Miracle-dz/UniFAR-FTUs huggingface dataset:
Hardness characterization parameters of Niobium Carbide and Niobium Nitride_ A first principles study

Niobium carbides and nitrides have been proposed as potential candidates for hardness and related applications, however, comprehensive studies are still needed for better understanding that may pave way for their re-engineering for the ultra hard industry. Here we present ab initio Density Functional Theory calculations that provide a comprehensive description of various hardness characterization parameters. Our results show that NbC in rocksalt (RS) had a higher shear modulus, Young's modulus, and Voigt-Reuss-Hill shear modulus compared to other phases of NbC and NbN considered in this work. Further, it was noted that NbC in RS had a higher value of Vickers hardness amongst the various phases NbC and NbN studied, thus identified as a potential candidate for hardness and related application. Finally, we showed that compounds with Vickers hardness (Hv) > 20 GPa were found to be brittle while those with Hv < 20GPa were ductile.
Circulating free DNA: a tumour biomarker for early detection and follow-up in colorectal cancer

Background: Circulating cell-free DNA (cfDNA) in plasma is under investigation as a “liquid biopsy” for monitoring cancers as a surrogate for the primary tumour. The aim of the study was to evaluate the potential of cfDNA for early detection and follow up of patients with colorectal cancers (CRC). Methods: 55 colonic and 29 rectal operable carcinomas were investigated comparing matched tumour tissue and cfDNA. A 69bp ALU repeat qPCR assay was used to quantify fragmented DNA. Allele specific locked nucleic acid/peptide nucleic acid (AS-LNA/PNA qPCR assays were used to detect hot spot mutations in KRAS, BRAF and PIK3CA, optimised using cell lines with known mutation status. Results for cfDNA were compared with clinicopathological features of CRC and overall survival. Results: Total cfDNA levels correlated with disease stage (p=0.003). Cell lines studies demonstrated a limit of mutant DNA detection of 1 genome equivalent (6pg total DNA). Using this threshold, at least one mutation was detected in cfDNA of 40% of cases of CRC. Mutations in cfDNA were more common in colonic cases than rectal cases (p=0.01) and with significantly higher levels of mutant cfDNA (p=0.02). ). In colonic tumours, cfDNA levels correlated with tumour stage (p=0.003), size (p=0.04) and LN status (p<0.005). However, only 6 (86%) with BRAF, 6 (45%) with KRAS and 3 (20%) with PIK3CA matched to the mutations found in the tumour tissue suggesting clonal evolution. PIK3CA mutations were detected for the first time in cfDNA in localised primary tumours including early stage of CRC. Potential use of cfDNA total levels to screen for early lymph nodes involvement demonstrated a ROC of 0.76, with a 75% sensitivity and 86% specificity, suggesting early detection of cancer prior to metastasis. No significant survival differences were observed for cohort cancers for mutant cfDNA. However, mutation in cfDNA of colonic cancers was associated with poor overall survival (p<0.05). Conclusion: This study has shown that cfDNA has a potential for use as a surrogate for the primary tumour in CRC, and for early detection of colonic cancer prior to metastasis. However, further study in a larger cohort is required to validate these findings.
Nutrient limitation or home field advantage: Does microbial community adaptation overcome nutrient limitation of litter decomposition in a tropical peatland?

Litter decomposition is an important control on carbon accumulation in tropical peatlands. Stoichiometric theory suggests that decomposition is regulated by elemental ratios in litter while the home field advantage (HFA) hypothesis predicts that decomposer communities are adapted to local conditions. To date, the relative importance of these contrasting theories for litter decomposition and therefore the carbon balance of tropical peatlands remain poorly understood. We conducted two in situ litter decomposition experiments in a lowland tropical peatland. The first experiment tested the importance of the stoichiometric theory using a factorial nutrient addition experiment at two sites with contrasting vegetation (Raphia taedigera and Campnosperma panamensis) to assess how nutrient addition affected microbial enzyme activity and litter mass loss at the peat surface and at 50 cm depth. The second experiment tested the importance of HFA by reciprocal translocation of leaf litter from R. taedigera and C. panamensis forests, which differed in both litter chemistry and soil nutrient availability, to separate the influence of litter chemistry and soil/site properties on litter mass loss. The activities of hydrolytic enzymes involved in the decomposition of large plant polymers were stimulated by nitrogen addition only where nitrogen availability was low relative to phosphorus, and were stimulated by phosphorus addition where phosphorus availability was low. The addition of nitrogen, but not phosphorus, increased leaf litter decomposition under waterlogged conditions at 50 cm depth, but not at the peat surface. Decomposition was greatest for autochthonous litter irrespective of site nutrient status, indicating that adaptation of the microbial community to low nutrients can partly overcome nutrient limitation, and suggesting that HFA can influence litter decomposition rates. Synthesis. Our study shows that leaf litter decomposition and the activity of microbial enzymes in tropical peatlands are constrained in part by nutrient availability. However, such nutrient limitation of litter decomposition can be overcome by adaptation of the microbial community.
Mycotic Granulomatosis and Seasonality are the Consistent Features of Epizootic Ulcerative Syndrome (EUS) in Fresh and Brackishwater Fish of Karnataka, India

Histopathological investigations carried out between 1992 and 1994 on a large number of fresh and brackishwater fish of Karnataka, India, have confirmed that the ulcerative syndrome sweeping through Karnataka since 1991 is the devastating epizootic ulcerative syndrome (EUS). The two key diagnostic features of EUS, namely, oomycete involvement and proliferative mycotic granulomatosis, have been consistently demonstrated in all af­fected fresh and brackishwater fishes of Karnataka. Interestingly, Indian major carps and tilapia present in these affected water bodies were refractory to EUS. Mycotic granulomatosis and seasonality have been identified as the key features of this syndrome.
Sexual Propagation of the Tunisian Spinescent Opuntia ficus-indica (L.) Mill., Morphogenetic Deployment and Polymorphism

The most common means of Opuntia ficus-indica (L.) Mill. propagation is through the use of asexually methods without genetic recombination which has been extensively studied for commercial purpose or to reduce erosion and desertification. However, seeds are important units to be considered for maintaining the species genetic variability. With the aim to undrestand the morphogenetic polymorphism deployment of the Tunisian spinescent Opuntia ficus-indica from the juvenile to the advanced stages, we search, firstly, the optimal conditions permetting to ensure the highest germination rate during the shortest period with sulphuric acid scarification in ten levels time of dipping. The best germinated rate (68.0%) is reached within 30 min of treatment exposure. Some germinated seeds showed polyembryony phenomenon. The highest rate (29.3%) was recorded after 25 and 30 min of pretreatment. Occurrence of morphogenetic abnormalities: tricotyledony, dissymmetried, coiled and adhered cotyledons in percentages varying from 12.8 to 20.0% was also reported. Secondly, a morphogenetic tracking of Opuntia ficus-indica young seedlings to adult plants during seven years (2009-2015) from the germination of seeds to the production of seeds was performed. This essay allowed us to report major seedling characteristics, their growth and phenotypic polymorphism: vertical succession of varying numbers of basal cladodes, future plant trunk formation, development and arrangement of secondary cladodes in the space, spinescence polymorphism and the first flowering and fruiting.
Effect of Three Desiccant Herbicides on Soybean (Glycine max) Seed Quality

Soybean [Glycine max (L.) Merr. ] cultivars ‘UFV1’ and ‘UFV2’ grown at Viçosa and Florestal, Brazil, and ‘Bonus' and ‘Wells' at Urbana, Illinois, were sprayed at growth stages R5.5 to R6 (full-pod) or R7 (50% defoliation) with the desiccant/herbicides glyphosate [N-(phosphonomethyl)glycine], paraquat (1,1′-dimethyl-4,4′-bipyridinium ion), or sodium chlorate:sodium borate (50:50, w/v). Desiccation of plants by paraquat significantly reduced seed weight and germination at all locations and increased the incidence of Alternaria and Phomopsis spp. at Urbana. Analysis of the combined data from the Brazilian locations showed a significant decrease in seed germination for all treatments except paraquat sprayed on the UFV2 at R7 and sodium chlorate: sodium borate sprayed on UFV1 at R7. Herbicide application at R7 did not result in consistent increases in seedborne Fusarium or Phomopsis spp. at any Brazilian location. Rainfall and temperature at seed maturation were more important variables in pod-to-seed infection by these fungi than increased rates of tissue senescence caused by the desiccants.
Rapid maxillary expansion effects on the upper airway dimensions and function in growing patients: An umbrella review

Objective: Because numerous published systematic reviews have assessed the effect of rapid maxillary expansion (RME) over upper airway dimensional changes, it is important to map and summarize their conclusions. In addition, the accepted methods used to evaluate the upper airway across the different systematic reviews will be outlined and areas of strengths and weaknesses on the topic identified. Methods: Systematic reviews in which RME treatment outcomes as related to upper airway dimensional changes or breathing function in children and adolescents were included in this umbrella systematic review. Studies that investigated upper airway changes using three-dimensional imaging (cone beam computed tomography, computed tomography, magnetic resonance imaging), acoustic rhinometry, rhinomanometry, and polysomnography correlated with RME effects were included. Studies on expansion using palatal anchorage with miniscrews and surgically assisted maxillary expansions were excluded, as well as studies including syndromic patients. Results: Sixty-six studies were found from the database searches. After managing duplicates, 33 studies were assessed based on the titles and abstracts, but only 16 reviews were considered for the next assessment phase (full text). From then, only 10 systematic reviews were finally included in this umbrella review. Conclusions: A significant amount of research has been published linking RME changes to increases in nasal respiratory capability, nasal volume, and linear transverse enlargement. However, methodologic inconsistencies and disagreements between the included studies (especially on the oropharyngeal dimensional changes after RME) lead to significant uncertainties about the consistency of the effect of RME changes, especially on the oropharynx region dimensions. It is not clear that the upper airway dimensional changes necessarily imply an improvement in actual breathing function.
Haptoglobin gene polymorphism influences the effect of malaria infection on host haptoglobin plasma level but not susceptibility to the disease

A cohort of 344 children aged less than five years were followed for one year to establish the relationship between haptoglobin genotype, haptoglobin plasma level and malaria infection and susceptibility. Haptoglobin genotyping was undertaken using PCR, with plasma haptoglobin levels measured using indirect ELISA. The number of children carrying the genotypes Hp 1-1 , Hp 1-2 and Hp 2-2 were 85, 171 and 88, respectively. The state of malaria infection was assessed using standard microscopy method to detect parasitemia. Higher plasma haptoglobin level tended to be associated with negative parasitemia (P=0.01). During malaria infection, haptoglobin level decreased in all individuals and, the decrease significantly varied by genotype, whereby the decrease was greater in Hp 2-2 individuals than the other genotypes. A longitudinal examination of blood smears revealed a slightly higher proportion of children carrying the Hp 2-2 genotype (12.4%) to be positive for malaria, as compared to children with the genotype Hp 1-1 (11.7%) and Hp 1-2 (11.6%). The present study has demonstrated that malaria infection in children affects the haptoglobin plasma level and the effect is influenced by haptoglobin genotype. The study has also revealed a limited influence of haptoglobin genotype to malaria infection and disease development. Keywords : Haptoglobin, malaria, parasitemia African Journal of Biotechnology Vol. 12(10), pp. 1115-1120
Low Bycatch Rates Add Up to Big Numbers for a Genus of Small Fishes

Nonselective fishing gears extract a great many small marine species, with limited documentation or assessment of their impacts. Among those species, seahorses (genus Hippocampus) are unusual because this genus has been the focus of scientific surveys and international trade regulation. Our review of published and unpublished data sources analyzed data on seahorse bycatch for five gear-type categories and 22 countries. The median catch per unit effort of seahorse bycatch across all five gear types was 0.96 seahorses per vessel−1 day−1. Nonetheless, fleet sizes were so large that annual catches were estimated at approximately 37 million seahorses across our sampled countries. Fisher interviews suggested that seahorse catches were declining (although information on changes in effort over time were not available). Furthermore, international export data did not capture the magnitude of seahorses in bycatch. Our work emphasizes the importance of evaluating bycatch, even for taxa where reported daily catch rate.
Genetic diversity studies among chickpea (Cicer arietinum L.) genotypes under rainfed and irrigated conditions for yield attributing and traits related to mechanical harvesting

Genetic diversity among 30 chickpea genotypes was assessed for yield attributing and traits related to mechanical harvesting during rabi 2016-17 under both rainfed and irrigated conditions as separate experiments. The genotypes were grown in randomized block design (RBD) with three replications. Genetic diversity study grouped 30 chickpea genotypes into five different clusters under both the tested environments. Days to 50 per cent flowering followed by days to maturity and 100 seed weight contributed maximum towards diversity under rainfed as well as irrigated conditions. Inter cluster average D2 values stretched between 7.42 and 20.11 under rain fed condition, while it was slightly higher and varied from 8.64 to 28 under irrigated condition. The most divergent clusters were IV and V under both the situations. The traits that are suitable for mechanical harvesting particularly, height of the first pod and plant height contributed more (8.3 per cent and 8.1 per cent respectively) towards the genetic divergence under irrigated than under rainfed condition (3 per cent and 5.5 per cent respectively). While the angle of the primary branch couldn’t show any influence on the divergence under both the tested environments. Promising genotypes with suitable traits for mechanical harvesting besides having yield advantage are‘NBeG 780’, ‘NBeG 857’, ‘NBeG 47’, ‘NBeG 863’ and ‘BG 3061’ of cluster I under rainfed and cluster II under irrigated, ‘GBM 2’ of cluster II in rainfed and cluster I in irrigated, ‘ICCL 85213’ and ‘NBeG 865’ of cluster III under rainfed, ‘DBGV 3104’ of cluster I under rainfed and ‘GL 12021’ of cluster V under both rainfed and irrigated are suggested for utilization in the crossing programs to breed varieties of chickpea for high yield with amenability to combine harvesting.
Comparative Efficacy of Organic and Inorganic Sources of Nutrients in Paddy (Oryza sativa L.)

The experiment was conducted at the research farm of Department of Organic Agriculture, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur during kharif 2014 to study the comparative efficacy of organic and inorganic sources of nutrients in paddy. The experiment consisted of eight treatments comprising of combinations of four nutrient management treatments viz., Organic nutrient management (soil treatment with jeevamrit & seed treatment with biofertilizer, vermicompost (VC) 10 t ha & 3 sprays of vermiwash at 15, 30, 45 days after sowing), Inorganic nutrient management (recommended NPK), Integrated nutrient management (5 tonnes VC + 50% of recommended NPK), Control (Farmer’s practices) (2.5 tonnes VC + 25% of recommended NPK) with two ecosystems i.e transplanted and direct seeded rice (rainfed) were tested in split plot design, replicated thrice. Growth, yield attributes, grain and straw yield of rice was increased in transplanted Original Research Article Sharma et al.; BJAST CJAST, 21(6): 1-8, 2017; Article no.CJAST. 33914 2 ecosystem and integrated nutrient management practice. The transplanted ecosystem recorded 18.64 per cent higher yield and 50.60 per cent higher net return per rupee invested over direct seeded rainfed ecosystem. Integrated nutrient management being statistically at par with organic nutrient management recorded the higher paddy yield over inorganic nutrient management and farmer’s practice. Integrated nutrient management recorded higher net returns per rupee invested (1.18) but remain statistically at par with organic nutrient management and inorganic nutrient management.
Reproductive biology of Cypripedium guttatum Sw. (Orchidaceae, Monocotyledones) at the northern border of its habitat.

The paper presents data on the reproductive biology of Cypripedium guttatum Sw. (Orchidaceae) in the Komi Republic, at the northern border of its habitat. Bees (Lasioglossum calceatum and L. brevicorne) are pollinators of C. guttatum in the region. The pollination efficiency is 21%. C. guttatum seeds are the largest ones among those of other orchid species in the region (1.11×0.22 mm). The size of seeds depends on the growing conditions of mother plants. The seed productivity of C. guttatum is rather high: every fruit contains 5 thousand seeds on the average, and more than 88% of them are of high quality. The seed crop is 2-22.6 thousand seeds per square meter.
Effect of Antimicrobial Agents on MinD Protein Oscillations in Escherichia coli

EFFECT OF ANTIMICROBIAL AGENTS ON MIND PROTEIN OSCILLATIONS IN ESCHERICHIA COLI Corey Kelly Advisor: University of Guelph, 2011 John Dutcher The Min protein system regulates cell division in the bacterium Escherichia coli. The protein MinD undergoes a pole-to-pole oscillation, antagonizing formation of the division septum at the cell poles, thereby confining the septum formation to the mid-cell. The MinD oscillation period is 40 s at room temperature in healthy cells, but has been shown to be sensitive to stress on the cell. By fluorescently labeling MinD with green fluorescent protein (GFP), we are able to measure the MinD oscillation period as an in situ metric of cell viability using high resolution total internal reflection fluorescence (TIRF) microscopy. We have made several improvements to the method by which we measure and analyse the MinD oscillation period. A microscopy flow cell was designed and constructed and it provides temperature control and stability to a precision of ±0.05 ◦C in addition to allowing controlled addition of bacterial cells and reagents of interest to the imaging region of the flow cell. This flow cell enabled us to make a precise measurement of the temperature dependence of the MinD oscillation period, for which we observed an Arrhenius dependence with an activation energy of 11.8 kcal/mol. We developed a centroid-tracking method, performed in a custom MATLAB program, to extract the values of the MinD oscillation periods from our time series of TIRF microscopy images. We measured the effect on the MinD oscillation period of exposure to the cationic antimicrobial peptide polymyxin B (PMB) and the related compound polymyxin B nonapeptide (PMBN), which does not exhibit antimicrobial activity. Exposure to PMB resulted in a 50 % increase in the average MinD oscillation period τ , while exposure to PMBN resulted in an 20 % decrease in τ . After exposure to PMB and PMBN, we measured the Arrhenius temperature dependence of the MinD temperature dependence, and calculated the associated activation energy EA. We found that exposure to PMB resulted in a 45 % increase inEA, whereas exposure to PMBN did not significantly change the value of EA. These results indicate that careful measurements of the MinD oscillation can yield information that can be helpful in evaluating the mechanism of action of antimicrobial compounds.
Effects of Different Mill Types on Ethanol Production Using Uncooked Dry‐Grind Fermentation and Characteristics of Residual Starch in Distiller's Dried Grains (DDG)

This study aimed to investigate impacts of milling methods on ethanol production using an uncooked dry-grind (cold fermentation) process and characterize residual starch in the distiller’s dried grains (DDG) coproduct. Four corn lines with different chemical compositions were ground with cyclone, ultra-centrifugal, or hammer mills equipped with a screen of 0.5 mm opening and used for the cold fermentation process. Greater starch hydrolysis and ethanol yield were obtained from cyclone-milled corn, resulting from larger damaged starch contents and smaller particle sizes of the ground corn. Corn grains and ground corn after five-month storage showed less starch hydrolysis than the freshly ground counterpart. Residual starch (2.8–8.0%) with large proportions of intact amylopectin contents (up to 42.5%) was found in the DDG from all types of milling. The results suggested that the entrapment of starch granules in ground corn and a low activity of amylolytic enzymes at a high ethanol concentration were accounta.
Genomic analysis of ribosomal DNA and its application to the investigation of disease pathogenesis

The synthesis of rRNA is critical to all growing organisms, accounting for well over half of all cellular transcription. Highlighting its central function in cellular life, dysregulation of rRNA biogenesis and subsequent ribosome assembly has been implicated in human genetic diseases and cancer. While the transcription of rRNA is highly regulated at the chromatin level, it has not been analyzed by genomic methods due to the exclusion of rDNA from current genome assemblies. This work describes a novel method of analysis that enables the alignment of high-throughput sequencing data to a single copy of rDNA in the context of the full human genome. Integrated analysis of genomic datasets reveals that the coding region of rDNA is contained within nucleosomepoor open chromatin with high transcriptional activity. We find that histone modifications are enriched not only at the rDNA promoter but also at novel sites within the noncoding intergenic spacer. The distribution of active modifications is more similar within and between cell types than that of repressive modifications. Using ChIP-seq, we show that the nucleolar protein UBF is bound to sites throughout the genome and may play a role in regulating the transcription of nucleoplasmic genes. Lastly, the insulator-binding protein CTCF is bound to a