bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anuran call properties as reliable indicators of environmental suitability for reproduction
Authors: Pekny Julianne E. , Todd Brian D. , Post Eric 
Published: June 2024

ABSTRACTThe annual onset of breeding activity by animals in seasonal environments is often accompanied by auditory signals such as stridulations in insects and vocalizations in birds, mammals, and anurans. In ectotherms, the seasonal timing of such activity by males signals to females the general favorability of environmental conditions for reproduction. Complementary to this, the acoustic characteristics of male auditory signals are presumed to indicate, primarily, the status or quality of males as mates or territorial competitors. Here, using male anurans as a case study, we present the novel hypothesis that characteristics of auditory signals that are modulated by temperature may also serve as bioclimatic indicators of the suitability of proximal abiotic conditions for reproduction by females. According to this hypothesis, thermal constraints on characteristics such as call rate and duration that are insuperable by males may imbue their calls with features that facilitate tracking of environmental conditions by females independently of information intended for communication by males. We integrate findings from empirical studies spanning multiple fields of ecology and evolution to demonstrate how temporal variation in call properties may directly influence female reproductive behavior and physiology. Finally, we outline how this proposed mechanism may enable environmental tracking, provide guidelines for future research to experimentally test this hypothesis, and discuss how findings from this research can translate into actionable conservation management for species of concern.
VASCilia (Vision Analysis StereoCilia): A Napari Plugin for Deep Learning-Based 3D Analysis of Cochlear Hair Cell Stereocilia Bundles
Authors: Kassim Yasmin M. , Rosenberg David B. , Das Samprita , Huang Zhuoling , Rahman Samia , Al Shammaa Ibraheem , Salim Samer , Huang Kevin , Renero Alma , Miller Cayla , Ninoyu Yuzuru , Friedman Rick A. , Indzhykulian Artur , Manor Uri 
Published: June 2024

ABSTRACTCochlear hair cells are essential for hearing, and their stereocilia bundles are critical for mechanotransduction. However, analyzing the 3D morphology of these bundles can be challenging due to their complex organization and the presence of other cellular structures in the tissue. To address this, we developed VASCilia (Vision Analysis StereoCilia), a Napari plugin suite that automates the analysis of 3D confocal microscopy datasets of phalloidin-stained cochlear hair cell bundles. VASCilia includes five deep learning-based models that streamline the analysis process, including: (1) Z-Focus Tracker (ZFT) for selecting relevant slices in a 3D image stack; (2) PCPAlignNet (Planar Cell Polarity Alignment Network) for automated orientation of image stacks; (3) a segmentation model for identifying and delineating stereocilia bundles; (4) a tonotopic Position Prediction tool; and (5) a classification tool for identifying hair cell subtypes. In addition, VASCilia provides automated computational tools and measurement capabilities. Using VASCilia, we found that the total actin content of stereocilia bundles (as measured by phalloidin staining) does not necessarily increase with bundle height, which is likely due to differences in stereocilia thickness and number. This novel biological finding demonstrates the power of VASCilia in facilitating detailed quantitative analysis of stereocilia. VASCilia also provides a user-friendly interface that allows researchers to easily navigate and use the tool, with the added capability to reload all their analyses for review or sharing purposes. We believe that VASCilia will be a valuable resource for researchers studying cochlear hair cell development and function, addressing a longstanding need in the hair cell research community for specialized deep learning-based tools capable of high-throughput image quantitation. We have released our code along with a manually annotated dataset that includes approximately 55 3D stacks featuring instance segmentation (https://github.com/ucsdmanorlab/Napari-VASCilia). This dataset comprises a total of 502 inner and 1,703 outer hair cell bundles annotated in 3D. As the first open-source dataset of its kind, we aim to establish a foundational resource for constructing a comprehensive atlas of cochlea hair cell images. Ultimately, this initiative will support the development of foundational models adaptable to various species, markers, and imaging scales to accelerate advances within the hearing research community.
“Modeling Diffusive Search by Non-Adaptive Sperm: Empirical and Computational Insights”
Authors: Brisard Benjamin M. , Cashwell Kylie D. , Stewart Stephanie M. , Harrison Logan M. , Charles Aidan C. , Dennis Chelsea V. , Henslee Ivie R. , Carrow Ethan L. , Belcher Heather A. , Bhowmick Debajit , Vos Paul W. , Majka Maciej , Bier Martin , Hart David M. , Schmidt Cameron A. 
Published: June 2024

AbstractDuring fertilization, mammalian sperm undergo a winnowing selection process that reduces the candidate pool of potential fertilizers from ∼106-1011cells to 101-102cells (depending on the species). Classical sperm competition theory addresses the positive or ‘stabilizing’ selection acting on sperm phenotypes within populations of organisms but does not strictly address the developmental consequences of sperm traits among individual organisms that are under purifying selection during fertilization. It is the latter that is of utmost concern for improving assisted reproductive technologies (ART) because ‘low fitness’ sperm may be inadvertently used for fertilization during interventions that rely heavily on artificial sperm selection, such as intracytoplasmic sperm injection (ICSI). Importantly, some form of sperm selection is used in nearly all forms of ART (e.g., differential centrifugation, swim-up, or hyaluronan binding assays, etc.). To date, there is no unifying quantitative framework (i.e., theory of sperm selection) that synthesizes causal mechanisms of selection with observed natural variation in individual sperm traits. In this report, we reframe the physiological function of sperm as a collective diffusive search process and develop multi-scale computational models to explore the causal dynamics that constrain sperm ‘fitness’ during fertilization. Several experimentally useful concepts are developed, including a probabilistic measure of sperm ‘fitness’ as well as an information theoretic measure of the magnitude of sperm selection, each of which are assessed under systematic increases in microenvironmental selective pressure acting on sperm motility patterns.Author SummaryFertilization in mammals requires many orders of magnitude more sperm than eggs to be fertilized. This study models collective sperm movement as a diffusive search process, combining experiments and simulations to explore how heterogeneity in motility patterns and microenvironmental complexity shape fertilization success. We introduce simple metrics to quantify sperm fitness and the magnitude of selection pressure imposed by the microenvironment, revealing that sperm phenotype distributions interact with environmental constraints to determine the range of sperm traits that ultimately support successful egg contact. These insights improve our understanding of sperm population dynamics and offer practical tools for optimizing assisted reproductive technologies in clinical and agricultural settings.
Targeted delivery of flagellin by nebulization offers optimized respiratory immunity and defense against pneumococcal pneumonia
Authors: Baldry Mara , Costa Charlotte , Zeroual Yasmine , Cayet Delphine , Pardessus Jeoffrey , Soulard Daphnée , Wallet Frédéric , Beury Delphine , Hot David , MacLoughlin Ronan , Heuzé-Vourc’h Nathalie , Sirard Jean-Claude , Carnoy Christophe 
Published: June 2024

AbstractNovel therapeutic strategies are urgently needed to combat pneumonia caused byStreptococcus pneumoniaestrains resistant to standard-of-care antibiotics. Previous studies have shown that targeted stimulation of lung innate immune defenses through intranasal administration of the Toll-like receptor 5 agonist flagellin, improves the treatment of pneumonia when combined with antibiotics. To promote translation to the clinic application, this study assessed the direct delivery of flagellin to the airways through nebulization using a vibrating mesh nebulizer in mice. Intranasal delivery achieved approximately 40% lung deposition of the administered flagellin dose, whereas nebulization yielded less than 1%. Despite these differences, nebulized flagellin induced a transient activation of lung innate immunity characterized by cytokine/chemokine production and neutrophil infiltration into airways analogous to intranasal administration. Furthermore, inhalation by nebulization resulted in an accelerated resolution of systemic pro-inflammatory responses. Lastly, adjunct therapy combining nebulized flagellin and amoxicillin proved effective against antibiotic-resistant pneumococcal pneumonia in mice. We posit that flagellin aerosol therapy represents a safe and promising approach to address bacterial pneumonia within the context of antimicrobial resistance.
A lever hypothesis for Synaptotagmin-1 action in neurotransmiter release
Authors: Jaczynska Klaudia , Esser Victoria , Xu Junjie , Sari Levent , Lin Milo M. , Rosenmund Christian , Rizo Josep 
Published: June 2024

AbstractNeurotransmiter release is triggered in microseconds by Ca2+-binding to the Synaptotagmin-1 C2domains and by SNARE complexes that form four-helix bundles between synaptic vesicles and plasma membranes, but the coupling mechanism between Ca2+-sensing and membrane fusion is unknown. Release requires extension of SNARE helices into juxtamembrane linkers that precede transmembrane regions (linker zippering) and binding of the Synaptotagmin-1 C2B domain to SNARE complexes through a ‘primary interface’ comprising two regions (I and II). The Synaptotagmin-1 Ca2+-binding loops were believed to accelerate membrane fusion by inducing membrane curvature, perturbing lipid bilayers or helping bridge the membranes, but SNARE complex binding orients the Ca2+-binding loops away from the fusion site, hindering these putative activities. Molecular dynamics simulations now suggest that Synaptotagmin-1 C2domains near the site of fusion hinder SNARE action, providing an explanation for this paradox and arguing against previous models of Sytnaptotagmin-1 action. NMR experiments reveal that binding of C2B domain arginines to SNARE acidic residues at region II remains after disruption of region I. These results and fluorescence resonance energy transfer assays, together with previous data, suggest that Ca2+causes reorientation of the C2B domain on the membrane and dissociation from the SNAREs at region I but not region II. Based on these results and molecular modeling, we propose that Synaptotagmin-1 acts as a lever that pulls the SNARE complex when Ca2+causes reorientation of the C2B domain, facilitating linker zippering and fast membrane fusion. This hypothesis is supported by the electrophysiological data described in the accompanying paper.Significance statementNeurotransmiter release requires SNARE complexes that fuse synaptic vesicles with the plasma membrane and the Ca2+-sensor synaptotagmin-1, which was thought to facilitate membrane fusion directly through its Ca2+-binding loops. However, binding of Synaptotagmin-1 to SNARE complexes orients these loops away from the fusion site. Using molecular dynamics simulations, we show that placing Synaptotagmin-1 at the fusion site hinders the action of SNARE complexes. Spectroscopic studies show that Ca2+binding to Synaptotagmin-1 can change its interactions with SNARE complexes and, together with molecular modeling, suggest that Synaptotagmin-1 acts as a lever, pulling SNARE complexes and thus facilitating their action on the membranes to induce fusion. Functional studies described in the accompanying paper support this hypothesis.
Abo1 ATPase facilitates the dissociation of FACT from chromatin
Authors: Jang Juwon , Kang Yujin , Zofall Martin , Cho Carol , Grewal Shiv , Lee Ja Yil , Song Ji-Joon 
Published: June 2024

AbstractThe histone chaperone FACT is a heterodimeric complex consisting of Spt16 and Pob3, crucial for preserving nucleosome integrity during transcription and DNA replication. Loss of FACT leads to cryptic transcription and heterochromatin defects. FACT was shown to interact with Abo1, an AAA+ family histone chaperone involved in nucleosome dynamics. Depletion of Abo1 causes FACT to stall at transcription start sites (TSS) and mimics FACT mutants, indicating a functional association between Abo1 and FACT. However, the precise role of Abo1 in FACT function remains poorly understood. Here, we reveal that Abo1 directly interacts with FACT and facilitates the dissociation of FACT from chromatin. Specifically, the N-terminal region of Abo1 utilizes its FACT interacting (FIN) helix to bind to the N-terminal domain (NTD) of Spt16. In addition, using single-molecule fluorescence imaging, we discovered that Abo1 facilitates the ATP-dependent dissociation of FACT from nucleosomes. Furthermore, we demonstrate that the interaction between Abo1 and FACT is essential for maintaining heterochromatin in fission yeast. In summary, our findings suggest that Abo1 regulates FACT turnover in an ATP-dependent manner, proposing a model of histone chaperone recycling driven by inter-chaperone interactions.
Reversing Pdgfrβ Signaling Restores Metabolically Active Beige Adipocytes by Alleviating ILC2 Suppression in Aged and Obese Mice
Authors: Benvie Abigail M. , Berry Daniel C. 
Published: June 2024

AbstractObjectivePlatelet Derived Growth Factor Receptor Beta (Pdgfrβ) suppresses the formation of cold temperature-induced beige adipocytes in aged mammals. We aimed to determine if deleting Pdgfrβ in aged mice could rejuvenate metabolically active beige adipocytes by activating group 2 innate lymphoid cells (ILC2), and whether this effect could counteract diet-induced obesity-associated beige fat decline.MethodsWe employed Pdgfrβ gain-of-function and loss-of-function mouse models targeting beige adipocyte progenitor cells (APCs). Our approach included cold exposure, metabolic cage analysis, and age and diet-induced obesity models to examine beige fat development and metabolic function under varied Pdgfrβ activity.ResultsAcute cold exposure alone enhanced metabolic benefits in aged mice, irrespective of beige fat generation. However, Pdgfrβ deletion in aged mice reestablished the formation of metabolically functional beige adipocytes, enhancing metabolism. Conversely, constitutive Pdgfrβ activation in young mice stymied beige fat development. Mechanistically, Pdgfrβ deletion upregulated IL-33, promoting ILC2 recruitment and activation, whereas Pdgfrβ activation reduced IL-33 levels and suppressed ILC2 activity. Notably, diet-induced obesity markedly increased Pdgfrβ expression and Stat1 signaling, which inhibited IL-33 induction and ILC2 activation. Genetic deletion of Pdgfrβ restored beige fat formation in obese mice, improving whole-body metabolism.ConclusionThis study reveals that cold temperature exposure alone can trigger metabolic activation in aged mammals. However, reversing Pdgfrβ signaling in aged and obese mice not only restores beige fat formation but also renews metabolic function and enhances the immunological environment of white adipose tissue (WAT). These findings highlight Pdgfrβ as a crucial target for therapeutic strategies aimed at combating age- and obesity-related metabolic decline.
Homogeneous large field-of-view and compact iSCAT-TIRF setup for dynamic single molecule measurements
Authors: De Angelis Giovanni , Abramo Jacopo , Miasnikova Mariia , Taubert Marcel , Eggeling Christian , Reina Francesco 
Published: June 2024

AbstractInterferometric Scattering Microscopy (iSCAT) enables prolonged and high frame rate Single Particle Tracking (SPT) for single molecule dynamics studies. Typically, iSCAT setups employ scanning illumination schemes to achieve uniform sample illumination. However, this implementation limits the field of view (FoV) and maximum sampling rate, while increasing hardware requirements and setup size. We demonstrate the realization of a large (60µm x 60µm) uniformly illuminated FoV through a passive refractive optical element in the iSCAT illumination path. This scanning-free iSCAT microscopy setup is further combined with an objective based Total Internal Reflection Fluorescence Microscopy (TIRF) channel for a complementary fluorescence readout, a focus-lock system, and a tailored control platform via the open-source ImSwitch software, and has a compact footprint. As a proof-of-principle, we highlight the performance of the setup through the acquisition of iSCAT images with a uniform contrast and a ≤10 nm localization precision throughout the whole FoV. The performance is further demonstrated through dynamic iSCAT SPT and imaging Fluorescence Correlation Spectroscopy of lipid diffusion in a model membrane system. Our iSCAT setup thus depicts an accurate and improved way of recording fast molecular dynamics in life sciences.
Production of ceramic bricks using nickel slags as contribution to decarbonization
Authors: Gurieva Victoria , Ilyina Anastasia , Klyuev Sergey , Saidumov Magomed , Khezhev Tolya , Nedoseko Igor , Fediuk Roman , Shamanov Vitaly , Yazyev Batyr 
Published: June 2024

PurposeThe study suggests that the high concentration of mining and metallurgical enterprises on the territory of the Russian Ural region determines the need to consider industrial waste, including nickel slag, as a possible raw material for the production of ceramic bricks. The article describes the properties of clays and nickel slag obtained at metallurgical enterprises in the Orenburg region and the features of their use as components in the composition of ceramic bricks.Design/methodology/approachTo achieve this purpose, such tasks as determining the technological parameters of production, conducting the X-ray phase and microstructural analysis of the obtained samples were solved.FindingsCompositions of ceramic mass using clay from the Khalilovsky deposit (Orenburg region) with the addition of nickel slag (20 and 40% by weight) have been developed, and their physical and mechanical properties (compressive strength, bending strength, water absorption and density) have been determined. With the help of modern research methods involving high-tech equipment, the microstructure is considered and the phase composition of the finished samples is determined. As a result of the conducted research, it was found that the composition of the selected clay and nickel slag in the obtained rational composition ensures the production of ceramic bricks of grades M175 and M200.Originality/valueThis is the first study on the use of nickel slag for the production of ceramic bricks. The results relate primarily to Russian feedstocks, but a methodology is presented that can be applied to other countries as well as to other silica-containing feedstocks.
Corporate governance and firm risk-taking: empirical evidence from India
Authors: Tiwari Reshma Kumari , Jha Ratish Kumar 
Published: June 2024

PurposeThis study aims to examine the impact of corporate governance (CG) on firm risk-taking in India.Design/methodology/approachThe present study is based on a panel data set of 100 non-financial Indian firms randomly selected from the top 500 firms listed on the Bombay Stock Exchange. The study uses two market-based measures to capture firm risk-taking – total risk and idiosyncratic risk. Generalised method of moments model is applied to examine the relationship between CG and firm risk-taking. Additionally, the fixed-effects model is applied to check the robustness of the results.FindingsThe study reveals a significant negative impact of CG index, CEO duality, multiple directorships, promoter ownership and institutional ownership on firm risk-taking. Whereas board size, board independence, board gender diversity and the number of board meetings do not significantly impact firm risk-taking.Originality/valueThis study contributes to the existing literature by providing a comprehensive view of how various CG attributes shape firm risk-taking in India. It examines eight CG variables: board size, board independence, board gender diversity, CEO duality, multiple directorships, number of board meetings, promoter ownership and institutional ownership. Furthermore, the study incorporates idiosyncratic risk as an additional measure of firm risk-taking, largely overlooked in the Indian context. Moreover, to the best of the authors’ knowledge, this is the first study to examine the impact of CG index on firm risk-taking in India.
Multi-scale wear mechanism of material surface and hinge interface based on TC4 alloy in space environment
Authors: Wang Dian , Huang Chuanjin , Hu Ning , Wei Qiang 
Published: June 2024

Purpose
The purpose of this paper is to clarify the influence of low earth orbit space environment on the wear mechanism of TC4 alloy material and crank rocker mechanism.

Design/methodology/approach
In this study, friction experiments were carried out on TC4 alloy friction discs and crank rocker mechanisms, both before and after exposure to atomic oxygen and proton irradiation. Nanoindentation, grazing incidence X-ray diffraction (GIXRD), and X-ray photoelectron spectroscopy were employed to systematically characterize alterations in mechanical properties, surface phase, and chemical composition.

Findings
The results show that the wear mechanism of TC4 alloy friction disc is mainly adhesive wear in vacuum environment, while the wear mechanism of crank rocker mechanism includes not only adhesive wear but also abrasive wear. Atomic oxygen exposure leads to the formation of more oxides on the surface of TC4 alloy, which form abrasive particles during the friction process. Proton irradiation will lead to a decrease in fatigue performance and an increase in hardness on the surface of TC4 alloy, thus causing fatigue wear on the surface of TC4 alloy, and more furrows appear on the crank rocker mechanism after proton irradiation. In the three environments, the characteristics of abrasive wear of the crank rocker mechanism are more obvious than those of the TC4 alloy friction disc.

Originality/value
These results highlight the importance of understanding the subtle effects of atomic oxygen and proton irradiation on the wear behavior of TC4 alloy and provide some insights for optimizing its performance in space applications.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-02-2024-0051/