bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tactile Mechanisms and Afferents Underlying the Rat Pup Transport Response
Authors: Ni Zheyi , Neifert Connor , Rosete Arturo , Albeely Abdalla M. , Yang Yu , Pratelli Marta , Brecht Michael , Clemens Ann M. 
Published: August 2024

AbstractJuvenile rodents and other altricial mammals react with calming, immobility and folding up of feet to parental pickup, a set of behaviors referred to as transport response. Here we investigate sensory mechanisms underlying the rat transport response. Grasping rat pups in anterior neck positions evokes strong immobility and folding up of feet, whereas more posterior grasping positions have lesser effects on immobility and foot position. Transport responses are enhanced by slow (1Hz) and even more so by fast (4Hz) gentle shaking and translation of the pup, features consistent with parental transport. In response to lateral grasping, the forepaw below the grasping position points downwards and the forepaw lateral to the grasping position points upwards and medially. Such forepaw adjustments put the pup’s center of gravity below the grasping point, optimizing pup transportability along with folding up of feet and tail lifting. Tactile stimuli on the back, belly, tail, whisker, dorsal forepaws and dorsal hind-paws do not significantly affect the behaviour of anterior-neck-held pups. Instead, ground contact or paw stimulation consistent with ground contact disrupts transport responses. We identify afferents mediating the transport response by examining membrane labelling with FM1-43 following anterior neck grasping. We observe a dense innervation of the anterior neck skin region (∼30 terminals/ mm2). We also observed an age-related decrease of cytochrome oxidase reactivity in the rat somatosensory cortical neck representation, a possible correlate to the developmental decrease in the pup transport response. We conclude anterior neck grasping and loss of ground contact trigger calming and postural adjustments for parental transport in rat pups, responses putatively driven from the densely innervated anterior neck skin.
The immunobiology of persistent intestinal infection byCampylobacter jejuniin the chicken
Authors: Gilroy Rachel , Wedley Amy , Jopson Sue , Hall Judith , Wigley Paul 
Published: August 2024

AbstractInfection of the intestinal tract of the chicken withCampylobacter jejuniis frequently prolonged with limited immune clearance from the caeca, the main site of colonisation. Previously it has been shown early infection of broiler chickens leads to a pro-inflammatory response, followed by regulatory and Th17 responses along with adaptive Th1 and Th2 cytokine responses. Here we show that infection up to 28 days post challenge leads to prolonged expression of IL-4 and high titre IgM and IgY serum antibody responses toC. jeuni, along with increased levels of total IgA in the gut of infected birds. Whilst early pro-inflammatory cytokine and chemokine responses largely wane, expression of both IL-10 and IL-17A remain high in the colonised caeca or caecal tonsils. Based on this and previous studies we hypothesize that the nature of the immune response toC.jeuniinfection is one that allows persistence in the gut, but limits inflammation and invasive infection from the gut through maintaining the intestinal barrier and producing secretory antibody. This protects the birds from campylobacteriosis, but the persistence in the gut for the production lifetime of chickens remains an unsolved public health issue.
Cyclic Electromagnetic DNA Simulation (CEDS) can regulate the Functions of Different miRNAs and DNA Motifs: Protein Signaling Pathways in RAW 264.7 Cells detected by IP-HPLC Analysis
Authors: Kim Yeon Sook , Lee Suk Keun 
Published: August 2024

AbstractBased on the hydrogen bonding magnetic resonance (HBMR) in double-stranded DNAs (dsDNAs) exhibiting unique base pair polarities, Cyclic Electromagnetic DNA Simulation (CEDS)1was designed to target nine miRNAs and four protein binding site sequences, which are known to have an anti-oncogenic or oncogenic role in cells. RAW 264.7 cells were cultured and treated with CEDS at 20-25 Gauss in a 5% CO2and 37℃ incubator for 20 min. Besides the cytological observation, the expressions of murine miRNAs and proteins were assessed by quantitative polymerase chain reaction (qPCR) and immunoprecipitation high-performance liquid chromatography (IP-HPLC) using 350 antisera, respectively. The results demonstrated that CEDS was found to increase the number of the corresponding mature and primary miRNAs and influenced the protein signaling in cells. For example, miR-34a-5p*-CEDS was able to downregulate 59 out of 43 target proteins (72.9%), and attenuated RAS-NFkB signaling axis, which subsequently led to the inactivation of proliferation-related signaling axis, protection-ER stress-survival signaling axis, telomere-glycolysis-fibrosis signaling axis, and FAS- and PARP-mediated apoptosis signaling axis. Conversely, miR-34a-5p*-CEDS activated the p53/Rb/E2F1-SHH/PTCH/GLI-Notch/Jagged proliferation signaling axis, epigenetic modification-RAS-p53 associated apoptosis signaling axis, and oncogenesis-senescence-innate immunity-chronic inflammation signaling axis. Among nine CEDS targeting mature miRNAs, miR-150-5p*-CEDSs exhibited a potent anti-oncogenic effect on RAW 264.7 cells, while miR-34a-5p*-, miR-181a-5p*-, miR-216a-5p*-, miR-365a-3p*-, and miR-655-3p*-CEDSs exhibited a dual effect, inducing both anti-oncogenic and oncogenic effects. Conversely, miR-155-5p*-CEDS appears to induce marked oncogenic effect, rather than anti-oncogenic effect. Among four CEDS targeting protein binding site sequences, p53 binding site sequence AGACATGCCT*-CEDS induced an oncogenic effect by upregulating proliferation, telomere, and oncogenesis signaling, while concomitantly inducing an anti-oncogenic effect by downregulating RAS and NFkB signaling and upregulating p53- and PARP-mediated apoptosis. Canonical E2Fs binding site sequence TTTC(C/G)CGC*-CEDS facilitated an oncogenic effect by enhancing RAS and NFkB signaling, resulting in the upregulation of proliferation, telomere, and senescence signaling. Consequently, it was found that CEDS using a miRNA or protein binding site sequence impacted the protein signaling in RAW 264.7 cells in a sequence-specific manner. It is therefore proposed that CEDS can target miRNAs and DNA motifs, influencing their hybridization and conformation, and subsequently regulate the protein signaling in the cells.
Monitoring DNA double strand break repair inSaccharomyces cerevisiaeat high throughput and high resolution
Authors: Ezra Yael Shalev , Saguy Alon , Levin Gaia , Weiss Lucien E. , Alalouf Onit , Shechtman Yoav 
Published: August 2024

ABSTRACTThe yeast mating type switching process is used as a biological model system to study eukaryotic DNA double strand break (DSB) repair, a process of fundamental importance in health and disease. However, tools for tracking the mating type switching process in real-time in live cells are limited. We developed methods to follow and quantify mating type switching occurrence in real-time, at the single live cell level, applicable for detection of rare events and population heterogeneity. First, we show, using a fluorescent reporter in live cells, that switching probability in strains tagged by a fluorescent repressor-operator system (FROS) is reduced, not only due to the integration of operator repeats, but also due to the overexpressed fluorescent molecules in the nucleus. Next, by applying wavefront shaping to imaging flow cytometry, we collected 3D data in high throughput, and were able to differentiate between MATa and MATα conformation and to detect DNA dynamics during switching with unprecedented spatial and temporal resolutions. Using a strain with theMAT-stkmutation, which gives rise to inefficient HO endonuclease DSB activity, we discriminated between two consecutive distances between the HMLα and the MAT loci upon DNA damage. We suggest that initial nearing between the loci occurs for both single and double strand breaks, and further and closer proximity occurs for DSB only, leading to mating type switching. Our approach can be adapted to other biological systems to study DSB repair with high precision, throughput and sensitivity.
DEK-rRNA interactions regulate ribosome biogenesis and stress response
Authors: Xu Nengwei , Chen Kunqi , Prell Malte , Liang Pengtao , Yang Shuhuai , Guo Shengjie , Lu Yuli , Dorle Soham , Idaghdour Samia , Kappes Ferdinand 
Published: August 2024

AbstractDNA/chromatin-based functions of the DEK oncogene, a unique nucleic acid-interacting factor in metazoans, have been widely investigated, yet its role in cellular RNA biology is under-studied. Herein we employed CLIP-seq alongside mutational, biochemical, and cellular approaches to gain deeper insights into the cellular DEK-RNA interplay. We confirm interaction of DEK with coding RNA, yet also report association with ribosomal RNA (rRNA) and thereby establishing a robust link between DEK and ribosome biology. Indeed, cells lacking DEK showed marked deficits in cytoplasmic ribosome quality and function. This phenotype was exclusively rescued by C-terminal DEK, harboring two RNA interaction domains, but not by an rRNA-binding deficient mutant. Mechanistically, we uncovered pleiotropic involvement of DEK in RNA polymerase I-mediated rRNA transcription and processing pathways. More specifically, we found direct interaction of DEK with RNA polymerase III-transcribed 5S rRNA and identified DEK as a regulator of the Impaired Ribosome Biogenesis Checkpoint (IRBC). Within this ribosomal stress pathway, DEK depletion results in free 5S RNP, triggering stabilization of p53 via inhibition of MDM2. In summary, our multilayer analysis revealed DEK as a potent cellular RNA binding protein and provides first evidence of DEK as a regulator of ribosome biogenesis and stress response via the 5S RNP-MDM2-p53 axis.
Complement activation at injury sites drives the phagocytosis of necrotic cell debris and resolution of liver injury
Authors: Vandendriessche Sofie , Mattos Matheus Silvério , Bialek Emilia Laura , Schuermans Sara , Proost Paul , Marques Pedro Elias 
Published: August 2024

AbstractCells die by necrosis due to excessive chemical or thermal stress, leading to plasma membrane rupture, release of intracellular components and severe inflammation. The clearance of necrotic cell debris is crucial for tissue recovery and injury resolution, however, the underlying mechanisms are still poorly understood, especially in vivo. This study examined the role of complement proteins in promoting clearance of necrotic cell debris by leukocytes and their influence on liver regeneration. We found that independently of the type of necrotic liver injury, either paracetamol (APAP) overdose or thermal injury, complement proteins C1q and (i)C3b were deposited specifically on necrotic lesions via the activation of the classical pathway. Importantly, C3 deficiency led to a significant accumulation of necrotic debris and impairment of liver recovery in mice, which was attributed to decreased phagocytosis of debris by recruited neutrophils in vivo. Monocytes and macrophages also took part in debris clearance, although the necessity of C3 and CD11b was dependent on the specific type of necrotic liver injury. Using human neutrophils, we showed that depletion of C1q or C3 caused a reduction in the volume of necrotic debris that is phagocytosed, indicating that complement promotes effective debris uptake by neutrophils in mice and humans. In summary, complement activation at injury sites is a pivotal event for necrotic debris clearance by phagocytes and determinant for efficient recovery from tissue injury.Abstract FigureKey pointsThe complement cascade is activated on necrotic cell debrisin vivovia the classical pathwayDeficiency in complement C3 impairs necrotic debris clearance and liver recovery after injuryComplement-mediated debris clearance is performed by neutrophils, monocytes and macrophagesHuman neutrophils depend on complement opsonization to phagocytose necrotic cell debris efficiently
Estimating Ancestral States of Complex Characters: A Case Study on the Evolution of Feathers
Authors: Cockx Pierre , Benton Michael J. , Keating Joseph N. 
Published: August 2024

AbstractFeathers are a key novelty underpinning the evolutionary success of birds, yet the origin of feathers remains poorly understood. Debates about feather evolution hinge upon whether filamentous integument has evolved once or multiple time independently on the lineage leading to modern birds. These contradictory results stem from subjective methodological differences in statistical ancestral state estimates. Here we conduct a comprehensive comparison of ancestral state estimation methodologies applied to stem-group birds, testing the role of outgroup inclusion, tree time scaling method, model choice and character coding strategy. Models are compared based on their Akaike Information Criteria (AIC), mutual information, as well as the uncertainty of marginal ancestral state estimates. Our results demonstrate that ancestral state estimates of stem-bird integument are strongly influenced by tree time scaling method, outgroup selection and model choice, while character coding strategy seems to have less effect on the ancestral estimates produced. We identify the best fitting models using AIC scores and a leave-one-out cross-validation approach (LOOCV). Our analyses broadly support the independent origin of filamentous integument in dinosaurs and pterosaurs and support a younger evolutionary origin of feathers than has been suggested previously. More generally, our study highlights that special care must be taken in selecting the outgroup, tree and model when conducting ASE analyses. With respect to model selection, our results suggest that considering a LOOCV approach, may yield more reliable results than simply comparing AIC scores when the analyses involve a limited number of taxa.
Mammalian PIEZO channels rectify anionic currents
Authors: Wijerathne Tharaka D. , Bhatt Aashish , Jiang Wenjuan , Luo Yun Lyna , Lacroix Jerome J. 
Published: August 2024

AbstractUnder physiological conditions, mammalian PIEZO channels (PIEZO1 and PIEZO2) elicit transient currents mostly carried by monovalent and divalent cations. PIEZO1 is also known to permeate chloride ions, with a Cl-/ Na+permeability ratio of about 0.2. Yet, little is known about how anions permeate PIEZO channels. Here, by separately measuring sodium and chloride currents using non-permanent counter-ions, we show that both PIEZO1 and PIEZO2 rectify chloride currents outwardly, favoring entry of chloride ions at voltages above their reversal potential, whereas little to no rectification was observed for sodium currents. Interestingly, chloride currents elicited by 9K, an anion-selective PIEZO1 mutant harboring multiple positive residues along intracellular pore fenestrations, also rectify but in the inward direction. Molecular dynamics simulation indicate that the inward rectification of chloride currents in 9K correlates with the largely positive electrostatic potential at the intracellular pore entrance, suggesting that rectification can be tuned by pore polarity. These results demonstrate that the pore of mammalian PIEZO channels inherently rectifies chloride currents.Statement of significanceMechanosensitive PIEZO ion channels play many important roles across cells and tissues. Their open pore facilitates the flow of cations down their electrochemical gradients, eliciting sodium-driven membrane depolarization and calcium-dependent signaling under physiological conditions. Yet, these channels also permeate chloride ions. In this study, we show that the two mammalian PIEZO channel homologs preferentially permeate chloride ions into the cells at voltages more positive than the chloride reversal potential. Although PIEZOs permeate cations more effectively than chloride ions, the influx of chloride ions mediated by PIEZOs could participate in certain physiological processes.
PHIStruct: Improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings
Authors: Gonzales Mark Edward M. , Ureta Jennifer C. , Shrestha Anish M.S. 
Published: August 2024

AbstractMotivationRecent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.ResultWe present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera. Compared against recent tools, PHIStruct exhibits the best balance of precision and recall, with the highest and most stable F1 score across a wide range of confidence thresholds and sequence similarity settings. The margin in performance is most pronounced when the sequence similarity between the training and test sets drops below 40%, wherein, at a relatively high-confidence threshold of above 50%, PHIStruct presents a 7% to 9% increase in class-averaged F1 over machine learning tools that do not directly incorporate structure information, as well as a 5% to 6% increase over BLASTp.Availability and ImplementationThe data and source code for our experiments and analyses are available athttps://github.com/bioinfodlsu/PHIStruct.
Design and analysis of double-permanent-magnet enhanced hybrid stepping machine with tangential and radial magnetization
Authors: Chai Xiaobao , Liu Jinglin , Guan RuiZhi , Xiao Minglang 
Published: August 2024

Purpose
To improve the output torque density of the machine and to be better suited for automation applications, this paper aims to propose a double-permanent-magnet enhanced hybrid stepping machine (DPMEHSM) with tangential and radial magnetization.

Design/methodology/approach
First, the structure of DPMEHSM is introduced and its operation principle is analyzed by describing the variation in stator poles versus time. Second, based on the similar electrical load and amount of PM, the size equations of the DPMEHSM are designed and the main parameters are presented. Third, the electromagnetic performances including the PM flux linkage distribution, magnetic density distribution, air-gap field, back electromotive force (back-EMF), detent torque, holding torque and output torque of DPMEHSM and stator-PM hybrid stepping machine (SPMHSM) are analyzed based on the finite element method.

Findings
The results show that the DPMEHSM has superiority in back-EMF, holding torque and output torque.

Originality/value
This paper proposes a DPMEHSM with tangential and radial magnetization to improve the output torque density.
From entrepreneurship to established business: duration, challenges and coping tactics according to resource providers and successful entrepreneurs
Authors: De Sordi José Osvaldo , Paulo Wanderlei Lima de , Jorge Carlos Francisco Bitencourt , Bandiera Jeremias  , André André Rodrigues dos 
Published: August 2024

Purpose
This paper aims to explore the perception of successful entrepreneurs and resource providers regarding the minimum operational time necessary to legitimize an enterprise as an established company, as well as the tactics used by the entrepreneurs to minimize the distrust of society during this initial period of the life cycle of the organization.

Design/methodology/approach
Data collection from two groups: (i) interviews with 62 entrepreneurs and founders of established companies; and (ii) a questionnaire completed by 77 sales managers of companies that provide businesses with resources (they practice business-to-business). Regarding analyses: (i) to analyze information, this study applied the content analysis technique; and (ii) for data, this study applied the one-sample t-test, mean comparison t-test, Pearson’s correlation test, chi-square test of association, Mann–Whitney U test and correspondence analysis technique.

Findings
In this study, a period of 42 months was identified for the legitimization of enterprises by society, in other words, the time necessary for enterprises to be recognized as an established company and a company of low risk by customers and resource providers. A set of managerial and behavioral actions practiced by successful entrepreneurs to face the difficulties they experience during the legitimization period was also identified.

Practical implications
In addition to establishing a period of 42 months for the legitimization of an enterprise in the eyes of society, a set of 15 strategies used by successful entrepreneurs was identified to combat the prejudice associated with the youthfulness of their companies. Of these, 12 are linked to managerial actions and 3 to the entrepreneur’s behavior. It should be highlighted that eight of these strategies are innovative and have yet to be addressed in the literature on mitigating risks associated with the liability of newness principle.

Originality/value
The authors discuss the legitimization of enterprises based on the perception of actors who play a fundamental role regarding entrepreneurial action: resource providers for companies, customers and successful entrepreneurs. This is a triangulation of sources, as well as a triangulation of collected data and qualitative and quantitative techniques, which sought to ensure the accuracy and reliability of the information that resulted from this analytical process.
Employee retention and company performance results: the mediating role of HRM outcomes in foreign subsidiaries of Central European MNCs
Authors: Stor Marzena 
Published: August 2024

PurposeThe main goal of the article is to identify, analyze and evaluate the mediating role of HRM outcomes in the relationships between employee retention (ER) and company performance results, with a specific focus on discerning any shifts or differences in this mediation across non-crisis and crisis times in the foreign subsidiaries of MNCs.Design/methodology/approachThe empirical research covered 200 MNCs headquartered in Central Europe. A Computer-Aided Telephone Interviewing (CATI) method was used for data collection. The raw data was adjusted using the Efficiency Index (EI) to accurately represent the relationships between the variables under study. The research hypotheses were examined, and the mediating effects were assessed through Partial Least Squares Structural Equation Modeling (PLS-SEM).FindingsThe research findings provide valuable insights by exploring the mediating role of HRM outcomes between ER and company performance results, highlighting HRM’s crucial role in enhancing results in finance, innovation and quality, particularly during crises. They underscore the strategic importance of HRM in fostering organizational resilience and innovation.Originality/valueThe study offers a new methodological contribution through introducing the EI for a precise quantitative evaluation of the relationships between ER, HRM and company performance results. However, the greatest added value of this article is the creation of the ER-HRM Mediation Theory of Organizational Resilience through Innovativeness in Crisis.