Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro

Abstract SARS-CoV-2 cause fatal infection in 213 countries accounting for the death of millions of people globally. In the present study, phytochemicals from spices were assessed for their ability to interact with SARS-CoV-2 MPro. Structure based virtual screening was performed with 146 phytochemicals from spices using Autodock Vina. Phytochemicals with binding energy ≥ −8.0 kcal/mol were selected to understand their interaction with MPro. Virtual screening was further validated by performing molecular docking to generate favorable docked poses and the participation of important amino acid residues. Molecular dynamics simulation for the docked poses was performed to study thermodynamic properties of the protein, ligand and protein-ligand complexes. The finding shows that cinnamtannin B2 and cyanin showed favorable binding affinity values with SARS-CoV-2 MPro. The results are comparable in terms of docked poses, important amino acid participation and thermodynamic properties with the standard control drugs remdesivir, benazepril and hydroxychloroquine diphosphate. Prime MM-GBSA was employed for end-point binding energy calculation. Binding to domain I and II of MPro were mediated through the OH, SH, NH2 and non-polar side chain of amino acids. Cinnamtannin B2 and cyanin binds to MPro with many sub sites within the active site with RMSD and RMSF within 4 Å. The results computed using Prime MM-GBSA show that cinnamtannin B2 (–68.54940214 kcal/mol) and cyanin (–62.1902835 kcal/mol) have better binding affinity in comparison to hydroxychloroquine diphosphate (–54.00912412 kcal/mol) and benazepril (–53.70242369 kcal/mol). The results provide a basis for exploiting cinnamtannin B2 and cyanin as a starting point potential candidate for the development of drug against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
Molecular Typing of Neisseria gonorrhoeae Clinical Isolates in Russia, 2018–2019: A Link Between penA Alleles and NG-MAST Types

This work aimed to study penA gene polymorphisms in clinical isolates of Neisseria gonorrhoeae collected in Russia in 2018–2019 and the contribution of the penA allele type to susceptibility to β-lactam antibiotics. A total of 182 isolates were analyzed. penA allele types were determined by sequencing, and the minimum inhibitory concentrations (MICs) of benzylpenicillin and ceftriaxone were measured. The influence of genetic factors on MICs was evaluated by regression analysis. All isolates were susceptible to ceftriaxone, and 40.1% of isolates were susceptible to penicillin. Eleven penA allele types were identified. The mosaic type XXXIV penA allele and the Gly120Lys substitution in PorB made the greatest contributions to increasing the ceftriaxone MIC; the presence of the blaTEM plasmid, Gly120Asp, Ala121Gly/Asn substitutions in PorB, and the adenine deletion in the promoter region of the mtrR gene caused an increase in the penicillin MIC. Among 61 NG-MAST types identified, the most frequent were types 228, 807, 9486, 1993, and 6226. A link between penA alleles and Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) types was established. Resistance to two groups of β-lactam antibiotics was associated with non-identical changes in penA alleles. To prevent the emergence of ceftriaxone resistance in Russia, NG-MAST genotyping must be supplemented with penA allele analysis.
Susceptibility to Being Lured Away by a Stranger: A Real-World Field Test of Selective Trust in Early Childhood

In this preregistered field study, we examined preschool children’s selective trust in a real-life situation. We investigated whether 3- to 6-year-old children (total N = 240) could be lured to a new location within their school grounds by an unfamiliar adult confederate. In a between-subjects manipulation, the confederate established either a high or a low level of personal credibility by providing information that the child knew to be either true or false. In Experiment 1, in which the confederate was female, children showed sensitivity to informational accuracy by being less willing to leave with an uninformed confederate, and this effect increased with age. In Experiment 2, in which the confederate was male, children were reluctant to leave regardless of informational accuracy. These findings point to real-world implications of epistemic-trust research and provide the first evidence regarding the early development of selective trust in a high-stakes naturalistic context.
Self-other distinction and borderline personality disorder features: Evidence for egocentric and altercentric bias in a self-other facial morphing task.

Self-other distinction (SOD) refers to the ability to distinguish one's own body, actions, and mental representations from those of others. Problems with SOD are considered to be a key feature of borderline personality disorder (BPD). However, empirical studies on SOD in BPD are scarce. Here, we present a study providing preliminary support for the usefulness and validity of a self-other facial morphing task to capture the capacity for SOD in a sample of nonclinical participants high (n = 30) and low (n = 32) in BPD features. Participants had to watch a video sequence in which their own face was gradually morphed into the face of an unfamiliar other (self-to-other) or vice versa (other-to-self), requiring them to indicate at which point they judged the morph to look more like the target face than the starting face. Consistent with predictions, results showed that participants in the high-BPD group judged the morph to look like themselves for longer in the self-to-other direction (suggestive of egocentric bias), but only with a relatively more attractive target face. In the other-to-self direction, the high-BPD group had more difficulty recognizing their own face (i.e., an altercentric bias), but this time only with the relatively less attractive face. Further research is needed to replicate these findings in clinical samples, but overall they suggest that the current task might be suited to investigate SOD problems in BPD. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
Multiple Sclerosis: Shall We Target CD33?

Background: Multiple sclerosis (MS) is a chronic disease of the central nervous system (CNS). Myeloid lineage cells (microglia and macrophages) may participate in the pathogenic mechanisms leading to MS. CD33 is a transmembrane receptor, mainly expressed by myeloid lineage cells. CD33 rs3865444 is a promoter variant previously associated with Alzheimer’s disease, whose role in MS remains obscure. Objective: To assess the role of CD33 rs3865444 in MS risk. Methods: We genotyped 1396 patients with MS and 400 healthy controls for the presence of the CD33 rs3865444 variant. Odds ratios (ORs) with the respective 95% confidence intervals (CIs), were calculated with the SNPStats software, assuming five genetic models (co-dominant, dominant, recessive, over-dominant, and log-additive), with the G allele as the reference allele. The value of 0.05 was set as the threshold for statistical significance. Results: CD33 rs3865444 was associated with MS risk in the dominant (GG vs. GT + TT; OR (95% C.I.) = 0.79 (0.63–0.99), p = 0.041) and the over-dominant (GG + TT vs. GT; OR (95% C.I.) = 0.77 (0.61–0.97), p = 0.03) modes of inheritance. Given that the GG genotype was more frequent and the GT genotype was less frequent in MS patients compared to controls—while the observed frequency of the TT genotype did not differ between the two groups—the observed difference in MS risk may be stemming from either the GG (as a risk factor) or the GT (as a protective factor) genotype of CD33 rs3865444. Conclusions: Our preliminary results suggest a possible contribution of CD33 rs3865444 to MS. Therefore, larger multiethnic studies should be conducted, investigating the role of CD33 rs3865444 in MS.
Modelling of Phase Contrast Imaging with X-ray Wavefront Sensor and Partial Coherence Beams

The Hartmann wavefront sensor is able to measure, separately and in absolute, the real δ and imaginary part β of the X-ray refractive index. While combined with tomographic setup, the Hartman sensor opens many interesting opportunities behind the direct measurement of the material density. In order to handle the different ways of using an X-ray wavefront sensor in imaging, we developed a 3D wave propagation model based on Fresnel propagator. The model can manage any degree of spatial coherence of the source, thus enabling us to model experiments accurately using tabletop, synchrotron or X-ray free-electron lasers. Beam divergence is described in a physical manner consistent with the spatial coherence. Since the Hartmann sensor can detect phase and absorption variation with high sensitivity, a precise simulation tool is thus needed to optimize the experimental parameters. Examples are displayed.
Mixed large cell neuroendocrine carcinoma and squamous cell carcinoma of the colon: detailed molecular characterisation of two cases indicates a distinct colorectal cancer entity

We present two rare cases of mixed large cell neuroendocrine carcinoma and squamous cell carcinoma of the colon. A literature search revealed only three published cases with similar histology but none of these reports provided profound molecular and mutational analyses. Our two cases exhibited a distinct, colon‐like immunophenotype with strong nuclear CDX2 and β‐catenin expression in more than 90% of the tumour cells of both components. We analysed the two carcinomas regarding microsatellite stability, RAS, BRAF and PD‐L1 status. In addition, next‐generation panel sequencing with Ion AmpliSeq™ Cancer Hotspot Panel v2 was performed. This approach revealed mutations in FBXW7, CTNNB1 and PIK3CA in the first case and FBXW7 and RB1 mutations in the second case. We looked for similar mutational patterns in three publicly available colorectal adenocarcinoma data sets, as well as in collections of colorectal mixed neuroendocrine‐non‐neuroendocrine neoplasms (MiNENs) and colorectal neuroendocrine carcinomas. This approach indicated that the FBXW7 point mutation, without being accompanied by classical adenoma–carcinoma sequence mutations, such as APC, KRAS and TP53, likely occurs at a relatively high frequency in mixed neuroendocrine and squamous cell carcinoma and therefore may be characteristic for this rare tumour type. FBXW7 codifies the substrate recognition element of an ubiquitin ligase, and inactivating FBXW7 mutations lead to an exceptional accumulation of its target β‐catenin which results in overactivation of the Wnt‐signalling pathway. In line with previously described hypotheses of de‐differentiation of colon cells by enhanced Wnt‐signalling, our data indicate a crucial role for mutant FBXW7 in the unusual morphological switch that determines these rare neoplasms. Therefore, mixed large cell neuroendocrine and a squamous cell carcinoma can be considered as a distinct carcinoma entity in the colon, defined by morphology, immunophenotype and distinct molecular genetic alteration(s).
Impact of Internet Use on Elderly Health: Empirical Study Based on Chinese General Social Survey (CGSS) Data

In the current era, the rapid spread of Internet technology has combined with various traditional industries; this provides new research perspectives and solutions for current problems, such as those in the elderly care industry. Elderly health is an important social problem in various countries, and governments have turned to the internet for new methods and better solutions. However, internet-use behavior has a certain influence on the elderly’s health status. This study investigates the effects of internet use on the elderly’s physical health, mental health, and self-rated health, along with the moderating role of individual cognitive ability in the above relationship. This study uses data from the Chinese General Social Survey (CGSS) in 2012 and 2015 as samples for analysis via the hierarchical regression method. The sample is from China and had 2821 and 3185 valid respondents in 2012 and 2015, respectively. Results show that internet use significantly affects the physical and mental health of the elderly and does not significantly affect self-rated health. In addition, individual cognitive ability plays a negative moderating role between internet use and physical and mental health. Finally, on the basis of results analysis and discussion, this study provides new recommendations to achieve targeted health improvements.
Outage Probability and Ergodic Capacity of a Two-User NOMA Relaying System with an Energy Harvesting Full-Duplex Relay and Its Interference at the Near User

In this paper, we consider a two-user downlink full-duplex (FD) non-orthogonal multiple access (NOMA) relay system where the FD relay uses an energy harvesting (EH) technique to assist the communication between the base station and far user over flat, independent and non-identically Rayleigh fading channels. Importantly, since the relay operates in FD mode, we take into account the effect of the interference caused by relay on the near user. Considering this EH-FD-NOMA relay system, we derive the exact mathematical expressions of the outage probabilities and ergodic capacities of near and far users. Monte–Carlo simulations verify the accuracy of our analytical method. Numerical results provided in this paper allow system designers to clearly see not only the impacts of the power distribution factor and the self-interference cancellation capacity of the relay but also the influence of the strength of inter-user interference at the near user on the outage performances and ergodic capacities of both users.
Shooting shots: Estimating alcoholic drink sizes in real life using event-level reports and annotations of close-up pictures.

INTRODUCTION AND AIMS Drinks consumed in real life are diverse, in terms of beverage type, container size and alcohol by volume. To date, most ecological momentary assessment studies have assessed drinking amounts with 'standard' drinks, although their event-level design allows for more advanced assessment schemes. The purpose of this empirical study is to compare participants' estimates of alcoholic drink characteristics, assessed using drink-specific questions, with estimates generated by annotators based on pictures of the same drinks. DESIGN AND METHODS On weekend nights, 186 young adults took 1484 close-up pictures of their drinks using a custom-built smartphone application. Participants reported the beverage type, drink size and alcohol by volume. Annotators described the beverage type, container size and filling level. Correspondence between participants' and annotators' estimates was explored using descriptive statistics, difference tests and correlations. RESULTS Annotators were unable to precisely identify the beverage types in most pictures of liqueurs, spirits and mixed drinks. Participants' drink size estimates converged with annotators' estimates of the container size for beer (41 cl corresponding to 16 g of pure alcohol) and mixed drinks (28 cl/35 g), and of the content size for wine (10 cl/9 g). However, annotators estimated larger sizes for liqueur/fortified wine (12 cl/14 g vs. 7 cl/9 g) and spirits (8 cl/26 g vs. 4 cl/10 g) than participants. DISCUSSION AND CONCLUSIONS Annotations of pictures should be considered as a complement to participants' reports rather than a substitute. Except for wine, real-life drinks vary largely and often exceed 10 g 'standard' drinks.
Individual and Area-level Factors Contributing to the Geographic Variation in Ambulatory Care Sensitive Conditions in Finland

Supplemental Digital Content is available in the text. Background: Measuring primary health care (PHC) performance through hospitalizations for ambulatory care sensitive conditions (ACSCs) remains controversial—recent cross-sectional research claims that its geographic variation associates more with individual socioeconomic position (SEP) and health status than PHC supply. Objectives: To clarify the usage of ACSCs as a PHC performance indicator by quantifying how disease burden, both PHC and hospital supply and spatial access contribute over time to geographic variation in Finland when individual SEP and comorbidities were adjusted for. Methods: The Finnish Care Register for Health Care provided hospitalizations for ACSCs (divided further into subgroups of acute, chronic, and vaccine-preventable causes) in 2011–2017. With 3-level nested multilevel Poisson models—individuals, PHC authorities, and hospital authorities—we estimated the proportion of the variance in ACSCs explained by selected factors at 3 time periods. Results: In age-adjusted and sex-adjusted analysis of total ACSCs the variances between hospital authorities was nearly twice that between PHC authorities. Individual SEP and comorbidities explained 19%–30% of the variance between PHC authorities and 25%–36% between hospital authorities; and area-level disease burden and arrangement and usage of hospital care a further 14%–16% and 32%–33%—evening out the unexplained variances between PHC and hospital authorities. Conclusions: Alongside individual factors, areas’ disease burden and factors related to hospital care explained the excess variances in ACSCs captured by hospital authorities. Our consistent findings over time suggest that the local strain on health care and the regional arrangement of hospital services affect ACSCs—necessitating caution when comparing areas’ PHC performance through ACSCs.
Early Percutaneous Tracheostomy in Coronavirus Disease 2019: Association With Hospital Mortality and Factors Associated With Removal of Tracheostomy Tube at ICU Discharge. A Cohort Study on 121 Patients.

OBJECTIVES Early tracheotomy, defined as a procedure performed within 10 days from intubation, is associated with more ventilator free days, shorter ICU stay, and lower mortality than late tracheotomy. During the coronavirus disease 2019 pandemic, it was especially important to save operating room resources and to have a shorter ICU stay for patients, when ICUs had insufficient beds. In this context of limited resources, early percutaneous tracheostomy could be an effective way to manage mechanically ventilated patients. Nevertheless, current recommendations suggest delaying or avoiding the tracheotomy in coronavirus disease 2019 patients. Aim of the study was to analyze the hospital mortality of coronavirus disease 2019 patients who had received early percutaneous tracheostomy and factors associated with removal of tracheostomy cannula at ICU discharge. DESIGN Cohort study. SETTING Coronavirus disease 2019 ICU. PATIENTS Adult patients with coronavirus disease 2019 3 days after ICU admission. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Three days after ICU admission, 164 patients were present in ICU and included in the analysis. One-hundred and twenty-one patients (74%) were tracheostomized, whereas the other 43 (26%) were managed with translaryngeal intubation only. In multivariable analysis, early percutaneous tracheostomy was associated with lower hospital mortality. Sixty-six of tracheostomized patients (55%) were discharged alive from the hospital. Age and male sex were the only characteristics that were independently associated with mortality in the tracheostomized patients (45.5% and 62.8% in tracheostomized and nontracheostomized patients, respectively; p = 0.009). Tracheostomy tube was removed in 47 of the tracheostomized patients (71%). The only variable independently associated with weaning from tracheostomy at ICU discharge was a faster start of spontaneous breathing after tracheotomy was performed. CONCLUSIONS Early percutaneous tracheostomy was safe and effective in coronavirus disease 2019 patients, giving a good chance of survival and of weaning from tracheostomy cannula at ICU discharge.
Incompatibility between proliferation and plant invasion is mediated by a regulator of appressorium formation in the corn smut fungus Ustilago maydis

Significance Many phytopathogenic fungi need specialized structures, called appressoria, to penetrate the plant before infection starts. For these structures, the fungus must carefully control when and where its cells divide, and it has been reported in different fungal phytopathogens that appressorium formation is subordinated to the cell cycle control. However, the molecular details about how this control operates were unknown. We described in the corn smut fungus U. maydis that Biz1, a regulator for the formation of appressorium, is phosphorylated by the kinase responsible for cell cycle progression. Biz1 is part of a negative feedback loop responsible for the final decision to invade or not the plant tissue. Targeting this process will lead to the development of antipenetrant fungicides. Plant pathogenic fungi often developed specialized infection structures to breach the outer surface of a host plant. These structures, called appressoria, lead the invasion of the plant by the fungal hyphae. Studies in different phytopathogenic fungi showed that appressorium formation seems to be subordinated to the cell cycle. This subordination ensures the loading in the invading hypha of the correct genetic information to proceed with plant infection. However, how the cell cycle transmits its condition to the genetic program controlling appressorium formation and promoting the plant’s invasion is unknown. Our results have uncovered how this process occurs for the appressorium of Ustilago maydis, the agent responsible for corn smut disease. Here, we described that the complex Clb2-cyclin-dependent kinase (Cdk)1, one of the master regulators of G2/M cell cycle progression in U. maydis, interacts and controls the subcellular localization of Biz1, a transcriptional factor required for the activation of the appressorium formation. Besides, Biz1 can arrest the cell cycle by down-regulation of the gene encoding a second b-cyclin Clb1 also required for the G2/M transition. These results revealed a negative feedback loop between appressorium formation and cell cycle progression in U. maydis, which serves as a “toggle switch” to control the fungal decision between infecting the plant or proliferating out of the plant.
Reconstruction of Oromandibular Defect After Tumor Resection by Sternomastoid-clavicular Flap

Supplemental Digital Content is available in the text Abstract The study aims to evaluate sternocleidomastoid-clavicular osteo-myocutaneous flap (SCM-OMCF) for reconstruction of mandibular defects after tumor resection. In the period between 2010 and 2018, thirteen patients with primary mandibular tumors underwent mandibular resection and reconstruction with SCM-OMCF. Patients were followed up for 10 to 66 months. Hospital was 13 ± 4 days. All patients started fluid in the 2nd day. The mean time to start oral fluid was 7.5 ± 0.8 day. Four (30.8%) patients suffered from complications (infection and salivary leak in 1 case due to partial flap loss, donor wound dehiscence in 1 case, deep venous thrombosis in 1 case and chest infection in 1 case). None of our cases experienced motor disability. Two cases (15.9%) underwent reoperations. The overall aesthetic outcome was found excellent in 5 cases, satisfactory in 5 cases and fair in 3 cases. The functional outcomes were satisfactory. Tumor recurrences were detected in 2 (15.9%) patients. Two patients died during follow up within 2 years after 1st surgery due to local and distant recurrences. SCM-OMCF is a versatile, safe and simple technique for reconstructing mandibular defects less than 11 cm.