Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Haplotypes Associated with Prenatal Death in Dairy Cattle and Identification of Deleterious Mutations in GART, SHBG and SLC37A2

The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10−4) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.
Optimal licensing innovation * of cost-reducing

We analyze licensing of a cost reducing innovation to an oligopolistic industry, and extend previous work by Kamien and Tauman (1986) and Katz and Shapiro (1986) in two directions. First, our analysis applies to a wider class of demand functions than linear ones. Second, we derive a simple optimal licensing mechanism for the patentee. We also examine three licensing mechanisms commonly discussed in the literature and observed in practice. Auctioning of a fixed number of licenses is compared to a fixed license fee and to a per unit royalty in terms of the patentee’s profit, licensees’ profit, industry structure, and the product’s price. The analysis is conducted in terms of a non-cooperative game involving the patentee and n identical firms. In this game the patentee acts as a Stackelberg leader selecting a licensing strategy by taking into account the reaction and competitive interaction of the firms. The competitive interaction among the firms is modeled explicitly, both as a quantity (Cournot) and as a price (Bertrand) subgame in a market for a homogeneous product. We examine the implications of the three licensing strategies and how they depend on the relative magnitude of the innovation, the number of firms, and the price elasticity of demand. Licensing by means of a royalty is inferior to the other modes, both for consumers and the patentee. The firms’ profits decline under both the auction and the fixed fee policies relative to their pre-innovation profits. Finally, it is shown that auctioning licenses is the patentee% optimal strategy when the magnitude of innovation is not too small. However, this does not hold for an arbitrary innovation.
Both Neurons and Astrocytes Exhibited Tetrodotoxin-Resistant Metabotropic Glutamate Receptor-Dependent Spontaneous Slow Ca2+ Oscillations in Striatum

The striatum plays an important role in linking cortical activity to basal ganglia outputs. Group I metabotropic glutamate receptors (mGluRs) are densely expressed in the medium spiny projection neurons and may be a therapeutic target for Parkinson's disease. The group I mGluRs are known to modulate the intracellular Ca2+ signaling. To characterize Ca2+ signaling in striatal cells, spontaneous cytoplasmic Ca2+ transients were examined in acute slice preparations from transgenic mice expressing green fluorescent protein (GFP) in the astrocytes. In both the GFP-negative cells (putative-neurons) and astrocytes of the striatum, spontaneous slow and long-lasting intracellular Ca2+ transients (referred to as slow Ca2+ oscillations), which lasted up to approximately 200 s, were found. Neither the inhibition of action potentials nor ionotropic glutamate receptors blocked the slow Ca2+ oscillation. Depletion of the intracellular Ca2+ store and the blockade of inositol 1,4,5-trisphosphate receptors greatly reduced the transient rate of the slow Ca2+ oscillation, and the application of an antagonist against mGluR5 also blocked the slow Ca2+ oscillation in both putative-neurons and astrocytes. Thus, the mGluR5-inositol 1,4,5-trisphosphate signal cascade is the primary contributor to the slow Ca2+ oscillation in both putative-neurons and astrocytes. The slow Ca2+ oscillation features multicellular synchrony, and both putative-neurons and astrocytes participate in the synchronous activity. Therefore, the mGluR5-dependent slow Ca2+ oscillation may involve in the neuron-glia interaction in the striatum.
Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N . caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N . caninum , which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N . caninum -derived reference isolates from around the world and 96 N . caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N . caninum . Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N . caninum samples. Geographic sub-structuring was present in the country populations according to pairwise F ST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal propagation for Spanish N . caninum MLGs in cattle.
The MODIS cloud products: algorithms and examples from Terra

The Moderate Resolution Imaging Spectroradiometer (MODIS) is one of five instruments aboard the Terra Earth Observing System (EOS) platform launched in December 1999. After achieving final orbit, MODIS began Earth observations in late February 2000 and has been acquiring data since that time. The instrument is also being flown on the Aqua spacecraft, launched in May 2002. A comprehensive set of remote sensing algorithms for cloud detection and the retrieval of cloud physical and optical properties have been developed by members of the MODIS atmosphere science team. The archived products from these algorithms have applications in climate change studies, climate modeling, numerical weather prediction, as well as fundamental atmospheric research. In addition to an extensive cloud mask, products include cloud-top properties (temperature, pressure, effective emissivity), cloud thermodynamic phase, cloud optical and microphysical parameters (optical thickness, effective particle radius, water path), as well as derived statistics. We will describe the various algorithms being used for the remote sensing of cloud properties from MODIS data with an emphasis on the pixel-level retrievals (referred to as Level-2 products), with 1-km or 5-km spatial resolution at nadir. An example of each Level-2 cloud product from a common data granule (5 min of data) off the coast of South America will be discussed. Future efforts will also be mentioned. Relevant points related to the global gridded statistics products (Level-3) are highlighted though additional details are given in an accompanying paper in this issue.
Elucidating Novel Serum Biomarkers Associated with Pulmonary Tuberculosis Treatment

In an unbiased approach to biomarker discovery, we applied a highly multiplexed proteomic technology (SOMAscan, SomaLogic, Inc, Boulder, CO) to understand changes in proteins from paired serum samples at enrollment and after 8 weeks of TB treatment from 39 patients with pulmonary TB from Kampala, Uganda enrolled in the Center for Disease Control and Prevention’s Tuberculosis Trials Consortium (TBTC) Study 29. This work represents the first large-scale proteomic analysis employing modified DNA aptamers in a study of active tuberculosis (TB). We identified multiple proteins that exhibit significant expression differences during the intensive phase of TB therapy. There was enrichment for proteins in conserved networks of biological processes and function including antimicrobial defense, tissue healing and remodeling, acute phase response, pattern recognition, protease/anti-proteases, complement and coagulation cascade, apoptosis, immunity and inflammation pathways. Members of cytokine pathways such as interferon-gamma, while present, were not as highly represented as might have been predicted. The top proteins that changed between baseline and 8 weeks of therapy were TSP4, TIMP-2, SEPR, MRC-2, Antithrombin III, SAA, CRP, NPS-PLA2, LEAP-1, and LBP. The novel proteins elucidated in this work may provide new insights for understanding TB disease, its treatment and subsequent healing processes that occur in response to effective therapy.
Implementation of SintromacWeb®, a new internet-based tool for oral anticoagulation therapy telecontrol: Study on system consistency and patient satisfaction

Summary Most computer- or internet-assisted systems for oral anticoagulation therapy (OAT) telemanagement have limitations when it comes to implementation within a healthcare center. It was the objective of this study to evaluate convenience and patient satisfaction with the use of SintromacWeb→, a new OAT telecontrol system, compared with the conventional control. SintromacWeb® consists of a point-of-care device for patient international normalized ratio (INR) self-testing and software that allows internet mediated interaction with physicians. Patients initiated the use of SintromacWeb→ and were followed up during a three-month period. A score-based questionnaire was completed in three controlled visits, and data were subsequently analysed. A total of 102 patients were enrolled. At first visit, 55.7% of the patients had their INR within normal range, and 64.9% at the final visit. Internal consistency of the questionnaire was good (Cronbach‘s α: 0.79). Scores in the questionnaire were independent of patient’s age, education level, working status and INR value. The most valued features of SintromacWeb® were: fewer visits to the hospital, simplicity and convenience of the system, and time administration for control tasks (86.7%, 82.7% and 77.6% of very satisfied patients, respectively). Also, patients showed indifference or were dissatisfied with the conventional system. At the final visit, 99% of patients declared that they were satisfied with their OAT control. Moreover, all patients continued using Sintrom -acWeb→ after completion of the study. In conclusion, SintromacWeb→ telecontrol is a new model for management of anticoagulated patients. It was highly accepted and can be used by all patients regardless of their sociodemographic characteristics.
Beyond unusual? Examining the role of attention in the weapon focus effect

The current study examined whether the weapon focus effect could be accounted for in terms of stimulus novelty. Participants viewed a slideshow of a simulated event while attending to a secondary task. In the critical slide, the target was shown holding a threatening object (weapon condition), a novel object (unusual condition) or a neutral object (control condition). Reaction times on the secondary task were impaired in the weapon and unusual conditions. Participants in the weapon condition had poorest recognition scores for the target's appearance when confidence was also taken into account. Results suggest that while both unusual and threatening objects command attention, the significance of a weapon can lead to impaired performance on less immediately informative aspects of a scene such as target appearance.
A new static strain measurement method of young's modulus based on the theory of the finite element

Measurement methods of Young's modulus about static state by beam bending, there are some issues such as having low precision, the range of application is limited, required the special equipment and specimen. Therefore, this paper presents a new strain Measurement Method of Young's modulus about static state based on the theory of Finite Element. Firstly, by studying the relationship among the load, strain, and the stiffness matrix in Finite Element, to establish a relationship between strain and the Young's modulus. Secondly, the paper analyzes the sources of error, and the impact of the raw measurement error and finite element calculation error on its results. Finally, the paper's result is verified by concrete examples, and it's been proved that this method doesn't require special equipments and specimens, with high testing accuracy, besides, it is widely applied to engineering practice.
Variability in the behavioural responses of three generalist herbivores to the most abundant coumarin in Daphne laureola leaves

We evaluated the responses of three generalist herbivores (Lepidoptera: Noctuidae) to the most abundant coumarin in young leaves of spurge‐laurel, Daphne laureola L. (Thymelaeaceae), a perennial shrub consistently fed upon by several noctuid species. Pseudenargia ulicis Staud and Noctua janthe Borkhausen are natural herbivores of the species in southeastern Spain, whereas Spodoptera littoralis Boisduval is a model species frequently used to address the antifeedant role of secondary compounds. Discrimination between control and coumarin‐coated D. laureola leaves was investigated by short‐term choice experiments. We found species‐specific behavioural responses to the treatment: P. ulicis preferred the control leaves, whereas S. littoralis did not discriminate between leaf treatments, although it clearly avoided coumarin when incorporated into an artificial diet, and N. janthe preferred the coumarin‐coated leaves. Furthermore, N. janthe larvae reduced consumption when the proportion of treated leaves ingested increased and consumption of S. littoralis larvae was also reduced in coumarin‐containing diet under no‐choice conditions. Our results highlight that different herbivore species feeding simultaneously on the same host plant respond differently to a single chemical defence compound, likely constraining a directional response of the plant to selection.
Latent Classes of Maltreatment: A Systematic Review and Critique

This article reviews and critically evaluates available research on latent classes of maltreatment. Three major databases (PsycINFO, Web of Knowledge, and Academic Search Complete) were used to identify studies on latent classes of maltreatment published before June 1, 2016. Of 365 potentially relevant studies, 14 met inclusion criteria for review. Our analysis was guided by the following questions: (a) What observed indicators are being used to model classes of maltreatment? (b) What are the most commonly identified classes of maltreatment? and (c) What are the predictors and outcomes of classes of maltreatment? Across the studies, findings demonstrated how person-centered methods (i.e., latent class/profile analysis) may facilitate the study of maltreatment by concurrently addressing several methodological limitations common to the study of maltreatment, while also addressing heterogeneity in experiences of maltreatment. After providing an account of existing trends within the literature employing person-centered methodology in the study of maltreatment, we offer a critique of extant research, note recent methodological developments, and make numerous recommendations for future research using person-centered approaches to understanding maltreatment.
Heart disease prediction using data mining techniques

The healthcare industry collects large amounts of Healthcare data, but unfortunately not all the data are mined which is required for discovering hidden patterns and effective decision making. We propose efficient genetic algorithm with the back propagation technique approach for heart disease prediction. This paper has analyzed prediction systems for Heart disease using more number of input attributes. The System uses medical terms such as Gender, blood pressure, cholesterol like13 attributes to predict the likelihood of patient getting a Heart disease.
Technical Validation of a Reverse-Transcription Quantitative Polymerase Chain Reaction In Vitro Diagnostic Test for the Determination of MiR-31-3p Expression Levels in Formalin-Fixed Paraffin-Embedded Metastatic Colorectal Cancer Tumor Specimens

MiR-31-3p expression has been shown to be a predictive biomarker for response to anti-epithelial growth factor receptor therapy in patients with RAS wild-type metastatic colorectal cancer (mCRC). To aid in the quantification of miR-31-3p expression in formalin-fixed paraffin-embedded (FFPE) primary tumor samples from patients with mCRC, a reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay was developed and validated. Assay development included the identification of a microRNA reference standard and the determination of an appropriate relative quantification cutoff for differentiating low versus high miR-31-3p expression. Sample specimens for the validation studies included both FFPE slides and shavings. Polymerase chain reaction (PCR) efficiency and linearity, analytical sensitivity and specificity, assay robustness, reproducibility, and accuracy were demonstrated across a number of test conditions and differing quantitative PCR platforms. The data from this study provide evidence as to the feasibility of quantifying the expression of miR-31-3p from FFPE tumor tissue using a standardized RT-qPCR assay.
An Ecological Visual Exploration Tool to Support the Analysis of Visual Processing Pathways in Children with Autism Spectrum Disorders

Recent improvements in the field of assistive technologies have led to innovative solutions aiming at increasing the capabilities of people with disability, helping them in daily activities with applications that span from cognitive impairments to developmental disabilities. In particular, in the case of Autism Spectrum Disorder (ASD), the need to obtain active feedback in order to extract subsequently meaningful data becomes of fundamental importance. In this work, a study about the possibility of understanding the visual exploration in children with ASD is presented. In order to obtain an automatic evaluation, an algorithm for free (i.e., without constraints, nor using additional hardware, infrared (IR) light sources or other intrusive methods) gaze estimation is employed. Furthermore, no initial calibration is required. It allows the user to freely rotate the head in the field of view of the sensor, and it is insensitive to the presence of eyeglasses, hats or particular hairstyles. These relaxations of the constraints make this technique particularly suitable to be used in the critical context of autism, where the child is certainly not inclined to employ invasive devices, nor to collaborate during calibration procedures.The evaluation of children’s gaze trajectories through the proposed solution is presented for the purpose of an Early Start Denver Model (ESDM) program built on the child’s spontaneous interests and game choice delivered in a natural setting.
Classical and Quantum Effects in Plasmonic Metals

The field of plasmonics exploits the unique optical properties of metallic nanostructures to concentrate and manipulate light at subwavelength length scales. Metallic nanostructures get their unique properties from their ability to support surface plasmons– coherent wave-like oscillations of the free electrons at the interface between a conductive and dielectric medium. Recent advancements in the ability to fabricate metallic nanostructures with subwavelength length scales have created new possibilities in technology and research in a broad range of applications. In the first part of this thesis, we present two investigations of the relationship between the charge state and optical state of plasmonic metal nanoparticles. Using experimental bias-dependent extinction measurements, we derive a potential- dependent dielectric function for Au nanoparticles that accounts for changes in the physical properties due to an applied bias that contribute to the optical extinction. We also present theory and experiment for the reverse effect– the manipulation of the carrier density of Au nanoparticles via controlled optical excitation. This plasmoelectric effect takes advantage of the strong resonant properties of plasmonic materials and the relationship between charge state and optical properties to eluci- date a new avenue for conversion of optical power to electrical potential. The second topic of this thesis is the non-radiative decay of plasmons to a hot-carrier distribution, and the distribution’s subsequent relaxation. We present first-principles calculations that capture all of the significant microscopic mechanisms underlying surface plasmon decay and predict the initial excited carrier distributions so generated. We also preform ab initio calculations of the electron-temperature dependent heat capacities and electron-phonon coupling coefficients of plasmonic metals. We extend these first-principle methods to calculate the electron-temperature dependent dielectric response of hot electrons in plasmonic metals, including direct interband and phonon-assisted intraband transitions. Finally, we combine these first-principles calculations of carrier dynamics and optical response to produce a complete theoretical description of ultrafast pump-probe measurements, free of any fitting parameters that are typical in previous analyses.
A core calculus of dependency

Notions of program dependency arise in many settings: security, partial evaluation, program slicing, and call-tracking. We argue that there is a central notion of dependency common to these settings that can be captured within a single calculus, the Dependency Core Calculus (DCC), a small extension of Moggi's computational lambda calculus. To establish this thesis, we translate typed calculi for secure information flow, binding-time analysis, slicing, and call-tracking into DCC. The translations help clarify aspects of the source calculi. We also define a semantic model for DCC and use it to give simple proofs of noninterference results for each case.