Miracle-dz/UniFAR-FTUs huggingface dataset:
Imputation-based fine-mapping suggests that most QTL in an outbred chicken Advanced Intercross Line are due to multiple, linked loci

The Virginia chicken lines have been divergently selected for juvenile body-weight for more than 50 generations. Today, the high-and low-weight lines show a 12-fold difference for the selected trait, 56-day body-weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several Quantitative Trait Loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the haplotype-diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker-density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to detect associations to 56-day body-weight. The approach revealed several statistically and population-structure independent associations and increased the resolution of most QTL. Further, most QTL were also found to contain multiple independent associations, implying a complex underlying architecture due to the combined effects of multiple, linked loci on independent haplotypes that still segregate in the selected lines. Article summary After 50 generations of bi-directional selection, the Virginia chicken lines display a 12-fold difference in bodyweight at 56 days of age. Birds from the high and low selected lines were crossed to found an Advanced Intercross Line, which has been maintained for 9 generations. Using high-density genotypes of the founders, we imputed genotypes in intercross birds that were only genotyped for a sparse set of markers. Using single and multi-marker association analyses, we replicated nine known body-weight QTL. Multiple statistically independent associations were revealed in eight of the QTL, suggesting that most are caused by multiple linked loci.
Glycerophosphodiesterase GDE2 affects pancreas differentiation in zebrafish

Notch signaling plays an essential role in the proliferation, differentiation and cell fate determination of various tissues, including the developing pancreas. One regulator of the Notch pathway is GDE2 (or GDPD5), a transmembrane ecto-phosphodiesterase that cleaves GPI-anchored proteins at the plasma membrane, including a Notch ligand regulator. Here we report that Gde2 knockdown in zebrafish embryos leads to developmental defects, particularly, impaired motility and reduced pancreas differentiation, as shown by decreased expression of insulin and other pancreatic markers. Exogenous expression of human GDE2, but not catalytically dead GDE2, similarly leads to developmental defects. These data reveal functional conservation between zebrafish and human GDE2, and suggest that strict regulation of GDE2 expression and catalytic activity is critical for correct embryonic patterning. In particular, our data uncover a role for GDE2 in regulating pancreas differentiation.
Muslim Friends: Their Faith and Feeling, An Introduction to Islam

de l’Affaire Galilée. Mais, surprise, le 16 avril 1757, la CongrEgation de l’lndex décida à la demande de Benoit XIV d’omettre dans l’lndex, qui sera publié en 1758, le décret gEnEral prohibant l’enseignement de l’immobilité du soleil et de la mobilité de la Terre, mais les oeuvres qui avaient été nommément condamnées ,. 1pTYBp11rprpnt ,. 1&dquo;,n<:. I’Tn,. 1pv <i Q71 rp n’pd n11p ion Tn’:>, 1¡;¡<. t<. t nl1. n+A--;+V’TT Michel Th&eacute;riault Facult&eacute; de droit canonique, Universit&eacute; Saint-Paul
Motion Estimation Architecture For Video Compression

A VLSI architecture which implements the full search block matching motion estimation algorithm in real time is proposed. The architecture consists of a 2D structure of basic cells (BCs), where each BC is capable of computing the mean absolute error. The interblock dependency is exploited and hence the architecture can meet the real-time requirement in various applications. Most importantly, the architecture is simple, modular, and cascadable. This makes possible VLSI implementation as a codec. >
Hypertension artérielle pulmonaire, moelle osseuse, précurseurs endothéliaux et sérotonine

La serotonine et les cellules souches derivees de la moelle osseuse participent de concert a l'hypertension arterielle pulmonaire. Notre travail a montre que l'absence du recepteur 5-HT 2B genere des alterations permanentes de la composition du sang et de la moelle osseuse dans les lignees myeloides et, en particulier, dans les cellules progenitrices endotheliales. Dans l'hypertension arterielle pulmonaire (HTAP), les recepteurs 5-HT 2B portes par les cellules de la moelle osseuse jouent un role fondamental. Ils contribuent a la differenciation / proliferation / mobilisation des precurseurs endotheliaux de la moelle. Ces cellules derivees de la moelle osseuse ont une fonction critique dans le developpement de l'HTAP et du remodelage vasculaire pulmonaire. Ces donnees indiquent que les cellules de la moelle osseuse jouent un role cle dans la pathogenese de l'HTAP et suggerent que les interactions entre la serotonine et BMPR2 (bone morphogenic protein type 2 receptor) pourraient se situer dans la moelle osseuse.
A Comparative Study of Reading Instruction Management for Selected Third-grade Students in an Urban School District

The specific purposes of the study were (1) to determine the effectiveness of ECRI (Exemplary Center for Reading Instruction), as compared to "traditional" (basal driven) classroom instruction based on a comparative analysis of norm-referenced test data; (2) to determine if there was a significant difference between Blacks, Hispanics and Caucasians on the Vocabulary and Reading Comprehension portions of the Iowa Test of Basic Skills among the third grade ECRI students; and (3) to provide valid information for those charged with the implementation of reading instruction in the Dallas Independent School District, Dallas, Texas.
Gene expression patterns associated with neurological disease in HIV infection

To provide new insight into the pathogenesis of neurocognitive impairments (NCI) in HIV infection, we used the Gene Set Enrichment Analysis (GSEA) algorithm to analyze pathway dysregulations in gene expression profiles of HIV-infected patients with or without NCI and HIV encephalitis (HIVE). While HIVE was characterized by widespread inflammation and tissue damage, gene expression evidence of induction of interferon (IFN), cytokines and tissue injury was apparent in all brain regions studied before the emergence of NCI. Various degrees of white matter changes were present in all HIV-infected subjects and were the primary manifestation in patients with NCI in the absence of HIVE. The latter showed a distinct pattern of immune activation with induction of chemokines, cytokines, β-defensins, and limited IFN induction. Altogether results indicate that significant neuroinflammation and neuronal suffering precede NCI. Patients with NCI without HIVE showed a predominantly white matter dysfunction with a distinct pattern of immune activation.
In Vitro Testing of Biomaterials for Neural Repair: Focus on Cellular Systems and High-Content Analysis

Abstract Biomimetic materials are designed to stimulate specific cellular responses at the molecular level. To improve the soundness of in vitro testing of the biological impact of new materials, appropriate cell systems and technologies must be standardized also taking regulatory issues into consideration. In this study, the biological and molecular effects of different scaffolds on three neural systems, that is, the neural cell line SH-SY5Y, primary cortical neurons, and neural stem cells, were compared. The effect of poly(L-lactic acid) scaffolds having different surface geometry (conventional two-dimensional seeding flat surface, random or aligned fibers as semi3D structure) and chemical functionalization (laminin or ECM extract) were studied. The endpoints were defined for efficacy (i.e., neural differentiation and neurite elongation) and for safety (i.e., cell death/survival) using high-content analysis. It is demonstrated that (i) the definition of the biological properties of biomaterials is profoundly influenced by the test system used; (ii) the definition of the in vitro safety profile of biomaterials for neural repair is also influenced by the test system; (iii) cell-based high-content screening may well be successfully used to characterize both the efficacy and safety of novel biomaterials, thus speeding up and improving the soundness of this critical step in material science having medical applications.
The mutation rate in human evolution and demographic inference

The germline mutation rate has long been a major source of uncertainty in human evolutionary and demographic analyses based on genetic data, but estimates have improved substantially in recent years. I discuss our current knowledge of the mutation rate in humans and the underlying biological factors affecting it, which include generation time, parental age and other developmental and reproductive timescales. There is good evidence for a slowdown in mean mutation rate during great ape evolution, but not for a more recent change within the timescale of human genetic diversity. Hence, pending evidence to the contrary, it is reasonable to use a present-day rate of approximately 0.5 × 10−9 bp−1 yr−1 in all human or hominin demographic analyses.
Ubiquitin-mediated proteolysis in Xenopus extract

The small protein modifier, ubiquitin, can be covalently attached to proteins in the process of ubiquitylation, resulting in a variety of functional outcomes. In particular, the most commonly-associated and well-studied fate for proteins modified with ubiquitin is their ultimate destruction: degradation by the 26S proteasome via the ubiquitin-proteasome system, or digestion in lysosomes by proteolytic enzymes. From the earliest days of ubiquitylation research, a reliable and versatile “cell-in-a-test-tube” system has been employed in the form of cytoplasmic extracts from the eggs and embryos of the frog Xenopus laevis. Biochemical studies of ubiquitin and protein degradation using this system have led to significant advances particularly in the study of ubiquitin-mediated proteolysis, while the versatility of Xenopus as a developmental model has allowed investigation of the in vivo consequences of ubiquitylation. Here we describe the use and history of Xenopus extract in the study of ubiquitin-mediated protein degradation, and highlight the versatility of this system that has been exploited to uncover mechanisms and consequences of ubiquitylation and proteolysis.
Functional consequences of pre- and postsynaptic expression of synaptic plasticity

Growing experimental evidence shows that both homeostatic and Hebbian synaptic plasticity can be expressed presynaptically as well as postsynaptically. In this review, we start by discussing this evidence and methods used to determine expression loci. Next, we discuss functional consequences of this diversity in pre- and postsynaptic expression of both homeostatic and Hebbian synaptic plasticity. In particular, we explore the functional consequences of a biologically tuned model of pre- and postsynaptically expressed spike-timing-dependent plasticity complemented with postsynaptic homeostatic control. The pre- and postsynaptic expression in this model predicts 1) more reliable receptive fields and sensory perception, 2) rapid recovery of forgotten information (memory savings) and 3) reduced response latencies, compared to a model with postsynaptic expression only. Finally we discuss open questions that will require a considerable research effort to better elucidate how the specific locus of expression of homeostatic and Hebbian plasticity alters synaptic and network computations.
Design of Bare-hand Gestures for Object Manipulation in Virtual Reality ⋆

With the advancement of markerless motion capture technology in recent years, gesture-based interactive technique has come into people’s daily life. In this paper, we conducted a two-stage study on the design of bare-hand gestures in Virtual Reality environment. In the first study, end users were asked to invent barehand gestures for the manipulation of virtual objects freely by themselves. Based on the experimental results, we established baseline criteria to distinguish different types of bare-hand gestures and then derived a user-defined gesture set from the collected data. In the second study, the user-defined gestures were validated in terms of good match, memorability, learnability, and comfort. Participants showed positive attitudes toward the user-defined gesture set. Finally, we report some design guidelines for gesture design and vision-based interface design.
Broad-spectrum inhibition of Phytophthora infestans by root endophytes

• Phytophthora infestans (Phy. infestans) is a devastating pathogen of tomato and potato. It readily overcomes resistance genes and applied agrochemicals. Fungal endophytes provide a largely unexplored avenue of control against Phy. infestans. Not only do endophytes produce a wide array of bioactive metabolites, they may also directly compete with and defeat pathogens in planta. • Twelve fungal endophyte isolates from different plant species were tested in vitro for their production of metabolites with anti-Phy. infestans activity. Four well-performing isolates were evaluated for their ability to suppress nine isolates of Phy. infestans on plates and in planta. • Two endophytes reliably inhibited all Phy. infestans on plates, of which Phoma eupatorii isolate 8082 was the most promising. It nearly abolished infection by Phy. infestans in planta. • Here we present a biocontrol agent, which can inhibit a broad-spectrum of Phy. infestans isolates. Such broadly acting inhibition is ideal, because it allows for effective control of genetically diverse pathogen isolates and may slow the adaptation by Phy. infestans.
Modelling applications of spreadsheets (in engineering)

Spreadsheets are essentially software packages for carrying out operations on rows and columns of numerical values. Although originally a financial modelling tool, they also have many applications in modelling engineering systems. The authors show that most commercially available spreadsheets are well provided with trigonometric, exponential and logarithmic functions, as well as with a range of arithmetic and logic operations for combining such functions. As a result, a spreadsheet is often a quick and convenient way of carrying out many types of calculation which commonly occur in electronics, telecommunications and control engineering. Furthermore, the standard graphics packages normally provided with spreadsheets make it particularly easy to display and use the results of such calculations.
Compositionally distinct nuclear pore complexes of functionally distinct dimorphic nuclei in ciliate Tetrahymena

SUMMARY STATEMENT Our study demonstrates compositional and structural differences of the nuclear pore complex between the functionally differentiated macronucleus and micronucleus within a single cytoplasm of ciliated protozoa. ABSTRACT The nuclear pore complex (NPC), a gateway for nucleocytoplasmic trafficking, is composed of about 30 different proteins called nucleoporins. It remains unknown whether the NPCs within a species are homogeneous or vary depending on the cell type, or physiological condition. Here, we present evidence for compositionally distinct NPCs that form within a single cell in a binucleated ciliate. In Tetrahymena thermophila, each cell contains both a transcriptionally-active macronucleus (MAC) and a germline micronucleus (MIC). By combining in silico analysis, mass spectrometry analysis for immuno-isolated proteins, and subcellular localization analysis of GFP fused proteins, we identified numerous novel components of MAC and MIC NPCs. Core members of the Nup107-160 scaffold complex were enriched in MIC NPCs. Strikingly, two paralogs of Nup214 and of Nup153 localized exclusively to either MAC or MIC NPCs. Furthermore, the transmembrane components Pom121 and Pom82 localize exclusively to MAC and MIC NPCs, respectively. Our results argue that functional nuclear dimorphism in ciliates is likely to depend on compositional and structural specificity of NPCs.
Independent component analysis and slow feature analysis

Within this thesis, we focus on the relation between independent component analysis (ICA) and slow feature analysis (SFA). To allow a comparison between both methods we introduce CuBICA2, an ICA algorithm based on second-order statistics only, i.e. cross-correlations. In contrast to algorithms based on higher-order statistics not only instantaneous cross-correlations but also time-delayed cross correlations are considered for minimization. CuBICA2 requires signal components with auto-correlation like in SFA, and has the ability to separate source signal components that have a Gaussian distribution. Furthermore, we derive an alternative formulation of the SFA objective function and compare it with that of CuBICA2. In the case of a linear mixture the two methods are equivalent if a single time delay is taken into account. The comparison can not be extended to the case of several time delays. For ICA a straightforward extension can be derived, but a similar extension to SFA yields an objective function that can not be interpreted in the sense of SFA. However, a useful extension in the sense of SFA to more than one time delay can be derived. This extended SFA reveals the close connection between the slowness objective of SFA and temporal predictability. Furthermore, we combine CuBICA2 and SFA. The result can be interpreted from two perspectives. From the ICA point of view the combination leads to an algorithm that solves the nonlinear blind source separation problem. From the SFA point of view the combination of ICA and SFA is an extension to SFA in terms of statistical independence. Standard SFA extracts slowly varying signal components that are uncorrelated meaning they are statistically independent up to second-order. The integration of ICA leads to signal components that are more or less statistically independent.
Analysis of mycobacterial infection-induced changes to host lipid metabolism in a 1 zebrafish infection model reveals a conserved role for LDLR in infection susceptibility 2

17 Changes to lipid metabolism are well-characterised consequences of human tuberculosis 18 infection but their functional relevance are not clearly elucidated in these or other host19 mycobacterial systems. The zebrafish-Mycobacterium marinum infection model is used 20 extensively to model many aspects of human-M. tuberculosis pathogenesis but has not been 21 widely used to study the role of infection-induced lipid metabolism. We find mammalian 22 mycobacterial infection-induced alterations in host Low Density Lipoprotein metabolism are 23 conserved in the zebrafish model of mycobacterial pathogenesis. Depletion of LDLR, a key 24 lipid metabolism node, decreased M. marinum burden, and corrected infection-induced 25 *Manuscript Click here to view linked References This accepted manuscript has been published in Fish & Shellfish Immunology https://doi.org/10.1016/j.fsi. 2018.09. 037 altered lipid metabolism resulting in decreased LDL and reduced the rate of macrophage 26 transformation into foam cells. Our results demonstrate a conserved role for infection27 induced alterations to host lipid metabolism, and specifically the LDL-LDLR axis, across 28 host-mycobacterial species pairings. 29 30
How Does Infection with Human Papillomavirus 16 and 18 Impact on DNA Damage and Repair in Cervical Cells and Peripheral Blood?

Human papillomavirus (HPV) infection is one of the most common sexually transmitted diseases worldwide and a prime cause of cervical cancer. The HPV DNA is detected in approximately 80-90% of all cervical cancers, with HPV 16 and 18 being the high risk conferring human carcinogens. DNA damage and diminished DNA repair mechanisms are potential biological surrogates of HPV infection that warrant further research in different tissues and populations. Notably, we do not know the extent to which the high risk HPV 16 and 18 differentially affect cervical cells versus other systems such as peripheral blood lymphocytes (PBLs). We evaluated DNA damage and repair in women who tested positive for HPV 16 or HPV 18 and healthy control women without HPV 16 or HPV 18 infection. We found that the DNA damage as measured by the Comet assay was markedly greater in cervical cells of women with HPV 16 (mean: 8.1 as% DNA in tail, 95% CI: 7.6-8.7) or HPV 18 infection (mean: 9.6, 95% CI: 8.9-10.2) than controls (mean: 6.7, 95% CI: 6.2-7.4) (p < 0.05). By contrast, in PBLs, we did not find a significant difference in DNA damage between women with HPV 16 or 18 infection versus controls, as measured by the Comet assay or the Conventional Chromosomal Aberration analysis (p > 0.05). We observed, however, the DNA repair capacity, as measured by the X-ray induced challenge (XRC) assay, was significantly impaired in PBLs from women with HPV 16 or 18 infection compared to controls (p < 0.05). This is the first comparative study, to the best of our knowledge, suggesting that the cervical swab cells might be better suited than peripheral lymphocytes as biosamples for detection of HPV 16 or 18 biological effects on DNA damage. In addition, these findings suggest that the Comet assay performed only in PBLs may potentially lead to false negative diagnosis of DNA damage. Taken together, these observations contribute to development of future diagnostic innovation and precision sampling strategies for robust detection of the biological effects of HPV 16 or 18 in women. We conclude by a brief discussion of implications for HPV clinical diagnostics and precision medicine innovation.
Analysis of the market difference using the stock board

The financial markets are fluctuating consistently. Therefore, it is difficult to analyze the financial market based on the same theory, without depending on the state of the market. So we use the concept ofmarket condition change. To estimate the points when the market change occurred in a real market is effective for market analysis. Thus, in this paper, we propose a method to detect the changes in market conditions. In the proposed method, we focuse on the stock board instead of the price data. From the stock board data, we classify short time series data to clusters by using k-means clustering method. Then, we generate Hidden Markov Model(HMM) from the transition probability of each clusters. By using the likelihood of HMM, we analyze the similarities of each time series data. We performed an experiment to evaluate the effectiveness of the method by discriminant analysis of time series data which created from opening session and continuous session. As a result, two time series data are discriminated with high accuracy. Finally, we compared the discriminate performance of proposed method with another discriminant analysis methods. We used three types of time series data of stock board and price data, before the Lehman's fall financial crisis. From the result, the proposed method shows the best performance in discriminating each financial data.