Miracle-dz/UniFAR-FTUs huggingface dataset:
Minimum Determinants of Transmissible Gastroenteritis Virus Enteric Tropism Are Located in the N-Terminus of Spike Protein

Transmissible gastroenteritis virus (TGEV) is an enteric coronavirus causing high morbidity and mortality in porcine herds worldwide, that possesses both enteric and respiratory tropism. The ability to replicate in the enteric tract directly correlates with virulence, as TGEVs with an exclusive respiratory tropism are attenuated. The tissue tropism is determined by spike (S) protein, although the molecular bases for enteric tropism remain to be fully characterized. Both pAPN and sialic acid binding domains (aa 506–655 and 145–155, respectively) are necessary but not sufficient for enteric tract infection. Using a TGEV infectious cDNA and enteric (TGEV-SC11) or respiratory (TGEV-SPTV) isolates, encoding a full-length S protein, a set of chimeric recombinant viruses, with a sequential modification in S protein amino terminus, was engineered. In vivo tropism, either enteric, respiratory or both, was studied by inoculating three-day-old piglets and analyzing viral titers in lung and gut. The data indicated that U655>G change in S gene (S219A in S protein) was required to confer enteric tropism to a respiratory virus that already contains the pAPN and sialic acid binding domains in its S protein. Moreover, an engineered virus containing U655>G and a 6 nt insertion at position 1124 (Y374-T375insND in S protein) was genetically stable after passage in cell cultures, and increased virus titers in gut by 1000-fold. We postulated that the effect of these residues in enteric tropism may be mediated by the modification of both glycosaminoglycan binding and S protein structure.
A Critical View of the Application of the APEX Software (Aqueous Photochemistry of Environmentally-Occurring Xenobiotics) to Predict Photoreaction Kinetics in Surface Freshwaters

The APEX (aqueous photochemistry of environmentally occurring xenobiotics) software computes the phototransformation kinetics of compounds that occur in sunlit surface waters. It is free software based on Octave, and was originally released in 2014. Since then, APEX has proven to be a remarkably flexible platform, allowing for the addressing of several environmental problems. However, considering APEX as a stand-alone software is not conducive to exploiting its full potentialities. Rather, it is part of a whole ecosystem that encompasses both the software and the laboratory protocols that allow for the measurement of substrate photoreactivity parameters. Coherently with this viewpoint, the present paper shows both how to use APEX, and how to experimentally derive or approximately assess the needed input data. Attention is also given to some issues that might provide obstacles to users, including the extension of APEX beyond the simple systems for which it was initially conceived. In particular, we show how to use APEX to deal with compounds that undergo acid–base equilibria, and with the photochemistry of systems such as stratified lakes, lakes undergoing evaporation, and rivers. Hopefully, this work will provide a reference for the smooth use of one of the most powerful instruments for the modeling of photochemical processes in freshwater environments. All authors have read and agreed to the published version of the manuscript.
AtMOB1 Genes Regulate Jasmonate Accumulation and Plant Development1[OPEN]

A core component of the Hippo pathway plays important roles in regulating jasmonate accumulation and plant development in Arabidopsis. The MOB1 proteins are highly conserved in yeasts, animals, and plants. Previously, we showed that the Arabidopsis (Arabidopsis thaliana) MOB1A gene (AtMOB1A/NCP1) plays critical roles in auxin-mediated plant development. Here, we report that AtMOB1A and AtMOB1B redundantly and negatively regulate jasmonate (JA) accumulation and function in Arabidopsis development. The two MOB1 genes exhibited similar expression patterns, and the MOB1 proteins displayed similar subcellular localizations and physically interacted in vivo. Furthermore, the atmob1a atmob1b (mob1a/1b) double mutant displayed severe developmental defects, which were much stronger than those of either single mutant. Interestingly, many JA-related genes were up-regulated in mob1a/1b, suggesting that AtMOB1A and AtMOB1B negatively regulate the JA pathways. mob1a/1b plants accumulated more JA and were hypersensitive to exogenous JA treatments. Disruption of MYC2, a key gene in JA signaling, in the mob1a/1b background partially alleviated the root defects and JA hypersensitivity observed in mob1a/1b. Moreover, the expression levels of the MYC2-repressed genes PLT1 and PLT2 were significantly decreased in the mob1a/1b double mutant. Our results showed that MOB1A/1B genetically interact with SIK1 and antagonistically modulate JA-related gene expression. Taken together, our findings indicate that AtMOB1A and AtMOB1B play important roles in regulating JA accumulation and Arabidopsis development.
Temperature and Rain Moderate the Effect of Neighborhood Walkability on Walking Time for Seniors in Barcelona

Walking is the most accessible form for seniors to engage in daily light or moderate physical activity. Walking activity depends on both individual and environmental factors, the latter including how walkable a given setting is. Recent papers have pointed at the relevance of also considering meteorological conditions in relation to the walking behavior of older adults. This paper explores the combined effect of neighborhood walkability, temperature and rain on daily walking time among seniors residing in Barcelona. Daily walking time was extracted from 7-day GPS (Global Positioning System) devices and accelerometer data of 227 seniors residing in the Barcelona Metropolitan Region (Spain). Temperature and rain data were extracted from official governmental weather stations. Mixed-effects linear regression models were adjusted to test the combined association between weather and walkability on daily walking time. Neighborhood walkability is positively associated with walking time among seniors, while rain generally deters it. Additionally, this study demonstrates that temperature and rain modify the effect of residential walkability on senior walking activity: low temperatures are particularly associated with lower walking activity among those residing in low walkable areas, while the presence of rain presents a negative association with walking time in high walkable environments. The combined effect of walkability and weather should be considered both in design actions that aim at improving walking infrastructure and also in prevention programs aimed at encouraging daily walking among seniors.
Chronic heart failure with diabetes mellitus is characterized by a severe skeletal muscle pathology

Patients with coexistent chronic heart failure (CHF) and diabetes mellitus (DM) demonstrate greater exercise limitation and worse prognosis compared with CHF patients without DM, even when corrected for cardiac dysfunction. Understanding the origins of symptoms in this subgroup may facilitate development of targeted treatments. We therefore characterized the skeletal muscle phenotype and its relationship to exercise limitation in patients with diabetic heart failure (D‐HF).
In vitro activity and In vivo efficacy of Isoliquiritigenin against Staphylococcus xylosus ATCC 700404 by IGPD target

Staphylococcus xylosus (S. xylosus) is a type of coagulase-negative Staphylococcus, which was previously considered as non-pathogenic. However, recent studies have linked it with cases of mastitis in cows. Isoliquiritigenin (ISL) is a bioactive compound with pharmacological functions including antibacterial activity. In this study, we evaluated the effect of ISL on S. xylosus in vitro and in vivo. The MIC of ISL against S. xylosus was 80 μg/mL. It was observed that sub-MICs of ISL (1/2MIC, 1/4MIC, 1/8MIC) significantly inhibited the formation of S. xylosus biofilm in vitro. Previous studies have observed that inhibiting imidazole glycerol phosphate dehydratase (IGPD) concomitantly inhibited biofilm formation in S. xylosus. So, we designed experiments to target the formation of IGPD or inhibits its activities in S. xylosus ATCC 700404. The results indicated that the activity of IGPD and its histidine content decreased significantly under 1/2 MIC (40 μg/mL) ISL, and the expression of IGPD gene (hisB) and IGPD protein was significantly down-regulated. Furthermore, Bio-layer interferometry experiments showed that ISL directly interacted with IGPD protein (with strong affinity; KD = 234 μM). In addition, molecular docking was used to predict the binding mode of ISL and IGPD. In vivo tests revealed that, ISL significantly reduced TNF-α and IL-6 levels, mitigated the destruction of the mammary glands and reversed the production of inflammatory cells in mice. The results of the study suggest that, ISL may inhibit S. xylosus growth by acting on IGPD, which can be used as a target protein to treat infections caused by S. xylosus.
Procrastination as a Threat to the Psychological Security of the Educational Environment

The present study provides an analysis of the concept of procrastination and its features, together with a discussion of the fundamental approaches to its investigation. It examines procrastination as a threat to the psychological security of the educational environment. The author presents the results of an empirical investigation of the characteristics of interpersonal relations in the educational environment, academic motivation, and general motivation of students with various degrees of procrastination. The subjects of the investigation were 95 students, of the average age of 18.2 years, in an institution of higher education dedicated to the humanities. The subjects were evaluated using the procrastination scale for student populations developed by C. Lay, the academic motivation scale of R.J. Vallerand, the self-evaluation survey of motivation of academic, intellectual, and professional activity developed by N.A. Bakshaeva and A.A. Verbitsky, and the “Survey of Interpersonal Relations in an Educational Environment” developed by G.S. Kozhukhar and V.V. Kovrov. The primary hypothesis of the study, that the interconnections of interpersonal relations in an educational environment with academic and general motivation would differ in the groups of students with different levels of procrastination, was confirmed. The differences in the evaluations of the quality of interpersonal relations, and indicators of academic and intellectual motivation of students with different levels of procrastination were of special particular significance. It was shown that, the higher the level of students’ procrastination, the greater the interaction between the negative aspects of interpersonal relations in the educational environment and the external academic motivation.
Establishing a Scientific Consensus on the Cognitive Benefits of Physical Activity

Research suggests that physical activity can be used as an intervention to increase cognitive function. Yet, there are competing views on the cognitive effects of physical activity and it is not clear what level of consensus exists among researchers in the field. The purpose of this study was two-fold: Firstly, to quantify the scientific consensus by focusing on the relationship between physical activity and cognitive function. Secondly, to investigate if there is a gap between the public’s and scientists’ interpretations of scientific texts on this topic. A two-phase study was performed by including 75 scientists in the first phase and 15 non-scientists in the second phase. Participants were asked to categorize article abstracts in terms of endorsement of the effect of physical activity on cognitive function. Results indicated that there was a 76.1% consensus that physical activity has positive cognitive effects. There was a consistent association between scientists’ and non-scientists’ categorizations, suggesting that both groups perceived abstracts in a similar fashion. Taken together, this study provides the first analysis of its kind to evaluate the level of consensus in almost two decades of research. The present data can be used to inform further research and practice.
Diet, Secondhand Smoke, and Glycated Hemoglobin (HbA1c) Levels among Singapore Chinese Adults

The combination of poor diet and exposure to secondhand smoke may increase hemoglobin A1c (HbA1c) levels, but few studies have explored this interaction. We explored an interaction among 574 never-smoking adults from the Singapore Chinese Health Study. At baseline (age 59 ± 8 years), intakes of omega-3 polyunsaturated fatty acids, vitamin C, vitamin E and fiber were estimated using a modified food frequency questionnaire. At follow-up (age 64 ± 9 years), HbA1c and cotinine were measured. A product term between cotinine (above or below the median value) and each nutrient (high or low intake) was included in separate linear regression models with HbA1c as the outcome. HbA1c among those with high cotinine and low omega-3 polyunsaturated fatty acids intakes were higher than would be expected due to the individual effects alone (p-for-interaction = 0.05). Among those with lower intakes of omega-3 polyunsaturated fatty acids, high cotinine levels were associated with 0.54% higher HbA1c levels (95% confidence interval [CI]: 0.02, 1.06). Conversely, among those with higher intakes of omega-3 polyunsaturated fatty acids, HbA1c differ not differ by exposure (−0.09%; 95% CI: −0.45, 0.30). No evidence of interaction was observed for other nutrients. Diets high in omega-3 polyunsaturated fatty acids may ameliorate secondhand smoke-induced increases in HbA1c.
Sources and Determinants of Discretionary Food Intake in a Cohort of Australian Children Aged 12–14 Months

Despite recommendations to the contrary, consumption of discretionary (energy-dense, nutrient-poor) foods begins for some children early in the weaning period, and the proportion of children consuming discretionary foods increases markedly in the second year of life. The purpose of this study was to determine intake and sources of discretionary foods in a cohort of 828 Australian toddlers (mean age: 13.1mo), and to identify determinants of discretionary food intake. At approximately 12 months of age, 3 non-consecutive days of dietary intake data were collected using a 24-h recall and 2-day food record, and the percentage total energy derived from discretionary foods was estimated. Linear regression was used to identify associations between discretionary food intake and socio-demographic determinants (mother’s age, level of education, country of birth, pre-pregnancy body mass index, socioeconomic position, parity, age of child when mother returned to work, and child’s sex) and age at which complementary foods were introduced. The average energy intake of children in this cohort was 4040 (±954.7 SD) kJ with discretionary foods contributing an average of 11.2% of total energy. Sweet biscuits, and cakes, muffins, scones and cake-type desserts contributed 10.8% and 10.2% of energy intake from discretionary foods, respectively. Other key contributors to energy intake from discretionary foods included sausages, frankfurters and saveloys (8.3%), vegetable products and dishes where frying was the main cooking technique (8.6%), butter (7.3%), and finally manufactured infant sweet or savory snack foods (9.3%). Higher intakes of discretionary food were associated with children having two or more siblings (p = 0.002), and being born to younger mothers (<25 years) (p = 0.008) and mothers born in Australia or the United Kingdom (p < 0.001). Parents, in particular young mothers and those with larger families, need practical guidance on how much of, and how often, these foods should be eaten by their children.
The Deoptimization of Rabies Virus Matrix Protein Impacts Viral Transcription and Replication

Rabies virus (RABV) matrix (M) protein plays several important roles during RABV infection. Although previous studies have assessed the functions of M through gene rearrangements, this interferes with the position of other viral proteins. In this study, we attenuated M expression through deoptimizing its codon usage based on codon pair bias in RABV. This strategy more objectively clarifies the role of M during virus infection. Codon-deoptimized M inhibited RABV replication during the early stages of infection, but enhanced viral titers at later stages. Codon-deoptimized M also inhibited genome synthesis at early stage of infection and increased the RABV transcription rates. Attenuated M through codon deoptimization enhanced RABV glycoprotein expression following RABV infection in neuronal cells, but had no influence on the cell-to-cell spread of RABV. In addition, codon-deoptimized M virus induced higher levels of apoptosis compared to the parental RABV. These results indicate that codon-deoptimized M increases glycoprotein expression, providing a foundation for further investigation of the role of M during RABV infection.
Connecting Cancer Pathways to Tumor Engines: A Stratification Tool for Colorectal Cancer Combining Human In Vitro Tissue Models with Boolean In Silico Models

To improve and focus preclinical testing, we combine tumor models based on a decellularized tissue matrix with bioinformatics to stratify tumors according to stage-specific mutations that are linked to central cancer pathways. We generated tissue models with BRAF-mutant colorectal cancer (CRC) cells (HROC24 and HROC87) and compared treatment responses to two-dimensional (2D) cultures and xenografts. As the BRAF inhibitor vemurafenib is—in contrast to melanoma—not effective in CRC, we combined it with the EGFR inhibitor gefitinib. In general, our 3D models showed higher chemoresistance and in contrast to 2D a more active HGFR after gefitinib and combination-therapy. In xenograft models murine HGF could not activate the human HGFR, stressing the importance of the human microenvironment. In order to stratify patient groups for targeted treatment options in CRC, an in silico topology with different stages including mutations and changes in common signaling pathways was developed. We applied the established topology for in silico simulations to predict new therapeutic options for BRAF-mutated CRC patients in advanced stages. Our in silico tool connects genome information with a deeper understanding of tumor engines in clinically relevant signaling networks which goes beyond the consideration of single drivers to improve CRC patient stratification.
Rapid Quantification of Riboflavin in Milk by Front-Face Fluorescence Spectroscopy: A Preliminary Study

The front-face fluorescence spectroscopy technique was used to establish a rapid prediction model of riboflavin concentration in milk without prior sample preparation. The prediction model developed was then compared with two conventional high performance liquid chromatography (HPLC)-based quantification methods. The method of standard addition allowed detecting a linear correlation between fluorescence intensity and riboflavin concentration in 12% (w/w) reconstituted low-heat milk powder. Validation of the model yielded an R2 of 0.99 with a standard error of prediction of 0.13 mg/L. The results suggest a potential use of front-face fluorescence spectroscopy as a simple method for off- and in-line determinations of riboflavin in milk.
Simultaneous intussusception associated with adenovirus infection in monozygotic twins

Abstract Rationale: Intussusception, a common cause of intestinal obstruction in children, typically requires medical reduction. Here, we describe the case of a pair of twins who had simultaneous intussusception and were positive for fecal adenovirus—strongly indicating that adenovirus infection may be a main cause of the intussusception. Patient concerns: Two 1-year-old twin girls were brought to Cathay General Hospital one after another on the same day. Both presented with intermittent abdominal pain, abdominal distension, diarrhea, and loss of appetite. Diagnoses: Their laboratory data were adenovirus positivity in rectal swab culture. Intussusception was diagnosed through a lower gastrointestinal series. Interventions: The twins were treated with reduction for intussusception. Outcomes: Both patients recovered well, without recurrence. Lessons: Most cases of intussusception are idiopathic. However, some potential risk factors—as strongly suggested by the current cases—are genetic factors and adenovirus infection.
The relationship between vitamin D, ratio of neutrophil to lymphocyte, and ratio of lymphocyte to monocyte in preoperative serum and prognosis of patients with breast conserving surgery in breast cancer

Objective: To explore the relationship between vitamin D, ratio of neutrophil to lymphocyte (NLR), and ratio of lymphocyte to monocyte (LMR) in preoperative serum and prognosis of patients with breast conserving surgery in breast cancer. Methods: 206 cases of breast conserving surgery in breast cancer were prospectively analyzed. Peripheral venous blood was collected 1-7 days before operation. Enzyme-linked immunosorbent assay (ELISA) was used to detect serum 25-hydroxyvitamin D3 (25(OH)D) levels, neutrophils, lymphocytes, monocytes, NLR and LMR levels in the peripheral blood and were detected by hematology analyzer. According to the levels of 25(OH)D, NLR and LMR in the patients’ peripheral blood, the receiver operating characteristic curve (ROC) for NLR and LMR was used to predict the overall survival (OS) in patients with breast cancer. Kaplan-Meier and Cox regression models were used for survival analysis of patients. Results: There were significant differences in the proportion of adjuvant radiotherapy and proportion of TNM staging between the high 25(OH)D group and the low 25(OH)D group (P<0.05). The median PFS and OS of the high 25(OH)D group were significantly longer than those of the low 25(OH)D group (P<0.05). The median PFS and OS of the low NLR group and LMR group were significantly longer than those of the high NLR group and low LMR group, respectively (P<0.05). Cox regression single factor analysis has shown that TNM staging, adjuvant radiotherapy, molecular typing, 25(OH)D, NLR and LMR were related factors affecting the prognosis of breast cancer patients (P<0.05). The optimal cutoff value for preoperative 25(OH)D, NLR and LMR to evaluate the prognosis of patients was 21.03 ng/mL (AUC=0.720, Sensitivity =58.82%, Specificity =78.16%), 2.76 (AUC=0.737, Sensitivity =64.71%, Specificity =82.76%) and 5.26 (AUC=0.718, Sensitivity =65.71%, Specificity =79.62%), respectively. High grading of the cancer, no adjuvant radiotherapy, different molecular typing, 25(OH) D<21.03 ng/mL, NLR≥2.76 and LMR<5.26 were independent prognostic factors affecting breast cancer (P<0.05). Conclusion: High grading of the cancer, no adjuvant radiotherapy, different molecular typing and 25(OH)D<21.03 ng/mL, NLR≥2.76, LMR<5.26 in preoperative peripheral blood are independent prognostic factors affecting OS in patients with breast cancer.