Miracle-dz/UniFAR-FTUs huggingface dataset:
An approach to increase the success rate of cultivation of soil bacteria based on fluorescence-activated cell sorting

Soil microbiota are considered a source of undiscovered bioactive compounds, yet cultivation of most bacteria within a sample remains generally unsuccessful. Two main reasons behind the unculturability of bacteria are the presence of cells in a viable but not culturable state (such as dormant cells) and the failure to provide the necessary growth requirements in vitro (leading to the classification of some bacterial taxa as yet-to-be-cultured). The present work focuses on the development of a single procedure that helps distinguish between both phenomena of unculturability based on viability staining coupled with flow cytometry and fluorescence-activated cell sorting. In the selected soil sample, the success rate of cultured bacteria was doubled by selecting viable and metabolically active bacteria. It was determined that most of the uncultured fraction was not dormant or dead but likely required different growth conditions. It was also determined that the staining process introduced changes in the taxonomic composition of the outgrown bacterial biomass, which should be considered for further developments. This research shows the potential of flow cytometry and fluorescence-activated cell sorting applied to soil samples to improve the success rate of bacterial cultivation by estimating the proportion of dormant and yet-to-be-cultured bacteria and by directly excluding dormant cells from being inoculated into growth media.
Air Quality Change in Seoul, South Korea under COVID-19 Social Distancing: Focusing on PM2.5

Seoul, the most populous city in South Korea, has been practicing social distancing to slow down the spread of coronavirus disease 2019 (COVID-19). Fine particulate matter (PM2.5) and other air pollutants measured in Seoul over the two 30 day periods before and after the start of social distancing are analyzed to assess the change in air quality during the period of social distancing. The 30 day mean PM2.5 concentration decreased by 10.4% in 2020, which is contrasted with an average increase of 23.7% over the corresponding periods in the previous 5 years. The PM2.5 concentration decrease was city-wide and more prominent during daytime than at nighttime. The concentrations of carbon monoxide (CO) and nitrogen dioxide (NO2) decreased by 16.9% and 16.4%, respectively. These results show that social distancing, a weaker forcing toward reduced human activity than a strict lockdown, can help lower pollutant emissions. At the same time, synoptic conditions and the decrease in aerosol optical depth over the regions to the west of Seoul support that the change in Seoul’s air quality during the COVID-19 social distancing can be interpreted as having been affected by reductions in the long-range transport of air pollutants as well as local emission reductions.
GM2 Gangliosidoses: Clinical Features, Pathophysiological Aspects, and Current Therapies

GM2 gangliosidoses are a group of pathologies characterized by GM2 ganglioside accumulation into the lysosome due to mutations on the genes encoding for the β-hexosaminidases subunits or the GM2 activator protein. Three GM2 gangliosidoses have been described: Tay–Sachs disease, Sandhoff disease, and the AB variant. Central nervous system dysfunction is the main characteristic of GM2 gangliosidoses patients that include neurodevelopment alterations, neuroinflammation, and neuronal apoptosis. Currently, there is not approved therapy for GM2 gangliosidoses, but different therapeutic strategies have been studied including hematopoietic stem cell transplantation, enzyme replacement therapy, substrate reduction therapy, pharmacological chaperones, and gene therapy. The blood–brain barrier represents a challenge for the development of therapeutic agents for these disorders. In this sense, alternative routes of administration (e.g., intrathecal or intracerebroventricular) have been evaluated, as well as the design of fusion peptides that allow the protein transport from the brain capillaries to the central nervous system. In this review, we outline the current knowledge about clinical and physiopathological findings of GM2 gangliosidoses, as well as the ongoing proposals to overcome some limitations of the traditional alternatives by using novel strategies such as molecular Trojan horses or advanced tools of genome editing.
Postactivation performance enhancement: Does conditioning one arm augment performance in the other?

The purpose was to determine whether postactivation performance enhancement is specific to the muscle being conditioned or if it is also observed within the homologous muscles of the contralateral limb (after accounting for the warm‐up and random error). We also investigated whether this differed based on training status or muscle size. One hundred seven participants (75 untrained; 32 trained) participated in four sessions. Visit 1 included baseline measurements and familiarization. Visits 2–4 included the completion of one of the three experimental conditions: (a) control, (b) same side and (c) crossover completed in a randomized order. The control condition completed all testing except for the conditioning contraction. The same side condition completed the conditioning contraction on the same side as the strength test. The crossover condition completed the conditioning on the arm opposite to the strength test. The variable of interest was the change from baseline in isokinetic strength. Our analysis indicated that of the hypotheses compared, the posterior probabilities (posterior probability of 0.506) favoured the hypothesis that the effect was local and greatest in those who were resistance trained [mean (SD) of 1.4 (2.2) Nm over the control in those resistance trained]. We found no relationship between muscle size and postactivation performance enhancement. In conclusion, there is an influence of training status pertaining to the postactivation performance enhancement effect but no influence from baseline muscle size. It appears unlikely that the effect is due to a systemic mechanism.
Substantial direct fitness gains of workers in a highly eusocial ant

Hamilton's theory of inclusive fitness suggests that helpers in animal societies gain fitness indirectly by increasing the reproductive performance of a related beneficiary. Helpers in cooperatively breeding birds, mammals and primitively eusocial wasps may additionally obtain direct fitness through inheriting the nest or mating partner of the former reproductive. Here, we show that also workers of a highly eusocial ant may achieve considerable direct fitness by producing males in both queenless and queenright colonies. We investigated the reproductive success of workers of the ant Temnothorax crassispinus in nature and the laboratory by dissecting workers and determining the origin of males by microsatellite analysis. We show that workers are capable of activating their ovaries and successfully producing their sons independently of the presence of a queen. Genotypes revealed that at least one fifth of the males in natural queenright colonies were not offspring of the queen. Most worker‐produced males could be assigned to workers that were unrelated to the queen, suggesting egg‐laying by drifting workers.
Dynamic monitoring of the effects of adherence to medication on survival in heart failure patients: A joint modeling approach exploiting time‐varying covariates

Adherence to medication is the process by which patients take their drugs as prescribed, and represents an issue in pharmacoepidemiological studies. Poor adherence is often associated with adverse health conditions and outcomes, especially in case of chronic diseases such as heart failure (HF). This turns out in an increased request for health care services, and in a greater burden for the health care system. In recent years, there has been a substantial growth in pharmacotherapy research, aimed at studying effects and consequences of proper/improper adherence to medication both for the increasing awareness of the problem and for the pervasiveness of poor adherence among patients. However, the way adherence is computed and accounted for into predictive models is far from being informative as it may be. In fact, it is usually analyzed as a fixed baseline covariate, without considering its time‐varying behavior. The purpose and novelty of this study is to define a new personalized monitoring tool exploiting time‐varying definition of adherence to medication, within a joint modeling approach. In doing so, we are able to capture and quantify the association between the longitudinal process of dynamic adherence to medication with the long‐term survival outcome. Another novelty of this approach consists of exploiting the potential of health care administrative databases in order to reconstruct the dynamics of drugs consumption through pharmaceutical administrative registries. In particular, we analyzed administrative data provided by Regione Lombardia ‐ Healthcare Division related to patients hospitalized for HF between 2000 and 2012.
Genotyping and antibiotic resistance patterns of Campylobacter fetus subsp.venerealis from cattle farms in India

Bovine genital campylobacteriosis caused by Campylobacter fetus subsp. venerealis (Cfv) is of considerable economic importance to the cattle industry worldwide. Cfv causes syndrome of temporary infertility in female cattle, early embryonic mortality, aberrant oestrus cycles, delayed conception, abortions and poor calving rates. In the present study, a total of 200 samples obtained from vaginal swabs, cervicovaginal mucous (CVM), preputial washes and semen straws were investigated that were obtained from organized cattle farm of MLRI, Manasbal and unorganized sectors. Out of a total of 200 samples, 49 (47·57%) vaginal swabs, 1 (3·33%) preputial wash and 8 (25%) carried out CVM samples were positive for Cfv, whereas none of the semen straws were positive for Cfv. A total of eleven isolates of Cfv were recovered. PFGE (Pulse field gel electrophoresis) analysis revealed four different pulsotypes (I–IV) circulating in the screened farms. A common pulsotype circulating among farms could not be established. Insertion element (ISCfe1), a 233 bp amplicon of Cfv, was sequenced and the sequence was deposited in GenBank (accession no: MK475662).
Association of New-Onset Atrial Fibrillation After Noncardiac Surgery With Subsequent Stroke and Transient Ischemic Attack.

Importance Outcomes of postoperative atrial fibrillation (AF) after noncardiac surgery are not well defined. Objective To determine the association of new-onset postoperative AF vs no AF after noncardiac surgery with risk of nonfatal and fatal outcomes. Design, Setting, and Participants Retrospective cohort study in Olmsted County, Minnesota, involving 550 patients who had their first-ever documented AF within 30 days after undergoing a noncardiac surgery (postoperative AF) between 2000 and 2013. Of these patients, 452 were matched 1:1 on age, sex, year of surgery, and type of surgery to patients with noncardiac surgery who were not diagnosed with AF within 30 days following the surgery (no AF). The last date of follow-up was December 31, 2018. Exposures Postoperative AF vs no AF after noncardiac surgery. Main Outcomes and Measures The primary outcome was ischemic stroke or transient ischemic attack (TIA). Secondary outcomes included subsequent documented AF, all-cause mortality, and cardiovascular mortality. Results The median age of the 452 matched patients was 75 years (IQR, 67-82 years) and 51.8% of patients were men. Patients with postoperative AF had significantly higher CHA2DS2-VASc scores than those in the no AF group (median, 4 [IQR, 2-5] vs 3 [IQR, 2-5]; P < .001). Over a median follow-up of 5.4 years (IQR, 1.4-9.2 years), there were 71 ischemic strokes or TIAs, 266 subsequent documented AF episodes, and 571 deaths, of which 172 were cardiovascular related. Patients with postoperative AF exhibited a statistically significantly higher risk of ischemic stroke or TIA (incidence rate, 18.9 vs 10.0 per 1000 person-years; absolute risk difference [RD] at 5 years, 4.7%; 95% CI, 1.0%-8.4%; HR, 2.69; 95% CI, 1.35-5.37) compared with those with no AF. Patients with postoperative AF had statistically significantly higher risks of subsequent documented AF (incidence rate 136.4 vs 21.6 per 1000 person-years; absolute RD at 5 years, 39.3%; 95% CI, 33.6%-45.0%; HR, 7.94; 95% CI, 4.85-12.98), and all-cause death (incidence rate, 133.2 vs 86.8 per 1000 person-years; absolute RD at 5 years, 9.4%; 95% CI, 4.9%-13.7%; HR, 1.66; 95% CI, 1.32-2.09). No significant difference in the risk of cardiovascular death was observed for patients with and without postoperative AF (incidence rate, 42.5 vs 25.0 per 1000 person-years; absolute RD at 5 years, 6.2%; 95% CI, 2.2%-10.4%; HR, 1.51; 95% CI, 0.97-2.34). Conclusions and Relevance Among patients undergoing noncardiac surgery, new-onset postoperative AF compared with no AF was associated with a significant increased risk of stroke or TIA. However, the implications of these findings for the management of postoperative AF, such as the need for anticoagulation therapy, require investigation in randomized trials.
Absolute and relative reliability of several measures of static postural stability calculated using a GYKO inertial sensor system.

PURPOSE The aim of this study was to analyse absolute and relative reliability of a number of postural static stability measures obtained from a GYKO inertial sensor system in young adults. METHODS The study examined 29 healthy non-athlete young adults. A test was performed for 30 s while standing on one foot, without moving, with eyes open and arms relaxed along the sides of the body. The examinations were performed twice, with a one-week interval. Relative reliability was measured using the intraclass correlation coefficient (ICC) and the 95% confidence interval (95% CI), whereas the absolute reliability was evaluated based on the standard error of measurement (SEM) and the minimal detectable change (MDC). RESULTS The results of this study showed moderate to good relative reliability scores for all the postural stability measures, with ICC values ranging from 0.62 to 0.70. For most of the analysed variables, SEM% ranged from ca. 10 to 14%. Relatively high SEM% values were obtained only for two variables (Area, Convex Hull Area). CONCLUSIONS The low costs of GYKO inertial sensor systems, the fast and easy installation, the mobility and high reliability of the measurement of postural stability show that it can be effective alternative to stabilographic platforms.
Prediction of immunogenicity for humanized and full human therapeutic antibodies

Immunogenicity is an important concern for therapeutic antibodies during drug development. By analyzing co-crystal structures of idiotypic antibodies and their antibodies, we found that anti-idiotypic antibodies usually bind the Complementarity Determining Regions (CDR) of idiotypic antibodies. Sequence and structural features were identified for distinguishing immunogenic antibodies from non-immunogenic antibodies. For example, non-immunogenic antibodies have a significantly larger cavity volume at the CDR region and a more hydrophobic CDR-H3 loop than immunogenic antibodies. Antibodies containing no Gly at the turn of CDR-H2 loop are often immunogenic. We integrated these features together with a machine learning platform to Predict Immunogenicity for humanized and full human THerapeutic Antibodies (PITHA). This method achieved an accuracy of 83% in leave-one-out experiment for 29 therapeutic antibodies with available crystal structures. The accuracy decreased to 65% for 23 test antibodies with modeled structures, because their crystal structures were not available, and the prediction was made with modeled structures. The server of this method is accessible at http://mabmedicine.com/PITHA.
iPSC-Derived Liver Organoids: A Journey from Drug Screening, to Disease Modeling, Arriving to Regenerative Medicine

Liver transplantation is the most common treatment for patients suffering from liver failure that is caused by congenital diseases, infectious agents, and environmental factors. Despite a high rate of patient survival following transplantation, organ availability remains the key limiting factor. As such, research has focused on the transplantation of different cell types that are capable of repopulating and restoring liver function. The best cellular mix capable of engrafting and proliferating over the long-term, as well as the optimal immunosuppression regimens, remain to be clearly well-defined. Hence, alternative strategies in the field of regenerative medicine have been explored. Since the discovery of induced pluripotent stem cells (iPSC) that have the potential of differentiating into a broad spectrum of cell types, many studies have reported the achievement of iPSCs differentiation into liver cells, such as hepatocytes, cholangiocytes, endothelial cells, and Kupffer cells. In parallel, an increasing interest in the study of self-assemble or matrix-guided three-dimensional (3D) organoids have paved the way for functional bioartificial livers. In this review, we will focus on the recent breakthroughs in the development of iPSCs-based liver organoids and the major drawbacks and challenges that need to be overcome for the development of future applications.
Leveraging Psychosocial Interventions to Motivate Instructor Participation in Teaching Professional Development

To promote undergraduate education reform, teaching professional development (TPD) efforts aim to encourage instructors to adopt evidence-based practices. However, many instructors do not attend TPD. There may be many reasons for this, including low intrinsic motivation to participate in TPD. Psychologists have dealt with motivational barriers in educational contexts using psychosocial interventions, brief activities that draw on a rich history of psychological research to subtly alter key, self-reinforcing psychological processes to yield long-term intrinsic motivation and behavioral changes. Psychosocial interventions, for example, have been used to alter students’ noncognitive attitudes and beliefs, such as attributions and mindset, which positively influence students’ motivation and academic performance. Here, we propose that insights from research on psychosocial interventions may be leveraged to design interventions that will increase instructors’ motivation to participate in TPD, thus enhancing existing pedagogical reform efforts. We discuss psychological principles and “best practices” underlying effective psychosocial interventions that could guide the development of interventions to increase instructors’ motivation to attend TPD. We encourage new interdisciplinary research collaborations to explore the potential of these interventions, which could be a new approach to mitigating at least one barrier to undergraduate education reform.
Reproducibility of isokinetic knee testing using the novel isokinetic SMM iMoment dynamometer

Isokinetic dynamometry is the gold standard for testing maximal strength in elite sport and rehabilitation settings. To be clinically useful, such tests should be valid and reliable. Despite some evidence regarding the relative test vs retest reliability of knee dynamometry, there is still a paucity of research regarding the absolute reliability parameters. The purpose of this study was to assess the absolute and relative intra-device reproducibility of isokinetic knee flexion and extension using the novel SMM iMoment dynamometer. A total of 19 participants (13 males and 6 females, aged 24 (2) years, height 178 (9) cm and weight 76 (11) kg) performed two identical knee isokinetic tests with at least a week of rest between measurements. Peak torque of knee extension and flexion were determined at 60°/s. Moderate (0.892) to excellent (0.988) relative reliability using the intraclass correlation coefficient (ICC) was obtained for peak knee torque. Absolute reliability assessed with a standard error of measurement (SEM %) was low, ranging from 2.54% to 6.93%, whereas the smallest real difference (SRD %) was moderate, ranging from 7.04% to 19.22%. Furthermore, there were no significant correlations between means and differences of two measurements, and Bland-Altman plots also showed no signs of heteroscedasticity. Our measurement protocol established the moderate to excellent reliability of the novel SMM iMoment isokinetic dynamometer. Therefore, this dynamometer can be applied in sport rehabilitation settings to measure maximal knee strength.
Altered tumor suppressor genes expression in Egyptian pesticide applicators exposed to organophosphate insecticides

Occupational exposure in spraying and application of non-arsenical insecticides has been classified as a probable human carcinogen. The fundamental molecular mechanisms involved the tumor-related genes. This study aimed to investigate the carcinogenesis effects related to chronic exposure to organophosphate (OP) pesticides in pesticide applicators. This was a cross-sectional study conducted on 27 pesticide applicators and 24 matched controls through the period from June to December 2018. The level of acetylcholinesterase (AChE) was determined and the effects of OPs exposure on messenger RNA (mRNA) expression of the DNA-damage responsive genes P53, P21, GADD45a, and MDM2 were determined using real-time quantitative polymerase chain reaction. A significant reduction of serum AChE enzyme activities was observed in chronically exposed subjects in comparison with the control group (p = 0.001). The expression of P53, P21 mRNA was significantly downregulated in the exposed group compared with the healthy nonexposed control group (p < 0.05). Conversely, the expression of MDM2 and GADD45a did not significantly differ between the exposed subjects and the control group (p > 0.05). No significant differences were noted between the exposed and control groups regarding the genotype or allele distributions of P53 Arg72Pro polymorphism. These results suggested that chronic exposure to OP insecticides may have mitogenic and carcinogenicity activity for the exposed cases due to downregulation of P53 and P21 but did not demonstrate any DNA damage properties for the exposed cases, and finally, a regular follow-up of the exposed cases for tumor markers is recommended.