Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of metabolomics data from twin families

Metabolomics is the comprehensive analysis of small molecules involved in metabolism, on the basis of samples that have been obtained from organisms in a given physiological state. Data obtained from measurements of trait levels in twin families can be used to elucidate the importance of genetic and environmental variation for individual differences in trait levels. I describe the results of various analyses using metabolomics data from twin families. These data originated from analysis of blood plasma lipids by liquid chromatography-mass spectrometry, and from analysis of blood plasma and urine by proton nuclear magnetic resonance spectroscopy. Data analyses with a newly developed method, based on hierarchical clustering analysis of family members, suggested that shared genetic variation and shared environmental variation are important for similarities in blood plasma lipid profiles among individuals. Also, a method called “quantile equating” was developed and applied that enables combination of semiquantitative metabolomics data sets originating from different measurement “blocks”. Univariate quantitative genetic analyses based on structural equation modeling revealed interesting differences in heritability among different metabolites. In multivariate analysis, relationships among genetic sources of phenotypic variation in different metabolites were investigated. These results bear relevance for the interpretation of the results from genome-wide association analyses.
Performance of Broccoli Cultivars in Spring and Fall Evaluations in Pennsylvania

S UMMARY . Recent hypothetical modeling suggests that increasing commercial broc- coli ( Brassica oleracea var. italica ) acreage in the eastern United States has the potential to notably reduce the costs of transportation within the broccoli supply chain. In this region, increasing broccoli acreage will require production improve-ments. Here, research was conducted to determine the best yielding commercially available cultivars for broccoli production. Eighteen to 19 cultivars of broccoli were evaluated in spring and fall evaluations using diverse production systems during 2014–15 in three locations across Pennsylvania. Data collected included production, yield, and quality attributes. Most interactions between site, year, and cultivar were signiﬁcant suggesting that environmental conditions inﬂuence broccoli yield, quality, and concentration of harvest. Overall, the cultivars evaluated were not different from, Imperial, the standard used, for marketable yield, head diameter, and concentration of harvest within a site year. Blue Wind was consistently the ﬁrst cultivar harvested, and Avenger and Emerald Jewel the last overall site years and growing seasons. These three cultivars may be good options for extending the growing season.
Milk composition and yield of the Red Sokoto (Maradi) goats in Nigeria

Eight adult Red Sokoto (Maradi) goats were used for lactation studies over three consecutive lactations of 15 weeks. At the start of the trial the goats weighed between 30 and 35 kg and were about two years old. The does were housed in individual pens with free access to salt licks and drinking water. Freshly cut grass Cynodon nlemfuensis ad libitum plus 1 kg of the concentrate (maize meal 58%, groundnut cake 18.5%, palm kernel cake 12% meat/bone meal 2.5%, vitamin mix 4% and salt 4%) was fed to each individual daily. The goats were hand milked twice daily and daily samples were bulked from each animal for subsequent analysis. The average weekly milk yield per head was 3.28 ± 1.78 kg. The composition of colostrum and milk are shown in Table 1.
The role of MEGF10 in skeletal muscle myopathy.

Mutations in the transmembrane protein MEGF10 (multiple epidermal growth factor-like protein 10) cause early-onset myopathy, areflexia, respiratory distress and dysphagia (EMARDD), an autosomal recessive congenital myopathy, characterized by reduced muscle fibre size. MEGF10 is reportedly expressed in satellite cells, playing a role in regulating cell proliferation and differentiation. The pattern of expression and the function of MEGF10 have not been clearly described. Cultured myoblasts, isolated single fibres and a muscle hyperplasia model were used to investigate changes in MEGF10 expression. Western blotting, immunofluorescence and RNAseq showed that MEGF10 was expressed at low levels in cultured myoblasts, suggesting that these cells are a poor model for studying endogenous MEGF10. Overexpression of GFP-tagged wildtype MEGF10 and MEGF10 containing pathogenic mutations decreased myoblasts cell motility and fusion. Isolated single fibres showed the presence of quiescent (Pax7+), committed and activated (MyoD+ or myogenin+) satellite cells after 2 - 4 days in culture. However, these cells did not consistently express MEGF10. A muscle hyperplasia model showed no MEGF10 expression in CD34+/Pax7+ or MyoD+ positive satellite cells, but MEGF10+/CD34- cells were present on these fibres. Finally, the expressed and purified extracellular domain (ECD) of MEGF10 was heavily post- translationally modified and facilitated myoblast attachment to a non- adherent surface. Pathogenic mutations in the ECD did not have a significant effect on myoblast fusion, whilst the wildtype ECD inhibited fusion. In conclusion, the choice of skeletal muscle model system is important in obtaining meaningful results. The discovery of MEGF10 expression in, as yet, unidentified CD34- cells on isolated fibres requires further study. MEGF10 is likely to respond to differing cues within the complex muscle environment to regulate myogenesis through cellular changes affecting differentiation and motility. Whilst EMARDD is a rare condition, insights into MEGF10 function may give insight into mechanisms of pathogenesis in a range of skeletal muscle diseases.
Toxicity and perturbation of the metabolite contents by a chitin synthesis inhibitor in the mosquito larvae of Culiseta longiareolata

Novaluron is an IGR of the benzoyl urea family, acting as a chitin synthesis inhibitor. The activity of a commercial formulation of Novaluron (10% EC) was tested, at different concentrations, ranging between 0.2 and 1.6 μg/l, against third and fourth-instar larvae of Culiseta longiareolata. (Diptera: Culicidae). The technical material showed a high level of activity with mortality recorded for both treated and following stages and happened after incomplete development. The LC50 values were 0.51 and 0.91 μg/l active ingredient for third and fourth instar larvae; and LC90 values were 2.32 and 4.30 μg/l respectively. In other experiments the compound was applied at LC50 and LC90 against the fourth instars larvae and its effects investigated on biochemical composition of larval body. Metabolite analyzes showed that novaluron affected significantly the amount of carbohydrates, lipids and proteins of fourth instars larvae starting from the day three following treatment. The carbohydrate and lipid amounts increased significantly whereas those of proteins decreased as compared with control series. For the same treated series a significant decrease was also recorded in the body weight with a decrease in development time. In the presence of chitin synthesis inhibitors, the last step of the chitin biosynthesis pathway is inhibited and the precursor is not converted in to chitin. It may either act on the hormonal level in the haemolymph to announce the synthesis, degradation or the inhibition of the metabolites. Than carbohydrates, lipids, proteins are under endocrine control and the exposure of the larvae to this xenobiotic product can modify the synthesis of these metabolites. The data obtained were discussed according to the mode of action of this insect growth regulator and the metabolism of lipids carbohydrates and proteins.
Considerations on neonatal ungulate capture method: potential for bias in survival estimation and cause-specific mortality

A recent study of Sitka black-tailed deer Odocoileus hemionus sitkensis demonstrated that opportunistic fawn capture yielded left-truncated data and ultimately resulted in overestimating fawn survival and spurious ecological model inference compared to neonates captured via vaginal implant transmitters (VITs). Given the ecological and economic value of ungulates worldwide and the importance of neonate survival to understanding population dynamics, the potential biases in survival estimates and causes of mortality caused by left-truncation must be transparent. Herein, we used a VIT-based dataset from white-tailed deer Odocoileus virginianus to examine potential problems with left-truncated data. We manipulated our original VIT-based dataset by randomly assigning age-at-capture to create three hypothetical opportunistic samples. We used the Kaplan—Meier estimator to quantify fawn survival to 16 weeks of age for the original and hypothetical datasets. Additionally, we compared the relative importance of mortality causes between the datasets. Survival for the original, VIT-based dataset was 0.121 (SE = 0.043), while hypothetical datasets yielded overestimates (ranging from 0.191 to 0.234). The hypothetical opportunistic samples overestimated coyote predation as a source of mortality, while underestimating starvation. Because management actions rely on accurate estimates of survival and causes of mortality, we recommend that neonatal survival studies consider biases caused by capture method. For robust estimates of survival, VIT-based samples appear to provide better estimates of survival, as opportunistic samples are biased high. We encourage future work to elucidate the potential for neonate capture technique to affect cause-specific mortality.
Managing mixed-stock fisheries: genotyping multi-SNP haplotypes increases power for genetic stock identification

A common challenge for fisheries management is resolving the relative contribution of closely related populations where accuracy of genetic assignment may be limited. An overlooked method for increasing assignment accuracy is the use of multi-SNP (single nucleotide polymorphism) haplotypes rather than single-SNP genotypes. Haplotypes increase power for detecting population structure, and loci derived from next-generation sequencing methods often contain multiple SNPs. We evaluated the utility of multi-SNP haplotyping for mixture analysis in western Alaska Chinook salmon (Oncorhynchus tshawytscha). Multi-SNP haplotype data increased the accuracy of mixture analysis for closely related populations by up to seven percentage points relative to single-SNP genotype data for a set of 500 loci; 90% accuracy was achievable with as few as 150 loci with multi-SNP haplotypes but required at least 300 loci with single-SNP genotypes. Individual assignment to reporting groups showed an even greater increase in accuracy .
Growth response of Catlacatla (Hamilton,1822) raised in manured tanks on low fishmeal diets,with a note on carcass composition and digestive enzyme activity

Low fishmeal diets (10%) with varied levels of maize (40-31%) and sardine oil (0-9%) were fed for 120 days to triplicate groups of catla ( Catla catla Hamilton,1822) fingerlings (average weight 1.84-1.90 g) stocked @ 1 fish per m 2 in cement tanks with soil base fertilised with poultry manure. Fish fed on diet containing 6% oil and 34% maize (T 2 ) showed the highest (p<0.05) growth, followed by those received 9/31 (T 3 ), 3/37 (T 1 ) and 0/40% (T 0 ) oil/maize supplemented diets. Food conversion ratio improved due to oil supplementation, while protein efficiency ratio was not affected significantly. Dietary lipid had a positive impact on carcass protein and lipid levels (p<0.05). Fish survival ranged from 90.73% in all the treatment groups to 92.58% in the control, without any significant (p>0.05) difference among them. Net fish production on termination of the experiment was lowest (820 g) in the control and the highest (1017.85 g) inT 2 treatment. Viscerosomatic index (VSI) varied from 3.59 (T 2 ) to 4.65% (T 0 ) and hepatosomatic index (HSI) from 1.13 (T 0 ) to 1.91% (T 3 ). RNA/DNA ratio was highest (3.05) in T 2 and lowest (1.84) in T 0 . An increase in intestinal amylase activity was observed in the treated fish, while intestinal protease and lipase activity showed increase only with higher levels of oil supplementation (6 and 9%). No difference (p>0.05) in enzyme activity was observed in the hepatopancreas of the control and treated fish. The results indicated beneficial effects of incorporating maize and fish oil in low fishmeal diet for catla.
Nutritional, managerial and hormonal strategies to mitigate the negative effects of heat stress on reproduction

This review aims to highlight past and recent research involving interrelationships of fertility and heat stress in dairy cattle. In addition, approaches to mitigate the negative effects of heat stress on reproduction in lactating dairy cattle will be discussed. With the continued increase in milk production per cow, sensitivity of the dairy cow to elevated climatic conditions has increased. Higher milk production associated with an increase in dry matter intake enhances metabolic heat production which aggravates thermoregulatory competence of lactating dairy cattle. A number of experiments have shown that milk production declines during summer months with a greater reduction in fertility. Intensive cooling of cattle still remains the superior strategy for improving both reproduction and milk production. Also, reducing the effects of heat stress prepartum appears to improve postpartum production performance; nonetheless, this period is often disregarded. Recent studies have evaluated both the energy demands and type of energy utilized during heat stress to support lactation. Increased demands for factors such as glucose and IGF-I during heat stress to sustain milk production may compromise early embryo development, in turn, increasing embryo loss. Recent research on manipulation of embryos in vitro with hormonal supplements has illustrated beneficial effects on fertility post transfer during summer. In addition, the use of various nutraceuticals and pharmaceuticals during summer has shown promise in negating summer fertility decline.
Health risk assessment of volatile organic compounds in urban areas

ABSTRACT The atmosphere is the first medium containing hazardous compounds entering the living environment. Metropolitan areas contain many industrial complex areas with high emissions of volatile organic compounds (VOCs), and consequently also large-scale exposure groups. As respiration is the most important part of the human exposure pathway, the atmosphere should be treated with greater importance than other media. It is therefore very important to monitor the emission of hazardous air pollutants (HAPs) and measure the concentration of VOCs in the atmosphere of such areas. It is essential to establish basic measures in order to protect public health as part of overall national safety management. This study utilized the national air pollution monitoring network data from Seoul, Incheon, and Gyeonggi, and investigated the differences in risk levels for humans considering various factors of the receptors, including gender and age. A total of 13 VOCs were categorized into carcinogens and noncarcinogens for risk assessment. The carcinogens 1,3-butadiene and benzene demonstrated a high level of cancer risk, ranging between 10−4 and 10−6, respectively. Noncarcinogens did not exceed Hazard Quotient (HQ) 1 in any area. The results will serve as important references for managing urban air environments and setting air quality standards.
Mating behaviour and reproductive output in insecticide‐resistant and ‐susceptible strains of the maize weevil (Sitophilus zeamais)

Insecticide resistance is a broadly recognised and well-studied management problem resulting from intensive insecticide use, which also provides useful evolutionary models of newly adapted phenotypes to changing environments. Two common assumptions in such models are the existence of fitness costs associated with insecticide resistance, which will place the resistant individuals at a disadvantage in insecticide-free environments, and the prevalence of random mating among insecticide-resistant and -susceptible individuals. However, cases of insecticide resistance lacking apparent fitness disadvantages do exist impacting the evolution and management of insecticide resistance. Assortative mating, although rarely considered, may also favour the evolution and spread of insecticide resistance. Thus, the possible existence of both conditions in the maize weevil (Sitophilus zeamais), a key pest of stored cereals, led to the assessment of the mating behaviour and reproductive fitness of insecticide-resistant and -susceptible weevil strains and their reciprocal crosses. The patterns of female and male mating choice also were assessed. Although mating behaviour within and between weevil strains was similar without mate choice, mating within the resistant strain led to higher reproductive output than within the susceptible strain; inter-strain matings led to even higher fertility. Thus, no apparent fitness cost associated with resistance seems to exist in these weevils, favouring the evolution of this phenotype that is further aided by the higher fertility of inter-strain matings. Mate choice reduced latency to mate and no inter-strain preference was detected, but female weevils were consistent in their mate selection between 1st and 2nd matings indicating existence of female mating preference among maize weevils. Therefore, if female mate selection comes to favour trait(s) associated with insecticide resistance, higher reproductive fitness will be the outcome of such matings favouring the evolution and spread of insecticide resistance among maize weevil populations reverting into a management concern.
Deep-sea polychaetes (Annelida) from the Malta Escarpment (western Ionian Sea)

Abstract The polychaete assemblages from an escarpment area in the western Ionian Sea are characterised in terms of species richness, evenness and trophic composition. Moreover, the first occurrence of the genus Barantolla in the Mediterranean Sea, and of Lumbrinerides carpinei and Exogone (Parexogone) campoyi in Italian waters, is reported. Aricidea trilobata Laubier and Ramos, 1974 is redescribed on the basis of new material with the new name Aricidea (Acmira) jeaneteae, together with a brief description of two deep-water species belonging to the genus Levinsenia.
The role of coastal areas in the Neogene-Quaternary mammal island populations of the central Mediterranean

Biogeographia vol. XXIII - 2002 (Pubblicato il 1” ottobre 2002) Biogeografia degli ambienti costieri The role of coastal areas in the Neogene—Quaternary mammal island populations of the central Mediterranean‘ FEDERICO MASlNl*, LAURA BONFlGLlO**, DARIA PETRUSO*, ANTONELLA CTNZLA **, LAURA ABBAZZl***, MASSIMO DELFiNO***, FLAVIANO FANFANl***, DANILO TORRE*** *Dz'pzzrti77m2r0 di Geolagizz e Geodesia, C50 Tukoiy I3], 1- 90134 Pzzlermo (Italy ) e—mzzz'[ﬁmz5z'nz' @um}gzz. it **Dz}uzrtz'mmto di Scimze dz/[:2 Term, Via Sperozze, 31- . /398166 Santﬂgara dzq M€55i7Zﬂ (ME) (Italy) e-mzzz'[: /zzzmz @/zzeczzrt. zmime. it ***Dipzzrrz'mem‘o di Scienze del/zz Term 6 M11520 di Storizz Nzzrzmz/6 rezizme Ge0—Pzz[e0I2r0Zogz'czz, Via G. Lzz Pin: 4, 1-5012] Firmze (Italy) e—mzzz'[: pzzleoz/ert@ce.rz't]. umﬁ. it Keywords: Vertebrate palaeontology, islands, neogenoquaternary, Mediterranean. models, case histories SUMMARY The fossil record, even with its severe limitations and uncertainties, provides the only direct access to the chronological and paleogeographical dimension of biological events and processes that took place in ancient insular environments in completely natural conditions. Terrestrial mammals, unlike other land vertebrates such as reptiles, have a high metabolic rate that requires large amounts of food and Water. This would lead one to expect that land mammals could not cross extended expanses of deep water. Differing abilities in colonising islands in large versus small mammals are also expected. One can roughly distinguish three groups of models to explain the occurrence of mammals on islands: 1) Insular mammals are the relics of a previous population (vicariance); 2) Mammals reached the island through filtering barriers ofvarious intensity (dispersals); 3) A third possible dispersal mechanism, is passive * Wor‘l( supported by grants CoFin MURST 1999 “Paleogeograﬁa del Mediterraneo centrale dal Miocene al Quaternario — Central Mediterranean paleogegraphy from Miocene to Quaternaryq.
Optimization of expression and purification of recombinant S1 domain of the porcine epidemic diarrhea virus spike (PEDV- S1) protein in Escherichia coli

ABSTRACT The PEDV-S1 protein, one of the members of a large family of PEDV, is significantly upregulated and has been targeted as a biomarker of cellular stress in several studies. Herein, conditions were optimized to increase the yield of recombinant PEDV-S1 protein in its native state, primarily focusing on the optimization of upstream processing parameters that lead to an increase in the specific as well as volumetric yield of the protein. The results showed that the production of PEDV-S1 was increased proportionally with increased incubation temperature up to 37 °C. Induction with 10 lM IPTG was sufficient to induce the expression of PEDV-S1 which was 100 times less than the normally used IPTG concentration. Furthermore, the results indicate that induction during early to late exponential phase produced relatively high levels of PEDV-S1 in soluble form. In addition, 5 h of post-induction incubation was found to be optimal to produce folded PEDV-S1 with higher specific and volumetric yield. Subsequently, highly pure and homogenous PEDV-S1 preparation was obtained using metal affinity and size exclusion chromatography. Taken together, the results showed successful production of electrophoretically pure recombinant PEDV-S1 protein in Escherichia coli (E. coli) in milligram quantities from shake flask liquid culture.
Pharmacokinetics and optimal dosage of kanamycin in domestic ruminant species.

Pharmacokinetics and optimal dosage of kanamycin were investigated in domestic ruminant species. In indigenous female adult Nili/Ravi buffaloes, Sahiwal cattle, Lohi sheep and Teddy goats, values of elimination half-life (t 1/2β), volume of distribution (V d) and total body clearance (Cl B) have been found to be greater than most respective values in their foreign counterparts. Elimination half-life values in domestic ruminants correspond to their respective glomerular filtration rate (GFR) values: the higher the GFR, the shorter the half-life. Comparison of half-life values in domestic ruminants with corresponding total body clearance values showed that shorter half-life should not be equated with higher clearance. To maintain the minimum inhibitory concentration (MIC) of 2 µg/ml of plasma, an optimal dosage regimen of 10.9, 10.2, 12.7 and 15.4 mg/kg body mass for priming and 9.31, 7.79, 11.7 and 14.7 mg/kg body mass for maintenance to be repeated at 12 hour interval have been suggested in buffaloes, cattle, sheep and goats, respectively.