Miracle-dz/UniFAR-FTUs huggingface dataset:
Perception of Online Learning Among Students From India Set Against the Pandemic

India is the second-most populous country in the world. There had been a tremendous shift towards online learning through Indian Government’s digital initiatives in general, and during COVID-19 lockdown in particular. An online self-report survey (n = 1,318) was conducted to assess students’ perception of online learning in this changed situation in comparison with traditional classroom learning. The study analysed eight independent variables on student’s perception towards online learning, viz., gender, nature of the settlement, economic background, religiosity, primary electronic device, technology-receptiveness, age, and educational institution, with each of these variables forming respective research hypotheses. Results revealed several exciting facets of students’ perceptions. Receptiveness towards online learning was significantly higher for students from urban areas compared with rural areas. Possible reasons for these results are discussed, impediments to student’s motivation with digital education are identified and the findings are contextualized in a broader perspective.
Diagnostic Efficacy of Xpert MTB/RIF Assay in Bronchoalveolar Lavage Fluid for Tracheobronchial Tuberculosis: A Retrospective Analysis

Background: The Xpert Mycobacterium tuberculosis/rifampin (MTB/RIF) assay has shown good diagnostic efficacy in brushing and biopsy tissue samples from patients with tracheobronchial tuberculosis (TBTB). However, its diagnostic value in bronchoalveolar lavage fluid (BALF) is still unclear. Therefore, the present retrospective study aimed to evaluate the diagnostic value of the Xpert MTB/RIF assay in BALF. Methods: The clinical data of 266 patients with suspected TBTB from January 2018 to October 2020 were pooled with complete details of bronchial brush and bronchoalveolar lavage samples. Smears of the bronchial brushings were stained with Auramine O stain to detect acid-fast bacilli (AFB), and BALF samples were used for culturing MTB with the BACTEC MGIT 960 system and the Xpert MTB/RIF assay. The diagnostic performance of these methods was assessed and compared. Results: A total of 266 patients suspected to have TBTB were enrolled in the final analysis. Of these patients, 179 patients were confirmed to have TBTB and 87 patients were non-TBTB. The sensitivity of the Xpert MTB/RIF assay in BALF (87.2%) was significantly higher than that of the brush smear for AFB (35.2%, p < 0.001). No significant difference was observed between the sensitivities of the Xpert MTB/RIF assay in BALF and MTB culture in BALF (87.2 vs. 84.9%, p = 0.542). The specificities of the Xpert MTB/RIF assay in BALF, MTB culture in BALF, and the bronchial brush smear were 97.7, 97.7, and 98.9%, respectively. The positive predictive value (PPV) and negative predictive value (NPV) of the Xpert MTB/RIF assay in BALF, MTB culture in BALF, and the bronchial brush smear were 98.7 and 78.7%, 98.7 and 75.9%, and 98.4 and 42.6%, respectively. Among the MTB culture-positive patients with TBTB detected by the Xpert assay, 27.0% (20/74) were identified to be resistant to RIF. Conclusions: The Xpert MTB/RIF assay in BALF enables a rapid and accurate diagnosis of TBTB and identification of RIF resistance, which is crucial for timely and proper treatment. Moreover, in patients with TBTB, BALF could be used as an alternative to bronchial brushing and biopsy tissues for the Xpert MTB/RIF assay.
Expression of Autophagy and Mitophagy Markers in Breast Cancer Tissues

Mitochondria play important roles in regulating cell bioenergetics status and reactive oxygen species (ROS) generation. ROS-induced mitochondrial damage is among the main intracellular signal inducers of autophagy. Autophagy is a cellular catabolic process that regulates protein and organelle turnover, while a selective form of autophagy, mitophagy, specifically targets dysfunctional mitochondrial degradation. This study aims to measure the levels of autophagy, mitophagy, oxidative stress, and apoptosis in invasive breast carcinoma tissues using immunohistochemistry (IHC). Tissue microarrays of 76 patients with breast cancer were stained with six IHC markers (MnSOD, Beclin-1, LC3, BNIP3, Parkin, and cleaved caspase 3). The expression intensity was determined for each tumor tissue and the adjacent tumor-matched control tissues. Intermediate and strong staining scores of MnSOD, Beclin-1, LC-3, BNIP-3, and Parkin were significantly higher in tumor tissues compared to the adjacent matched control. The scoring intensity was further classified into tissues with negative staining and positive staining, which showed that positive scores of Beclin-1 and Parkin were significantly high in tumor tissues compared to other markers. Positive association was also noted between BNIP-3 and Beclin-1 as well as LC-3 and cleaved caspase-3 immunostaining. To our knowledge, this is one of the first studies that measure both mitophagy and autophagy in the same breast cancer tissues and the adjacent matched control. The findings from this study will be of great potential in identifying new cancer biomarkers and inspire significant interest in applying anti-autophagy therapies as a possible treatment for breast cancer.
Immune System Disequilibrium—Neutrophils, Their Extracellular Traps, and COVID-19-Induced Sepsis

Equilibrium within the immune system can often determine the fate of its host. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen responsible for the coronavirus disease 2019 (COVID-19) pandemic. Immune dysregulation remains one of the main pathophysiological components of SARS-CoV-2-associated organ injury, with over-activation of the innate immune system, and induced apoptosis of adaptive immune cells. Here, we provide an overview of the innate immune system, both in general and relating to COVID-19. We specifically discuss “NETosis,” the process of neutrophil release of their extracellular traps, which may be a more recently described form of cell death that is different from apoptosis, and how this may propagate organ dysfunction in COVID-19. We complete this review by discussing Stem Cell Therapies in COVID-19 and emerging COVID-19 phenotypes, which may allow for more targeted therapy in the future. Finally, we consider the array of potential therapeutic targets in COVID-19, and associated therapeutics.
The Role of Atopy in COPD and Asthma

Common to several allergic diseases is the generation of immunoglobulin E (IgE) by plasma cells, when exposed to an innocuous antigen. Asthma and chronic obstructive pulmonary disease (COPD) are two prevalent chronic airway inflammatory diseases. Asthma is mediated in some patients through eosinophilic inflammatory mechanisms that include allergic sensitization and Th2-mediated immune airway response. COPD, on the other hand is mainly considered a Th1-mediated inflammatory process with neutrophilic predominance or a non-Th2 inflammation, occasionally associated with the presence of airway bacteria or viruses. IgE production appears to play an important role in the development of both COPD and asthma, as it has been associated to respiratory symptoms, lung function, bacterial and viral infections, airway remodeling and bronchial hyperreactivity in both diseases. The aim of this review is to summarize all current data concerning the role of specific and total IgE in COPD and asthma and to highlight similarities and differences in view of possible therapeutic interventions.
Child Adjustment During COVID-19: The Role of Economic Hardship, Caregiver Stress, and Pandemic Play

The coronavirus disease 2019 (COVID-19) led to many lifestyle changes and economic hardships for families with young children. Previous research on risk and resilience highlights that children's adjustment to family hardships is influenced by caregiver stress, but individual child behaviors and characteristics may protect children from negative outcomes. Interestingly, many children have been reported to incorporate COVID-19 themes in their pretend play. Theory suggests children may do so to cope with pandemic-related stress, but no empirical studies have explored this possibility. The purpose of this study was to understand the process by which COVID-19 economic hardships experienced by a family were related to children's emotional well-being and development and to investigate how this process may vary as a function of children's engagement in pandemic-related pretend play. Caregivers (N = 99; mostly high earning families) of preschoolers ages 3–6 years (51% girls, 82% White) living in the United States participated in an online survey at two time points during the pandemic. Result revealed that COVID-19 economic hardships were related to increased caregiver stress, which, in turn, was associated with children's emotional distress and poorer self-regulation. However, engaging in pandemic-related pretend play appeared to protect children's well-being by weakening the adverse association between caregivers' stress and children's emotional distress. Thus, addressing caregiver stress levels and allowing children an outlet to cope with challenges through pretend play could have crucial protective effects on early development and well-being during times of crisis.
How to Identify Patients at High Risk of Developing Nasal-Type, Extranodal Nature Killer/T-Cell Lymphoma-Associated Hemophagocytic Syndrome

Nasal-type, extranodal nature killer (NK)/T-cell lymphoma-associated hemophagocytic syndrome (NK/T-LAHS) is a rare and life-threatening disease, requiring investigation of risk stratification. We conducted a retrospective study and proposed nomograms to predict NK/T-LAHS. The discriminative ability and calibration of the nomograms for prediction were tested using C statistics and calibration plots. We analyzed 533 patients with extranodal NK/T-cell lymphoma (ENKTL), out of which 71 were diagnosed with hemophagocytic syndrome (HPS), with a cumulative incidence of 13.3%. Significant difference for 2-year survival was found between patients with and without HPS (14.7% vs. 77.5%). Analyses showed that Eastern Cooperative Oncology Group (ECOG) performance status (PS) ≥2, B symptoms, and bone marrow (BM) invasion were significantly associated with NK/T-LAHS. We used these data as the basis to establish a nomogram of risk index for ENKTL (RINK). In 335 patients with available data for Epstein-Barr virus DNA (EBV-DNA), we found high viral copies (≥4,450 copies/ml) were correlated with NK/T-LAHS. When these data were added to RINK, we developed another nomogram that included EBV-DNA data (RINK-E). The nomograms displayed good accuracy in predicting NK/T-LAHS with a C-statistics of 0.919 for RINK and a C-statistics of 0.946 for RINK-E, respectively. The calibration chart also showed an excellent consistency between the predicted and observed probabilities. The proposed nomograms provided individualized risk estimate of HPS in patients with ENKTL.
Genetic Mechanism for the Cyclostome Cerebellar Neurons Reveals Early Evolution of the Vertebrate Cerebellum

The vertebrate cerebellum arises at the dorsal part of rhombomere 1, induced by signals from the isthmic organizer. Two major cerebellar neuronal subtypes, granule cells (excitatory) and Purkinje cells (inhibitory), are generated from the anterior rhombic lip and the ventricular zone, respectively. This regionalization and the way it develops are shared in all extant jawed vertebrates (gnathostomes). However, very little is known about early evolution of the cerebellum. The lamprey, an extant jawless vertebrate lineage or cyclostome, possesses an undifferentiated, plate-like cerebellum, whereas the hagfish, another cyclostome lineage, is thought to lack a cerebellum proper. In this study, we found that hagfish Atoh1 and Wnt1 genes are co-expressed in the rhombic lip, and Ptf1a is expressed ventrally to them, confirming the existence of r1’s rhombic lip and the ventricular zone in cyclostomes. In later stages, lamprey Atoh1 is downregulated in the posterior r1, in which the NeuroD increases, similar to the differentiation process of cerebellar granule cells in gnathostomes. Also, a continuous Atoh1-positive domain in the rostral r1 is reminiscent of the primordium of valvula cerebelli of ray-finned fishes. Lastly, we detected a GAD-positive domain adjacent to the Ptf1a-positive ventricular zone in lampreys, suggesting that the Ptf1a-positive cells differentiate into some GABAergic inhibitory neurons such as Purkinje and other inhibitory neurons like in gnathostomes. Altogether, we conclude that the ancestral genetic programs for the formation of a distinct cerebellum were established in the last common ancestor of vertebrates.
Traumatic Injury to the Developing Brain: Emerging Relationship to Early Life Stress

Despite the high incidence of brain injuries in children, we have yet to fully understand the unique vulnerability of a young brain to an injury and key determinants of long-term recovery. Here we consider how early life stress may influence recovery after an early age brain injury. Studies of early life stress alone reveal persistent structural and functional impairments at adulthood. We consider the interacting pathologies imposed by early life stress and subsequent brain injuries during early brain development as well as at adulthood. This review outlines how early life stress primes the immune cells of the brain and periphery to elicit a heightened response to injury. While the focus of this review is on early age traumatic brain injuries, there is also a consideration of preclinical models of neonatal hypoxia and stroke, as each further speaks to the vulnerability of the brain and reinforces those characteristics that are common across each of these injuries. Lastly, we identify a common mechanistic trend; namely, early life stress worsens outcomes independent of its temporal proximity to a brain injury.
Research on Influencing Factors and Classification of Patients With Mild and Severe COVID-19 Symptoms

Objective To analyze the epidemiological history, clinical symptoms, laboratory testing parameters of patients with mild and severe COVID-19 infection, and provide a reference for timely judgment of changes in the patients’ conditions and the formulation of epidemic prevention and control strategies. Methods A retrospective study was conducted in this research, a total of 90 patients with COVID-19 infection who received treatment from January 21 to March 31, 2020 in the Ninth People’s Hospital of Dongguan City were selected as study subject. We analyzed the clinical characteristics of laboratory-confirmed patients with COVID-19, used the oversampling method (SMOTE) to solve the imbalance of categories, and established Lasso-logistic regression and random forest models. Results Among the 90 confirmed COVID-19 cases, 79 were mild and 11 were severe. The average age of the patients was 36.1 years old, including 49 males and 41 females. The average age of severe patients is significantly older than that of mild patients (53.2 years old vs 33.7 years old). The average time from illness onset to hospital admission was 4.1 days and the average actual hospital stay was 18.7 days, both of these time actors were longer for severe patients than for mild patients. Forty-eight of the 90 patients (53.3%) had family cluster infections, which was similar among mild and severe patients. Comorbidities of underlying diseases were more common in severe patients, including hypertension, diabetes and other diseases. The most common symptom was cough [45 (50%)], followed by fever [43 (47.8%)], headache [7 (7.8%)], vomiting [3 (3.3%)], diarrhea [3 (3.3%)], and dyspnea [1 (1.1%)]. The laboratory findings of patients also included leukopenia [13(14.4%)] and lymphopenia (17.8%). Severe patients had a low level of creatine kinase (median 40.9) and a high level of D-dimer. The median NLR of severe patients was 2.82, which was higher than that of mild patients. Logistic regression showed that age, phosphocreatine kinase, procalcitonin, the lymphocyte count of the patient on admission, cough, fatigue, and pharynx dryness were independent predictors of COVID-19 severity. The classification of random forest was predicted and the importance of each variable was displayed. The variable importance of random forest indicates that age, D-dimer, NLR (neutrophil to lymphocyte ratio) and other top-ranked variables are risk factors. Conclusion The clinical symptoms of COVID-19 patients are non-specific and complicated. Age and the time from onset to admission are important factors that determine the severity of the patient’s condition. Patients with mild illness should be closely monitored to identify those who may become severe. Variables such as age and creatine phosphate kinase selected by logistic regression can be used as important indicators to assess the disease severity of COVID-19 patients. The importance of variables in the random forest further complements the variable feature information.
The Comparison Between Different Hospital Market Definition Approaches: An Empirical Analysis of 11 Representative Diseases in Sichuan Province, China

Objective: This study aims to provide empirical evidence for the controversy about whether the inference is consistent if alternative hospital market definition methods are employed, and for which definition method is the best alternative to the predicted patient flow approach. Data sources: Collecting data from the discharge data of inpatients and hospital administrative data of Sichuan province in China in the fourth quarter of 2018. Study Design: We employed Herfindahl–Hirschman Index (HHI) as the proxy of market competition used as an example to measure the hospital market structure. Correlation coefficients of HHIs based on different definition methods were assessed. The corresponding coefficient of each HHI estimated in identical regression models was then compared. In addition, since the predicted patient flow method has been argued by the literature of its advantages compared with the previous approaches, we took the predicted patient flow as a reference to compare with the other approaches. Data Extraction Methods: We selected the common diseases with a significant burden, and 11 diseases were included (902,767 hospitalizations). Principal Findings: The correlation coefficients of HHIs based on different market definition methods are all significantly greater than 0, and the coefficients of HHIs are different in identical regression models. Taking the predicted patient flow approach as a reference, we found that the correlation coefficients between HHIs based on fixed radius and predicted patient flow approach is larger than others, and their parameter estimates are all consistent. Conclusion: Although the HHIs based on different definition methods are significantly and positively correlated, the inferences about the effectiveness of market structure would be inconsistent when alternative market definition methods are employed. The fixed radius would be the best alternative when researchers want to use the predicted patient flow method to define the hospital market but are hindered by the data limitations and computational complexity.
First Coronavirus Active Survey in Rodents From the Canary Islands

Since the beginning of the 21st century five new coronaviruses inducing respiratory diseases in humans have been reported. These emergences has promoted research on coronaviruses in wildlife. We started the first eco-epidemiological study to screen the presence of coronaviruses circulating in mice and rats of four Canary Islands. Between 2015 and 2019, we obtained fecal samples of three rodent species (150 Mus musculus, 109 Rattus rattus and 1 Rattus norvegicus) captured in urban and rural areas. Fecal samples were analyzed by nRT-PCR and the resulting sequences were compared to known diversity using Bayesian phylogenetic methods. We only found coronavirus RNA in house mice from El Hierro (10.53%), Tenerife (7.02%) and Lanzarote (5.26%) islands. All coronaviruses detected belong to the species Murine coronavirus belonging to the genus Betacoronavirus and subgenus Embecovirus, being all positive house mice captured in anthropogenic environment. The phylogenetic analysis shows that murine coronaviruses from the Canary Islands are related to European murine coronaviruses. Albeit data are still scarce in the region, the most probable origin of M. coronavirus present in the Canary Islands is continental Europe. According to temporal Bayesian phylogenetics, the differentiation between Canary and continental viruses seems to be quite recent. Moreover, murine coronaviruses from El Hierro, Tenerife and Lanzarote islands tend to segregate in different clades. This enlightens the potential role of rodents or other possibly invasive species in disseminating infectious diseases to remote places through exchanges with the continent. It is important to consider these aspects in the sanitary control of islands, for health and biodiversity preservation concerns.
Methods and Analysis of The First Competition in Predicting Generalization of Deep Learning

Deep learning has been recently successfully applied to an ever larger number of problems, ranging from pattern recognition to complex decision making. However, several concerns have been raised, including guarantees of good generalization , which is of foremost importance. Despite numerous attempts, conventional statistical learning approaches fall short of providing a satisfactory explanation on why deep learning works. In a competition hosted at the Thirty-Fourth Conference on Neural Information Processing Systems (NeurIPS 2020)
Improved Analysis of the Tsallis-INF Algorithm in Stochastically Constrained Adversarial Bandits and Stochastic Bandits with Adversarial Corruptions

We derive improved regret bounds for the Tsallis-INF algorithm of Zimmert and Seldin (2021). We show that in adversarial regimes with a $(\Delta,C,T)$ self-bounding constraint the algorithm achieves $\mathcal{O}\left(\left(\sum_{i\neq i^*} \frac{1}{\Delta_i}\right)\log_+\left(\frac{(K-1)T}{\left(\sum_{i\neq i^*} \frac{1}{\Delta_i}\right)^2}\right)+\sqrt{C\left(\sum_{i\neq i^*}\frac{1}{\Delta_i}\right)\log_+\left(\frac{(K-1)T}{C\sum_{i\neq i^*}\frac{1}{\Delta_i}}\right)}\right)$ regret bound, where $T$ is the time horizon, $K$ is the number of arms, $\Delta_i$ are the suboptimality gaps, $i^*$ is the best arm, $C$ is the corruption magnitude, and $\log_+(x) = \max\left(1,\log x\right)$. The regime includes stochastic bandits, stochastically constrained adversarial bandits, and stochastic bandits with adversarial corruptions as special cases. Additionally, we provide a general analysis, which allows to achieve the same kind of improvement for generalizations of Tsallis-INF to other settings beyond multiarmed bandits.