Miracle-dz/UniFAR-FTUs huggingface dataset:
Root Foraging Precision of Pinus pumila (Pall.) Regel Subjected to Contrasting Light Spectra

Root foraging behavior in heterogeneous patterns of soil nutrients is not well understood for undergrowth in alpine forests, where light spectra may generate an interactive effect on root foraging precision. A dwarf alpine species, Pinus pumila (Pall.) Regel. , was cultured in pots where nitrogen (N)–phosphorus (P)–potassium (K) nutritional granules (N–P2O5–K2O, 14–13–13) were added to both halves of an inner space at a rate of 67.5 mg N (homogeneous) or 135 mg N to a random half (heterogeneous). Potted seedlings were subjected to either a green-and-blue light spectrum with a red-to-green light ratio of 4.24 (15.3% red, 64.9% green, and 19.8% blue) or a red-light enriched spectrum (69.4% red, 30.2% green, and 0.4% blue) both at irradiations of 200.43 µmol m−2 s−1. The root foraging precision was assessed by the difference in the fine root morphology or weight between the two halves. The foraging precision was assessed by both fine root length and surface area and was promoted in seedlings subjected to the heterogeneous pattern in the red-light enriched spectrum. Seedlings subjected to the green-and-blue light spectrum showed lower shoot growth, biomass, and root morphology but had higher shoot and root N and P concentrations. The heterogenous pattern resulted in greater seedling growth and fine root morphology as well as N and P concentrations compared to the homogeneous pattern. We conclude that P. pumila has a strong ability to forage nutrients in heterogenous soil nutrients, which can be further promoted by a spectrum with higher red-light proportions.
Bioformulations with Beneficial Microbial Consortia, a Bioactive Compound and Plant Biopolymers Modulate Sweet Basil Productivity, Photosynthetic Activity and Metabolites

Increasing attention is being given to the development of innovative formulations to substitute the use of synthetic chemicals to improve agricultural production and resource use efficiency. Alternatives can include biological products containing beneficial microorganisms and bioactive metabolites able to inhibit plant pathogens, induce systemic resistance and promote plant growth. The efficacy of such bioformulations can be increased by the addition of polymers as adjuvants or carriers. Trichoderma afroharzianum T22, Azotobacter chroococcum 76A and 6-pentyl-α-pyrone (6PP; a Trichoderma secondary metabolite) were administrated singularly or in a consortium, with or without a carboxymethyl cellulose-based biopolymer (BP), and tested on sweet basil (Ocimum basilicum L.) grown in a protected greenhouse. The effect of the treatments on basil yield, photosynthetic activity and secondary metabolites production was assessed. Photosynthetic efficiency was augmented by the applications of the bioformulations. The applications to the rhizosphere with BP + 6PP and BP + T22 + 76A increased the total fresh weight of basil by 26.3% and 23.6%, respectively. Untargeted LC-MS qTOF analysis demonstrated that the plant metabolome was significantly modified by the treatments. Quantification of the profiles for the major phenolic acids indicated that the treatment with the T22 + 76A consortium increased rosmarinic acid content by 110%. The use of innovative bioformulations containing microbes, their metabolites and a biopolymer was found to modulate the cultivation of fresh basil by improving yield and quality, thus providing the opportunity to develop farming systems with minimal impact on the environmental footprint from the agricultural production process.
Clusters of Physical Frailty and Cognitive Impairment and Their Associated Comorbidities in Older Primary Care Patients

(1) Objectives: We aimed to identify clusters of physical frailty and cognitive impairment in a population of older primary care patients and correlate these clusters with their associated comorbidities. (2) Methods: We used a latent class analysis (LCA) as the clustering technique to separate different stages of mild cognitive impairment (MCI) and physical frailty into clusters; the differences were assessed by using a multinomial logistic regression model. (3) Results: Four clusters (latent classes) were identified: (1) highly functional (the mean and SD of the “frailty” test 0.58 ± 0.72 and the Mini-Mental State Examination (MMSE) test 27.42 ± 1.5), (2) cognitive impairment (0.97 ± 0.78 and 21.94 ± 1.95), (3) cognitive frailty (3.48 ± 1.12 and 19.14 ± 2.30), and (4) physical frailty (3.61 ± 0.77 and 24.89 ± 1.81). (4) Discussion: The comorbidity patterns distinguishing the clusters depend on the degree of development of cardiometabolic disorders in combination with advancing age. The physical frailty phenotype is likely to exist separately from the cognitive frailty phenotype and includes common musculoskeletal diseases.
Molecular Characterization of the env Gene of Bovine Leukemia Virus in Cattle from Pakistan with NGS-Based Evidence of Virus Heterogeneity

Characterization of the global genetic diversity of the bovine leukemia virus (BLV) is an ongoing international research effort. Up to now BLV sequences have been classified into eleven distinct genotypes. Although BLV genotyping and molecular analysis of field isolates were reported in many countries, there is no report describing BLV genotypes present in cattle from Pakistan. In this study we examined 27 env gene sequences from BLV-infected cattle coming from four farms located in Khyber Pakhtunkwa, Gilgit Baltisan and Punjab provinces. Phylogenetic analyses revealed the classification of Pakistani sequences into genotypes G1 and G6. The alignment with the FLK-BLV sequence revealed the presence of 45 mutations, namely, seven in genotype G1 and 33 in genotype G6. Five mutations were found in both, G1 and G6 genotypes. Twelve amino acid substitutions were found in the analyzed sequences, of which only one P264S was specific for sequences from Pakistan. Furthermore, a certain degree of nucleotide heterogeneity was identified by NGS. These results highlight the need for further study on the importance of genetic variability of BLV, especially in the context of its pathogenicity and potential effect on serological detection.
Effect of Mineral and Organic Fertilization on desi and kabuli Chickpea (Cicer arietinum L.): Plant Growth and Production, Hydration Properties, Bioactive Compounds, and Antioxidant Activity

Composting is a strategic technology to convert organic waste into environmentally friendly soil improvers, mitigating the pressure on landfills and contributing to sustainability. This research evaluates the effects of different doses of mineral/organic fertilizers on two chickpea types: desi and kabuli. A randomized block design with three replications and six conditions was adopted: non-fertilized control, two mineral fertilizations (M1, M2), and three organic fertilizations (B1, B2, B3). M1 and B1 provided for comparable NPK amounts. Fertilization and variety significantly influenced plant growth and production, and seed hydration. Fertilization had a lower influence on bioactive compounds. The highest seed yields were obtained with M2 (30–40–100 kg ha−1 of N, P2O5, and K2O, respectively. An addition of 40 kg ha−1 of P2O5 (M1) had no effect on seed yield. B1 (10 Mg ha−1 of Bio Vegetal) and M1 led to the same yield, which did not increase using higher doses of green compost. Mineral and organic fertilizations favored hydration and swelling of chickpeas. Desi chickpea showed a significantly higher seed yield but a lower seed weight than kabuli. Organic fertilization, combined with the recovery of peculiar chickpeas, which are more productive and richer in bioactive compounds, promotes a more sustainable food system.
Development of Bacteriophage Virus-Like Particle Vaccines Displaying Conserved Epitopes of Dengue Virus Non-Structural Protein 1

Dengue virus (DENV) is a major global health problem, with over half of the world’s population at risk of infection. Despite over 60 years of efforts, no licensed vaccine suitable for population-based immunization against DENV is available. Here, we describe efforts to engineer epitope-based vaccines against DENV non-structural protein 1 (NS1). NS1 is present in DENV-infected cells as well as secreted into the blood of infected individuals. NS1 causes disruption of endothelial cell barriers, resulting in plasma leakage and hemorrhage. Immunizing against NS1 could elicit antibodies that block NS1 function and also target NS1-infected cells for antibody-dependent cell cytotoxicity. We identified highly conserved regions of NS1 from all four DENV serotypes. We generated synthetic peptides to these regions and chemically conjugated them to bacteriophage Qβ virus-like particles (VLPs). Mice were immunized two times with the candidate vaccines and sera were tested for the presence of antibodies that bound to the cognate peptide, recombinant NS1 from all four DENV serotypes, and DENV-2-infected cells. We found that two of the candidate vaccines elicited antibodies that bound to recombinant NS1, and one candidate vaccine elicited antibodies that bound to DENV-infected cells. These results show that an epitope-specific vaccine against conserved regions of NS1 could be a promising approach for DENV vaccines or therapeutics to bind circulating NS1 protein.
Longitudinal Change of Mental Health among Active Social Media Users in China during the COVID-19 Outbreak

During the COVID-19 pandemic, every day, updated case numbers and the lasting time of the pandemic became major concerns of people. We collected the online data (28 January to 7 March 2020 during the COVID-19 outbreak) of 16,453 social media users living in mainland China. Computerized machine learning models were developed to estimate their daily scores of the nine dimensions of the Symptom Checklist—90 (SCL-90). Repeated measures analysis of variance (ANOVA) was used to compare the SCL-90 dimension scores between Wuhan and non-Wuhan residents. Fixed effect models were used to analyze the relation of the estimated SCL-90 scores with the daily reported cumulative case numbers and lasting time of the epidemic among Wuhan and non-Wuhan users. In non-Wuhan users, the estimated scores for all the SCL-90 dimensions significantly increased with the lasting time of the epidemic and the accumulation of cases, except for the interpersonal sensitivity dimension. In Wuhan users, although the estimated scores for all nine SCL-90 dimensions significantly increased with the cumulative case numbers, the magnitude of the changes was generally smaller than that in non-Wuhan users. The mental health of Chinese Weibo users was affected by the daily updated information on case numbers and the lasting time of the COVID-19 outbreak.
The Discharge of Pulverized Coal from a Pressurized Aerated Hopper

An aerated discharge system was established in this paper to investigate the discharge of pulverized coal from a pressurized aerated hopper. Two opposite effects of aerated gas on solid were first revealed. “Fluidized pressurization”, which effectively fluidized the solid and improved the subsequent hopper discharge, was then developed. The effect of hopper pressure on the discharge of pulverized coal was studied. Our experimental results showed that the gas volumetric flow rate increased and the gas superficial velocity decreased with the increase of the hopper pressure in the range of 0–1800 kPa. It was confirmed that more energy was needed; the uncertainty and instability was increased to discharge pulverized coal at higher pressures. Gas momentum flux was defined and used to describe the effect of aeration. The optimum gas momentum flux, which was independent of the hopper pressure, was obtained on the basis of the experimental data. The optimum gas volumetric flow rates and the optimum gas superficia.
A Precision Medicine Approach to Optimize Modulator Therapy for Rare CFTR Folding Mutants

Trikafta, a triple-combination drug, consisting of folding correctors VX-661 (tezacaftor), VX-445 (elexacaftor) and the gating potentiator VX-770 (ivacaftor) provided unprecedented clinical benefits for patients with the most common cystic fibrosis (CF) mutation, F508del. Trikafta indications were recently expanded to additional 177 mutations in the CF transmembrane conductance regulator (CFTR). To minimize life-long pharmacological and financial burden of drug administration, if possible, we determined the necessary and sufficient modulator combination that can achieve maximal benefit in preclinical setting for selected mutants. To this end, the biochemical and functional rescue of single corrector-responsive rare mutants were investigated in a bronchial epithelial cell line and patient-derived human primary nasal epithelia (HNE), respectively. The plasma membrane density of P67L-, L206W- or S549R-CFTR corrected by VX-661 or other type I correctors was moderately increased by VX-445. Short-circuit current measurements of HNE, however, uncovered that correction comparable to Trikafta was achieved for S549R-CFTR by VX-661 + VX-770 and for P67L- and L206W-CFTR by the VX-661 + VX-445 combination. Thus, introduction of a third modulator may not provide additional benefit for patients with a subset of rare CFTR missense mutations. These results also underscore that HNE, as a precision medicine model, enable the optimization of mutation-specific modulator combinations to maximize their efficacy and minimize life-long drug exposure of CF patients.
STAT-1 Knockout Mice as a Model for Wild-Type Sudan Virus (SUDV)

Currently there is no FDA-licensed vaccine or therapeutic against Sudan ebolavirus (SUDV) infections. The largest ever reported 2014–2016 West Africa outbreak, as well as the 2021 outbreak in the Democratic Republic of Congo, highlight the critical need for countermeasures against filovirus infections. A well-characterized small animal model that is susceptible to wild-type filoviruses would greatly add to the screening of antivirals and vaccines. Here, we infected signal transducer and activator of transcription-1 knock out (STAT-1 KO) mice with five different wildtype filoviruses to determine susceptibility. SUDV and Marburg virus (MARV) were the most virulent, and caused 100% or 80% lethality, respectively. Zaire ebolavirus (EBOV), Bundibugyo ebolavirus (BDBV), and Taï Forest ebolavirus (TAFV) caused 40%, 20%, and no mortality, respectively. Further characterization of SUDV in STAT-1 KO mice demonstrated lethality down to 3.1 × 101 pfu. Viral genomic material was detectable in serum as early as 1 to 2 days post-challenge. The onset of viremia was closely followed by significant changes in total white blood cells and proportion of neutrophils and lymphocytes, as well as by an influx of neutrophils in the liver and spleen. Concomitant significant fluctuations in blood glucose, albumin, globulin, and alanine aminotransferase were also noted, altogether consistent with other models of filovirus infection. Finally, favipiravir treatment fully protected STAT-1 KO mice from lethal SUDV challenge, suggesting that this may be an appropriate small animal model to screen anti-SUDV countermeasures.
Vitamin Intake and Loss of Muscle Mass in Older People with Type 2 Diabetes: A Prospective Study of the KAMOGAWA-DM Cohort

The aim of this prospective cohort study was to examine the relationships between the intakes of various vitamins and the loss of muscle mass in older people with type 2 diabetes (T2DM). The change in skeletal muscle mass index (SMI, kg/m2) (kg/m2/year) was defined as follows: (SMI at baseline (kg/m2) − SMI at follow-up (kg/m2))/follow-up period (year). The rate of SMI reduction (%) was calculated as follows (the change in SMI (kg/m2/year)/SMI at baseline (kg/m2)) × 100. The rate of SMI reduction ≥ 1.2% was considered as the loss of muscle mass. Among 197 people with T2DM, 47.2% of them experienced the loss of muscle mass at the 13.7 ± 5.2 month follow-up. Vitamin B1 (0.8 ± 0.3 vs. 0.8 ± 0.3 mg/day, p = 0.031), vitamin B12 (11.2 ± 8.3 vs. 13.4 ± 7.5 μg/day, p = 0.049), and vitamin D (16.5 ± 12.2 vs. 21.6 ± 13.0 μg/day, p = 0.004) intakes in people with the loss of muscle mass were significantly lower than those without. Vitamin D intake was related to the loss of muscle mass after adjusting for sex, age, exercise, alcohol, smoking, body mass index, SMI, glucagon-like peptide-1 agonist, sodium glucose cotransporter-2 inhibitor, insulin, HbA1c, creatinine, energy intake, and protein intake (adjusted odds ratio 0.93, 95% confidence interval: 0.88–0.97, p = 0.003). This study showed that vitamin D intake was related to the loss of muscle mass in older people with T2DM. Vitamin B12 intake tended to be related to the loss of muscle mass, although vitamin A, vitamin B2, vitamin B6, vitamin C, and vitamin E intake were not related.
The Role of MSC in Wound Healing, Scarring and Regeneration

Tissue repair and regeneration after damage is not completely understood, and current therapies to support this process are limited. The wound healing process is associated with cell migration and proliferation, extracellular matrix remodeling, angiogenesis and re-epithelialization. In normal conditions, a wound will lead to healing, resulting in reparation of the tissue. Several risk factors, chronic inflammation, and some diseases lead to a deficient wound closure, producing a scar that can finish with a pathological fibrosis. Mesenchymal stem/stromal cells (MSCs) are widely used for their regenerative capacity and their possible therapeutically potential. Derived products of MSCs, such as exosomes or extravesicles, have shown a therapeutic potential similar to MSCs, and these cell-free products may be interesting in clinics. MSCs or their derivative products have shown paracrine beneficial effects, regulating inflammation, modifying the fibroblast activation and production of collagen and promoting neovascularization and re-epithelialization. This review describes the effects of MSCs and their derived products in each step of the wound repair process. As well, it reviews the pre-clinical and clinical use of MSCs to benefit in skin wound healing in diabetic associated wounds and in pathophysiological fibrosis.
Review on Perioperative and Oncological Outcomes of Robotic Gastrectomy for Cancer

Background. Minimally invasive gastrectomy is currently considered a valid option to treat gastric cancer and is gaining increasing acceptance. Recent reports have suggested that the application of robots may confer some advantages over conventional laparoscopy, but the role of robotic surgery in clinical practice is still uncertain. We aimed to critically review the relevant evidence comparing robotic to standard laparoscopic surgery in performing radical gastrectomy. Methods. The Pubmed/Medline electronic databases were searched through February 2021. Paper conference and the English language was the only restriction applied to our search strategy. Results. According to the existing data, robotic gastrectomy seems to provide some benefits in terms of blood loss, rate of conversion, procedure-specific postoperative morbidity, and length of hospital stay. Robotic gastrectomy is also associated with a longer duration of surgery and a higher economic burden as compared to its laparoscopic counterpart. No significant differences have been disclosed in terms of long-term survivals, while the number of lymph nodes retrieved with robotic gastrectomy is generally higher than that of laparoscopy. Conclusions. The current literature suggests that robotic radical gastrectomy appears as competent as the conventional laparoscopic procedure and may provide some clinical advantages. However, due to the relative paucity of high-level evidence, it is not possible to draw definitive conclusions.
Limited Association between Schizophrenia Genetic Risk Factors and Transcriptomic Features

Schizophrenia is a polygenic disorder with many genomic regions contributing to schizophrenia risk. The majority of genetic variants associated with schizophrenia lie in the non-coding genome and are thought to contribute to transcriptional regulation. Extensive transcriptomic dysregulation has been detected from postmortem brain samples of schizophrenia-affected individuals. However, the relationship between schizophrenia genetic risk factors and transcriptomic features has yet to be explored. Herein, we examined whether varying gene expression features, including differentially expressed genes (DEGs), co-expression networks, and central hubness of genes, contribute to the heritability of schizophrenia. We leveraged quantitative trait loci and chromatin interaction profiles to identify schizophrenia risk variants assigned to the genes that represent different transcriptomic features. We then performed stratified linkage disequilibrium score regression analysis on these variants to estimate schizophrenia heritability enrichment for different gene expression features. Notably, DEGs and co-expression networks showed nominal heritability enrichment. This nominal association can be partly explained by cellular heterogeneity, as DEGs were associated with the genetic risk of schizophrenia in a cell type-specific manner. Moreover, DEGs were enriched for target genes of schizophrenia-associated transcription factors, suggesting that the transcriptomic signatures of schizophrenia are the result of transcriptional regulatory cascades elicited by genetic risk factors.
Mining of Leaf Rust Resistance Genes Content in Egyptian Bread Wheat Collection

Wheat is a major nutritional cereal crop that has economic and strategic value worldwide. The sustainability of this extraordinary crop is facing critical challenges globally, particularly leaf rust disease, which causes endless problems for wheat farmers and countries and negatively affects humanity’s food security. Developing effective marker-assisted selection programs for leaf rust resistance in wheat mainly depends on the availability of deep mining of resistance genes within the germplasm collections. This is the first study that evaluated the leaf rust resistance of 50 Egyptian wheat varieties at the adult plant stage for two successive seasons and identified the absence/presence of 28 leaf rust resistance (Lr) genes within the studied wheat collection. The field evaluation results indicated that most of these varieties demonstrated high to moderate leaf rust resistance levels except Gemmeiza 1, Gemmeiza 9, Giza162, Giza 163, Giza 164, Giza 165, Sids 1, Sids 2, Sids 3, Sakha 62, Sakha 69, Sohag 3 and Bany Swif 4, which showed fast rusting behavior. On the other hand, out of these 28 Lr genes tested against the wheat collection, 21 Lr genes were successfully identified. Out of 15 Lr genes reported conferring the adult plant resistant or slow rusting behavior in wheat, only five genes (Lr13, Lr22a, Lr34, Lr37, and Lr67) were detected within the Egyptian collection. Remarkedly, the genes Lr13, Lr19, Lr20, Lr22a, Lr28, Lr29, Lr32, Lr34, Lr36, Lr47, and Lr60, were found to be the most predominant Lr genes across the 50 Egyptian wheat varieties. The molecular phylogeny results also inferred the same classification of field evaluation, through grouping genotypes characterized by high to moderate leaf rust resistance in one cluster while being highly susceptible in a separate cluster, with few exceptions.