bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiation-induced gastrointestinal (GI) syndrome as a function of age
Authors: Li Hongyan , Kucharavy Herman C. , Hajj Carla , Zhao Liyang , Hua Guoqiang , Glass Ryan , Paty Phillip B. , Fuks Zvi , Kolesnick Richard , Hubbard Karen , Haimovitz-Friedman Adriana 
Published: January 2023

AbstractPrevious studies show increased sensitivity of older mice (28–29 months) compared with young adult mice (3 months, possessing a mature immune system) to radiation-induced GI lethality. Age-dependent lethality was associated with higher levels of apoptotic stem cells in small intestinal crypts that correlated with sphingomyelinase activity, a source of pro-apoptotic ceramide. The objective of this study is to determine whether the cycling crypt base columnar cells (CBCs) in aging animals are specifically more sensitive to radiation effects than the CBCs in young adult mice, and to identify factors that contribute to increased radiosensitivity. Mortality induced by subtotal body radiation was assessed at different doses (13 Gy, 14 Gy, and 15 Gy) in young adult mice versus older mice. Each dose was evaluated for the occurrence of lethal GI syndrome. A higher death rate due to radiation-induced GI syndrome was observed in older mice as compared with young adult mice: 30 vs. 0% at 13 Gy, 90 vs. 40% at 14 Gy, and 100 vs. 60% at 15 Gy. Radiation-induced damage to crypts was determined by measuring crypt regeneration (H&E staining, Ki67 expression), CBC biomarkers (lgr5 and ascl2), premature senescence (SA-β-gal activity), and apoptosis of CBCs. At all three doses, crypt microcolony survival assays showed that the older mice had fewer regenerating crypts at 3.5 days post-radiation treatment. Furthermore, in the older animals, baseline CBCs numbers per circumference were significantly decreased, correlating with an elevated apoptotic index. Analysis of tissue damage showed an increased number of senescent CBCs per crypt circumference in older mice relative to younger mice, where the latter was not significantly affected by radiation treatment. It is concluded that enhanced sensitivity to radiation-induced GI syndrome and higher mortality in older mice can be attributed to a decreased capacity to regenerate crypts, presumably due to increased apoptosis and senescence of CBCs.
Visualization of translation and protein biogenesis at the ER membrane
Authors: Gemmer Max , Chaillet Marten L. , van Loenhout Joyce , Cuevas Arenas Rodrigo , Vismpas Dimitrios , Gröllers-Mulderij Mariska , Koh Fujiet A. , Albanese Pascal , Scheltema Richard A. , Howes Stuart C. , Kotecha Abhay , Fedry Juliette , Förster Friedrich 
Published: January 2023

AbstractThe dynamic ribosome–translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome1,2. It governs the synthesis, translocation, membrane insertion, N-glycosylation, folding and disulfide-bond formation of nascent proteins. Although individual components of this machinery have been studied at high resolution in isolation3–7, insights into their interplay in the native membrane remain limited. Here we use cryo-electron tomography, extensive classification and molecular modelling to capture snapshots of mRNA translation and protein maturation at the ER membrane at molecular resolution. We identify a highly abundant classical pre-translocation intermediate with eukaryotic elongation factor 1a (eEF1a) in an extended conformation, suggesting that eEF1a may remain associated with the ribosome after GTP hydrolysis during proofreading. At the ER membrane, distinct polysomes bind to different ER translocons specialized in the synthesis of proteins with signal peptides or multipass transmembrane proteins with the translocon-associated protein complex (TRAP) present in both. The near-complete atomic model of the most abundant ER translocon variant comprising the protein-conducting channel SEC61, TRAP and the oligosaccharyltransferase complex A (OSTA) reveals specific interactions of TRAP with other translocon components. We observe stoichiometric and sub-stoichiometric cofactors associated with OSTA, which are likely to include protein isomerases. In sum, we visualize ER-bound polysomes with their coordinated downstream machinery.
Externally-triggerable optical pump-probe scanning tunneling microscopy with a time resolution of tens-picosecond
Authors: Iwaya Katsuya , Yokota Munenori , Hanada Hiroaki , Mogi Hiroyuki , Yoshida Shoji , Takeuchi Osamu , Miyatake Yutaka , Shigekawa Hidemi 
Published: January 2023

AbstractPhotoinduced carrier dynamics of nanostructures play a crucial role in developing novel functionalities in advanced materials. Optical pump-probe scanning tunneling microscopy (OPP-STM) represents distinctive capabilities of real-space imaging of such carrier dynamics with nanoscale spatial resolution. However, combining the advanced technology of ultrafast pulsed lasers with STM for stable time-resolved measurements has remained challenging. The recent OPP-STM system, whose laser-pulse timing is electrically controlled by external triggers, has significantly simplified this combination but limited its application due to nanosecond temporal resolution. Here we report an externally-triggerable OPP-STM system with a temporal resolution in the tens-picosecond range. We also realize the stable laser illumination of the tip-sample junction by placing a position-movable aspheric lens driven by piezo actuators directly on the STM stage and by employing an optical beam stabilization system. We demonstrate the OPP-STM measurements on GaAs(110) surfaces, observing carrier dynamics with a decay time of $$\sim 170$$

∼
170

ps and revealing local carrier dynamics at features including a step edge and a nanoscale defect. The stable OPP-STM measurements with the tens-picosecond resolution by the electrical control of laser pulses highlight the potential capabilities of this system for investigating nanoscale carrier dynamics of a wide range of functional materials.
Proselfs depend more on model-based than model-free learning in a non-social probabilistic state-transition task
Authors: Oguchi Mineki , Li Yang , Matsumoto Yoshie , Kiyonari Toko , Yamamoto Kazuhiko , Sugiura Shigeki , Sakagami Masamichi 
Published: January 2023

AbstractHumans form complex societies in which we routinely engage in social decision-making regarding the allocation of resources among ourselves and others. One dimension that characterizes social decision-making in particular is whether to prioritize self-interest or respect for others—proself or prosocial. What causes this individual difference in social value orientation? Recent developments in the social dual-process theory argue that social decision-making is characterized by its underlying domain-general learning systems: the model-free and model-based systems. In line with this “learning” approach, we propose and experimentally test the hypothesis that differences in social preferences stem from which learning system is dominant in an individual. Here, we used a non-social state transition task that allowed us to assess the balance between model-free/model-based learning and investigate its relation to the social value orientations. The results showed that proselfs depended more on model-based learning, whereas prosocials depended more on model-free learning. Reward amount and reaction time analyses showed that proselfs learned the task structure earlier in the session than prosocials, reflecting their difference in model-based/model-free learning dependence. These findings support the learning hypothesis on what makes differences in social preferences and have implications for understanding the mechanisms of prosocial behavior.
Dynamics of immune responses are inconsistent when trauma patients are grouped by injury severity score and clinical outcomes
Authors: Yang Ya-Wen , Wu Che-Hsiung , Tsai Huei-Ting , Chen Ying-Ru , Chang Yu-Ping , Han Yin-Yi , Wu Tiffany E. , Hu Ray-Heng 
Published: January 2023

AbstractThe injury severity score (ISS) is used in daily practice to evaluate the severity of trauma patients; however, the score is not always consistent with the prognosis. After injury, systemic inflammatory response syndrome (SIRS) and compensatory anti-inflammatory response syndrome (CARS) are related to the prognosis of trauma patients. We aimed to evaluate the associations between the immune response and prognosis in trauma patients. Patients who admitted to the Trauma Intensive Care Unit (ICU) were eligible. Whole blood samples were collected at admission, and then 6, 12, 24, 48 and 72 h after admission. Natural killer (NK) cells, lymphocyte subset population and cytokines release were identified using flow cytometry. We grouped patients by their ISS (≤ 25 and > 25 as very severe injury) and ICU stay (≤ 10 days as a short ICU stay and > 10 days as a long ICU stay) for evaluation. Fifty-three patients were enrolled. ICU stay but not ISS was close correlated with activity daily living (ADL) at discharge. Patients with a long ICU stay had an immediate increase in NK cells followed by lymphopenia which persisted for 48 h. Immediate activation of CD8+ T cells and then exhaustion with a higher programmed cell death-1 (PD-1) expression and suppression of CD4+ T cells with a shift to an anti-inflammatory Th2 phenotype were also observed in the patients with a long ICU stay. When the patients were grouped by ISS, the dynamics of immune responses were inconsistent to those when the patients were grouped by ICU stay. Immune responses are associated with the prognosis of trauma patients, however the currently used clinical parameters may not accurately reflect immune responses. Further investigations are needed to identify accurate predictors of prognosis in trauma patients.
Effect of different end-capped donor moieties on non-fullerenes based non-covalently fused-ring derivatives for achieving high-performance NLO properties
Authors: Khalid Muhammad , Shafiq Iqra , Umm-e-Hani  , Mahmood Khalid , Hussain Riaz , ur Rehman Muhammad Fayyaz , Assiri Mohammed A. , Imran Muhammad , Akram Muhammad Safwan 
Published: January 2023

AbstractA series of derivatives (DOCD2–DOCD6) with D–π–A configuration was designed by substituting various efficient donor moieties via the structural tailoring of o-DOC6-2F. Quantum-chemical approaches were used to analyze the optoelectronic properties of the designed chromophores. Particularly, M06/6-311G(d,p) functional was employed to investigate the non-linear optical (NLO) response (linear polarizability ⟨α⟩, first (βtot) and second ($$\upgamma$$
γ
tot) order hyperpolarizabilities) of the designed derivatives. A variety of analyses such as frontier molecular orbital (FMO), absorption spectra, transition density matrix (TDMs), density of states (DOS), natural bond orbital (NBO) and global reactivity parameters (GRPs) were employed to explore the optoelectronic response of aforementioned chromophores. FMO investigation revealed that DOCD2 showed the least energy gap (1.657 eV) among all the compounds with an excellent transference of charge towards the acceptor from the donor. Further, DOS pictographs and TDMs heat maps also supported FMO results, corroborating the presence of charge separation states along with efficient charge transitions. NBO analysis showed that π-linker and donors possessed positive charges while acceptors retained negative charges confirming the D–π–A architecture of the studied compounds. The λmax values of designed chromophores (659.070–717.875 nm) were found to have broader spectra. The GRPs were also examined utilizing energy band gaps of EHOMO and ELUMO for the entitled compounds. Among all the derivatives, DOCD2 showed the highest values of βtot (7.184 × 10–27 esu) and $$\upgamma$$
γ
tot (1.676 × 10–31 esu), in coherence with the reduced band gap (1.657 eV), indicating future potentiality for NLO materials.
Viable cryopreserved human bone graft exhibit superior osteogenic properties in mandibular lateral augmentation
Authors: Deluiz Daniel , Delcroix Gaëtan J.-R. , Fraga Samira R. G. , D’Ippolito Gianluca , Grau-Monge Cristina , Bonnin-Marquez Andrea , Reiner Teresita , Amadeu Thaís , Tinoco Eduardo M. B. , Schiller Paul Christian 
Published: January 2023

AbstractLack of bone volume to place dental implants is frequently a problem in the reconstruction of edentulous patients. Even though autografts are the gold standard for jaw regeneration, morbidity associated with the harvesting site stimulates the demand for other substitutes. The aim of this study is to characterize the incorporation and the osteogenic ability of a viable cryopreserved human bone graft (VC-HBG) in the mandibular augmentation in rats. Bone chips from fresh human vertebrae cadaveric donors were processed, cryoprotected and deep-frozen at − 80 °C maintaining its cell viability. A jaw augmentation model was used in 20 athymic nude rats allocated into 2 groups to either receive the VC-HBG or an acellular graft as control (A-HBG). The assessment of the grafts' incorporation was performed at 4 and 8 weeks by micro-CT, histomorphometry and immunohistochemistry. Bone volume gain was significantly higher for the VC-HBG group at both time points. At 4 weeks, the A-HBG group presented significantly higher mineral density, but at 8 weeks, the VC-HBG group showed significantly higher values than the A-HBG. There was no statistical difference between VC-HBG and A-HBG groups at 4-weeks for remaining graft particles, while at 8 weeks, the VC-HBG group showed significantly less graft remnants. Collagen I, osteopontin and tartrate-resistant acid phosphatase expression were significantly higher in the VC-HBG group at both time points, while osteocalcin expression was significantly higher in the VC-HBG group at 8-weeks compared to the A-HBG group. This experimental research demonstrated that the VC-HBG shows positive osteogenic properties, greater bone formation, higher rate of bone remodeling and a better overall incorporation in rats' mandibles compared to the A-HBG.
Data mining combines bioinformatics discover immunoinfiltration-related gene SERPINE1 as a biomarker for diagnosis and prognosis of stomach adenocarcinoma
Authors: Zhai Yiyan , Liu Xinkui , Huang Zhihong , Zhang Jingyuan , Stalin Antony , Tan Yingying , Zhang Fanqin , Chen Meilin , Shi Rui , Huang Jiaqi , Wu Chao , Wu Zhishan , Lu Shan , You Leiming , Wu Jiarui 
Published: January 2023

AbstractStomach adenocarcinoma (STAD) is a type of cancer which often at itsadvanced stage apon diagnosis and mortality in clinical practice. Several factors influencethe prognosis of STAD, including the expression and regulation of immune cells in the tumor microenvironment. We here investigated the biomarkers related to the diagnosis and prognosis of gastric cancer, hoping to provide insights for the diagnosis and treatment of gastric cancer in the future. STAD and normal patient RNA sequencing data sets were accessed from the cancer genome atlas (TCGA database). Differential genes were determined and obtained by using the R package DESeq2. The stromal, immune, and ESTIMATE scores are calculated by the ESTIMATE algorithm, followed by the modular genes screening using the R package WGCNA. Subsequently, the intersection between the modular gene and the differential gene was taken and the STRING database was used for PPI network module analysis. The R packages clusterProfiler, enrichplot, and ggplot2 were used for GO and KEGG enrichment analysis. Cox regression analysis was used to screen survival-related genes, and finally, the R package Venn Diagram was used to take the intersection and obtain 7 hub genes. The time-dependent ROC curve and Kaplan–Meier survival curve were used to find the SERPINE1 gene, which plays a critical role in prognosis. Finally, the expression pattern, clinical characteristics, and regulatory mechanism of SERPINE1 were analyzed in STAD. We revealed that the expression of SERPINE1 was significantly increased in the samples from STAD compared with normal samples. Cox regression, time-dependent ROC, and Kaplan–Meier survival analyses demonstrated that SERPINE1 was significantly related to the adverse prognosis of STAD patients. The expression of SERPINE1 increased with the progression of T, N, and M classification of the tumor. In addition, the results of immune infiltration analysis indicated that the immune cells’ expression were higher in high SERPINE1 expression group than that in low SERPINE1 expression group, including CD4+ T cells, B cells, CD8+ T cells, macrophages, neutrophils and other immune cells. SERPINE1 was closely related to immune cells in the STAD immune microenvironment and had a synergistic effect with the immune checkpoints PD1 and PD-L1. In conclusion, we proved that SERPINE1 is a promising prognostic and diagnostic biomarker for STAD and a potential target for immunotherapy.
Liver fibrosis is closely related to metabolic factors in metabolic associated fatty liver disease with hepatitis B virus infection
Authors: Lv Haifeng , Jiang Yanming , Zhu Geli , Liu Shiyi , Wang Dian , Wang Jie , Zhao Ke , Liu Jing 
Published: January 2023

AbstractThis case–control study aimed to identify the clinical characteristics and explore the risk factors for liver fibrosis in metabolic associated fatty liver disease (MAFLD) patients with hepatitis B virus (HBV) infection. The patients were grouped into MAFLD + HBV and MAFLD (without HBV infection). Propensity score matching (PSM) was used to match baseline features between the groups. We included 401 patients with biopsy-proven MAFLD, 179 of whom had HBV infection. A total of 83 pairs were successfully matched via PSM, and steatosis scores and ballooning in the MAFLD + HBV group were lower than those in the MAFLD group, while the inflammation scores and liver fibrosis stages were higher. After adjusted for confounding factors, HBV infection was associated with a higher risk of significant liver fibrosis in patients with MAFLD [odds ratio (OR): 3.140, P = 0.003]. Overall, 43.58% (78/179) of patients in the MAFLD + HBV group had significant liver fibrosis. Further multivariate regression analysis, hypertension (OR: 2.640; P = 0.031), type 2 diabetes (OR: 4.939; P = 0.035), and elevated glutamyl-transferase levels (OR: 3.980; P = 0.001) were risk factors for liver fibrosis in the MAFLD + HBV group. This suggests metabolic rather than viral factors are more closely associated with liver fibrosis in MAFLD patients with HBV infection.
Iterated cross validation method for prediction of survival in diffuse large B-cell lymphoma for small size dataset
Authors: Chang Chin-Chuan , Chen Chien-Hua , Hsieh Jer-Guang , Jeng Jyh-Horng 
Published: January 2023

AbstractEfforts have been made to improve the risk stratification model for patients with diffuse large B-cell lymphoma (DLBCL). This study aimed to evaluate the disease prognosis using machine learning models with iterated cross validation (CV) method. A total of 122 patients with pathologically confirmed DLBCL and receiving rituximab-containing chemotherapy were enrolled. Contributions of clinical, laboratory, and metabolic imaging parameters from fluorine-18 fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) scans to the prognosis were evaluated using five regression models, namely logistic regression, random forest, support vector classifier (SVC), deep neural network (DNN), and fuzzy neural network models. Binary classification predictions for 3-year progression free survival (PFS) and 3-year overall survival (OS) were conducted. The 10-iterated fivefold CV with shuffling process was conducted to predict the capability of learning machines. The median PFS and OS were 41.0 and 43.6 months, respectively. Two indicators were found to be independent predictors for prognosis: international prognostic index and total metabolic tumor volume (MTVsum) from FDG PET/CT. For PFS, SVC and DNN (both with accuracy 71%) have the best predictive results, of which outperformed other algorithms. For OS, the DNN has the best predictive result (accuracy 76%). Using clinical and metabolic parameters as input variables, the machine learning methods with iterated CV method add the predictive values for PFS and OS evaluation in DLBCL patients.
Diversity enables the jump towards cooperation for the Traveler’s Dilemma
Authors: Ramírez María Alejandra , Smerlak Matteo , Traulsen Arne , Jost Jürgen 
Published: January 2023

AbstractSocial dilemmas are situations in which collective welfare is at odds with individual gain. One widely studied example, due to the conflict it poses between human behaviour and game theoretic reasoning, is the Traveler’s Dilemma. The dilemma relies on the players’ incentive to undercut their opponent at the expense of losing a collective high payoff. Such individual incentive leads players to a systematic mutual undercutting until the lowest possible payoff is reached, which is the game’s unique Nash equilibrium. However, if players were satisfied with a high payoff -that is not necessarily higher than their opponent’s- they would both be better off individually and collectively. Here, we explain how it is possible to converge to this cooperative high payoff equilibrium. Our analysis focuses on decomposing the dilemma into a local and a global game. We show that players need to escape the local maximisation and jump to the global game, in order to reach the cooperative equilibrium. Using a dynamic approach, based on evolutionary game theory and learning theory models, we find that diversity, understood as the presence of suboptimal strategies, is the general mechanism that enables the jump towards cooperation.
Containerized cloud-based honeypot deception for tracking attackers
Authors: Priya V. S. Devi , Chakkaravarthy S. Sibi 
Published: January 2023

AbstractDiscovering malicious packets amid a cloud of normal activity, whether you use an IDS or gather and analyze machine and device log files on company infrastructure, may be challenging and time consuming. The vulnerability landscape is rapidly evolving, and it will only become worse as more and more developing technologies, such as IoT, Industrial Automation, CPS, Digital Twins, etc are digitally connected. A honey trap aids in identifying malicious packets easily as, after a few rapid calibrations to eliminate false positives. Besides analyzing and reporting particular invasion patterns or toolkits exploited, it also assists in preventing access to actual devices by simulating the genuine systems and applications functioning in the network thus delaying as well as baffling the invader. In order to analyze and evaluate the hackers’ behavior, an ensemble of research honeypot detectors has been deployed in our work. This paper delivers a robust outline of the deployment of containerized honeypot deployment, as a direct consequence, these are portable, durable, and simple to deploy and administer. The instrumented approach was monitored and generated countless data points on which significant judgments about the malevolent users’ activities and purpose could be inferred.