bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Simple Model for the Emergence of Relaxation‐Oscillator Convection
Authors: Spaulding‐Astudillo F. E. , Mitchell J. L. 
Published: November 2024

AbstractEarth's tropics are characterized by quasi‐steady precipitation with small oscillations about a mean value, which has led to the hypothesis that moist convection is in a state of quasi‐equilibrium (QE). In contrast, very warm simulations of Earth's tropical convection are characterized by relaxation‐oscillator‐like (RO) precipitation, with short‐lived convective storms and torrential rainfall forming and dissipating at regular intervals with little to no precipitation in between. We develop a model of moist convection by combining a zero‐buoyancy model of bulk‐plume convection with a QE heat engine model, and we use it to show that QE is violated at high surface temperatures. We hypothesize that the RO state emerges when the equilibrium condition of the convective heat engine is violated, that is, when the heating rate times a thermodynamic efficiency exceeds the rate at which work can be performed. We test our hypothesis against one‐ and three‐dimensional numerical simulations and find that it accurately predicts the onset of RO convection. The proposed mechanism for RO emergence from QE breakdown is agnostic of the condensable, and can be applied to any planetary atmosphere undergoing moist convection. To date, RO states have only been demonstrated in three‐dimensional convection‐resolving simulations, which has made it seem that the physics of the RO state requires simulations that can explicitly resolve the three‐dimensional interaction of cloudy plumes and their environment. We demonstrate that RO states also exist in single‐column simulations of radiative‐convective equilibrium with parameterized convection, albeit in a different surface temperature range and with much longer storm‐free intervals.
Prospective prediction of childhood body mass index trajectories using multi-task Gaussian processes
Authors: Leroy Arthur , Gupta Varsha , Tint Mya Thway , Ooi Delicia Shu Qin , Yap Fabian , Lek Ngee , Godfrey Keith M. , Chong Yap Seng , Lee Yung Seng , Eriksson Johan G. , Álvarez Mauricio A. , Michael Navin , Wang Dennis 
Published: November 2024

Abstract

Background
Body mass index (BMI) trajectories have been used to assess the growth of children with respect to their peers, and to anticipate future obesity and disease risk. While retrospective BMI trajectories have been actively studied, models to prospectively predict continuous BMI trajectories have not been investigated.

Materials and methods
Using longitudinal BMI measurements between birth and age 10 y from a mother-offspring cohort, we leveraged a multi-task Gaussian process approach to develop and evaluate a unified framework for modeling, clustering, and prospective prediction of BMI trajectories. We compared its sensitivity to missing values in the longitudinal follow-up of children, compared its prediction performance to cubic B-spline and multilevel Jenss-Bayley models, and used prospectively predicted BMI trajectories to assess the probability of future BMIs crossing the clinical cutoffs for obesity.

Results
MagmaClust identified 5 distinct patterns of BMI trajectories between 0 to 10 y. The method outperformed both cubic B-spline and multilevel Jenss-Bayley models in the accuracy of retrospective BMI trajectories while being more robust to missing data (up to 90%). It was also better at prospectively forecasting BMI trajectories of children for periods ranging from 2 to 8 years into the future, using historic BMI data. Given BMI data between birth and age 2 years, prediction of overweight/obesity status at age 10 years, as computed from MagmaClust’s predictions exhibited high specificity (0.94), negative predictive value (0.89), and accuracy (0.86). The accuracy, sensitivity, and positive predictive value of predictions increased as BMI data from additional time points were utilized for prediction.

Conclusion
MagmaClust provides a unified, probabilistic, non-parametric framework to model, cluster, and prospectively predict childhood BMI trajectories and overweight/obesity risk. The proposed method offers a convenient tool for clinicians to monitor BMI growth in children, allowing them to prospectively identify children with high predicted overweight/obesity risk and implement timely interventions.
Hippocampal area CA2 activity supports social investigation following an acute social stress
Authors: Radzicki Daniel , McCann Katharine E. , Alexander Georgia M. , Dudek Serena M. 
Published: November 2024

AbstractNeuronal activity in the hippocampus is critical for many types of memory acquisition and retrieval and influences an animal’s response to stress. Moreover, the molecularly distinct principal neurons of hippocampal area CA2 are required for social recognition memory and aggression in mice. To interrogate the effects of stress on CA2-dependent behaviors, we chemogenetically manipulated neuronal activity in vivo during an acute, socially derived stressor and tested whether memory for the defeat was influenced. One day after an acute social defeat (aSD), defeated mice spent significantly less time investigating another mouse when compared to non-defeated control mice. We found that this avoidant phenotype persisted for up to one month following a single defeat encounter. When CA2 pyramidal neuron activity was inhibited with Gi-DREADD receptors during the defeat, subject mice exhibited a significantly higher amount of social avoidance one day later when compared to defeated littermates not expressing DREADDs. Moreover, CA2 inhibition during defeat caused a reduction in submissive defense behaviors in response to aggression. In vitro electrophysiology and tracing experiments revealed a circuit wherein CA2 neurons connect to caudal CA1 projection neurons that, in turn, project to corticolimbic regions including the anterior cingulate cortex. Finally, socially avoidant, defeated mice exhibited significant reductions in cFos expression in caudal hippocampal and limbic brain areas during a social investigation task 24 h after aSD. Taken together, these results indicate that CA2 neuronal activity is required to support behavioral resilience following an acute social stressor and that submissive defensive behavior during the defeat (vs. fleeing) is a predictor of future resilience to social stress. Furthermore, CA2 preferentially targets a population of caudal CA1 projection neurons that contact cortical brain regions where activity is modulated by an acute social stressor.
Lfng-expressing centroacinar cell is a unique cell-of-origin for p53 deficient pancreatic cancer
Authors: Chung Wen-Cheng , Zhang Shubing , Atfi Azeddine , Xu Keli 
Published: November 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies with limited understanding of etiology. Studies in mice showed that both acinar and ductal cells of the pancreas can be targeted by combination of oncogenic Kras and p53 mutations to form PDAC. How the transforming capacities of pancreatic cells are constrained, and whether a subset of cells could serve as a prime target for oncogenic transformation, remain obscure. Here we report that expression of a Notch modulator, Lunatic Fringe (Lfng), is restricted to a limited number of cells with centroacinar location and morphology in the adult pancreas. Lfng-expressing cells are preferentially targeted by oncogenic Kras along with p53 deletion to form PDAC, and deletion of Lfng blocks tumor initiation from these cells. Notch3 is a functional Notch receptor for PDAC initiation and progression in this context. Lfng is upregulated in acinar- and ductal-derived PDAC and its deletion suppresses these tumors. Finally, high LFNG expression is associated with high grade and poor survival in human patients. Taken together, Lfng marks a centroacinar subpopulation that is uniquely susceptible to oncogenic transformation when p53 is lost, and Lfng functions as an oncogene in all three lineages of the exocrine pancreas.
The impact of the early environment on oxytocin receptor epigenetics and potential therapeutic implications
Authors: Nance Madelyn G. , Sullivan Kelsey M. , Puglia Meghan H. 
Published: November 2024

Abstract
Oxytocin research is rapidly evolving and increasingly reveals that epigenetic modifications to the oxytocin receptor gene (OXTR) are functional, plastic, and reliable components of oxytocinergic system function. This review outlines how OXTR epigenetics are shaped by the early life environment, impact social-developmental outcomes, and have strong potential to serve as therapeutic targets. We first establish the malleability of OXTR epigenetics in infancy in both animal models and humans through research demonstrating the impact of the early life environment on OXTR DNA methylation (OXTRm) and subsequent social behavior. Next, we detail how OXTRm serves as a predictive mechanism for neurodevelopmental outcomes in animal models of social behavior such as the prairie vole, and summarize the role of OXTRm in psychiatric disorders, emotional processing, and attachment behavior in humans. We discuss the potential of further OXTRm research to improve oxytocin therapeutics by highlighting how a deeper knowledge of OXTRm could improve the therapeutic potential of exogenous oxytocin, how OXTRm may impact additional cellular mechanisms with therapeutic potential including control of the perinatal GABA switch, and how early life therapies may target the tuning of endogenous OXTRm. Finally, we review limitations of previous oxytocin research and make recommendations for future research.

Impact

Previous research into oxytocin therapeutics has been hampered by methodological difficulties that may be improved by assay of the oxytocin receptor gene (OXTR) and its methylation (OXTRm)

Key sites of OXTRm modification link early life exposures to developmental and behavioral outcomes

OXTRm appears to have a critical period of development in early life

Epigenetic modification of the oxytocin receptor gene could serve as a powerful target for therapeutic interventions
Structure-dynamics relation in metallic glass revealed by 5-dimensional scanning transmission electron microscopy
Authors: Nakazawa Katsuaki , Mitsuishi Kazutaka , Iakoubovskii Konstantin , Kohara Shinji , Tsuchiya Koichi 
Published: November 2024

Abstract
Dynamical and structural heterogeneities play an important role in glass transition phenomena. However, the relation between these heterogeneities is not fully revealed. In this study, we simultaneously observed these heterogeneities near the glass transition temperature in Zr50Cu40Al10 using five-dimensional scanning transmission electron microscopy, which can record the spatiotemporal distribution of diffraction patterns. The heterogeneities were visualized with sub-nanometer resolution, and a correlation between them was measured up to the glass transition temperature. We verified that ordered structures had slow dynamics, and the order decreased as the temperature increased.
scPair: Boosting single cell multimodal analysis by leveraging implicit feature selection and single cell atlases
Authors: Hu Hongru , Quon Gerald 
Published: November 2024

AbstractMultimodal single-cell assays profile multiple sets of features in the same cells and are widely used for identifying and mapping cell states between chromatin and mRNA and linking regulatory elements to target genes. However, the high dimensionality of input features and shallow sequencing depth compared to unimodal assays pose challenges in data analysis. Here we present scPair, a multimodal single-cell data framework that overcomes these challenges by employing an implicit feature selection approach. scPair uses dual encoder-decoder structures trained on paired data to align cell states across modalities and predict features from one modality to another. We demonstrate that scPair outperforms existing methods in accuracy and execution time, and facilitates downstream tasks such as trajectory inference. We further show scPair can augment smaller multimodal datasets with larger unimodal atlases to increase statistical power to identify groups of transcription factors active during different stages of neural differentiation.
Effectiveness of treat-to-target cholesterol-lowering interventions on cardiovascular disease and all-cause mortality risk in the community-dwelling population: a target trial emulation
Authors: Yang Zhao , Deng Qiujv , Hao Yongchen , Yang Na , Han Lizhen , Jia Pingping , Zhou Pan , Hao Yiming , Wang Ziyu , Zhao Wenlang , Qi Yue , Liu Jing 
Published: November 2024

AbstractLittle is known about the long-term effectiveness of risk-based treat-to-target cholesterol-lowering interventions on cardiovascular risk. Here, we show the emulated effectiveness of guideline-recommended low-density and non-high-density lipoprotein cholesterol-lowering interventions using the absolute risk reduction (ARR) and the restricted mean event-free time-based number needed to treat (NNT). With 5,375 participants, the 29-year risks for cardiovascular disease (CVD), all-cause mortality, and atherosclerotic CVD were 18.6%, 25.6%, and 17.7%, respectively. Long-term treat-to-target interventions showed significant reductions in CVD (ARR −2.3%, 95%CI −3.4% to −0.8%; NNT 115), all-cause mortality (−3.0%, −4.3% to −1.8%; 95), and atherosclerotic CVD (−2.6%, −3.5% to −1.2%; 104). Such effects appear more pronounced in women, smokers, and those with body mass index < 24 kg/m² or higher adherence rates.
Loss of cytoplasmic actin filaments raises nuclear actin levels to drive INO80C-dependent chromosome fragmentation
Authors: Hurst Verena , Gerhold Christian B. , Tarashev Cleo V. D. , Challa Kiran , Seeber Andrew , Yamazaki Shota , Knapp Britta , Helliwell Stephen B. , Bodenmiller Bernd , Harata Masahiko , Shimada Kenji , Gasser Susan M. 
Published: November 2024

AbstractLoss of cytosolic actin filaments upon TORC2 inhibition triggers chromosome fragmentation in yeast, which results from altered base excision repair of Zeocin-induced lesions. To find the link between TORC2 kinase and this yeast chromosome shattering (YCS) we performed phosphoproteomics. YCS-relevant phospho-targets included plasma membrane-associated regulators of actin polymerization, such as Las17, the yeast Wiscott-Aldrich Syndrome protein. Induced degradation of Las17 was sufficient to trigger YCS in presence of Zeocin, bypassing TORC2 inhibition. In yeast, Las17 does not act directly at damage, but instead its loss, like TORC2 inhibition, raises nuclear actin levels. Nuclear actin, in complex with Arp4, forms an essential subunit of several nucleosome remodeler complexes, including INO80C, which facilitates DNA polymerase elongation. Here we show that the genetic ablation of INO80C activity leads to partial YCS resistance, suggesting that elevated levels of nuclear G-actin may stimulate INO80C to increase DNA polymerase processivity and convert single-strand lesions into double-strand breaks.
TORC2 inhibition triggers yeast chromosome fragmentation through misregulated Base Excision Repair of clustered oxidation events
Authors: Shimada Kenji , Tarashev Cleo V. D. , Bregenhorn Stephanie , Gerhold Christian B. , van Loon Barbara , Roth Gregory , Hurst Verena , Jiricny Josef , Helliwell Stephen B. , Gasser Susan M. 
Published: November 2024

AbstractCombinational therapies provoking cell death are of major interest in oncology. Combining TORC2 kinase inhibition with the radiomimetic drug Zeocin results in a rapid accumulation of double-strand breaks (DSB) in the budding yeast genome. This lethal Yeast Chromosome Shattering (YCS) requires conserved enzymes of base excision repair. YCS can be attenuated by eliminating three N-glycosylases or endonucleases Apn1/Apn2 and Rad1, which act to convert oxidized bases into abasic sites and single-strand nicks. Adjacent lesions must be repaired in a step-wise fashion to avoid generating DSBs. Artificially increasing nuclear actin by destabilizing cytoplasmic actin filaments or by expressing a nuclear export-deficient actin interferes with this step-wise repair and generates DSBs, while mutants that impair DNA polymerase processivity reduce them. Repair factors that bind actin include Apn1, RFA and the actin-dependent chromatin remodeler INO80C. During YCS, increased INO80C activity could enhance both DNA polymerase processivity and repair factor access to convert clustered lesions into DSBs.
Enabling biocontained plant virus transmission studies through establishment of an axenic whitefly (Bemisia tabaci) colony on plant tissue culture
Authors: Thompson Natalie S. , Krum David , Chen Yun-Ru , Torres Mariela C. , Trauger Marena A. , Strike Dalton , Weston Zachary , Polston Jane E. , Curtis Wayne R. 
Published: November 2024

AbstractWhiteflies (Bemisia tabaci) and the diseases they transmit are a major detriment to crop yields and a significant contributor to world hunger. The highly evolved interactions of host plant, phloem-feeding insect vector with endosymbionts and persistently transmitted virus represent a tremendous challenge for interdisciplinary study. Presented here is the establishment of a colony of axenic whiteflies on tissue-cultured plants. Efficient colony establishment was achieved by a surface sterilization of eggs laid on axenic phototrophically tissue-cultured plants. The transfer of emerging whiteflies through coupled tissue culture vessels to new axenic plants facilitates robust subculturing and produces hundreds of whitefly adults per month. Whitefly proliferation on more than two dozen plant species is shown as well as in vitro testing of whitefly preference for different plants. This novel multi-organism system provides the high-level of biocontainment required by Federal permitting to conduct virus transmission experiments. Axenic whitefly adults were able to acquire and transmit a begomovirus into tissue-cultured plants, indicating that culturable gut microorganisms are not required for virus transmission. The approach described enables a wide range of hypotheses regarding whitefly phytopathology without the expense, facilities, and contamination ambiguity associated with current approaches.
Hydrodynamics of cruise swimming and turning maneuvers in Euchaeta antarctica
Authors: Mohaghar Mohammad , Webster Donald R. 
Published: November 2024

AbstractThe hydrodynamic disturbance generated by the adult copepod Euchaeta antarctica during cruise swimming is quantified. Kinematic results are compared to previous results reported for different Euchaeta species. The results reveal a linear relationship between cruise speed and prosome length across Euchaeta species, indicating a size-proportional trend that is indicative of a complicated interaction of species size and environmental factors such as fluid temperature and viscosity. The detailed fluid flow measurements using the tomographic Particle Image Velocimetry (tomo-PIV) technique provide insight into copepod cruise propulsion during turning events in comparison to straight motions. During straight swimming, E. antarctica demonstrates streamlined flow patterns and reduced vorticity in the near-body fluid shear layer, which is beneficial for sustained motion and energy conservation. In contrast, turning maneuvers are characterized by maximum flow velocities reaching 1.5 times greater values than during straight cruising with increased flow field complexity and enhanced vorticity. The viscous dissipation rate generated in the flow disturbance is also greater during turning events, with the total dissipation rate reaching $$\bf3.5-3.8\times 10^{-8}$$

3.5
-
3.8
×

10

-
8

W compared to $$\bf2.6-2.8\times 10^{-8}$$

2.6
-
2.8
×

10

-
8

W during straight cruising. The flow disturbance also generates a hydrodynamic cue that prey may sense in order to avoid the predator E. antarctica. For the adult E. antarctica, the hydrodynamic cue extends to a volume that is 11–13 times larger than the copepod exoskeleton volume during the straight swimming motion and 22–25 times larger during the turn events.
Stabilized 30 µJ dissipative soliton resonance laser source at 1064 nm
Authors: Pokryszka Piotr , Xu Yingchu , Chang Wonkeun , Krzempek Karol 
Published: November 2024

AbstractWe demonstrate the first successful stabilization of a dissipative soliton resonance (DSR) mode-locked (ML) laser source using straightforward techniques. Our setup employed a figure-8 (F8) resonator configuration and a nonlinear optical loop mirror (NOLM) to achieve stable mode-locking, generating 1064 nm rectangular pulses with a 3 ns duration at a repetition frequency of ~ 1 MHz. The pulses were boosted in an all-fiber amplifier chain and reached 30 µJ and 10 kW peak power per pulse at 30 W average output power. We addressed a critical gap in the literature by actively stabilizing key DSR pulse parameters: average output power (improved by a factor of 51), pulse repetition frequency (improved by 7583 using cross-phase modulation for synchronization), and pulse duration (improved by a factor of ~ 4). Additionally, we included a numerical analysis to explore the pulse formation mechanisms in DSR ML lasers working in a F8 configuration. Our findings show that non-complex all-in-fiber DSR ML lasers can reliably produce high-energy pulses with stable, repeatable parameters, making them suitable for future applications e.g. in nonlinear frequency conversion, laser micromachining, or LIDAR.
Unique insights into morphological characterization and functional adaptation of the scaly shank skin in aquatic and terrestrial birds
Authors: Madkour Fatma A. 
Published: November 2024

AbstractThe avian skin is a vital barrier against external effects and undergoes modification to adapt to the different ecosystems. The current study focused on the comprehensive study of the scaly shank skin of aquatic birds, Egyptian Balady Duck (EBD) as well as terrestrial birds, Broad Breasted White Turkey (BBWT) via gross anatomy, histology, and scanning electron microscopy with ED-XRF analysis. The shank skin color was yellow to black in EBD and creamy-white in BBWT. Gross anatomy exhibited two types of scales around the shank: scute and scutella scales in EBD and four types: scute, scutella, reticula, and cancella (interstitial) scales in BBWT. Most scales were non-overlapped and separated by sulci in both birds except those on the dorsum of the shank of BBWT. SEM of the descaled skin revealed an irregular surface due to keratinocytes defining a polygonal texture in EBD and Langerhans cells (a large oval-shaped cell body with abundant long projections) attached to neighboring keratinocytes in BBWT. Histologically, the epidermal and dermal layers varied among the different skin aspects of the shanks of both birds. Langerhans cells were seen within the basal cell layer of the stratum germinativum and collagen fibers of the dermal stratum superficiale. Melanocytes were observed in the stratum basale in EBD. In both birds, abundant telocytes and fibroblasts were distributed within the dermal layers, with excessive adipose tissue in the dermis of the shank skin of EBD. According to the results of the ED-XRF analysis of the scaly shank skin, elements and oxides were present in both species. In conclusion, the findings of the present study reflect the correlations between the functional morphology of shank skin and the bird habitats.