Miracle-dz/UniFAR-FTUs huggingface dataset:
Heat stress in poultry and the beneficial effects of ascorbic acid (vitamin C) supplementation during periods of heat stress

Pakistan is an agro-livestock based economy with a poultry share of 55% of the total agricultural GDP (21%). The environment in Pakistan remains hot and humid during July to August, which renders the survival of poultry critical during these months, as birds are more susceptible to changing environments than other domestic animals. Heat stress is a combination of high environmental temperature and humidity, hindering proper thermoregulatory processes. It diminishes immunity, feed intake, weight gain, egg production, number of chicks per hen, hatchability of fertile eggs, egg and carcass quality, mineral balance, and increases panting and mortality and affects semen quality and fertility in male birds. Ascorbic acid (vitamin C), a white crystalline compound (also known as L-ascorbic acid) is primarily synthesised in the chicken by the kidneys, however, during heat stress, endogenous ascorbic acid becomes insufficient to meet the bird's requirements. Vitamin C ameliorates heat stress induced problems such as poor immunity, feed intake, weight gain, oxidative stress, rectal and body temperature, fertility and semen quality, carcass weight and mortality in birds.
Germination and seed bank depletion of holly (Ilex aquifolium L.) in four microhabitat types

The germination dynamics of Ilex aquifolium L. were studied in central Spain using a 3-year field sowing experiment. Ten triads of bags (n = 30 seeds per bag) were buried randomly in four different microhabitats: inside the holly woodland, along the forest edge, in open grassland and under isolated shrubs. Bags were harvested annually, and seeds were analysed for seed viability, embryo development changes and germination. Holly seeds did not germinate until the second year. Embryo development and seed germination were faster at the forest edge, with a total germination proportion of 63% of sown seeds. Germination in the holly woodland (48%), under the shrubs (46%) and in grassland (46%) were very similar. Thus, recruitment of Ilex populations in this region is not limited by requirements for germination. After the third year, the seed bank was reduced by 80–90% of the initial seeds, so it can be considered as a short-persistent seed bank. Holly seed behaviour can enhance recruitment in semi-open areas, such as forest edges. Linked to the short persistence of its seed bank, this species can be considered an intermediate strategist between mature forest specialists and early successional species. This work contributes to a deeper knowledge of the germination ecology of I. aquifolium, in an effort to determine the relative importance of germination/ dormancy processes within holly population dynamics.
Can climate explain interannual local extinctions among bird species?

Geographical variations in species richness are strongly related to temperature and precipitation. On ecological time‐scales, these variations in species richness should reflect rates of immigration and local extinction (extirpation). Here we ask whether the probability of local extinction in passerine birds covaries with climate. Specifically, we test whether local extinctions increase with climatic harshness or with the climatic distance from a species' optimal climate.
Milk thistle (Silybum marianum (L.) Gaertn.) as a weed in sustainable crop rotation.

Milk thistle - Silybum marianum (L.) Gaertn. can be a winter annual or a biennial medicinal plant. The assessment of the occurrence of milk thistle in sustainable crop rotation was conducted at the Experimental Base of Faculty of Agrobiology and Food Resources, SUA in Nitra in the years 2008- 2011. This study was focused on milk thistle as a weed in the sustainable farming system with the crop rotation of maize for grain, pea for grain, durum wheat and milk thistle. An actual weed infestation of maize, pea and durum wheat stands with milk thistle was evaluated before preemergence application of herbicides, in the spring time. Second screening of actual weed infestation of all stands in sustainable crop rotation with milk thistle was done before crops harvest. Screening of each field was made on 1 m 2 area with three replications. The three randomly established sample quadrants were situated minimally 10 m from field margin and apart from each other, respectively. The level of infestation was evaluated according to average density of weeds per square meter. Obtained data was statistically analyzed by Statistica 7.0, ANOVA, LSD test (p=0.05). As a plant from the family Asteraceae has a great
The polyphyletic origin of the “Cheilostomata” (Bryszoa)

The relative appearance of the parietal muscles in the development of the zooids has been studied in several ctenostomatous and “cheilostomatous” species. A comparison of the different on-togenetical sequences demonstrated that a “cheilostomatous” type of organization of the zooids with a great probability has been achieved in minimum three times independentl and originated from different ctenostomatous sub-grous: the Membranidea from plesiomorgic victorelloids (ancestors of Bulbella with not yet developed peristomial tube), the Inoviceiata (Aetea) from advanced forms of victorelloids with reduced primary parietal muscles (perhaps stcies related to Pottsiella), and Penetrantia from arachnidioid or vesicularioid ancestors (? ). Therefore, the classical orders α“Ctenostomata” and “Cheilostomata” represent only “stage groups” but no monohyletic systematical units. Because of the new concept and interpretation I propose a new name for the united group: Cteno-Cheilostomata, supra-ord. nov.
Avaliação química e sensorial de ovos obtidos por diferentes tratamentos

Eggs are a very important economic product for the country and the production system presents different options. The research had the objective of evaluating, chemically and sensorially, eggs from traditional, semi-organic and organic systems. One hundred and forty four white and red traditional, semi-organic and organic eggs were collected at their production site. Chemical analyses of proximal composition and minerals were carried out. Retinol, a and b carotene contents were determined by high performance liquid chromatography. Hedonic and ordination tests were carried out. The experimental design was in complete random blocks. Results were submitted to Tukey (p < 0.05) and chi-square tests. Chemical analyses did not exhibit differences for water, ash, carbohydrate and iron, however there were differences (p < 0.05) for protein, lipids, calcium and magnesium. Retinol contents did not present significant differences and a and b carotene were not detected. Cholesterol contents presented significant differences, but the sensory analysis did not. Hence, the production system alters protein, lipid, magnesium, calcium and cholesterol contents, but does not alter vitamin A and sensorial characteristics.
Darrieus type vertical axis wind turbine (VAWT) design

The potential of wind energy in Indonesia is generally relatively less compared to other countries in the subtropical region. With the Darrieus VAWT Type Vertical Axis Wind Turbine, the turbine does not have to be directed to the wind to be effective. Mill with vertical axis, generator and gearbox can be placed near the ground, so the tower does not need to support it and is more accessible for maintenance purposes. Gearbox or transmission is one of the main components of the motor which is referred to as a power transfer system, the transmission functions to move and change the power of the rotating motor. To get a large turbine torque, a gearbox design (large size on the turbine, and a smaller size on the rotor generator) is needed. The number of blades used will also affect the effectiveness of the turbine in capturing the wind. With the number of 3 blades, get torque above 40 rpm, at wind speeds of 4.5 to 5 m/s.
Safety and Allograft Function Post Native Lung Pneumonectomy, A Single Lung Transplant Center Experience

Background: Single lung transplantation is a valuable treatment option for end stage lung disease cases of which bilateral lung transplantation is not necessarily indicated. The main disadvantage of single lung transplantation is complications related to the native lung. The most common complications are infection and malignancy which tend to behave aggressively and often require surgical intervention. Safety and feasibility of surgery in lung transplant recipients has been shown in several case reports, however there is very little data regarding native lung pneumonectomy (NPL) and we found no data to date, describing allograft function post-procedure. Methods: We retrospectively extracted data on lung transplant recipients at the Rabin Medical Center, Israel between May, 1997 and June, 2017. We collected and analyzed demographic information, indication for lung transplant and pneumonectomy, postoperative complications and allograft function. Results: We identified 12 patients who required native lung pneumonectomy. By the end of the study, five of 12 patients (42%) were alive. Seven patients were deceased: 3 (25%) did not survive the post-operative period. One patient died from bronchopleural fistula complications eight months after NLP; two died from progressive malignant disease. One patient died from chronic lung allograft dysfunction. Of nine patients who survived NLP to hospital discharge two patients with underlying emphysema had increase in FEV1; six developed significant allograft dysfunction with an average drop in forced expiratory volume in the first second (FEV1) of 29% (range 22-41%) at 3 month post NLP, one patient had a < 10% decline. Conclusion: In conclusion, native lung pneumonectomy is feasible in carefully selected group of patients. It can lead to significant lung allograft dysfunction and we recommend case-by-case decision, where the risk of post-procedure complications, including the possibility of allograft loss, is weighed against the primary disease burden and expected survival without surgery.
The mineral content and vitamin d on bone flour fish yellowfin tuna

Vitamin D is in charge of regulating the amount of calcium in the blood, bones, and intestines, besides this vitamin is also useful for increasing the number of cells of phosphate in the bones. Vitamin D is the only vitamin that is produced naturally by the human body, while under the light of the Sun. The purpose of this study is to conduct an analysis of the mineral content and vitamin D on bone flour fish yellowfin tuna. The results of mineral content of flour of the highest fish bones found on calcium and phosphorus (222.54; 107.08 mg/kg), while vitamin D with the best value found in the NaOH treatment (0.119 g/ml), whereas citric acid treatment is (0.173 g/ml) and treatment the control value (0.069 g/ml).
The digestive tract and life history of small mammals

The type of food, differentiation of the large intestine and stomach, and methane production, as well as life history data, are considered in Insectivora, Rodentia and Lagomorpha. When food containing plant cell wall material is eaten, there is either a differentiation of the stomach or the large intestine. In animals with low body mass and little differentiation of the gastrointestinal tract, methane production is low, but structures essential for microbial digestion of plant cell wall material, such as haustration of the colon or formation of a caecum, can be found in many methane-producers. Animals with a body mass 50 days for the weaning process. Caviomorpha, Thryonomyidae and Hystricidae seem to have 'opened the door' to the use of low quality food by microbial fermentation, but some of them have to 'pay' for this extension of the food range by an extended weaning period, which also means an extended dependency on the mother.
In Vitro Study of Bile Salt Hydrolase (BSH) Activity of BSH Isogenic Lactobacillus plantarum 80 Strains and Estimation of Cholesterol Lowering through Enhanced BSH Activity

Growth and bile salt hydrolase (BSH) activity of the isogenic Lactobacillus plantarum 80 (LP80) strains were studied in vitro . In pure culture experiments viability and growth performance of the BSH - LP80 strain was negatively affected by the presence of conjugated bile salts. The LP80 wild type (WT) and BSH overproducing LP80 (pCBHl) strains did not show a die-off upon supplementation of bile salts. The latter strains hydrolysed glyco-conjugated deoxycholate (GDCA) more readily than tauro-conjugated deoxycholate (TDCA), indicating substrate specificity of the enzyme. BSH activities towards TDCA of LP80 WT and LP80 (pCBHl) stationary phase cells were 0.17 and 1.02 μmol/mg CDW.h respectively; activities towards GDCA of the respective strains were 3.52 and 54.80 μmol/mg CDW.h respectively. The study of BSH activity as a function of growth revealed a marked difference in behaviour between LP80 WT and LP80 (pCBHl) with LP80 WT hydrolysing GDCA when reaching the exponential phase, whereas LP80 (pCBHl) immediately started to hydrolyse GDCA. TDCA hydrolysis increased after GDCA hydrolysis was completed. BSH activity of LP80 (pCBHl) in a mixed microbial association, resembling that of the small intestine, was comparable to that determined under pure culture conditions, indicating that BSH activity will probably not be influenced by the presence of the normal intestinal microbiota. Based on the BSH activity of LP80 (pCBHl) and on physiological data on the bile salt-cholesterol metabolism interrelationship, it was calculated that a daily intake of a realistic amount of highly BSH active Lactobacillus cells, e.g. in the form of yoghurt, might lead to a significant reduction of cholesterol. Hence, this in vitro study indicates that altering BSH activity can be a valid (micro) biological alternative treatment for patients with severe hypercholesterolaemia. Keywords - Bile salt hydrolysis, Lactobacilli, Cholesterol, Hypercholesterolaemia, Probiotic food products.
Purification and characterization of intracellular nitrilases from rhodococcus sp. - potential role of periplasmic nitrilase

Two bacterial species Rhodococcus rhodochrous and Rhodococcus fascianswere evaluated for the production of nitrilase enzyme (EC 3.5.5.2) from benzonitrile. This is the first time report on comparative analyses of intracellular nitrilases in two different Rhodococcus species which showed the involvement of periplasmic nitrilases towards nitrile degradation rather than cytoplasmic nitrilases. The periplasmic nitrilases of R. rhodochrous showed nearly 50% more activity as compared to R. fascians. In comparison to R. fascians, R. rhodochrous was found to be better towards nitrile production and degradation as observed under different physiological conditions. The optimum nitrile degradation was recorded at 40EsC and at pH 8.0. The nitrilase enzyme produced by R. rhodochrous was found to be fairly thermostable, as an incubation temperature of 45EsC did not affect the activity of nitrilase enzyme produced by it adversely. The pre-incubation temperature resulted in a decrease of nitrilase activity. The substrate concentration of 40 mM was found to be optimum for hydrolyzing benzonitrile. These findings may prove beneficial from enzymology and industrial biotechnology point of view so as to render both the environment free from harmful nitrile compounds. Key words: Benzonitrile, cytoplasmic, periplasmic, nitrilase, rhodococcus
Effects of Artificial Escape Dens on Swift Fox Populations in Northwest Texas

Abstract Throughout the range of swift fox (Vulpes velox), coyotes (Canis latrans) are the primary source of swift fox mortality. Coyotes may suppress swift fox populations where densities are high. Because coyote numbers have increased since wolves (Canis lupus) have been exterminated, we hypothesized that escape habitats may limit swift foxes. To test our hypothesis, we installed artificial escape dens in 3 spatially separated (treated) areas on the Rita Blanca National Grasslands in Dallam County, Texas, USA. From January 2002 to August 2004, we captured, radiocollared, and monitored 55 swift foxes. Annual swift fox survival in artificial escape-den–treated areas (Ŝ = 0.81) was higher than in untreated areas (Ŝ = 0.52, P = 0.07). Relative swift fox abundance was higher in treated than untreated areas in 2002 (Yates' χ2 = 4.61, P = 0.03) and in 2003 (Yates' χ2 = 4.70, P = 0.03) but not in 2004 (Yates' χ2 = 2.67, P = 0.10). However, recruitment rates were no different between treated and untreated areas in 2002 (Yates' χ2 = 0.21, P = 0.65) or 2003 (Yates' χ2 = 0.41, P = 0.52). Ninety-five percent fixed-kernel estimates of home-range sizes revealed no difference (P = 0.91) between treated and untreated areas, but swift foxes increased their distribution by moving into an area that had been unoccupied for at least 3 years before this study. Our results suggest that artificial escape dens contributed to increasing swift fox distributions in our study area.
A Representational Model of Grid Cells Based on Matrix Lie Algebras

The grid cells in the mammalian medial entorhinal cortex exhibit striking hexagon firing patterns when the agent navigates in the open field. It is hypothesized that the grid cells are involved in path integral so that the agent is aware of its self-position by accumulating its self-motion. Assuming the grid cells form a vector representation of self-position, we elucidate a minimally simple recurrent model for path integral, which models the change of the vector representation given the self-motion, and we discern two matrix Lie algebras and their Lie groups that are naturally coupled together. This enables us to connect the path integral model to the dimension reduction model for place cells via group representation theory of harmonic analysis. By reconstructing the kernel functions for place cells, our model learns hexagon grid patterns that characterize the grid cells. The learned model is capable of near perfect path integral, and it is also capable of error correction.
Large surface magnetization in noncentrosymmetric antiferromagnets

Thin-film antiferromagnets (AFs) with Rashba spin-orbit coupling are theoretically investigated. We demonstrate that the relativistic Dzyaloshinskii-Moriya interaction (DMI) produces a large surface magnetization and a boundary-driven twist state in the antiferromagnetic Neel vector. We predict a magnetization on the order of $2.3\cdot 10^4$ A/m, which is comparable to the magnetization of ferromagnetic semiconductors. Importantly, the magnetization is characterized by ultra-fast terahertz dynamics and provides new approaches for efficiently probing and controlling the spin dynamics of AFs as well as detecting the antiferromagnetic DMI. Notably, the magnetization does not lead to any stray magnetic fields except at corners where weak magnetic monopole fields appear.
On the Role of Sparsity and DAG Constraints for Learning Linear DAGs

Learning graphical structure based on Directed Acyclic Graphs (DAGs) is a challenging problem, partly owing to the large search space of possible graphs. Recently, NOTEARS (Zheng et al., 2018) formulates the structure search problem as a continuous optimization task using the least squares objective and a proper characterization of DAGs. However, the formulation requires a hard DAG constraint and may lead to optimization difficulties. In this paper, we study the asymptotic roles of the sparsity and DAG constraints for learning DAG models in the linear Gaussian and non-Gaussian cases, and investigate their usefulness in the finite sample regime. Based on the theoretical results, we formulate a likelihood-based score function, and show that one only has to apply sparsity and DAG regularization terms to recover the underlying DAGs. This leads to an unconstrained optimization problem that is much easier to solve. Using gradient-based optimization and GPU acceleration, our procedure can easily handle thousand of nodes while retaining a high accuracy. Extensive experiments validate the effectiveness of our proposed method and show that the DAG-regularized likelihood objective is indeed favorable over the least squares one with the hard DAG constraint.
XRayGAN: Consistency-preserving Generation of X-ray Images from Radiology Reports

To effectively train medical students to become qualified radiologists, a large number of X-ray images collected from patients with diverse medical conditions are needed. However, due to data privacy concerns, such images are typically difficult to obtain. To address this problem, we develop methods to generate view-consistent, high-fidelity, and high-resolution X-ray images from radiology reports to facilitate radiology training of medical students. This task is presented with several challenges. First, from a single report, images with different views (e.g., frontal, lateral) need to be generated. How to ensure consistency of these images (i.e., make sure they are about the same patient)? Second, X-ray images are required to have high resolution. Otherwise, many details of diseases would be lost. How to generate high-resolutions images? Third, radiology reports are long and have complicated structure. How to effectively understand their semantics to generate high-fidelity images that accurately reflect the contents of the reports? To address these three challenges, we propose an XRayGAN composed of three modules: (1) a view consistency network that maximizes the consistency between generated frontal-view and lateral-view images; (2) a multi-scale conditional GAN that progressively generates a cascade of images with increasing resolution; (3) a hierarchical attentional encoder that learns the latent semantics of a radiology report by capturing its hierarchical linguistic structure and various levels of clinical importance of words and sentences. Experiments on two radiology datasets demonstrate the effectiveness of our methods. To our best knowledge, this work represents the first one generating consistent and high-resolution X-ray images from radiology reports. The code is available at this https URL.
Constraining Variational Inference with Geometric Jensen-Shannon Divergence

We examine the problem of controlling divergences for latent space regularisation in variational autoencoders. Specifically, when aiming to reconstruct example $x\in\mathbb{R}^{m}$ via latent space $z\in\mathbb{R}^{n}$ ($n\leq m$), while balancing this against the need for generalisable latent representations. We present a regularisation mechanism based on the skew geometric-Jensen-Shannon divergence $\left(\textrm{JS}^{\textrm{G}_{\alpha}}\right)$. We find a variation in $\textrm{JS}^{\textrm{G}_{\alpha}}$, motivated by limiting cases, which leads to an intuitive interpolation between forward and reverse KL in the space of both distributions and divergences. We motivate its potential benefits for VAEs through low-dimensional examples, before presenting quantitative and qualitative results. Our experiments demonstrate that skewing our variant of $\textrm{JS}^{\textrm{G}_{\alpha}}$, in the context of $\textrm{JS}^{\textrm{G}_{\alpha}}$-VAEs, leads to better reconstruction and generation when compared to several baseline VAEs. Our approach is entirely unsupervised and utilises only one hyperparameter which can be easily interpreted in latent space.