Miracle-dz/UniFAR-FTUs huggingface dataset:
Anxiety and depression among patient’s companions during admission to the ICU in the Omicron wave of COVID-19: A cross-sectional study in Aleppo University Hospital

Background After the COVID-19 pandemic, anxiety and depression have reached high levels, especially after the last wave, Omicron. Healthcare workers in contact with COVID-19 patients or those who come in contact with them may exhibit high levels of anxiety and depression. Therefore, we aimed to assess anxiety and depression symptoms among ICU companions of COVID-19 patients. Methods From 30 November 2021 to 1 March 2022, sixth-year medical students at Aleppo University Hospital conducted interviews with the companions of COVID-19 patients who they brought their patient to the ICU centre as part of a cross-sectional quantitative study using the PHQ-9 and GAD-7 tools to gauge their level of anxiety and depression among companions of COVID-19 patients. The data were analyzed using the SPSS program. In addition, logistic regression models were used to study possible factors of anxiety and depression symptoms during COVID-19. Results The total number was 997 participants in contact with COVID-19 patients. The mean score of the depression assessment tool (PHQ-9) in our questionnaire was 9.5 with a range of 0 to 27. At the same time, the anxiety assessment tool (GAD-7) had a mean score of 9.1, ranging from 0 to 21. A binary logistic regression was used to predict the relationship between depression and anxiety and various factors. We found that the companions with medical specialties were substantially less likely to develop anxiety than other companions [AOR = 0.459; 95%CI (0.23–0.9)], in addition females were substantially higher likely to develop depression than males [AOR = 1.322; 95%CI (0.992–1.762)]. 45.4% of companions had moderate to severe anxiety, in additon 50.8% of companions had moderate to severe depression. Conclusion Our research reveals that moderate to severe anxiety and sadness are present in roughly half of the COVID19 patients’ companions. Females, people with children, and hard workers were more inclined to feel anxious than others, and those who are not in the medical field were more likely to suffer from depression than others, thus it is critical to assist these groups during the present outbreaks (Omicron and Monkeybox).
Bootstrapping One-Loop QCD Amplitudes

We review the recently developed bootstrap method for the computation of high-multiplicity QCD amplitudes at one loop. We illustrate the general algorithm step by step with a six-point example. The method combines (generalized) unitarity with on-shell recursion relations to determine the not cut-constructible, rational terms of these amplitudes. Our bootstrap approach works for arbitrary configurations of gluon helicities and arbitrary numbers of external legs.
In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors

Bacterial type VI secretion systems (T6SSs) are contractile nanomachines that deliver proteinic substrates into target prokaryotic or eukaryotic cells and the surrounding milieu. The genus Campylobacter encompasses 39 recognized species and 13 subspecies, with many belonging to a group known as ‘emerging Campylobacter pathogens’. Within Campylobacter , seven species have been identified to harbour a complete T6SS cluster but have yet to be comparatively assessed. In this study, using systematic bioinformatics approaches and the T6SS-positive Campylobacter jejuni 488 strain as a reference, we explored the genus-wide prevalence, similarity and make-up of the T6SS amongst 372 publicly available ‘complete’ Campylobacter genomes. Our analyses predict that approximately one-third of Campylobacter species possess a T6SS. We also putatively report the first identification of a T6SS in four species: Campylobacter cuniculorum, Campylobacter helveticus, Campylobacter armoricus and Campylobacter ornithocola . The Campylobacter T6SSs cluster into three distinct organizations (I–III), of which two break down into further variants. Thirty T6SS-containing genomes were found to harbour more than one vgrG gene, with Campylobacter lari strain NCTC 11845 possessing five. Analysis of the C. jejuni Pathogenicity Island-1 confirmed its conservation amongst T6SS-positive C. jejuni strains, as well as highlighting its diverse genetic composition, including additional putative effector–immunity pairs (e.g. PoNe and DUF1911 domains). Effector–immunity pairs were also observed neighbouring vgrGs in several other Campylobacter species, in addition to putative genes encoding nucleases, lysozymes, ATPases and a ferric ATP-binding cassette uptake system. These observations highlight the diverse genetic make-up of the T6SS within Campylobacter and provide further evidence of its role in pathogenesis.
Draft Genome Sequences of Eight Mycobacterium montefiorense Strains Isolated from Salamanders in Captivity

Mycobacterium montefiorense is a nontuberculous mycobacterium that causes infections in fish and salamanders. Here, we report annotated draft genome sequences of eight strains that were isolated in 2014 and 2018 from salamanders reared in an aquarium in Japan. ABSTRACT Mycobacterium montefiorense is a nontuberculous mycobacterium that causes infections in fish and salamanders. Here, we report annotated draft genome sequences of eight strains that were isolated in 2014 and 2018 from salamanders reared in an aquarium in Japan.
eIF4A3 Promotes RNA Viruses’ Replication by Inhibiting Innate Immune Responses

Production of type I IFN is pivotal for the cellular antiviral immunity. Virus infection leads to the activation of transcription factor IRF3 and subsequent production of type I IFN to eliminate viral infection. ABSTRACT Viral infection activates the type I interferons (IFNs) and cellular antiviral responses. Eukaryotic initiation factor 4A-III (eIF4A3) has been shown to promote influenza A virus (IAV) replication by promoting viral mRNA splicing and spliced mRNA nuclear export. Here, we identified eIF4A3 as a negative regulator of virus-triggered type I IFN induction. Our study found that eIF4A3 promoted multiple RNA viruses’ replication by binding to IFN regulatory factor 3 (IRF3) and impaired the interaction between tank-binding kinase 1 (TBK1) and IRF3, leading to attenuation of the phosphorylation of IRF3 by TBK1, the formation of IRF3 dimer, and the nuclear translocation of IRF3. This impaired its biological functions in the nucleus, which blocked IRF3 binding to interferon-stimulated response element (ISRE) and the interaction of IRF3 and CBP/p300, resulting in inhibiting the transcription of IFN-β and downstream IFN-stimulated genes (ISGs), thereby impairing innate antiviral immune responses against RNA viruses. These findings reveal a previously unknown function of eIF4A3 in host innate immunity and establish a mechanistic link between eIF4A3 and IRF3 activation that expands potential therapeutic strategies for viral infectious diseases. IMPORTANCE Production of type I IFN is pivotal for the cellular antiviral immunity. Virus infection leads to the activation of transcription factor IRF3 and subsequent production of type I IFN to eliminate viral infection. Thus, the regulation of IRF3 activity is an important way to affect type I IFN production. IRF3 activation requires phosphorylation, dimerization, and nuclear translocation. Here, we first reported that eIF4A3, a member of DEAD box family, served as a negative regulator of antiviral innate immune responses by inhibiting IRF3 activation. Mechanistically, eIF4A3 binds to IRF3 to impair the recruitment of IRF3 by TBK1, which is independent of eIF4A3 ATP binding, ATPase, and RNA helicase activities. Our study delineates a common mechanism of eIF4A3 promoting replication of different RNA viruses and provides important insights into the negative regulation of host antiviral innate immune responses against virus infections.
Incidence and risk factors for central nervous system relapse in patients with primary mediastinal large B‐cell lymphoma in the rituximab era

Central nervous system (CNS) involvement is rare in primary mediastinal large B‐cell lymphoma (PMLBCL). We aimed to evaluate the incidence of CNS relapse as first treatment failure event and the effect of the induction chemotherapy regimen, central nervous system ‐ international prognostic index (CNS‐IPI) and other clinical and laboratory variables on the risk of CNS relapse in 564 PMLBCL patients treated with immunochemotherapy. Only 17 patients (3.0%) received CNS prophylaxis. During a 55‐month median follow‐up only 8 patients experienced CNS relapse as first event, always isolated. The 2‐year cumulative incidence of CNS relapse (CI‐CNSR) was 1.47% and remained unchanged thereafter. The CI‐CNSR was not affected by the chemotherapy regimen (R‐CHOP or R‐da‐EPOCH). None of the established International Prognostic Index factors for aggressive lymphomas predicted CNS relapse in PMLBCL. The 2‐year CI‐CNSR in patients with versus without kidney involvement was 13.3% versus 0.96% (p < 0.001); 14.3% versus 1.13% with versus without adrenal involvement (p < 0.001); and 10.2% versus 0.97% with versus without either kidney or adrenal involvement. CNS‐IPI was also predictive (2‐year CI‐CNSR in high‐risk vs. intermediate/low‐risk: 10.37% vs. 0.84%, p < 0.001). However, this association may be driven mainly by kidney and/or adrenal involvement. In conclusion, in PMLBCL, CNS relapse is rare and appears to be strongly associated with kidney and/or adrenal involvement.
microshades: An R Package for Improving Color Accessibility and Organization of Microbiome Data

When creating figures, it is important to consider that individuals with color vision deficiency (CVD) may not perceive all colors. While there are several CVD-friendly color palettes, they are often insufficient for working with microbiome data. Here, we introduce microshades, an R package for creating CVD-accessible microbiome figures. ABSTRACT When creating figures, it is important to consider that individuals with color vision deficiency (CVD) may not perceive all colors. While there are several CVD-friendly color palettes, they are often insufficient for working with microbiome data. Here, we introduce microshades, an R package for creating CVD-accessible microbiome figures.
Microscopic origin of isotropic non-Heisenberg behavior in highly correlated systems

We have reanalyzed the microscopic origin of the isotropic deviations that are observed from the energy spacings predicted by the HDVV Hamiltonian. Usually, a biquadratic spin operator is added to the HDVV Hamiltonian to account for such deviations. It is shown here that this operator cannot describe the effect of the excited atomic non-Hund states which brought the most important contribution to the deviations. For systems containing more than two magnetic centers, non-Hund states cause additional interactions that are of the same order of magnitude as the biquadratic exchange and should have significant effects on the macroscopic properties of extended systems.
Maternal immune activation leads to defective brain–blood vessels and intracerebral hemorrhages in male offspring

Intracerebral hemorrhages are recognized risk factors for neurodevelopmental disorders and represent early biomarkers for cognitive dysfunction and mental disability, but the pathways leading to their occurrence are not well defined. We report that a single intrauterine exposure of the immunostimulant Poly I:C to pregnant mice at gestational day 9, which models a prenatal viral infection and the consequent maternal immune activation, induces the defective formation of brain vessels and causes intracerebral hemorrhagic events, specifically in male offspring. We demonstrate that maternal immune activation promotes the production of the TGF‐β1 active form and the consequent enhancement of pSMAD1‐5 in males' brain endothelial cells. TGF‐β1, in combination with IL‐1β, reduces the endothelial expression of CD146 and claudin‐5, alters the endothelium–pericyte interplay resulting in low pericyte coverage, and increases hemorrhagic events in the adult offspring. By showing that exposure to Poly I:C at the beginning of fetal cerebral angiogenesis results in sex‐specific alterations of brain vessels, we provide a mechanistic framework for the association between intragravidic infections and anomalies of the neural vasculature, which may contribute to neuropsychiatric disorders.
A multi‐scale analysis of basketball throw in virtual reality for tracking perceptual‐motor expertise

To benefit from virtual reality (VR) as a complementary tool for training, coaches must determine the proper tools and variables for tracking sports performance. We explored the basketball shooting at several scales (basket‐ball, ball‐player, and player systems) by monitoring success‐rate, and ball and body kinematics. We measured how these scales of analysis allowed tracking players' expertise and perceptual sensitivity to basket distance. Experienced and novice players were instructed to naturally throw and swish an instrumented ball in a stereoscopically rendered virtual basket. We challenged their perceptual‐motor systems by manipulating the distance of the virtual basket while keeping the surrounding environment unchanged. The success‐rate accounted for the players' shooting adjustments to the manipulation of basket distance and allowed tracking their expertise. Ball kinematics also reflected the manipulation of distance and allowed detecting gender, but did not reflect the players' expertise. Finally, body kinematics variables did not echo players' adjustments to the distance manipulation but reflected their expertise and gender. The results gained at each scale of analysis are discussed with regard to the simulator's construct, biomechanical, and psychological fidelity.
Structural and Functional Analysis of Peptides Derived from KEX2-Processed Repeat Proteins in Agaricomycetes Using Reverse Genetics and Peptidomics

Two recent bioinformatics studies have demonstrated that KEX2-processed repeat proteins are widespread in the fungal kingdom. However, despite the prevalence of KEPs in fungal genomes, only few KEP-derived peptides have been detected and studied so far. ABSTRACT Bioactivities of fungal peptides are of interest for basic research and therapeutic drug development. Some of these peptides are derived from “KEX2-processed repeat proteins” (KEPs), a recently defined class of precursor proteins that contain multiple peptide cores flanked by KEX2 protease cleavage sites. Genome mining has revealed that KEPs are widespread in the fungal kingdom. Their functions are largely unknown. Here, we present the first in-depth structural and functional analysis of KEPs in a basidiomycete. We bioinformatically identified KEP-encoding genes in the genome of the model agaricomycete Coprinopsis cinerea and established a detection protocol for the derived peptides by overexpressing the C. cinerea KEPs in the yeast Pichia pastoris. Using this protocol, which includes peptide extraction and mass spectrometry with data analysis using the search engine Mascot, we confirmed the presence of several KEP-derived peptides in C. cinerea, as well as in the edible mushrooms Lentinula edodes, Pleurotus ostreatus, and Pleurotus eryngii. While CRISPR-mediated knockout of C. cinerea kep genes did not result in any detectable phenotype, knockout of kex genes caused defects in mycelial growth and fruiting body formation. These results suggest that KEP-derived peptides may play a role in the interaction of C. cinerea with the biotic environment and that the KEP-processing KEX proteases target a variety of substrates in agaricomycetes, including some important for mycelial growth and differentiation. IMPORTANCE Two recent bioinformatics studies have demonstrated that KEX2-processed repeat proteins are widespread in the fungal kingdom. However, despite the prevalence of KEPs in fungal genomes, only few KEP-derived peptides have been detected and studied so far. Here, we present a protocol for the extraction and structural characterization of KEP-derived peptides from fungal culture supernatants and tissues. The protocol was successfully used to detect several linear and minimally modified KEP-derived peptides in the agaricomycetes C. cinerea, L. edodes, P. ostreatus, and P. eryngii. Our study establishes a new protocol for the targeted search of KEP-derived peptides in fungi, which will hopefully lead to the discovery of more of these interesting fungal peptides and allow a further characterization of KEPs.
Positive interactions between corals and damselfish increase coral resistance to temperature stress

By the century's end, many tropical seas will reach temperatures exceeding most coral species' thermal tolerance on an annual basis. The persistence of corals in these regions will, therefore, depend on their abilities to tolerate recurrent thermal stress. Although ecologists have long recognized that positive interspecific interactions can ameliorate environmental stress to expand the realized niche of plants and animals, coral bleaching studies have largely overlooked how interactions with community members outside of the coral holobiont shape the bleaching response. Here, we subjected a common coral, Pocillopora grandis, to 10 days of thermal stress in aquaria with and without the damselfish Dascyllus flavicaudus (yellowtail dascyllus), which commonly shelter within these corals, to examine how interactions with damselfish impacted coral thermal tolerance. Corals often benefit from nutrients excreted by animals they interact with and prior to thermal stress, corals grown with damselfish showed improved photophysiology (Fv/Fm) and developed larger endosymbiont populations. When exposed to thermal stress, corals with fish performed as well as control corals maintained at ambient temperatures without fish. In contrast, corals exposed to thermal stress without fish experienced photophysiological impairment, a more than 50% decline in endosymbiont density, and a 36% decrease in tissue protein content. At the end of the experiment, thermal stress caused average calcification rates to decrease by over 80% when damselfish were absent but increase nearly 25% when damselfish were present. Our study indicates that damselfish‐derived nutrients can increase coral thermal tolerance and are consistent with the Stress Gradient Hypothesis, which predicts that positive interactions become increasingly important for structuring communities as environmental stress increases. Because warming of just a few degrees can exceed corals' temperature tolerance to trigger bleaching and mortality, positive interactions could play a critical role in maintaining some coral species in warming regions until climate change is aggressively addressed.
Analysis of a Multi-Class Queueing System

The stability properties of the bandwidth allocation algorithm First Fit are analyzed for the distributions concentrated on three sizes for the requests. We give the explicit expression of the ergodicity condition of this model; it involves a quadratic functional of the input parameters. The stochastic processes describing these systems are string valued Markov process. To analyze these processes we introduce the notion of a smooth initial state. Starting from a smooth initial state the fluid limits of this systems can be investigated. The fluid limits of interest are random dynamical systems in $\R^2$ which are products of random $2\times2$ matrices.
Evaluating the effectiveness of physical exercise in improving standardized testing performances through attention indices

In the United States, standardized tests have risen in prevalence, extending their importance from education placement to employment. Attention is crucial to improving testing performance. Past studies have established that acute, coordinative, aerobic exercise improves attention, which is measured by the D2 Attention Test, emotional analysis, reading time, and eye movement tracking. No studies have drawn connections between physical exercise's quantifiable improvement in attention to improvements in standardized tests; therefore, this study would attempt to do so.
One-Step Rapid and Sensitive ASFV p30 Antibody Detection via Nanoplasmonic Biosensors

African swine fever (ASF) is a serious transnational disease caused by the African swine fever virus (ASFV), which is highly contagious in wild boars and domestic pigs. There is currently no available vaccine for ASF; therefore, development efforts are a key priority as ASFV continues to evolve and diversify. ABSTRACT African swine fever (ASF) is one of the most serious transnational swine diseases in the world. The case fatality rate of susceptible pigs is up to 100%. Currently, no commercial vaccine is available, so the prevention and control of ASF mainly relies on early diagnosis and culling of infected pigs. As the ASF virus continues to evolve, develop, and diversify, nucleic acid testing becomes less efficient. Here, we developed a method for the rapid and direct optical measurement of African swine fever virus (ASFV) antibody in vitro. This one-step procedure requires nearly no sample preparation and involves p30 protein-specific label-free integration into standard 96-well plates. Using a nanoplasmonic biosensor with extraordinary optical transmission (EOT) effect, one-step sample addition, ASFV antibody was detected within 20 min. The positive antibody showed a satisfactory sensitivity and linear relationship in the dilution ratio of 1:100–1:16000. It was used for the detection of clinical serum samples with a coincidence rate of 96.6%. The measurement results can be automatically analyzed and displayed on a conventional microplate meter computer and connected device. Our detection method can be widely applied in point-of-care testing (POCT) of ASFV antibody in pig farms. IMPORTANCE African swine fever (ASF) is a serious transnational disease caused by the African swine fever virus (ASFV), which is highly contagious in wild boars and domestic pigs. There is currently no available vaccine for ASF; therefore, development efforts are a key priority as ASFV continues to evolve and diversify. The ASF antibody rapid detection platform comprising the nanoplasmonic biosensor with extraordinary optical transmission effect can greatly reduce the detection time and improve detection flux while maintaining detection sensitivity and specificity. The one-step sample addition can effectively avoid cross contamination of samples in the detection process. The detection method provides a solution for the rapid and accurate real-time monitoring of ASF in pig farms.
Highly Compressive Visual Self-localization Using Sequential Semantic Scene Graph and Graph Convolutional Neural Network

In this paper, we address the problem of image sequence-based self-localization from a new highly compressive scene representation called sequential semantic scene graph (S3G). Highly-compressive scene representation is essential for robots to perform long-term and huge-numbers of VPR tasks in virtual-training and real-deploy environments. Recent developments in deep graph convolutional neural networks (GCNs) have enabled a highly compressive visual place classifier (VPC) that can use a scene graph as the input modality. However, in such a highly compressive application, the amount of information lost in the image-to-graph mapping is significant and can damage the classification performance. To address this issue, we propose a pair of similarity-preserving mappings, image-to-nodes and image-to-edges, such that the nodes and edges act as absolute and relative features, respectively, that complement each other. Moreover, the proposed GCN-VPC is applied to a new task of viewpoint planning of the query image sequence, which contributes to further improvement in the VPC performance. Experiments using the public NCLT dataset validated the effectiveness of the proposed method.