Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Analysis to Study the Molecular Response in the Gill and Hepatopancreas Tissues of Macrobrachium nipponense to Salinity Acclimation

Macrobrachium nipponense is an economically important prawn species and common in Chinese inland capture fisheries. During aquaculture, M. nipponense can survive under freshwater and low salinity conditions. The molecular mechanism underlying the response to salinity acclimation remains unclear in this species; thus, in this study, we used the Illumina RNA sequencing platform for transcriptome analyses of the gill and hepatopancreas tissues of M. nipponense exposed to salinity stress [0.4‰ (S0, control group), 6‰ (S6, low salinity group), and 12‰ (S12, high salinity group)]. Differentially expressed genes were identified, and several important salinity adaptation-related terms and signaling pathways were found to be enriched, such as “ion transport,” “oxidative phosphorylation,” and “glycometabolism. ” Quantitative real-time PCR demonstrated the participation of 12 key genes in osmotic pressure regulation in M. nipponense under acute salinity stress. Further, the role of carbonic anhydrase in response to salinity acclimation was investigated by subjecting the gill tissues of M. nipponense to in situ hybridization. Collectively, the results reported herein enhance our understanding of the mechanisms via which M. nipponense adapts to changes in salinity.
Recognition of Cattle's Feeding Behaviors Using Noseband Pressure Sensor With Machine Learning

Automatic monitoring of feeding behavior especially rumination and eating in cattle is important to keep track of animal health and growth condition and disease warnings. The noseband pressure sensor is not only able to accurately sense the pressure change of the cattle's jaw movements, which can directly reflect the cattle's chewing behavior, but also has strong resistance to interference. However, it is difficult to keep the same initial pressure while wearing the pressure sensor, and this will pose a challenge to process the feeding behavior data. This article proposed a machine learning approach aiming at eliminating the influence of initial pressure on the identification of rumination and eating behaviors. The method mainly used the local slope to obtain the local data variation and combined Fast Fourier Transform (FFT) to extract the frequency-domain features. Extreme Gradient Boosting Algorithm (XGB) was performed to classify the features of rumination and eating behaviors. Experimental results showed that the local slope in combination with frequency-domain features achieved an F1 score of 0.96, and recognition accuracy of 0.966 in both rumination and eating behaviors. Combined with the commonly used data processing algorithms and time-domain feature extraction method, the proposed approach improved the behavior recognition accuracy. This work will contribute to the standardized application and promotion of the noseband pressure sensors.
Ablation of Outflow Tract Arrhythmias in Patients With and Without Structural Heart Disease—A Comparative Analysis

Introduction Catheter ablation of ventricular arrhythmias emerging from the ventricular outflow tracts and adjacent structures is very effective and considered almost curative in patients without structural heart disease (SHD). Outcomes of patients with SHD undergoing ablation of outflow tract arrhythmias are not known. Methods Consecutive patients (2019–2021) undergoing catheter ablation of ventricular arrhythmias in a single high-volume center were retrospectively analyzed. Patients with ablation of outflow tract arrhythmias were identified and divided in individuals with and without SHD. Procedural parameters and acute outcome were compared. Results We identified 215 patients with outflow tract arrhythmias (35.3% female, mean age 58.3 ± 16.0 years). Of those, 93 (43.3%) had SHD. Patients with SHD and outflow tract arrhythmias were older (65.0 ± 12.8 vs. 53.3 ± 16.3 years; p < 0.001), more often male (82.8 vs. 50.0%; p < 0.001) and had more comorbidities than patients without SHD (arterial hypertension: 62.4 vs. 34.4%, p < 0.001; diabetes: 22.6 vs. 8.2%, p = 0.005; chronic lung disease: 20.4 vs. 7.4%, p = 0.007). Outflow tract arrhythmias in patients with SHD had their origin more often in the left ventricle (68.8 vs. 53.3%, p = 0.025). The acute success rate was similar in both patient groups (93.4 vs. 94.2%, p = 0.781). Patients with SHD were discharged later {median length of hospital stay with SHD 5 [6 (interquartile range)] days, without SHD 2 [4] days, p < 0.001}. Periprocedural complications were numerically more frequent in patients with SHD [with SHD 12 (12.9%), without SHD 8 (6.6%), p = 0.154]. Conclusion Outflow tract arrhythmia ablation has a high success rate irrespective of the presence of SHD. Longer hospital stay and potentially a higher risk of periprocedural complications should be considered when discussing this treatment option with patients.
Screening the Potential Biomarkers of COVID-19-Related Thrombosis Through Bioinformatics Analysis

A high proportion of critically ill patients with coronavirus disease 2019 (COVID-19) experience thrombosis, and there is a strong correlation between anticoagulant therapy and the COVID-19 survival rate, indicating that common COVID-19 and thrombosis targets have potential therapeutic value for severe COVID-19.Gene expression profiling data were downloaded from Gene Expression Omnibus (GEO), and common differentially expressed genes (co-DEGs) were identified. The potential biological functions of these co-DEGs were explored by functional enrichment analysis, and protein–protein interaction (PPI) networks were constructed to elucidate the molecular mechanisms of the co-DEGs. Finally, hub genes in the co-DEG network were identified, and correlation analysis was performed.We identified 8320 upregulated genes and 7651 downregulated genes from blood samples of COVID-19 patients and 368 upregulated genes and 240 downregulated genes from blood samples of thrombosis patients. The enriched cellular component terms were mainly related to cytosolic ribosomes and ribosomal subunits. The enriched molecular function terms were mainly related to structural constituents of ribosomes and electron transfer activity. Construction of the PPI network and identification of hub genes ultimately confirmed that RPS7, IGF1R, DICER1, ERH, MCTS1, and TNPO1 were jointly upregulated hub genes, and FLNA and PXN were jointly downregulated hub genes.The identification of novel potential biomarkers provides new options for treating COVID-19-related thrombosis and reducing the rate of severe COVID-19.
Necroptosis is Related to Anti-PD-1 Treatment Response and Influences the Tumor Microenvironment in Head and Neck Squamous Cell Carcinoma

The latest research suggesting that necroptosis plays a vital role in immune response. However, the influence of necroptosis on tumor microenvironment (TME) remodeling and immunotherapy is still unclear. We analyzed the variations in the expression of 26 necroptosis-related molecules in HNSCC and the influence of genome changes. We investigated HNSCC samples and determined that there are two necroptosis phenotypes in HNSCC cancer, and there are significant differences in cell infiltration characteristics and survival in different necroptosis phenotypes. We used the single‐sample gene set enrichment analysis to measure the level of necroptosis in patients with NecroticScore, we confirmed that the NecroticScore can predict the prognosis of HNSCC patients and the response to immunotherapy. Patients with a high NecroticScore are more sensitive to immunotherapy and have a better prognosis. Our study suggests a significant correlation between the expression imbalance of necroptosis-related molecules and suggests necroptosis plays an important role in modeling the TME. In addition, we construct a risk prediction model which could stratify patients with HNSCC and predict patient prognosis according to this necroptosis-related molecules. In conclusion, evaluating necroptosis modification patterns contributes to enhancing our understanding of TME and can guide more effective immunotherapy strategies.
Cognitive and Neuropsychiatric Features of COVID-19 Patients After Hospital Dismission: An Italian Sample

Background and Aims Recent studies suggest cognitive, emotional, and behavioral impairments occur in patients after SARS-CoV-2 infection. However, studies are limited to case reports or case series and, to our knowledge, few of them have control groups. This study aims to assess the prevalence of neuropsychological and neuropsychiatric impairment in patients after hospitalization. Methods We enrolled 29 COVID+ patients (M/F: 17/12; age 58.41 ± 10.00 years; education 11.07 ± 3.77 years, 2 left handers) who needed hospitalization but no IC, about 20 days post-dismission, and 29 COVID− healthy matched controls. Neuropsychological and neuropsychiatric assessments were conducted via teleneuropsychology using the following tests: MMSE, CPM47, RAVLT, CDT, Digit-Span Forward/Backward, Verbal fluencies; BDI-II, STAI. People with previous reported cognitive impairment and neurological or psychiatric conditions were excluded. Clinical and demographics were collected. Comparison between groups was conducted using parametric or non-parametric tests according to data distribution (T-test, Mann Withney-U test; Chi-square goodness of fit). Within COVID+ group, we also evaluated the correlation between the cognitive and behavioral assessment scores and clinical variables collected. Results Among COVID+, 62% had at least one pathological test (vs. 13% in COVID−; p = 0.000) and significantly worst performances than COVID− in RAVLT learning (42.55 ± 10.44 vs. 47.9 ± 8.29, p = 0.035), RAVLT recall (8.79 ± 3.13 vs. 10.38 ± 2.19, p = 0.03), and recognition (13.69 ± 1.47 vs. 14.52 ± 0.63, p = 0.07). STAI II was higher in COVID− (32.69 ± 7.66 vs. 39.14 ± 7.7, p = 0.002). Chi-square on dichotomous values (normal/pathological) showed a significant difference between groups in Digit backward test (pathological 7/29 COVID+ vs. 0/29 COVID−; p = 0.005). Conclusions Patients COVID+ assessed by teleneuropsychology showed a vulnerability in some memory and executive functions (working memory, learning, delayed recall, and recognition). Intriguingly, anxiety was higher in the control group. Our findings therefore confirm the impact of COVID-19 on cognition even in patients who did not need IC. Follow-up is needed to evaluate the evolution of COVID-19-related cognitive deficit. Clinical Trial Registration [ClinicalTrials.gov], identifier [NCT05143320].
Tricuspid Annular Abnormalities in Isolated Left Ventricular Non-compaction—Insights From the Three-dimensional Speckle-Tracking Echocardiographic MAGYAR-Path Study

Introduction Prominent trabecular left ventricular (LV) meshwork and deep intertrabecular LV recesses are featuring LV non-compaction (LVNC). The aim of this study was to evaluate tricuspid annular (TA) morphological and functional abnormalities by three-dimensional speckle-tracking echocardiography (3DSTE) in patients with LVNC without right ventricular (RV) involvement. Materials and Methods This study consisted of 21 patients with isolated LVNC, from which 6 cases were excluded due to inferior image quality. The remaining patient group consisted of 15 subjects with a mean age of 52.1 ± 11.4 years (9 males). LVNC was defined according to the Jenni's criteria. Their results were compared to 21 age- and gender-matched healthy controls (mean age: 52.4 ± 3.9 years, 14 males). Complete routine 2-dimensional Doppler echocardiographic examination was performed in all the patients with isolated LVNC and healthy controls. End-systolic and end-diastolic TA dimensions were assessed on selected planes derived from full-volume 3D echocardiographic datasets during 3DSTE. Results Patients with isolated LVNC showed significantly dilated end-systolic and end-diastolic TA diameter and area, which were accompanied with preserved TA functional properties and associated with right atrial (RA) volumes. TA plane systolic excursion (TAPSE) showed mild correlations with TA fractional area change (TAFAC) and TA fractional shortening (TAFS). No correlations could be demonstrated between TAPSE and TA morphological features. Extent of LVNC did not correlate with any echocardiographic parameters. Conclusion TA is dilated with preserved sphincter-like function in patients with isolated LVNC. Longitudinal (TAPSE) and sphincter-like (TAFAC and TAFS) TA movements correlate with each other. TA dilation is associated with an increased RA volumes respecting cardiac cycle.
Editorial: User Modeling and Recommendations

1 Faculty of Computer Science and Biomedical Engineering, Institute of Interactive Systems and Data Science, Graz University of Technology, Graz, Austria, Web Information Systems, Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, Delft, Netherlands, HICUP Lab, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
Prediction of Left Atrial Fibrosis and Success of Catheter Ablation by Speckle Tracking Echocardiography in Patients Imaged in Persistent Atrial Fibrillation

Background Non-invasive evaluation of left atrial structural and functional remodeling should be considered in all patients with persistent atrial fibrillation (AF) to optimal management. Speckle tracking echocardiography (STE) has been shown to predict AF recurrence after catheter ablation; however in most studies, patients had paroxysmal AF, and STE was performed while patients were in sinus rhythm. Aim The aim of this study was to evaluate the ability of STE parameters acquired during persistent AF to assess atrial fibrosis measured by low voltage area, and to predict maintenance of sinus rhythm of catheter ablation. Methods A total of 94 patients (69 men, 65 ± 9 years) with persistent AF prospectively underwent measurement of Global Peak Atrial Longitudinal Strain (GPALS), indexed LA Volume (LAVI), E/e′ ratio, and LA stiffness index (the ratio of E/e′ to GPALS) by STE prior to catheter ablation, while in AF. Low-voltage area (LVA) was assessed by electro-anatomical mapping and categorized into absent, moderate (>0 to <15%), and high (≥15%) atrial extent. AF recurrence was evaluated after 3 months of blanking. Results Multivariable regression showed that LAVI, GPALS, and LA stiffness independently predicted LVA extent after correcting for age, glomerular filtration rate, and CHA2DS2-VASc score. Of all the parameters, LA stiffness index had the highest diagnostic accuracy (AUC 0.85), allowing using a cut-off value ≥0.7 to predict moderate or high LVA with 88% sensitivity and 47% specificity, respectively. In multivariable Cox analysis, both GPALS and LA stiffness were able to significantly improve the c statistic to predict AF recurrence (n = 40 over 9 months FU) over CHARGE-AF (p < 0.001 for GPALS and p = 0.01 for LA stiffness) or CHA2DS2-VASc score (p < 0.001 for GPALS and p = 0.02 for LA stiffness). GPALS and LA stiffness also improved the net reclassification index (NRI) over the CHARGE-AF index (NRI 0.67, 95% CI [0.33–1.13] for GPALS and NRI 0.73, 95% CI [0.12–0.91] for LA stiffness, respectively), and over the CHA2DS2-VASc score (NRI 0.43, 95% CI [−0.14 to 0.69] for GPALS and NRI 0.52, 95% CI [0.10–0.84], respectively) for LA stiffness to predict AF recurrence at 9 months. Conclusion STE parameters acquired during AF allow prediction of LVA extent and AF recurrence in patients with persistent AF undergoing catheter ablation. Therefore, STE could be a valuable approach to select candidates for catheter ablation.
Staphylococcal Complement Evasion Protein Sbi Stabilises C3d Dimers by Inducing an N-Terminal Helix Swap

Staphylococcus aureus is an opportunistic pathogen that is able to thwart an effective host immune response by producing a range of immune evasion molecules, including S. aureus binder of IgG (Sbi) which interacts directly with the central complement component C3, its fragments and associated regulators. Recently we reported the first structure of a disulfide-linked human C3d17C dimer and highlighted its potential role in modulating B-cell activation. Here we present an X-ray crystal structure of a disulfide-linked human C3d17C dimer, which undergoes a structurally stabilising N-terminal 3D domain swap when in complex with Sbi. These structural studies, in combination with circular dichroism and fluorescence spectroscopic analyses, reveal the mechanism underpinning this unique helix swap event and could explain the origins of a previously discovered N-terminally truncated C3dg dimer isolated from rat serum. Overall, our study unveils a novel staphylococcal complement evasion mechanism which enables the pathogen to harness the ability of dimeric C3d to modulate B-cell activation.
Linear Growth Trajectories, Catch-up Growth, and Its Predictors Among North Indian Small-for-Gestational Age Low Birthweight Infants: A Secondary Data Analysis

Background Low birthweight small-for-gestational-age (SGA-LBW) (birthweight below the 10th percentile for gestational age; SGA-LBW) infants are at an increased risk of poor postnatal growth outcomes. Linear growth trajectories of SGA-LBW infants are less studied in South Asian settings including India. Objectives To describe the linear growth trajectories of the SGA-LBW infants compared with appropriate-for-gestational-age LBW (AGA-LBW) infants during the first 6 months of life. In addition, we estimated catch-up growth (ΔLAZ > 0.67) in SGA-LBW infants and their performance against the WHO linear growth velocity cut-offs. Additionally, we studied factors associated with poor catch-up growth in SGA-LBW infants. Methods The data utilized came from an individually randomized controlled trial that included low birthweight (LBW) infants weighing 1,500–2,250 g at birth. A total of 8,360 LBW infants were included. For comparison between SGA-LBW and AGA-LBW infants, we presented unadjusted and adjusted estimates for mean differences (MDs) or risk ratios (RRs) for the outcomes of length, linear growth velocity, length for age z-score (LAZ) score, and stunting. We estimated the proportion of catch-up growth. Generalized linear models of the Poisson family with log links were used to identify factors associated with poor catch-up growth in SGA-LBW infants. Results Low birthweight small-for-gestational-age infants had a higher risk of stunting, lower attained length, and a lower LAZ score throughout the first 6 months of life compared with AGA-LBW infants, with differences being maximum at 28 days and minimum at 6 months of age. The linear growth velocity in SGA-LBW infants compared with AGA-LBW infants was significantly lower during the birth–28 day period [MD −0.19, 95% confidence interval (CI): −0.28 to −0.10] and higher during the 3- to 6-month period (MD 0.17, 95% CI: 0.06–0.28). Among the SGA-LBW infants, 55% showed catch-up growth for length at 6 months of age. Lower wealth quintiles, high birth order, home birth, male child, term delivery, non-exclusive breastfeeding, and pneumonia were associated with the higher risk of poor catch-up in linear growth among SGA-LBW infants. Conclusion Small for gestational age (SGA) status at birth, independent of gestational age, is a determinant of poor postnatal linear growth. Promotion of institutional deliveries, exclusive breastfeeding, and prevention and early treatment of pneumonia may be helpful to improve linear growth in SGA-LBW infants during early infancy. Clinical Trial Registration [https://clinicaltrials.gov/], identifier [NCT02653534].
A Decrease in Hemodynamic Response in the Right Postcentral Cortex Is Associated With Treatment-Resistant Auditory Verbal Hallucinations in Schizophrenia: An NIRS Study

Background Treatment-resistant auditory verbal hallucinations (TRAVHs) might cause an increased risk of violence, suicide, and hospitalization in patients with schizophrenia (SCZ). Although neuroimaging studies have identified the neural correlation to the symptom of AVH, functional brain activity that correlates particularly in patients with TRAVH remains limited. Functional near-infrared spectroscopy (fNIRS) is a portable and suitable measurement, particularly in exploring brain activation during related tasks. Hence, our researchers aimed to explore the differences in the cerebral hemodynamic function in SCZ-TRAVH, patients with schizophrenia without AVH (SCZ-nAVH), and healthy controls (HCs), to examine neural abnormalities associated more specifically with TRAVH. Methods A 52-channel functional near-infrared spectroscopy system was used to monitor hemodynamic changes in patients with SCZ-TRAVH (n = 38), patients with SCZ-nAVH (n = 35), and HC (n = 30) during a verbal fluency task (VFT). VFT performance, clinical history, and symptom severity were also noted. The original fNIRS data were analyzed using MATLAB to obtain the β values (the brain cortical activity response during the VFT task period); these were used to calculate Δβ (VFT β minus baseline β), which represents the degree of change in oxygenated hemoglobin caused by VFT task. Result Our results showed that there were significant differences in Δβ values among the three groups at 26 channels (ch4, ch13-15, 18, 22, ch25–29, 32, ch35–39, ch43–51, F = 1.70 to 19.10, p < 0.043, FDR-corrected) distributed over the prefrontal–temporal cortical regions. The further pairwise comparisons showed that the Δβ values of 24 channels (ch13–15, 18, 22, 25, ch26–29, ch35–39, ch43–49, ch50–51) were significantly lower in the SCZ group (SCZ-TRAVH and/or SCZ-nAVH) than in the HC group (p < 0.026, FDR-corrected). Additionally, the abnormal activation in the ch22 of right postcentral gyrus was correlated, in turn, with severity of TRAVH. Conclusion Our findings indicate that specific regions of the prefrontal cortex may be associated with TRAVH, which may have implications for early intervention for psychosis.
Protocol for Comparing the Efficacy of Three Reconstruction Methods of the Digestive Tract (Kamikawa Versus Double-Tract Reconstruction Versus Tube-Like Stomach) After Proximal Gastrectomy

Background Appropriate gastrointestinal reconstruction after proximal gastrectomy can effectively reduce the incidence of postoperative complications in patients with proximal early gastric cancer. However, there is still great controversy about the choice of digestive tract reconstruction after proximal gastrectomy, and there is no clinical consensus on the choice of digestive tract reconstruction after proximal gastrectomy. Currently, there is a lack of large-sample, prospective, randomized controlled studies to compare the efficacy of Kamikawa, double-tract reconstruction, and tube-like stomach reconstruction after proximal gastrectomy. Methods/design This study will investigate the efficacy of three reconstruction methods after proximal gastrectomy in a prospective, multicenter, randomized controlled trial, which will enroll 180 patients with proximal early gastric cancer. Patients will be randomly divided into three groups: Group A (Kamikawa, n = 60), Group B (double-tract reconstruction, n = 60), and Group C (tube-like stomach, n = 60). The general information, past medical history, laboratory findings, imaging findings, and surgical procedures of the patients will be recorded and analyzed. The incidence of reflux esophagitis will be recorded as the primary endpoint. The incidence of anastomotic leakage, anastomotic stenosis, operative time and intraoperative blood loss will be recorded as secondary endpoints. Discussion This study will establish a large-sample, prospective, randomized controlled trial to compare the efficacy of Kamikawa, double-tract reconstruction, and tube-like stomach reconstruction after proximal gastrectomy. Trial registration This study was approved by the Chinese Clinical Trial Registry and registered on April 30, 2021. The registration number is ChiCTR2100045975.