bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cortical spheroids show strain-dependent cell viability loss and neurite disruption following sustained compression injury
Authors: González-Cruz Rafael D. , Wan Yang , Calvao Dominick , Burgess Amina , Renken William , Vecchio Francesca , Franck Christian , Kesari Haneesh , Hoffman-Kim Diane 
Published: November 2023

AbstractSustained compressive injury (SCI) in the brain is observed in numerous injury and pathological scenarios, including tumors, ischemic stroke, and traumatic brain injury-related tissue swelling. Sustained compressive injury is characterized by tissue loading over time, and currently, there are fewin vitromodels suitable to study neural cell responses to strain-dependent sustained compressive injury. Here, we present anin vitromodel of sustained compressive neural injury via centrifugation. Spheroids were made from neonatal rat cortical cells seeded at 4000 cells/spheroid and cultured for 14 daysin vitro. A subset of spheroids was centrifuged at 209 or 419 rad/s for 2 minutes. Modeling the physical compression of the spheroids via finite element analyses, we found that spheroids centrifuged at 209 and 419 rad/s experienced pressures of 38 kPa and 149 kPa, respectively, and compressive strains of 18% and 35%, respectively. Quantification of LIVE-DEAD assay and Hoechst 33342 nuclear staining showed that centrifuged spheroids exhibited significantly higher DNA damage than control spheroids at 2, 8, and 24 hours post-injury. Immunohistochemistry of β3-tubulin networks at 2, 8, and 24 hours post-centrifugation injury showed increasing degradation of microtubules over time with increasing compressive strain. Our findings show that cellular injuries occur as a result of specific levels and timings of sustained compressive tissue strains. This experimental compressive injury model provides anin vitroplatform to examine cellular injury to gain insights into brain injury that could be targeted with therapeutic strategies.
Pangenome- and genome-based taxonomic classification inference for the marine bacterial strain KMM 296 producing a highly active PhoA alkaline phosphatase and closely relatedCobetiaspecies
Authors: Nedashkovskaya O.I. , Balabanova L.A. , Otstavnykh N. Y. , Zhukova N.V. , Seitkalieva A.V. , Noskova Yu.A. , Tekutyeva L.A 
Published: November 2023

AbstractA strictly aerobic, Gram-stain-negative, rod-shaped and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of musselCrenomytilus grayanus, was investigated in details due to its ability to produce a highly active alkaline phosphatase of the structural family PhoA. A previous taxonomic study placed the strain to the speciesCobetia marina, a member of the familyHalomonadaceaeof the classGammaproteobacteria. However, the comprehensive phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain KMM 296 is most closely related toCobetia amphilectiNRIC 815Twith the 16S rRNA gene sequence similarity of 100%. The mussel isolate grew with 0.5-19% NaCl and at 4 - 42°C and hydrolysed Tweens 20 and 40, and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C18:1ω7c, C12:03-OH, C18:1ω7c, C12:0and C17:0cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and unidentified aminolipid, phospholipid, and lipids. The major respiratory quinone was Q-8. According to phylogenetic evidence and similarity in the chemotaxonomic and genotypic properties of the mussel isolate and its nearest neighbors, the strain KMM 296 represents a member of the speciesC. amphilecti. A comparative analysis of the type strains genomes of the speciesC. amphilectiandC. litoralisshowed that they belong to a single species. In addition, a high similarity of the genome sequences ofC. pacificaNRIC 813TandC. marinaLMG 2217Talso allows suggesting the affiliation of these two species to one species. Based on the rules of priority,C. litoralisshould be reclassified as a later heterotypic synonym ofC. amphilecti, andC. pacificais a later heterotypic synonym ofC. marina. The emended descriptions of the speciesC. amphilectiandC. marinaare also proposed.
Investigating the Role of Neck Muscle Activation and Neck Damping Characteristics in Brain Injury Mechanism
Authors: Bahreinizad Hossein , Chowdhury Suman K. 
Published: November 2023

AbstractPurposeThis study aimed to investigate the role of neck muscle activity and neck damping characteristics in traumatic brain injury (TBI) mechanisms.MethodsWe used a previously validated head-neck finite element (FE) model that incorporates various components such as scalp, skull, cerebrospinal fluid, brain, muscles, ligaments, cervical vertebrae, and intervertebral discs. Impact scenarios included a Golf ball impact, NBDL linear acceleration, and Zhang’s linear and rotational accelerations. Three muscle activation strategies (no-activation, low-to-medium, and high activation levels) and two neck damping levels by perturbing intervertebral disc properties (high: hyper-viscoelastic and low: hyper-elastic) strategies were examined. We employed Head Injury Criterion (HIC), Brain Injury Criterion (BrIC), and maximum principal strain (MPS) as TBI measures.ResultsIncreased neck muscle activation consistently reduced the values of all TBI measures in Golf ball impact (HIC: 4%-7%, BrIC: 11%-25%, and MPS (occipital): 27%-50%) and NBDL study (HIC: 64%-69%, BrIC: 3%-9%, and MPS (occipital): 6%-19%) simulations. In Zhang’s study, TBI metric values decreased with the increased muscle activation from no-activation to low-to-medium (HIC: 74%-83%, BrIC: 27%-27%, and MPS (occipital): 60%-90%) and then drastically increased with further increases to the high activation level (HIC: 288%-507%, BrIC: 1%-25%, and MPS (occipital): 23%-305%). Neck damping changes from low to high decreased all values of TBI metrics, particularly in Zhang’s study (up to 40% reductions).ConclusionOur results underscore the pivotal role of neck muscle activation and neck damping in TBI mitigation and holds promise to advance effective TBI prevention and protection strategies for diverse applications.
Atom filtering algorithm and GPU-accelerated calculation of simulation atomic force microscopy images
Authors: Amyot Romain , Kodera Noriyuki , Flechsig Holger 
Published: November 2023

AbstractSimulation atomic force microscopy computationally emulates experimental scanning of a biomolecular structure to produce topographic images that can be correlated with measured images. Its application to the enormous amount of available high-resolution structures, as well as to molecular dynamics modelling data, facilitates the quantitative interpretation of experimental observations by inferring atomistic information from resolution-limited measured topographies. The computation required to generate a simulated AFM image generally includes the calculation of contacts between the scanning tip and all atoms from the biomolecular structure. However, since only contacts with surface atoms are relevant, a filtering method shall highly improve the efficiency of simulation AFM computations. In this report we address this issue and present an elegant solution based on graphics processing unit (GPU) computations that significantly accelerates the computation of simulation AFM images. The method not only allows for visualization of biomolecular structures combined with ultra-fast synchronized calculation and graphical representation of corresponding simulated AFM images (live simulation AFM), but, as we demonstrate, can also reduce the computational effort during automatized fitting of atomistic structures into measured AFM topographies by orders of magnitude. Hence, the developed method will play an important role in post-experimental computational analysis involving simulation AFM. Implementation is realized in our BioAFMviewer software package for simulation AFM of biomolecular structures and dynamics.
Trans-omic analysis reveals opposite metabolic dysregulation between feeding and fasting in liver associated with obesity
Authors: Bai Yunfan , Morita Keigo , Kokaji Toshiya , Hatano Atsushi , Ohno Satoshi , Egami Riku , Pan Yifei , Li Dongzi , Yugi Katsuyuki , Uematsu Saori , Inoue Hiroshi , Inaba Yuka , Suzuki Yutaka , Matsumoto Masaki , Takahashi Masatomo , Yoshihiro Izumi , Bamba Takeshi , Hirayama Akiyoshi , Soga Tomoyoshi , Kuroda Shinya 
Published: November 2023

SUMMARYDysregulation of liver metabolism associated with obesity during feeding and fasting leads to the breakdown of metabolic homeostasis. However, the underlying mechanism remains unknown. Here, we measured multi-omics data in the liver of wild-type and leptin-deficient obese (ob/ob) mice atad libitumfeeding, and constructed a differential regulatory trans-omic network of metabolic reactions. We compared the trans-omic network at feeding with that at 16 h-fasting constructed in our previous study. Intermediate metabolites in glycolytic and nucleotide metabolism decreased inob/obmice at feeding but increased at fasting. Allosteric regulation reversely shifted between feeding and fasting, generally showing activation at feeding while inhibition at fasting inob/obmice. Transcriptional regulation was similar between feeding and fasting, generally showing inhibiting transcription factor regulations, activating enzyme protein regulations inob/obmice. The opposite metabolic dysregulation between feeding and fasting characterizes breakdown of metabolic homeostasis associated with obesity.
Adapting genetic algorithms for artificial evolution of visual patterns under selection from wild predators
Authors: Briolat Emmanuelle S. , Hancock George R. A. , Troscianko Jolyon 
Published: November 2023

AbstractCamouflage is a widespread and well-studied anti-predator strategy, yet identifying which patterns provide optimal protection in any given scenario remains challenging. Besides the virtually limitless combinations of colours and patterns available to prey, selection for camouflage strategies will depend on complex interactions between prey appearance, background properties and predator traits, across repeated encounters between co-evolving predators and prey. Experiments in artificial evolution, pairing psychophysics detection tasks with genetic algorithms, offer a promising way to tackle this complexity, but sophisticated genetic algorithms have so far been restricted to screen-based experiments. Here, we present methods to test the evolution of colour patterns on physical prey items, under selection from wild predators in the field. Our techniques expand on a recently-developed open-access pattern generation and genetic algorithm framework, modified to operate alongside artificial predation experiments. In this system, predators freely interact with prey, and the order of attack determines the survival and reproduction of prey patterns into future generations. We demonstrate the feasibility of these methods with a case study, in which free-flying birds feed on artificial prey deployed in semi-natural conditions, against backgrounds differing in three-dimensional complexity. Wild predators reliably participated in this experiment, foraging for 11 to 16 generations of artificial prey and encountering a total of 1,296 evolved prey items. Changes in prey pattern across generations indicated improvements in several metrics of similarity to the background, and greater edge disruption, although effect sizes were relatively small. Computer-based replicates of these trials, with human volunteers, highlighted the importance of starting population parameters for subsequent evolution, a key consideration when applying these methods. Ultimately, these methods provide pathways for integrating complex genetic algorithms into more naturalistic predation trials. Customisable open-access tools should facilitate application of these tools to investigate a wide range of visual pattern types in more ecologically-relevant contexts.
The Impact of Visually Simulated Self-Motion on Predicting Object Motion
Authors: Jörges Björn , Harris Laurence R. 
Published: November 2023

AbstractTo interact successfully with moving objects in our environment we need to be able to predict their behavior. Predicting the position of a moving object requires an estimate of its velocity. When flow parsing during self-motion is incomplete – that is, when some of the retinal motion created by self-motion is incorrectly attributed to object motion – object velocity estimates become biased. Further, the process of flow parsing should add noise and lead to object velocity judgements being more variable during selfmotion. Biases and lowered precision in velocity estimation should then translate to biases and lowered precision in motion extrapolation. We investigated this relationship between self-motion, velocity estimation and motion extrapolation with two tasks performed in a realistic virtual reality (VR) environment: first, participants were shown a ball moving laterally which disappeared after a certain time. They then indicated by button press when they thought the ball would have hit a target rectangle positioned in the environment. While the ball was visible, participants sometimes experienced simultaneous visual lateral self-motion in either the same or in the opposite direction of the ball. The second task was a two-interval forced choice task in which participants judged which of two motions was faster: in one interval they saw the same ball they observed in the first task while in the other they saw a ball cloud whose speed was controlled by a PEST staircase. While observing the single ball, they were again moved visually either in the same or opposite direction as the ball or they remained static. We found the expected biases in estimated time-to-contact, while for the speed estimation task, this was only the case when the ball and observer were moving in opposite directions. Our hypotheses regarding precision were largely unsupported by the data. Overall, we draw several conclusions from this experiment: first, incomplete flow parsing can affect motion prediction. Further, it suggests that time-to-contact estimation and speed judgements are determined by partially different mechanisms. Finally, and perhaps most strikingly, there appear to be certain compensatory mechanisms at play that allow for much higher-than-expected precision when observers are experiencing self-motion – even when self-motion is simulated only visually.
Influence of Nursing Explanation Skills on Incident Occurrence
Authors: Fujimoto Manabu , Shimamura Mika , Yuki Fumiko 
Published: November 2023

ObjectivesA routine nursing task is providing explanations to patients, their families, and other healthcare professionals. Inaccurate explanations can adversely affect the quality of healthcare and patient safety. Despite the significance of good explanatory skills in nursing, supporting empirical data are limited. Therefore, this study aimed to develop a psychological scale and investigate the impact of explanatory skills on incidents.MethodsIn the preliminary investigation, responses obtained from experienced nurses were analyzed to compile 87 scale items. Study 1 involved an online explanatory skills survey with a sample of 1,000 nursing professionals. Study 2 comprised a field survey involving 159 nursing staff members working in a comprehensive hospital.ResultsNine sub-skills were identified and categorized under two factors: “compassion” and “mental model sharing.” Seven of these sub-skills were found to be shared, and the remaining two were specific to interactions with patients/families or healthcare professionals. Clinical ladder progression was associated with both compassion and mental model sharing, whereas years of practical experience was only related to mental model sharing. Furthermore, compassion was identified as a factor that increased the probability of the occurrence of various incidents through interactional failures. In contrast, mental model sharing enhanced the probability of severe incidents stemming from judgmental failures and minor incidents from conceptual failures.ConclusionsThis study developed a psychological scale to measure nursing professionals’ explanation skills in communication with patients, their families, and other medical staff. It elucidated their impact on incident occurrence through miscommunication. The findings need to be practically verified through fieldwork in nursing education.
Polygenic burden of short tandem repeat expansions promote risk for Alzheimer’s disease
Authors: Guo Michael H. , Lee Wan-Ping , Vardarajan Badri , Schellenberg Gerard D. , Phillips-Cremins Jennifer 
Published: November 2023

AbstractStudies of the genetics of Alzheimer’s disease (AD) have largely focused on single nucleotide variants and short insertions/deletions. However, most of the disease heritability has yet to be uncovered, suggesting that there is substantial genetic risk conferred by other forms of genetic variation. There are over one million short tandem repeats (STRs) in the genome, and their link to AD risk has not been assessed. As pathogenic expansions of STR cause over 30 neurologic diseases, it is important to ascertain whether STRs may also be implicated in AD risk. Here, we genotyped 321,742 polymorphic STR tracts genome-wide using PCR-free whole genome sequencing data from 2,981 individuals (1,489 AD case and 1,492 control individuals). We implemented an approach to identify STR expansions as STRs with tract lengths that are outliers from the population. We then tested for differences in aggregate burden of expansions in case versus control individuals. AD patients had a 1.19-fold increase of STR expansions compared to healthy elderly controls (p=8.27×10−3, two-sided Mann Whitney test). Individuals carrying > 30 STR expansions had 3.62-fold higher odds of having AD and had more severe AD neuropathology. AD STR expansions were highly enriched within active promoters in post-mortem hippocampal brain tissues and particularly within SINE-VNTR-Alu (SVA) retrotransposons. Together, these results demonstrate that expanded STRs within active promoter regions of the genome promote risk of AD.
Fecal microbiota transplantation from individual with bipolar disorder and healthy control elicits distinct behaviors and metabolite profiles in mice
Authors: Bukowski-Thall Grace , Fellendorf Frederike T. , Gorkiewicz Sarah , Ip Kenny Chi Kin , Schmidt Laura , Durdevic Marija , Habisch Hansjörg , Mörkl Sabrina , Wagner-Skacel Jolana , Bengesser Susanne A. , Lenger Melanie , Dalkner Nina , Gorkiewicz Gregor , Högenauer Christoph , Madl Tobias , Moissl-Eichinger Christine , Farzi Aitak , Reininghaus Eva Z. 
Published: November 2023

AbstractBipolar disorder (BD) is a chronic mood disorder characterized by recurrent episodes of depression and (hypo-) mania. The gut microbiome is a potential avenue through which metabolic signaling, inflammatory pathways, environmental factors, and genetics influence BD pathogenesis via the gut-brain axis. Fecal microbiota transplantation (FMT) is a powerful translational tool for investigating the connections between the gut microbiome and BD, and there is evidence FMT can transfer affective symptoms of BD from humans to mice. In this study, we compared the behavior, gut-brain metabolomic profiles, and inflammatory marker expression in two groups of adult female C57BL/6J mice, one receiving FMT from a human donor with BD in a mixed episode ( HAM-D = 20, YMRS = 14) and another receiving FMT from a mentally healthy weight and age-matched control donor without BD (HAM-D and YMRS = 0). Here, we demonstrate that mice receiving FMT from individuals with BD had an increased abundance of Bacteroidota and decreased abundances ofParabacteroides merdaeandAkkermansia muciniphilaassociated with altered levels of fecal metabolites, short-chain fatty acids, and related gut hormone expression relative to mice receiving control donor FMT. BD mice also exhibited differential regulation of several metabolites and inflammatory markers in the amygdala, with glycine being the most prominently affected. Furthermore, BD mice displayed increased anxiety-like behavior and decreased sociability, indicating that aspects of the behavioral phenotype of BD are transferable from humans to mice via FMT. Taken together, these findings implicate gut-brain signaling in the physiological and behavioral changes observed in our BD-FMT mouse model.
Diving into bacterial dormancy: emergence of osmotically stable wall-less forms in an aquatic environment
Authors: Carvalho Filipe , Carreaux Alexis , Sartori-Rupp Anna , Tachon Stéphane , Gazi Anastasia D. , Courtin Pascal , Nicolas Pierre , Dubois-Brissonnet Florence , Barbotin Aurélien , Desgranges Emma , Gloux Karine , Schouler Catherine , Carballido-López Rut , Chapot-Chartier Marie-Pierre , Milohanic Eliane , Bierne Hélène , Pagliuso Alessandro 
Published: November 2023

AbstractBacteria can respond to environmental stresses by entering a dormant state, called viable but non-culturable (VBNC) state, in which they no longer grow in routine culture media. VBNC pathogens pose thus a significant risk for human and animal health as they are not detected by standard growth-based techniques and can “wake up” back into a vegetative and virulent state. Although hundreds of species were reported to become VBNC in response to different stresses, the molecular mechanisms governing this phenotypic switch remain largely elusive.Here, we characterized the VBNC state transition process in the Gram-positive pathogenListeria monocytogenesin response to nutritional deprivation. By combining fluorescence microscopy, cryo-electron tomography and analytical biochemistry, we found that starvation in mineral water drivesL. monocytogenesinto a VBNC state via a mechanism of cell wall (CW) shedding that generates osmotically stable CW-deficient (CWD) coccoid forms. This phenomenon occurs in multipleL. monocytogenesstrains and in otherListeriaspecies, suggesting it may be a stress-adapting process transversal to theListeriagenus. Transcriptomic and gene-targeted approaches revealed the stress response regulator SigB and the autolysin NamA as major moderators of CW loss and VBNC state transition. Finally, we show that this CWD dormant state is transient as VBNCListeriarevert back to a walled, vegetative and virulent state after passage in embryonated eggs.Our findings provide unprecedented detail on the mechanisms governing the transition to a VBNC state, and reveal that dormant CWD bacterial forms can naturally arise in aquatic environments without osmotic stabilization. This may represent an alternative strategy for bacterial survival in oligotrophic conditions, which can potentially generate public health-threatening reservoirs of undetectable pathogens.