Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproductive Phenology of Eleutherodactylus bransfordii in Northeastern Costa Rica

-Eleutherodactylus bransfordii is an abundant leaf-litter frog at the La Selva Biological Reserve in northeastern Costa Rica. I studied a sample of 842 frogs collected from November 1973 to December 1974 to determine size and structure of the population and seasonality of reproduction in E. bransfordii. Individuals were measured snout-to-vent (SVL) and dissected to determine reproductive condition. Frogs were classified as adult female (SVL > 20.0 mm, oviducts wide and convoluted, ovaries containing large eggs or yolking follicles), adult male (SVL > 17.0 mm, nuptial pads well developed), or juvenile. The number of ovarian eggs was positively correlated with female body size. Female body size did not vary significantly among months, but the number of ovarian eggs did. Testis length varied significantly among months and was shorter in December 1973 than in other months. All three age-sex classes were captured in all months, and juveniles accounted for more than 50% of the monthly sample in 11 of 14 months. Juveniles in the smallest size class (SVL 10.0 mm) were collected in all months except October 1974, and were most abundant in February 1974. More frogs were collected during the dry season than in the wet season. Although the year-round occurrence of frogs suggests continuous reproduction, more juveniles were captured in the dry season suggesting some seasonality in reproductive output. , . , 99 i ia s a eptiles
1-Deoxysphingolipids cause autophagosome and lysosome accumulation and trigger NLRP3 inflammasome activation

ABSTRACT 1-Deoxysphingolipids (deoxySLs) are atypical sphingolipids of clinical relevance as they are elevated in plasma of patients suffering from hereditary sensory and autonomic neuropathy (HSAN1) or type 2 diabetes. Their neurotoxicity is described best but they inflict damage to various cell types by an uncertain pathomechanism. Using mouse embryonic fibroblasts and an alkyne analog of 1-deoxysphinganine (doxSA), the metabolic precursor of all deoxySLs, we here study the impact of deoxySLs on macroautophagy/autophagy, the regulated degradation of dysfunctional or expendable cellular components. We find that deoxySLs induce autophagosome and lysosome accumulation indicative of an increase in autophagic flux. The autophagosomal machinery targets damaged mitochondria that have accumulated N-acylated doxSA metabolites, presumably deoxyceramide and deoxydihydroceramide, and show aberrant swelling and tubule formation. Autophagosomes and lysosomes also interact with cellular lipid aggregates and crystals that occur upon cellular uptake and N-acylation of monomeric doxSA. As crystals entering the lysophagosomal apparatus in phagocytes are known to trigger the NLRP3 inflammasome, we also treated macrophages with doxSA. We demonstrate the activation of the NLRP3 inflammasome by doxSLs, prompting the release of IL1B from primary macrophages. Taken together, our data establish an impact of doxSLs on autophagy and link doxSL pathophysiology to inflammation and the innate immune system. Abbreviations: alkyne-doxSA: (2S,3R)-2-aminooctadec-17yn-3-ol; alkyne-SA: (2S,3R)-2- aminooctadec-17yn-1,3-diol; aSA: alkyne-sphinganine; ASTM-BODIPY: azido-sulfo-tetramethyl-BODIPY; CerS: ceramide synthase; CMR: clonal macrophage reporter; deoxySLs: 1-deoxysphingolipids; dox(DH)Cer: 1-deoxydihydroceramide; doxCer: 1-deoxyceramide; doxSA: 1-deoxysphinganine; FB1: fumonisin B1; HSAN1: hereditary sensory and autonomic neuropathy type 1; LC3: MAP1LC3A and MAP1LC3B; LPS: lipopolysaccharide; MEF: mouse embryonal fibroblasts; MS: mass spectrometry; N3635P: azido-STAR635P; N3Cy3: azido-cyanine 3; N3picCy3: azido-picolylcyanine 3; NLRP3: NOD-like receptor pyrin domain containing protein 3; P4HB: prolyl 4-hydroxylase subunit beta; PINK1: PTEN induced putative kinase 1; PYCARD/ASC: PYD and CARD domain containing; SPTLC1: serine palmitoyltransferase long chain base subunit 1; SQSTM1: sequestosome 1; TLC: thin layer chromatography.
Methionine concentration in the pre-starter diet: its effect on broiler breast muscle development

The effect of feeding diets of variable methionine concentration on breast muscle development was assessed in Ross 308 broiler chicks. Four isonitrogenous and isoenergetic starter diets were formulated to contain 7.8, 5.9, 4.6, and 3.4 g methionine/kg diet, and were provided for the first 7 days post-hatch. At 7 days of age all birds were placed on an industry standard starter diet with 5.9 g methionine/kg diet until 14 days, and then provided standard broiler grower (until 28 days) and finisher (until 42 days) diets. Birds were weighed periodically throughout the study and feed intake and feed conversion ratio were determined. Ten birds per treatment were sacrificed and weighed on 0, 1, 4, 7, 14, 21, 28, 35, and 42 days. The pectoralis major (breast muscle) was then removed from the carcass and weighed. Samples of breast muscle were collected for genetic and histological analysis. Expression of the myogenic marker genes, myogenic differentiation factor 1 and myogenin, which regulate satellite cell activity, and the adipogenic marker gene, peroxisome proliferator-activated receptor gamma (PPARγ), was measured. Histological assessment of breast muscle morphology and fat deposition morphology was also performed. No effect of dietary treatment was observed on body or breast muscle weight, feed intake or feed conversion ratio. Marker gene expression was also similar in all treatment groups, except for PPARγ. Significantly higher expression of PPARγ was observed at 0 days in the 5.9 g methionine/kg diet treatment, before dietary treatments were provided. Expression of PPARγ did not differ among treatment groups on any subsequent day. Methionine dietary treatment had no effect on the morphological structure of the breast muscle, or intramuscular fat deposition. These results suggest that under the conditions of this study, satellite cell activity in the early post-hatch chick, and subsequent muscle development, were not responsive to the variable methionine manipulations tested in the pre-starter period.
Effects of full-fat canola seed with an exogenous enzyme supplementation on performance, carcass characteristics and thyroid hormones of broiler chickens.

This research was performed to determine the effects of full-fat canola seed with enzyme supplementation on performance, carcass characteristics and thyroid hormones (T3 and T4) in broiler chickens. Two hundred and forty one_day-old chicks (ROSS 308) were used in a 2×4 factorial design with three replicates per each treatment. Treatments were 2 levels of enzyme supplementation (0 and 5 g/kg of diet) and 4 inclusion rates of full-fat canola seed (0, 30, 60 and 90 g/kg of diet). The results showed improved (P<0.05) broiler performance by inclusion of full-fat canola seed. Linear improvement was noted in feed conversion ratio (P<0.05) with an increase in dietary levels of canola seed. However, effect of enzyme supplementation on growth performance was not significant (P>0.05). Carcass characteristics, except for liver and pancreas percentage, did not influence by either full-fat canola seed levels or enzyme supplementation. The results of thyroid hormones indicated that use of canola seed, irrespective of enzyme supplementation, in diets changed T3 and T4 concentration at 7 and 42 days of age in broilers. In conclusion, use of full-fat canola seed in broiler diets had positive effect on growth performance.
Evaluation of Leaf Proteome in Wheat Genotypes Under Drought Stress

Drought stress in plants, the change (increase or decrease) in the production of plant proteins. Proteomics in recent years one of the most powerful tools that help us to study the changes in protein In order to investigate the proteome of wheat leaves in response to terminal drought, two genotypes susceptible and resistant wheat genotypes were evaluated under irrigated (non-stress) and rain-fed (stress) conditions. After applying stress and extraction of leaf proteins, two-dimensional gels were prepared and scanned. Analysis of gel images was performed using Same Spot Progenesis. About 657 protein spots were identified by the software. After alignment of the spots and their correspondence, 148 spot were identified visually and by using the software and statistical analysis was carried out. Five spots with Fold ≥ 1/5 at P ≤ 0/05 were identified, of which 4 spots were significant at P ≤ 0/05 and 1 spot was significant at P ≤ 0/01.
Structural Basis for the Recognition and removal of damaged bases from DNA by a DNA Repair Enzyme, 3-Methyladenine DNA glycosylase from Escherichia coli

Escherichia coli 3-methyladenine DNA glycosylase II is a DNA repair enzyme that removes numerous alkylated bases from DNA. The three-dimensional structure, mutagenesis and model building studies suggest that the active site is located in a cleft between the two helical domains and that the enzyme flips the target base out of the DNA duplex into the active-site cleft. The structural similarity among a variety of DNA glycosylases shows the existence of a DNA glycosylase family, whose members recognize diverse sets of substrates.
Cardiorespiratory Fitness, Adiposity, and Heart Rate Variability: The Coronary Artery Risk Development in Young Adults Study.

PURPOSE The importance of cardiorespiratory fitness versus adiposity in determining heart rate variability (HRV) is unclear. METHODS From the Coronary Artery Risk Development in Young Adults study, an observational cohort study, we included 2316 participants (mean age = 45.2 ± 3.6 yr at year 20, 57% female, 43% Black) with HRV measured in 2005-2006 (year 20) and graded exercise test duration (GXTd) and adiposity measures (body mass index and waist circumference) obtained in 1985-1986 (baseline) and 2005-2006. HRV measures (SD of all normal RR intervals [SDNN] and square root of the mean value of the squares of differences between all successive RR intervals [RMSSD]) were obtained from resting 30-s 12-lead ECG. Cross-sectional associations between GXTd, adiposity, and HRV were assessed at year 20. Longitudinal changes in GXTd and adiposity measures were categorized as ≥10% increase, <10% change (no change), or ≥10% decrease. We used multivariable logistic regression to assess associations of GXTd and adiposity measures with unfavorable versus more favorable HRV (lower 25th percentile vs upper 75th percentile). RESULTS A 1-SD increment in GXTd was associated with 22% and 32% lower odds of unfavorable SDNN and RMSSD, respectively; associations remained significant after adjustment for adiposity. A 1-SD increment in adiposity measures was associated with 16%-28% higher odds of unfavorable RMSSD; associations were not significant after adjustment for GXTd. Compared with no change/increase in GXTd, longitudinal decrease in GXTd was significantly associated with 55% and 94% higher odds of unfavorable SDNN and RMSSD, respectively, at year 20. These associations remained significant after adjusting for adiposity. CONCLUSION Cardiorespiratory fitness may be a stronger determinant of HRV than adiposity. Intervention studies are needed to better determine the differential effects of improved cardiorespiratory fitness versus weight loss on HRV.
Effects of single and mixed infections of Bean pod mottle virus and Soybean mosaic virus on host‐plant chemistry and host–vector interactions

Co‐infection by vector‐borne plant viruses is common, yet few studies have explored the effects of mixed infections on host‐plant phenotypes or plant–vector interactions. We documented the effects of single and mixed infection by Bean pod mottle virus (BPMV) and Soybean mosaic virus (SMV) on key biochemical plant traits and the behaviour and performance of virus vectors (BPMV: Epilachna varivestis, SMV: Aphis glycines) in order to understand how virus‐induced changes in plant phenotypes might influence (i) the acquisition and transmission of each virus by its respective vector in single infections, (ii) the likelihood of secondary infection for plants singly infected with either virus and (iii) the implications of co‐infection for virus transmission by vectors. Single infection by either BPMV or SMV increased host‐plant palatability for E. varivestis, potentially enhancing vector acquisition of BPMV from BPMV‐infected plants as well as the risk of secondary BPMV infection in plants infected with SMV. However, co‐infected plants were no more palatable to beetle vectors than mock‐inoculated plants. BPMV infection had minimal impacts on A. glycines. SMV infection reduced A. glycines population growth, but increased aphid feeding preferences for infected plants, a pattern likely not conducive to the (non‐persistent) transmission of SMV. Co‐infection eliminated the negative effects of single SMV infection on aphid population growth, and aphids exhibited a feeding preference for co‐infected (relative to mock‐inoculated) plants. Our results demonstrate that virus effects on host phenotype and vector behaviour can be modified by the presence of a co‐infecting virus, with potentially important implications for disease transmission.
Gaps in our Knowledge of Genetics underlying Common Familial Cancer

Copyright: © 2012 Neklason DW. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. It has long been recognized that cancers have a familial component; some cancers more strikingly than others. This is composed of both shared genetic and environmental factors. Twin studies (monozygotic versus dizygotic) have found statistically significant effects of heritable factors in prostate (42%), colorectal (33%), and breast (27%) cancers [3]. Mendelian genetic factors account for a small proportion of these heritable factors, most notably BRCA1 and BRCA2, APC, and the most common mismatch repair genes (MLH1, MSH2, PMS2, and MSH6). Although mutations in these genes confer a high relative risk of cancer, the fact that they are rare makes their population-attributable fraction low [2]. Case-control genome-wide association studies (GWAS) have characterized the other extreme of hereditary cancers-common genetic variants in the population which are associated with small increases in cancer risk [1]. With the GWAS, the relative risk estimates are on the order of 1.2 to 1.7, explaining only a small proportion of heritable risk. There is a large gap between these two extremes, representing 10 40% of the heritable risk that has yet to be defined. This is in part because cancer is a complex disease involving the interplay of multiple genetic and environmental factors. With the development of affordable whole genome sequencing technology, some of this may be teased apart in the not-so-distant future, but based on the low relative risk findings from the GWAS, its clinical utility is still in question.
Nuances of microalgal technology in food and nutraceuticals: a review

PurposeThe purpose of this paper is to acquaint the readers with the insights regarding the interventions of microalgal technology for production of metabolites and functional ingredients from microalgae for food and nutraceutical application and exploration of microalgae biomass for food application.Design/methodology/approachVarious information databases such as journals, library catalogues and professional websites were used to collect information pertaining to application of microalgae in food and nutraceutical sector. Systematic review was made with recent studies covering the vital aspects of art of microalgae cultivation for metabolite production, functional ingredients from microalgae, market scenario and utilisation of microalgae biomass for the valorisation of the food products. Key points have been discussed after every section to highlight the practical implications to make this review more insightful for the readers.FindingsMicroalgal technology provides sustainable solution for its application in food and nutraceutical sector. The heart of metabolite production lies in the optimisation of cultivation conditions of microalgae. Wide array of functional components are obtained from microalgae. Microalgae offer an alternative source for omega-3 fatty acids. Microalgae is widely exploited for production of pigments, namely, ß-carotene, astaxanthin, lutein, phycocyanin and chlorophyll, that have important implication as natural colourants and nutraceuticals in food. Larger diversity of sterols found in microalgae confers bioactivity. Microalgae is finding its place in market shelves as nutraceuticals where its functional ingredients are in the form of powder, tablets, extract and beverages and in innovative products such as microalgae protein and fat, culinary algae oil and butter. Sprulina and Chlorella are popular choice for the supplementation of food products with microalgae biomass.Originality/valueThis is a comprehensive review that highlights the application of microalgal technology for the development of healthy food products and presents holistic intervention in food and nutraceutical sector.
Handbook of Water Use and Conservation

Review: Handbook of Water Use and Conservation By Amy Vickers Reviewed by Russell A. Cohen Massachusetts Department of Fisheries, USA Amy Vickers. Handbook of Water Use and Conservation. Amherst, MA: WaterPlow Press, 2001. 446 pp. ISBN 1-931579-07-5 (hardcover). US$99.95. Recycled paper. paper. 'Water is our most precious resource' is a refrain expressed by many-from engineers and poets to politicians-yet humanity's actions have often belied those words. Amidst the world's growing population and increasing demand for more water, many regions around the globe are facing the hard realities of groundwater depletion, chronic drought, dried-up rivers, poor water quality, mounting infrastructure costs, and diminishing alternatives for additional supplies. As we peer into the 21st century, water conservation is looking far more like an imperative than an option (p. xv). So begins Amy Vickers' Handbook of Water Use and Conservation, to date the most authoritative, encyclopedic reference work available on this subject. The Handbook contains detailed descriptions of hundreds of water-efficiency technologies and practices for all customer groups-residential, landscape, industrial, commercial, institutional, and agricultural. Vickers backs up her claim that water conservation represents The Great Untapped Water Supply (p. xv) by presenting hundreds of proven water efficiency measures that reduce and control both short-term water demand (such as during drought and peak conditions) as well as long-term demand for each type of customer. Potential water savings and related costs are provided too, so you can know which measures will provide the best benefit/cost ratio for any type of customer. Vickers points out that many, if not most, water conservation measures have a relatively short payback time, often two years or less. As someone from a densely populated state where profligate household water use increasingly threatens the natural integrity of our streams and other hydric ecosystems, I found the Handbook's sections on domestic water use (and abuse) particularly valuable. Here's a brief example: The American obsession with lawns and lawn care products has come under scrutiny in recent years because of concerns about wasted water and the burdens of time, cost, and pollution that a well-manicured green lawn exacts from its owner and the natural environment (p.145). Vickers points out that lawn watering represents one of the biggest non-essential uses of water in many communities as well as the fact that keeping a lawn green with no brown spots during midsummer is often a costly, losing battle, even with regular
Propagation Methods Affect Fruit Morphology and Antioxidant Properties but Maintain Clonal Fidelity in Lowbush Blueberry

The berry morphology (size and weight), phytochemical content (polyphenols, flavonoids, anthocyanins, and proanthocyanidins), and antioxidant activity of lowbush blueberry (Vaccinium angustifolium Ait.) wild clone QB 9C and cultivar Fundy, propagated by tissue culture (TC) and softwood cutting (SC), were studied over two growing seasons to evaluate the effect of propagation methods on fruit yield and the content of antioxidant metabolites. Number of flower clusters, number of berries and berry weight per plant, diameter and weight of individual berry were higher in SC plants than those of TC plants. Significant interaction between genotypes and propagation methods were observed for total phenolic and flavonoid content of fruits. Berries from TC plants contained more polyphenols and flavonoids than those of SC plants. Twenty microsatellite markers were used to assess the clonal fidelity of TC regenerants and SC plants. The identical monomorphic amplification profiles within the TC plants of each genotype confirmed the clonal fidelity of micropropagated blueberry plants. These results indicate that propagation methods affected the morphology and antioxidant metabolites but maintained trueness-to-type genetic makeup in blueberry.
Evaluating The Effects Of Magnetic Susceptibility In Uxo Discrimination Problems

Past unexploded ordnance (UXO) clearance projects have demonstrated that the ability to detect UXO can be seriously hindered by the presence of magnetic rocks and soils. In particular, magnetic material affects the decay curve characteristics in electromagnetic surveys and this can adversely affect inversion calculations that try to estimate parameters of the UXO or answer the question of whether the item is UXO or scrap. Our research is in two parts. Firstly, we carry out numerical 1D forward modelling to evaluate the distortions of signals due to laterally uniform magnetic material. In the second part of the talk we examine how the distortions in the signal affect our inversion algorithms used for UXO discrimination.
Diffusion in zeolites : towards a microscopic understanding

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