Miracle-dz/UniFAR-FTUs huggingface dataset:
Discrimination and Sympathy for Violent Radicalization Among College Students in Quebec (Canada)

Abstract The present study examines the moderating role of total, intrinsic, and extrinsic religiosity in the relation between perceived discrimination and sympathy for violent radicalization (VR) among college students in Quebec, Canada. A total of 931 students responded to an online questionnaire and were included in this study. Linear mixed-effects models were conducted to account for the clustered nature of the data, and moderation was assessed via interaction analysis using cross-product terms in the models. Findings indicated that both intrinsic and extrinsic religiosity had a protective role in the link between perceived discrimination and sympathy for VR and buffered the effects of sadness in response to discrimination on sympathy for VR, but not the effects of anger in response to discrimination. These results provide evidence of the protective role of religiosity in Canada, a social context characterized by an increase in religious discrimination, but which also supports religious diversity.
Sub-nanosecond acousto-electric carrier redistribution dynamics and transport in polytypic GaAs nanowires

The authors report on a combined structural, optical and acousto-electric study of polytypic GaAs nanowires. Two types of nanowires with different zincblende and wurtzite crystal phase mixing are identified by transmission electron microscopy and photoluminescence spectroscopy. The nanowires exhibit characteristic recombination channels which are assigned to different types of spatially direct recombination (electron and hole within the same crystal phase segment) and spatially indirect recombination (electron and holes localized in different segments). Contact-free acousto-optoelectric spectroscopy is employed to resolve spatiotemporal charge carrier dynamics between different recombination channels induced by a piezoelectric surface acoustic wave. The observed suppression of the emission and its dynamic temporal modulation shows unambiguous fingerprints of the local bandedge variations induced by the crystal phase mixing. A nanowire, which exhibits a variation from a near-pristine zinc blende crystal structure to a highly mixed crystal phase, shows a clear dependence on the propagation direction of the acoustic wave. In contrast, no pronounced directionality is found for a nanowire with an extended near-pristine zincblende segment. The experimental findings are corroborated by solving the drift and diffusion equations of electrons and holes induced by the surface acoustic wave. The key characteristics observed in our experimental data are well reproduced in the numerical simulations by assuming two general bandedge modulations and realistic parameters for the bandedge discontinuities and transport mobilities of electrons and holes. This evidences that even all relevant physical processes are accounted for in the model.
Determinants of Leptomeningeal Collateral Status Variability in Ischemic Stroke Patients

ABSTRACT: Background: Collateral status is an indicator of a favorable outcome in stroke. Leptomeningeal collaterals provide alternative routes for brain perfusion following an arterial occlusion or flow-limiting stenosis. Using a large cohort of ischemic stroke patients, we examined the relative contribution of various demographic, laboratory, and clinical variables in explaining variability in collateral status. Methods: Patients with acute ischemic stroke in the anterior circulation were enrolled in a multi-center hospital-based observational study. Intracranial occlusions and collateral status were identified and graded using multiphase computed tomography angiography. Based on the percentage of affected territory filled by collateral supply, collaterals were graded as either poor (0–49%), good (50–99%), or optimal (100%). Between-group differences in demographic, laboratory, and clinical factors were explored using ordinal regression models. Further, we explored the contribution of measured variables in explaining variance in collateral status. Results: 386 patients with collateral status classified as poor (n = 64), good (n = 125), and optimal (n = 197) were included. Median time from symptom onset to CT was 120 (IQR: 78–246) minutes. In final multivariable model, male sex (OR 1.9, 95% CIs [1.2, 2.9], p = 0.005) and leukocytosis (OR 1.1, 95% CIs [1.1, 1.2], p = 0.001) were associated with poor collaterals. Measured variables only explained 44.8–53.0% of the observed between-patient variance in collaterals. Conclusion: Male sex and leukocytosis are associated with poorer collaterals. Nearly half of the variance in collateral flow remains unexplained and could be in part due to genetic differences.
Imaging the living plant cell: From probes to quantification

Abstract At the center of cell biology is our ability to image the cell and its various components, either in isolation or within an organism. Given its importance, biological imaging has emerged as a field of its own, which is inherently highly interdisciplinary. Indeed, biologists rely on physicists and engineers to build new microscopes and imaging techniques, chemists to develop better imaging probes, and mathematicians and computer scientists for image analysis and quantification. Live imaging collectively involves all the techniques aimed at imaging live samples. It is a rapidly evolving field, with countless new techniques, probes, and dyes being continuously developed. Some of these new methods or reagents are readily amenable to image plant samples, while others are not and require specific modifications for the plant field. Here, we review some recent advances in live imaging of plant cells. In particular, we discuss the solutions that plant biologists use to live image membrane-bound organelles, cytoskeleton components, hormones, and the mechanical properties of cells or tissues. We not only consider the imaging techniques per se, but also how the construction of new fluorescent probes and analysis pipelines are driving the field of plant cell biology.
Antiviral effect of a commercially phytotherapeutic compound against feline immunodeficiency virus

Abstract The feline immunodeficiency virus (FIV) is a widespread lentivirus of felids. Due to its worldwide diffusion and the lack of an effective preventive and therapeutic protocol, it has a high impact on the cats’ health. Several therapeutical protocols have been proposed, among those, phytotherapeutic compounds have been tested with the purpose to find a possible natural treatment. The most studied active compounds are derived from Ganoderma lucidum, Cordyceps sinensis, and Trametes versicolor. The present study aims to investigate in vitro antiviral effects of a commercially available compound HELP-TH1 (Camon, S.p.A., Italy) against FIV. The antiviral effect of HELP-TH1 was evaluated by quantifying and comparing the viral load of control groups, infected and not-treated cells, vs both experimental groups, infected and treated cells. Our data indicate that HELP-TH1 reduce the viral load in the experimental conditions demonstrating its antiviral effect. Graphical Abstract
Knock down analysis reveals critical phases for specific oskar noncoding RNA functions during Drosophila oogenesis

Abstract The oskar transcript, acting as a noncoding RNA, contributes to a diverse set of pathways in the Drosophila ovary, including karyosome formation, positioning of the microtubule organizing center (MTOC), integrity of certain ribonucleoprotein particles, control of nurse cell divisions, restriction of several proteins to the germline, and progression through oogenesis. How oskar mRNA acts to perform these functions remains unclear. Here, we use a knock down approach to identify the critical phases when oskar is required for three of these functions. The existing transgenic shRNA for removal of oskar mRNA in the germline targets a sequence overlapping a regulatory site bound by Bruno1 protein to confer translational repression, and was ineffective during oogenesis. Novel transgenic shRNAs targeting other sites were effective at strongly reducing oskar mRNA levels and reproducing phenotypes associated with the absence of the mRNA. Using GAL4 drivers active at different developmental stages of oogenesis, we found that early loss of oskar mRNA reproduced defects in karyosome formation and positioning of the MTOC, but not arrest of oogenesis. Loss of oskar mRNA at later stages was required to prevent progression through oogenesis. The noncoding function of oskar mRNA is thus required for more than a single event.
Interactions of nisin with meat components and their effect on activity

Nisin is a bacteriocin produced by Lactococcus lactis subsp. lactis, with antimicrobial activity against many Gram-positive bacteria, including bacterial spores. Nisin has been successfully used in numerous products, such as processed cheeses, dairy products and canned foods. However, its effectiveness in meat products is variable due to interactions with certain meat components. The aim of this project therefore was to determine a number of factors reported to reduce nisin activity in meat and meat products, evaluate the extent of interference with its efficacy and introduce multicomponent preserving systems that improve its antimicrobial action. Loss of nisin activity in meat has been partly ascribed before to the formation of a nisin- glutathione adduct. Activity is lost more quickly in raw meat than in cooked meat and this has been taken as evidence that the reaction is enzyme-mediated. Horizontal agar diffusion method and MALDI-TOF MS confirmed the formation of the nisin-glutathione adduct which was shown not to be enzyme mediated. Retention of activity in cooked meat was shown to be due to loss of free sulfhydryl groups during heat processing as a result of the reaction of glutathione with proteins and not a result of the inactivation of endogenous enzymes, as indicated by measuring the free thiol content. Microbial enzymes did not appear to play a role as similar losses were seen in raw and cooked meat extracts containing undetectable levels of microorganisms. Enumeration of viable counts indicated that increased nisin concentrations were required for the total inhibition of L. monocytogenes following incubation of nisin with glutathione. The inhibitory effect of glutathione on nisin activity was removed in the presence of ascorbic and dehydroascorbic acid, sometimes with enhancement of nisin's bactericidal effect. However, there was no evidence for a direct reaction between glutathione and dehydroascorbic acid. The addition of ascorbic acid and dehydroascorbic acid in raw meat extract as well as in raw and thermally processed meat slurry was shown to exert the same protective effect seen with laboratory media. The synergy between nisin, ascorbic and dehydroascorbic acid was more pronounced at chill temperatures. Simultaneous application of antioxidants and nisin delayed the recovery of nisin-injured L. monocytogenes cells especially at low temperatures. Antioxidants, at the levels used, had no bactericidal effect on their own, but they did retard growth by decreasing growth rate and increasing lag phase. This was probably due to antioxidants diverting energy from injuiy repair-related functions. The effectiveness of the combination of nisin with propyl gallate was completely negated in whole fat UHT milk due to interactions of nisin with fat. Overall, the findings of this study clearly show that nisin performs better when its use is supplemented with other preservation agents or methods, since its amphiphilic properties make it vulnerable to interactions with other food macromolecules resulting in reduced efficacy.
Surface Modification of Polyhydroxyalkanoates toward Enhancing Cell Compatibility and Antibacterial Activity

Biomaterials for in vivo application should induce positive interaction with various histocytes and inhibit bacteria inflection as well. Cells and/or bacteria response to the extracellular environment is therefore the basic principle to design the biomaterials surface in order to induce the specific biomaterial–biological interaction. Polyhydroxyalkanoate (PHAs) are of growing interests because of their natural origin, biodegradability, biocompatibility, and thermoplasticity; however, quite inert and intrinsic hydrophobic characteristics have hindered their extensive usage in medical applications. Surface modification of PHAs tailors the chemistry, wettability, and topography without altering the bulk properties, and introduces specific proteins/peptides and/or antibacterial agents to mediate cell–matrix interactions. This review describes the recent developments on the surface modification of PHAs to construct cell compatible and antibacterial surfaces.
Crystal Structure and Molecular Mechanism of Phosphotransbutyrylase from Clostridium acetobutylicum

Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium Clostridium acetobutylicum has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase (phosphate butyryltransferase, PTB) plays a crucial role in butyrate metabolism by catalyzing the reversible conversion of butyryl-CoA into butyryl phosphate. Here, we report the crystal structure of PTB from the Clostridial host for ABE fermentation, C. acetobutylicum, (CaPTB) at a 2.9 Å resolution. The overall structure of the CaPTB monomer is quite similar to those of other acyltransferases, with some regional structural differences. The monomeric structure of CaPTB consists of two distinct domains, the N- and C-terminal domains. The active site cleft was formed at the interface between the two domains. Interestingly, the crystal structure of CaPTB contained eight molecules per asymmetric unit, forming an octamer, and the size-exclusion chromatography experiment also suggested that the enzyme exists as an octamer in solution. The structural analysis of CaPTB identifies the substrate binding mode of the enzyme and comparisons with other acyltransferase structures lead us to speculate that the enzyme undergoes a conformational change upon binding of its substrate.
Outbreak of Mucormycosis in Coronavirus Disease Patients, Pune, India

We provide an overview of the epidemiology and clinical course of mucormycosis in the coronavirus disease (COVID-19) pandemic era. We conducted a retrospective chart review of 178 patients with clinical or diagnostic, endoscopically or histopathologically confirmed rhino-sino-orbital or cerebral mucormycosis after COVID-19 treatment during the second wave of COVID-19 in Pune, India. Median time to symptom onset from COVID-19 detection was 28 days. Moderate or severe COVID-19 was seen in 73% of patients and diabetes in 74.2%. A total of 52.8% received steroids. Eschar over or inside the nose was seen in 75%, but baseline clinical and laboratory parameters were mostly unremarkable. Bone penetration was present in ≈90% of cases, 30% had soft-tissue swelling of the pterygopalatine fossa and 7% had cavernous sinus thrombosis, and 60% had multifocal mucormycosis. Of the 178 study cases, 151 (85%) underwent surgical debridement. Twenty-six (15%) died, and 16 (62%) of those had multifocal mucormycosis.
Introducing medical students to cadaveric dissection: Which aspects of an orientation are most beneficial?

We appreciate the insight and comments shared by Patera and Khamuani (2021) in response to the article, "Fear of death and examination performance in a gross anatomy course with cadaveric dissection" (Allison et al., 2021). In their letter, Patera and Khamuani (2021) presented a few concerns regarding this article, which included: (1) lack of insight into why students' fear of death had increased, (2) findings were contradictory to previously published results, (3) information concerning an introduction to the anatomy course was omitted, and (4) the questionnaire structure and manner of distribution may have influenced students' responses.
A versatile and scalable single-cell data integration algorithm based on domain-adversarial and variational approximation

Single-cell technologies provide us new ways to profile transcriptomic landscape, chromatin accessibility, spatial expression patterns in heterogeneous tissues at the resolution of single cell. With enormous generated single-cell datasets, a key analytic challenge is to integrate these datasets to gain biological insights into cellular compositions. Here, we developed a domain-adversarial and variational approximation, DAVAE, which can integrate multiple single-cell datasets across samples, technologies and modalities with a single strategy. Besides, DAVAE can also integrate paired data of ATAC profile and transcriptome profile that are simultaneously measured from a same cell. With a mini-batch stochastic gradient descent strategy, it is scalable for large-scale data and can be accelerated by GPUs. Results on seven real data integration applications demonstrated the effectiveness and scalability of DAVAE in batch-effect removing, transfer learning and cell-type predictions for multiple single-cell datasets across samples, technologies and modalities. Availability: DAVAE has been implemented in a toolkit package "scbean" in the pypi repository, and the source code can be also freely accessible at https://github.com/jhu99/scbean. All our data and source code for reproducing the results of this paper can be accessible at https://github.com/jhu99/davae_paper.
Anti-Tuberculosis Activity of Pediococcus acidilactici Isolated from Young Radish Kimchi against Mycobacterium tuberculosis

Tuberculosis is a highly contagious disease caused by Mycobacterium tuberculosis. It affects about 10 million people each year and is still one of the leading causes of death worldwide. About 2 to 3 billion people (equivalent to 1 in 3 people in the world) are infected with latent tuberculosis. Moreover, as the number of multidrug-resistant, extensively drug-resistant, and totally drug-resistant strains of M. tuberculosis continues to increase, there is an urgent need to develop new anti-tuberculosis drugs that are different from existing drugs to combat antibiotic-resistant M. tuberculosis. Against this background, we aimed to develop new anti-tuberculosis drugs using probiotics. Here, we report the anti-tuberculosis effect of Pediococcus acidilactici PMC202 isolated from young radish kimchi, a traditional Korean fermented food. Under coculture conditions, PMC202 inhibited the growth of M. tuberculosis. In addition, PMC202 inhibited the growth of drug-sensitive and -resistant M. tuberculosis- infected macrophages at a concentration that did not show cytotoxicity and showed a synergistic effect with isoniazid. In a 2-week, repeated oral administration toxicity study using mice, PMC202 did not cause weight change or specific clinical symptoms. Furthermore, the results of 16S rRNA-based metagenomics analysis confirmed that dysbiosis was not induced in bronchoalveolar lavage fluid after oral administration of PMC202. The anti-tuberculosis effect of PMC202 was found to be related to the reduction of nitric oxide. Our findings indicate that PMC202 could be used as an anti-tuberculosis drug candidate with the potential to replace current chemicalbased drugs. However, more extensive toxicity, mechanism of action, and animal efficacy studies with clinical trials are needed.
Osteology and relationships of Revueltosaurus callenderi (Archosauria: Suchia) from the Upper Triassic (Norian) Chinle Formation of Petrified Forest National Park, Arizona, United States

Once known solely from dental material and thought to represent an early ornithischian dinosaur, the early‐diverging pseudosuchian Revueltosaurus callenderi is described from a minimum of 12 skeletons from a monodominant bonebed in the upper part of the Chinle Formation of Arizona. This material includes nearly the entire skeleton and possesses a combination of plesiomorphic and derived character states that help clarify ingroup relationships within Pseudosuchia. A phylogenetic analysis recovers R. callenderi in a clade with Aetosauria and Acaenasuchus geoffreyi that is named Aetosauriformes. Key autapomorphies of R. callenderi include a skull that is longer than the femur, a complete carapace of dermal armor including paramedian and lateral rows, as well as ventral osteoderms, and a tail end sheathed in bone. Histology of the femur and associated osteoderms demonstrate that R. callenderi was slow growing and that the individuals from the bonebed were not young juveniles but had not ceased growing. A review of other material assigned to Revueltosaurus concludes that the genus cannot be adequately diagnosed based on the type materials of the three assigned species and that only R. callenderi can be confidently referred to Revueltosaurus.
Predictive radiomics signature for treatment response to nivolumab in patients with advanced renal cell carcinoma.

INTRODUCTION The anti-PD-1 immune checkpoint inhibitor nivolumab is currently approved for the treatment of patients with metastatic renal cell carcinoma (mRCC); approximately 25% of patients respond. We hypothesized that we could identify a biomarker of response using radiomics to train a machine learning classifier to predict nivolumab response outcomes. METHODS Patients with mRCC of different histologies treated with nivolumab in a single institution between 2013 and 2017 were retrospectively identified. Patients were labelled as responders (complete response [CR]/particle response [PR]/durable stable disease [SD]) or non-responders based on investigator tumor assessment using RECIST 1.1 criteria. For each patient, lesions were contoured from pre-treatment and first post-treatment computed tomography (CT) scans. This information was used to train a radial basis function support vector machine classifier to learn a prediction rule to distinguish responders from non-responders. The classifier was internally validated by a 10-fold nested cross-validation. RESULTS Thirty-seven patients were identified; 27 (73%) met the inclusion criteria. One hundred and four lesions were contoured from these 27 patients. The median patient age was 56 years, 78% were male, 89% had clear-cell histology, 89% had prior nephrectomy, and 89% had prior systemic therapy. There were 19 responders vs. eight non-responders. The lesions selected were lymph nodes (60%), lung metastases (23%), and renal/adrenal metastases (17%). For the classifier trained on the baseline CT scans, 69% accuracy was achieved. For the classifier trained on the first post-treatment CT scans, 66% accuracy was achieved. CONCLUSIONS The set of radiomic signatures was found to have limited ability to discriminate nivolumab responders from non-responders. The use of novel texture features (two-point correlation measure, two-point cluster measure, and minimum spanning tree measure) did not improve performance.
Prediction of Reaction Yield for Buchwald‐Hartwig Cross‐coupling Reactions Using Deep Learning

Chemical reaction yield is one of the most important factors for determining reaction conditions. Recently, several machine learning‐based prediction models using high‐throughput experiment (HTE) data sets were reported for the prediction of reaction yield. However, none of them were at a practical level in terms of predictive ability. In this study, we propose a message passing neural network (MPNN) model for chemical yield prediction, focusing on the Buchwald‐Hartwig cross‐coupling HTE data set. As an initial atom embedding in MPNN model, we propose to use the Mol2Vec feature vectors pre‐trained using a large compound database. Predictive ability of the proposed model was higher than that of previously reported five models for the three out of five data sets. Moreover, visualization of important atoms based on self‐attention mechanism was in favor of Mol2Vec as an atom embedding rather than other embeddings including previously employed simple representations.