Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multiple Peptides Vaccine against nCOVID-19 Designed from the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics Approach

Due to the current COVID-19 pandemic, the rapid discovery of a safe and effective vaccine is an essential issue, consequently, this study aims to predict potential COVID-19 peptide-based vaccine utilizing the Nucleocapsid phosphoprotein (N) and Spike Glycoprotein (S) via the Immunoinformatics approach. To achieve this goal, several Immune Epitope Database (IEDB) tools, molecular docking, and safety prediction servers were used. According to the results, The Spike peptide peptides SQCVNLTTRTQLPPAYTNSFTRGVY is predicted to have the highest binding affinity to the B-Cells. The Spike peptide FTISVTTEI has the highest binding affinity to the MHC I HLA-B1503 allele. The Nucleocapsid peptides KTFPPTEPK and RWYFYYLGTGPEAGL have the highest binding affinity to the MHC I HLA-A0202 allele and the three MHC II alleles HLA-DPA1*01:03/DPB1*02:01, HLA-DQA1*01:02/DQB1- *06:02, HLA-DRB1, respectively. Furthermore, those peptides were predicted as non-toxic and non-allergen. Therefore, the combination of those peptides is predicted to stimulate better immunological responses with respectable safety.
Genomic Methods Identify Homologous Recombination Deficiency in Pancreas Adenocarcinoma and Optimize Treatment Selection

Purpose: Genomic methods can identify homologous recombination deficiency (HRD). Rigorous evaluation of their outcome association to DNA damage response–targeted therapies like platinum in pancreatic ductal adenocarcinoma (PDAC) is essential in maximizing therapeutic outcome. Experimental Design: We evaluated progression-free survival (PFS) and overall survival (OS) of patients with advanced-stage PDAC, who had both germline- and somatic-targeted gene sequencing. Homologous recombination gene mutations (HRm) were evaluated: BRCA1, BRCA2, PALB2, ATM, BAP1, BARD1, BLM, BRIP1, CHEK2, FAM175A, FANCA, FANCC, NBN, RAD50, RAD51, RAD51C, and RTEL1 HRm status was grouped as: (i) germline versus somatic; (ii) core (BRCAs and PALB2) versus non-core (other HRm); and (iii) monoallelic versus biallelic. Genomic instability was compared using large-scale state transition, signature 3, and tumor mutation burden. Results: Among 262 patients, 50 (19%) had HRD (15% germline and 4% somatic). Both groups were analyzed together due to lack of difference in their genomic instability and outcome. Median [95% confidence interval (CI)] follow-up was 21.9 (1.4–57.0) months. Median OS and PFS were 15.5 (14.6–19) and 7 (6.1–8.1) months, respectively. Patients with HRD had improved PFS compared with no HRD when treated with first-line (1L) platinum [HR, 0.44 (95% CI: 0.29–0.67); P < 0.01], but not with 1L-non-platinum. Multivariate analysis showed HRD patients had improved OS regardless of their first-line treatment, but most had platinum exposure during their course. Biallelic HRm (11%) and core HRm (12%) had higher genomic instability, which translated to improved PFS on first-line platinum (1L-platinum) versus 1L-non-platinum. Conclusions: Pathogenic HRm identifies HRD in patients with PDAC with the best outcome when treated with 1L-platinum. Biallelic HRm and core HRm further enriched benefit from 1L-platinum from HRD.
Molecular diversity and genetic structure of Saccharum complex accessions

Sugarcane is an important crop for food and energy security, providing sucrose and bioethanol from sugar content and bioelectricity from lignocellulosic bagasse. In order to evaluate the diversity and genetic structure of the Brazilian Panel of Sugarcane Genotypes (BPSG), a core collection composed by 254 accessions of the Saccharum complex, eight TRAP markers anchored in sucrose and lignin metabolism genes were evaluated. A total of 584 polymorphic fragments were identified and used to investigate the genetic structure of BPSG through analysis of molecular variance (AMOVA), principal components analysis (PCA), a Bayesian method using STRUCTURE software, genetic dissimilarity and phylogenetic tree. AMOVA showed a moderate genetic differentiation between ancestors and improved accessions, 0.14, and the molecular variance was higher within populations than among populations, with values of 86%, 95% and 97% when constrasting improved with ancestors, foreign with ancestors and improved with foreign, respectively. The PCA approach suggests clustering in according with evolutionary and Brazilian breeding sugarcane history, since improved accessions from older generations were positioned closer to ancestors than improved accessions from recent generations. This result was also confirmed by STRUCTURE analysis and phylogenetic tree. The Bayesian method was able to separate ancestors of the improved accessions while the phylogenetic tree showed clusters considering the family relatedness within three major clades; the first being composed mainly by ancestors and the other two mainly by improved accessions. This work can contribute to better management of the crosses considering functional regions of the sugarcane genome.
Comparative investigation of the late embryogenesis of Leptodora kindtii (Focke, 1844) (Crustacea: Branchiopoda), with notes on types of embryonic development and larvae in Cladocera

The embryonic development of the parthenogenetic eggs of Leptodora kindtii has been investigated by observing living embryos removed from the female brood pouch. The sequence of morphological changes was analysed, as was the time at which the activity of certain organs began. The timing of these events at 20–22°C is documented. These data were compared with similar information obtained for some representatives of Ctenopoda and Anomopoda. The sequence of appearance of rudiments of organs on the ventral side of the embryos is similar in all these groups but the timing of shedding of the embryonic membranes differs. Hatching from the inner egg membranes takes place at the late metanauplius stage in Leptodora as in Ctenopoda and Cyclestherida, while in Anomopoda this stage is embryonized. The development of Leptodora is more like that of Ctenopoda than of Anomopoda. The embryos of all the above‐mentioned groups begin to grow at approximately the same morphological stage. A new scheme for the periodization of the embryogenesis of L. kindtii is proposed, which includes four well‐separated stages. Previously, the same number of developmental stages has been reported for Ctenopoda and Anomopoda. In Leptodora, as well as in Ctenopoda, the first two of these occur within the egg membranes. Cyclestheria has at least one embryonic moult and one embryonic stage more than Leptodora and other cladocerans. Embryonic stages 3 and 4 of the parthenogenetic eggs of L. kindtii represent a peculiar type of secondary larvae developing inside the female's brood pouch. The appearance of a free‐living nauplius in L. kindtii arises from its mode of hatching from the gamogenetic egg.
Nutrient sensing pathways regulating adult reproductive diapause in C. elegans

Genetic and environmental manipulations, such as dietary restriction (DR), can improve both health span and lifespan in a wide range of organisms, including humans. Changes in nutrient intake trigger often overlapping metabolic pathways that can generate distinct or even opposite outputs depending on several factors, such as when DR occurs in the lifecycle of the organism or the nature of the changes in nutrients. Due to the complexity of metabolic pathways and the diversity in outputs, the underlying mechanisms regulating diet-associated pro-longevity are not yet well understood. Adult reproductive diapause (ARD) in the model organism Caenorhabditis elegans is a DR model that is associated with lengthened lifespan and reproductive potential (Angelo and Van Gilst 2009). As the metabolic pathways regulating ARD have not yet been explored in depth, we performed a candidate-based genetic screen analyzing select nutrient-sensing pathways to determine their contribution to the regulation of ARD. Focusing on the three phases of ARD (initiation, maintenance, and recovery), we find that ARD initiation is regulated by fatty acid metabolism, sirtuins, AMPK, and the O-linked N-acetyl glucosamine (O-GlcNAc) pathway. Although ARD maintenance was not significantly influenced by the nutrient sensors in our screen, we found that ARD recovery was modulated by energy sensing, stress response, insulin-like signaling, and the TOR pathway. We also discovered that fatty acid β-oxidation regulates ARD initiation through a pathway involving the O-GlcNAc cycling enzyme, OGT-1, acting with the nuclear hormone receptor NHR-49. Consistent with these findings, our analysis revealed a change in levels of neutral lipids associated with ARD entry defects. Our findings thus identify novel conserved genetic pathways required for ARD entry and recovery and identify new genetic interactions that provide insight into the role of OGT and OGA.
Are Community Gardening and Horticultural Interventions Beneficial for Psychosocial Well-Being? A Meta-Analysis

Recent literature has revealed the positive effect of gardening on human health; however, empirical evidence on the effects of gardening-based programs on psychosocial well-being is scant. This meta-analysis aims to examine the scientific literature on the effect of community gardening or horticultural interventions on a variety of outcomes related to psychosocial well-being, such as social cohesion, networking, social support, and trust. From 383 bibliographic records retrieved (from 1975 to 2019), seven studies with a total of 22 effect sizes were selected on the basis of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Meta-analytic findings on 11 comparisons indicate a positive and moderate effect of horticultural or gardening interventions on psychosocial well-being. Moderation analysis shows a greater effect size in individualistic than collectivistic cultures. A greater effect size was also observed in studies involving community gardening compared to horticultural intervention. Nevertheless, an effect of publication bias and study heterogeneity has been detected. Despite the presence of a large number of qualitative studies on the effect of horticulture/gardening on psychosocial well-being, quantitative studies are lacking. There is a strong need to advance into further high-quality studies on this research topic given that gardening has promising applied implications for human health, the community, and sustainable city management.
Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains however poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on SNP Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 SSRs using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.
Relationship between Performance on the Mini-Mental State Examination Sub-Items and Activities of Daily Living in Patients with Alzheimer’s Disease

Mini-mental state examination (MMSE) subitems provide useful information about the cognitive status of patients with Alzheimer’s disease (AD). If the relationship between MMSE subitems and activities of daily living (ADL) can be shown, the performance of sub-items can predict ADL status and may provide useful information for early ADL intervention. Therefore, the purpose of this study was to investigate the relationship between MMSE subitem scores and ADL. The study sample consisted of 718 patients with AD. Logistic regression analysis using the Physical Self-maintenance Scale (PSMS) and Lawton’s Instrumental ADL (L-IADL) was performed with each of the subitems as the dependent variables and the MMSE subitem as the independent variable. As a result, the subitems of MMSE, which are strongly related to each item in PSMS differed (e.g., toilet: registration odds ratio 3.00, grooming: naming 3.66). In the case of L-IADL, most items were strongly associated with “writing” (e.g., shopping: odds ratio 4.29, laundry 3.83). In clinical practice, we often focus only on the total MMSE score in patients with AD. However, the relationship between each MMSE subitem and ADL suggested in this study may be useful information that can be linked to ADL care from the performance of the MMSE subitem.
Effect of Replacing a Soy Diet with Vicia Faba and Pisum Sativum on Performance, Meat and Fat Traits of Cinta Senese Pigs

The aim of this study was to investigate the effect of diets containing genetically modified organism-free legumes as a replacement of soybean on the basis of performance, carcass composition and quality of local pig meat (Cinta Senese). Twenty-four Cinta Senese barrows were divided into 3 dietary groups and were each fed with a diet containing different protein sources: soybean meal (SOY), Vicia faba (FABA) and Pisum sativum (PEA) (8 pigs for each group). The diets were isonitrogenous and isocaloric and contained approximately 14.5% crude protein and 14.8 MJ/kg of digestible energy (on dry matter). Each group was reared outdoors in a paddock of 3500 m2. In vivo performances were not different among groups. At slaughter, differences in subcutaneous fat thickness appeared only in the outer layer, at the last thoracic vertebra level, which was lowest in the PEA group. No differences were found in the sample joint composition. With regard to the chemico-physical traits of meat and fat, the FABA group had the highest values of redness in lean and backfat, while the PEA group showed higher moisture and lower fat content in meat compared to the SOY group. Differences in the fatty acid profile of backfat were found only for the C16:1 percentage that was higher in FABA than SOY pigs. In conclusion, Vicia faba and Pisum sativum could be a good alternative to soybean in the growing-fattening of Cinta Senese pigs.
Bacillus amyloliquefaciens RWL-1 as a New Potential Strain for Augmenting Biochemical and Nutritional Composition of Fermented Soybean

Soybean (Glycine max L.) is a good source of natural antioxidants and commonly consumed as fermented products such as cheonggukjang, miso, tempeh, and sufu in Asian countries. The aim of the current study was to examine the influence of novel endophytic bacterial strain, Bacillus amyloliquefaciens RWL-1 as a starter for soybean fermentation. During fermentation, the cooked soybeans were inoculated with different concentrations (1%, 3%, and 5%) of B. amyloliquefaciens RWL-1. The changes in 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging activities, total phenolic contents, isoflavones (Daidzin, Genistin, Glycitin, Daidzein, Glycitein, and Genistein), amino acids (aspartic acid, threonine, serine, glutamic acid, glycine, alanine, cysteine, valine, methionine, isoleucine, leucine, tyrosine, phenylalanine, lysine, histidine, arginine, and proline) composition, and minerals (calcium, copper, iron, potassium, magnesium, manganese, sodium, nickel, lead, arsenic, and zinc) were investigated. The level of antioxidants, total phenolic contents, isoflavones, and total amino acids were higher in fermented soybean inoculated with 1% B. amyloliquefaciens RWL-1 after 60 h of fermentation as compared to control, 3% and 5% B. amyloliquefaciens RWL-1. Additionally, fermented soybean inoculated with 5% B. amyloliquefaciens RWL-1 showed the highest values for mineral contents. Changes in antioxidant activities and bioactive compounds depended on the concentration of the strain used for fermentation. From these results, we conclude that fermented soybean has strong antioxidant activity, probably due to its increased total phenolic contents and aglycone isoflavone that resulted from fermentation. Such natural antioxidants could be used in drug and food industries and can be considered to alleviate oxidative stress.
Consensus multiplex PCR–restriction fragment length polymorphism (RFLP) for rapid detection of plant mitochondrial DNA polymorphism

A fast, simple, and efficient approach, termed consensus multiplex PCR–RFLP, was developed and employed to detect mitochondrial (mt)DNA variation in three orchid species, Spiranthes hongkongensis, S. sinensis, and S. spiralis. Using multiplex PCR, three pairs of consensus mitchondrial primers were added simultaneously into each reaction tube to amplify three nonoverlapping introns located in the NADH dehydrogenase genes. Fragment length differences in the multiplex PCR amplicons were directly detectable between S. spiralis and the other two species. Further restriction analysis of the multiplex PCR amplicons revealed sufficient mtDNA polymorphism, suitable for phylogenetic studies at the interspecific level. This approach is well suited for large‐scale population surveys of mitochondrial genome diversity in plants. Additionally, the maternal mode of inheritance of organelle genomes renders this approach valuable for rapid identification of the origin and specific parentage of hybrid or allopolyploid species.
Ectomycorrhizal fungi in New Zealand: Current perspectives and future directions

Abstract The occurrence and host plant associations of ectomycorrhizal (ECM) fungi in New Zealand are reviewed. Seventy‐six genera of fungi thought to be ECM are recorded as associated with plants in New Zealand, including 1 zygomycete, 11 ascomycete, and 64 basidiomycete genera. Forty‐two genera are recorded in association with Nothofagus spp. , Leptospermum scoparium, and/or Kunzea eri‐coides. Ten genera are recorded in association only with introduced tree species (Pinus radiata, Pseu‐dotsuga menziesii, and others) and 24 genera are associated with either native or introduced species. Generally, ECM fungal species have either native or introduced trees as hosts, but exceptions exist. In particular, Amanita muscaria is a potential unas‐sessed threat to native ECM fungal communities. We review invasive ECM fungi and their roles in facilitating the invasion of introduced trees.
Effect of thyroxine and thiourea on liver and muscle energy stores in the freshwater catfish, Heteropneustes fossillis

The hepato-somatic index (HSI) and the lipid, glycogen and protein contents of liver and muscle were studied in Heteropneustes fossilis in response to various doses of thyroxine, thiourea, and thyroxine in combination with thiourea. These treatments did not change the HSI of H. fossilis. A low dose (5 yg/fish) of thyroxine had no effect on the lipid content of liver and muscle or on the glycogen content of liver, but it increased liver and muscle protein contents significantly. Mid (10 p.g/fish) and high (50 yg/fish) doses of thyroxine decreased the lipid and glycogen levels of the liver and the lipid content of muscle whereas the same doses did not alter liver and muscle proteins. All the tested doses of thyroxine, thiourea, and thyroxine in combination with thiourea did not affect the glycogen level of muscle. This experiment showed that thiourea treatment failed to alter the lipid and glycogen levels of tissues, but was very effective in depleting the protein content of liver and muscle. The influence of thyroxine in combination with thiourea on the lipid and glycogen content of liver and on muscle lipid was similar to that of thyroxine alone. Only a low dose of thyroxine with thiourea restored liver protein level. A high dose of thyroxine with thiourea did not check the decline of liver protein. Thiourea blockade in muscle was
Estimation of the position effect and action mode of a semi-lethal factor locus on a DNA polymorphism linkage map in silkworm, Bombyx mori

Distorted segregation has been repeatedly observed in molecular marker linkage mapping of various plants and animals where distant crosses were made. It may be caused by a semi-lethal factor acting in the filial generations. Although general methods have been developed to find semi-lethal factors, so far no method is available to estimate semi-lethal factors in the organisms, for example Bombyx mori and Drosophila melanogaster, in which no crossing-over occurs in meiosis in either of the sexes. In this report, a method is presented for estimating the recombination values between a semi-lethal factor locus and neighboring dominant molecular markers, e.g. RAPDs and AFLPs, and the relative viability of gametes or zygotes affected by the semi-lethal factor in an F2 population for such species by using the maximum likelihood method associated with the expectation maximization (EM) algorithm. Five selection models of gamete or zygote were considered, and the most likely one was determined by goodness of fit of the observed counts of phenotypes to the expected ones under the models. The method was applied to segregation data of RAPD markers of an F2 population with 101 individuals developed from the `C108' × `p50' cross in silkworm, B. mori. The presence of two semi-lethal factor loci (L 1 and L2) located on the linkage groups 22a and 27b causing partial selection was suggested. The semi-lethal factors L1 and L2 were theoretically predicted to affect viability of male gametes and zygotes, respectively.