Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Characterization and Phylogenetic Analysis of Some Agaricomycetes (Mushroom) Fungi from Kogi State, Central Nigeria

The diversity and distribution of mushroom-forming fungi of the three senatorial zones of Kogi state was studied. A multi-stage sampling technique was used to assess twelve randomly selected plots mapped out across the study area during the rainy and early dry seasons of 2014, 2015 and 2016. Identification of selected mushrooms was done through morphological and molecular characterization. Fungi description was initially based on morphometric characters. For the molecular characterization, rDNA was used in a micro satellite PCR technique using ITS1 and ITS4. Forty wild mushrooms were amplified using genomic DNA isolated from their mycelial culture. The amplified products revealed 450 to 650 base pairs. The molecular data obtained from Randomly Amplified Polymorphic DNA (RAPD) using microsatellite DNA amplification techniques characterized a total forty wild mushrooms species most of which had 99% similarity with other mushrooms when subjected to blasting. -----------------------------------------------------------------------* Corresponding author. International Journal of Sciences: Basic and Applied Research (IJSBAR) (2017) Volume 35, No 2, pp 276-292 277 Mushroom sample 14S (Trametes sp) matched 100% Trametes polyzona ascension number JN848329.1 while 2S, S8, 22S, 20S, S3 and S6 mushroom samples have 99% percentage similarities with Daldinia eschscholtzii (KP012909.1), Leiotrametes flavida (KC589131.1), Lentinus squarrosulus (JQ428823.1 1), Lentinus sp. (JQ428823.1 2), Auricularia polytricha (FJ617296.1) and Tricholoma matsutake (MF037408.1) respectively. Furthermore, the result of the molecular analysis and phylogenetic relationship revealed that two (2) new species of mushrooms, never reported were been identified.
Investigating pericyte progenitor cells in glioma angiogenesis and postnatal brain development

The current study established that a transgenic mouse model, Nes-CreERT2 Tdtomato, is of use to trace the fate of nestin-expressing cells in glioma progression and postnatal brain development. Through a series of cell type identification tests, using immunofluorescence labelling and confocal microscopy, it was shown that these nestin-positive cells generate new pericytes, but initially do not have a pericyte identity, this is corroborated by the following findings: (1) In the Nes-CreERT2 Tdtomato mouse model, the number of traced cells (RFP positive cells) increased during the intracranial tumor growth. At an early time point (7 days) few of the RFP positive cells co-localized with pericyte markers while at a later time point (21 days) most of the RFP positive cells co-localized with pericyte markers, which indicated that the new pericytes in glioma derived from the pericyte progenitor cells (defined as RFP positive and pericyte marker negative cells) in the Nes-CreERT2 Tdtomato mouse model; (2) In the JnesCreERT2 Tdtomato mouse model, the traced cells were found to express astrocyte-markers like GFAP but not pericyte markers, which indicated that the traced cells in the JnesCreERT2 Tdtomato mouse model were originally neural stem cells rather than pericyte progenitor cells. Hence, only the Nes-CreERT2 Tdtomato mouse model is useful to study pericyte development in the brain. (3) The cells traced with the NesCreERT2-tdTomato mouse model over a postnatal period develop into pericytes in the brain, which indicates that the NesCreERT2-tdTomato strain is a useful model to trace the pericyte lineage both in pathological neoangiogenesis during glioma growth and in physiological postnatal angiogenesis. (4) In this study RFP-expressing pericyte marker positive cells were detected in the postnatal mouse retina, indicating that RFP-traced pericytes play an important role in both pathological angiogenesis and physiological vascular development of retina.
Convergent Evolution of a Eusuchian-Type Secondary Palate within Shartegosuchidae

ABSTRACT Shartegosuchids are a poorly known, early-branching group of Asian and North American crocodylomorphs. Shartegosuchids have been hypothesized to have eusuchian-type secondary palates, but a paucity of described material makes assessing this difficult. Our fieldwork in western Mongolia recovered cranial material of a new Shartegosuchus specimen from the Ulan Malgait Formation, which we CT-scanned and digitally reconstructed to investigate its palatal morphology. We then incorporated this new anatomical information into a revised phylogenetic dataset to assess its affinities. Our study confirms that Shartegosuchus has a posteriorly placed choana that is fully enclosed by the pterygoids, but differs from Eusuchia in possessing a secondary palatal fenestra and reduced palatine bones. Shartegosuchus, together with Adzhosuchus, Fruitachampsa, and Nominosuchus, forms the monophyletic group Shartegosuchidae. Shartegosuchidae is nested within a larger clade Shartegosuchoidea, and this clade is an earlier-diverging lineage than Eusuchia, showing that a eusuchian-type secondary palate evolved multiple times in crocodylomorphs, including very early in the group's evolutionary history. The co-occurrence of Nominosuchus in the Ulan Malgait Formation and the Shishigou Formation allows us to assign an early Oxfordian age to Shartegosuchus. The independent evolution of a eusuchian-type secondary palate in an oreinorostral group suggests that the link between platyrostry and a closed secondary palate has been overstated.
Recovering genomic clusters of secondary metabolites from lakes: a Metagenomics 2.0 approach

Background Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolism still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. Results With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from the lake samples. A total of 18 NRPS, 19 PKS and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Conclusions Our approach revealed a great potential to recover and study secondary metabolites genes from any aquatic ecosystem.
Method of reducing foam formation during the esterification of free fatty acids in triglycerides

A method for reducing foam by esterification of free fatty acids in triglycerides with C1-C8 aliphatic alcohols odioles; said method comprising the steps of (a) providing a catalyst quecomprende ion exchange resin of sulfonic acid type gel having 0.25% to 2.75% crosslinker; and (b) contacting said catalyst with a reaction mixture comprising: (i) a triglyceride having at least 1% free fatty acids; and (ii) an alcohol or aliphatic diol C1-C8, under suitable conditions paraesterificacion.
Biogenesis of a mitochondrial DNA inheritance machinery in the mitochondrial outer membrane

Mitochondria cannot form de novo but require mechanisms that mediate their inheritance to daughter cells. The parasitic protozoan Trypanosoma brucei has a single mitochondrion with a single-unit genome that is physically connected across the mitochondrial membranes to the basal body of the flagellum. This connection, termed tripartite attachment complex (TAC), is essential for the segregation of the replicated mitochondrial genomes prior to cytokinesis. Here we identify a protein complex consisting of three integral mitochondrial outer membrane proteins - TAC60, TAC42 and TAC40 - which are essential subunits of the TAC. TAC60 contains separable mitochondrial import and TAC-sorting signals and its biogenesis depends on the main outer membrane protein translocase. TAC40 is a member of the mitochondrial porin family, whereas TAC42 represents a novel class of mitochondrial outer membrane β-barrel proteins. Consequently TAC40 and TAC42 contain C-terminal β-signals. Thus in trypanosomes the highly conserved β-barrel protein assembly machinery plays a major role in the biogenesis of its unique mitochondrial genome segregation system.
Diet dependent sex ratios in Tigriopus californicus: Evidence for environmental sex determination in a system with polygenic sex determination

By controlling the inheritance of sex, the sex determination mechanism constrains sex allocation strategies and sex ratio adaptation; however, sex ratio selection also influences the evolution of sex determination mechanisms. Much of the sex determination literature focuses on how sex determination mechanisms transition between genetic and environmental factors (i.e. GSD vs. ESD), and if genetic sex factors are involved, how many (e.g. chromosomal vs polygenic systems). The study of sex allocation largely focuses on deviations in sex ratio from a theoretically 1:1 evolutionarily stable strategy, such as when sex ratios reflect ‘cost’ differences between the sexes. Tigriopus californicus is a tidepool copepod with polygenic sex determination, and shows wide variability in sex ratios in the field and lab that cannot be explained by genetic and stochastic processes alone, which suggests that an environmental variable might influence sex ratio. Females and their offspring were fed diets of different nutritional quality in a crossed design, and the sex ratio of each clutch was recorded for up to 8 clutches from a given female: this design allowed the influence of female diet vs. that of her offspring to be distinguished. The clutch sex ratio changed over the laying order according to the offspring’s diet, which is evidence for environmental sex determination in this species. Sex ratio also showed the influence of maternal diet, consistent with sex allocation theory. While dietary carotenoids showed no association with sex ratio or clutch size, long chain polyunsaturated fatty acids (particularly EPA and DHA) were implicated as the agent of sex ratio effect, providing a direction for future studies. The situation of T. californicus at the intersection of major themes in sex evolution makes this system an ideal model for selection studies.
The polymorphism of JAK2 rs56118985 may be a predictive marker of the treatment responses of acute myeloid leukemia patients

Background: The Janus kinase/Signal transducer and activator of transcription (JAK/STAT) signaling pathway plays a role in ontogeny and developmental biology, hematopoietic regulation and the immune response. In this study, we aimed to investigate whether the genetic polymorphism rs56118985 (Glycine ⇒ Aspartic acid) in the JAK2 gene is associated with the therapeutic outcomes of Ara-C-based chemotherapy regimens in acute myeloid leukemia (AML). Methods: A total of 552 AML patients were included in our study. Genotypes were determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Results: The frequency of the GG genotype was significantly higher in patients with intermediate and good therapeutic responses. In contrast, the GA genotype was found in the unfavorable response group, high ratio of blast group and was significantly associated with the poor therapeutic response group. Patients with the GA genotype were significantly more likely to die early (P Conclusions: In conclusion, the polymorphism of JAK2 rs56118985 may be a predictive marker of the treatment responses of AML patients.
Release of carbon and nitrogen from fodder radish (Raphanus sativus) shoots and roots incubated in soils with different management history

ABSTRACT Plant roots are generally considered to decompose slower than shoots and contribute more to accumulation of soil organic matter, and management history is expected to shape the structure and function of decomposer communities in soil. Here we study the effect of chemical characteristics of shoots and roots from fodder radish (Raphanus sativus oleiformis L.), a widely used cover crop, on the release of their C and N after addition to soil. Shoots and roots were incubated for 180 d at 20°C using four soils with different management histories (organic versus mineral fertiliser, with and without use of cover crops), and the release of CO2 and extractable mineral N was determined. More shoot C than root C was mineralised during the first 10 d of incubation. After 180 d, 58% of the C input was mineralised with no difference between shoots and roots. At the end of incubation, shoots had released more N (42% of shoot N) than roots (28% of root N). Moreover, management history did not affect net mineralisation of added plant C. Residues incubated in soil with a management history involving cover crops showed an enhanced net N mineralisation. Therefore, long-term decomposition of C added in radish shoots and roots is unaffected by differences in chemical characteristics or soil management history. However, the net mineralisation of N in shoots is faster than for N in roots, and net N mineralisation of added materials is higher in soil with than without a history of cover crops. Abbreviations: CC: cover crop; IF: inorganic fertilizer; M: manure
An optimized method to quantify large numbers of amphibian eggs

Reducing time spent performing menial, yet time-consuming tasks improves efficiency not only in productivity, but also in funding. For amphibian ecologists, counting eggs is a common and laborious task. We developed a fast and cost-efficient method to quantify large numbers of eggs using freely available software. Our method had high agreement with hand counts, but dramatically faster processing times, especially as counts increased. Percent error also decreased with increasing counts. Overall, this method significantly improves speed, accuracy and will be useful for many researchers examining amphibian reproduction .
Inefficiency of evolutionarily relevant selection in ungulate trophy hunting

Differentially harvesting individual animals with specific traits has led some to argue that such selection can cause evolutionary change that may be detrimental to the species, especially if those traits are related positively to individual fitness. Most hunters are not selective in the type of animal they take, satisfied instead to harvest any legal animal. In a few exceptions, however, regulations may limit hunters to harvest animals of a minimum size or age regardless of their personal choice. Using information from a broad range of aquatic and terrestrial systems exposed to a myriad of potential and operational selective pressures, several authors have made expansive generalizations about selective harvest and its applicability to ungulates. Harvest-based selection can potentially be intensive enough to be relevant in an evolutionary sense, but phenotypic changes consistent with hunter selection are otherwise confounded with multiple environmental influences. Factors such as age, genetic contribution of females, nutrition, maternal effects, epigenetics, patterns of mating success, gene linkage, gene flow, refugia, date of birth, and other factors affecting selection interact with harvest to impede unidirectional evolution of a trait. The intensity of selection determines potential for evolutionary change in a meaningful temporal framework. Indeed, only under severe intensity, and strict selection on a trait, could human harvest prompt evolutionary changes in that trait. Broad generalizations across populations or ecological systems can yield erroneous extrapolations and inappropriate assumptions. Removal of males expressing a variety of horn or antler sizes, including some very large males, does not inevitably represent directional artificial selection unless the selective pressures are intensive enough to cause a unidirectional shift in allele frequencies that may act on some relevant life-history trait or process. Here I review the topic of harvest-based selection in male ungulates and discuss the inefficiency of trophy hunting in changing genetic expression of phenotype. © 2017 The Wildlife Society.
Impacts of domestication on population genetics of a traditional Chinese medicinal herb, Atractylodes macrocephala (Asteraceae)

As a medicinal herb, Atractylodes macrocephala Koidz. experienced centuries of cultivation in China, and germplasm resources of all cultivated populations have degraded over time as a consequence of domestication processes. This study used chloroplast DNA and microsatellites to clarify not only the effects of domestication on population genetics, but also determine the geographic origins of landraces. The results revealed that cultivated populations (except the “Pingzhu” landrace) showed higher genetic diversity than their wild counterparts and low levels of genetic differentiation occurred between cultivated and wild groups. Furthermore, STRUCTURE and UPGMA analyses grouped all wild populations into three genotypic clusters, two of which (in Shaanxi and Hunan Province) shared the same gene pool with cultivated A. macrocephala, suggesting that wild populations in Central China have been involved in the origin of cultivated A. macrocephala. Moreover, the wild population from Qimen, Anhui Province and the cultivated “Pingzhu” landrace harbor unique gene pools and rare alleles that could be useful in future breeding efforts. This large‐scale analysis of population genetics on a medicinal herb that has a centuries‐long history of human‐mediated selection will facilitate utilization and conservation of the valuable genetic resources of medicinal species.
Real-time 3D Reconstruction of Aerial Transmission Lines

High-precision 3D real-time reconstruction system can complete the reconstruction of small-scale space, but it cannot meet the 3D real-time reconstruction of outdoor large-scale environment. The operating environment of high-altitude operation transmission lines is relatively harsh, and when carrying on the operation robot that replaces maintenance personnel, it is necessary to establish a system that can meet the outdoor large-scale 3D real-time reconstruction, and the reconstruction accuracy should be able to meet the conditions of use. Therefore, we propose a large-scale 3D real-time reconstruction system based on RGB-D sensor and IMU information fusion, using ORBSLAM algorithm to reconstruct the dense map by feature matching of the point cloud observed by the depth camera, and then using OctoMap to convert it into a real-time octree map, and using incremental storage to synthesize a large-scale 3D map.
Molecular mechanism of cell-cell adhesion mediated by cadherin-23

Adherin-junctions are traditionally described by the homophilic-interactions of classical cadherin-proteins at the extracellular region. However, the role of long-chain non-classical cadherins like cadherin-23(Cdh23) is not explored as yet even though it is implicated in tissue-morphogenesis, cancer, and force-sensing in neuronal tissues. Here, we identified a novel antiparallel-binding interface of Cdh23 homodimer in solution by combining biophysical and computational methods, in-vitro cell-binding, and mutational modifications. The dimer consists of two electrostatic-based interfaces extended up to two terminal domains, atypical to classical-cadherins known so far, and forms the strongest interactions in cadherin-family as measured using single-molecule force-spectroscopy. We further identified single point-mutation, E78K, that completely disrupts this binding. Interestingly, the mutation, S77L, found in skin cancers falls within the binding interface of the antiparallel-dimer. Overall, we provide the molecular architecture of Cdh23 at the cell-cell junctions which are likely to have far-reaching applications in the fields of mechanobiology and cancer.
Habitat selection of riparian birds at restoration sites along the Trinity River, California

Riparian habitats in the western United States are imperiled, yet they support the highest bird diversity in arid regions, making them a conservation priority. Riparian restoration efforts can be enhanced by information on species response to variation in habitat features. We examined the habitat selection of four riparian birds known as management indicators at restoration and reference sites along the Trinity River, California. We compared vegetation structure and composition at nest sites, territories, and random points to quantify used versus available habitat from 2012 to 2015. Vegetation in focal species' territories differed between site types, and from available habitat, indicating nonrandom site choice. Birds selected aspects of more structurally complex habitats, such as greater canopy cover, canopy height, and tree species richness. Yellow‐breasted Chats preferred greater shrub cover, and Yellow Warblers preferred greater cover by non‐native Himalayan blackberry. Territory preferences on restoration sites were often a subset of those on reference sites. One exception was canopy height, which was taller on restoration site territories than random points for all species, suggesting that birds preferentially used patches of remnant habitat. Few variables were significant in nest site selection. Restoration plantings along the Trinity River were only 3–10 years old during this study, and have not developed many of the characteristics of mature riparian habitat preferred by birds, but may improve in habitat value over time. Understanding habitat selection is especially important in recently human‐modified environments, where indirect cues used to assess habitat quality may become disassociated from actual habitat quality, potentially creating ecological traps.
Some Aspects of Nephrotoxicity of Paracetamol and Ketoprofen in Patients with Rheumathoid Arthritis

Abstract Introduction. To determine the effect of initial therapy with Paracetamol and Ketoprofen on glomerular and tubular integrity in rheumatoid arthritis (RA), to quantify nephrotoxicity of these two drugs by measurement of enzymuria, which correlates with the damage of tubular epithelium. Microalbuminuria is used as a marker for glomerular damage, and urine excretion of N-Acetyl-b-D-glucosaminidase (NAG) as an indicator of proximal tubular damage. Methods. Using colorimetric method for determination of NAG, and immunoturbidimetric method for microalbuminuria, samples of 70 participants were examined (35 RA patients treated with Paracetamol only, 35 RA patients treated with Ketoprofen). The follow-up was in 5 time-intervals in the course of 24 weeks. Results. There was a moderate correlation between NAG and microalbuminuria (r=0.16) in the group of patients treated with Paracetamol only, and a moderate correlation (r=0.28) in the group of patients treated with Ketoprofen. NAG enzymuria in size, by number of patients Registered, and time of appearance, was greater and appeared earlier in the Ketoprofen group compared to the Paracetamol group. Conclusions. Ketoprofen is more potent NAG inductor and provokes greater tubular enzymuria than Paracetamol. Results from our study confirm safety in use of Paracetamol and Ketoprofen in everyday clinical practice.