Miracle-dz/UniFAR-FTUs huggingface dataset:
Glutathione S-transferase M1-T1 null genotypes and susceptibility to Hodgkin’s lymphoma

(GSTs) have an important role in the detoxification of a wide variety of toxins and carcinogens. Studies have been indicated that genetic variation in the GST gene family may lead to susceptibility in HL. Hereby, we investigated the association of GSTT1 and GSTM1 null genotypes with HL in the Iranian population. This case-control study consisted of 76 patients suffering from HL and 120 healthy individuals as a control group. Genomic DNA was extracted and genotyping of GSTT1 and GSTM1 genes for the identification of their null genotypes was carried out using multiplex PCR method. Our findings indicated that GSTM1 null genotype is associated with risk of developing HL in our population (P=0.025; OR=2.00; 95%CI=1.110-3.602); however, no association was found for GSTT1 null genotype. Our study also showed that the GSTM1 null genotype increased the risk of disease in the individuals younger than 45 years, and it had a positive association with low ESR. GSTM1 null genotype may have the key role in increasing the risk of HL in the Iranian population.
Net displacement and temporal scaling: Model fitting, interpretation and implementation

Net displacement is an integral component of numerous ecological processes and is critically dependent on the tortuosity of a movement trajectory and hence on the temporal scale of observation. Numerous attempts have been made to quantitatively describe net displacement while accommodating tortuosity, typically evoking a power law, but scale‐dependency in tortuosity limits the utility of approaches based on power law relationships that must assume scale‐invariant tortuosity. We describe a phenomenological model of net displacement that permits both scale‐variant and scale‐invariant movement. Movement trajectories are divided into pairs of relocations specifying start‐ and end‐points, and net displacements between points are calculated across a vector of time intervals. A bootstrap is implemented to create new datasets that are independent both across and within time intervals, and the model is fitted to the bootstrapped dataset using log–log regression. We apply this model to simulated trajectories and both fine‐grain and coarse‐grain trajectories obtained from an Aldabra giant tortoise Aldabrachelys gigantea, African elephants Loxodonta africana, black‐backed jackals Canis mesomelas and Northern elephant seals Mirounga angustirostris. The model was able to quantify the characteristics of net displacement from simulated movement trajectories corresponding to both scale‐variant (e.g. correlated random walks) and scale‐invariant (e.g. random walk) movement models. Furthermore, the model produced identical outputs across time vectors corresponding to different intervals and absolute ranges of time for scale‐invariant models. The model characterized the tortoise as generally exhibiting long scale‐invariant steps, which was corroborated by visual comparison of model outputs to observed trajectories. Elephants, jackals and seals exhibited movement parameters consistent with their known movement behaviours (nomadism, territoriality and widely ranging searching). We describe how the model may be used to compare movements within and between species, for example by partitioning movement into scale‐variant and scale‐invariant components, and by calculating a unitless net displacement scaled to the basal movement capacities of an animal. We also identify several useful derived quantities and realistic parameter ranges and discuss how the model may be implemented in a variety of ecological studies.
Structural determinants of ion permeation in CRAC channels

CRAC channels generate Ca2+ signals critical for the activation of immune cells and exhibit an intriguing pore profile distinguished by extremely high Ca2+ selectivity, low Cs+ permeability, and small unitary conductance. To identify the ion conduction pathway and gain insight into the structural bases of these permeation characteristics, we introduced cysteine residues in the CRAC channel pore subunit, Orai1, and probed their accessibility to various thiol-reactive reagents. Our results indicate that the architecture of the ion conduction pathway is characterized by a flexible outer vestibule formed by the TM1-TM2 loop, which leads to a narrow pore flanked by residues of a helical TM1 segment. Residues in TM3, and specifically, E190, a residue considered important for ion selectivity, are not close to the pore. Moreover, the outer vestibule does not significantly contribute to ion selectivity, implying that Ca2+ selectivity is conferred mainly by E106. The ion conduction pathway is sufficiently narrow along much of its length to permit stable coordination of Cd2+ by several TM1 residues, which likely explains the slow flux of ions within the restrained geometry of the pore. These results provide a structural framework to understand the unique permeation properties of CRAC channels.
The role of activating transcription factor 3 in mouse skeletal muscle

Exercise has anti-inflammatory properties useful to prevent and treat some chronic diseases. The expression of activating transcription factor 3 (ATF3) increases in skeletal muscle after exercise. In many tissues, ATF3 regulates the inflammatory response. Whether ATF3 contributes to the anti-inflammatory properties of exercise in skeletal muscle was unknown. To understand the role of ATF3 in skeletal muscle, we used a mutant mouse model unable to express ATF3 (ATF3-KO). We found that the expression of some inflammation-related genes was higher in ATF3-KO than control mice postexercise. ATF3-KO mice also had an impaired molecular adaptation to training in skeletal muscle. Our data suggest ATF3 is an important regulator of the inflammation postexercise, which could influence training adaptation in skeletal muscle. Since inflammation is involved in the pathogenesis of many diseases, the identification of ATF3 as an exercise-induced anti-inflammatory factor is relevant for future studies.
Oxidative stress and antioxidant enzyme defence system in seminal plasma of common carp (Cyprinus carpio) and rainbow trout (Oncorhynchus mykiss) during spawning season

Shaliutina-Kolešová A. , Rui N. , Ashtiani S. , Rodina M. , Cosson J., Linhart O. (2018): Oxidative stress and antioxidant enzyme defence system in seminal plasma of common carp (Cyprinus carpio) and rainbow trout (Oncorhynchus mykiss) during spawning season. Czech J. Anim. Sci., 63, 78–84. Assessment of seminal oxidative stress indicators is emerging as a valuable prognostic tool in assisted reproductive technology. We investigated levels of oxidative stress caused by reactive oxygen species (ROS) and the antioxidant enzyme defence system comprising superoxide dismutase (SOD), glutathione reductase (GR), and glutathione peroxidase (GPx) in seminal plasma (SP) of common carp Cyprinus carpio and rainbow trout Oncorhynchus mykiss over the course of the spawning season. Oxidation was determined in lipids and proteins by assessing thiobarbituric acid reactive species (TBARS) and the 2,4-dinitrophenylhydrazine carbonyl groups, respectively. Levels of SOD were assessed by the autoxidation of pyrogallol. Determination of GR and GPx was based on the rate of NADPH oxidation. We observed clear alterations in lipids and proteins over the course of the spawning season in both species. The highest levels of TBARS and CP were recorded late in the season. SOD was not significantly altered in either species. The activity of GR was higher in carp SP late in spawning compared to other times (P < 0.05), while in rainbow trout, GR significantly increased (24.13 ± 2.8 mU/mg protein) in mid-season. A significantly lower GPx activity (9.18 ± 1.32 mU/mg protein) was found in rainbow trout SP early in the spawning season, but no significant differences in GPx were observed over the course of the season in carp. These results provide further understanding of the role of fish SP antioxidants and present new data on the oxidant and antioxidant balance in SP during the spawning season that may be of value in the development of methods for artificial reproduction of teleost species.
Impact of strain and dose of live yeast and yeast derivatives on in vitro ruminal fermentation of a high-grain diet at two pH levels

Abstract: The objective of this study was to determine the effects of live yeast (LY) or yeast derivatives (YD) on gas production (GP), dry matter (DM) disappearance (DMD), fermentation characteristics, and microbial profiles in batch culture. The study was a completely randomized design with a factorial arrangement: 2 media pH × 5 yeasts × 4 dosages. An additional treatment of monensin (Mon) was added as a positive control for each pH level. Media pH was low (5.8) and high (6.5); the yeasts were three LY (LY1-3) and two YD (YD4-5); and doses were 0, 4 × 106, 8 × 106, and 1.6 × 107 cfu mL-1 for LY and 0, 15, 30, and 60 mg bottle-1 for YD. Substrate consisted of 10% silage and 90% concentrate (DM basis) and samples were incubated for 24 h. Media pH of 6.5 vs. 5.8, increased (P < 0.01) GP, DMD, and volatile fatty acid (VFA) concentrations but decreased (P < 0.01) NH3-N concentration and copy numbers of Ruminococcus albus, Ruminococcus flavefaciens, and Selenomonas ruminantium. Increasing dose of LY2 linearly (P < 0.05) increased DMD. Total VFA concentration was greater with LY2 (P < 0.01) than LY3 and YD5 at pH 6.5. Overall, adding yeast products improved (P < 0.05) DMD at pH 5.8, and increased VFA concentration compared with Mon. These results indicate that in vitro GP and DMD of a high-grain diet varied with source and dose of yeast supplementation. Some yeast products have the potential to improve fermentation of feedlot diets when supplemented at appropriate doses.
Detection of the Trp-2027-Cys Mutation in Fluazifop-P-Butyl–Resistant Itchgrass (Rottboellia cochinchinensis) Using High-Resolution Melting Analysis (HRMA)

Abstract Itchgrass [Rottboellia cochinchinensis (Lour.) Clayton] is recognized as one of the most noxious and troublesome annual weeds in tropical and subtropical regions. Acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicides have been frequently used for managing R. cochinchinensis POST in a variety of crops, resulting in evolved resistance to these herbicides. Recently, resistance to fluazifop-P-butyl has been demonstrated for this weed, as the result of a G-to-C single-nucleotide polymorphism (SNP) that leads to the Trp-2027-Cys substitution in the ACCase enzyme. This study was conducted to develop a high-resolution melting analysis (HRMA) for the detection of the mutation underlying the Trp-2027-Cys substitution. The HRMA assay allowed differentiating between fluazifop-P-butyl–resistant (C mutant) and susceptible (G wild type) R. cochinchinensis plants. HRMA accuracy was confirmed with DNA sequencing of the target-site mutation, and no false positives or negatives were observed. Our results illustrated how HRMA is effective detecting the Trp-2027-Cys substitution in an R. cochinchinensis resistance, and how this technique can be of great value for developing high-throughput programs for monitoring evolution and dispersion of target site–based herbicide resistance at large scales.
Oral health status & treatment needs of patient attending anti retro-viral therapy among HIV patient in Government Medical College, Bhopal - A cross-sectional study

India has the third largest HIV epidemic in the world. The HIV/AIDS epidemic constitutes one of the most formidable challenges to development and social progress. Antiretroviral therapy (ART) is the most common treatment provided to HIV/AIDS patients. Oral lesions strongly associated to HIV/AIDS. Moreover, no evidential record of any study on AIDS patients attending retro viral therapy at Bhopal is present. So, a pioneer attempt has been made to assess the oral health status & treatment needs of patients attending anti-retro viral therapy in ART cell, G.M. C Bhopal. Material & methods: A Descriptive cross-sectional study design was employed. Total 320 patients were examined. All patient who reported in unit, since last 3 year were included in the study. data was collected and recorded using printed proforma. Consisted of WHO Oral Health Assessment form 1997. The collected data were coded, and statistical analysis was carried out using Statistical Package of Social Science (SPSS Version 22) chi-square, T test, unpaired T test, ANOVA is used. The statistical significance was fixed at 0.05. Results: A total of 320 study subjects were examined, 202(63.1%) were male and 118(36.8%) were females. 124(38.75%) had ulceration erosion on vermillion border. Total 145(45.3%) AIDS Patients had TMJ symptoms of pain. 7(2.1%) had malignant tumor, 11(3.2%) had leukoplakia, 18(5.8%) had lichen plannus, 98(30.06%) had ulceration, 67(20%) had candidiasis, 57(17.8%) had abscess. Total periodontal disease prevalence was 78.8 %,. Mean DMFT was 3.50±2.18, 50(15.6%) had dental trauma. Overall, one surface filling, two surface filling, extraction & pulp care restorations were most frequent treatment need. Conclusion: The study shows that HIV positive patients have poor oral health status. The use of antiretroviral drugs further depletes their oral health and is responsible for development of periodontal diseases, dental caries and oromucosal lesions. *Correspondence to: Vijayta Sharva, Senior Lecturer, Public Health Dentistry, Peoples Dental Academy, Bhopal (M.P.), India, E-mail: vijaytasharva@gmail.com
Validation of hair tubes for small mammal population studies

Survey techniques available to sample mammals have multiplied during the last decades. They offer new opportunities for sampling and monitoring populations, but before widespread use they need to be validated and calibrated to more traditional approaches. We conducted a quantitative assessment of hair tubes designed to monitor common small mammals by comparing results to live-trapping data. Hair tubes are inexpensive, easy to use, and noninvasive, which offers benefits regarding animal ethics. We considered the shape of the tube, application in field conditions, and validated hair-tube results in 3 different habitats based on experimental and field sampling in 2 countries. Tube size selected species entering into the tubes, with shrews detected in small tubes only and rodents in larger tubes. The number of tubes visited (with hair sample) was proportional to the number of individuals captured in live traps. Overall, tubes performed better than traps, detecting individuals where traps did not, making this technique promising for inventory of rare species. The sampling pattern was robust across wood, grassland, and cultivated field habitats and across seasons, which suggests that the proportion of hair tubes visited is a robust indicator of relative abundance of small mammals. In the context of population studies, hair tubes cannot replace trapping because the identification of species or individuals from hair collected in tubes is difficult and costly. We recommend combining hair tubes with livetrapping for increased efficiency and before species identification based on DNA sampling is applied to large-scale population studies.
The relationship between cheliped color and body size in female Callinectes sapidus and its role in reproductive behavior

The Relationship between Cheliped Color and Body Size in Female Callinectes sapidus and Its Role in Reproductive Behavior. (August 2003) Kirsten Laurene Williams, B.S., Humboldt State University Chair of Advisory Committee: Dr. Mary K. Wicksten Many species use color during courtship displays, with the more colorful individuals often selected as potential mates. Female blue crabs, Callinectes sapidus, display prominent red markings on their chelipeds, which is absent in males. I tested the hypothesis that females use this sexual dimorphism as an effective signal to potential mates. Body size was positively correlated with size of the colorful pattern on the crusher dactyl. Digital imaging techniques were used to examine and quantify a pattern of coloration in the female blue crab. Morphometric measurements were made using digital images of the carapace and chelae of crabs collected along the Gulf of Mexico coast in Galveston, Texas. Color complexity was examined on digital images of the chelae using Adobe® Photoshop® and Image J. Specific wavelengths were selected and their presence within the attribute quantified and evaluated. To determine whether male blue crabs prefer more colorful females, males were given a choice between females of different female coloration. Males displayed more often and directed more courtship displays towards the more colorful females. I hypothesize that male blue crabs use cheliped coloration as a visual cue for mate selection.
The changing role of fins in growing loliginid squid (Mollusca; Cephalopoda).

From the deep sea giants to the smallest planktonic larvae, virtually all squid need and use fins for swimming, despite being archetypal jet-propelled animals. Fins vary, not only in final adult shape (i.e. small, triangular; long, marginal; or large, rhomboid) and throughout ontogenetic growth, but also with the lifestyle of the squid species. The morphometric changes occurring to both body and fins in 126 loliginid squid (Loligo forbesi, L. pealei, L. vulgaris reynaudii, L. opalescens, Lolliguncula brevis and Sepioteuthis lessoniana) were studied over a billion-fold size range in this thesis. These species all belong to the Family Loliginidae and are shallow-water, coastal species with similar lifestyles. The shape of the fins in these species is very similar and an optimal width to length ratio was indicated for these long-finned adults. Also, the final fin length appears to be determined, not by species, but by the size the squid attains during growth.
Disorders in the System of Mineral and Bone Metabolism Regulators—FGF-23, Klotho and Sclerostin—in Chronic Kidney Disease: Clinical Significance and Possibilities for Correction

The chapter discusses the current understanding of the system of mineral and bone metabolism regulators—FGF-23, Klotho and sclerostin—disturbances in chronic kidney disease (CKD). In the chapter we presented the date, including our own results, which allow to suggest the change in the ratio of FGF-23-Klotho-sclerostin in CKD as an early biomarker not only for the chronic kidney damage but also for high cardiovascular (CV) risk. Results of studies show that disorders in FGF-23-Klotho-sclerostin ratio correlate with the frequency and severity of hypertension, vascular calcification, cardiac remodel - ling, anaemia, malnutrition, inflammation strong aggravate CV risk in CKD. It was found independent from blood pressure (BP) action of increased serum FGF-23 on the myocardium as well as the correlation of serum high-sensitive troponin I with increased serum FGF-23 and low Klotho levels in CKD patients. At the same time, it was shown that renoprotective therapy, including renin-angiotensin blockers, low-protein diet with amino/keto acid supplementation and phosphate binders, erythropoiesis stimulators, vitamin D metabolites used to get the target levels of BP, serum phosphorus, haemoglobin, parathyroid hormone and nutritional status disorders correction can reduce the risk of CV events, as the major cause of death in CKD patients.
Muyocopron garethjonesii sp. nov. (Muyocopronales, Dothideomycetes) on Pandanus sp.

During a survey of microfungi on leaves of Pandanus species in the Nabanhe Valley at Xishuangbanna, Yunnan Province, China in August 2016, we collected and isolated a new saprobic taxon belonging in Muyocopron (Muyocopronaceae). Both morphological characters and phylogenetic analyses of LSU and SSU sequence data provide strong evidence to place the new taxon in Muyocopron where it is described as M. garethjonesii. A description, photoplates of the macroand micro-characteristics, and a phylogenetic tree to resolve the placement of M. garethjonesii are provided.
Foliar spray of gibberellic acid influences morphological attributes and foliage yield of coriander (Coriandrum sativum L.)

A field experiment was conducted at the research field of Sher-e- Bangla Agricultural University, Dhaka during the period from December 1, 2016 to January 11, 2017 to investigate the effect of gibberellic acid (GA3) on vegetative growth, morphological attributes and foliage (leaf) yield of coriander (Coriandrum sativum L.). The experimental treatments consisted of eight different doses of GA3 viz., 0 (distilled water spray), 5, 10, 15, 20, 25, 30 and 35 ppm. The variety Rosina (Pahuja Co., India) was used as planting material and different doses of GA3 were applied on the plants at 25 and 30 days after sowing. The experiment was laid out in Randomized Complete Block Design with three replications. GA3 had significant effect on vegetative growth, morphology, foliage yield and yield contributing characters of coriander. Plant height, number of leaves plant-1, leaf length, plant spread and single plant weight were found maximum from the application of GA3 at 20 ppm, which was closely followed by 25 ppm GA3. Application of GA3 at 20 ppm produced the highest weight of foliage m-2. A strong positive correlation of foliage yield was observed with plant height, number of leaves plant-1, leaf length, plant spread, single plant weight and weight of foliage m-2. Application of GA3 at 20 ppm gave maximum foliage yield (9.34 t ha-1) which was followed by GA3 at 15 ppm (8.46 t ha-1) and 25 ppm (8.06 t ha-1), and the minimum foliage yield was recorded from control (distilled water spray) (4.90 t ha-1). Application of GA3 at 20 ppm increased foliage yield over control by 47.54 %. A quadratic relationship between applied GA3 concentration and foliage yield was found; the regression equation was y = 4.87 + 0.375x – 0.009x2 from which it came up to be optimum dose of GA3 as 20.83 ppm.Res. Agric. , Livest. Fish.5(1): 1-9, April 2018
Reducing stomatal density in Hordeum vulgare improves drought tolerance and water use efficiency

Manipulation of the expression of the epidermal patterning factor (EPF) family of secreted signalling peptides in order to regulate stomatal density has previously been demonstrated to improve water use efficiency in Arabidopsis thaliana (Franks et al., 2015). Following the sequencing of the barley genome an ortholog of EPF2 was identified and overexpressed. HvEPFL1 overexpression limits both entry into, and progression through, the stomatal lineage. Lines overexpressing HvEPFL1 showed significant increases over controls in terms of both water use efficiency and drought tolerance, without a detrimental effect on grain yield. This suggests that the manipulation of stomatal density could be utilised in order to futureproof crops against future climate change.