Miracle-dz/UniFAR-FTUs huggingface dataset:
Cultivar Variation in Tomato Seed Coat Permeability Is an Important Determinant of Jasmonic Acid Elicited Defenses Against Western Flower Thrips

Induction of defenses is one of the most widely accepted eco-friendly approaches for management of pests and diseases. Seeds are receptive to resistance-inducing chemicals and could offer broad-spectrum protection at the early stages of development. However, seed treatment with elicitors has previously been shown to differentially influence induced defense responses among cultivars and thus, could hamper commercial exploitation. In this context, the objective of the present study was to evaluate the genotype-dependent ability of jasmonic acid (JA) to induce resistance against western flower thrips (WFT) at the seed stage. We examined the variation in inducibility of resistance in eight commercial tomato cultivars. Causal factors accounting for discrepancies in JA-induced responses at the seed stage were phenotypically and biochemically evaluated. Seed receptivity to exogenous JA appeared to be cultivar dependent. Thrips associated silver damage was only reduced in JA seed-treated plants of cultivar Carousel. Enhancement of resistance, was not associated with activation of defense-related traits such as polyphenol oxidase activity (PPO), trichomes or volatiles. Sulfuric acid scarification, prior to JA seed incubation, significantly augmented the embryonic responsiveness to JA in cv. Moneymaker without an adverse effect on growth. Hence, these results support the hypothesis that seed coat permeability is a key factor for successfully inducing JA mediated thrips defenses. The outcome of our study is of translational value as it creates opportunities for the seed industry to perform pre-treatments on non-responsive cultivars as well as for tomato breeding programs to select for genetic traits that affect seed permeability.
Molecular Characterization of Extended-Spectrum β-Lactamase–Producing Escherichia coli and Klebsiella pneumoniae Among the Pediatric Population in Qatar

Introduction Although extended-spectrum β-lactamase (ESBL)–producing Enterobacterales are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited. Aim To determine the molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the pediatric population of Qatar. Methods Whole-genome sequencing was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018. Results A total of 327 ESBL producers were sequenced: 254 E. coli and 73 K. pneumoniae. Non-susceptibility rates to non-β-lactam antibiotics for both species were 18.1 and 30.1% for gentamicin, 0.8 and 4.1% for amikacin, 41.3 and 41.1% for ciprofloxacin, and 65.8 and 76.1% for cotrimoxazole. The most common sequence types (STs) were ST131 (16.9%), ST38 and ST10 (8.2% each) in E. coli and ST307 (9.7%), and ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBLs were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Among other β-lactamases, TEM-1B and OXA-1 were coproduced in 41 and 19.6% of isolates. The most common plasmid-mediated quinolone resistance genes cocarried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harbored genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only two of 57 isolates harboring aac(6′)-Ib-cr were non-susceptible to amikacin. Chromosomal mutations in genes encoding DNA gyrase and topoisomerase IV enzymes were detected in 96.2% fluoroquinolone-non-susceptible E. coli and 26.7% fluoroquinolone-non-susceptible K. pneumoniae. Conclusion Our data show that CTX-M enzymes are largely the most prevalent ESBLs in children in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited, given the frequent coproduction of OXA-1 and TEM-1B enzymes and coresistance to antibiotic classes other than β-lactams.
Impact of COVID-19 Social Distancing Restrictions on Training Habits, Injury, and Care Seeking Behavior in Youth Long-Distance Runners

Purpose: The COVID-19 pandemic impacted the sporting and exercise activities of millions of youth. Running is an activity that could be maintained while social distancing restrictions were implemented during the pandemic. If running-related injuries do occur, these restrictions may also influence the access to care or care seeking behavior of this population. Therefore, the purpose of this study was to determine if the social distancing restrictions during the 2020 COVID-19 pandemic influenced training habits, injury, and care seeking behavior in youth long-distance runners. Methods: A customized, open online questionnaire was provided to runners 9–19 years of age who participated in long-distance running activities including team/club cross-country, track and field (distances ≥800 m), road races, or recreational running. Participants responded to questions about demographics, running habits, RRIs, and health care provider visits 6-months before as well as during social distancing restrictions due to COVID-19. Wilcoxon signed rank tests compared differences for ratio data and Chi-square tests were used to compare proportions before and during COVID-19 social distancing restrictions. Statistical significance was set at p ≤ 0.05. Results: A total of 287 youth long-distance runners (male = 124, female = 162, unspecified = 1; age = 15.3 ± 1.7 years; running experience = 5.0 ± 2.3 years) participated. Compared to their pre-COVID-19 responses, youth long-distance runners reported lower distances run per week (p < 0.001), fewer runs per week (p < 0.001), fewer hard runs per week (p < 0.001), fewer number of injuries (p < 0.001), and fewer injuries per 1,000 km (p = 0.002) during the COVID-19 social distancing restrictions. A lower proportion of participants reported in-person health care provider visits (p < 0.001) and a lower proportion of visits were made to an athletic trainer during COVID-19 social distancing restrictions compared to prior to COVID-19 (p < 0.001). Conclusion: The COVID-19 pandemic resulted in significant decreases in both training and injuries which were different compared to previous reports in an adult population. Many of the runners who sustained an injury during COVID-19 social distancing restrictions did not seek care, with the most prominent reduction in visits to an athletic trainer. This could impact future injury and chronic pain.
Detection of Antibiotic-Resistance by MALDI-TOF Mass Spectrometry: An Expanding Area

Several MALDI-TOF MS-based methods have been proposed for rapid detection of antimicrobial resistance. The most widely studied methods include assessment of β-lactamase activity by visualizing the hydrolysis of the β-lactam ring, detection of biomarkers responsible for or correlated with drug-resistance/non-susceptibility, and the comparison of proteomic profiles of bacteria incubated with or without antimicrobial drugs. Antimicrobial-resistance to a number of antibiotics belonging to different classes has been successfully tested by MALDI-TOF MS in a variety of clinically relevant bacterial species including members of Enterobacteriaceae family, non-fermenting Gram-negative bacteria, Gram-positive cocci, anaerobic bacteria and mycobacteria, opening this field to further clinically important developments. Early detection of drug-resistance by MALDI-TOF MS can be particularly helpful for clinicians to streamline the antibiotic therapy for a better outcome of patients with systemic infection, in all cases where a prompt and effective antibiotic treatment is essential to preserve organ function and/or patient survival.
Supplementation of Yeast Cell Wall Fraction Tends to Improve Intestinal Health in Adult Dogs Undergoing an Abrupt Diet Transition

When owners decide to change their pet's food, a rapid transition may cause gastrointestinal distress. Yeast products may help with digestive upset during diet transition due to the bioactive compounds they possess, which may lead to improved intestinal morphology and integrity, modified gut microbiota, and modulated immune responses. The objective of this study was to determine the effects of a yeast cell wall fraction supplement on measures of gut integrity and fecal characteristics of adult dogs undergoing an abrupt diet transition. Twelve adult female beagles (mean age: 5.16 ± 0.87 years; mean body weight: 13.37 ± 0.68 kg) were used in a replicated 4 × 4 Latin square design with four 28-day experimental periods. During days 1–14, dogs were fed a dry kibble diet and supplemented with a placebo (cellulose; 125 mg/d) or yeast product (365 mg/d; equivalent to 0.2% of diet). During days 15–28, dogs remained on their placebo or yeast treatments but were rapidly transitioned to a canned diet or high-fiber diet. Fresh fecal samples were collected on days 13, 16, 20, 24, and 27 for measurement of pH, dry matter, calprotectin, immunoglobulin A (IgA), Escherichia coli, and Clostridium perfringens. Blood samples were collected on days 14, 17, and 28 to measure serum lipopolysaccharide-binding protein concentrations. All data were analyzed using the Mixed Models procedure of SAS 9.4. Fecal pH, dry matter, calprotectin, IgA, and E. coli were not affected (P > 0.05) by treatment before diet transition. Dogs supplemented with yeast cell wall fraction tended to have higher (P = 0.06) fecal C. perfringens counts than the controls. After diet transition, most parameters were not altered (P > 0.05) by treatment except that yeast-supplemented dogs tended to have higher (P = 0.06) fecal IgA than controls. Our results suggest that the yeast product may modestly improve intestinal health after an abrupt diet transition in adult dogs by enhancing intestinal immunity.
LncRNA PPP1R14B-AS1 Promotes Tumor Cell Proliferation and Migration via the Enhancement of Mitochondrial Respiration

PPP1R14B-AS1 is an antisense long non-coding RNA with unknown functions. Herein, gene differential analyses were performed using the data of patients with liver cancer and lung adenocarcinoma (LUAD) from The Cancer Genome Atlas database. PPP1R14B-AS1 was found to be upregulated and also overexpressed in 10 other types of cancers. In addition, PPP1R14B-AS1 overexpression was associated with poor overall prognosis in eight cancers. Furthermore, PPPAR14B-AS1 upregulation was positively associated with worsening development of liver and LUAD cancers and related to poor disease-free survival. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that PPP1R14B-AS1 strongly participated in regulating cell aerobic respiration processes, such as mitochondrial electron respiration chain and NADH dehydrogenation processes. Cell cytoplasmic and nuclear RNA purification assessment results revealed that PPP1R14B-AS existed in the cell nucleus and cytoplasm. The knockdown of PPP1R14B-AS1 in HepG2 and A549 cells using PPP1R14B-AS1-specific siRNAs decreased mitochondrial respiration as demonstrated by the reduction in basal respiration and ATP production. Moreover, PPP1R14B-AS1 downregulation did not obviously affect cell glycolysis ability. Finally, PPP1R14B-AS1 inhibition inhibited HepG2 and A549 cell migration and proliferation. In summary, our study found for the first time that PPP1R14B-AS1 could be a potential biomarker for cancer diagnosis and that PPP1R14B-AS1 inhibition could be a potentially effective therapy.
Evaluation of Staphylococcal Bacteriophage Sb-1 as an Adjunctive Agent to Antibiotics Against Rifampin-Resistant Staphylococcus aureus Biofilms

Rifampin plays a crucial role in the treatment of staphylococcal implant-associated infection, as it is the only antibiotic capable of eradicating Staphylococcus aureus biofilms. However, the emergence of rifampin resistance strongly limits its use. Combinatorial therapy of antibiotics and bacteriophages may represent a strategy to overcome the resistance. Here, we evaluated the activity of staphylococcal bacteriophage Sb-1 in combination with different antibiotics against the biofilms of 10 rifampin-resistant S. aureus clinical strains, including MRSA and MSSA. S. aureus biofilms formed on porous glass beads were exposed to antibiotics alone or combined with Sb-1 simultaneously or staggered (first Sb-1 for 24 h followed by antibiotic). Recovered bacteria were detected by measuring growth-related heat production at 37°C (isothermal microcalorimetry) and the biofilm eradication was assessed by sonication of beads and plating of the resulting sonication fluid. Minimum biofilm eradication concentration (MBEC) was defined as the lowest concentration of antibiotic required to kill all adherent bacteria, resulting in absence of growth after plating the sonication fluid. Tested antibiotics presented high MBEC values when administered alone (64 to > 1,024 μg/ml). The simultaneous or staggered combination of Sb-1 with daptomycin showed the highest activity against all MRSA biofilms, whereas the exposure to Sb-1 with vancomycin showed no improved anti-biofilm activity. Staggered administration of Sb-1 and flucloxacillin, cefazolin, or fosfomycin improved the antibiofilm activity in four out of six MSSA, whereas simultaneous exposure exhibited similar or lesser synergy. In conclusion, the combinatorial effect of Sb-1 and antibiotics enabled to eradicate rifampin-resistant S. aureus biofilms in vitro.
A Modified Pathological N Stage Including Status of Tumor Deposits in Colorectal Cancer With Nodal Metastasis

Background The American Joint Committee on Cancer 8th classification states that colorectal cancer (CRC) is classified as N1c stage when regional lymph nodes (LNs) are negative and tumor deposits (TDs) are positive. However, how to classify TDs when regional LNs are positive remains unclear. The current study aimed to investigate the possibility of combining positive LNs and positive TDs to develop a modified pathological N (mpN) stage for CRC. Methods We retrospectively analyzed 9,198 patients with stage III CRC from the Surveillance, Epidemiology, and End Results program who underwent surgery (6,440 in the training cohort and 2,758 the validation cohort). The combination of positive LNs and TD status was defined as mpN stage. Overall survival (OS) according to mpN and pathological N (pN) stages was analyzed by the Kaplan–Meier method. The area under the curves (AUCs) and Akaike’s information criterion (AIC) were applied to assess the predictive discrimination abilities and goodness-of-fit of the model. The clinical benefits were measured using decision curve analyses. The validation cohort was used to validate the results. Results AUC analysis showed that the prognostic discrimination of mpN stage (AUC = 0.628, 95% confidence interval (CI), 0.616–0.640) was better than that of pN stage (AUC = 0.618, 95% CI, 0.606–0.630, p = 0.006) for OS. The AIC demonstrated that mpN stage (AIC = 30,217) also showed superior model-fitting compared with pN stage (AIC = 30,257) and decision curve analyses revealed that mpN stage had better clinical benefits than pN stage. Similar results were found in the validation cohort. Conclusions Among patients with CRC and LN metastasis, mpN stage might be superior to pN stage for assessing prognosis and survival, suggesting that TD status should be included in the pN stage.
Comparison of Dimensionality Reduction Techniques on Audio Signals

: Analysis of audio signals is widely used and very effective technique in several domains like health-care, transportation, and agriculture. In a general process the output of the feature extraction method results in huge number of relevant features which may be difﬁcult to process. The number of features heavily correlates with the complexity of the following machine learning method. Di-mensionality reduction methods have been used successfully in recent times in machine learning to reduce complexity and memory usage and improve speed of following ML algorithms. This paper attempts to compare the state of the art dimensionality reduction techniques as a building block of the general process and analyze the usability of these methods in visualizing large audio datasets.
Not too close and not too far: comfort-distance towards virtual humans and anthropomorphic robot

Nowadays, machines like humanoid and non-humanoid robots no longer belong to an imagined futuristic scenario but to many real contexts of our time. This leads to the reconsideration of the relationship between humans and machines from a human-centered perspective. Indeed, despite the fact that evidence has shown that people perceive robots as social beings and that robots are designed to ensure a pleasant and positive atmosphere, little is known about the human comfort (i.e. positive or negative proxemics preferences) in interacting with human-like machines. More specifically, here we wondered whether the robot’s appearance could serve as a socio-emotional cue to influence individuals’ proxemics preferences. The present study tried to address this issue considering the Interpersonal-comfort space (IPS) as a reliable measure of the quality of social interactions. To this end participants were asked to provide the comfort-dis-tance judgement while being approached by an anthropomorphic robot, a non-anthropomorphic robot and male and female virtual confederates showing positive or negative facial expressions. Results suggest that participant’s comfort distance can be ideally ordered along a line from a negative pole with non-anthro-pomorphic robot and angry humans to a positive pole with neutral and happy humans. It is interesting to note that the comfort distance from the anthropomorphic robot seems to be between these two poles.
Teprotumumab reduces extraocular muscle and orbital fat volume in thyroid eye disease

Purpose Thyroid eye disease (TED) is a progressive, debilitating and potentially vision-threatening autoimmune disease. Teprotumumab, a novel human monoclonal antibody, has been shown to reverse the clinical manifestations of TED. Patients receiving teprotumumab have been shown in two multicenter, randomized placebo-controlled trials to have decreased proptosis, diplopia and inflammation after 24 weeks of treatment. This study aims to analyse volumetric and inflammatory changes on orbital imaging prior to and after teprotumumab treatment from one of these trials. Design Retrospective review. Subjects Six patients enrolled in the phase III teprotumumab clinical trial (OPTIC, NCT03298867) with active TED who received 24 weeks of teprotumumab and had pre- and post-treatment orbital imaging (CT or MRI). Additionally, 12 non-TED patients (24 orbits) were analysed as a comparative control group. Methods 3D volumetric calculations of the extraocular muscles (EOMs), orbital fat, and bony orbit were measured using previously validated image processing software. 3D volumetric results and changes in EOM inflammation were compared with clinical measurements of TED. Results Total EOM volume within each orbit was markedly reduced post-teprotumumab in all patients (n=six patients, 12/12 orbits, p<0.02). There was no statistical difference in post-treatment EOM volume when compared to non-TED controls. Total orbital fat volume was also reduced in 11 of 12 studied orbits (n=six patients, p=0.04). Overall EOM inflammation based on MRI signal intensity ratio was reduced in 8/8 orbits (n=four patients, p<0.01). Conclusion Orbital imaging demonstrated decreased EOM volumes and orbital fat tissue volumes after teprotumumab treatment.
Massively parallel characterization of regulatory dynamics during neural induction

The molecular components governing neural induction remain largely unknown. Here, we applied a suite of genomic and computational tools to comprehensively identify these components. We performed RNA-seq, ChIP-seq (H3K27ac, H3K27me3) and ATAC-seq on human embryonic stem cells (hESCs) at seven early neural differentiation time points (0-72 hours) and identified thousands of induced genes and regulatory regions. We analyzed the function of ~2,500 selected regions using massively parallel reporter assays at all time points. We found numerous temporal enhancers that correlated with similarly timed epigenetic marks and gene expression. Development of a prioritization method that incorporated all genomic data identified key transcription factors (TFs) involved in neural induction. Individual overexpression of eleven TFs and several combinations in hESCs found novel neural induction regulators. Combined, our results provide a comprehensive map of genes and functional regulatory elements involved in neural induction and identify master regulator TFs that are instrumental for this process. One Sentence Summary Using numerous genomic assays and computational tools we characterized the dynamic changes that take place during neural induction.
The associations between cyberbullying/cyber victimization and emotion attribution to a fictional cyberbully and to a fictional cyber victim in a community sample of preadolescents

The present study was realized starting from research on emotion processes related to moral reasoning in cyberbullying, using a task of emotion attribution (i.e., positive and negative emotions) to a fictional cyberbully and a fictional cyber victim. Specifically, we investigated whether the involvement in cyberbullying or in cyber victimization was associated with differences in the emotion attribution task. 528 middle school students (282 girls, mean age = 12.58 years, DS = 1.16 years) took part in the study. The results of a MANOVA showed that youths perpetrating cyberbullying, compared to non-involved peers, attributed higher positive emotions and lower negative emotions to the fictional cyberbully. Moreover, youths involved in both cyberbullying and cyber victimization (i.e., the so-called cyberbully-victims) compared to pure cyber victims had higher likeability to attribute positive emotions to a fictional cyber victim. The findings were discussed in light of the role of morality and moral disengagement in both traditional bullying and cyberbullying research, expanding the role of emotion attribution beyond moral emotions. Furthermore, the importance of carefully considering cyber victims’ impairments in emotion attribution processes as possible risk factors for the development of a cyberbully-victim condition was advanced.