and moderate flow. On average, corals under OA calcified 18 % less and grew 23 % less in surface area than those at ambient pH. We observed species-specific interactive effects of OA and flow on coral physiology. P:R ratios decreased after 12 weeks of OA inA. cytherea(22 %) andP. cylindrica(28 %) under moderate flow, but were unaffected by OA under low flow. P:R ratios were stable inP. verrucosa. These results suggest that short periods of decreased water flow may modulate OA effects on some coral species, indicating that flow variability is a factor to consider when assessing long-term effects of climate change.
Male and female variability in response to chronic stress and morphine in C57BL/6J, DBA/2J, and their BXD progeny
Authors: Morel Carole , Parise Lyonna F. , Van der Zee Yentl , Issler Orna , Cai Min , Browne Caleb , Blando Anthony , Leclair Katherine , Haynes Sherod , Williams Robert W. , Mulligan Megan K. , Russo Scott J. , Nestler Eric J. , Han Ming-Hu 
Published: February 2024

AbstractDrug addiction is a multifactorial syndrome in which genetic predispositions and exposure to environmental stressors constitute major risk factors for the early onset, escalation, and relapse of addictive behaviors. While it is well known that stress plays a key role in drug addiction, the genetic factors that make certain individuals particularly sensitive to stress and thereby more vulnerable to becoming addicted are unknown. In an effort to test a complex set of gene x environment interactions—specificallygene x chronic stress—here we leveraged a systems genetics resource: BXD recombinant inbred mice (BXD5, BXD8, BXD14, BXD22, BXD29, and BXD32) and their parental mouse lines, C57BL/6J and DBA/2J. Utilizing the chronic social defeat stress (CSDS) and chronic variable stress (CVS) paradigms, we first showed sexual dimorphism in the behavioral stress response between the mouse strains. Further, we observed an interaction between genetic background and vulnerability to prolonged exposure to non-social stressors. Finally, we found that DBA/2J and C57BL/6J mice pre-exposed to stress displayed differences in morphine sensitivity. Our results support the hypothesis that genetic variation in predisposition to stress responses influences morphine sensitivity and is likely to modulate the development of drug addiction.