Miracle-dz/UniFAR-FTUs huggingface dataset:
Stimuli-sensing channels

European Bioinformatics Institute, New York University Langone Medical Center, Ontario Institute for Cancer Research, Oregon Health and Science University. The contents of this document may be freely copied and distributed in any media, provided the authors, plus the institutions, are credited, as stated under the terms of Creative Commons Attribution 4.0 International (CC BY 4.0) License. For more information see our license. This is just an excerpt of a full-length report for this pathway. To access the complete report, please download it at the Reactome Textbook. 15/11/2022
Despotic behaviour and the evolution of migration patterns in birds

The despotic distribution described by Fretwell and Lucas (1970) and the ideal free distribution of individuals differing in competitive ability (Parker and Sutherland 1986) were applied to the evolution of migration patterns. In both theories, dominant individuals monopolize the best resources but dominance is mediated by prior occupancy in the former and by body size in the latter. Additional parameters used were latitudinal suitability gradients for both breeding and wintering, and costs of migration between sites. When migration costs are high, leap-frog migration is the most likely pattern to develop. Chain migration develops when either of two intricate conditions are fulfilled: (1) Both the breeding and the wintering suitability gradients increase towards the north and dominance is due to body size. (2) Breeding suitability increases towards the north and wintering suitability towards the south and dominance is due to prior occupancy. Under special circumstances, no stable pattern is likely to develop.
Effects of alternative dietary lipid sources on lipid metabolism and regulation of food intake in larvae and juvenile senegalese sole (Solea senegalensis)

This study analyses the effects of dietary lipid level and source on lipid absorption and metabolism in Senegalese sole (Solea senegalensis). Juvenile fish were fed 4 experimental diets containing either 100% fish oil (FO) or 25% FO and 75% vegetable oil (VO; rapeseed, linseed and soybean oils) at two lipid levels (~8% or ~18%). Effects were assessed on fish performance, body proximate composition and lipid accumulation, activity of hepatic lipogenic and fatty acid oxidative enzymes and, finally, on the expression of genes related to lipid metabolism in liver and intestine, and to intestinal absorption, both pre– and post–prandially. Increased dietary lipid level had no major effects on growth and feeding performance (FCR), although fish fed FO had marginally better growth. Nevertheless, diets induced significant changes in lipid accumulation and metabolism. Hepatic lipid deposits were higher in fish fed VO, associated to increased hepatic ATP citrate lyase activity and up–regulated carnitine palmitoyltransferase 1 (cpt1) mRNA levels post–prandially. However, lipid level had a larger effect on gene expression of metabolic (lipogenesis and β–oxidation) genes than lipid source, mostly at fasting. High dietary lipid level down–regulated fatty acid synthase expression in liver and intestine, and increased cpt1 mRNA in liver. Large lipid accumulations were observed in the enterocytes of fish fed high lipid diets. This was possibly a result of a poor capacity to adapt to high dietary lipid level, as most genes involved in intestinal absorption were not regulated in response to the diet.
The Epidermal Growth Factor Receptor Responsive miR-125a Represses Mesenchymal Morphology in Ovarian

The epithelial-to-mesenchymal transition (EMT) that occurs during embryonic development is recapitulated during tumor metastasis. Important regulators of this process include growth factors, transcription factors, and adhesion molecules. New evidence suggests that microRNA (miRNA) activity contributes to metastatic progression and EMT; however, the mechanisms leading to altered miRNA expression during cancer progression remain poorly understood. Importantly, overexpression of the epidermal growth factor receptor (EGFR) in ovarian cancer correlates with poor disease outcome and induces EMT in ovarian cancer cells. We report that EGFR signaling leads to transcriptional repression of the miRNA miR-125a through the ETS family transcription factor PEA3. Overexpression of miR-125a induces conversion of highly invasive ovarian cancer cells from a mesenchymal to an epithelial morphology, suggesting miR-125a is a negative regulator of EMT. We identify AT-rich interactive domain 3B (ARID3B) as a target of miR-125a and demonstrate that ARID3B is overexpressed in human ovarian cancer. Repression of miR-125a through growth factor signaling represents a novel mechanism for regulating ovarian cancer invasive behavior.
Mass Customization of Sheet Metal Parts by Numerically Controlled Driving [004-0047]

The manufacturing technique of driving is one of the oldest procedures for sheet metal forming and has been used for millenia. It is still utilized for niche applications but it has lost its importance today. The driving process is almost completely carried out manually and thus usually only appropriate for very small quantities. Since individualization of products is strongly gaining in significance, forming processes have to be found which are independent from expensive tools and machines. To use driving of sheet metal for individual manufacture, the grade of automation of the forming process has to be increased. Numerically controlled driving will need a conclusive simulation base. The multitude of influence factors, e.g. thickness and geometry of the sheet, forming forces, friction, strain hardening etc. and their influence on the process have to be identified and evaluated. Forming strategies will have to be automatically derived from the desired part geometry.
Promotion of Fruit Ripening of Ornamental Peppers by Ethephon

Fruit ripening of ornamental pepper (Capsicum annuum L.) was accelerated by the application of ethephon 3 to 6 weeks after anthesis. Concentrations as low as 75 μ1·liter−1 were effective, but 600 μ1·liter−1 resulted in foliar and fruit damage. Concentrations of 150 and 300 μ1·liter−1 were most effective, regardless of cultivar. Fruit <3 cm long were less sensitive to ethephon than more mature fruit. Raising the pH of the treatment solution from 3.3 to 6.3 resulted in increased effectiveness of the chemical, mainly due to an increased response by the larger fruit. Production time was reduced ≈1 day for every 5% increase in colored fruit due to ethephon. Chemical names used: 2-(chloroethyl)phosphonic acid (ethephon).
MOLECULAR AND GENETIC ASPECTS OF RIPENING AND QUALITATIVE TRAITS IN PEACH AND NECTARINE FRUITS

Expressed Sequence Tags (ESTs) and cDNA-AFLP analysis have been used to study gene expression during peach fruit ripening. An EST repertoire (1007 sequences) has been constructed using transcripts in nectarine fruit cv. 'Fantasia' at climacteric stage. The EST repertoire was reduced to 696 unigenes: in these 579 (83%) were singletons. EST analysis confirmed that in peach ripe fruit, genes involved in ethylene biosynthesis and cell wall metabolism are highly represented. Three transcription factors (TFs) homologous to SEPALLATA3, atb2, bHLH61 belonging to MADS, bZIP and bHLH families, respectively, have been identified. The abundance of the related transcripts suggests that these TFs play a regulatory role of ripening, as reporter in other fruits species. The EST repertoire has been included in a sequence database assembled by the Italian Consortium for Prunus spp genomic study to generate the first peach fruit microarray (μPEACH 1.0). EST analysis has been integrated with cDNA-AFLP to study a selection of the nectarine cv. 'Fantasia', named sir, characterized by a block of ripening. Data pointed out that the sir fruit phenotype might be due to disturbance in the onset of senescence.
The Influence of Elevated CO2 Concentration on Growth of Seven Grasses and One Clover Species in a Cool Maritime Climate

Abstract The effect of elevated CO2 concentration on the growth of eight common species and cultivars in Norwegian meadows—Festuca pratensis “Salten” and “Fure”, Festuca rubra “Koket” and “Leik”, Festuca arundinaceae “Vantage”, Festuca duruiscula “Barfina”, Poa pratensis “Lavang”, Agrostis capillaris “Aros”, Dactylis- glomerata “Apelsvoll”, and Trifolium repens “Grasslands Huia”—was studied during 11 weeks (April 26-early July). The study was performed in ten 9 m2 large field chamber units in a cool (11.3°C) maritime climate under long days (15.1–18.1 h), on the south-west coast of Norway (59°N, 6°E). The different species responded differently to elevated CO2 with respect to tillering, which was enhanced in A. capillaris (81%), D. glomerata (23%) and F. pratensis (36%), but was not significantly affected in the other species. The sward length was significantly decreased by high CO2 concentration, by 20% in P. pratensis, 36% in A. capillaris, 29% in D. glomerata, 26% in F. duruiscula, 36% in F. pratensis .
Morphologic and Habitat Characteristics of Black Sea's Endemic Goby Neogobius platyrostris (Gobiidae)

The flat-snout goby (Neogobius platyrostris), which is an endemic species for the Black Sea, inhabits in marine ecosystem. The aim of the present study is to provide data on live colouration, head lateral line system, sexual dimorphism, morphometric and meristic features and habitat preferences of this goby.
Effect of different feeds on growth, survival and production of African catfish (Clarias gariepinus Burchell)

An experiment was conducted to study the effect of different feeds on growth survival and production of African catfish (C. gariepinus) in six cemented tanks (3m 2 each) over a period of 120 days. Three different feeds namely Feed A (Saudi-Bangla fish feed, 33.43% protein), Feed B (formulated feed, 40.12% protein) and Feed C (chicken raw intestine, 59.58% protein) were applied to treatments I, II and III respectively. Each of the tanks was stocked with 24 fry with mean initial body weight of 2.56 ±0.06 g. Feeds were supplied to the fish ad- libitum daily in two instalments. Significantly highest weight gain was obtained in treatment III, however, survival rate was low compared to other treatments. The feed conversion ratio (FCR) values ranged from 2.52-6.4. Survival rate of fish varied between 83 and 96%. Treatment II yielded the highest (5000 kg/ha/120 days) production with the highest survival rate of fish. On the basis of survival rate and production, it is suggested that the formulated feed (Feed B) is suitable for the culture of C. gariepinus in cemented tanks.
Effect of Freezing on Infectivity of Toxoplasma Gondii Tissue Cysts in Pork.

To study the effect of low temperatures on infectivity of Toxoplasma gondii tissue cysts, pork from infected pigs was mixed with infected mouse brains and homogenized thoroughly. Twenty-gram samples of infected homogenized meat which were sealed in plastic pouches, pressed to a uniform thickness resulting in samples having the dimensions of ~. 2 × 16 × 18 cm, were subjected to temperatures of -1 to -171.1 °C for 1 s to 67.2 d. Treated samples were digested in HCl-pepsin solution and infectivity assayed in mice. A regression model from these data is described by the least squares linear regression: Square root of time for the inactivation of T. gondii (h) = 26.72 + 2.16 temperature (°C) with r = 0.77. T. gondii tissue cysts remained viable usually up to 22.4 d at -1 and -3.9°C and 11.2 d at -6.7°C but were usually rendered nonviable by freezing at -12.37°C. These data demonstrate that T. gondii tissue cysts are inactivated by freezing more readily than encysted Trichinella spiralis larvae.
Mineral Element and Total Phenolic Composition and Antioxidant Capacity of Seeds and Aerial Plant Parts of Perennial Legumes

ABSTRACT Naturally derived bioactive compounds with antioxidant activity and mineral component have a positive effect on human health. Consequently, legumes, including perennial species, have been used as healthy food or medicinal plants. Red clover (Trifolium pratense) and lucerne (Medicago sativa) have been researched more thoroughly for food components and supplements than zigzag clover (T. medium), black medick (M. lupulina), liquorice milkvetch (Astragalus glycyphyllos), cicer milkvetch (A. cicer), and sainfoin (Onobrychis viciifolia). However, information is scarce about the distribution of mineral elements and phenolics in plants of these species as well as the antioxidant capacity of their extracts. In this study, we determined the mineral composition and total phenolic concentration in seeds and whole aerial plant parts and morphological fractions of these perennial legumes, as well as the antioxidant activity of extracts of the above-mentioned plant parts. The legume accessions chosen for this study were rich in potassium (K), calcium (Ca), magnesium (Mg), phosphorus (P), zinc (Zn), and iron (Fe), especially at branching growth stage, and thus could be used for mineral fortification of staple foods. Astragalus species, particularly seeds of A. glycyphyllos, were the richest source of Fe. Trifolium pratense, T. medium, O. viciifolia, and A. cicer were valuable source of total phenolics and antioxidants. The flower and leaf extracts of red clover exhibited very strong 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity. In general, the tested perennial legumes and their plant parts have rich mineral composition and bioactive properties, and they can be used as functional ingredients to accommodate the need for a particular mineral element or a bioactive property.
Beach strandings as an indicator of at-sea mortality of sea turtles

Estimates of the number of federally protected sea turtles drowned during the 1991-1992 winter trawl fishery for summer flounder off North Carolina were compared to the number of turtles stranded on beaches adjacent to the fishing grounds. The objective was to evaluate how well beach strandings functioned as an indicator of fishery-induced mortality. The number of dead turtles that washed up on the beaches represented a maximum of 7-13% of the estimated fishery-induced mortalities. We attribute this discrepancy to offshore bottom currents, which normally transport lifeless turtles away from the beach during the winter. We conclude that turtle strandings during the winter on the northern beaches of North Carolina are a poor indicator of at-sea mortalities, and that they may not be entirely related to the winter trawl fishery for summer flounder.
Kinetika Immunoglobulin Kuning Telur Antiparvovirus Anjing Pada Anjing (KINETICS OF ANTICANINE PARVOVIRUS YOLK IMMUNOGLOBULIN IN DOGS)

Kinetic study on Anti CPV IgY has been performed on six dogs aged 5-10 months. The IgY was injectedintravenously at dose of 21.4mg /10kg body weight. IgY levels in the blood were determined by ELISA. Aresearch was conducted to find out the kinetics of Anti CPV IgY in dogs blood. The kinetics of IgY wascalculated by using regression analysis to determine the association on the levels of IgY in serum againsttime at injection. The results showed that kinetic parameters were calculated based on first order kinetics.The constant elimination rate of IgY was at the range between 0.007 to 0.015 / h. IgY concentration in thedogs blood was from 0.746 to 0.992 mg / mL. The half-life of IgY was from 1.65 to 4.01 / d. Volumedistribution of IgY was between 21.47 to 28,55 / mL. Total IgY in the dog bodies (AUC) was from 42,60 to142,00 mg / mL.h. The duration of the IgY in the dog’s body was 3.08 to 8.51 days. Clearance time of IgY was0.15 to 0.50 mL / h. In conclusion the kinetics of anti CPV IgY in dog’s body follow one compartment andfirst order model, which are only distributed in the blood with the half-life at 2.5 days, and IgY has lesspossibility to accumulate in the body compared to the IgG.
Determination of organic materials quality based on nutrient recovery, mineral fertilizer equivalency and maize (Zea mays L.) allometry

ABSTRACT Crop production in Sub-Saharan Africa is primarily limited by soil fertility decline. In view of this, the fertilizer value of locally available organic materials (OMs) was assessed for their nutrient release to crop growth. Crop residues and farmyard manure (FYM) were evaluated along with mineral fertilizers to grow a test crop maize variety – Gibe 2. The maize allometric parameters, nutrient ratios (NRs), nutrient recovery (NRy) and mineral fertilizer equivalency (MFE) were used to assess the mineral fertilizer value (MFV) of OMs. MFE of OMs was estimated as the available mineral N and P out of the fraction of total nitrogen and phosphorus applied relative to mineral fertilizers supply. The results revealed that maize allometry, NRy and MFE were significantly influenced by fertilizer sources. OM amendment resulted in poor maize allometry and low NRy. Interestingly, MFE of OM amended ranged from −201% with chickpea (CHP) residue to 63% with FYM. The results demonstrate that CHP has the poorest quality, while FYM is a good-quality OM as a fertilizer source.
Factors influencing germination of Canavalia brasiliensis, Leucaena leucocephala, Clitoria ternatea and Calopogonium mucunoides seeds

Several factors affecting germination of C. brasiliensis, L. leucocephala, C. ternatea and C. mucunoides seeds were investigated. They all show primary dormancy which is broken different treatments. Chemical scarification produced by hot water or sulphuric acid facilitate seed germination better than mechanical procedures. Temperature was another essential factor, 28°C providing the optimum condition. On the other hand, salinity affects seed germination, althoug some seeds showed relative tolerance to high salt concentrations.
Effect of rumen degradable protein with or without fermentable carbohydrate supplementation on blood metabolites and embryo survival in cattle

High intakes of dietary protein, particularly rumen degradable protein (RDP), lead to elevations in systemic concentrations of ammonia and (or) urea and these may be increased further if associated with inadequate fermentable energy intake. High systemic concentrations of ammonia and urea have been associated with reduced reproductive performance in cattle. The objective of this study was to examine the effect of RDP and fermentable energy intake on a range of blood metabolites and on embryo survival in heifers. Oestrous synchronized, nulliparous beef heifers (no. = 162) were randomly assigned in a 2 ✕ 2 factorial designed experiment to two levels of RDP and two levels of fermentable energy. Grass silage-based diets were supplemented with either 0 (0U) or 240 (240U) g dietary urea (460 g/kg N) and these in turn with either 0 (0P) or 3 (3P) kg dry matter of molassed sugar-beet pulp pellets (MSBP) per day. The four treatments were, therefore, (1) 0U + 0P (no. = 43), (2) 0U + 3P (no. = 44), (3) 240U + 0P (no. = 40) (4) 240U + 3P (no. = 35), respectively. Systemic concentrations of ammonia, urea, insulin, glucose and progesterone were measured. Heifers were given artificial insemination (AI) and embryo survival measured by ultrasonography at 30 and again at 40 days after AI. Systemic ammonia and urea were elevated (P 0·05). Plasma glucose was not affected by urea or MSBP treatment (P > 0·05) but was affected by day and time of sampling (P > 0·05). Plasma concentration of insulin was not affected by urea or MSBP supplementation or by day or time of sampling (P > 0·05). Plasma concentration of progesterone was not affected by diet or time of sampling (P > 0·05). The overall embryo survival rate was 62% and was not affected by dietary urea or fermentable carbohydrate or by systemic concentrations of ammonia, urea, glucose, insulin or progesterone (P > 0·05).
Predictive modeling of metagenomes

Human-associated microbial communities have been implicated in a variety of chronic diseases, including inflammatory bowel diseases, obesity, and autoimmune disorders like diabetes. Environmental communities are also important for bioconversion of waste products in biofuel production. However, microbiomes are highly complex systems involving mutualism and competition between many constituent organisms, and a variety of fundamental and interesting computational challenges remain in the modeling of pathogenicity and community-wide response to perturbations. In this thesis we discuss several computational and statistical approaches to predictive modeling of microbiome behavior using high-throughput metagenomic and transcriptomic sequencing data, including models that leverage biological structures such as phylogenies and gene ontologies to help extract features and constrain model complexity. We also demonstrate several applications of these approaches to real biological problems. We successfully apply predictive modeling to new studies of human-associated and environmental microbial communities in several interdisciplinary collaborations with colleagues at numerous institutions around the world. These include a prominent study of the species and genes present in diverse mammalian gut communities, a study of the effects of yogurt consumption on gut microbial taxa and gene expression (i.e. transcriptomics) in humans and mice, and a large cross-sectional global survey of the human gut microbiota in varied populations. We also develop SourceTracker, a Bayesian approach to predictive modeling of mixtures of microbial communities with important applications in forensics, pollution studies, public health, and detection of sample contamination. This dissertation introduces predictive modeling of human-associated and environmental microbial communities, increasing our ability to understanding the diversity and distribution of the human microbiota, and especially the systematic changes that occur in different physiological and disease states. We expect this type of predictive modeling to have far-reaching effects on health and disease.
Mechanism for Preventing Fungal Infection with Halocrusticida okinawaensis in Larvae of Swimming Crab by Adjusting pH of Rearing Water to 9.25

The mechanism for preventing fungal infection with Halocrusticida okinawaensis in larvae of swimming crab (Portunus trituberculatus) by adjusting pH of rearing water to 9.25 was investigated. The number of zoospores discharged in pH 9.25 sea water was not different from that in pH 8.00 sea water. Survival of zoospores at pH 9.25 sea water was about 1/3 of the survival at pH 8.00. Motility of zoospores was observed at 60 min after inoculation in pH 8.00 sea water, but at pH 9.25 motility was not observed after 30 min. The number of adhering zoospores on carapace of adult swimming crab in pH 9.25 sea water was not different from that in pH 8.00 sea water. These results with previous findings indicate that inhibition of the germination of encysted zoospores and reduction of the number of surviving zoospores in pH 9.25 sea water plays an important and secondary roles, respectively, in preventing fungal infection with H, okinawaensis in swimming crab larvae.