Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis of severe acute respiratory syndrome coronavirus 2 infection

Purpose of review The spike glycoprotein plays a critical role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by recognizing the angiotensin converting enzyme 2 (ACE2) receptor and mediating fusion of the viral envelope with the cell membrane. It is also the major target for neutralizing antibodies and vaccines. This review summarizes recent studies on the structure and function of spike glycoprotein, which revealed the structural basis of SARS-CoV-2 infection. Recent findings SARS-CoV-2 spike glycoprotein, similar to those of SARS-CoV and Middle East respiratory syndrome coronavirus, spontaneously samples different prefusion states with the receptor-binding domain (RBD) adopting ‘up’ or ‘down’ conformations, and the RBD ‘down’ to ‘up’ conformational change is required for ACE2 binding. Receptor binding and spike glycoprotein priming by host proteases such as furin and transmembrane protease serine 2 induce pre to postfusion conformational changes of the spike trimer that enable membrane fusion. Interactions between SARS-CoV-2 RBD and ACE2 were elucidated at atomic resolution using high-resolution crystal structures. These structures, together with adapted and remodeled SARS-CoV-2 strains, further revealed critical residues of the spike glycoprotein for SARS-CoV-2 infection and cross-species transmission. Summary Recent studies on SARS-CoV-2 spike glycoprotein provide important structural knowledge for a better understanding of the molecular mechanisms of SARS-CoV-2 infection and cross-species transmission.
Triplex Real-Time PCR Approach for the Detection of Crucial Fungal Berry Pathogens—Botrytis spp., Colletotrichum spp. and Verticillium spp.

Phytopathogens cause undeniably serious damage in agriculture by harming fruit cultivations and lowering harvest yields, which as a consequence substantially reduces food production efficiency. Fungi of the Botrytis, Colletotrichum and Verticillium genera are a main concern in berry production. However, no rapid detection method for detecting all of these pathogens simultaneously has been developed to date. Therefore, in this study, a multiplex real-time PCR assay for this purpose was established. Universal fungal primers for the D2 region of the large subunit ribosomal DNA and three multiplexable fluorogenic probes specific for the chosen fungi were designed and deployed. The triplex approach for the molecular detection of these fungi, which was developed in this study, allows for the rapid and effective detection of crucial berry pathogens, which contributes to a more rapid implementation of protective measures in plantations and a significant reduction in losses caused by fungal diseases.
Positive correlation between dispersal and body size in Green Frogs (Rana clamitans) naturally colonizing an experimental landscape

Dispersers are often assumed to have the mean phenotype observed across the entire metapopulation, despite growing evidence of dispersal–phenotype correlations. We examined three dispersal–phenotype correlations in Green Frogs (Rana clamitans Latreille, 1801 = Lithobates clamitans (Latreille, 1801)). Two were in traits that have been previously tied to fitness (body size and body condition), while a third (relative hindlimb length) has been linked to movement performance. We constructed a spatially dispersed array of experimental ponds in close proximity to source ponds known to support Green Frog breeding populations. Over the course of two breeding seasons (four sampling periods), we measured phenotypes of all Green Frogs that had colonized the experimental ponds and a sample of individuals from the source ponds. After only 1 month, a positive correlation was detected between dispersal and body size within the population of dispersers occupying the experimental ponds. After a 2nd month, this positive dispersal – body size correlation was also present when comparing the population of dispersers to the population of nondispersers remaining at the source ponds. Even if generated solely by plasticity, a positive correlation between dispersal and body size (a trait tightly linked to fitness) has the ability to alter metapopulation capacity and thus the probability of regional species persistence.
Strabismus surgery in Angelman syndrome: More than ocular alignment

Purpose To report and evaluate strabismus surgery in children with Angelman syndrome, in order to optimize and standardize surgical approach. Other purposes are to understand the possible relation between ocular findings and motor ability, and between improvement in ocular alignment and changes in motor skills in this population. Design Observational cross-sectional study. Methods Medical records of pediatric patients with Angelman syndrome, who underwent strabismus surgery, were investigated. Collected data included: genotype, gender, age at the time of surgery, refractive error, pre-operative strabismus, surgical procedure, surgical outcome, gross and fine motor development assessment pre- and post-operatively. Results Seventeen subjects, aged 3–15 years, were investigated. Fourteen patients were exotropic, three esotropic. Most patients presented astigmatism. Considering the exaggerated response to standard amounts of surgery and the risk of consecutive strabismus on long term follow-up reported by previous studies in children with developmental delay, a reduction of the amount of strabismus surgery was applied. Post-operatively, all patients presented with a significative reduction of the baseline deviation angle, with all esotropic patients and 7 exotropic patients (59%) achieving orthotropia. The surgical outcomes were variable according to the type and the amount of baseline strabismus, but no case presented with exaggerated surgical response. At baseline, patients showed important delays in all motor abilities, and, post-operatively, presented a significant improvement in walking and fine motor tasks. Pre- and post-operative motor abilities were negatively correlated to astigmatism, anisometropia, and amount of deviation. Conclusions According to our data, the standard nomograms for strabismus surgery may be successfully applied in subjects with Angelman syndrome and exotropia. Our data suggest that the reduction of the deviation angle improves motor skills in strabismic pediatric patients with Angelman syndrome.
The p-curve is Not “Just Fine”

Figure 1: “P-curve Handles Heterogeneity Just Fine” (http://datacolada.org/67) according to Simonsohn, Nelson, and Simmons but their own simulation makes clear there is nothing “fine” about p-curve estimates: perfect estimates would fall on the 45-degree line while p-curve estimates look like random scatter. Note: To reproduce the above figure, run the R code (http://datacolada.org/appendix/Colada%2067%20%20Shorter%20-%202017%2012%2019.R) associated with the SNS blog post and then run: plot(r0$pcurve, r0$true, pch=16, main="p-curve Estimate vs. Truth"). Preface: This is a long form response to a recent post of Andrew Gelman. The original idea for the post was to feature a dialogue between the three of us and Uri Simonsohn with additional commentary by Andrew; the below reflects that. Unfortunately, the dialogue did not work out. Andrew proceeded with his own post and solicited brief comments from each of us. We note that several of us on opposing teams are friends and admire one another’s work, and nothing in this comment has a personal element to it. In “p-Curve and Effect Size” (2014), SNS purport to introduce a new method, the so-called pcurve, that adjusts for the upward bias in meta-analytic effect size estimates that results from publication bias (i.e., the tendency for statistically significant and directionally consistent results to be over-represented in the published literature). However, as we have written (McShane, Böckenholt, & Hansen, 2016), the method is not new and it is terribly flawed in the sense that it ● ● ●
High-quality nursing mode is helpful to improve the joint function and quality of life of patients after hip replacement

Objective: With the increasing number of patients undergoing hip replacement, the demand for highquality nursing is also raising. This study aimed to explore the application value of high-quality nursing mode in the nursing of patients undergoing hip replacement. Methods: Altogether 144 patients who underwent hip replacement in our hospital from January 2018 to January 2019 were selected as the research objects. Among them, those in the conventional group (n=68) received conventional nursing and those in the high-quality group (n=76) received highquality nursing. The effects of the two nursing modes on the quality of patients’ nursing were compared. Results: After nursing intervention, the evaluation of hip joint function, pain management, adverse emotions, quality of life and nursing satisfaction in the high-quality group were better than those in the conventional group. In addition, the number of cases of joint swelling and incision infection in the high-quality group was lower than that in the conventional group. Conclusion: Compared with conventional nursing model, high-quality nursing model can provide better hip joint function, quality of life and nursing satisfaction for patients undergoing hip replacement, and can be popularized in clinical practice.
Multivariate Multiple Test Procedures

Dependencies among data points are present in virtually all modern statistical applications. This holds especially true for studies with multiple endpoints which are all measured for the same observational units. For example, consider the case of a gene expression study. In that context, expression levels of m genes are measured for n individuals. The goal of the study typically is to detect statistically significant expression differences, either in a two-groups model or in a one-group model under different experimental conditions. Due to biological and technological reasons, the expression levels will typically exhibit strong dependencies, at least for genes which are functionally related; cf. [67]. We will discuss multiple tests which take such dependencies explicitly into account. Such multiple tests are called multivariate multiple tests, because they rely on joint distributions or on approximations thereof.
Modeling the Radiative Transfer in Leaves in the 300nm to 2.5µm Wavelength Region taking into Consideration Chlorophyll Fluorescence - The Leaf Model SLOPE

The model SLOPE (Stochastic model for Leaf Optical Properties Extended for fluorescence) is based on the concept of Marcov Chains. It describes the radiative transfer in leaves and calculates transmittance and reflectance spectra between 300nm and 2. 5µm. Input parameters are e.g. the concentrations and in vivo absorption spectra of chlorophylls, carotenoids and water in four leaf layers. The validation of the model shows very good agreement between calculated and measured spectra. The model supports the hypothesis, leaves are optimized for maximum light absorption. The model is applied in the development of new algorithms to interpret remote sensing data
Changes in Protein Non-Covalent Bonds and Aggregate Size during Dough Formation

This research investigated changes in the amounts and sizes of monomeric proteins and protein aggregates during dough mixing, with a focus on the contribution of non-covalent bonds in the aggregation of gluten proteins. High protein flour (HF) and low protein flour (LF) were used in this study. As dough mixing progressed from flour to overmixed dough, the total amount of protein aggregates increased while the amount of monomeric protein decreased. Omega-gliadin was the major monomeric protein that decreased in quantity. Interestingly, the amount of larger-sized protein aggregates decreased and that of smaller-sized protein aggregates increased. The amount of gluten protein macro-polymer aggregated through strong non-covalent bonds decreased whereas aggregates formed with weaker non-covalent bonds increased. LF dough behaved similar to HF dough. Large-sized gluten protein aggregates disaggregated due to the weakening of non-covalent bonds and became smaller. Omega-gliadin was incorporated into gluten protein aggregates during dough mixing.
The role of immigration and reinforcement in the population dynamics of a long‐lived bird: implications for the conservation of threatened species

Understanding population dynamics requires knowledge of the differential effects of survival, productivity and dispersal on population growth. This is particularly important for the conservation of small and recently established populations, where stochastic births and deaths may result in negative growth and even extinction. Here, we investigated the population dynamics of a small population of Eurasian cranes Grus grus in the UK and the effect of a population reinforcement in population growth. We also estimated the probability that the conservation status of cranes improves in the future. We developed stochastic population models to assess the population dynamics and the effect of adding 90 individuals between 2010 and 2014. The best‐supported models suggest that the crane population is self‐sustaining with an annual adult survival of 0.88, but suffers from low productivity. In addition, much of the population increase has been driven by immigration of birds from continental Europe. We found that population reinforcement resulted in a 50% increase in the projected population size, from 178 to 275 breeding pairs over the next 50 years. We showed that the relative contribution of immigration to population growth declined from 43%, when the translocated birds were not considered, to 29%, when they were included in the breeding pool. Moreover, after the population reinforcement, the probability of the population improving its conservation status increased from just above zero to 32%. In light of the recent increase in translocation programs worldwide, our study highlights the need to consider population dynamics to successfully predict the increase in population size when management strategies, such as reintroductions and reinforcements, are planned.
Impact of Time to Initiation of Treatment on the Quality of Life of Women with Breast Cancer

Introduction: Breast cancer is the most common malignancy in women. Due to the large number of women living with breast cancer and the increasing incidence of this cancer, it is very important to understand the factors determining the quality of life (QOL) of patients. The aim of the study. The aim of the study was to determine the impact of time to initiation of treatment on the quality of life of women with breast cancer. Materials and methods. The study involved 324 women with breast cancer, treated at the Podkarpackie Oncology Centre in Brzozów, Poland. The study was conducted using a diagnostic survey, using a standardised questionnaire to measure the quality of life of women treated for breast cancer, i.e., the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC) QLQ-C30 and the QLQ-BR23 module, as well as a proprietary survey questionnaire. Statistical analysis was performed using the Statistica 10.0 software (StatSoft Inc., 2011). A p value of <0.05 was considered statistically significant. Results: The examined women had a reduced overall quality of life and health (M = 53.88). The quality of life was higher in women who consulted a doctor the earliest after noticing initial symptoms of the disease, i.e., up to one week (M = 57.58), compared to patients who delayed the decision (over four weeks; M = 47.8) (p = 0.002). The quality of life was also considered higher by women who received treatment within two weeks of diagnosis (M = 56.79) and was lower for patients who waited for treatment for more than two months (M = 43.68). Statistically significant relationships were demonstrated for functional scales and disease intensity. Conclusions: Women diagnosed with breast cancer had a considerably lower overall quality of life. A relatively higher quality of life was experienced by patients who consulted a doctor the earliest after discovering symptoms of the disease and those whose waiting time for treatment was shorter. In a systematic manner, the individual stages of diagnosis should be maximally reduced and breast cancer treatment initiated without delay.
Antibiotic resistance evasion is explained by rare mutation frequency and not by lack of compensatory mechanisms

Drug resistant infections represent one of the most challenging medical problems of our time. D-cycloserine is an antibiotic used for decades without appearance and dissemination of antibiotic resistant strains, making it an ideal model compound to understand what drives resistance evasion. We investigated why Mycobacterium tuberculosis fails to become resistant to D-cycloserine. To address this question we employed a combination of bacterial genetics, genomics, biochemistry and fitness analysis in vitro, in macrophages and in mice. Altogether, our results suggest that the ultra-low mutation frequency associated with D-cycloserine resistance is the dominant factor delaying the appearance of clinical resistance to this antibiotic in bacteria infecting humans, and not lack of potential compensatory mechanisms. One Sentence Summary We show that the lack of D-cycloserine resistance in Mycobacterium tuberculosis is due its ultra-low mutation frequency rather than lack of compensatory mechanisms.
HEALTH OUTCOMES AMONG FORMER FEMALE COLLEGIATE GYMNASTS: THE INFLUENCE OF SPORT SPECIALIZATION, CONCUSSION, AND DISORDERED EATING

Background: Over 1,500 collegiate gymnasts compete each year. Injury rates among these athletes are high, yet little is known about their long-term health outcomes. Hypothesis/Purpose: The purpose of our study was to describe health-related outcomes of former collegiate gymnasts and to evaluate how early sport specialization, concussion history, and disordered eating (DE) influence current health. We hypothesized that gymnasts who specialize early would report more injuries and would have worse physical health currently; that gymnasts who sustained concussions will be more likely to seek mental health treatment during their sport careers; and that gymnasts with DE would report more injuries. Methods: 473 former female collegiate gymnasts completed a survey (Table 1) that was distributed through social media. Participants were grouped according to early (<14 years) or late (> or equal to 14 years) specialization, whether they sustained a concussion during gymnastics participation, and whether they reported a history of DE or not. We determined the number of participants who had time-loss injuries, menstrual dysfunction, reasons for retirement from sport, functional outcome measures, and whether participants had sought mental health care during college. Results: The median age of gymnastics specialization was 8 years [interquartile range=6-11 years]. A significantly greater proportion of early specializers sustained injuries requiring surgery (60% vs. 44%; p=0.02), however, the proportion of time-loss injuries sustained during college, reasons for retirement, and current pain and physical function scores did not significantly differ between the early and late specializers (Table 2). Forty-two percent of participants sustained a concussion. Those with a concussion were more likely to have sought mental health treatment during college (32% vs. 23%; p=0.03), and to have a diagnosis of anxiety disorder (16% vs. 9%; p=0.01) than those with no concussion history (Table 3). Thirty-four percent reported DE during college. Those in the DE group had an increased risk of osteoporosis during college (4% vs 0%; p=0.003), secondary amenorrhea (16% vs 9%; p=0.02), and had an increased risk of time-loss injury (78% vs 65%; p=0.004) (Table 4). In addition, they had worse PROMIS pain (11.5 vs 10.2; p=0.007) and physical function scores (12.2 vs 11; p=0.01) after college. Conclusion: It is important for clinicians, coaches, and gymnasts to be aware of the risks of early specialization, concussions, and DE, all of which are common in former collegiate gymnasts. Counseling regarding these risks and prevention strategies for these health problems should be a focus of further research.
Personal and Lifestyle Determinants of HIV Transmission Risk in Spanish University Students

The increase in human immunodeficiency virus (HIV) transmission cases poses a serious public health concern. Although several previous studies have been conducted with the aim of identifying the risk factors for HIV transmission, the number of cases has been increasing, especially in youth. The present study is aimed at the identification of personal and lifestyle determinants of HIV transmission risk in a sample of 335 Spanish university students selected by convenience sampling from a public university located in Alicante (Spain). Sociodemographic factors, lifestyles, and variables of HIV risk of transmission were evaluated. Group differences on risk of HIV transmission were evaluated between participants depending on their sociodemographic characteristics (age, sex, relationship status, employment status, economic status, and sexual orientation) and lifestyle (diet, physical exercise, smoking, alcohol consumption, and stress). Linear regression models were conducted in order to identify those personal and lifestyle variables related to HIV transmission risk. The obtained results indicate that, generally, being older, in a relationship, and employed were factors related to a high risk of HIV transmission. Regarding lifestyle, poor diet, lower intensity of physical exercise, higher alcohol intake, and smoking were fundamentally associated with a higher risk of HIV transmission, through lower use of condoms and higher frequency of risky sexual behaviors. Hence, participants who develop an unhealthy lifestyle exhibit twice the probability of being at a high risk of HIV transmission, especially regarding these previously indicated behaviors. The present study points out the relevance of sociodemographic characteristics and lifestyles of university students in their proneness to developing risky behaviors for HIV infection. Future studies should be developed with larger, randomized, and more representative samples, in order to obtain significant information for the development of effective preventive strategies oriented toward the increase in the adherence to healthy lifestyles and HIV prevention.