Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Wide Association and Next Generation Sequencing Approaches to Map Determinants of Ascites in Broiler Chickens

These studies have investigated different candidate genomic regions for their contributions to ascites in broilers. Ascites syndrome is a manifestation of idiopathic pulmonary arteriole hypertension that concerns the poultry industry worldwide. Investigations have demonstrated the disease to be genetically regulated and to exhibit moderate to high heritabilities. Although previous studies have indicated a few chromosomes to be involved with ascites, no genes have been identified to date with direct links to the disease. This dissertation presents a collection of studies that determine the genomic and genetic interactions for regions on chromosome 2 and 9 for ascites phenotypes in broiler chickens. The dissertation further focuses on developing genetic markers for selection of broilers for ascites-resistance. To achieve these aims, the studies described here use two high throughput approachesgenome-wide association and whole genome re-sequencing. A previously identified region on chromosome 9 was further investigated with fine mapping using SNPs. A region on chromosome 2 was investigated using 2 different SNPs. Neither of these regions was found to contain more than a minor association with ascites. Re-evaluation of chromosome 2 and 9 by whole genome resequencing identified multiple regions. One of the most intriguing regions was further evaluated and found to contain the most significant association with ascites ever identified. The region contains the CPQ gene. The data support three different alleles for CPQ with two of those alleles associated with resistance to ascites. Those two alleles appear to be expressed at higher levels in three tissues critical for oxygen homeostasis. Taken together, this collection of studies provides an insight and adds to our current understanding of the molecular correlates of the disease. The markers developed in these studies will be useful in breeding schemes for ascites resistance in the broiler industry. ©2017 by Shatovisha Dey All Rights Reserved
Study of the Effect of Inhibitory Activity on Palm Pollen Phoenix Sylvestris in Some Bacterial Isolates from Male Reproductive Infections

The aim of this study was to investigate the inhibitory activity of the hot alcoholic and water extracts (cold and hot)and acetonic extracts of Phoenix Sylvestris to the bacteria isolated from the Staphylococcus aureus and Streptococcus pyogenes , Which is a common cause of genital tract infection, Klebsiella spp and Enterobacter spp Cause inflammation and urinary tract infections. from the Sadr City Medical Hospital in Najaf, for its clinical importance as the cause of genital infection, where 320 samples of patients with symptoms and signs of genital tract infection were collected. The result was 46 isolates from The highest bacterial infection in the infected patients was Staphylococcus aureus (17) isolates and 40%, followed by Streptococcus pyogenes with 15 isolates and 32%, respectively. Followed by Klebsiella spp bacteria with a number of isolates (9) and a percentage of 19%. The lowest infection rate among bacterial patients was Enterobacter spp with (5) isolates and (9%) of the total number of bacterial infection patients (46). The The minimum inhibitory concentration MIC was determined for Acetonic and Alcoholic extracts against bacteria and was between 12.5-50 mg / ml. The hot water extract was (50 μg / ml) for the Staphylococcus aureus bacteria and the Streptococcus pyogenes , The concentration 50 mg / ml did not show effect on the bacteria Enterobacter spp and Enterobacter spp. , MBC was determined with 25-50 mg / ml of acetone extract. MBC for hot alcohol extract was 25 mg / ml and cold alcohol extract was 50 mg / ml for bacteria, Streptococcus pyogenes, Enterobacter spp, Staphylococcus aureus, Enterobacter spp. The hot water extract was negative for all bacteria tested for 50 mg / ml concentration. The results of the first preliminary detection of cold and hot alcohol extract showed that it contains effective substances (Flavonids, Steriod, alkaloids, Aminoacid, saponin, glycosideTanins and Terpenoid), the hot water extract is to contain it (Tanins, Flavonids and saponin) only. The acetone extract contained Tanins, Flavonid, saponin, Terpenoid.
Spectral sensitivities of ants – a review

Ants constitute one of the most intriguing animal groups with their advanced social lifes, different life histories and sensory modalities, one of which is vision. Chemosensation dominates all other modalities in the accomplishment of different vital tasks, but vision, varying from total blindness in some species to a relatively well-developed vision providing ants the basis for visually-guided behaviors, is also of importance. Although studies on ant vision mainly focused on recognition of and guidance by landmark cues in artificial and/or natural conditions, spectral sensitivities of their compound eyes and ocelli were also disclosed, but to a lesser extent. In this review, we have tried to present current data on the spectral sensitivities of the different ant species tested so far and the different methodological approaches. The results, as well as the similarities and/or discrepancies of the methodologies applied, were compared. General tendencies in ants’ spectral sensitivities are presented in a comparative manner and the role of opsins and ant ocelli in their spectral sensitivity is discussed in addition to the sensitivity of ants to long wavelengths. Extraocular sensitivity was also shown in some ant species. The advantages and/or disadvantages of a dichromatic and trichromatic color vision system are discussed from an ecological perspective.
Neograd: Gradient Descent with a Near-Ideal Learning Rate

Since its inception by Cauchy in 1847, the gradient descent algorithm has been without guidance as to how to efficiently set the learning rate. This paper identifies a concept, defines metrics, and introduces algorithms to provide such guidance. The result is a family of algorithms (Neograd) based on a {\em constant $\rho$ ansatz}, where $\rho$ is a metric based on the error of the updates. This allows one to adjust the learning rate at each step, using a formulaic estimate based on $\rho$. It is now no longer necessary to do trial runs beforehand to estimate a single learning rate for an entire optimization run. The additional costs to operate this metric are trivial. One member of this family of algorithms, NeogradM, can quickly reach much lower cost function values than other first order algorithms. Comparisons are made mainly between NeogradM and Adam on an array of test functions and on a neural network model for identifying hand-written digits. The results show great performance improvements with NeogradM.
At Which Level Should We Extract? An Empirical Analysis on Extractive Document Summarization

Extractive methods have been proven effective in automatic document summarization. Previous works perform this task by identifying informative contents at sentence level. However, it is unclear whether performing extraction at sentence level is the best solution. In this work, we show that unnecessity and redundancy issues exist when extracting full sentences, and extracting sub-sentential units is a promising alternative. Specifically, we propose extracting sub-sentential units based on the constituency parsing tree. A neural extractive model which leverages the sub-sentential information and extracts them is presented. Extensive experiments and analyses show that extracting sub-sentential units performs competitively comparing to full sentence extraction under the evaluation of both automatic and human evaluations. Hopefully, our work could provide some inspiration of the basic extraction units in extractive summarization for future research.
On the unusual effectiveness of type-aware operator mutations for testing SMT solvers

We propose type-aware operator mutation, a simple, but unusually effective approach for testing SMT solvers. The key idea is to mutate operators of conforming types within the seed formulas to generate well-typed mutant formulas. These mutant formulas are then used as the test cases for SMT solvers. We realized type-aware operator mutation within the OpFuzz tool and used it to stress-test Z3 and CVC4, two state-of-the-art SMT solvers. Type-aware operator mutations are unusually effective: During one year of extensive testing with OpFuzz, we reported 1092 bugs on Z3’s and CVC4’s respective GitHub issue trackers, out of which 819 unique bugs were confirmed and 685 of the confirmed bugs were fixed by the developers. The detected bugs are highly diverse — we found bugs of many different types (soundness bugs, invalid model bugs, crashes, etc.), logics and solver configurations. We have further conducted an in-depth study of the bugs found by OpFuzz. The study results show that the bugs found by OpFuzz are of high quality. Many of them affect core components of the SMT solvers’ codebases, and some required major changes for the developers to fix. Among the 819 confirmed bugs found by OpFuzz,184 were soundness bugs, the most critical bugs in SMT solvers,and 489 were in the default modes of the solvers. Notably, OpFuzz found 27 critical soundness bugs in CVC4, which has proved to be a very stable SMT solver.
Fluoroscopy Based Guidance for Percutaneous Cement Injection in Minimally Invasive Hip Refixation

At the Leiden University Medical Centre (LUMC) a novel method for refixating hip prostheses is being developed. A hip prosthesis can loosen due to bone resorption. This creates fibrotic tissue adjacent to the cement, which is holding the prosthesis in place. Instead of replacing the complete hip prosthesis, new cement is injected in the area which contains the fibrotic tissue. This refixates the prosthesis and extends its lifetime. Currently a CT scanner is used during the procedure to position needles which are used to inject the cement. Monitoring cement injection can be a difficult task, because dense materials like the hip prosthesis obstruct the view on the fluoroscope. To improve the reliability and reduce the procedure time we have developed a software tool to help the surgeon plan and verify the cement injection. This tool can simulate the view on the fluoroscopy C-arm, based on preoperative CT data. The Digitally Reconstructed Radiographs (DRRs) can be augmented with cement, needles and tissue overlays. The main goal is twofold. First of all we aim to provide the surgeon with an optimal planning for the viewing angle of the fluoroscopy C-arm. Secondly we want to provide the ability to perform postoperative analysis and verification of the cement injection. We can provide optimal angles based on the visibility of needles, accuracy of the detectable needle position and the certainty of the cement filling of the target area. We also provide designs for needle attachments to make the tilting angle of a needle more visible on the projection images recorded by a fluoroscope.
Scaling factors in HYDRUS to simulate a reduction in hydraulic conductivity during infiltration from recharge wells and infiltration basins

Managed aquifer recharge (MAR) represents a promising technique to cope with increasing water stress worldwide. However, it can be challenging to operate MAR systems, especially concerning clogging. Clogging reduces the infiltration capacity and system efficiency of a MAR facility. Processes that cause clogging are difficult to quantify and assess, and their simulations in MAR schemes have so far been limited. The variably saturated water flow model HYDRUS‐2D was therefore modified to include time‐variable hydraulic conductivities to more realistically represent clogging at the infiltration interface of infiltration basins and recharge wells. An exponential function with a time‐variable scaling factor was implemented into HYDRUS to vary the soil hydraulic conductivity over time during simulations. The new approach was tested, in combination with the reservoir boundary condition, by simulating two‐dimensional cross‐sections of two three‐dimensional laboratory experiments representing recharge from infiltration basins and injection wells. With the help of the time‐variable scaling factor, the increasing ponding depth in both experiments due to progressive clogging was reproduced. Hypothetical simulations with various well configurations, soils, and injection rates indicate that clogging influences the infiltration volumes and subsurface infiltration area, which should be considered during the planning of MAR systems. The approach can be used to evaluate the resulting infiltration capacity numerically and to help with the operation and design of MAR facilities. However, further research is required to fully understand and integrate the processes that lead to clogging at MAR facilities into numerical simulations.
Air Traffic Control Competencies Measurements based on Functional Near-Infrared Spectroscopy

Air traffic control officers (ATCOs) are rigorously selected from the vast number of applicants and extensively trained, in order to have the required psychological and behavioural characteristics for this stressful occupation, as well as specialised performance competencies while controlling air traffic, such as situational awareness, workload management, problem-solving and decision-making. Recent studies have demonstrated the possible improvements of ATCO selection and training processes by using physiological, speech and oculometric features related to stress resilience, cognitive load, visual attention and fatigue. The functional near-infrared spectroscopy (fNIRS) is a brain imaging technique which provides a good insight into brain activation by measuring the haemoglobin concentration in the prefrontal cortex, which is one of the key brain areas responsible for complex cognitive behaviour, decision-making, working memory, and stress regulation. This paper focuses on the ATC performance competencies that could be measured with the fNIRS, demonstrates computational processing of signals obtained with this technique, and discusses the applicability of fNIRS measurements in the current ATC selection and training procedures. The experimental paradigm and the results obtained from the paradigm demonstrate that fNIRS shows differences in brain activation among individuals during cognitive tasks, thus allowing the more objective performance measurement.
Exploring Antagonistic Candidate Fungi for Controling Pathogenic Fungi (Colletotricum gloeosporioides) Causing Anthracnose Disease in Kintamani Siam Orange Plants (Citrus Nobillis Lour Var. Hass)

Orange plantation center in Bali are located in Bangli Regency, Kintamani District. Kintamani orange plantations cultivated three types of oranges: tangerine, selayer, and mandarin oranges. The famous orange in Bali today is Kintamani orange, tangerine type. The typical flavor and aroma of Kintamani tangerine make it is favored by consumers from various regions. Based on the information from Bangli District Agriculture Office and the results of field surveys in the last two years (in 2013 and 2014), cultivation of orange in Kintamani has been infected with anthracnose disease. The disease is characterized by symptoms whereby brown twigs spread to the leaves and fruit, and the fruits which are about to be harvested rot simultaneously and eventually fall due to decay. This condition causes farmers to suffer significant losses. The cause of anthracnose on Kintamani orange is Colletotrichum gloeosporioides . The Control of these diseases has been carried out by farmers with various synthetic fungicides but the disease is still widespread. It is feared that the uncontrolled use of synthetic pesticides can harm the environment, cause resistance to C. gloeosporioides fungi, and kill non-target beneficial micro-organism. It is necessary to conduct research that aims to control anthracnose biologically to maintain the ecological balance and environmental safety. Based on the results of this research by exploring the fungi on healthy plants around orange trees infected with anthracnose diseases, nine isolates of antagonist candidate fungus were obtained based on colony color of fungal hyphae (IS1, IS2, IS3, IS4, IS5. IS6, IS7, IS8, IS9). Based on the test results of the in vitro dual culture, two candidates of antagonistic fungal isolates were selected, the isolates IS4 and IS7. It was because on day 7 after the second dual culture, these two isolates had the highest percentage of inhibition, 89.22% and 85.11 % respectively. Based on the conventional and molecular identifications, it is known that the two candidate isolates of antagonistic fungus (IS4 and IS7) belong to one species of the Aspergillus aculeatus.
Allelopathic potential of some multipurpose tree species (MPTS) on wheat and some of its associated weeds

Allelopathic potential of aqueous extracts of leaves of Prosopis juliflora and Eucalyptus camaldulensis and bark of Acacia nilotica @ 0, 150, 100 and 50 g L. The dry plant materials were ground and soaked for 24 hours in water. Ten seeds each of Triticum aestivum, Avena fatua, and Carthamus oxycantha were used as test species. The data were recorded on germination percentage, seedling length (mm) and biomass (mg) plant. There were two identical runs of the experiment. The inhibition was recorded in all the species tested for all the parameters studied, but it was most pronounced in the germination percentage. Carthamus oxycantha was the most inhibited species. Wheat was the most tolerant. Only 20% seeds as compared to the respective check germinated in this species when exposed to E. camaldulensis @150 g L. All other concentrations of P. juliflora and E. camaldulensis proved severely inhibitory to germination of C. oxycantha. For other parameters the inhibition was observed at the higher concentrations of P. juliflora and E. camaldulensis. Acacia nilotica emerged as the weakest species in inhibiting the growth parameters of the tested species.
Toric genera Buchstaber, Victor M and Panov, Taras E and Ray, Nigel 2009

Our primary aim is to develop a theory of equivariant genera for stably complex manifolds equipped with compatible actions of a torus T k. In the case of omnioriented quasitoric manifolds, we present computations that depend only on their defining combinatorial data; these draw inspiration from analogous calculations in toric geometry, which seek to express arithmetic, elliptic, and associated genera of toric varieties in terms only of their fans. Our theory focuses on the universal toric genus Φ, which was introduced independently by Krichever and Löffler in 1974, albeit from radically different viewpoints. In fact Φ is a version of tom Dieck’s bundling transformation of 1970, defined on T k-equivariant complex cobordism classes and taking values in the complex cobordism algebra Ω∗ U (BT k +) of the classifying space. We proceed by combining the analytic, the formal group theoretic, and the homotopical approaches to genera, and refer to the index theoretic approach as a recurring source of insight and motivation. The resultant flexibility allows us to identify several distinct genera within our framework, and to introduce parametrised versions that apply to bundles equipped with a stably complex structure on the tangents along their fibres. In the presence of isolated fixed points, we obtain universal localisation formulae, whose applications include the identification of Krichever’s generalised elliptic genus as universal amongst genera that are rigid on SU -manifolds. We follow the traditions of toric geometry by working with a variety of illustrative examples wherever possible. For background and prerequisites we attempt to reconcile the literature of east and west, which developed independently for several decades after the 1960s.
Protection, adaptation or cell death as response to toxins: Dependence of time and dose

People are constantly exposed to various toxic substances, for instance toxins related to recent food scandals or cigarette smoke. In early evolution, oxygen was a toxic substance, too. Fortunately, human cells have developed adequate protective systems against oxygen, such as glutathione and thioredoxine. The dynamic protection balance against oxygen is also being used to adjust to other toxins. The method of adjustment depends on the substance, time and dose. This dissertation examines the effects of acrolein (in cigarette smoke), silver nanoparticles (in electronics) and flavonoids (in fruit and vegetables). The study results show that low doses of these substances induce protective systems.
EFFECTS OF PROTEIN INTAKE ON GLUTATHIONE CONCENTRATION AND GLUTATHIONE ENZYME ACTIVITY IN MICE

The aim of the paper was to determine whether multi-generation selection for high body weight gains in experimental mice affects changes in reduced glutathione concentration and glutathione enzyme activity in the liver and kidney of subjects maintained on different protein level in their diets. The experiment involved 200 mice obtained from the Institute of Genetics and Animal Breeding of the Polish Academy of Sciences in Jastrzebiec (Poland). 100 6-9 week-old Swiss male mice were sampled from a line selected for 24 generations for increased body weight (weights were 35±3.2 g) and 100 control subjects came from a randomly mated, non-selected line (weights were 25±2 g). The selected and non-selected mice received either a standard (16%) or low (10%) protein diet (n=10 animals per each subgroup) for 21 consecutive days. These diets were almost isocaloric (14.04 and 13.47 MJ/kg). The animals were decapitated. In their liver and kidney homogenates, reduced glutathione (GSH) concentration and glutathione transferase, peroxidase and reductase activity were determined. The reduction of protein level (from 16% to 10%) in diets of animals decreased GSH concentration and glutathione enzyme (transferase and peroxidase) activity in the liver and kidney of selected and non-selected mice. Glutathione reductase revealed a higher activity in the kidney of non-selected mice maintained on the low-protein diet.It may be suggested that GSH concentration and glutathione enzyme activity play an important role in cellular biochemical adaptation, significantly reacting to disturbances of physiological homeostasis. Prolonged selection for increased body weight did not influence the studied parameters.
STATE FEEDBACK CONTROL OF THE GLUCOSE-INSULIN SYSTEM R . 652 Novembre 2006

The paper investigates the problem of tracking a desired level of plasma glucose concentration. The model for the glucose-insulin system considered here, and recently published, belongs to the class of single-distributed delay models. The control law is obtained according to the feedback linearization theory. Both the cases of hyperglycemic and hypoglycemic patients have been considered. Simulations support theoretical results and show the physical reliability of the approach proposed.
Risk assessment due to transmission of vibrations from olive electrical and pneumatic harvesters to the Hand-Arm System (HAV): definition and evaluation of levels and exposure time

The paper is focused on exposure to vibration during the olive harvest for farmers of Azienda Agraria of Università Politecnica of Marche to highlight the importance of the exposure to vibrations transmitted to the hand-arm system in agriculture and its consequences on human health. To assess the exposure to mechanical vibration transmitted to operators during the olive harvest, measurements were done using a vibration measuring equipment during the regular working activity. The vibration samplings were carried out on electric and pneumatic harvesters. The measured data were compared with the prevention values for the safety requirements fixed by the normative. The analysis of the results shows that the electric harvesters transmit vibrations equivalent and in some cases higher than ones provided by the pneumatic harvesters. The paper, evaluating the risk to the hand-arm system due to vibrations, give an overview of the exposure of workers to the risks arising from vibrations to which operators are exposed when using olive harvesters.