Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of Claudin-2 in intestinal metaplastic mucosa of Cdx2-transgenic mouse stomach

Abstract Objective. Cdx2 is expressed in human intestinal metaplastic mucosa and induces intestinal metaplastic mucosa in Cdx2-transgenic mouse stomach. Claudin-2 is a structural component of tight junctions in the intestine and Cdx2 activates the Claudin-2 promoter in the human intestinal epithelial cell line Caco-2. Our aim is to evaluate the expression of Claudin-2 in intestinal metaplastic mucosa of Cdx2-transgenic mouse stomach. Material and methods. The Claudin-2 expression in the normal gastric mucosa and normal intestinal mucosa of wild type mice and the intestinal metaplastic mucosa of Cdx2-transgenic mice was analyzed by immunohistochemistry, Western blotting and quantitative real-time PCR (qRT-PCR). Results. Claudin-2 was expressed in the base of the glands in intestine and intestinal metaplasia while it was not expressed in the body of stomach. Claudin-2 expression was found in the antrum of stomach, while it was weaker than that in the intestine and the intestinal metaplasia. Claudin-2 was also detected in intestinal metaplasia, colon and ileum by both Western blotting and qRT-PCR while it was not detected in gastric body. Conclusion. These results suggest that Cdx2 plays an important role in the expression of Claudin-2 in vivo.
A Theo-Cymatic Reading of Prolegomena of St. John's Gospel: and Implications for Cosmology Etc.

The science of cymatics, the study of visible sound, is beginning to yield clues to one of the most challenging questions in science: what triggered the creation of life on earth? The hypothetical model we have developed was inspired by ancient traditions and demonstrates that sound and cymatic forces could have worked together to become the dynamic force that created the first stirrings of life and also the Universe.
Microwave characterization of ink-jet printed CPW on PET substrates

This paper describes microwave characterization of coplanar waveguide (CPW) lines formed by ink-jet printed technology on flexible polyethylene terephthalate (PET) substrates. The reel-to-reel printing process uses inkjet printing as a precursor for 2μm copper plating, which allows significantly lowered resistances as compared to traditional inks. A multiline TRL calibration technique has been used to characterize the propagation constant and reflection coefficient of the CPW lines. With the aid of four sets of measurements at two identical labs, it is shown that the fabricated samples have contact repeatability, permitting redundant multiline calibrations.
The plasticity of intellectual development: insights from preventive intervention.

Debates regarding the plasticity of intelligence are often fired by a confusion between 2 distinct realms of development, that is, between developmental functions (e.g., a group's average IQ over time) and individual differences (e.g., the relative rank ordering of individual IQs within a group). Questions concerning the stability of these 2 realms are statistically independent. Thus there are 2 kinds of intellectual plasticity, and there may be no developmental convergences between them. In the present study, data from an early intervention program were used to investigate the 2 kinds of plasticity separately and to examine certain possible convergences between them. The program involved children at risk for developmental retardation who were randomly assigned at birth to 2 rearing conditions (i.e., educational daycare vs. no educational intervention) and whose intellectual development was then studied longitudinally to 4 years of age. Our findings indicate that developmental functions are moderately alterable through systemic early education, particularly after infancy, whereas individual differences are moderately stable, again particularly after infancy. They also indicate that the 2 kinds of plasticity are independent; the alteration of developmental functions through daycare affects neither the stability nor the determinants of individual differences. We discuss the implications that these findings have for current models of mental development, for the nature-nurture debate, and for arguments concerning the efficacy of early intervention programs.
Zika virus NS4A hijacks host ANKLE2 to promote viral replication

Zika virus (ZIKV) is infamous among flaviviruses for its unique association with congenital birth defects, notably microcephaly. We previously mapped ZIKV-host protein interactions and identified the interaction between ZIKV NS4A and host ANKLE2, which itself has established ties to congenital microcephaly. In fruit flies, NS4A induces microcephaly phenotypes in an ANKLE2-dependent manner. This suggests that NS4A interacts with ANKLE2 to dysregulate cell behavior and contributes to abnormal host neurodevelopment. Here, we explore the role of ANKLE2 in ZIKV replication to understand the biological significance of the interaction from the viral perspective. We show that knockdown of ANKLE2 reduces replication of two ZIKV strains, across multiple MOIs and timepoints. We observe that localization of ANKLE2 is drastically shifted to sites of NS4A accumulation during infection. We investigate which domains of ANKLE2 mediate this behavior and the interaction with NS4A. Using co-immunoprecipitation, we show that deletion of either the transmembrane or LEM domain has little impact on the interaction, but deletion of both significantly reduces interaction with NS4A. We show that the C-terminal transmembrane domains of NS4A stabilize the interaction with ANKLE2. Finally, we explore this interaction in other flaviviruses and observe ANKLE2 interacts with NS4A across four additional mosquito-borne flaviviruses. Together, these results suggest NS4A interacts with ANKLE2 through a combination of its transmembrane and LEM domains, bringing it to sites of ZIKV replication to promote replication through an unknown mechanism. Taken together with our previous results, our findings indicate that, in the process of hijacking ANKLE2 for replication, ZIKV disrupts its physiological function to cause disease. Importance The ZIKV epidemic led to the astonishing revelation that congenital ZIKV infection is associated with devastating birth defects, including microcephaly. Microcephaly is the condition in which head and brain size are severely reduced, and is often accompanied by intellectual disability. The molecular mechanisms by which ZIKV replicates and causes microcephaly are still incompletely understood. We previously identified the protein interaction between ZIKV NS4A and host ANKLE2, which is associated with congenital microcephaly. In flies, NS4A induces microcephaly in an ANKLE2-dependent manner, suggesting this interaction is crucial for ZIKV pathogenesis. Here, we explore the relevance of this physical interaction for virus replication. We find that ANKLE2 promotes ZIKV replication, concentrates at sites of NS4A accumulation during infection, and interacts with NS4A via its N-terminal domain. Thus, this represents a rare example of a ZIKV-host protein interaction that impacts both disease and virus replication.
In Search of Automatic Rhythm Analysis Methods for Turkish and Indian Art Music

Abstract The aim of this paper is to identify and discuss various methods in computational rhythm description of Carnatic and Hindustani music of India, and Makam music of Turkey. We define and describe three relevant rhythm annotation tasks for these cultures—beat tracking, meter estimation, and downbeat detection. We then evaluate several methodologies from the state of the art in Music Information Retrieval (MIR) for these tasks, using manually annotated datasets of Turkish and Indian music. This evaluation provides insights into the nature of rhythm in these cultures and the challenges to automatic rhythm analysis. Our results indicate that the performance of evaluated approaches is not adequate for the presented tasks, and that methods that are suitable to tackle the culture specific challenges in computational analysis of rhythm need to be developed. The results from the different analysis methods enable us to identify promising directions for an appropriate exploration of rhythm analysis in Turkish, Carnatic and Hindustani music.
Intuitive Ordering of Scaffolds and Scaffold Similarity Searching Using Scaffold Keys

Scaffold Keys-scaffold descriptors based on simple topological parameters such as number of ring and chain atoms, number and type of heteroatoms, and other simple structural features-are presented. Scaffold Keys enable intuitive ordering of scaffolds from small and simple to large and complex, ordering that is consistent with the way medicinal chemists themselves classify scaffolds. Scaffold Keys may be also used as descriptors for scaffold similarity searches, providing results compatible with expectations of chemists and well-suited for use in scaffold bioisosteric replacement and scaffold hopping. Scaffold Keys also support visualization of large chemical data sets. Scaffold Keys descriptors are easy to understand by chemists as well as easy to implement.
Dynamic Network Selection for Multicast Services in Wireless Cooperative Networks

In next generation mobile multimedia communications, different wireless access networks are expected to cooperate. However, it is a challenging task to choose an optimal transmission path in this scenario. This paper focuses on the problem of selecting the optimal access network for multicast services in the cooperative mobile and broadcasting networks. An algorithm is proposed, which considers multiple decision factors and multiple optimization objectives. An analytic hierarchy process (AHP) method is applied to schedule the service queue and an artificial neural network (ANN) is used to improve the flexibility of the algorithm. Simulation results show that by applying the AHP method, a group of weight ratios can be obtained to improve the performance of multiple objectives. And ANN method is effective to adaptively adjust weight ratios when users' new waiting threshold is generated.
A Restart Procedure for the Finite Mass Method

The finite mass method is a gridless Lagrangian method to simulate compressible flows that has been developed by Gauger, Leinen, and Yserentant [SIAM J. Numer. Anal. , 37 (2000), pp. 1768-1799]. It is based on a discretization of mass, not of space as with classical discretization schemes. Mass is subdivided into little mass packets of finite extension each of which is equipped with finitely many internal degrees of freedom. These mass packets move under the influence of internal and external forces and the laws of thermodynamics and can change their size, orientation, and shape to follow the motion of the fluid. The ability of the mass packets to deform with the flow is the reason for the high accuracy of the finite mass method but also requires that the computation is newly set up from time to time. Such restart procedures are described in this article.
GLCM ARCHITECTURE FOR IMAGE EXTRACTION

In this paper we are extracting the image features using different algorithms that are specified with architectural models with internal modules represented. The main objective involves calculating the different features for a given image. Digital image has several features where a feature is a characteristic that can capture a certain visual property of an image either globally for the whole image, or locally for objects or regions. A key function in different image applications is Feature extraction. There are different algorithms to extract texture features such as Structural, Statistical methods [3]. Feature extraction is a key function in various image processing applications. A feature is an image characteristic that can capture certain visual property of the image. Texture is an important feature of many image types, which is the pattern of information or arrangement of the structure found in a picture. Texture features are used in different applications such as image processing, remote sensing and contentbased image retrieval. These features can be extracted in several ways. The most common way is using a Gray Level Co-occurrence Matrix (GLCM). GLCM contains the second-order statistical information of neighboring pixels of an image. Textural properties can be calculated from GLCM to understand the details about the image content. [6]. The Gray Level Co occurrence Matrix is a second order Statistical method. These features are implemented in VERILOG language. The tools used for implementation of the paper are XILINX ISE.
Substitut versus greffon autologue dans le traitement des récessions de classe I et II de Miller : à propos de la matrice Mucoderm®

Le recours a des tissus autologues presente de nombreux avantages et est considere comme le gold standard. Cependant, le recours a des matrices acellulaires d’origine xenogenique en chirurgie plastique parodontale nous a permis de s’affranchir d’un site donneur, avec les avantages qui en decoulent. De plus, la disponibilite illimitee de ces produits permet de traiter des recessions multiples, etendues a un quadrant, voire un maxillaire complet, ce qui semblerait etre leur indication majeure. Enfin, ces alternatives majorent la satisfaction et le confort du patient. Le manque de recul clinique sur ces nouvelles matrices xenogeniques nous a incite a initier un projet de recherche clinique comparant la greffe de tissu autologue a la matrice Mucoderm® dans le cadre de recessions de classe I et II de Miller. Cette etude clinique prospective randomisee en bouche divisee a demontre des resultats semblables en termes de recouvrement avec neanmoins de meilleurs resultats pour la greffe conjonctive en termes de recouvrement complet. On obtient, dans les 2 cas, un gain de tissu keratinise en hauteur et en epaisseur equivalent. Cependant lorsque l’on integre des criteres subjectifs tels que la douleur, les donnees sont en faveur de la matrice en raison de l’absence de prelevement. Enfin, la stabilite des resultats a long terme reste encore a definir. Ce sont des procedes nouveaux qui necessitent d’autres investigations pour conclure sur leur efficacite reelle. De plus, les resultats prometteurs qui se dessinent au sujet de ces substituts doivent etre valides scientifiquement par les etudes de bons niveaux de preuve qui sont en cours, menees sur des echantillons de patients importants.
Development of complement therapeutics for inhibition of immune‐mediated red cell destruction

A major objective of my National Blood Foundation (NBF)‐funded proposal was to produce recombinant soluble forms of a complement regulatory protein called complement receptor 1 (CR1) that carries the Knops blood group system antigens to perform antibody neutralization studies. By generating these recombinant proteins, we were able to inhibit several Knops antibodies in patient serum samples, thereby demonstrating their usefulness for clinical use. Interestingly, the recombinant CR1 proteins generated through NBF funding were also found to strongly reduce complement‐mediated red cell destruction in a mouse hemolytic transfusion model. In this review, I will outline our NBF‐funded studies, give an overview of recent advances from our group and others in the development of complement therapeutics, and highlight their potential use in the transfusion medicine setting.
Gene expression of herpes simplex virus. II. UV radiological analysis of viral transcription units

The transcriptional organization of the genome of herpes simplex virus type 1 was analyzed by measuring the sensitivity of viral polypeptide synthesis to UV irradiation of the infecting virus. Herpes simplex virus type 1 was irradiated with various doses of UV light and used to infect xeroderma pigmentosum fibroblasts. Immediate early transcription units were analyzed by having cycloheximide present throughout the period of infection, removing the drug at 8 h postinfection, and pulse-labeling proteins with [35S]methionine. Delayed early transcription units were analyzed in similar studies by having 9-beta-D-arabinofuranosyladenine present during the experiment to block replication of the input irradiated genome. The viral polypeptides were separated by gel electrophoresis and quantitated by densitometry of the gel autoradiograms. The following results were obtained. (i) The UV target sizes for the viral transcription units analyzed ranged from 1.44 to 5.65 kilobase pairs. This implies that the corresponding primary transcripts have minimum molecular weights ranging from 0.46 x 10(6). (ii) The genes for the four viral proteins, 165, 145, 116, and 71 (molecular weight x 10(3), exhibited UV target sizes that agree with their calculated gene size or measured mRNA size or both and thus must reside in promoter-adjacent positions. (iii) The transcription units for the remaining genes analyzed showed target sizes that range from 0.42 to 2.59 kilobase pairs greater than needed to encode the respective proteins. This probably is a reflection of their distances from promoters or the presence of intervening sequences or both. It further suggests that these genes are transcribed as precursor RNA molecules that are larger than their mRNA's. (iv) The results indicate that none of the immediate early genes analyzed can be cotranscribed, whereas some of the delayed early genes might be cotranscribed. No evidence was found for the existance of large, multigene transcription units.
Distinct changes in evoked and resting globus pallidus activity in early and late Parkinson's disease experimental models

The main clinical manifestations of Parkinson's disease are caused by alterations of basal ganglia activity that are tied in with the progressive loss of mesencephalic dopaminergic neurons. Recent theoretical and modeling studies have suggested that changes in resting neuronal activity occurred later in the course of the disease than those evoked by phasic cortical input. However, there is no empirical support for this proposal. Here we report a marked increase in the responsiveness of globus pallidus neurons to electrical motor cortex stimulation, in the absence of noticeable changes in resting activity, in anesthetized rats that had consistently shown a deficit in forelimb use during behavioral testing before the experiments, and had ∼45% dopamine neurons spared in the substantia nigra. Pallidal neurons were also over‐responsive to motor cortex stimulation and lost spatial selectivity for cortical inputs in rats with extensive nigrostriatal damage. After partial lesions, over‐responsiveness was mainly due to an increased proportion of neurons showing excitatory responses, while extensive lesions led to an increased likelihood of inhibitory responding neurons. Changes in resting neuronal activity, comprising pauses disrupting tonic discharge, occurred across different global brain states, including an activated condition which shares similarities with natural patterns of cortical activity seen in awake states and rapid eye‐movement sleep, but only after massive nigrostriatal degeneration. These results suggest that a loss of functional segregation and an abnormal temporal encoding of phasic cortical inputs by globus pallidus neurons may contribute to inducing early motor impairment in Parkinson's disease.
Single and Multi Column Neural Networks for Content-based Music Genre Recognition

This working note reports approaches of team KART to MediaEval2017 AcousticBrainz Genre Task and their results. To solve the problem, we mainly considered the sparsity and noise of data, network design for the multi-label classification, and implementation of successful Deep Neural Network (DNN) models. We propose three steps of preprocessing and depict two different approaches: a single-column model and a multi-column model.
Draft Genome Sequence of Acinetobacter calcoaceticus Strain P23, a Plant Growth-Promoting Bacterium of Duckweed

ABSTRACT Acinetobacter calcoaceticus strain P23 is a plant growth-promoting bacterium, which was isolated from the surface of duckweed. We report here the draft genome sequence of strain P23. The genome data will serve as a valuable reference for understanding the molecular mechanism of plant growth promotion in aquatic plants.
Short- Versus Long-Term Credit and Economic Performance: Evidence from the WAEMU

This paper studies the link between financial development and economic growth in the West African Economic and Monetary Union (WAEMU). Using panel data for WAEMU countries over the period 1995-2006, the results suggest that while financial development does support growth in the region, long-term bank financing has a greater impact on economic growth than short-term financing because long-term projects have higher returns adjusted for risks. Given that in the WAEMU short-term credit accounts for about 70 percent of credit to the private sector, WAEMU countries are less able to reap the full benefits of improvements in their financial systems. The results also highlight the importance of macroeconomic stability, a creditor-friendly environment, political stability, and the availability of long-term financial resources in fostering banks' supply of long-term loans.
Apports de la modélisation causale dans l’évaluation des immunothérapies à partir de données observationnelles

De nouveaux traitements comme l’immunotherapie ont ete proposes en oncologie. Ils sont bases sur les mecanismes de regulation du systeme immunitaire. Cependant tous les patients ne repondent pas a ces nouveaux traitements. Afin de pouvoir les identifier, on mesure l’association des marqueurs immunologiques exprimes a la reponse au traitement ainsi qu’a la toxicite a l’instaurationdu traitement et leur evolution sous traitement. En situation observationnelle, l’absence de tirage au sort empeche la comparabilite des groupes et l'effet mesure est juste une mesure d'association. Les methodes d’inference causalepermettent dans certains cas, apres avoir identifie les sources de biais de par la construction de diagrammes acycliques diriges (DAG), d'atteindre l’interchangeabilite conditionnelle entre exposes et non exposes etpermettent l’estimation d’effets causaux. Dans les cas les plus simples ou le nombre de variables est faible, il est possible de dessiner leDAG a partir d’expertise. Dans les situations ou le nombre de variables explosent, des algorithmes d’apprentissage ont ete proposes pour retrouver la structure de ces graphes. Neanmoins ces algorithmes font d’une part l’hypothese qu’aucune information n’est connue et n’ont ete developpes que dans les cas ou les covariables sont mesures a un seul temps. L’objectif de cette these est donc de developper ces methodes d’apprentissages de graphes a des donnees repetees, puis d’integrer des connaissances a priori pour ameliorer l’estimation de ceux-ci. Une fois les graphes appris les modeles causaux peuvent etre appliques sur les biomarkers immunologiques repetes pour detecter ceux qui sont associes a lareponse et/ou la toxicite.