bluuebunny/crossref_metadata_2025_split huggingface dataset:
C iii] λ1909 emission as an alternative to Ly α in the reionization era: the dependence of C iii] and Ly α at 3 &lt; z &lt; 4 from the VANDELS survey
Authors: Cunningham M H , Saxena A , Ellis R S , Pentericci L 
Published: April 2024

ABSTRACT
The velocity offset of Ly α emission from a galaxy’s systemic redshift is an excellent tracer of conditions that enable the escape of Ly α photons from the galaxy, and potentially the all-important hydrogen ionizing Lyman continuum photons. However at z ≥ 6, Ly α is often heavily attenuated by the neutral intergalactic medium. Here we investigate the utility of C iii] λλ1907, 1909 emission, usually the brightest ultraviolet (UV) line after Ly α, as a proxy estimating the Ly α velocity offset (ΔvLy α). To do so, we use analogues of reionization era galaxies based upon 52 star-forming galaxies with robust C iii] detections drawn from the VANDELS survey. Our sample spans a broad UV magnitude range of −18.5 &lt; MUV &lt; −22.0, with a sample average value of EW(C iii]) = 5.3 Å. We find a slight increase of EW(C iii]) with increasing EW(Ly α), but find a large range of EW(C iii]) ∼ 1–13 Å particularly at EW(Ly α) &lt; 10 Å. Using the C iii] line peak as the systemic redshift, we calculate ΔvLy α and recover the previously reported trend of decreasing ΔvLy α with increasing EW(Ly α). Interestingly, we find an anticorrelation between ΔvLy α and EW(C iii]), which also displays a dependence on the UV absolute magnitude. We derive a multivariate fit to obtain ΔvLy α using both EW(C iii]) and MUV, finding that ΔvLy α is more strongly dependent on EW(C iii]), with a weaker but non-negligible dependence on MUV. We find that for a fixed EW(C iii]), UV-bright Ly α emitting galaxies show smaller values of ΔvLy α,which suggests that such galaxies may be undergoing more bursty star-formation compared to the UV-fainter ones, akin to a population of extremely UV-bright galaxies identified at z &gt; 10.
The heat shock factor 20-HSF4-cellulose synthase A2 module regulates heat stress tolerance in maize
Authors: Li Ze , Li Zerui , Ji Yulong , Wang Chunyu , Wang Shufang , Shi Yiting , Le Jie , Zhang Mei 
Published: April 2024

Abstract
Temperature shapes the geographical distribution and behavior of plants. Understanding the regulatory mechanisms underlying the plant heat stress response is important for developing climate-resilient crops, including maize (Zea mays). To identify transcription factors (TFs) that may contribute to the maize heat stress response, we generated a dataset of short- and long-term transcriptome changes following a heat treatment time course in the inbred line B73. Co-expression network analysis highlighted several TFs, including the class B2a heat shock factor (HSF) ZmHSF20. Zmhsf20 mutant seedlings exhibited enhanced tolerance to heat stress. Furthermore, DNA affinity purification sequencing and Cleavage Under Targets and Tagmentation assays demonstrated that ZmHSF20 binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three class A Hsf genes, including ZmHsf4, repressing their transcription. We showed that ZmCesA2 and ZmHSF4 promote the heat stress response, with ZmHSF4 directly activating ZmCesA2 transcription. In agreement with the transcriptome analysis, ZmHSF20 inhibited cellulose accumulation and repressed the expression of cell wall-related genes. Importantly, the Zmhsf20 Zmhsf4 double mutant exhibited decreased thermotolerance, placing ZmHsf4 downstream of ZmHsf20. We proposed an expanded model of the heat stress response in maize, whereby ZmHSF20 lowers seedling heat tolerance by repressing ZmHsf4 and ZmCesA2, thus balancing seedling growth and defense.
Do Institutional Investors Process and Act on Information? Evidence from M&A Targets
Authors: Kim Kirak , Luu Ellie , Xu Fangming 
Published: April 2024

Abstract
We document important links between targets’ institutional ownership and takeover-bid outcomes. Firms’ institutional ownership increases the likelihood of receiving stock-for-stock bids. The impact becomes stronger when information asymmetries are higher, whereas we find little support for alternative channels, such as bidder misvaluation or target-side adverse selection. The information channel is further buttressed in our analyses of institutions’ share-retention decisions, targets’ demand for top-tier advisors, collar provisions, and targets’ share of expected synergies. Our findings suggest that institutions’ information advantage facilitates rational payment design and targets’ bargaining power gains, alleviating deadweight losses associated with stock-for-stock offers.
Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and PPARα knockout mouse hepatocytes
Authors: Heintz Melissa M , Klaren William D , East Alexander W , Haws Laurie C , McGreal Steven R , Campbell Rebecca R , Thompson Chad M 
Published: April 2024

Abstract
Recent in vitro transcriptomic analyses for the short-chain polyfluoroalkyl substance, HFPO-DA (ammonium, 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate), support conclusions from in vivo data that HFPO-DA-mediated liver effects in mice are part of the early key events of the peroxisome proliferator-activated receptor alpha (PPARα) activator-induced rodent hepatocarcinogenesis mode of action (MOA). Transcriptomic responses in HFPO-DA-treated rodent hepatocytes have high concordance with those treated with a PPARα agonist and lack concordance with those treated with PPARγ agonists or cytotoxic agents. To elucidate whether HFPO-DA-mediated transcriptomic responses in mouse liver are PPARα-dependent, additional transcriptomic analyses were conducted on samples from primary PPARα knockout (KO) and wild-type (WT) mouse hepatocytes exposed for 12, 24, or 72 h with various concentrations of HFPO-DA, or well-established agonists of PPARα (GW7647) and PPARγ (rosiglitazone), or cytotoxic agents (acetaminophen or d-galactosamine). Pathway and predicted upstream regulator-level responses were highly concordant between HFPO-DA and GW7647 in WT hepatocytes. A similar pattern was observed in PPARα KO hepatocytes, albeit with a distinct temporal and concentration-dependent delay potentially mediated by compensatory responses. This delay was not observed in PPARα KO hepatocytes exposed to rosiglitazone, acetaminophen, d-galactosamine. The similarity in transcriptomic signaling between HFPO-DA and GW7647 in both the presence and absence of PPARα in vitro indicates these compounds share a common MOA.
Cadmium inhibits calcium activity in hippocampal CA1 neurons of freely moving mice
Authors: Matsushita Megumi T , Xia Zhengui 
Published: April 2024

Abstract
Cadmium (Cd) is a ubiquitous toxic heavy metal and a potential neurotoxicant due to its wide use in industrial manufacturing processes and commercial products, including fertilizers. The general population is exposed to Cd through food and smoking due to high transfer rates of Cd from contaminated soil. Cd has been shown to mimic calcium ions (Ca2+) and interfere with intracellular Ca2+ levels and Ca2+ signaling in in vitro studies. However, nothing is known about Cd’s effects on Ca2+ activity in neurons in live animals. This study aimed to determine if Cd disrupts Ca2+ transients of neurons in CA1 region of the hippocampus during an associative learning paradigm. We utilized in vivo Ca2+ imaging in awake, freely moving C57BL/6 mice to measure Ca2+ activity in CA1 excitatory neurons expressing genetically encoded Ca2+ sensor GCaMP6 during an associative learning paradigm. We found that a smaller proportion of neurons are activated in Cd-treated groups compared with control during fear conditioning, suggesting that Cd may contribute to learning and memory deficit by reducing the activity of neurons. We observed these effects at Cd exposure levels that result in blood Cd levels comparable with the general U.S. population levels. This provides a possible molecular mechanism for Cd interference of learning and memory at exposure levels relevant to U.S. adults. To our knowledge, our study is the first to describe Cd effects on brain Ca2+ activity in vivo in freely behaving mice.
This study provides evidence for impairment of neuronal calcium activity in hippocampal CA1 excitatory neurons in freely moving mice following cadmium exposure.
Simulation in pediatric anesthesiology: current state and visions for the future
Authors: Daly Guris Rodrigo J. , George Preeta , Gurnaney Harshad G. 
Published: April 2024

Purpose of review
Simulation is a well established practice in medicine. This review reflects upon the role of simulation in pediatric anesthesiology in three parts: training anesthesiologists to care for pediatric patients safely and effectively; evaluating and improving systems of care for children; and visions for the future.

Recent findings
Simulation continues to prove a useful modality to educate both novice and experienced clinicians in the perioperative care of infants and children. It is also a powerful tool to help analyze and improve upon how care is provided to infants and children. Advances in technology and computational power now allow for a greater than ever degree of innovation, accessibility, and focused reflection and debriefing, with an exciting outlook for promising advances in the near future.

Summary
Simulation plays a key role in developing and achieving peak performance in the perioperative care of infants and children. Although simulation already has a great impact, its full potential is yet to be harnessed.
Post-traumatic Bullous Pilomatrixoma Exploring the Pathogenesis
Authors: Martínez-Ortega Jesús I. , Ortega-Valerio Grisell , Ramirez-Cibrian Arely G. 
Published: April 2024

Abstract:
This report demonstrates the rare variant of bullous pilomatrixoma in a 10-year-old boy who presented with a rapidly growing, red-colored, bullous nodule on his neck after trauma. The exact etiology of this subtype of pilomatrixoma is unclear, but previous studies have suggested that mechanical trauma may trigger its development.
Walking on thin endometrium
Authors: Ata Baris , Mathyk Begum , Telek Savci , Kalafat Erkan 
Published: April 2024

Purpose of review
Endometrial thickness has been regarded a predictor of success in assisted reproductive technology cycles and it seems a common practice to cancel embryo transfer when it is below a cut-off. However, various cut-offs have been proposed without a causal relationship between endometrial thickness and embryo implantation being established, casting doubt on the current dogma.

Recent findings
Methodological limitations of the available studies on endometrial thickness are increasingly recognized and better designed studies do not demonstrate a cut-off value which requires cancelling an embryo transfer.

Summary
Endometrium is important for implantation and a healthy pregnancy; however, ultrasound measured thickness does not seem to be a good marker of endometrial function.
Abnormal Cerebrospinal Fluid Cytology in Functional Movement Disorders
Authors: Serranová Tereza , Slovák Matěj , Forejtová Zuzana , Sieger Tomáš , Dušek Petr , Srpová Barbora , Mrázová Kateřina , Růžička Evžen , Šonka Karel , Espay Alberto J. , Nytrová Petra 
Published: April 2024

Objective
The role of inflammation and neuroimmune mechanisms, which have been documented in various neuropsychiatric disorders including the seizure subtype of functional neurological disorder, remains unclear in functional movement disorders (FMD). To explore these mechanisms, we analyzed selected inflammatory markers in cerebrospinal fluid (CSF) in patients with FMD.

Methods
We compared CSF markers in 26 patients with clinically established FMD (20 females; mean [SD] age = 43.3 [10.9], disease duration = 3.9 [3], range = 0.1–11 years; mean follow-up after lumbar puncture = 4.3 [2] years, range = 0.5–7 years) and 26 sex- and age-matched clinical controls with noninflammatory nonneurodegenerative neurological disorders, mostly sleep disorders.

Results
Sixty-five percent of FMD patients versus 15% of controls showed cytological abnormalities (i.e., increased white blood cells [WBC] count, signs of WBC activation, or both; odds ratio [OR] = 9.85, 95% confidence interval = 2.37–52.00, p < .01, corrected), with a significantly higher frequency of an isolated lymphocytic activation, 35% versus 0% (OR = ∞, 95% confidence interval = 2.53–∞, p < .05, corrected). There were no differences in CSF protein and albumin levels, quotient albumin, IgG index, and oligoclonal bands. CSF abnormalities were not associated with more severe motor symptoms or a higher frequency of depression in FMD.

Conclusions
Our results suggest a possible involvement of immune mechanisms in the pathophysiology of (at least a subtype of) FMD that deserves further investigation.
Machine learning-driven COVID-19 early triage and large-scale testing strategies based on the 2021 Costa Rican Actualidades survey
Authors: Pasquier Carlos , Solís Maikol , Vilchez Vivian , Núñez-Corrales Santiago 
Published: April 2024

AbstractThe COVID-19 pandemic underscored the importance of mass testing in mitigating the spread of the virus. This study presents mass testing strategies developed through machine learning models, which predict the risk of COVID-19 contagion based on health determinants. Using the data from the 2021 “Actualidades” survey in Costa Rica, we trained models to classify individuals by contagion risk. After theorize four possible strategies, we evaluated these using Monte Carlo simulations, analyzing the distribution functions for the number of tests, positive cases detected, tests per person, and total costs. Additionally, we introduced the metrics,efficiencyandstock capacity, to assess the performance of different strategies. Our classifier achieved an AUC-ROC of 0.80 and an AUC-PR of 0.59, considering a disease prevalence of 0.26. The fourth strategy, which integrates RT-qPCR, antigen, and RT-LAMP tests, emerged as a cost-effective approach for mass testing, offering insights into scalable and adaptable testing mechanisms for pandemic response.
Combined visualization of genomic and epidemiological data for outbreaks
Authors: Suster Carl J.E. , Watt Anne E. , Wang Qinning , Chen Sharon C.-A. , Kok Jen , Sintchenko Vitali 
Published: April 2024

AbstractIn epidemiological investigations, pathogen genomics can provide insights and test epidemiological hypotheses that would not have been possible through traditional epidemiology. Tools to synthesize genomic analysis with other types of data are a key requirement of genomic epidemiology. We propose a new ‘phylepic’ visualization that combines a phylogenomic tree with an epidemic curve. The combination visually links the molecular time represented in the tree to the calendar time in the epidemic curve, a correspondence that is not easily represented by existing tools. Using an example derived from a foodborne bacterial outbreak, we demonstrated that the phylepic chart communicates that what appeared to be a point-source outbreak was in fact composed of cases associated with two genetically distinct clades of bacteria. We provide an R package implementing the chart. We expect that visualizations that place genomic analyses within the epidemiological context will become increasingly important for outbreak investigations and public health surveillance of infectious diseases.
Nanopore Guided Annotation of Transcriptome Architectures
Authors: Abebe Jonathan S. , Alwie Yasmine , Fuhrmann Erik , Leins Jonas , Mai Julia , Verstraten Ruth , Schreiner Sabrina , Wilson Angus C. , Depledge Daniel P. 
Published: April 2024

ABSTRACTHigh-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs, without recoding or amplification bias, and resulting data may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails on individual RNA molecules. Existing software solutions for generating high-resolution transcriptome annotations are poorly suited to small gene dense organisms such as viruses due to the challenge of identifying distinct transcript isoforms where alternative splicing and overlapping RNAs are prevalent. To resolve this, we identified key characteristics of DRS datasets and developed a novel approach to transcriptome. We demonstrate, using a combination of synthetic and original datasets, that our novel approach yields a high level of precision and recall when reconstructing both gene sparse and gene dense transcriptomes from DRS datasets. We further apply this approach to generate a new high resolution transcriptome annotation of the neglected pathogen human adenovirus type F 41 for which we identify 77 distinct transcripts encoding at least 23 different proteins.
MGPfactXMBD: A Model-Based Factorization Method for scRNA Data Unveils Bifurcating Transcriptional Modules Underlying Cell Fate Determination
Authors: Ren Jun , Zhou Ying , Hu Yudi , Yang Jing , Fang Hongkun , Lyu Xuejing , Guo Jintao , Shi Xiaodong , Li Qiyuan 
Published: April 2024

AbstractManifold-learning is particularly useful to resolve the complex cellular state space from single-cell RNA sequences. While current manifold-learning methods provide insights into cell fate by inferring graph-based trajectory at cell level, challenges remain to retrieve interpretable biology underlying the diverse cellular states. Here, we described MGPfactXMBD, a model-based manifold-learning framework and capable to factorize complex development trajectories into independent bifurcation processes of gene sets, and thus enables trajectory inference based on relevant features. MGPfactXMBDoffers more nuanced understanding of the biological processes underlying cellular trajectories with potential determinants. When bench-tested across 239 datasets, MGPfactXMBDshowed advantages in major quantity-control metrics, such as branch division accuracy and trajectory topology, outperforming most established methods. In real datasets, MGPfactXMBDrecovered the critical pathways and cell types in microglia development with experimentally valid regulons and markers. Furthermore, MGPfactXMBDdiscovered evolutionary trajectories of tumor-associated CD8+T cells and yielded new subtypes of CD8+T cells with gene expression signatures significantly predictive of the responses to immune checkpoint inhibitor in independent cohorts. In summary, MGPfactXMBDoffers a manifold-learning framework in scRNA-seq data which enables feature selection for specific biological processes and contributing to advance our understanding of biological determination of cell fate.
Vinegar injections can be used safely to control outbreaks of crown-of-thorns starfish (Acanthaster solaris) during the peak spawning season
Authors: Dumas Pascal , Durbano Amaury , Bourgeois Bertrand , Gossuin Hugues , Peignon Christophe 
Published: April 2024

AbstractConcerns are mounting over the effects of COTS outbreaks, prompting the need for integrated management strategies. Although direct control methods are short-term and localized, they remain one of the few operational tools that can be easily implemented by local actors. Vinegar injections have recently emerged as highly effective method; however their impact on reproductive behavior remains untested. Here, we investigated the short-term spawning response of mature COTS to double injections of household vinegar. First, COTS abundances and reproductive status were monitored during a massive outbreak affecting New Caledonia’s reefs. In-situ and laboratory experiments were then conducted to determine whether injected COTS would eventually release their eggs and trigger synchronized spawning among mature individuals in close proximity. Our results indicated that injections had no significant effect on spawning behavior, even in densely populated aggregations (>4000 COTS.ha-1). In the field, starfish exhibited ripe gonads with high gamete content (up to 35% of body weight) three days after conspecifics were injected. In the laboratory, mature COTS kept with injected, decaying individuals in a confined volume did not expel their gametes after two days. This suggests that vinegar injections could be used at any time, even during peak spawning, without risking synchronized spawning in the affected areas.
Terroir and rootstock effects on leaf shape in California Central Valley vineyards
Authors: Migicovsky Zoë , Swift Joel F. , Awale Mani , Helget Zachary , Klein Laura L. , Pinkner Leah , Woodhouse Karoline , Cousins Peter , Fennell Anne Y. , Miller Allison J. , Chitwood Daniel H. 
Published: April 2024

SummaryEmbedded in a single leaf shape are the latent signatures of genetic, developmental, and environmental effects. In viticulture, choice of location and rootstock are important decisions that affect the performance and production of the shoot. We hypothesize that these effects influence plant morphology, as reflected in leaf shape.We sample 1879 leaves arising from scion and rootstock combinations from commercial vineyards in the Central Valley of California. Our design tests 20 pairwise contrasts between Cabernet Sauvignon and Chardonnay scions from San Joaquin, Merced, and Madera counties from vines grafted to Teleki 5C, 1103 Paulsen, and Freedom rootstocks.Using geometric morphometric approaches, we visualize a morphospace in which, in addition to clear separation of Cabernet Sauvignon and Chardonnay scion leaf shapes, an orthogonal source of shape variation affects both varieties. Comparing the Procrustes distances to within and between group means, the additional source of variance is found to arise from location and rootstock effects.We describe and visualize a specific shape feature, the angle of the proximal lobe to the midvein that defines the closure of the petiolar sinus, that is attributable to location and rootstock effects and orthogonal to and separate from genetic, developmental, or allometric effects attributable to leaf size.Societal Impact Statement (EN)The innumerable effects of terroir—including climate, soil, microbial environment, biotic interactions, and cultivation practice—collectively alter plant performance and production. A more direct agricultural intervention is grafting, in which genetically distinct shoot and root genotypes are surgically combined to create a chimera that alter shoot performance at a distance. Selection of location and rootstock are intentional decisions in viticulture to positively alter production outcomes. Here, we show that terroir and rootstock alter the shapes of grapevine leaves in commercial vineyards throughout the California Central Valley, documenting the profound effects of these agricultural interventions that alter plant morphology.