Near-optimal Assembly for Shotgun Sequencing with Noisy Reads

Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption of no errors in the reads (noiseless reads). In this work, we show that even when there is noise in the reads, one can successfully reconstruct with information requirements close to the noiseless fundamental limit. A new assembly algorithm, X-phased Multibridging, is designed based on a probabilistic model of the genome. It is shown through analysis to perform well on the model, and through simulations to perform well on real genomes

Non-conformal coarse-grained potentials for water

Water is a notoriously difficult substance to model both accurately and efficiently. Here, we focus on descriptions with a single coarse-grained particle per molecule using the so-called Approximate Non-Conformal (ANC) and generalized Stockmayer potentials as the starting points. They are fitted using the radial density function and the density of the atomistic SPC/E model by downhill simplex optimization. We compare the results with monatomic water (mW), ELBA, as well as with direct Iterative Boltzmann Inversion (IBI) of SPC/E. The results show that symmetrical potentials result in non-transferable models, that is, they need to be reparametrized for new state-points. This indicates that transferability may require more complex models. Furthermore, the results also show that the addition of a point dipole is not sufficient to make the potentials accurate and transferable to different temperatures (300 K-500 K) and pressures without an appropriate choice of properties as targets during model optimization

Physicochemical properties and chemical composition of muscle tissue of young pigs of large white breed and their correlation with some serum enzymes

The aim of the study was to investigate the biochemical parameters of blood serum, physicochemical properties and chemical composition of muscle tissue of young white pigs of English origin, as well as to calculate the level of correlations between the main quantitative traits. The experimental part of the work was carried out in LTd “AF” Dzerzhynets” Dnipropetrovsk region, Research Center for Biosafety and Environmental Control of Agricultural Resources Dnipro State Agrarian and Economic University, Ltd “Globinsky Meat Plant” Poltava region, laboratory of zootechnical analysis of the Institute of Pig Breeding and Agriculture and livestock laboratories of the Institute of Cereals NAAS. Blood sampling for biochemical studies was performed in 5-month-old animals, serum activity of aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase and α-amylase was determined. Physicochemical properties and chemical composition of the longest muscle of the back (m. Longissimus dorsi) were studied on the indicators of “moisture holding capacity, %”, “color intensity, units. ext. × 1000”, “tenderness”, c, “fat content, %”, “total moisture content, %”, “protein content, %”, “heat loss, %”, and “energy value of muscle tissue, kcal”. It was found that the biochemical parameters of blood serum of young pigs of large white breed at 5 months of age correspond to the physiological norm of clinically healthy animals. Thus, the activity of aspartate aminotransferase (AST) is 1.33 ± 0.074 mmol/h/l, alanine aminotransferase (ALT) – 1.87 ± 0.063 mmol/h/l, alkaline phosphatase – 291.99 ± 12.517 IU/l,α-amylase – 169.82 ± 5.005 g/h×l. Studies of physicochemical properties and chemical composition of samples of the longest back muscle of young pigs of large white breed show that the number of high quality samples in terms of “moisture holding capacity, %” is equal to 12.0%, “color intensity, units. ext. × 1000” – 16.0 %, “tenderness, c” – 12.0 % and “fat content, %” – 16.0 %. Significant correlations were established between the following pairs of features: moisture holding capacity, % × protein content, % (-0.484 ± 0.1825, tr = 2.65), moisture holding capacity, % × heat loss, % -0.416 ± 0.1896, tr = 2.19), fat content, % × moisture holding capacity, %, (-0.450 ± 01862, tr = 2.42), fat content, % × energy value, kcal (0.836 ± 0.1144, tr = 7.31), alanine aminotransferase (ALT) activity, mmol/h/l × pH, units of acidity, (0.443 ± 0.1859, tr = 2.37), alkaline phosphatase activity, units/l × color intensity, units. ext. × 1000 (-0.483 ± 0.1826, tr = 2.65), alkaline phosphatase activity, units/l × P, % (0.484 ± 0.1825, tr = 2.65)

Level of phenotypic manifestation of feeding and meat qualities of young pigs of different intrabreed differentiation according to some multi-component evaluation indexes

The paper deals with the results of the search for fattening and meat qualities of young pigs of Large White breeds of different interbreeding differentiation according to some integrated indicators, the level of correlations between traits, and the economic efficiency of research results is calculated. The experimental part of the work was performed in agricultural formations of the Dnipropetrovsk region and the laboratory of animal husbandry of the State Establishment Institution “Institute of Grain Crops of NAAS of Ukraine”. Evaluation of young pigs for fattening and meat qualities was carried out taking into account the following indicators: average daily gain of live weight during the period of control fattening, kg, age achievement of live weight 100 kg, days, the thickness of the lard at the level of 6–7 thoracic vertebrae, mm, the length of the chilled carcass, cm. A comprehensive evaluation of young pigs for fattening and meat qualities was performed according to the Tyler and Sazer-Fredin indices. Economic efficiency of research results and biometric processing of the obtained data were carried out according to generally accepted methods. It was found that young pigs of the Large White breed of the controlled population at the age of 100 kg exceeded the minimum requirements of the elite class by 6.13%, the thickness of the lard at the level of 6-7 thoracic vertebrae – 32.25 % and the length of the chilled carcass – 3.92 %. A significant difference between animals of different interbreeding differentiation according to the Tyler index (groups I and III) was set up by the average daily gain of live weight during the control period of fattening (91.7 g), age of 100 kg live weight (7.3 days), lard thickness at the level of 6–7 thoracic vertebrae (3.4 mm), length of the chilled carcass (1.7 cm), length of bacon half of chilled carcass (2.7 cm). Taking into account the interbreed differentiation according to the Sazer-Fredin index, it is found that young pigs of the II group prevailed over their peers of I in terms of average daily increase in live weight during the period of control fattening by 4.03 %, age of achievement of live weight of 100 kg – 3.67 % and length of the chilled carcass – 0.2 %. The pairwise correlation coefficient between fattening and meat qualities of young pigs and evaluation indices ranges from -0.710 (tr = 10.24) to +0.844 (tr = 20.98). The maximum increase in additional products was obtained from young pigs of the first experimental group according to the Tyler index (+5.03 %) and the second experimental group according to the Sazer-Fredin index (+1.12 %). The cost of additional products got from the young pigs of these groups, provided that the selling price per 1 kg of live weight of young pigs at the time of the search was 47.5 UAH is +247.51 and +55.42 UAH/head, respectively

Feeding and meat qualities of young pigs of different genotypes according to melanocortin 4 receptor (Mc4r) gene and interbreed differentiation according to the coefficient of decrease in growth intensity in early ontogenesis

The paper presents the results of studies of fattening and meat qualities of young large white pigs of different genotypes for the melanocortin receptor 4 (Mc4r) gene and the decline in growth intensity in early ontogeny. The research was carried out in the agricultural formations of the Dnipropetrovsk region, the Jazz meat processing plant, the laboratory of the genetics of the Institute of Pig Breeding and APV of the National Academy of Sciences, and the laboratory of animal husbandry of the State Institution “Institute of Grain Crops of the National Academy of Sciences”. The work was carried out following the scientific research program of the National Academy of Sciences No. 30, “Innovative technologies of breeding, industrial and organic production of pig farming products” (“Pig farming”). Assessment of animals for fattening and meat quality was carried out taking into account the following characteristics: average daily gain of live weight during the period of control fattening, g; the age of reaching 100 kg live weight, days, length of the chilled carcass, cm; length of the bacon half of the cooled carcass, cm; thickness of lard at the level of 6–7 thoracic vertebrae, mm. The coefficient of decline in growth intensity was calculated according to the method of Yu. K. Sviechin. Biometric research results were processed using generally accepted methods. It was established that according to live weight at 4 and 6 months of age, fattening and meat qualities (age of reaching a live weight of 100 kg, days; lard thickness at the level of 6–7 thoracic vertebrae, mm; length of the chilled carcass, cm) young pigs the controlled population belongs to the I class and the elite class. The coefficient of growth decline in animals of the controlled population ranges from 108.57 to 142.51 points. The data analysis shows that according to the live weight at 4 and 6 months of age, the age of reaching the live weight of 100 kg, the fat thickness at the level of 6–7 thoracic vertebrae, and the length of the chilled carcass, the young pigs of the controlled population belong to the I class and the elite class. Animals of the Mc4r АГ genotype prevail over peers of the Mc4r AA genotype in terms of fattening and meat qualities by an average of 5.90 %. The interbreed differentiation of young pigs by the coefficient of the intensity of growth decline (∆K) shows that the difference between the animals of the experimental groups in terms of the average daily gain in live weight is 23.3 g (td = 2.62), the age of reaching 100 kg live weight is 2.7 days (td = 1.59), the length of the cooled carcass is 1.4 mm (td = 2.12). The number of reliable correlations between fattening and meat qualities, coefficient of the intensity of growth decline (∆K), and Tyler B. index is 75.0 %, which indicates the possibility of their use in selection and breeding work. The use of young pigs of the Mc4r АG genotype and animals of the I group, in which the coefficient of the intensity of growth decline (∆K) ranges from 115.61 to 123.27 points, provides additional production at the level of +3.68 – +1.75 % respectively

Vortex-induced vibrations of a freely vibrating cylinder near a plane boundary: experimental investigation and theoretical modelling

This work reports on experiments that were performed with a freely vibrating cylinder exposed to currents and placed near a plane boundary parallel to the cylinder axis. It is observed that the proximity of the boundary affects the vertical response of the cylinder in two ways: (i) for gaps between 0.75 and 2 diameters (D), the amplitude of oscillation is reduced; (ii) for gaps smaller than 0.75D, the cylinder impacts the boundary, resulting in an increase of amplitudes and frequencies of oscillations as the flow is accelerated. The in-line force acting on the cylinder is also examined, and the dependency of its harmonic components on the flow velocity and distance to the boundary is evaluated. Besides the typical amplification of the mean component inside the lock-in region, it is also observed that as the cylinder is placed closer to the boundary, the harmonic component with the frequency of the vertical oscillations increases, while the component with twice that frequency decreases in similar amount. Based on the experimental observations, an existing wake-oscillator model for vortex-induced vibrations is enhanced in order to account for the effect of the boundary. The proposed model introduces an effective damper that is activated when the cylinder reaches a certain distance from the boundary, and a damper/spring set representing the rigidity of the boundary and the dissipation of energy due to impact

System of antioxidant protection of the body of piglets under the action of feed additive “Butaselmevit-plus”

The aim of the study was to investigate the effect of the feed additive “Butaselmevit-plus” on the state of the antioxidant defense system of piglets during weaning. The experiments were conducted on the basis of the LTD “KOSHET” Mukachevo district of Zakarpattia region. Two groups of piglets were formed – control and experimental, in the amount of 10 individuals in each group, selected on the principle of analogs – age, breed and body weight. Animals were fed according to the norms for this age of pigs. On the 28th day of life, the piglets were weaned from the sow and regrouped from different nests for further maintenance during fattening and rearing with a change in the structure of the diet, which served as technological stress for the animal's body. Piglets of the experimental group, from 21 to 40 days of age, were additionally fed the feed additive “Butaselmevit-plus” at a dose of 100 mg/kg body weight per day. The material for the study was blood, which was taken in the morning before feeding the animals by puncture of the cranial vena cava for 20 days of life (the period before weaning), for 25 days of life (the period before weaning), for 30 days of life (2 days after weaning), for 35 days of life (7 days after weaning), 40 days of life (12 days after weaning). It is proved that feeding piglets feed additive “Butaselmevit-plus” enhanced the antioxidant status of piglets after weaning. It was found that under conditions of technological stress, the use of feed additive “Butaselmevit-plus” in the amount of 100 mg/kg body weight per day improves the antioxidant defense of the body, as evidenced by an increase in blood 35-day-old piglets superoxide dismutase activity by 26.7 % (P < 0.001), catalase – by 39.5 % (P < 0.001), glutathione peroxidase – by 51.7 % (P < 0.05), glutathione reductase – by 52.9 % (P < 0.05), the content of reduced glutathione – at 58.3 % (P < 0.001). These results confirm the effectiveness of the use of milk thistle, methionine, selenium, and vitamins A, E, and D3 in the feed additive “Butaselmevit-plus” to piglets in the period before and after weaning to activate the protective systems of their body

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software

In the current work we report on our participation in the SAMPL7 challenge calculating absolute free energies of the host–guest systems, where 2 guest molecules were probed against 9 hosts-cyclodextrin and its derivatives. Our submission was based on the non-equilibrium free energy calculation protocol utilizing an averaged consensus result from two force fields (GAFF and CGenFF). The submitted prediction achieved accuracy of 1.38kcal/mol in terms of the unsigned error averaged over the whole dataset. Subsequently, we further report on the underlying reasons for discrepancies between our calculations and another submission to the SAMPL7 challenge which employed a similar methodology, but disparate ligand and water force fields. As a result we have uncovered a number of issues in the dihedral parameter definition of the GAFF 2 force field. In addition, we identified particular cases in the molecular topologies where different software packages had a different interpretation of the same force field. This latter observation might be of particular relevance for systematic comparisons of molecular simulation software packages. The aforementioned factors have an influence on the final free energy estimates and need to be considered when performing alchemical calculations