Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen Use Efficiency and the Genetic Variation of Maize Expired Plant Variety Protection Germplasm

Nitrogen use efficiency (NUE) in maize ( Zea mays L.) is an important trait to optimize yield with minimal input of nitrogen (N) fertilizer. Expired Plant Variety Protection (ex-PVP) Act-certified germplasm may be an important genetic resource for public breeding sectors. The objectives of this research were to evaluate the genetic variation of N-use traits and to characterize maize ex-PVP inbreds that are adapted to the U.S. Corn Belt for NUE performance. Eighty-nine ex-PVP inbreds (36 stiff stalk synthetic (SSS), and 53 non-stiff stalk synthetic (NSSS)) were genotyped using 26,769 single-nucleotide polymorphisms, then 263 single-cross maize hybrids derived from these inbreds were grown in eight environments from 2011 to 2015 at two N fertilizer rates (0 and 252 kg N ha −1 ) and three replications. Genetic utilization of inherent soil nitrogen and the yield response to N fertilizer were stable across environments and were highly correlated with yield under low and high N conditions, respectively. Cluster analysis identified inbreds with desirable NUE performance. However, only one inbred (PHK56) was ranked in the top 10% for yield under both N-stress and high N conditions. Broad-sense heritability across 12 different N-use traits varied from 0.11 to 0.77, but was not associated with breeding value accuracy. Nitrogen-stress tolerance was negatively correlated with the yield increase from N fertilizer.
Preliminary association analysis of microsatellites and Mycobacterium avium subspecies paratuberculosis infection in the native Garfagnina goats

ABSTRACT Paratuberculosis disease occurs with high frequency in many places of the world and it is a chronic infection of ruminants, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to investigate the association between MAP-resistant or MAP-susceptible goats and short tandem repeats (STR) markers. Blood samples were collected from 48 adult goats (27 positive and 21 negative) of the Italian native Garfagnina goat breed from a single flock that had experienced annual mortalities due to MAP infection. Diagnosis was achieved by serological tests and by post-mortem examination of affected animals. To investigate possible genetic influences on susceptibility or resistance of goats to MAP disease, 12 STR markers were used. For each marker, allele and genotypes frequencies between MAP-positive and MAP-negative groups of animals were compared using the chi-square test and Fisher’s exact tests. In this study, two microsatellite loci SRCRSP05 and ETH10 were associated with the disease playing an interesting role in the susceptibility or resistance to the disease. Although the present study should be considered preliminary, our results reveal for the first time that two microsatellite loci were associated with the development of lesions due to MAP in the Garfagnina goat breed.
Advances in Molecular Imaging Strategies in Immune Checkpoint Therapy

Tumor cells avoid being detected and eliminated by the innate immune system, and as a result, are able to proliferate in the body. Immune checkpoint inhibitor therapies eliminate cancer cells by activating immune cells in the body; however, this treatment is not suitable against all cancer types. This reflects a dire need for the development of non-invasive molecular imaging tools in the visualization of immune checkpoints expression, which will then allow practitioners to improve clinical assessments, screen interest groups and provide therapeutic predictions, furthering the development of personalized medicine. Therefore, the analyzing the efficacy of various tracers and the optimization of antibodies have recently become popular topics of research in the field of antibody-based imaging. This review summarizes the current mechanism of immune checkpoint-based treatments, and preclinical studies on immune checkpoint imaging.
Dark butterflies camouflaged from predation in dark tropical forest understories

1. Morphological characteristics, especially coloration, are related to thermoregulation and camouflage, both of which are crucial for species survival and fitness. In cool environments such as the understorey of closed rainforests, darker organisms have thermal advantages and may be able to absorb heat more efficiently. However, such habitats are also suitable for darker organisms with respect to camouflage, making it difficult to elucidate whether the association of dark‐coloured organisms with shady environments is a consequence of thermal stress or predation pressure, or both.
vOX2- a potential immune regulatory protein involved in Kaposi's sarcoma-associated herpesvirus pathogenesis

Kaposi's sarcoma -associated herpesvirus (KSHV), the newest member of the human herpesviruses, was first identified in 1994, and has been shown to be the etiological agent of Kaposi's Sarcoma (KS); a tumour most commonly associated with the onset of AIDS. KSHV is also involved in the development of other malignancies, including Multicentric Castleman's disease (MCD) and primary effusion lymphoma (PEL), both of which are B -cell lymphoproliferative disorders. The study of KSHV, as is the case with other herpesviruses from the Gammaherpesvirinae subfamily, is severely limited due to their species specificity and restricted growth in vitro. This has led to the increasing use of closely related murine gammaherpesviruses as a model system to study gammaherpesvirus pathogenesis. A common feature of the gammaherpesviruses is their incorporation of cellular homologous genes during viral evolution, presumably aiding in viral replication and dissemination. One such gene found in KSHV is vOX2, which has homology with the human OX2 gene (hOX2, also recently termed CD200). There are also homologous genes found in mice (mCD200) and rats (rCD200). This membrane bound protein is expressed on a wide variety of cell types, excluding myeloid derived cells. Recent studies have indicated that CD200 plays an important regulatory role in macrophage and microglia activation, through its interaction with a receptor (CD200R) found to be expressed predominantly on macrophage and microglia. Studies on the viral gene, vOX2, have indicated that this glycoprotein has a similar structure to the human CD200, an immunoglobulin superfamily gene, containing two extracellular domains, a single transmembrane region and a short cytoplasmic tail. In order to investigate the potential role of vOX2 in an in vivo system, a novel murid herpesvirus, murine gammaherpesvirus -76 (MHV -76), was utilised. MHV -76 is a natural deletion mutant of murine gammaherpesvirus -68 (MHV -68), lacking four unique genes and eight viral tRNA -like genes from the left end of the MHV -68 genome. This deletion has provided an opportunity to generate a recombinant MHV -76 virus expressing vOX2 (MHV76 -vOX2) and a selectable
Fast Memory Integration Facilitated by Schema Consistency

Many of our everyday decisions are based not only on memories of direct experiences, but on memories that are integrated across multiple distinct experiences. Sometimes memory integration between existing memories and newly learnt information occurs rapidly, without requiring inference at the time of a decision. Such fast memory integration is known to be supported by the hippocampus but not the neocortex. In this study, we explore an alternative mechanism of fast memory integration, through related prior knowledge (i.e., schema), which is associated with neocortical learning. Paired associates were selected to be schema consistent or inconsistent, and confirmed with a latent semantic analysis of text corpora. We observed that after enabling fast learning by using material that is consistent with a schema, faster memory integration can occur. This result suggests that the hippocampus-mediated integration of new information is not the only available mechanism that supports fast memory integration.
The comparison of two glucose measurement systems: POCT devices versus central laboratory

Abstract Background Glucose meters are used for two purposes: point-of-care testing and the self-monitoring of glucose, both of which are very important in the management of diabetes, hypoglycemia, or hyperglycemia and in therapeutic decisions. Objective The aim of this study was to determine the test reliability of glucose meters and to compare their results with those of the clinical laboratory method. Material and methods Evaluation was made of five different types of glucose meters which are generally used for hospitalized patients. Capillary and venous specimens were obtained concurrently from each patient. The former were analyzed in the glucose meters, and the latter in the laboratory analyzer. Results Of 1837 glucose meters read-outs, 1748 capillary and venous comparisons were evaluated. The majority of the glucose meter measurements were within acceptable limits. The error percentage distribution of glucose meters indicated that the accuracy of glucose meters is higher in the prediabetic/diabetic measurement range than at normo-/hypoglycemic levels. Conclusion In general, the glucose meters and laboratory method were observed to be compatible. However, health care professionals and self-monitoring diabetic patients should be aware of the evaluation of glucose meter results, and should cross-check, as frequently as possible, with laboratory values.
Faculty Opinions recommendation of miR-145 and miR-143 regulate smooth muscle cell fate and plasticity.

, SUMMARY microRNAs are regulators of myriad cellular events, but evidence for a single microRNA that can efficiently differentiate multipotent cells into a specific lineage or regulate direct reprogramming of cells into an alternate cell fate has been elusive. Here, we show that miR-145 and miR-143 are co-transcribed in multipotent cardiac progenitors before becoming localized to smooth muscle cells, including neural crest stem cell–derived vascular smooth muscle cells. miR-145 and miR-143 were direct transcriptional targets of serum response factor, myocardin and Nkx2.5, and were downregulated in injured or atherosclerotic vessels containing proliferating, less differentiated smooth muscle cells. miR-145 was necessary for myocardin-induced reprogramming of adult fibroblasts into smooth muscle cells and sufficient to induce differentiation of multipotent neural crest stem cells into vascular smooth muscle. Furthermore, miR-145 and miR-143 cooperatively targeted a network of transcription factors, including Klf4, myocardin, and Elk-1 to promote differentiation and repress proliferation of smooth muscle cells. These findings demonstrate that miR-145 can direct the smooth muscle fate and that miR-145 and miR-143 function to regulate the quiescent versus proliferative phenotype of smooth muscle cells.
The evolution of genomic anatomy : linkage, expression and rates of evolution.

Many attempts to test selectionist and neutralist models employ estimates of synonymous (Ks) and non-synonymous (Ka) substitution rates of orthologous genes. For example, a stronger Ka-Ks correlation than expected under neutrality has been argued to indicate a role for selection and the absence of a Ks-GC4 correlation has been argued to be inconsistent with neutral models for isochore evolution. However, both of these results, we have shown previously, are sensitive to the method by which Ka and Ks are estimated. Using a maximum likelihood (ML) estimator (GY94) we found a positive correlation between Ks and GC4 and only a weak correlation between Ka and Ks, lower than expected under neutral expectations. This ML method is computationally slow. Recently, a new ad hoc approximation of this ML method has been provided (YNOO). This is effectively an extension of Li’s protocol but that also allows for codon usage bias. This method is computationally near-instantaneous and therefore potentially of great utility for analysis of large datasets. Here we ask whether this method might have such applicability. To this end we ask whether it too recovers the two unusual results. We report that when the ML and earlier ad hoc methods disagree, YNOO recovers the results described by the ML methods, i.e. a positive correlation between GC4 and Ks and only a weak correlation between Ks and Ka. If the ML method can be trusted, then YNOO can also be considered an adequately reliable method for analysis of large datasets. Assuming this to be so we also analyze further the patterns. We show, for example, that the positive correlation between GC4 and Ks is probably in part a mutational bias, there being more methyl induced CpG —* TpG mutations in GC rich regions. As regards the evolution of isochores, it seems inappropriate to use the claimed lack of a correlation between GC and Ks as definitive evidence either against or for any model. If the positive correlation is real then, we argue, this is hard to reconcile with the biased gene conversion model for isochore formation as this predicts a negative correlation. © 2000 Elsevier Science B.V. All rights reserved. Keywords-. Covariation of GC content; Silent site substitution rate; Evolution; Isochores
Effects of Lactarius deliciosus and Rhizopogon roseolus ectomycorrhyzal fungi on seeds and seedlings of Scots and stone pines inoculated with Fusarium oxysporum and Fusarium verticillioides

Two isolates of the edible ectomycorrhizal fungi (ECM), Lactarius deliciosus and Rhizopogon roseolus, were tested against Fusarium oxysporum and F. verticillioides, causal agents of damping-off on seeds and seedlings of Scots pine (Pinus sylvestris) and stone pine (Pinus pinea). The effects of ECM on Fusarium spp. in the rhizosphere of Scots and stone pines were evaluated by: (1) co-inoculating ECM and Fusarium when seeding (seed test) and (2) co-inoculating eight-week-old seedlings (seedling test). The seed tests showed significant reduction of Scots pine seed germination when treated with F. verticillioides, but this effect was absent when co-inoculated with R. roseolus. Higher germination rates were observed in stone pine when F. oxysporum was co-inoculated with L. deliciosus than the pathogen inoculation alone. In the seedling test, Scots and stone pines were not apparently affected by Fusarium spp. No obvious changes in plant growth-related variables were observed in either assay. Root colonization of Scots and stone pine seedlings by R. roseolus was 15.5% and 12% for the seed assay, as well as 21.6% and 11% for the seedling assay. Lactarius deliciosus mycorrhizal roots were found only in Scots pine seedlings (10%). Rhizopogon roseolus and L. deliciosus are two promising fungi for pine seedling protection against Fusarium damping-off at nurseries.
Study and exploitation of diverse soil environments for novel natural product discovery using metagenomic approaches

Natural products with antimicrobial activity have played an important role in the treatment of infection since their discovery. The increasing emergence of pathogens resistant to multiple antibiotics has raised awareness of the urgent need for novel antibiotics. Soil microorganisms are the major source of antibiotics and Actinobacteria in particular have an impressive capacity for production of diverse bioactive secondary metabolites. However, culture-independent studies have shown a greater microbial diversity present in soil with potential for novel chemical structures and these can be explored further using metagenomic approaches capturing genes without the need to cultivate the host. Different metagenomic tools were used to study and explore microbial secondary metabolite diversity in soil. In particular, amplicon sequencing of 16S rRNA gene, NRPS and PKS biosynthetic genes allowed the identification of novel potential phylogenetic drivers of secondary metabolite diversity in the less characterized phyla Verrucomicrobia and Bacteroidetes and potential geographic hotspots harbouring unique biosynthetic diversity such as Antarctica and Cuba. The exploitation of these hotspots presented some bottlenecks in the form of DNA extraction efficiency, library creation, screening and heterologous expression. These were overcome by comparative analysis of different eDNA extraction methods to optimise fragment size and purity combined with development of new cloning tools for both DNA capture and expression. Modification of the microbial community through the amendment of the soil with chitin, highlighted the beneficial effect of microbial enrichment allowing a higher recovery of eDNA and higher detection of the biosynthetic gene of interest related to secondary metabolite production. Further additions were made to the metagenomic molecular toolbox in the form of BAC vectors (pBCaBAC and pBCkBAC) which were tested with suitable heterologous host systems (Streptomyces sp. and the engineered Pseudomonas putida species) potentially facilitating heterologous expression. In conclusion this is the first study to identify the drivers of microbial secondary metabolite diversity in situ and provided a comparative analysis of a range of diverse soil types. This approach paired with new developments in metagenomic technologies will make a substantial contribution to improving the likelihood for discovery and exploitation of new drugs for treating multi-resistant pathogenic bacteria.
Addressing the mycotoxin deoxynivalenol contamination with soil-derived bacterial and enzymatic transformations targeting the C3 carbon

The search for feasible biological means of detoxifying mycotoxins has attained successful accomplishments in the past twenty years due to the involvement of many teams coming from diverse backgrounds and research expertise. The recently witnessed breakthroughs in the field of bacterial genomics (including next-generation sequencing), proteomics, and computational biology helped all in shaping the current understanding of how microorganisms/mycotoxins/environmental factors intertwined and interact together, hence paving the road for some substantial discoveries. This perspective review summarises the advances that were observed in the past two decades within the deoxynivalenol (DON) bio-detoxification field. It highlights the research efforts and progresses that were made in the arena of the aerobic oxidation and epimerization of this mycotoxin at the C3 carbon carried out by multiple Devosia species. Moreover, it sets practical examples and discusses how the recent standing-knowledge of bacterial detoxif.
The coevolution of data and hypotheses in bayesian cultural evolution

Culture is a special evolutionary system that is composed of two types of replicators: public structures in the world, such as artifacts and behaviors, and private structures in the mind, such as brain states or grammars. In this paper, I utilize a mathematical equivalence between replicator dynamics and Bayesian inference to specify a model where cultural artifacts and learners’ hypotheses co-evolve.
Centrality and the shortest path approach on the human interactome

A network is one of the most convenient way to represent interactions between biological entities in systems biology. A network of molecular interactions is a graph in which the vertices are biological component and the edges correspond to the interactions between them. Many notions and approaches for network analysis came to systems biology from the theory of graphs – a field of mathematics that study graphs. We focused on the study of the shortest path approach in this work. We investigated whether this approach yields valid molecular paths. To perform this, the shortest paths in the human interactome (derived from HPRD and HIPPIE databases) were found between all relevant combinations of proteins taken from eight well-studied highly conserved signaling pathways from the KEGG database (NF-kappa B, MAPK, Jak-STAT, mTOR, ErbB, Wnt, TGF-beta and the signaling part of the apoptotic process). Canonical paths were systematically compared with the shortest counterparts and centrality of vertices and paths in subnetworks induced by the shortest paths were analyzed. We found that the sets of the shortest paths contain the canonical counterparts only for very short canonical paths (length 2-3 interactions). We also found that high centrality vertices tend to belong to canonical counterparts, to less extent this can also be said about high centrality paths.
A novel method for estimating LDC levels: total cholesterol and non-HDLC can be used to predict the normal LDLC level in apparently healthy population

Background Triglycerides (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDLC), and low-density lipoprotein cholesterol (LDLC) are usually ordered together to test lipid metabolism in physical examination and clinical application. LDLC is a component of TC and its change is closely correlated to TC. Objective We aim to predict the normal LDLC level by using TG, TC, HDLC and non-HDLC (nonHDLC) in this study. Methods TG, TC, HDLC, and LDLC data were obtained from Laboratory Information System (LIS) based on 4 years (Octo, 1, 2013-Sept, 30, 2017) period health check-up TG, TC, HDLC, and LDLC(direct clearance method) were measured using TBA2000FR biochemical analyzer. The nonHDLC was calculated with TC minus HDLC. Correlation between TG, TC, nonHDLC, and LDLC were analyzed using Spearman’s rank approach. Receiver operating characteristics curve analysis was used to evaluate the predictive of TG, TC and nonHDLC for the normal LDLC level(less than 130mg/dL). Results Both TC(r = 0.870) and nonHDLC (r = 0.893) were significantly positively correlated with LDLC. Area under curve of TC and nonHDLC can be used to predict normal LDLC level. Optimal thresholds were 182.5 mg/dL(4.72 mmol/L) for TC and 135.3 mg/dL(3.50 mmol/L) for nonHDLC. Based on these optimal thresholds, less than 0.5% and 0.4% of tests with elevated LDLC might be missed, but the missing elevated LDLC is not too high(less than 147.3 mg/dL). Conclusion If the nonHDLC is less than 135.3mg/dL(3.50 mmol/L) and/or TC is less than 182.5mg/dL(4.72 mmol/L) for the apparently healthy populations the LDLC level will be less than 130mg/dL(3.36 mmol/L). Total cholesterol and non-HDLC can be used to predict the normal LDLC level in apparently healthy population is a novel method for estimating LDC level.
Constructing and Visualizing Cancer Genomic Maps in 3D Spatial Context by Phenotype-based High-throughput Laser-aided Isolation and Sequencing (PHLI-seq)

A spatially resolved analysis of the heterogeneous cancer genome, in which the data are connected to the three-dimensional space of a tumour, is crucial to understand cancer biology and the clinical impact of cancer heterogeneity on patients. However, despite recent progress in spatially resolved transcriptomics, spatial mapping of genomic data in a high-throughput and high-resolution manner has been challenging due to current technical limitations. Here, we describe a novel approach, phenotype-based high-throughput laser-aided isolation and sequencing (PHLI-seq), which enables high-throughput isolation of a single-cell or a small number of cells and their genome-wide sequence analysis to construct genomic maps within cancer tissue in relation to the phenotypes of the cells. By applying PHLI-seq, we reveal the heterogeneity of breast cancer tissues at a high resolution and map the genomic landscape of the cells to their corresponding spatial locations and phenotypes in the tumour mass. Additionally, with different staining modalities, the genotypes of the cells can be connected to corresponding phenotypic information of the tissue. Together with the spatially resolved genomic analysis, we can infer the histories of heterogeneous cancer cells in two or three dimensions, providing significant insight into cancer biology and precision medicine.