Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Differentially Expressed Genes in Different Types of Broiler Skeletal Muscle Fibers Using the RNA-seq Technique

The difference in muscle fiber types is very important to the muscle development and meat quality of broilers. At present, the molecular regulation mechanisms of skeletal muscle fiber-type transformation in broilers are still unclear. In this study, differentially expressed genes between breast and leg muscles in broilers were analyzed using RNA-seq. A total of 767 DEGs were identified. Compared with leg muscle, there were 429 upregulated genes and 338 downregulated genes in breast muscle. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in cellular processes, single organism processes, cells, and cellular components, as well as binding and catalytic activity. KEGG analysis shows that a total of 230 DEGs were mapped to 126 KEGG pathways and significantly enriched in the four pathways of glycolysis/gluconeogenesis, starch and sucrose metabolism, insulin signalling pathways, and the biosynthesis of amino acids. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differential expression of 7 selected DEGs, and the results were consistent with RNA-seq data. In addition, the expression profile of MyHC isoforms in chicken skeletal muscle cells showed that with the extension of differentiation time, the expression of fast fiber subunits (types IIA and IIB) gradually increased, while slow muscle fiber subunits (type I) showed a downward trend after 4 days of differentiation. The differential genes screened in this study will provide some new ideas for further understanding the molecular mechanism of skeletal muscle fiber transformation in broilers.
Dosimetric evaluation of vaginal cuff brachytherapy planning in cervical and endometrial cancer patients

Purpose The aim of the study was to perform a prospective analysis of dosimetric consequences of rectal enema administration before vaginal cuff brachytherapy (VCB), the dose distribution in organs at risk (OARs), and the presence of air gaps (AGs) in patients with cervical or endometrial cancer. Material and methods In total, 75 patients treated in 2019 were randomly divided into two groups including 38 patients with and 37 without an enema before VCB. All patients received post-operative high-dose-rate (HDR). Single-channel vaginal cylinders with active length of 2.75 cm were used. Prescription dose was 7 Gy at 5 mm depth from the applicator surface in all directions. Treatment plans were based on computed tomography (CT). Results Enema performed before cylinder insertion had no effect on rectosigmoid Dmax or D2cm3. Rectosigmoid median V100 was 0.5 cm3 (range, 0-2.7 cm3). V100 ≥ 1 cm3 in 22 and ≥ 2 cm3 in 6 patients, with Dmax up to 19.7 Gy (282%) were observed. No effect of bladder volume in the range of 27-256 cm3 on Dmax or D2cm3 was found. The median bladder V100 was 0.1 cm3 (range, 0-1.4 cm3). There were 62 (83%) patients with AGs, with 24% at the top of the vagina and 75% on the remaining length of the vagina. Most of the AGs were small (≤ 3 mm), but in 5 (8%) cases, they were bigger than 5 mm. Conclusions VCB planning with the use of CT is essential. CT can facilitate the selection of optimal cylinder size to reduce the occurrence of large AGs. A few percent of plans require correction of dose distribution because of hot spots in OARs and the presence of AGs. Enema before cylinder insertion does not influence rectosigmoid Dmax and D2cm3. The analysis revealed no bladder volume effect on bladder doses Dmax and D2cm3.
Effects of experimental infections with larvae of Eustrongylides ignotus Jäegerskiold, 1909 and Contracaecum multipapillatum (Drasche, 1882) Baylis, 1920 in rabbits

Rabbits were infected per os with 10 Eustrongylides ignotus L4 and with 50 Contracaecum multipapillatum L3 per rabbit, recovered from naturally infected freshwater fishes (Hoplias malabaricus) in order to evaluate the patogenicity of these two nematode species in mammalian host. Two rabbits (20%) infected with E. ignotus died before the fourth day post-inoculation (one after 51 and the other after 78 hours). Six rabbits (60%) were inappetent until the fifth day following experimental inoculation. No clinical signs in rabbits inoculated with C. multipapillatum were observed; nevertheless, eight (80%) animals were positive for this nematode species. Rabbits inoculated with E. ignotus, had gastric congestion with hematoma of the gastric wall in 60% of the cases. Peritoneum was congested in 20% of the animals with the presence of peritoneal abscess in 10% of the cases. All inoculated animals showed hyperemia of the gastric mucosa with hemorrhagic gastritis due to infections with E. ignotus. In C. multipapillatum inoculated animals, the hyperemia was followed by disruption of the epithelial mucosa in the sites of parasite attachment. In the gastric mucosa, miscellaneous leukocitary infiltrates, with multifocal necrosis reaching the submucosa in the infections with C. multipapillatum were observed under bright field microscopy. Perforating lesions in several organs, mainly in the gastric wall, pancreas and liver, always in the presence of a mixed inflammatory process, intensely fibrous, with hemorrhage and necrosis were observed in animals infected with E. ignotus.
Genetic influence of vitamin D receptor gene polymorphisms on osteoporosis risk

Objective: Osteoporosis is the most common type of bone disorder characterized by low bone mineral density (BMD). It is a multifactorial disease and caused by the interaction of environmental and genetic factors. It has been reported that mutations in the vitamin D receptor (VDR) gene highly affect the metabolism of minerals, which reduces bone density. Therefore, this study aimed to determine the association of VDR gene polymorphisms TaqI (rs731236) and ApaI (rs7975232) with osteoporosis risk in the Saudi population. Methods: This case–control study involved 73 individuals with osteoporosis and 73 healthy controls in Jeddah, KSA. DNA extracted from peripheral blood was used to determine the genotypes and allele frequencies of VDR variants by polymerase chain reaction-restriction fragment length polymorphisms. Osteoporosis was confirmed by measuring BMD using dual-energy X-ray absorptiometry. The results were interpreted using the Hardy–Weinberg equilibrium assumption with P < 0.05 considered as significant. Results: A significant increase in the genotype frequencies of the ApaI (Aa) and (aa) was observed among osteoporotic patients compared to controls (P = 0.002 and P < 0.0001, respectively). Only the homozygous (tt) genotype of TaqI was significantly higher in those with osteoporosis than in the controls (P = 0.001). The minor “a” allele of ApaI and the “t” allele of TaqI were significantly more common in the patients as compared to controls (P < 0.0001 and P = 0.01, respectively). Conclusion: VDR polymorphisms ApaI and TaqI were found to be significantly determinant risk factors for osteoporosis progression in the Saudi population.
Zooplankton structure in heated lakes with differing thermal regimes and water retention

Zooplankton structure in heated lakes with differing thermal regimes and water retention The aim of the study was to determine the impact water retention time and increased water temperature had on the composition and abundance of zooplankton. Crustacea and Rotifera were examined from lakes Ślesińskie and Licheńskie, which are part of the water cooling system for the Konin and Pątnów power plants. Lake Ślesińskie is included in the cooling system periodically (from May to September) when the long cooling cycle is in operation, and its waters are heated moderately (< 25°C) with a water retention time of about two weeks. The zooplankton biomass in this basin in summer ranges from 1.5 to 4.0 mg dm-3 and was lower than that noted in May (< 25 mg dm-3) before the lake was included in the water cooling system. In Lake Licheńskie, which is heated continuously (< 30°C) and has a water retention time of about 5 days, the zooplankton abundance (< 100 indiv. dm-3) and biomass (< 0.5 mg dm-3) noted was low. In addition to temperature, one of the factors that affects zooplankton development in both lakes is the short water retention time. Struktura zooplanktonu w podgrzanych jeziorach o zróżnicowanej termice i retencji wód Celem pracy było określenie wpływu retencji i podwyższonej temperatury wody na skład i obfitość zooplanktonu. Zbadano skorupiaki i wrotki jezior Ślesińskiego i Licheńskiego, wchodzących w skład systemu chłodzącego Elektrowni Konin i Pątnów. Jezioro Ślesińskie włączane okresowo (maj-wrzesień) w cykl dużego obiegu wód pochłodniczych charakteryzuje się umiarkowanym stopniem podgrzania (< 25°C) i kilkunastodniową retencją wód (ok. 14 dni). Biomasa zooplanktonu wahała się latem w tym zbiorniku od 1,5 do 4,0 mg dm-3 i była niższa od notowanej w maju (< 25 mg dm-3), przed włączeniem jeziora w system schładzania wód pochłodniczych. W Jeziorze Licheńskim, stale podgrzewanym (< 30°C) o 5-dniowej retencji wód, notowano niską liczebność (< 100 osobn. dm-3) i biomasę (< 0,5 mg dm-3) zooplanktonu. W obu jeziorach, oprócz temperatury, czynnikiem modyfikującym rozwój zooplanktonu była niska retencja wód w zbiornikach.
Microbial communities in high altitude altiplanic wetlands in northern Chile : phylogeny, diversity and function

The phylogeny, diversity and function of microbial communities from several altiplanic wetlands was examined using an array of different but complimentary techniques. Results highlighted that microbial diversity exhibited a specific pattern in each wetland. Bacteria were dominant over Archaea in both freshwater and saline systems. Bacterial and archaeal diversity were both higher in sediment than in water samples. Lago Chungara, Laguna de Piacota and Bofedal de Parinacota are freshwater wetlands located at high altitude (>4400 m) in the north of Chile. They support microbial communities closely related to psychrophilic bacteria (e.g. Psychrobacter sp., Pseudomonas congelans, Flavobacterium psychrolimnae) in water and Proteobacteria and Actinobacteria in sediment samples. Salar de Huasco and Salar de Ascotan are located further south at an altitude of 3800 m and exhibit a wide range of salinities (varying between freshwater to 120 gL-1 of total dissolved salts). Microbial communities in these sites were characterized by bacteria tolerant to salt (e.g. halophilic Bacteria: Halomonas sp., halophilic Archaea: Halorubrum sp.). Cytophaga-Flavobacteria-Bacteroidetes was the most frequent group reported at the sites. In-depth studies focussing on the Salar de Huasco revealed a particular diversity of Archaea, characterized by a number of sequences related to uncultured groups and ammonia-oxidizing Crenarchaeota. Cyanobacteria from the Salar de Huasco were closely related to Cyanobacteria previously described from Antarctica. Isolates of halophilic bacteria and phototrophic bacteria displayed an elevated tolerance to different salt concentrations. The particular microbial diversity found in high altitude wetlands provides a new and exciting area of research.
A SAR Image Target Recognition Approach via Novel SSF-Net Models

With the wide application of high-resolution radar, the application of Radar Automatic Target Recognition (RATR) is increasingly focused on how to quickly and accurately distinguish high-resolution radar targets. Therefore, Synthetic Aperture Radar (SAR) image recognition technology has become one of the research hotspots in this field. Based on the characteristics of SAR images, a Sparse Data Feature Extraction module (SDFE) has been designed, and a new convolutional neural network SSF-Net has been further proposed based on the SDFE module. Meanwhile, in order to improve processing efficiency, the network adopts three methods to classify targets: three Fully Connected (FC) layers, one Fully Connected (FC) layer, and Global Average Pooling (GAP). Among them, the latter two methods have less parameters and computational cost, and they have better real-time performance. The methods were tested on public datasets SAR-SOC and SAR-EOC-1. The experimental results show that the SSF-Net has relatively better robustness and achieves the highest recognition accuracy of 99.55% and 99.50% on SAR-SOC and SAR-EOC-1, respectively, which is 1% higher than the comparison methods on SAR-EOC-1.
Effect of maceration on nitrogen fractions in hay and silage

An intensive mechanical conditioning treatment, referred to as maceration, was applied at mowing to alfalfa or timothy in order to enhance drying rate, reduce wilting time and possibly reduce respiration losses and proteolysis. In 1995, a laboratory trial was conducted using two levels of force (1750 and 3500 Newton) and five levels of conditioning: a control (no conditioning), one passage, three passages, five passages and seven passages through two steel knurled rolls. All forages were dried in a controlled environment at 30 °C and conserved as hay. The level of force did not affect the chemical composition of the forages obtained. However the nitrogen (N) fractions were affected by the level of maceration. As the level of conditioning increased, the soluble N fractions (A and B1) of both forages decreased (P < 0.001). Meanwhile, the slowly degradable N fraction (B3) increased linearly (P < 0.001) in timothy and quadratically (P < 0.003) in alfalfa. The fraction of unavailable N (fraction C) also increa.
Identifying the optimal donor for natural killer cell adoptive therapy to treat paediatric B‐ and T‐cell acute lymphoblastic leukaemia

Natural killer (NK) cells are an attractive source of cells for an ‘off the shelf’ cellular therapy because of their innate capacity to target malignant cells, and ability to be transferred between donors and patients. However, since not all NK cells are equally effective at targeting cancer, selecting the right donor for cellular therapy is critical for the success of the treatment. Recently, cellular therapies utilising NK cells from cytomegalovirus (CMV)‐seropositive donors have been explored. However, whether these NK cells are the best source to treat paediatric acute lymphoblastic leukaemia (ALL) remains unclear.
Morphological appraisal of Collembola phylogeny with special emphasis on Poduromorpha and a test of the aquatic origin hypothesis

Phylogenetic relationships within Collembola were determined through the cladistic analysis of 131 morphological characters and 67 exemplar taxa representing the major families of the group, with special emphasis on Poduromorpha. The results show that the order Poduromorpha is monophyletic and the sister group to the remaining Collembola, with Entomobryomorpha monophyletic and the sister group to the clade Neelipleona + Symphypleona. In Entomobryomorpha, Actaletidae is the sister group of the remaining families. In Poduromorpha, Tullbergiinae is monophyletic as well as Onychiurinae and the group Tetrodontophorinae + Onychiurinae which is the sister group of the remaining Poduromorpha; Tetrodontophorinae is paraphyletic; Onychiuridae is polyphyletic; Isotogastruridae is not an intermediate between Poduromorpha and Entomobryomorpha, it is the sister group of Tullbergiinae; Odontellidae is monophyletic and the sister group to the clade Neanuridae + Brachystomellidae; in Neanuridae, Frieseinae and the group Pseudachorutinae + Morulinae + Neanurinae are monophyletic; Morulinae is the sister group of Neanurinae; Pseudachorutinae is paraphyletic; Hypogastruridae is polyphyletic; Podura aquatica (Poduridae) is not ‘primitive’, it clusters with the genera Xenylla and Paraxenylla in Hypogastruridae. On the basis of these relationships and the position of the aquatic species, the most parsimonious hypothesis is a terrestrial edaphic origin for the springtails.
Effect of ambient temperature and urea supplementation on the intake and digestion of alkali-treated straw by Brahman cattle and swamp buffaloes

SUMMARY Four adult swamp buffaloes (Bubalus bubalis) and four adult Brahman cattle (Bos indicus), maintained in climate rooms, were provided ad libitum with a pelleted NaOH-treated barley straw ration (10·7 g N/kg dry matter) supplemented with sulphur, minerals and vitamins and 0, 14·5 or 22 g urea/kg. The animals were given each diet when housed at 32 °C and, in addition, were given the urea unsupplemented diet at 22 °C. All animals received all treatments for periods of 21 days, measurements being made during the last 8 days, after the animals had been given single doses of two nonabsorbable markers (Cr-fibre and Co-EDTA). Intake, digestibility and gastro-intestinal passage rate were low on the unsupplemented N-deficient (10·7 g N/kg dry matter) diet at both temperatures. Urea supplementation to provide diets of 17·3 and 20·7 g N/kg dry matter was associated with increased intake and digestibility of the feed and increased rate of passage of digesta through the gut. Despite differences in respiration rate and plasma thyroxine (T4) and triiodothyronine (T3) concentrations at the two temperatures, no effects of temperature on intakes and digestion of the unsupplemented diet were seen. Differences between species were seen in respiration rate at 32 °C and plasma T4, which were higher, and mean retention time of Cr in the gut at 22 °C and water intakes, which were lower, in Brahman cattle than in buffaloes. There were no significant species differences in response to dietary urea supplementation.
Which Feature Location Technique is Better?

Feature location is a fundamental step in software evolution tasks such as debugging, understanding, and reuse. Numerous automated and semi-automated feature location techniques (FLTs) have been proposed, but the question remains: How do we objectively determine which FLT is most effective? Existing evaluations frequently use bug fix data, which includes the location of the fix, but not what other code needs to be understood to make the fix. Existing evaluation measures such as precision, recall, effectiveness, mean average precision (MAP), and mean reciprocal rank (MRR) will not differentiate between a FLT that ranks higher these related elements over completely irrelevant ones. We propose an alternative measure of relevance based on the likelihood of a developer finding the bug fix locations from a ranked list of results. Our initial evaluation shows that by modeling user behavior, our proposed evaluation methodology can compare and evaluate FLTs fairly.
A Linear Response Bandit Problem

We consider a two–armed bandit problem which involves sequential sampling from two non-homogeneous populations. The response in each is determined by a random covariate vector and a vector of parameters whose values are not known a priori. The goal is to maximize cumulative expected reward. We study this problem in a minimax setting, and develop rate-optimal polices that combine myopic action based on least squares estimates with a suitable “forced sampling” strategy. It is shown that the regret grows logarithmically in the time horizon n and no policy can achieve a slower growth rate over all feasible problem instances. In this setting of linear response bandits, the identity of the sub-optimal action changes with the values of the covariate vector, and the optimal policy is subject to sampling from the inferior population at a rate that grows like n.
Predicting Covariance Matrices with Financial Conditions Indexes

This discussion paper resulted in a publication in the 'Journal of Empirical Finance' (2014). Volume 29, pages 435-447. We model the impact of financial conditions on asset market volatility and correlation. We propose extensions of (factor-)GARCH models for volatility and DCC models for correlation that allow for including indexes that measure financial conditions. In our empirical application we consider daily stock returns of US deposit banks during the period 1994-2011, and proxy financial conditions by the Bloomberg Financial Conditions Index (FCI) which comprises the money, bond, and equity markets. We find that worse financial conditions are associated with both higher volatility and higher average correlations between stock returns. Especially during crises the additional impact of the FCI indicator is considerable, with an increase in correlations by 0.15. Moreover, including the FCI in volatility and correlation modeling improves Value-at-Risk forecasts, particularly at short horizons.
Algorithms for Robot Coverage Under Movement and Sensing Constraints

This thesis explores the problem of generating coverage paths—that is, paths that pass within some sensor footprint of every point in an environment—for mobile robots. It both considers models for which navigation is a solved problem but motions are constrained, as well for models in which navigation must be considered along with coverage planning because of the robot’s unreliable sensing and movements. The motion constraint we adopt for the former is a common constraint, that of a Dubins vehicle. We extend previous work that solves this coverage problem as a traveling salesman problem (TSP) by introducing a practical heuristic algorithm to reduce runtime while maintaining near-optimal path length. Furthermore, we show that generating an optimal coverage path is NP-hard by reducing from the Exact Cover problem, which provides justification for our algorithm’s conversion of Dubins coverage instances to TSP instances. Extensive experiments demonstrate that the algorithm does indeed produce path lengths comparable to optimal in significantly less time. In the second model, we consider the problem of coverage planning for a particular type of very simple mobile robot. The robot must be able to translate in a commanded direction (specified in a global reference frame), with bounded error on the motion direction, until reaching the environment boundary. The objective, for a given environment map, is to generate a sequence of motions that is guaranteed to cover as large a portion of that environment as possible, in spite of the severe limits on the robot’s sensing and actuation abilities. We show how to model the knowledge available to this kind of robot about its own
The acute effects of resistant starch on appetite and satiety

The aim of the present study was to investigate the acute effects (24h) of supplementation with a non-viscous dietary ﬁbre (resistant starch type 2; RS2) on appetite and satiety compared with placebo (rapidly-digestible starch) supplementation. On two separate occasions, at least 1 week apart, twenty healthy young adult males (age range 19–31 years, BMI range 19–27kg/m 2 ) consumed either 48g RS2 or the placebo over two meals in a randomised single-blind balanced cross-over study. The supplements were consumed as part of standardised breakfast and lunch. Appetite was assessed every 30 min by subjective ratings using visual analogue scales and blood samples were taken to measure changes in gut peptide levels and metabolites. Following the 7h postprandial period subjects were provided with a large pre-weighed ad libitum test meal to quantify intake. Food and drink consumption were then recorded for the remainder of the day to obtain overall 24h dietary intake. Subjects were also requested to complete bowel diaries on the day of the study and the following day to monitor gastrointestinal effects. Following RS2 supplementation there was a lower intake at the ad libitum test meal compared with the placebo supplementation (5250kJ (1255kcal) v . 5568kJ (1331kcal); P = 0.06). There was also a signiﬁcantly lower overall 24h energy intake with the RS2 supplement compared with the placebo (12 598kJ (3011kcal) v . 13895 kJ (3321kcal); P = 0.05), which was mostly explained by a reduced fat intake (97g v . 110g; P = 0.02). However, these reductions in intake were not accompanied by differences between the supplements for any of the subjective appetite ratings. The supplements were well tolerated by all subjects. There was a signiﬁcantly lower insulin response following the RS2 supplementation compared