Miracle-dz/UniFAR-FTUs huggingface dataset:
Ligand dependent gene regulation by transient ERα clustered enhancers

Unliganded nuclear receptors have been implicated in ligand-dependent gene regulation. However, the underlying mechanisms are not fully understood. Here we demonstrate that unliganded ERα binds to specific sites in the genome thereby pre-marking them as future functional enhancers. Upon ligand exposure, ERα binds to several EREs relatively proximal to the pre-marked, or persistent, ERα-bound sites. Interestingly, the persistent sites interact extensively, via chromatin looping, with the proximal transiently bound sites forming ERα clustered enhancers in 3D. CRISPR-based deletion of TFF1 persistent site disrupts the formation of its clustered enhancer resulting in the loss of E2-dependent induced expression of TFF1 and its neighboring genes within the same cluster. The clustered enhancers overlap with nuclear ERα puncta that coalesce in a ligand-dependent manner. Furthermore, formation of clustered enhancers, as well as puncta, coincide with the active phase of signaling and their later disappearance results in the loss of gene expression even though persistent sites remain bound by ERα. Our results establish the role of persistent unliganded ERα binding in priming enhancer clusters in 3D that drive transient, but robust, gene expression in a ligand-dependent fashion.
Feed quantitative restriction and coenzyme Q10 level on performance, plasma lipoproteins and organ weights of broiler chicks

An experiment was conduct in order to investigate the effects of feed restriction level and duration and dietary coenzyme Q10 level on growth performance, organ characteristics and plasma lipoproteins. A factorial arangment based on a completely randomized design was performed using two levels of feed restriction (10 and 20% less than the standard Ross strain 308 guidelines), two levels of restriction duration (7 and 14 days) and three levels of coenzyme Q10 (0, 20 and 40 mg/kg feed). The results of the experiment showed that restriction intensity had significant effect on feed intake in first, second and sixth weeks of age (P<0.05), body weight gain in second and sixth weeks of age (P<0.05), and feed conversion ratio in first week of age (P<0.05). Restriction duration had significant effect on feed intake in third week of age (P<0.05), and feed conversion ratio in third and sixth weeks of age (P<0.05). Coenzyme Q level had significant effect on feed intake in first and sixth weeks of age (P<0.05), body weight gain in second, fifth and sixth weeks of age (P<0.05), and feed conversion ratio in second and sixth weeks of age (P<0.05). In conclusion, considering the positive effects of feed restriction and coenzyme Q10 on broiler yield, the simaltaneous use of feed restriction strategy and dietary coenzyme Q10 can be considered as a management program in order to improvement of broiler productivity.
Weed diversity of the family Poaceae in Bangladesh Agricultural University campus and their ethnobotanical uses

A taxonomic study on the weeds of the family Poaceae growing throughout the Bangladesh Agricultural University campus was carried out to determine species diversity of grasses in the campus. A total of 81 species under 46 genera and 2 subfamilies of the family Poaceae were collected and identified; their uses in various ailments were also recorded. Out of the three subfamilies, no weed from the subfamily Bambusoideae was found. Among the genera, Digitaria, Eragrostis, Brachiaria, Panicum, Echinochloa and Sporobolus were most dominant in context to number of species with a total of 29 species. While 28 genera were represented by single species each in BAU campus; of these 15 genera were in Bangladesh as well. Some of them are major and obnoxious weeds in different crop fields including staples rice and wheat. The flowering period will be helpful for the management of respective weed population. Many of these weed species have high economical, ethnomedicinal and other uses. The phenological study of these weed taxa will be helpful in managing weeds of the family Poaceae of this campus as well as the whole country without affecting the agro-ecosystem by keeping the weed population below a threshold level. J.Bangladesh Agril. Univ. 16(3): 372–379, December 2018
Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

The use of relative abundance data from next generation sequencing (NGS) can lead to misinterpretations of microbial community structures, as the increase of one taxon leads to the concurrent decrease of the other(s) in compositional data. Although different DNA- and cell-based methods as well as statistical approaches have been developed to overcome the compositionality problem, and the biological relevance of absolute bacterial abundances has been demonstrated, the human microbiome research has not yet adopted these methods, likely due to feasibility issues. Here, we describe how quantitative PCR (qPCR) done in parallel to NGS library preparation provides an accurate estimation of absolute taxon abundances from NGS data and hence provides an attainable solution to compositionality in high-throughput microbiome analyses. The advantages and potential challenges of the method are also discussed.
Mutant Resources of Spring Wheat to Improve Grain Quality and Morphology

The objective of this study was to broaden genetic variation of spring common wheat, evaluate and identify among M 5 mutant lines those with high-yield and improved grain quality characteristics. New lines were generated by initial treatment of variety of Eritrospermum-35 adapted to conditions of Kazakhstan by irradiation with 100-Gy and 200-Gy doses from a 60 Co source. Yield-associated traits including grain number and weight per main spike, grain weight (GW) per plant, and the thousand-kernel weight; grain size and grain shape variations; as well as quality characteristics such as grain protein content (GPC), iron, and zinc concentrations were evaluated. Mutant lines with high iron and zinc concentrations and high protein content were identified as those which have 1.6–3.4 and 1.4–2.9 times more as well as 3.7–16.9% more higher data of target con- centrations than parental variety had, respectively. Several mutant lines showed signifi cant increase in both grain iron and zinc concentrations. The positive correlation of grain quality parameters with grain area, length, and width suggest that they are related to each other. Wheat grain can be biofortified with micronutrients without negative impact on crop productivity using new mutant lines. Mutation breeding can significantly con tribute to human health malnutrition and improve nutrition quality diet.
WHICH ONE MAY BE THE BEST QUALITY PARAMETER OF RISKY FOODS IN TERMS OF MOLD: AFLATOXINS, PATULIN, OCHRATOXIN A AND ERGOSTEROL

Agricultural products can be exposed to mycotoxins produced by several kinds of molds as seconder toxic compound, as a result of the development of various toxigenic molds during the stages of preharvest, harvest and storage. Therefore, it is important to determine the presence of mold in foods quickly because of the deterioration of aroma, flavor, appearance and textural structure as well as the mycotoxins. Due to infection of 25% of the agricultural products with mycotoxins in the world wide and global population rising increasingly, researchers indicate importance of safety and adequate food production in the future. Some important mycotoxins are aflatoxins (AFs), patulin and ochratoxin A (OTA). Aflatoxins, which are mycotoxins produced by molds, causes significant quality and economic loss and have unfavorable effects on human health. Patulin, often detected in apple and apple products, is a mycotoxin produced by several species of Aspergillus, Penicillium and Byssochlamys. OTA is a nephrotoxic and nephrocarcinogenic mycotoxin which is predominantly produced by the two ubiquitous fungal genera, Aspergillus and Penicillium. Additionally, the other chemical component for determination of mold growth is ergosterol, a constituent of cell membrane of molds, provides a quick assay for presence of molds. The aim of this study is to compare the aflatoxins, patulin, ochratoxin A and ergosterol in risk foods in terms of mold as a microbiological quality parameter and to state the most effective metabolite as quality parameter.
Delivery of paclitaxel and cetuximab by nanodiamond enhances mitotic catastrophe and tumor inhibition in colorectal cancer

Nanomaterials provide the opportunities to improve the efficacies for cancer therapy. Nanodiamond (ND) is a promising carbon nanomaterial developed for novel cancer treatment. Here, we show ND‐carried paclitaxel (PTX), a mitotic blocker, and cetuximab (Cet) (a specific EGFR antibody) that enhances mitotic catastrophe and tumor inhibition in human colorectal cancer (CRC). ND‐PTX induced the mitotic catastrophe and apoptosis in a variety of human CRC cell lines; in contrast, ND alone did not induce cell death. ND‐PTX blocked the mitotic progression, caused abnormal chromosomes separation and subsequently induced the caspase‐3 activation and PARP protein cleavage for apoptosis induction. ND‐PTX inhibited the xenografted human CRC tumors in nude mice. Furthermore, ND‐PTX‐Cet enhanced the cellular uptake ability and apoptosis induction and tumor growth inhibition in the EGFR‐expressed colorectal cancer cells. The mitotic marker of phospho‐histone H3 proteins was highly elicited by ND‐PTX‐Cet in CRC tissues. These results demonstrate that ND is a promising nanocarrier of PTX and Cet for developing novel CRC therapy.
Butanol production by Clostridium pasteurianum NRRL-598 using corn steep liquor as nutrient source

Butanol has become an interesting substitute for ethanol in additives and fuel applications due to its physical chemical properties. Several Clostridium strains are able to produce ABE (acetone, butanol and ethanol) solvents by fermentation. Efforts have been made to reduce cost of butanol biotechnological production in order to become this route competitive when compared to petrochemical technology. This study aimed to evaluate the use of corn steep liquor, a residue of corn industry, as unique nutrient source in culture medium for butanol production by Clostridium pasteurianum NRRL B-598. The strain is capable of producing butanol using only corn steep liquor as nutrient source. The yield was 0.30 gButanol/gglucose and the butanol productivity was 0.11 g.L . h using 20 g.L of corn steep liquor.
Design Technique for a Shaped-Reflector Antenna With a Three-Layer Cable Net Structure

Considering the contoured beam design technique applied to deployable mesh reflector antennas, this article presents a design method for a shaped reflector with a three-layer cable net configuration. First, the concave–convex surface of the mesh reflector antenna required to meet the far-field pattern in an area of interest is designed based on the direct expansion method. Then, a typical application of a rotationally symmetric reflector is designed and analyzed to produce a coverage beam for the continental United States (CONUS). Second, an improved geometry for the three-layer cable net is established by the design scheme. Next, the pretension iterative optimization of the three-layer-shaped cable net structure is carried out by combining the equilibrium matrix method and a topology optimization method. Finally, using the design results of this article as a manufacturing case, we develop a prototype and measure the shape accuracy of the mesh-shaped reflector. The experimental results indicate that the far-field pattern of the prototype contoured beam antenna is close to the computations, which demonstrates the correctness and effectiveness of the proposed design technique.
The specific roles of cohesin-SA1 and cohesin-SA2 in gene regulation and genome organization

The use of Chromosome Conformation Capture (3C)-derived techniques for probing 3D genome structure has shed new light on the principles of genome organization. DNA looping is recognized as the major mechanism responsible for this organization in which topologically associated domains (TADs) and compartments are acknowledged as hierarchical levels of genome folding at a megabase scale. The cohesin complex, working together with the insulator protein CTCF, has shown to be essential for partitioning the genome into chromatin loops and TADs. Cohesin is a ring-shaped protein complex best known for its role in sister chromatin cohesion that consists of four subunits: SMC1, SMC3, RAD21 and SA. In somatic vertebrate cells, the SA subunit can be either SA1 or SA2, thus giving rise to two different cohesin variants, cohesin-SA1 and cohesin-SA2. Studies in human and mouse cells have suggested that these variants have non-redundant functions, at least regarding cohesion. However, their differential contributions to gene regulation and genome organization have not been explored. In order to address this question, we first analysed the genome-wide distribution of the two cohesin variants in three human cell lines and found that cohesin-SA1 is almost exclusively present at CTCF-bound sites. In contrast, only a fraction of cohesin-SA2 colocalizes with cohesin-SA1 and CTCF, while another one occupies non-CTCF positions that are instead bound by transcriptional regulators. This population is enriched at active enhancers, in particular at super-enhancer elements responsible for establishment of cell identity. Importantly, cohesin-SA2 can reach CTCF positions in the absence of SA1, but cohesin-SA1 cannot occupy non-CTCF positions when SA2 is absent. Differential affinity of SA1 and SA2 for cohesin-releasing factor WAPL, CTCF and transcriptional regulators may contribute to the observed differences in the dynamics of their association to chromatin. Downregulation of cohesin-SA2 has a more pronounced effect on the transcriptome of MCF10A cells and leads to deregulation of core cell-identity genes. Using 4C and Hi-C analyses we also explored the consequences of cohesin variant depletion on local and global genome organization. Our results suggest that cohesin-SA1 works together with CTCF to define TADs while cohesin-SA2 facilitates more transient and local regulatory contacts. In summary, we propose that cohesin-SA2 contributes to cell-type specific gene regulation in a CTCFindependent fashion, a function that cannot be assumed by cohesin-SA1. Our work provides a new perspective on understanding the contribution of cohesin mutations to the pathology of human cancers.
Prediction of stress concentration at fillets using a neural network for efficient finite element analysis

In finite element analysis, small fillets make mesh generation difficult and accurate evaluation of stress concentration at fillets requires refined meshes. Simplified analysis is often performed using a corner model where the fillets are removed. In the analysis using a corner model, mesh division becomes easier and the number of elements is reduced, which shortens the calculation time. However, the stress concentrations cannot be evaluated, and stress singularities occur at corners. We have developed a method for predicting the stress at a fillet based on the simulation of a simplified corner model and the use of a neural network. We use the stress distribution at a corner as the neural network input such that the method can be applied to arbitrary object shapes, loading, and boundary conditions. We trained and validated the neural network using simple corner and fillet models. It was shown that stress distribution at a corner can express the difference in loading conditions. In addition, we found that the method can predict stress at fillets of models that were not used for the neural network training. These results show the possibility that the method enables efficient stress concentration evaluation in finite element analysis.
Antiretroviral drug activity and potential for pre-exposure prophylaxis against COVID-19 and HIV infection

Abstract COVID-19 is the disease caused by SARS-CoV-2 which has led to 2,643,000 deaths worldwide, a number which is rapidly increasing. Urgent studies to identify new antiviral drugs, repurpose existing drugs, or identify drugs that can target the overactive immune response are ongoing. Antiretroviral drugs (ARVs) have been tested in past human coronavirus infections, and also against SARS-CoV-2, but a trial of lopinavir and ritonavir failed to show any clinical benefit in COVID-19. However, there is limited data as to the course of COVID-19 in people living with HIV, with some studies showing a decreased mortality for those taking certain ARV regimens. We hypothesized that ARVs other than lopinavir and ritonavir might be responsible for some protection against the progression of COVID-19. Here, we used chemoinformatic analyses to predict which ARVs would bind and potentially inhibit the SARS-CoV-2 main protease (Mpro) or RNA-dependent-RNA-polymerase (RdRp) enzymes in silico. The drugs predicted to bind the SARS-CoV-2 Mpro included the protease inhibitors atazanavir and indinavir. The ARVs predicted to bind the catalytic site of the RdRp included Nucleoside Reverse Transcriptase Inhibitors, abacavir, emtricitabine, zidovudine, and tenofovir. Existing or new combinations of antiretroviral drugs could potentially prevent or ameliorate the course of COVID-19 if shown to inhibit SARS-CoV-2 in vitro and in clinical trials. Further studies are needed to establish the activity of ARVs for treatment or prevention of SARS-CoV-2 infection . Communicated by Ramaswamy H. Sarma
Dietary oils ameliorate aluminum chloride-induced memory deficit in wistar rats

Background: Alzheimer's disease (AD) is a progressive neurodegenerative disorder of the brain and is the most common form of dementia. There is no known cure for AD, and therefore, alternate therapies are warranted. Multiple reports state that nutritional or dietary interventions may have therapeutic potential and particularly associating high intake of n-3 polyunsaturated fatty acids to reduce risk for AD. In this direction, we have attempted to study the neuroprotective effects of dietary supplementation with canola oil, olive oil and rice bran oil in an aluminum chloride (AlCl3)-induced dementia model in Wistar rats. Materials and Methods: In the present study, spatial memory of AlCl3-treated animals, given supplementation with dietary oils, was evaluated using the Morris water maze. In addition, brain antioxidant parameters, acetylcholinesterase activity and serum biochemical markers were evaluated at the end of the study. Results: All dietary oils used in the present study showed ameliorative effect on the decline in spatial memory due to AlCl3treatment. However, among the three oils, canola oil exerted the most protective effect toward AlCl3-induced neuronal damage by improving spatial memory and brain antioxidant status. Apart from serum glucose, none of the biochemical parameters were altered by AlCl3or by dietary oil supplementation. Conclusion: The study highlights the protective effect of dietary oils rich in unsaturated fats against Alzheimer's dementia. Canola oil showed highest neuroprotective activity against AlCl3-induced dementia in rats. Abbreviation used: AD: Alzheimer's disease; ALA: Alpha-linoleic acid; DHA: Docosahexaenoic acid; PUFA: Polyunsaturated fatty acids; MWM: Morris water maze; AchE: Acetylcholinesterase; UFAW: University Federation for Animal Welfare.
Evaluation of tomato (Solanum lycopersicum L.) Hybrids for quality parameter in Allahabad agro climatic condition

The experiment was conducted under Randomized Block Design with three replications during winter season of the year 2017-18 in Departmental Research field of Department of Horticulture, Naini Agricultural Institute, Sam Higginbottom University of Agricultural Technology and Sciences, Allahabad. Twenty-five hybrid varieties of tomato were evaluated for quality parameters under total soluble solids, acidity, ascorbic acid and fruit shape index. Hybrid H20 (Excel - 204) is found to be best for most of the quality parameters such as it had maximum ascorbic acid (26.900 mg) and total soluble solids (6.073° Brix). Fruit shape index was high in hybrid H₁₀ (CHAITANYA) (1.053) and acidity was minimum in hybrid H₂₄ (Arka Rakshak) (0.740 %).
Bayesian decision theoretic design of two-founder experimental crosses given diallel data

In designing experimental crosses of inbred strains of model organisms, researchers must make a number of decisions. These include the selection of the appropriate strains, the cross design (eg. F2 intercross), and the number of progeny to collect (sample size). These decisions strongly influence the potential for a successful quantitative trait locus (QTL) mapping experiment; good design decisions will lead to efficient and effective science. Thus experimental design deserves careful consideration and planning. Experimental outcomes can be quantified through utility functions using a Bayesian decision theoretic approaches. For QTL mapping experiments, the power to map a QTL is an appealing utility function to maximize. Using any utility function to aid in experimental design will be dependent on assumptions, such as the QTL effect size in the case of power. Rather than arbitrarily selecting QTL effect size values, they can be estimated from pilot data using a Bayesian hierarchical model. The information in the pilot data can be propagated to the utility function, using Markov Chain Monte Carlo (MCMC) to sample from the posterior distribution. Key features of this approach include: 1) distributional summaries of utility, which are preferable to point estimates, and 2) a comprehensive search of the experimental space of crosses of inbred lines for well-designed experiments. We evaluate this Bayesian theoretic approach using diallel crosses as the pilot data. We present results from simulations as well as present examples from both Mendelian and complex traits in the founder strains of the mouse Collaborative Cross. All analyses were performed using our R package, DIDACT (Diallel-Informed Decision theoretic Approach for Crosses Tool), developed to perform Bayesian cross selection based on diallel pilot data.
Análisiscomparativodelas propiedades mecánicas de geopolímeros queincorporannanowhiskersdeSiCynanopartículasdeTiO2

Un geopolímero a base de metacaolin fue fabricado con 5 proporciones de dos nanomateriales diferentes. Por un lado, nanowhiskersde carburo de silicio y, por otro lado, nanopartículas de dióxido de titanio. Ambos fueron colocados en agua y recibieron energía ultrasónica para ser dispersados. Fueron analizadas los efectos sobre las propiedades mecánicas y la cinética de reacción. Comparados con la matriz de referencia, los resultados evidenciaron una tendencia al incremento de la resistencia a la flexión. Probablemente por la geometría de los nanowhiskersde SiC y el refinamiento de poros por las partículas de nano-TiO2. Las curvas de calorimetría mostraron que al incorporar nanopartículas de TiO2se obtuvo una reducción del 92 % en el calor total, mientras que, los nanowhiskers de SiC produjeron una reducción del 25 % en el calor total.