Miracle-dz/UniFAR-FTUs huggingface dataset:
Using SSR Marker to Trace Chinese Shrimp Fenneropenaeus chinensis Released in Natural Sea -A Feasible Strategy for Assessment of Release Effect in Natural Resources Recovery Program

Enhancement release has been proven effective in natural resources recovery of Chinese shrimp Fenneropenaeus chinensis in the last several decades in China, however, to assess the effectiveness of enhancement release, we still need to develop a high-efficient and easy-operational method to replace those physical-tagging release method with labor intensive, size-and number-limited. In the present study, single (with maternal known) parentage identification using eight simple sequence repeat (SSR) markers genotype fingerprint was used to trace Chinese shrimp released in Bohai Bay in 2013. A total of 884 shrimp spawners were collected from two hatcheries in Tianjin City respectively after enhancement release of shrimp larvae in May 2013. A total of 844 shrimp samples were recaptured around the release location approximately 4 months after the shrimp larvae were released into the natural sea. Genotype data of 8 SSR loci of the 1, 726 samples were used for maternal-offspring parentage identification using CEervus 3.0 software. The allele number in each locus ranged from 8 to 68 with an average value of 33.25, which produced the cumulative exclusion probability with one parent known of all these sight loci up to 99%. Among the 844 recaptured shrimp samples, 448 (♂:♀=212:232, gender information was lost for 4 samples) were successfully traced to their 337 maternal parents using a logarithm of odds (LOD) > 3.0 threshold. Among these 337 maternal parents, 253 had a single offspring, 62 had two offspring, 18 had three offspring, 3 had four offspring, and 1 had five offspring. For the first time, a large number of released shrimp were identified from recapture samples, and this study showed that it is possible to trace all released Chinese shrimp without using any type of physical tag in enhancement release activities. This not only means more precise recapture ratio assessment than ever expected, but also this method demonstrates an effective method for large-scale hatchery release as well as for organisms used in hatchery enhancement which are not suitable for physical tagging.
The evolution of fatty acid metabolism in chordathes

Gene duplication and loss are powerful drivers of evolutionary change. The role of loss in phenotypic diversification is notably illustrated by the enzymatic repertoire involved in vertebrate digestion. Among these we find the pepsin family of aspartic proteinases, including chymosin. Previous studies demonstrated that chymosin, a neonatal digestive pepsin, is inactivated in some primates, including humans. This pseudogenization event was hypothesized to result from the acquisition of maternal immune IgG transfer. By investigating 94 mammalian subgenomes we reveal an unprecedented level of cmy erosion in placental mammals, with numerous independent events of gene loss taking place in primates, dermoptera, rodentia, cetacea and perissodactyla. Our findings strongly suggest that the recurrent inactivation of cmy correlates with the evolution of the passive transfer of IgG and uncover a noteworthy case of evolutionary cross-talk between the digestive and the immune system, modulated by gene loss. PROTEIN DIGESTION AND GASTRIC PROTEASES VI
Conservation of woodland birds in a fragmented rural landscape

Increasingly, conservation efforts are being extended towards agricultural and pastoral areas outside large reserves. This indicates a change from the view of the landscape as islands of native habitat in a hostile matrix, to one in which the landscape is regarded as a patchwork of differing levels of disturbance. This latter view considers the whole of the landscape as the biological resource. These trends are discussed in relation to land bird species near Armidale on the New England Tablelands, north-east New South Wales, Australia. We assess the conservation status of 137 species of land birds. Of these, six species are locally extinct, 18 are thought to be declining and 35 are vulnerable due to their dependence on healthy woodland. Only 33 species are abundant and widely distributed on the Tablelands. The remaining 45 species tend to be habitat specialists that are marginal to the Armidale Plateau, and may never have been common in the study area. Most of the species that are dependent on large areas of continuous woodland (>400 ha) are in this last group, and it is demonstrated that an emphasis on these species may result in a conservation strategy that is inappropriate for most of the land birds in the region. Indeed, this could result in the extinction of species that at present are secure. An alternative strategy, specific to areas outside large reserves, is proposed that aims to maintain local species richness. In this management plan, priority is given to core species that are tolerant of intermediate levels of habitat fragmentation.
Preliminary study of the impact of pig or goat manure fertilization of a meadow on oribatid mites

Abstract We investigated the impact of pig or goat manure fertilization of a meadow with doses of 80 kg N ha−1, 140 kg N ha−1, and 200 kg N ha−1 (plots 1-6) on oribatid mites. A control plot (0) was left unfertilized. The manure was applied to the meadow in the early spring of 2012, and soil samples were collected in the spring of 2012 and 2013. In total, 6053 oribatid mites were examined, including 1163 juveniles. The effect of fertilizing on the Oribatida depended on the dose of manure, but not on its type. A low dose of pig or goat manure did not affect the density of Oribatida, whereas the other doses decreased it, but only the highest doses decreased it significantly, compared to the control. Species diversity decreased with the dose of manure. In total, 24 species of Oribatida were found and some species reacted differently to both types of manure. For example, a low dose of pig manure significantly increased the density of Eupelops occultus, whereas the density of other species significantly decreased under the influence of the highest dose of pig manure (Achipteria coleoptrata), highest doses of pig and goat manure (Galumna obvia, Liebstadia similis), and medium and highest doses of goat manure (Scheloribates laevigatus).
Accuracy of a family-based genotype imputation algorithm

Genomic selection has been recently applied to dairy cattle breeding and is expected to substantially increase genetic gain. To estimate genomic breeding values, dense DNA marker panels are usually required to exploit the linkage disequilibrium (LD) between quantitative trait loci (QTL) and markers (Hayes et al. (2008)). A dense marker map is also a prerequisite for fine mapping in order to precisely locate QTL (e.g., Meuwissen and Goddard (2000)). Even though high-density genotyping is now feasible for dairy cattle, genotyping thousands of individuals with a high-density panel is still expensive. To bring down genotyping costs, a reference population can be genotyped with a high-density panel while other animals are genotyped with a low-density panel in which markers are evenly spaced. Then, using information from the reference population, genotypes for untyped loci can be inferred for individuals genotyped with the low-density panel (e.g., Habier et al. (2009)). Despite current advances in genotyping technology, missing data are fairly common in association studies. Usually missing genotypes are not randomly distributed and the failure rate for some individuals can be as high as 10% or even more. Implementation of fine mapping and genomic selection in presence of missing data can be challenging. Genotype imputation is simply a method for inferring missing genotypes to increase genome coverage and it is a powerful tool to increase the power of genome-wide association studies. Imputation can be used for three main purposes: 1) to infer the missing genotypes of markers that were not successfully called during genotyping, 2) to infer the genotypes of ungenotyped parents that have a sufficiently large number of genotyped progeny and 3) to infer genotypes for untyped loci in individuals genotyped with a low-density panel using a reference population genotyped for a high-density marker panel. The first case is for a situation where the rate of missing genotypes for some individuals is high. The second case is for a situation where DNA samples for some important ancestors are not available. The third case may be the most important one, and is primarily designed to reduce genotyping costs. The persistency of imputation accuracy over successive generations is of interest in this third case. Imputation algorithms can be classified as LD-based and family-based. Genetic linkage can effectively help with the imputation of long segments of haplotypes because of the small number of recombinations in the pedigree of close relatives. Therefore, when individuals are highly related, a modest number of markers for the low-density panel should be enough for accurate imputation (Li et al. (2009)). The objective of this article was to evaluate the accuracy of a family-based imputation algorithm for situations 2 and 3 described above.
Three new records of Gobiidae from Malta with morphology, colouration and identification of the smallest known juveniles of two small gobiid species

– individuals of small juvenile gobies, some of them just 10 mm long, were collected during a study on infralittoral cobble bed fauna around the Maltese islands between July and September 2011. These repre sent the first records of three gobiid species for Malta, including Gobius couchi Miller & el Tawil, 1974 and the smallest known juveniles of Millerigobius macrocephalus (Kolombatović, 1891) and Zebrus zebrus (Risso, 1827). Morphology and colouration, including diagnostic features and photographs, are provided for these spe- cies and the problems of identification of small juveniles are discussed. ont été collectés durant une étude de la faune des fonds de galets infralittoraux autour des îles maltaises entre juillet et septembre 2011. Ces derniers représentent pour Malte les premières signalisations de trois espèces de gobies: Gobius couchi Miller & el Tawil, 1974, les plus petits juvéniles connus de Millerigobius macrocephalus (Kolombatović, 1891) et de Zebrus zebrus (Risso, 1827). la morphologie et la coloration, comprenant les caractères utiles à la diagnose et les photo- graphies, sont décrites pour ces espèces et les problèmes d’identification des petits juvéniles sont discutés.
Freshwater crayfish invasions in South Africa: past, present and potential future

Freshwater crayfish invasions have been studied around the world, but less so in Africa, a continent devoid of native freshwater crayfish. The present study reviews historical and current information on alien freshwater crayfish species introduced into South Africa and aims to indicate which areas are at risk from invasion. As is the case elsewhere, South Africans have shown a keen interest in both farming and keeping freshwater crayfish as pets, which has resulted in Cherax cainii, Cherax destructor, Cherax quadricarinatus and Procambarus clarkii being introduced to the country. There is evidence of successful establishment in the wild for C. quadricarinatus and P. clarkii in different parts of the country. Species distribution models suggest that the eastern part of the country and parts of the Eastern and Western Cape are at higher risk of invasion. At present, illegal translocations represent the most likely pathway of crayfish spread in South Africa. A continued risk of invasion by freshwater crayfish species in South Africa is highlighted, which reinforces the need for more research, as well as for strong mitigation measures, such as stronger policing of existing regulations, management or eradication where feasible and public education.
Bovine epithelial cell responses to colonisation by Escherichia coli 0157:H7

E. colt 0157:H7 was the first identified pathogen of a group that have come to be referred to as Enterohaemorrhagic E. coli (EHEC) and was identified in 1983 as being associated with Haemolytic ureamic syndrome (HUS). This bacterium carries the potent cytotoxin Shigalike toxin (Stx), also known as verotoxin, which through the inhibition of protein synthesis causes cell necrosis in the endothelium of the renal vasculature and this leads to the triad of symptoms — renal failure, thrombocytopenia and microangiopathic haemolytic anaemia. EHEC is also associated with Haemorrhagic colitis in humans as endothelium of both the colonic vasculature and the renal system express Gb3 receptors. These receptors bind the toxin and internalisation of the toxin allows the inhibition of protein synthesis. EHEC is a food borne zoonosis and its reservoir host is the bovine and faecal contamination of the environment, the food chain and direct contact with cattle are the most recognised routes for human infection to occur. The bovine host is asymptomatically colonised in the field and detection and removal is problematic, any future intervention strategy to remove this pathogen from the national herd is likely to be expensive and labour
Sirtuin1, Inducible Nitric Oxide Synthase in Newly Diagnosed Iraqi Diabetic Patients

In Mammals Sirtuins (SIRTs) are members of the silent information regulator two family Sirtuin1 regulate a variety of cellular functions. It shows anti-oxidative, anti-inflammatory, and anti-apoptotic effects against cellular damage.SIRT1 conserves the cells by the mitochondrial biogenesis organizing, cellular energy and oxido reduction state. Vascular tissues are protected by SIRT1 too. In diabetic patients mutation in exon1 of SIRT1 (L107P) in insulin-generating cells conducted in over production of nitric oxide synthase (iNOS), TNF-α. Assessment of SIRT1 protein levels in newly diagnosed Iraqi diabetic in regards to family history Age, gender, and duration of disease, and its correlation with biochemical parameter in the same group. Measurement of iNOS, TNF-α. This study involved totally 40 volunteers. This group were subdivided (20) volunteers as newly diagnosis (DMT1) duration disease ˂1 year, group1 was subdivided to 10 male and 10 female: (10 with family history and 10 without family history) and group two healthy volunteers. Group1 All DMT1 were under insulin treatment. Healthy Volunteers (20) included in this study as control groups. None Healthy Volunteers were alcoholic, smoke, or having a history of (CVD) cardiovascular disease, thyroid disease, and hormonal abnormalities problems were exempted from this study.In the present study SIRT1, TNF-alpha, iNOS were measured by enzyme linked immune absorbent assay (ELISA). Biochemical parameters fasting glucose, body mass index (BMI), urea, creatinine and lipid profile that were measured by spectrophotometer technique in patients and healthy volunteers groups.The Statistical Analysis System- SAS (2012) program was used to effect of difference factors in study parameters. Least significant difference –LSD test (ANOVA) was used to significant compare between means. Estimate of correlation coefficient between difference parameters in this study.The results showed that a highly significant increase in levels of FBG, Urea, creatinine and lipid profile except HDL was decrease levels, BMI was decrease in newly diagnosis DMT1 with healthy volunteers groups. A significant decrease in SIRT1 protein, and a highly significant increase in TNF-alpha and iNOS in newly diagnosis DMT1 with healthy volunteers groups. A highly negative significantly correlation coefficient between SIRT1 and F.G. , TG. , VLDL,TG/HDL, A.I. and negative significantly correlation duration, urea, creatinine,T.CH., LDL. And non-significant correlation with age, BMI, HDL, CH/HDL and LDL/HDL. Effect of gender were insignificant of SIRT1. Effect of family history in patients. SIRT1 were all insignificant in patients with family history as with non-family history group. SIRT1 could decreases in the sera of DMT1 patients with family history, the decreased SIRT1 level reflect a mutation in SIRT1 gene, the decreases in SIRT1 on increases the incident of DMT1 complication.
Formation and Reversion of VBNC Cells of Salmonella Typhimurium Preincubated in Different Substrates

Objectives: Salmonella is one of the main dangerous opportunistic microorganisms, and it can persist in viable but nonculturable (VBNC) state in different foodstuffs, water, human or animal organisms etc. Thus it is important to know more about this form of bacterial existence. Methodology: In this study Salmonella Typhimurium 79 strain was used, in which RP4 plasmid was introduced. Prior to entering nonculturability inducing conditions cells of the strain were preincubated in one of the substrates that are typical sources of Salmonella contamination. Several additives and conditions were evaluated in order to revert nonculturable Salmonella into vegetative state. Results: Influence of preincubation in different substrates on speed and totality of entry into nonculturable state was determined. It was shown that preincubation in soil had the greatest impact on the Salmonella population. Control population, preincubated in nutrient broth, was the slowest to enter nonculturable state. Tested reversion factors had effects at different concentrations. The most efficient, though the slowest, way to revert Salmonella was to incubate VBNC cells in 0.9% NaCl. Conclusion: Obtained data reveal some reasons for strain differences in speed of formation of VBNC cells. Reversion was achieved using several supplements and conditions.
Reference evapotranspiration estimates by means of Hargreaves-samani and Penman-monteith fao methods with missing data in the northwestern Mato Grosso do Sul

We aimed to assess the performance of different methodologies to estimate the reference evapotranspiration (ET0) in different seasons for at 1, 3, 6 and 10 days for the Northwestern Mato Grosso do Sul. We used a set of daily data obtained from the networks of the Brazilian National Institute of Meteorology for Água Clara, Cassilândia, Chapadão do Sul, Paranaíba and Três Lagoas locations. The meteorological data used were: maximum and minimum air temperatures, wind speed, solar radiation, and relative humidity. The methodologies used for the ET0 estimation were Hargreaves-Samani and Penman-Monteith (PM-FAO) using all the meteorological data needed and missing data on relative humidity, solar radiation and wind speed. To compare ET0 values estimated by means of equations tested against the PM-FAO method we analyzed the parameters of linear regression equation “β0” and “β1”, coefficient of determination (r2), standard-error of estimate (SEE) and coefficient of performance (c). The PM-FAO method with missing data (relative humidity and wind speed) were the best alternatives to estimate ET0, followed by the PM-FAO method with missing solar radiation data in all timescales during fall and winter seasons. The HargreavesSamani method is not recommended to be used in its original form to estimate ET0 in the Northwestern Mato Grosso do Sul, in none of the timescales and seasons.
Temporal and Spatial Change in Diameter Growth of Boreal Scots Pine, Norway Spruce, and Birch under Recent-Generation (CMIP5) Global Climate Model Projections for the 21st Century

We investigated how climate change affects the diameter growth of boreal Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies (L.) H. Karst. ), and silver birch (Betula pendula Roth) at varying temporal and spatial scales. We generated data with a gap-type ecosystem model for selected locations and sites throughout Finland. In simulations, we used the current climate and recent-generation (CMIP5) global climate model projections under three representative concentration pathways (RCPs) forcing scenarios for the period 2010–2099. Based on this data, we developed diameter growth response functions to identify the growth responses of forests under mild (RCP2.6), moderate (RCP4.5), and severe (RCP8.5) climate change at varying temporal and spatial scales. Climate change may increase growth primarily in the north, with a clearly larger effect on birch and Scots pine than Norway spruce. In the south, the growth of Norway spruce may decrease largely under moderate and severe climate change, in contrast to that of birch. The growth of Scots pine may also decrease slightly under severe climate change. The degree of differences between tree species and regions may increase along with the severity of climate change. Appropriate site-specific use of tree species may sustain forest productivity under climate change. Growth response functions, like we developed, provide novel means to take account of climate change in empirical growth and yield models, which as such include no climate change for forest calculations.
Hay Rake-Type Effect on Ash and Forage Nutritive Values of Alfalfa Hay

High levels of ash content are problematic in hay since ash provides no nutritional benefit to livestock. Hay raking may impact ash content, but the effect of different hay rake types on ash content is unknown. The objectives were to determine the effect of rake type on ash content and forage nutritive values of alfalfa (Medicago sativa L.) hay. Replicated trials were conducted on two cuttings of alfalfa in Minnesota, Pennsylvania, and Wisconsin. During raking, two swath rows were combined using one of the following rake types: wheel, sidebar, rotary, or merger. Samples were collected during the four phases of hay harvest: standing forage, post-cut, post-raked, and post-baled or chopped and analyzed for ash content and forage nutritive values. Ash content was different in five of the six sites-cuttings post-raking (P ≤ 0.05). The hay merger and sidebar rake resulted in the least amount of ash (90–136 g kg–¹) while the wheel rake (100–153 g kg–¹) resulted in the greatest amount of ash. Differences in forage nutritive values were rarely observed due to rake type and ranged from 200–241 g kg–¹ crude protein (CP), 374–480 g kg–¹ NDF, and 393 to 532 g kg–¹ neutral detergent fiber digestibility (NDFd) post-raking. First cutting alfalfa differed in relative forage quality (RFQ) post-raking where the hay merger and sidebar rake tended to result in greater RFQ values (121–165) compared with the wheel rake (114–160; P ≤ 0.05). Using a hay merger or sidebar rake to combine swaths resulted in less ash content compared with a wheel rake; however, rake type rarely resulted in differences in forage nutritive values.