Miracle-dz/UniFAR-FTUs huggingface dataset:
Body condition (Wr) and reproductive potential of bighead and silver carp hybrids: Postzygotic selection in the Mississippi River Basin

Abstract Invasive bighead (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are reproductively isolated in their native range, but form a bimodal, multigenerational hybrid swarm within the Mississippi River Basin (MRB). Despite observed F1 hybrid superiority in experimental settings, effects of postzygotic selection on bighead and silver carp hybrids have not been tested in a natural system. Individual parent and hybrid genotypes were resolved at 57 species‐specific loci and used to evaluate postzygotic selection for body condition (Wr) and female reproductive potential (presence of spawning stage gonads and gonadosomatic index [GSI]) in the MRB during 2009–2011. Body condition in the Marseilles Reach, Illinois River declined with a decrease in species‐specific allele frequency from 1.0 to 0.4 for each species and early generation hybrids (F1, F2, and first‐generation backcross) had lower mean Wr than late generation hybrids (2nd+ generation backcrosses) and parentals. Proportions of stage IV and stage V (spawning stage) female gonads differed between bighead and silver carp, but not among parentals and their early and late generation hybrids within the MRB. Mean GSI values did not differ between parentals and hybrids. Because reproductive potential did not differ between hybrids and parentals, our results suggest that early generation hybrids occur in low frequency either as a factor of poor condition (Wr) and postreproductive survival, infrequent reproductive encounters by parental bighead and silver carp, or selection pressures acting on juvenile or immature life stages. Our results suggest that a combination of genetic and environmental factors may contribute to the postzygotic success of bighead and silver carp hybrids in the Mississippi River Basin.
Genome‐Wide Measurement and Computational Analysis of Transcription Factor Binding and Chromatin Accessibility in Lymphocytes

Cells of the adaptive immune system, including CD4+ and CD8+ T cells, as well as B cells, possess the ability to undergo dynamic changes in population size, differentiation state, and function to counteract diverse and temporally stochastic threats from the external environment. To achieve this, lymphocytes must be able to rapidly control their gene‐expression programs in a cell‐type‐specific manner and in response to extrinsic signals. Such capacity is provided by transcription factors (TFs), which bind to the available repertoire of regulatory DNA elements in distinct lymphocyte subsets to program cell‐type‐specific gene expression. Here we provide a set of protocols that utilize massively parallel sequencing–based approaches to map genome‐wide TF‐binding sites and accessible chromatin, with consideration of the unique aspects and technical issues facing their application to lymphocytes. We show how to computationally validate and analyze aligned data to map differentially enriched/accessible sites, identify enriched DNA sequence motifs, and detect the position of nucleosomes adjacent to accessible DNA elements. These techniques, when applied to immune cells, can enhance our understanding of how gene‐expression programs are controlled within lymphocytes to coordinate immune function in homeostasis and disease. © 2019 by John Wiley & Sons, Inc.
Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation

Significance Steroids are mainly produced by animals, while bacteria are major steroid consumers in the biosphere. Anaerobic environments are major reservoirs for estrogens; however, prior to this study, biochemical mechanisms involved in anaerobic estrogen catabolism remained completely unknown. Here, we characterized anaerobic estrogen catabolic pathway in denitrifying Denitratisoma sp. strain DHT3, which includes the transformation of estrogens into androgens via a cobalamin-dependent methylation. Data presented here complete the central pathways for bacterial steroid catabolism and reveal an unprecedented role of cobalamin in microbial steroid metabolism. Sex steroids are involved in bidirectional metabolic interactions between bacteria and their eukaryotic hosts; the discovery of retroconversion of estrogens into androgens in bacteria portends unexplored microbe–host metabolic interdependencies via this cobalamin-dependent estrogen methylation reaction. Steroid estrogens modulate physiology and development of vertebrates. Conversion of C19 androgens into C18 estrogens is thought to be an irreversible reaction. Here, we report a denitrifying Denitratisoma sp. strain DHT3 capable of catabolizing estrogens or androgens anaerobically. Strain DHT3 genome contains a polycistronic gene cluster, emtABCD, differentially transcribed under estrogen-fed conditions and predicted to encode a cobalamin-dependent methyltransferase system conserved among estrogen-utilizing anaerobes; an emtA-disrupted DHT3 derivative could catabolize androgens but not estrogens. These data, along with the observed androgen production in estrogen-fed strain DHT3 cultures, suggested the occurrence of a cobalamin-dependent estrogen methylation to form androgens. Consistently, the estrogen conversion into androgens in strain DHT3 cell extracts requires methylcobalamin and is inhibited by propyl iodide, a specific inhibitor of cobalamin-dependent enzymes. The identification of the cobalamin-dependent estrogen methylation thus represents an unprecedented metabolic link between cobalamin and steroid metabolism and suggests that retroconversion of estrogens into androgens occurs in the biosphere.
Role of TGF-β in the motility of ShcD-overexpressing 293 cells

The newly identified Src homology and collagen (Shc) family member ShcD was observed to be upregulated in 50% of vertical growth phase and metastatic melanomas. The aim of the present study was to investigate the mechanism by which ShcD mediates cell motility. 293 cell lines were altered to stably express GFP (GF) or GFP-ShcD (G5). Treatment of the cells with transforming growth factor (TGF)β2 promoted extracellular signal-regulated kinase (ERK) phosphorylation and, to a lesser extent, Smad2 phosphorylation in GFP-ShcD-expressing cells but not in GFP-overexpressing cells. GFP-ShcD-expressing cells exhibited upregulated expression of certain epithelial-mesenchymal transition-related genes, such as snail family transcriptional repressor 1 and SLUG, than GFP-expressing cells. Higher levels of ERK were found in the nuclear fraction of GFP-ShcD-expressing cells than that of GFP-expressing cells. Overall, GFP-ShcD-expressing cells demonstrated enhanced migration compared with GFP-expressing cells. A slight increase in cell migration was observed in both cell lines (GF and G5) when the cells were allowed to migrate towards conditioned medium derived from TGFβ2-treated GFP-ShcD expressing cells. Collectively, ShcD upregulation was proposed to induce cell migration by affecting the expression of certain epithelial-mesenchymal transition-related genes. Thus, our findings may improve understanding of the role of ShcD in cell migration.
Dupilumab to target interleukin 4 for inflammatory bowel disease? Hypothesis based on a translational message

Dupilumab is a human monoclonal antibody that has recently been approved for the treatment of mild-to-severe atopic dermatitis. Dupilumab inhibits the interleukin (IL)-4/IL-13 signalling by binding specific subunits of the receptors. IL-4 is involved in the regulation of both innate and adaptive intestinal immune system, thus its possible role in the pathogenesis of inflammatory bowel disease (IBD) has been investigated. Several polymorphisms of IL-4 have been found in patients with IBD. Furthermore, the crucial role of IL-4 has been demonstrated in Th2-driven models of colitis as well as in Th1-related models of this disease. Finally, many studies have shown the increased production of IL-4 in two models of experimental colitis: the dextran sulphate sodium – related colitis and the oxazolone-related colitis. In the latter, a dual antagonist of IL-4/IL-13 has proved to ameliorate the course of the disease. In conclusion, IL-4 antagonists might play a role in the treatment of IBD, especially in ulcerative colitis, which shows a classic pattern of Th2-related disease. and suggests
Carrier Recombination and Diffusion in Wet-Cast Tin Iodide Perovskite Layers Under High Intensity Photoexcitation

Tin iodide perovskite CH3NH3SnI3 is often considered as a replacement for toxic lead halide perovskites. Tin iodide is not only suitable for production of solar cells, but also it emits in the near-infrared spectral region, which is unique among the metal halide perovskites. On the downside, the CH3NH3SnI3 layers tend to be of high unintentional p-type doping, which significantly limits the solar cell efficiency. On the other hand, it is little known how this doping could affect other optical and electrical properties important for light-emitting applications. Here, we present an optical study of carrier diffusion and recombination pathways by time-resolved photoluminescence, differential transmission, and light induced transient grating techniques at excitations close to the lasing regime. We investigate several CH3NH3SnI3 layers formed by a solvent bathing method and using different antisolvents, causing different structural quality and doping level of the layers. We observe the amplified spontaneous em.
Investigating the influence of Thomson effect on the performance of a thermoelectric generator in a waste heat recovery system

ABSTRACT Since thermoelectric technology is a clean method to produce electrical energy, many researchers have been attracted to this field, recently. Different modelling and simplifying studies have been done to gain the best performance and optimum geometry of thermoelectric devices, but Thomson heat has not been considered, seriously. In this paper, using an analytical model, the effect of Thomson heat on the power and efficiency of a thermoelectric generator is investigated and amount of its influence in different conditions is explained. To compare different materials with the aspect of the rate of Thomson heat influence, Bi-Te and Pb-Te alloys are considered. It is seen that in different conditions, Thomson heat has different effects on the system efficiency. In low temperature ranges (lower than 650 K), although it has negative influence on the power and efficiency for both materials, Bi-Te has better performance than the other one. For the temperature ranges higher than 650 K, Pb-Te can be appropriate material since Thomson heat has positive effect on the power and efficiency for it.
Neurobehavioral Effects of Prolonged Exposure to Solid Air Freshener in Mice

Background: Air fresheners are products with fragrances used to mask unpleasant odor in the environment. However, air fresheners contain diverse chemical substances that pose health challenges to the users; hence are of public health significance. Although previous studies have shown that air fresheners affect the lungs, liver and reproductive organs, the neurobehavioral effects of these agents are yet to be evaluated in details. This study evaluated the neurobehavioral effects and biochemical changes in mice exposed to a solid commercially available air freshener (SAF). Methods: Male Swiss mice were divided into 6 groups (n = 7). Mice in groups 2-6 were exposed to powdered SAF (10, 25, 50, 100 and 200 g) via inhalation in their cages for 28 days. Mice in group 1 (control) were not exposed to SAF. The neurobehavioral changes: spontaneous motor activity (SMA), memory, anxiety and depression were evaluated on day 28. The mice brains were then proccessed for determination of malondialdehyde, nitrite, glutathione contents, and the activities of catalase and acetyl-cholinesterase. Results: SAF (25-200g) significantly (p<0.05) impaired SMA compared with control. Mice exposed to SAF exhibited increased anxiety and depression-like symptoms relative to control (p<0.05). It also impaired memory and increased acetylcholinesterase activity (p<0.05). Moreover, SAF increased the levels of nitrite and malondialdehyde accompanied by decreased antioxidant molecules (glutathione and catalase) in mouse brain. Conclusion: These findings suggest that SAF produced neurobehavioral deficits, increased oxidative stress and altered cholinergic system, posing potential health hazards to the regular consumers.
Identifying Factors Affecting the Quality of Teaching in Basic Science Education: Physics, Biological Sciences, Mathematics, and Chemistry

Basic science education provides the most fundamental knowledge for preparing students to pursue departmental major courses. Considering that basic science courses are laboratory classes conducted alongside theory classes, the factors affecting instructor–student communication and feedback can vary between theory and laboratory classes. We applied the ordinary least squares model to the refined data of basic science courses. We drew on variables reflecting instructor–student interaction such as class size, type of subject, and instructor characteristics to analyze the factors affecting student satisfaction with theory and laboratory classes. The analysis results indicated that the educational environment of a large-sized class could be improved by subdividing it into smaller groups to facilitate feedback. The use of online platforms to supplement offline courses provides an additional mechanism for the exchange of feedback and positively affects student satisfaction. We also confirmed empirically that the instructor–student communication which takes place during laboratory work, in contrast to the one-sided conveyance of course materials by the instructor in lectures, was a crucial factor in the quality of education. These results are linked to the demand for knowledge in engineering education, the student’s educational performance, and the labor market performance needed to establish a sustainable system in engineering education.
Drying Effect on Yields and Chemical Composition of Essential Oils Extracted from the Moroccan Mentha spicata (L.) Aerial Parts

Abstract Spearmint (Mentha spicata L.) is one of the most used species in Morocco. The whole herb and essential oil are used in flavoring tea and also have medicinal, cosmetic and industrial importance. In this study, the influence of drying on essential oil (EO) yields and chemical composition of spearmint was assessed. The spearmint aerial parts were harvested at flowering stage from two regions of Middle-Atlas: Meknes (Latitude: 33°53’42; Longitude: 5°33’17"; Altitude: 522 m) and Azrou (Latitude: 33°25’59"; Longitude: 5°13’01"; Altitude: 1278 m) and subjected to shadow drying method. The oils were extracted by hydrodistillation from dry leaves and flowers of the herb then analyzed using GC/MS. The obtained essential oil yield increased from 2.4 % to 4.48 % and 1.54 % to 3.8 %, respectively for M. spicata L. from Azrou and that from Meknes during six days of drying. The main compounds were carvone ranged from 47.30 % to 67.14 % and from 64.97 % to 69.19 %, limonene from 4.48 % to 9.03 % and 6.33 % to 15.43 %, then trans-4-caranone about 2.84 % to 4.63 % and 0.82 % to 2.08 % respectively for Azrou and Meknes spearmint. The high concentration of these compounds was observed on the fifth day for M. spicata from Azrou while for that from Meknes: the carvone rate reached its maximum on the 2nd day and limonene on the 3rd day. Moreover, some compounds appeared during of drying process as menthone and pulegone. So, the drying in shade process of spearmint can be suitable and recommended for high-oil yield and active components.
Anti-hyperuricemicactivity of granule formulated from Anonnamuricata L. fruit juice on hyperuricemia induce Sprague-Dawleys rat

The Annona muricata or soursop fruit has long been used in folk medicine for the treatment of variable ailments including hyperuricemia. Recent study has successfully formulated the soursop fruit juice into more practical preparation of instant granule drink. The aim of this study was toinvestigate the antihyperuricemic activity of instant granuleformulated from soursopfruit juice on hyperuricemia induce Sprague Dawleys rat. The soursop granulewas produced from fresh fruit juice with the addition of carboxymethyl cellulose (CMC), citric acid, sucralose and maltodextrin. Different doses of granule (90mg/200g b.wt.180 mg/200g b. wt. and 270 mg//200g b. wt.) were administeredorally to potassium oxonate-induced Sprague Dawley rats. The uric acid level of rats wasmeasured subsequently on the day 4, 8, and 12 of treatment period. The soursop fruit juice produced bright white granule with tipically fresh sour sweet taste, 2.9% water content (<5%), 1.91% ashcontent, 3.13 ml/s solubility, 29.3% angle of repose, and stable in the storage at 15C for two months. The soursop granule have shown significant antihyperuricemic activityin both male and female Sprague Dawley rats. The highest percentage of uric acid level decrease occurs at day 8in male rats treated with 270 mg soursop granule and at day 12 in female rats treated with 180 mglevel of soursop granule respectively. The overall the results show thatthe soursop granule has a potent as antihyperuricemic natural medicine which works in gender and time dependent manner, and can be developed to substitute synthetic antihypertensive drugs.
Effects of Limonene on the PAHs mutagenicity risk in Roasted Fish Skin

Traditional edible barbecue products use with lemon juice not only make the barbecue more delicious but also reduce the risk of PAHs in the barbecue products. One of the major economics crops in Taiwan, the waste from citrus fruits was very tremendous mass. However, the peelings of citrus fruits are rich in essential oil, especially, the limonene is the major. Whether the anti-carcinogenesis activities of terpene, such as limonene, in citrus fruits essential oil extraction. This study to demonstrate the PAHs content in fish skin increased markedly after being roasted at 210℃ for 20 minutes and greater mutagenicity risk of roasted fish skin was observed by Ame's test. The reduction of mutagenicity risk of roasted fish skin, which the antimutagenic abilities of substances in descending order were limonene > cold pressure oil > lemon >grapefruit. The antimutagenicity rate and ability of the three extracts were limonene: 18–23%; cold-pressed lemon oil: 18–22%; and steam distilled lemon essential oil: 8–16%. The obvious anti- mutagenicity effects against the PAHs mutagenicity of roasted fish skins can be found in citrus fruits essential oil extraction.
Evaluating a low‐cost portable NIR spectrometer for the prediction of soil organic and total carbon using different calibration models

This study aims to assess the performance of a low‐cost, micro‐electromechanical system‐based, near infrared spectrometer for soil organic carbon (OC) and total carbon (TC) estimation. TC was measured on 151 soil profiles up to the depth of 1 m in NSW, Australia, and from which a subset of 24 soil profiles were measured for OC. Two commercial spectrometers including the AgriSpecTM (ASD) and NeoSpectraTM (Neospectra) with spectral wavelength ranges of 350–2,500 and 1,300–2,500 nm, respectively, were used to scan the soil samples, according to the standard contact probe protocol. Savitzky–Golay smoothing filter and standard normal variate (SNV) transformation were performed on the spectral data for noise reduction and baseline correction. Three calibration models, including Cubist tree model, partial least squares regression (PLSR) and support vector machine (SVM), were assessed for the prediction of soil OC and TC using spectral data. A 10‐fold cross‐validation analysis was performed for evaluation of the models and devices accuracies. Results showed that Cubist model predicts OC and TC more accurately than PLSR and SVM. For OC prediction, Cubist showed R2 = 0.89 (RMSE = 0.12%) and R2 = 0.78 (RMSE = 0.16%) using ASD and NeoSpectra, respectively. For TC prediction, Cubist produced R2 = 0.75 (RMSE = 0.45%) and R2 = 0.70 (RMSE = 0.50%) using ASD and NeoSpectra, respectively. ASD performed better than NeoSpectra. However, the low‐cost NeoSpectra predictions were comparable to the ASD. These finding can be helpful for more efficient future spectroscopic prediction of soil OC and TC with less costly devices.
Automated segmentation of intraretinal cystoid macular edema based on Gaussian mixture model

We introduce a method based on Gaussian mixture model (GMM) clustering and level-set to automatically detect intraretina fluid on diabetic retinopathy (DR) from spectral domain optical coherence tomography (SD-OCT) images in this paper. First, each B-scan is segmented using GMM clustering. The original clustering results are refined using location and thickness information. Then, the spatial information among every consecutive five B-scans is used to search potential fluid. Finally, the improved level-set method is used to obtain the accurate boundaries. The high sensitivity and accuracy demonstrated here show its potential for detection of fluid.
Microcrystalline Cellulose as Pharmaceutical Excipient

Microcrystalline cellulose (MCC) is a pure partially depolymerized cellulose synthesized from α-cellulose precursor (type Iβ), obtained as a pulp from fibrous plant material, with mineral acids using hydrochloric acid to reduce the degree of polymerization. The MCC can be synthesized by different processes such as reactive extrusion, enzyme mediated, steam explosion, and acid hydrolysis. It is commonly manufactured by spray-drying the neutralized aqueous slurry of hydrolyzed cellulose. The MCC is a valuable additive in pharmaceutical, food, cosmetic, and other industries. MMC obtained from different sources will differ considerably in chemical composition, structural organization, and physicochemical properties (crystallinity, moisture content, surface area and porous structure, molecular weight, etc.). The high demand of microcrystalline cellulose used in pharmaceutical industries has led to the utilization of locally and naturally occurring materials in the production of microcrystalline cellulose. Many studies on the physicochemical properties of locally produced MCC derived from natural sources have been extensively evaluated in the development of a new natural source for MCC as a substitution of wood, the most abundant one.
Sized dependence and microstructural defects on highly photocatalytic activity based on multisized CdTe quantum dots sensitized TiO2

A series of sensitized TiO2 NPs with enhanced photocatalytic activity were prepared by different sized CdTe QDs with bifunctional ligand interlinking. The microstructures and morphologies of four different sizes of CdTe QDs and CdTe QDs sensitized TiO2 NPs were characterized systematically by fluorescence spectroscopy, UV‐Vis diffuse reflectance spectroscopy, FT‐IR, XRD, XPS, FE‐SEM, HRTEM, BET, and positron annihilation lifetime spectroscopy (PALS). The photocatalytic performance of CdTe QDs sensitized TiO2 NPs was investigated by degrading MO and MB in aqueous solution under visible light irradiation. The process of degradation complied with the first‐order reaction kinetics. Four different sized CdTe QDs sensitized TiO2 exhibited higher photocatalytic activities than TiO2. Particularly, yellow emitting CdTe QDs (3.28 nm) sensitized TiO2 (CT_1.5) showed the best photocatalytic performance, which may be attributed to the optimal NP size, and has a moderate light absorption and electron injection. The effect of microstructural defects on CdTe QDs sensitized TiO2 has been confirmed effectively by positron lifetime measurements.