bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of Tolerogenic Dendritic Cells under the Persistent Inflammation Stimulation
Authors: Miao Shumin , Chang Zenan , Gu Bin , Jiang Jinlong , Pei Fei , Liu Yishan , Zhou Yu , liu Zimeng , Si Xiang , Guan Xiangdong , Wu Jianfeng 
Published: February 2024

Abstract
Immunosuppression, commonly accompanied by persistent inflammation, is a key feature in the later phase of sepsis. However, the pathophysiological mechanisms underlying this phenomenon remain unclear. Dendritic cells (DCs), specifically tolerogenic DCs (tolDCs), play a crucial role in this process by regulating immune responses through inducing T cell anergy and releasing anti-inflammatory cytokines. Nevertheless, the existing cell models are inadequate for investigating tolDCs during the immunosuppressive phase of sepsis. Therefore, this study aimed to develop a novel in vitro model to generate tolDCs under chronic inflammatory conditions. We have successfully generated tolDCs by exposing them to sublethal lipopolysaccharide (LPS) for 72 h while preserving cell viability. Considering that Interleukin-10-induced tolDCs (IL-10-tolDCs) are a well-established model, we compared the immunological tolerance between LPS-tolDCs and IL-10-tolDCs. Our findings indicated that both LPS-tolDCs and IL-10-tolDCs exhibited reduced expression of maturation markers, whereas their levels of inhibitory markers were elevated. Furthermore, the immunoregulatory activities of LPS-tolDCs and IL-10-tolDCs were found to be comparable. These dysfunctions include impaired antigen presenting capacity and suppression of T cell activation, proliferation, and differentiation. Notably, compared with IL-10-tolDCs, LPS-tolDCs showed a reduced response in maturation and cytokine production upon stimulation, indicating their potential as a better model for research. Overall, in comparison with IL-10-tolDCs, our data suggest that the immunological dysfunctions shown in LPS-tolDCs could more effectively elucidate the increased susceptibility to secondary infections during sepsis. Consequently, LPS-tolDCs have emerged as a promising therapeutic target for ameliorating the immunosuppressed state in septic patients.
What Are Risk Factors for Graft Loss in Patients Who Underwent Simultaneous Splenectomy During Living-donor Liver Transplantation?
Authors: Toshima Takeo , Harada Noboru , Itoh Shinji , Tomiyama Takahiro , Toshida Katsuya , Morita Kazutoyo , Nagao Yoshihiro , Kurihara Takeshi , Tomino Takahiro , Kosai-Fujimoto Yukiko , Mimori Koshi , Yoshizumi Tomoharu 
Published: February 2024

Background.
The consensus that portal venous pressure modulation, including splenectomy (Spx), prevents portal hypertension-related complications after living-donor liver transplantation (LDLT) has been established. However, little evidence about the risk factors for graft loss after simultaneous Spx during LDLT is available. This study aimed to identify the independent predictors of graft loss after simultaneous Spx during LDLT.

Methods.
Data of 655 recipients who underwent LDLT between 1997 and 2021 were collected and separated into the simultaneous Spx group (n = 461) and no-Spx group (n = 194).

Results.
The simultaneous Spx group had significantly lower serum total bilirubin levels, drained ascites volumes, and prothrombin time-international normalized ratios on postoperative day 14 than the no-Spx group (P < 0.001 for each). Incidences of small-for-size graft syndrome (P < 0.001), acute cellular rejection (P = 0.002), and sepsis (P = 0.007) were significantly lower in the Spx group. Graft survival of the Spx group was significantly better than that of the no-Spx group (P < 0.001; hazard ratio [HR], 1.788; 95% confidence interval, 1.214-2.431). A multivariate analysis revealed that 3 variables, platelet count ≤4.0 × 104/mm3 (P = 0.029; HR, 2.873), donor age ≥60 y old (P = 0.013; HR, 6.693), and portal venous pressure at closure ≥20 mm Hg (P = 0.010; HR, 3.891), were independent predictors of graft loss within 6 mo after simultaneous Spx during LDLT.

Conclusions.
Spx is a safe inflow modulation procedure with a positive impact on both postoperative complications and prognosis for most patients. However, patients with the 3 aforementioned independent factors could experience graft loss after LDLT.
Twenty-four-hour Normothermic Ex Vivo Heart Perfusion With Low Flow Functional Assessment in an Adult Porcine Model
Authors: Spencer Brianna L. , Wilhelm Spencer K. , Urrea Kristopher A. , Chakrabortty Vikramjit , Sewera Sebastian , Mazur Daniel E. , Niman Joseph B. , Bartlett Robert H. , Rojas-Peña Alvaro , Drake Daniel H. 
Published: February 2024

Background.
Cold static storage and normothermic ex vivo heart perfusion are routinely limited to 6 h. This report describes intermittent left atrial (LA) perfusion that allows cardiac functional assessment in a working heart mode.

Methods.
Using our adult porcine model, general anesthesia was induced and a complete cardiectomy was performed following cardioplegic arrest. Back-table instrumentation was completed and normothermic ex vivo heart perfusion (NEHP) was initiated in a nonworking heart mode (Langendorff). After 1 h of resuscitation and recovery, LA perfusion was initiated and the heart was transitioned to a coronary flow-only working heart mode for 30 min. Baseline working heart parameters were documented and the heart was returned to nonworking mode. Working heart assessments were performed for 30 min every 6 h for 24 h.

Results.
Twenty-four-hour NEHP on 9 consecutive hearts (280 ± 42.1 g) was successful and no significant differences were found between working heart parameters at baseline and after 24 h of perfusion. There was no difference between initial and final measurements of LA mean pressures (5.0 ± 3.1 versus 9.0 ± 6.5 mm Hg, P = 0.22), left ventricular systolic pressures (44.3 ± 7.2 versus 39.1 ± 9.0 mm Hg, P = 0.13), mean aortic pressures (30.9 ± 5.8 versus 28.1 ± 8.1 mm Hg, P = 0.37), and coronary resistance (0.174 ± 0.046 versus 0.173 ± 0.066 mL/min/g, P = 0.90). There were also no significant differences between lactate (2.4 ± 0.5 versus 2.6 ± 0.4 mmol/L, P = 0.17) and glucose (173 ± 75 versus 156 ± 70 mg/dL, P = 0.37).

Conclusions.
A novel model using intermittent LA perfusion to create a coronary flow-only working heart mode for assessment of ex vivo cardiac function has been successfully developed.
Maintenance Electroconvulsive Therapy in Catatonia
Authors: Gil-Badenes Joaquín , Giménez-Palomo Anna , Duque Lucía , Pujol-Fontrodona Gabriel , Martínez-Amorós Erika , Bioque Miquel 
Published: February 2024

Objectives
This study aims to conduct a descriptive analysis of the clinical features and treatment responses in 6 patients with catatonia who received maintenance electroconvulsive therapy (ECT).

Methods
Our study included all patients who underwent maintenance ECT (mECT) at the Hospital Clínic de Barcelona between September 2020 and September 2022 following a catatonic episode.

Results
The study cohort comprised 5 patients with schizophrenia and 1 patient with major depressive disorder. Among patients with schizophrenia, the first catatonic episode occurred several years after their initial paranoid psychotic episode, whereas the patient with depression experienced a rapid progression from the first depressive episode to catatonia. After acute ECT, 4 patients achieved complete symptomatic remission, 1 patient exhibited a partial response, and another maintained a severe catatonic state. Maintenance ECT was indicated because of the high risk of severe relapses. The mean frequency of mECT sessions was 9.83 (SD, 5.60) days. Notably, 66.67% of the patients were concurrently receiving clozapine as part of their pharmacological treatment. Among patients with schizophrenia, mECT sessions could not be extended beyond 7 to 10 days, whereas the depressed patient could space ECT sessions up to 21 days without experiencing a relapse.

Conclusions
Maintenance ECT proves to be a safe and well-tolerated strategy for preventing relapses in severe catatonic patients who have previously stabilized with acute ECT. Further research is needed to develop clinical guidelines that define optimal application strategies for mECT in catatonia.
Healthy dietary choices involve prefrontal mechanisms associated with long-term reward maximization but not cognitive control
Authors: Takehana Ai , Tanaka Daiki , Arai Mariko , Hattori Yoshiki , Yoshimoto Takaaki , Matsui Teppei , Sadato Norihiro , Chikazoe Junichi , Jimura Koji 
Published: February 2024

AbstractTaste and health are critical factors to be considered when choosing foods. Prioritizing healthiness over tastiness requires self-control. It has also been suggested that self-control is guided by cognitive control. We then hypothesized that neural mechanisms underlying healthy food choice are associated with both self-control and cognitive control. Human participants performed a food choice task and a working memory (WM) task during functional MRI scanning. Their degree of self-control was assessed behaviorally by the value discount of delayed monetary rewards in intertemporal choice. Prioritizing healthiness in food choice was associated with greater activity in the superior, dorsolateral, and medial prefrontal cortices. Importantly, the prefrontal activity was greater in individuals with smaller delay discounting (i.e., high self-control) who preferred a delayed larger reward to an immediate smaller reward in intertemporal choice. On the other hand, WM activity did not show a correlation with delay discounting or food choice activity, which was further supported by supplementary results that analyzed data from the Human Connectome Project. Our results suggest that the prefrontal cortex plays a critical role in healthy food choice, which requires self-control, but not cognitive control, for maximization of reward attainments in a remote future.
Asymmetric Fin Shape changes Swimming Dynamics of Ancient Marine Reptiles’ Soft Robophysical Models
Authors: Sprumont Hadrien , Allione Federico , Schwab Fabian , Wang Bingcheng , Mucingat Claudio , Lunati Ivan , Scheyer Torsten , Ijspeert Auke , Jusufi Ardian 
Published: February 2024

AbstractAnimals have evolved highly effective locomotion capabilities in terrestrial, aerial, and aquatic environments. Over life’s history, mass extinctions have wiped out unique animal species with specialized adaptations, leaving paleontologists to reconstruct their locomotion through fossil analysis. Despite advancements, little is known about how extinct megafauna, such as the Ichthyosauria one of the most successful lineages of marine reptiles, utilized their varied morphologies for swimming. Traditional robotics struggle to mimic extinct locomotion effectively, but the emerging soft robotics field offers a promising alternative to overcome this challenge. This paper aims to bridge this gap by studyingMixosauruslocomotion with soft robotics, combining material modeling and biomechanics in physical experimental validation. Combining a soft body with soft pneumatic actuators, the soft robotic platform described in this study investigates the correlation between asymmetrical fins and buoyancy by recreating the pitch torque generated by extinct swimming animals. We performed a comparative analysis of thrust and torque generated byCarthorhyncus, Utatsusaurus, Mixosaurus, Guizhouichthyosaurus, andOphthalmosaurustail fins in a flow tank. Experimental results suggest that the pitch torque on the torso generated by hypocercal fin shapes such as found in model systems ofGuizhouichthyosaurus, MixosaurusandUtatsusaurusproduce distinct ventral body pitch effects able to mitigate the animal’s non-neutral buoyancy. This body pitch control effect is particularly pronounced inGuizhouichthyosaurus, which results suggest would have been able to generate high ventral pitch torque on the torso to compensate for its positive buoyancy. By contrast, homocercal fin shapes may not have been conducive for such buoyancy compensation, leaving torso pitch control to pectoral fins, for example. Across the range of the actuation frequencies of the caudal fins tested, resulted in oscillatory modes arising, which in turn can affect the for-aft thrust generated.
Privacy Preserving Epigenetic PaceMaker Stronger Privacy and Improved Efficiency
Authors: Goldenberg Meir , Mualem Loay , Shahar Amit , Snir Sagi , Akavia Adi 
Published: February 2024

AbstractDNA methylation data plays a crucial role in estimating chronological age in mammals, offering real-time insights into an individual’s aging process. The Epigenetic Pacemaker (EPM) model allows inference of the biological age as deviations from the population trend. Given the sensitivity of this data, it is essential to safeguard both inputs and outputs of the EPM model. In a recent study by Goldenberg et al., a privacy-preserving approach for EPM computation was introduced, utilizing Fully Homomorphic Encryption (FHE). However, their method had limitations, including having high communication complexity and being impractical for large datasets Our work presents a new privacy preserving protocol for EPM computation, analytically improving both privacy and complexity. Notably, we employ a single server for the secure computation phase while ensuring privacy even in the event of server corruption (compared to requiring two non-colluding servers in Goldenberg et al.). Using techniques from symbolic algebra and number theory, the new protocol eliminates the need for communication during secure computation, significantly improves asymptotic runtime and and offers better compatibility to parallel computing for further time complexity reduction. We have implemented our protocol, demonstrating its ability to produce results similar to the standard (insecure) EPM model with substantial performance improvement compared to Goldenberg et al. These findings hold promise for enhancing data security in medical applications where personal privacy is paramount. The generality of both the new approach and the EPM, suggests that this protocol may be useful to other uses employing similar expectation maximization techniques.
Analysis of genetic variation inMacadamiashows evidence of extensive reticulate evolution
Authors: Manatunga Sachini Lakmini , Furtado Agnelo , Topp Bruce , Alam Mobashwer , Mason Patrick J. , Kharabian-Masouleh Ardashir , Henry Robert J 
Published: February 2024

AbstractThe genusMacadamiain the Proteaceae family includes four species. To explore diversity in macadamia genetic resources, a total of 166 wild genotypes, representing all four species, were sequenced. The four species were clearly distinguished as four separate clades in a phylogenetic analysis of nuclear gene CDS.M. integrifoliaandM. tetraphyllaformed a clade that had diverged from a clade includingM. ternifoliaandM. jansenii.The greatest diversity in nuclear and chloroplast genomes was found in the more widely distributedM. integrifoliawhile the rareM. janseniishowed little diversity. The chloroplast phylogeny revealed a much more complex evolutionary history. Multiple chloroplast capture events have resulted in chloroplast genome clades including genotypes from different species. This suggests extensive reticulate evolution inMacadamiadespite the emergence of the four distinct species that are supported by the analysis of their nuclear genomes. The chloroplast genomes showed strong associations with geographical distribution reflecting limited maternal gene movement in these species having large seeds. The nuclear genomes showed lesser geographical differences, probably reflecting longer distance movement of pollen. This improved understanding of the distribution of diversity inMacadamiawill aid conservation of these rare species now found in highly fragmented rainforest remnants.HighlightsWhole genome sequencing of population of the four species in the Macadamia genus allowed phylogenetic relationships to be determined and revealed significant reticulate evolution.
An ability to respond begins with inner alignment: How phase synchronisation effects transitions to higher levels of agency
Authors: Tissot Tazzio , Levin Mike , Buckley Chris , Watson Richard 
Published: February 2024

AbstractHow do multiple active components at one level of organisation create agential wholes at higher levels of organisation? For example, in organismic development, how does the multi-scale autonomy of the organism arise from the interactions of the molecules, cells and tissues that an organism contains? And, in the major evolutionary transitions, how does a multicellular organism, for example, arise as an evolutionary unit from the selective interests of its unicellular ancestors? We utilise computational models as a way to think about this general question. We take a deliberately minimalistic notion of an agent: a competency to take one of two possible actions to minimise stress. Helping ourselves to this behaviour at the microscale, we focus on conditions where this same type of agency appears spontaneously at a higher level of organisation. We find that a simple process of positive feedback on the timing of individual responses, loosely analogous to the natural phase synchronisation of weakly coupled oscillators, causes such a transition in behaviour. The emergent collectives that arise become, quite suddenly, able to respond to their external stresses in the same (minimal) sense as the original microscale units. This effects a dramatic rescaling of the system behaviour, and a quantifiable increase in problem-solving competency, serving as a model of how higher-level agency emerges from a pool of lower-level agents or active matter. We discuss how this dynamical ‘waking-up’ of higher-level collectives, through the alignment of their internal dynamics, might relate to reproductive/cell-cycle synchronisation in evolutionary transitions and development.
From Sight to Insight: A Multi-task Approach with the Visual Language Decoding Model
Authors: Huang Wei , Yang Pengfei , Tang Ying , Qin Fan , Li Hengjiang , Wu Diwei , Ren Wei , Wang Sizhuo , Zhao Yuhao , Wang Jing , Liu Haoxiang , Li Jingpeng , Zhu Yucheng , Zhou Bo , Sun Jingyuan , Li Qiang , Cheng Kaiwen , Yan Hongmei , Chen Huafu 
Published: February 2024

AbstractVisual neural decoding aims to unlock the mysteries of how the human brain interprets the visual world. While early studies made some progress in decoding visual activity for singular type of information, they failed to concurrently reveal the multi-level interweaving linguistic information in the brain. Here, we developed a novel Visual Language Decoding Model (VLDM) capable of decoding categories, semantic labels, and textual descriptions from visual perceptual activities simultaneously. We selected the large-scale NSD dataset to ensure the efficiency of the decoding model in joint training and evaluation across multiple tasks. For category decoding, we achieved the effective classification of 12 categories with an accuracy of nearly 70%, significantly surpassing the chance level. For label decoding, we attained the precise prediction of 80 specific semantic labels with a 16-fold improvement over the chance level. For text decoding, the scores of the decoded text surpassed the corresponding baseline levels by remarkable margins on six evaluation metrics. This study contributes significantly to extensive applications in multi-layered brain-computer interfaces, potentially leading to more natural and efficient human-computer interaction experiences.
Predicting genetic biodiversity in salamanders using geographic, climatic, and life history traits
Authors: Parsons Danielle J. , Green Abigail E. , Carstens Bryan C. , Pelletier Tara A. 
Published: February 2024

AbstractThe geographic distribution of genetic variation within a species reveals information about its evolutionary history, including responses to historical climate change and dispersal ability across various habitat types. We combine genetic data from salamander species with geographic, climatic, and life history data collected from open-source online repositories to develop a machine learning model designed to identify the traits that are most predictive of unrecognized genetic lineages. We find evidence of hidden diversity distributed throughout the clade Caudata that is largely the result of variation in climatic variables. We highlight some of the difficulties in using machine-learning models on open-source data that are often messy and potentially taxonomically and geographically biased.
LineageVAE: Reconstructing Historical Cell States and Transcriptomes toward Unobserved Progenitors
Authors: Majima Koichiro , Kojima Yasuhiro , Minoura Kodai , Abe Ko , Hirose Haruka , Shimamura Teppei 
Published: February 2024

AbstractSingle-cell RNA sequencing (scRNA-seq) enables comprehensive characterization of the cell state. However, its destructive nature prohibits measuring gene expression changes during dynamic processes such as embryogenesis. Although recent studies integrating scRNA-seq with lineage tracing have provided clonal insights between progenitor and mature cells, challenges remain. Because of their experimental nature, observations are sparse, and cells observed in the early state are not the exact progenitors of cells observed at later time points. To overcome these limitations, we developed LineageVAE, a novel computational methodology that utilizes deep learning based on the property that cells sharing barcodes have identical progenitors. This approach transforms scRNA-seq observations with an identical lineage barcode into sequential trajectories toward a common progenitor in a latent cell state space. Using hematopoiesis and reprogrammed fibroblast datasets, we demonstrate the capability of LineageVAE to reconstruct unobservable cell state transitions, historical transcriptome, and regulatory dynamics toward progenitor cell states at single-cell resolution.
Profiling Glioma Stem Cell Dynamics via 3D-based Cell Cycle Reporter Assays
Authors: Lubanska Dorota , Roye-Azar Antonio , Alrashed Sami , Cieslukowski Alan , Soliman Mohamed , deCarvalho Ana C. , Shamisa Abdalla , Kulkarni Swati , Porter Lisa A. 
Published: February 2024

SummarySuccessful containment of unwanted cell cycle progression in tumours such as glioblastoma (GBM) requires targeted therapeutic approaches which rely on understanding cell cycle dynamics in response to microenvironmental stimuli. Glioma Stem Cells (GSCs) can drive tumour initiation, recurrence, therapy resistance, and are often attributed to the heterogeneity and plasticity of GBM.In vitromodels using patient-derived GSCs provide a life relevant tool for exploration of complex molecular mechanisms underlying the aggressive characteristics of GBM. Introduction of 3D tissue culture systems permits the study of spatial complexity of the tumour mass and enables control over diverse conditions within the surrounding microenvironment. This chapter demonstrates detailed methods to study spatio-temporal changes to the cell cycle dynamics using available fluorescent cell cycle reporter systems in combination with bioinformatics-based signal intensity and localization analysis. We present a successful approach that investigates the 3D cell cycle dynamics of GSC populations. This approach utilizes GBM neurosphere and organoid cultures, which are assessed over time and under therapeutic pressure. These models can be further explored, manipulated, and customized to serve specific experimental designs.