Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-Species Phylogeography of Arid-Zone Sminthopsinae (Marsupialia: Dasyuridae) Reveals Evidence of Refugia and Population Expansion in Response to Quaternary Change

Historical population contraction and expansion events associated with Pleistocene climate change are important drivers of intraspecific population structure in Australian arid-zone species. We compared phylogeographic patterns among arid-adapted Dasyuridae (Sminthopsis and Planigale) with close phylogenetic relationships and similar ecological roles to investigate the drivers of phylogeographic structuring and the importance of historical refugia. We generated haplotype networks for two mitochondrial (control region and cytochrome b) and one nuclear (omega-globin) gene from samples distributed across each species range. We used ΦST to test for a genetic population structure associated with the four Pilbara subregions, and we used expansion statistics and Bayesian coalescent skyline analysis to test for signals of historical population expansion and the timing of such events. Significant population structure associated with the Pilbara and subregions was detected in the mitochondrial data for most species, but not with the nuclear data. Evidence of population expansion was detected for all species, and it likely began during the mid-late Pleistocene. The timing of population expansion suggests that these species responded favorably to the increased availability of arid habitats during the mid-late Pleistocene, which is when previously patchy habitats became more widespread. We interpret our results to indicate that the Pilbara region could have acted as a refugium for small dasyurids.
Utility of CT in the diagnosis of prosthetic valve abnormalities

Patients with prosthetic heart valves (PHV) are at an increased risk of endocarditis and dysfunction. Knowledge about the etiology of dysfunction and extent of endocarditis can have distinct treatment implications. Echocardiography has limitations due to PHV‐related artifacts. We hypothesized that computed tomography (CT) will have incremental value over echocardiography for evaluation of PHV abnormalities with surgical findings as the reference standard.
Characterization and antibiogram of Salmonella spp. from poultry specimens.

Department of Veterinary Microbiology, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences (WBUAFS), Kolkata 700 037, India. AICRP on Post Harvest Technology in Department of Fish Processing Technology, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences (WBUAFS), Kolkata 700 094, India. Department of Veterinary Pathology, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences (WBUAFS), Kolkata 700 037, India.
Annexin A1: A Bane or a Boon in Cancer? A Systematic Review

Annexin A1 has been extensively investigated as an anti-inflammatory protein, but its role in different types of cancer has not been consolidated in a single systematic review to date. Thus, the aim of this paper is to systematically review and critically analyse 18 studies (in-vivo and in-vitro) to consolidate, in a concerted manner, all the information on differential expression of Annexin A1 in different types of cancer and the role this protein plays in tumorigenesis. Pubmed, Scopus, Web of Science, and ScienceDirect were used for the literature search and the keywords used are “annexin A1,” “lipocortin 1,” “cancer,” “malignancy,” “neoplasm,” “neoplasia,” and “tumor. ” A total of 1128 articles were retrieved by implementing a standard search strategy subjected to meticulous screening processes and 442 articles were selected for full article screening. A total of 18 articles that adhered to the inclusion criteria were included in the systematic review and these articles possessed low to moderate bias. These studies showed a strong correlation between Annexin A1 expression and cancer progression via modulation of various cancer-associated pathways. Differential expression of Annexin A1 is shown to play a role in cellular proliferation, metastasis, lymphatic invasion, and development of resistance to anti-cancer treatment. Meta-analysis in the future may provide a statistically driven association between Annexin A1 expression and malignancy progression.
A Deep Learning Ensemble for Network Anomaly and Cyber-Attack Detection

Currently, expert systems and applied machine learning algorithms are widely used to automate network intrusion detection. In critical infrastructure applications of communication technologies, the interaction among various industrial control systems and the Internet environment intrinsic to the IoT technology makes them susceptible to cyber-attacks. Given the existence of the enormous network traffic in critical Cyber-Physical Systems (CPSs), traditional methods of machine learning implemented in network anomaly detection are inefficient. Therefore, recently developed machine learning techniques, with the emphasis on deep learning, are finding their successful implementations in the detection and classification of anomalies at both the network and host levels. This paper presents an ensemble method that leverages deep models such as the Deep Neural Network (DNN) and Long Short-Term Memory (LSTM) and a meta-classifier (i.e., logistic regression) following the principle of stacked generalization. To enhance the capabilities of the proposed approach, the method utilizes a two-step process for the apprehension of network anomalies. In the first stage, data pre-processing, a Deep Sparse AutoEncoder (DSAE) is employed for the feature engineering problem. In the second phase, a stacking ensemble learning approach is utilized for classification. The efficiency of the method disclosed in this work is tested on heterogeneous datasets, including data gathered in the IoT environment, namely IoT-23, LITNET-2020, and NetML-2020. The results of the evaluation of the proposed approach are discussed. Statistical significance is tested and compared to the state-of-the-art approaches in network anomaly detection.
Efficacy of Dupilumab on Different Phenotypes of Atopic Dermatitis: One-Year Experience of 221 Patients

Background: The clinical features of adult-onset atopic dermatitis (AD) are heterogeneous and the diagnosis can be a challenge. A new biologic drug (dupilumab) has been approved for moderate to severe AD in adult patients. The efficacy and safety have been demonstrated in clinical trials, but these studies do not reflect conditions in daily practice and do not consider the different clinical manifestations of AD. Objectives: Analyzing the dupilumab activity in a real-world setting and comparing its efficacy on different AD phenotypes. Methods: We retrospectively evaluated 221 AD patients treated with dupilumab, stratified into six clinical phenotypes: classic, generalized eczema inflammatory and lichenoid patterns, prurigo, nummular eczema, and erythroderma. At baseline and at weeks 4, 16, and 52, the disease severity was assessed through the Eczema Area and Severity Index (EASI) and the quality of life was assessed through the Dermatology Life Quality Index (DLQI) questionnaire, Peak Pruritus Numerical Rating Scale (itch NRS), and Peak Sleep NRS. Results: We found a significant improvement after 16 weeks of treatment (p < 0.0001) in all six phenotypes for all the assessed scores mentioned above, persisting up to week 52. The best improvement was seen in the more severe phenotypes, particularly the erythrodermic one. Conclusions: The present study confirmed the efficacy and safety of dupilumab in the treatment of severe AD. Its strength was in the stratification of AD patients in six different phenotypes based on their clinical presentation, all of whom markedly improved in terms of both clinically evident and reported symptoms, as well as their quality of life.
Mycobacteriosis in Aquatic Invertebrates: A Review of Its Emergence

Mycobacteriosis is a chronic bacterial disease reported in aquatic and terrestrial animals, including humans. The disease affects a wide range of cultured and wild organisms worldwide. Mycobacteriosis is well-known in aquatic vertebrates (e.g., finfish, marine mammals), while in the last few years, reports of its presence in aquatic invertebrates have been on the rise, for both freshwater and marine species. The number of cases is likely to increase as a result of increased awareness, surveillance and availability of diagnostic methods. Domestication of wild aquatic species and the intensification of modern aquaculture are also leading to an increase in the number of reported cases. Moreover, climate changes are affecting fresh and marine aquatic ecosystems. The increasing reports of mycobacteriosis in aquatic invertebrates may also be influenced by global climate warming, which could contribute to the microbes’ development and survival rates, pathogen transmission and host susceptibility. Several species of the genus Mycobacterium have been diagnosed in aquatic invertebrates; a few of them are significant due to their wide host spectrum, economic impact in aquaculture, and zoonotic potential. The impact of mycobacteriosis in aquatic invertebrates is probably underestimated, and there is currently no effective treatment other than facility disinfection. In this review, we provide an overview of the diversity of mycobacterial infections reported in molluscs, crustaceans, cnidarians, echinoderms and sponges. We highlight important issues relating to its pathological manifestation, diagnosis and zoonotic considerations.
Monitoring of Target-Site Mutations Conferring Insecticide Resistance in Spodoptera frugiperda

Simple Summary Fall armyworm, Spodoptera frugiperda, is an invasive moth species and one of the most destructive pests of maize. It is native to the Americas but recently invaded (sub)tropical regions in Africa, Asia and Oceania. Fall armyworm larvae feeding on maize plants cause substantial economic damage and are usually controlled by the application of insecticides and genetically modified (GM) maize expressing Bacillus thuringiensis (Bt) proteins, selectively targeting fall armyworm. It has developed resistance to many different classes of insecticides and Bt proteins as well; therefore, it is important to check field populations for the presence of mutations in target proteins conferring resistance. Here, we developed molecular diagnostic tools allowing us to test the frequency of resistance alleles in field-collected populations, either alive or preserved in alcohol. We tested 34 different populations collected on four different continents for the presence of mutations conferring resistance to common classes of insecticides and Bt proteins. We detected resistance mutations which are quite widespread, whereas others are restricted to certain geographies or even completely absent. The established molecular methods show robust results in samples collected across a broad geographical range and can be used to support decisions for sustainable fall armyworm control and applied resistance management. Abstract Fall armyworm (FAW), Spodoptera frugiperda, a major pest of corn and native to the Americas, recently invaded (sub)tropical regions worldwide. The intensive use of insecticides and the high adoption of crops expressing Bacillus thuringiensis (Bt) proteins has led to many cases of resistance. Target-site mutations are among the main mechanisms of resistance and monitoring their frequency is of great value for insecticide resistance management. Pyrosequencing and PCR-based allelic discrimination assays were developed and used to genotype target-site resistance alleles in 34 FAW populations from different continents. The diagnostic methods revealed a high frequency of mutations in acetylcholinesterase, conferring resistance to organophosphates and carbamates. In voltage-gated sodium channels targeted by pyrethroids, only one population from Indonesia showed a mutation. No mutations were detected in the ryanodine receptor, suggesting susceptibility to diamides. Indels in the ATP-binding cassette transporter C2 associated with Bt-resistance were observed in samples collected in Puerto Rico and Brazil. Additionally, we analyzed all samples for the presence of markers associated with two sympatric FAW host plant strains. The molecular methods established show robust results in FAW samples collected across a broad geographical range and can be used to support decisions for sustainable FAW control and applied resistance management.
A Phase II Study of Glembatumumab Vedotin for Metastatic Uveal Melanoma

Glembatumumab vedotin (CDX-011, GV) is a fully human Immunoglobulin G2 monoclonal antibody directed against glycoprotein NMB coupled via a peptide linker to monomethyl auristatin E (MMAE), a potent cytotoxic microtubule inhibitor. This phase II study evaluated the overall response rate and safety of GV, glycoprotein NMB (GPNMB) expression, and survival in patients with metastatic uveal melanoma. Eligible patients with metastatic uveal melanoma who had not previously been treated with chemotherapy received GV 1.9 mg/kg every three weeks. The primary endpoint was the objective response rate (ORR). Secondary endpoints included GPNMB expression, progression-free survival (PFS), overall survival (OS), and toxicity analysis. GPNMB expression was assessed pre- and post-treatment via immunohistochemistry for patients with available tumor tissue. Out of 35 patients who received treatment, two patients had confirmed partial responses (PRs; 6%), and 18 patients had a stable disease (SD; 51%) as the best objective response. 38% of the patients had stable disease >100 days. The grade 3 or 4 toxicities that occurred in two or more patients were neutropenia, rash, hyponatremia, and vomiting. The median progression-free survival was 3.1 months (95% CI: 1.5–5.6), and the median overall survival was 11.9 months (95% CI 9.0–16.9) in the evaluable study population. GV is well-tolerated in metastatic uveal melanoma. The disease control rate was 57% despite a low objective response rate. Exploratory immune correlation studies are underway to provide insight into target saturation, combination strategies, and antigen release.
Natural killer cell immunotypes related to COVID-19 disease severity

Understanding innate immune responses in COVID-19 is important to decipher mechanisms of host responses and interpret disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections but might also contribute to immunopathology. Using 28-color flow cytometry, we here reveal strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients. This pattern was mirrored in scRNA-seq signatures of NK cells in bronchoalveolar lavage from COVID-19 patients. Unsupervised high-dimensional analysis of peripheral blood NK cells furthermore identified distinct NK cell immunotypes that were linked to disease severity. Hallmarks of these immunotypes were high expression of perforin, NKG2C, and Ksp37, reflecting increased presence of adaptive NK cells in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed across COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This study provides a detailed map of the NK cell activation landscape in COVID-19 disease. The NK cell activation landscape in acute SARS-CoV-2 infection is associated with COVID-19 disease severity.
EDTA-Anticoagulated Whole Blood for SARS-CoV-2 Antibody Testing by Electrochemiluminescence Immunoassay (ECLIA) and Enzyme-Linked Immunosorbent Assay (ELISA)

While lateral flow test formats can be utilized with whole blood and low sample volumes, their diagnostic characteristics are inferior to immunoassays based on chemiluminescence immunoassay (CLIA) or enzyme-linked immunosorbent assay (ELISA) technology. CLIAs and ELISAs can be automated to a high degree but commonly require larger serum or plasma volumes for sample processing. We addressed the suitability of EDTA-anticoagulated whole blood as an alternative sample material for antibody testing against SARS-CoV-2 by electro-CLIA (ECLIA; Roche, Rotkreuz, Switzerland) and ELISA (IgG and IgA; Euroimmun, Germany). Simultaneously drawn venous serum and EDTA-anticoagulated whole blood samples from 223 individuals were included. Correction of the whole blood results for hematocrit led to a good agreement with the serum results for weakly to moderately positive antibody signals. In receiver-operating characteristic curve analysis, all three assays displayed comparable diagnostic accuracy (area under the curve (AUC)) using corrected whole blood and serum (AUCs: 0.97 for ECLIA and IgG ELISA; 0.84 for IgA ELISA). In conclusion, our results suggest that the investigated assays can reliably detect antibodies against SARS-CoV-2 in hemolyzed whole blood anticoagulated with EDTA. Correction of these results for hematocrit is suggested. This study demonstrates that the automated processing of whole blood for identification of SARS-CoV-2 antibodies with common ECLIA and ELISA methods is accurate and feasible.
COVID-19 and Inflammatory Bowel Disease: Patient Knowledge and Perceptions in a Single Center Survey

Background and objectives: Spreading of SARS-CoV-2 infection from China to countries with a higher prevalence of inflammatory bowel disease (IBD) has generated concern among gastroenterologists and patients. The aim of this survey is to evaluate knowledge about clinical importance of COVID-19, disease management, prevention measures, and anxiety level during pandemic among patients with IBD. Material and methods: From 15th March to 15th April 2020, a questionnaire survey was administered to 200 patients with IBD by email or phone application. The questionnaire consisted of five sections: (1) anthropometric, demographic and clinical characteristics, (2) knowledge about clinical importance of COVID-19, (3) IBD management, (4) prevention measures, (5) anxiety level during pandemic. Results: One hundred forty two questionnaires were completed. Ninety-seven patients (68.3%) were males with a mean age of 46 years (SD 13; range 17–76). Fifty-four individuals (38%) were affected by Crohn disease and 88 (62%) by Ulcerative Colitis. Most patients reported high knowledge about clinical importance of COVID-19 (80%), IBD management (72%), and prevention measures (97%). Sixty-two percent of them showed moderate-high level of anxiety. High education level was independently associated with high knowledge about clinical importance of COVID-19 (odds ratio [OR] 5, 95% confidence interval [CI] 1.49–16.6, p = 0.009) and older age (OR 1, 95%, CI 1.01–1.1, p = 0.01), while the receipt of e-format educational material with low knowledge about clinical importance of COVID-19 (OR 3, 95%, CI 1.08–9.3, p = 0.03). Displaying an active disease appeared to be independently associated with low knowledge of IBD management (OR 5.8, 95% CI 1.4–22.8, p = 0.01) and no variables other than an older age was independently associated with higher level of anxiety (OR 1.04, 95% CI 1.009–1.09, p = 0.01). Conclusions: High educational level and aging promote knowledge about clinical importance of COVID-19, while e-format educational material does not. Taken together with findings that an active disease status compromises knowledge of IBD management and the high level of anxiety related to increasing age, these data suggest the need of further supporting patient-oriented strategies in IBD during Covid-19 pandemic.
The Penicillium chrysogenum Q176 Antimicrobial Protein PAFC Effectively Inhibits the Growth of the Opportunistic Human Pathogen Candida albicans

Small, cysteine-rich and cationic antimicrobial proteins (AMPs) from filamentous ascomycetes promise treatment alternatives to licensed antifungal drugs. In this study, we characterized the Penicillium chrysogenum Q176 antifungal protein C (PAFC), which is phylogenetically distinct to the other two Penicillium antifungal proteins, PAF and PAFB, that are expressed by this biotechnologically important ascomycete. PAFC is secreted into the culture broth and is co-expressed with PAF and PAFB in the exudates of surface cultures. This observation is in line with the suggested role of AMPs in the adaptive response of the host to endogenous and/or environmental stimuli. The in silico structural model predicted five β-strands stabilized by four intramolecular disulfide bonds in PAFC. The functional characterization of recombinant PAFC provided evidence for a promising new molecule in anti-Candida therapy. The thermotolerant PAFC killed planktonic cells and reduced the metabolic activity of sessile cells in pre-established biofilms of two Candida albicans strains, one of which was a fluconazole-resistant clinical isolate showing higher PAFC sensitivity than the fluconazole-sensitive strain. Candidacidal activity was linked to severe cell morphology changes, PAFC internalization, induction of intracellular reactive oxygen species and plasma membrane disintegration. The lack of hemolytic activity further corroborates the potential applicability of PAFC in clinical therapy.
Energy Density and Nutrient Contents of Selective Chinese New Year Snacks

Background: In this study, the energy density and nutrient contents of thirty Chinese New Year (CNY) snacks commonly consumed in the Asian region during the CNY festive season were measured. Methods: Calorie Answer™, Gas Chromatography-Mass Spectrometry (GC-MS) and Inductively coupled plasma-mass spectrometry (ICP-MS) were the main methods applied in this study. Results: All snacks showed high energy density (kJ/100 g) and the nutrient content, including macro-and micronutrients of these snacks were remarkably different. The most abundant minerals in these snacks include sodium, magnesium, potassium, and calcium. Palmitic (C16:0), oleic (C18:1) and linoleic (C18:2) acids were the main fatty acids and trans-fat was only identified in Butter cookies. Conclusions: This study provides a large database on macro- and micronutrient contents in CNY snacks consumed in the Asian region that has not been previously reported. Our results indicate that the snacks were generally energy-dense and nutrient-poor. This study provides necessary information to enable the reformulation of snacks with lower saturated fat and sodium content. It is also a source of information for consumers to select healthier snacks.