Miracle-dz/UniFAR-FTUs huggingface dataset:
High Migration and Invasion Ability of PGCCs and Their Daughter Cells Associated With the Nuclear Localization of S100A10 Modified by SUMOylation

Our previous studies have confirmed that cobalt chloride (CoCl2) or chemoradiotherapy could induce the formation of polyploid tumor giant cells (PGCCs). Polyploid giant cancer cells are a special subpopulation of cancer cells that contribute to solid tumor heterogeneity. The size of PGCC was at least three times larger than regular diploid cancer cells. PGCCs have the properties of cancer stem cells (CSCs) and can express CSC markers CD44 and CD133. Daughter cells derived from PGCCs have strong proliferation, infiltration and migration abilities. However, the detailed molecular mechanism of daughter cells expressing mesenchymal phenotype and displaying strong abilities of proliferation and migration is unclear. As a plasminogen receptor, S100A10 which is closely associated with the invasion and metastasis of malignant tumors, was highly expressed in PGCCs with their daughter cells. In this study, CoCl2 was used to induce the formation of PGCCs in LoVo and HCT116 CRC cells. Cell functional experiments, co-immunoprecipitation, MG132 and ginkgolic acid treatment, western blot, and ChIP-Seq were used to identify the mechanism of S100A10 nuclear location. The proliferation and migration abilities of PGCCs and their daughter cells decreased significantly after S100A10 knockdown. In the control cells, S100A10 was mainly ubiquitinated, while in PGCCs and daughter cells, S100A10 was mainly SUMOylated, which was associated with S100A10 nuclear location. After SUMO1 was inhibited, the nuclear S100A10 in PGCCs and daughter cells decreased, and their proliferation and migration abilities significantly decreased. ChIP-Seq combined with real-time fluorescent quantitative PCR showed that S100A10 regulated the expression of neutrophil defensin 3 (DEFA3), receptor-type tyrosine-protein phosphatase N2 (PTPRN2), and rho guanine nucleotide exchange factor 18 (ARHGEF18), which were associated with actin dynamics and cytoskeleton remodeling. The expression of S100A10 in the nuclei and cytoplasm of rectal cancer after neoadjuvant chemoradiation (nCRT) and liver metastases increased compared with that in rectal cancer without nCRT. Taken together, the expression and nuclear localization of S100A10 modified by SUMOylation were associated with the high proliferation and migration of PGCCs and their daughter cells, and the differentiation, metastases, and relapse of CRCs by regulating the expression of ARHGEF18, PTPRN2, and DEFA3.
Physiological and Genomic Characterization of a Hyperthermophilic Archaeon Archaeoglobus neptunius sp. nov. Isolated From a Deep-Sea Hydrothermal Vent Warrants the Reclassification of the Genus Archaeoglobus

Hyperthermophilic archaea of the genus Archaeoglobus are the subject of many fundamental and biotechnological researches. Despite their significance, the class Archaeoglobi is currently represented by only eight species obtained as axenic cultures and taxonomically characterized. Here, we report the isolation and characterization of a new species of Archaeoglobus from a deep-sea hydrothermal vent (Mid-Atlantic Ridge, TAG) for which the name Archaeoglobus neptunius sp. nov. is proposed. The type strain is SE56T (=DSM 110954T = VKM B-3474T). The cells of the novel isolate are motile irregular cocci growing at 50–85°C, pH 5.5–7.5, and NaCl concentrations of 1.5–4.5% (w/v). Strain SE56T grows lithoautotrophically with H2 as an electron donor, sulfite or thiosulfate as an electron acceptor, and CO2/HCO3− as a carbon source. It is also capable of chemoorganotrophic growth by reduction of sulfate, sulfite, or thiosulfate. The genome of the new isolate consists of a 2,115,826 bp chromosome with an overall G + C content of 46.0 mol%. The whole-genome annotation confirms the key metabolic features of the novel isolate demonstrated experimentally. Genome contains a complete set of genes involved in CO2 fixation via reductive acetyl-CoA pathway, gluconeogenesis, hydrogen and fatty acids oxidation, sulfate reduction, and flagellar motility. The phylogenomic reconstruction based on 122 conserved single-copy archaeal proteins supported by average nucleotide identity (ANI), average amino acid identity (AAI), and alignment fraction (AF) values, indicates a polyphyletic origin of the species currently included into the genus Archaeoglobus, warranting its reclassification.
Comprehensive Analysis of the Value of SMYD Family Members in the Prognosis and Immune Infiltration of Malignant Digestive System Tumors

Background The SET and MYND domain-containing (SMYD) gene family comprises a set of genes encoding lysine methyltransferases. This study aimed to clarify the relationship between the expression levels of SMYD family members and the prognosis and immune infiltration of malignant tumors of the digestive system. Methods The Oncomine, Ualcan, Kaplan–Meier Plotter, cBioPortal, Metascape, and TIMER databases and tools were used to analyze the correlation of SMYD family mRNA expression, clinical stage, TP53 mutation status, prognostic value, gene mutation, and immune infiltration in patients with esophageal carcinoma (ESCA), liver hepatocellular carcinoma (LIHC), and stomach adenocarcinoma (STAD). Results In ESCA, the mRNA expression of SMYD2/3/4/5 was significantly correlated with the incidence rate, that of SMYD2/3 with the clinical stage, that of SMYD2/3/4/5 with TP53 mutation status, that of SMYD2/4/5 with overall survival (OS), and that of SMYD1/2/3/4 with relapse-free survival (RFS). In LIHC, the mRNA expression of SMYD1/2/3/4/5 was significantly correlated with the incidence rate, that of SMYD2/4/5 with the clinical stage, that of SMYD3/5 with TP53 mutation status, that of SMYD2/3/4/5 with OS, and that of SMYD3/5 with RFS. In STAD, the mRNA expression of SMYD2/3/4/5 was significantly correlated with the incidence rate, that of SMYD1/4 with the clinical stage, that of SMYD1/2/3/5 with TP53 mutation status, that of SMYD1/3/4 with OS, and that of SMYD1/3 with RFS. Furthermore, the function of SMYD family mutation-related genes in ESCA, LIHC, and STAD patients was mainly related to pathways, such as mitochondrial gene expression, mitochondrial matrix, and mitochondrial translation. The expression of SMYD family genes was significantly correlated with the infiltration of six immune cell types and eight types of immune check sites. Conclusion SMYD family genes are differentially expressed and frequently mutated in malignant tumors of the digestive system (ESCA, LIHC, and gastric cancer). They are potential markers for prognostic prediction and have important significance in immunity and targeted therapy.
Plasticity of GluN1 at Ventral Hippocampal Synapses in the Infralimbic Cortex

Although the infralimbic cortex (IL) is not thought to play a role in fear acquisition, recent experiments found evidence that synaptic plasticity is occurring at ventral hippocampal (vHPC) synapses in IL during auditory fear acquisition as measured by changes in the N-methyl-D-aspartate (NMDA) receptor-mediated currents in male rats. These electrophysiological data suggest that fear conditioning changes the expression of NMDA receptors on vHPC-to-IL synapses. To further evaluate the plasticity of NMDA receptors at this specific synapse, we injected AAV particles expressing channelrhodopsin-EYFP into the vHPC of male and female rats to label vHPC projections with EYFP. To test for NMDA receptor changes in vHPC-to-IL synapses after fear learning, we used fluorescence-activated cell sorting (FACS) to quantify synaptosomes isolated from IL tissue punches that were positive for EYFP and the obligatory GluN1 subunit. More EYFP+/GluN1+ synaptosomes with greater average expression of GluN1 were isolated from male rats exposed to auditory fear conditioning (AFC) than those exposed to context and tones only or to contextual fear conditioning (CFC), suggesting that AFC increased NMDA receptor expression in males. In a second experiment, we found that pairing the tones and shocks was required to induce the molecular changes and that fear extinction did not reverse the changes. In contrast, females showed similar levels of EYFP+/GluN1+ synaptosomes in all behavioral groups. These findings suggest that AFC induces synaptic plasticity of NMDA receptors in the vHPC-to-IL projection in males, while female rats rely on different synaptic mechanisms.
Plasma Amino Acids Metabolomics' Important in Glucose Management in Type 2 Diabetes

The perturbation in plasma free amino acid metabolome has been observed previously in diabetes mellitus, and is associated with insulin resistance as well as the onset of cardiovascular disease in this population. In this study, we investigated, for the first time, changes in the amino acid profile in a group of people with and without type 2 diabetes (T2D) with normal BMI, from Jordan, who were only managed on metformin. Twenty one amino acids were evaluated in plasma samples from 124 people with T2D and 67 healthy controls, matched for age, gender and BMI, using amino acids analyser. Total amino acids, essential amino acids, non-essential amino acids and semi-essential amino acids were similar in T2D compared to healthy controls. Plasma concentrations of four essential amino acids were increased in the presence of T2D (Leucine, p < 0.01, Lysine, p < 0.001, Phenylalanine, p < 0.01, Tryptophan, p < 0.05). On the other hand, in relation to non-essential amino acids, Alanine and Serine were reduced in T2D (p < 0.01, p < 0.001, respectively), whereas Aspartate and Glutamate were increased in T2D compared to healthy controls (p < 0.001, p < 0.01, respectively). A semi-essential amino acid, Cystine, was also increased in T2D compared to healthy controls (p < 0.01). Citrulline, a metabolic indicator amino acid, demonstrated lower plasma concentration in T2D compared to healthy controls (p < 0.01). These amino acids were also correlated with fasting blood glucose and HbA1c (p < 0.05). Glutamate, glycine and arginine were correlated with the duration of metformin treatment (p < 0.05). No amino acid was correlated with lipid profiles. Disturbances in the metabolism of these amino acids are closely implicated in the pathogenesis of T2D and associated cardiovascular disease. Therefore, these perturbed amino acids could be explored as therapeutic targets to improve T2D management and prevent associated cardiovascular complications.
Cross-Cultural Comparison of How Mind-Body Practice Affects Emotional Intelligence, Cognitive Well-Being, and Mental Well-Being

The study tested cross-cultural differences between Israeli and Indian participants in the outcomes of mind-body practice (MBP) on emotional intelligence (EI), cognitive well-being, and mental well-being, as well as the predictive role of gender and MBP on cognitive and mental well-being. It drew on a sample of 699 Indian and Israeli participants (ages 18–65) from urban settings and used questionnaires to measure cognitive well-being, demographics, EI, and mental well-being. EI was assessed using the Self Report Emotional Intelligence (SREIT); cognitive well-being was assessed using the Personal Well-being Index; mental well-being was assessed using the Warwick-Edinburgh Mental Well-being Scale (WEMWBS). The effect of demographic variables was tested using the two-sample T-test or the Chi-square test. The associations between EI, mental, and cognitive subscales were evaluated using the Pearson correlation coefficient and linear regression with stepwise selection. Results indicated MBP affected EI in both cultures, but Indian participants showed higher EI, and Israeli participants showed lower EI. Israelis also reported higher mental well-being. Future research should examine EI as ability (we examined it as a trait) thus contributing to a better understanding of the similarities and differences between trait and ability EI in different cultures. Future work should also probe gender differences.
Differential Effects of Focused Attention and Open Monitoring Meditation on Autonomic Cardiac Modulation and Cortisol Secretion

Mindfulness-based interventions (MBIs) have been used widely as a useful tool for the alleviation of various stress-related symptoms. However, the effects of MBIs on stress-related physiological activity have not yet been ascertained. MBIs primarily consist of focused-attention (FA) and open-monitoring (OM) meditation. Since differing effects of FA and OM meditation on brain activities and cognitive tasks have been mentioned, we hypothesized that FA and OM meditation have also differing effects on stress-related physiological activity. In this study, we examined the effects of FA and OM meditation on autonomic cardiac modulation and cortisol secretion. Forty-one healthy adults (aged 20–46 years) who were meditation novices experienced 30-min FA and OM meditation tasks by listening to instructions. During resting- and meditation-states, electrocardiogram transducers were attached to participants to measure the R-R interval, which were used to evaluate heart rate (HR) and perform heart rate variability (HRV) analyses. Saliva samples were obtained from participants pre- and post-meditation to measure salivary cortisol levels. Results showed that FA meditation induced a decrease in HR and an increase in the root mean square of successive differences (rMSDD). In contrast, OM meditation induced an increase in the standard deviation of the normal-to-normal interval (SDNN) to rMSSD ratio (SDNN/rMSSD) and a decrease in salivary cortisol levels. These results suggest that FA meditation elevates physiological relaxation, whereas OM meditation elevates physiological arousal and reduces stress.
Predicting lncRNA–Protein Interaction With Weighted Graph-Regularized Matrix Factorization

Long non-coding RNAs (lncRNAs) are widely concerned because of their close associations with many key biological activities. Though precise functions of most lncRNAs are unknown, research works show that lncRNAs usually exert biological function by interacting with the corresponding proteins. The experimental validation of interactions between lncRNAs and proteins is costly and time-consuming. In this study, we developed a weighted graph-regularized matrix factorization (LPI-WGRMF) method to find unobserved lncRNA–protein interactions (LPIs) based on lncRNA similarity matrix, protein similarity matrix, and known LPIs. We compared our proposed LPI-WGRMF method with five classical LPI prediction methods, that is, LPBNI, LPI-IBNRA, LPIHN, RWR, and collaborative filtering (CF). The results demonstrate that the LPI-WGRMF method can produce high-accuracy performance, obtaining an AUC score of 0.9012 and AUPR of 0.7324. The case study showed that SFPQ, SNHG3, and PRPF31 may associate with Q9NUL5, Q9NUL5, and Q9UKV8 with the highest linking probabilities and need to further experimental validation.
Lateral Lymph Node Metastases in T1a Papillary Thyroid Carcinoma: Stratification by Tumor Location and Size

Objective To analyze the incidence and risk factors for lateral lymph node metastases (LNMs) in T1a papillary thyroid carcinoma (PTC) with a focus on tumor location and size. Materials and Methods The incidence of lateral LNM in 345 cases of T1a PTC was retrospectively analyzed. Univariate and multivariate analyses were performed to assess the relationships between lateral LNM and clinicopathological characteristics. Results The incidence of skip metastasis to lateral LNM in T1a PTC located in the upper lobe was 12.1% (8/66). Logistic regression analysis indicated tumor size >5 mm (OR = 5.04, 95% CI = 1.79 to 14.18, P = 0.002), upper lobe location (OR = 7.68, 95% CI = 3.05–19.34, P < 0.001) and the number of central neck LNM (<2: OR = 24.79, 95% CI = 8.23–74.60, P < 0.001; ≥2: OR = 4.99, 95% CI = 1.95–12.73, P < 0.001) were independently associated with lateral LNM. Comparing the lateral and central LNM stratification based on tumor location revealed that both the incidences of lateral (33.3%) and central (30.3%) LNM of T1a PTC located in the upper lobe were higher than those of T1a PTC located in the middle and lower lobes. Of T1a PTC located in the upper lobe, the incidence of lateral LNM was 33.3% (22/66), which was higher than that [30.3% (20/66)] of central LNM. This finding is reversed in all T1a PTC cases and T1a PTC cases with tumor located in the middle and lower lobes. Conclusion A particularly high likelihood of lateral LNM was observed in T1a PTC patients with tumor located in the upper lobe of the thyroid gland, especially the tumor >5 mm in size, which could be considered a risk factor for lateral LNM in the clinical management of T1a PTC.
Lifestyle Interventions Improving Cannabinoid Tone During COVID-19 Lockdowns May Enhance Compliance With Preventive Regulations and Decrease Psychophysical Health Complications

Studies investigating the psychosomatic effects of social isolation in animals have shown that one of the physiologic system that gets disrupted by this environment-affective change is the Endocannabinoid System. As the levels of endocannabinoids change in limbic areas and prefrontal cortex during stressful times, so is the subject more prone to fearful and negative thoughts and aggressive behavior. The interplay of social isolation on the hypothalamic-pituitary-adrenal axis and cannabinoid tone triggers a vicious cycle which further impairs the natural body's homeostatic neuroendocrine levels and provokes a series of risk factors for developing health complications. In this paper, we explore the psychosomatic impact of prolonged quarantine in healthy individuals, and propose management and coping strategies that may improve endocannabinoid tone, such as integration of probiotics, cannabidiol, meditation, and physical exercise interventions with the aim of supporting interpersonal, individual, and professional adherence with COVID-19 emergency public measures whilst minimizing their psycho-physical impact.
Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance (mcr)-9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy

A collection of 177 genomes of Salmonella Typhimurium and its monophasic variant isolated in 2014–2019 from Italian poultry/livestock (n = 165) and foodstuff (n = 12), previously screened for antimicrobial susceptibility and assigned to ST34 and single-locus variants, were studied in-depth to check the presence of the novel mcr-9 gene and to investigate their genetic relatedness by whole genome sequencing (WGS). The study of accessory resistance genes revealed the presence of mcr-9.1 in 11 ST34 isolates, displaying elevated colistin minimum inhibitory concentration values up to 2 mg/L and also a multidrug-resistant (MDR) profile toward up to seven antimicrobial classes. Five of them were also extended-spectrum beta-lactamases producers (blaSHV–12 type), mediated by the corresponding antimicrobial resistance (AMR) accessory genes. All mcr-9-positive isolates harbored IncHI2-ST1 plasmids. From the results of the Mash analysis performed on all 177 genomes, the 11 mcr-9-positive isolates fell together in the same subcluster and were all closely related. This subcluster included also two mcr-9-negative isolates, and other eight mcr-9-negative ST34 isolates were present within the same parental branch. All the 21 isolates within this branch presented an IncHI2/2A plasmid and a similar MDR gene pattern. In three representative mcr-9-positive isolates, mcr-9 was demonstrated to be located on different IncHI2/IncHI2A large-size (∼277–297 kb) plasmids, using a combined Illumina–Oxford Nanopore WGS approach. These plasmids were also compared by BLAST analysis with publicly available IncHI2 plasmid sequences harboring mcr-9. In our plasmids, mcr-9 was located in a ∼30-kb region lacking different genetic elements of the typical core structure of mcr-9 cassettes. In this region were also identified different genes involved in heavy metal metabolism. Our results underline how genomics and WGS-based surveillance are increasingly indispensable to achieve better insights into the genetic environment and features of plasmid-mediated AMR, as in the case of such IncHI2 plasmids harboring other MDR genes beside mcr-9, that can be transferred horizontally also to other major Salmonella serovars spreading along the food chain.
Challenges and Opportunities for Information Systems Research During and After Coronavirus

Abstract The COVID-19 pandemic has affected world-wide business and management immensely. Furthermore, challenges and opportunities for information systems research during and after coronavirus have emerged. To better understand the impacts of COVID-19 pandemic in the field of information systems (IS), and also as a part of the 2020 AIS SIG-ISAP Workshop on Information Systems in Asia Pacific (ISAP) being held prior ICIS-2020, we organized a panel to address this important issue with three distinguished information systems researchers. The panelists identified and discussed the challenges and opportunities for information systems research during and after Coronavirus. In addition, constructive suggestions for aspiring young scholars who aim to publish their works in top-tier IS journals have been proposed, which may benefit the IS community in large.
Self-Reported Onset of Paroxysmal Atrial Fibrillation Is Related to Sleeping Body Position

Background: Because stretch of the atrial myocardium is proarrhythmic for atrial fibrillation (AF) and a left lateral body position increases atrial dimensions in humans, we hypothesized that left lateral recumbence is a frequent AF-triggering body position in AF patients. Methods: We performed a questionnaire study of symptomatic paroxysmal AF (episodes of AF < 1 week) patients scheduled for a first AF ablation therapy at Catharina Hospital, Eindhoven, the Netherlands and at University Hospital, Bordeaux, France. Results: Ninety-four symptomatic paroxysmal AF patients were included [mean age 61 ± 11 years, median AF history of 29(48) months, 31% were females]. Twenty-two percent of patients reported a specific body position as a trigger of their AF symptoms. The triggering body position was left lateral position in 57% of cases, supine position in 33%, right lateral position in 10%, and prone position in 5% (p = 0.003 overall difference in prevalence). Patients with positional AF had a higher body mass index compared to patients without nocturnal/positional AF [28.7(4.2) and 25.4(5.2) kg/m2, respectively, p = 0.025], but otherwise resembled these patients. Conclusion: Body position, and the left lateral position, in particular, is a common trigger of AF in symptomatic AF patients. Moreover, positional AF is associated with overweight. Understanding of the underlying mechanisms of positional AF can contribute to AF treatment and prevention.