Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling neuro-immune interactions during Zika virus infection

Although Zika virus (ZIKV) infection is often asymptomatic, in some cases, it can lead to birth defects in newborns or serious neurologic complications in adults. However, little is known about the interplay between immune and neural cells that could contribute to the ZIKV pathology. To understand the mechanisms at play during infection and the antiviral immune response, we focused on neural precursor cells (NPCs)-microglia interactions. Our data indicate that human microglia infected with the current circulating Brazilian ZIKV induces a similar pro-inflammatory response found in ZIKV-infected human tissues. Importantly, using our model, we show that microglia interact with ZIKV-infected NPCs and further spread the virus. Finally, we show that Sofosbuvir, an FDA-approved drug for Hepatitis C, blocked viral infection in NPCs and therefore the transmission of the virus from microglia to NPCs. Thus, our model provides a new tool for studying neuro-immune interactions and a platform to test new therapeutic drugs.
A Learning Algorithm for Relational Logistic Regression: Preliminary Results

Relational logistic regression (RLR) is a representation of conditional probability in terms of weighted formulae for modelling multi-relational data. In this paper, we develop a learning algorithm for RLR models. Learning an RLR model from data consists of two steps: 1- learning the set of formulae to be used in the model (a.k.a. structure learning) and learning the weight of each formula (a.k.a. parameter learning). For structure learning, we deploy Schmidt and Murphy's hierarchical assumption: first we learn a model with simple formulae, then more complex formulae are added iteratively only if all their sub-formulae have proven effective in previous learned models. For parameter learning, we convert the problem into a non-relational learning problem and use an off-the-shelf logistic regression learning algorithm from Weka, an open-source machine learning tool, to learn the weights. We also indicate how hidden features about the individuals can be incorporated into RLR to boost the learning performance. We compare our learning algorithm to other structure and parameter learning algorithms in the literature, and compare the performance of RLR models to standard logistic regression and RDN-Boost on a modified version of the MovieLens data-set.
Vers une meilleure connaissance de la spécificité des interactions protéiques dans la signalisation cellulaire - les domaines PDZ au centre des approches informatiques et expérimentales

Les domaines PDZ reconnaissent des motifs C-terminaux (PBMs), a l'origine de nombreuses interactions qui sont souvent impliquees dans la regulation de la polarite cellulaire. Dans cette these, nous avons etudie divers aspects de la specificite des interactions PDZ-PBM. Nous avons mis en evidence les faibles performances de deux predicteurs d'interaction entre PDZs et PBMs, consideres sous leurs formes les plus courtes. Ensuite, nous avons developpe des protocoles bases sur les methodes BIAcore et HoldUp pour valider experimentalement et a grande echelle des predicteurs d'interaction PDZ-PBM et pour etudier l'influence du contexte de sequence (comme les sequences flanquantes ou les domaines voisins) des PDZs et des PBMs sur l’affinite et la specificite de leurs interactions. Nous avons identifie des interactions potentielles impliquant les proteines humaines a PDZ MAGI1 et SCRIB soulignant leur implication dans les reseaux de signalisation des proteines G. Une revue de la litterature, combinee avec nos propres resultats, a revele des mecanismes par lesquels le contexte de sequence influence les affinites et specificites des interactions impliquant les PDZs. Nous avons discute ces mecanismes dans une revue publiee. Les connaissances obtenues a partir de cette these pourront influencer positivement de futures etudes sur les interactions PDZ-PBM, en particulier, et sur les interactions domaine-motif lineaire en general.
Direkte Partizipation abhängig Beschäftigter: Konzept, organisatorische Realisierung und die Wirkung auf Arbeitszufriedenheit und Gesundheitsressourcen

Restrukturierungen von Unternehmen gehen haufig mit dem Versprechen einher, Teilhabechancen der ausfuhrenden Beschaftigten an Konsultationen und Entscheidungen in der Arbeit - d.h. direkte Partizipation - zu vergrosern. Man erhofft sich davon: motiviertere, zufriedenere und gesundere Beschaftigte, hohere Produktivitat sowie geringere Kosten. In diesem Papier wird zunachst der Begriff der direkten Partizipation erlautert und in einen historischen Kontext gestellt. Sodann werden gangige Wege, direkte Partizipation in Unternehmen organisatorisch zu vergrosern, vorgestellt. Schlieslich wird auf Basis organisationspsychologischer Ansatze und einschlagiger empirischer Studien untersucht, wie sich organisatorische oder auch nur wahrgenommene Erweiterungen direkter Partizipation auf die subjektive Befindlichkeit der Beschaftigten auswirken. Die Befunde sprechen fur einen moderaten Effekt von Partizipation auf die Motivation und das Befinden von Beschaftigten.
An appraisal of three methods of rating facial deformity in patients with repaired complete unilateral cleft lip and palate.

OBJECTIVES To evaluate the reliability of clinical assessment, two-dimensional color transparencies and three-dimensional imaging for evaluating the residual facial deformity in patients with repaired complete unilateral cleft lip and palate (UCLP) and compare the ratings of facial deformity made by health care professionals with those made by lay assessors. PATIENTS AND PARTICIPANTS Thirty-one randomly selected subjects aged 10 to 30 years with repaired complete UCLP. Five professionals and five laypersons evaluated each subject's residual cleft-related facial deformity using clinical assessment, two-dimensional color transparencies, and three-dimensional images. MAIN OUTCOME MEASURES The facial deformity of the full face, lip, nose, and midface were scored using a 5-point ordinal scale on two occasions with a 1-month interval. Intra- and interexaminer agreements were calculated from weighted kappa statistics. Bootstrap permutation tests were used to detect any differences in agreement. RESULTS Assessment of facial deformity showed good reproducibility across the three assessment media (kappa = 0.42 to 0.83, SE 0.08). Clinical assessment among lay assessors, however, was poor to moderate (kappa = 0.16 to 0.58, SE 0.07). For all assessors, there was no difference in the two nonclinical media relative to the standard clinical assessment for assessments of the full face (p =.377). For assessments of the lip or nose, transparency scores were in greater agreement with the clinical scores than were the three-dimensional assessment scores (p =.017 and.011, respectively). For rating the midface, the three-dimensional scores were in greater agreement with the clinical scores than were the color transparencies scores (p =.047). CONCLUSIONS In comparison with lay assessors, clinical assessment among professionals was more reproducible. This was not so for nonclinical media. The equivalence of using the color transparencies and three-dimensional media relative to the clinical assessment depends on the region of the face being considered.
Collaborative Knowledge Management: Evaluation of Automated Link Discovery in the Wikipedia

Using the Wikipedia as a corpus, the Link-the-Wiki track, launched by INEX in 2007, aims at producing a standard procedure and metrics for the evaluation of (automated) link discovery at different element levels. In this paper, we describe the preliminary procedure for the assessment, including the topic selection, submission, pooling and evaluation. Related techniques are also presented such as the proposed DTD, submission format, XML element retrieval and the concept of Best Entry points (BEPS). Due to the task required by LTW, it represents a considerable evaluation challenge. We propose a preliminary procedure of assessment for this stage of the LTW and also discuss the further issues for improvement. Finally, an efficiency measurement is introduced for investigation since the LTW task involves two studies: the selection of document elements that represent the topic of request and the nomination of associated links that can access different levels of the XML document.
Reliable State Feedback Control of T–S Fuzzy Systems With Sensor Faults

This paper is concerned with reliable state feedback control synthesis for Takagi and Sugeno (T-S) fuzzy systems with sensor multiplicative faults. By considering the influence of sensor faults on both the system states and premise variables of fuzzy controllers, a class of new convex reliable stabilization conditions are proposed for T-S fuzzy systems using the properties of fuzzy product inference engines. Furthermore, the obtained result is extended to the H∞ reliable control case. The resulting controllers are reliable in that they provide guaranteed asymptotic stability and H∞ performance when all sensors are operational, as well as when some sensor experiences failures. Different from the proposed approach, the influence of sensor faults on premise variables is not considered in the existing results; then, it might not guarantee the stability and control performance for T-S fuzzy systems with premise variables dependent on the system states. A numerical example is given to illustrate the effectiveness of the proposed method.
Getting Reading Right from the Start: Effective Early Literacy Interventions

I. The Context for Current Interventions. 1. Early Literacy Interventions: Aims and Issues, Barbara M. Taylor & Elfrieda H. Hiebert. 2. Compensatory and Special Education: Is There Accountability for Learning and Belief in Children's Potential? , Anne McGill-Franzen, SUNY - Albany. II. Tutoring and Small Group Interventions. 3. At-Risk University Students Tutoring At-Risk Elementary School Children: What Factors Make it Effective? , Connie Juel, University of Virginia. 4. Implementation of Reading Recovery in the New York Area, Trika Smith-Burke & Angela M. Jaggar, New York University. 5. A Small Group Literacy Intervention With Chapter 1 Students, Elfrieda H. Hiebert. 6. Early Intervention in Reading: Supple- mental Instruction for Groups of Low-Achieving Students Provided by First-Grade Teachers, Barbara Taylor, Jean Strait & Mary Anne Medo, University of Minnesota. III. Extending Interventions Across Schools. 7. Success for All: Policy Implications for Getting Reading Right the First Time, Robert E. Slavin, Nancy A. Madden, Nancy L. Karweit, Lawrence J. Dolan & Barbara A. Wasik, Center for Research on Effective Schooling for Disadvantaged Students, Johns Hopkins University. 8. Interactive Writing: A Transition Tool for Assisting Children in Learning to Write and Read, Gay Su Pinnell & Andrea McCarrier, The Ohio State University. 9. Promoting Early Literacy Development Among Spanish-Speaking Children: Lessons From Two Studies. Claude Goldenberg, University of California at Los Angeles. 10. Interventions and the Restructuring of American Literacy Instruction, Elfrieda H. Hiebert & Barbara M. Taylor.
Preference-based Search using Example-Critiquing with Suggestions

We consider interactive tools that help users search for their most preferred item in a large collection of options. In particular, we examine example-critiquing, a technique for enabling users to incrementally construct preference models by critiquing example options that are presented to them. We present novel techniques for improving the example-critiquing technology by adding suggestions to its displayed options. Such suggestions are calculated based on an analysis of users' current preference model and their potential hidden preferences. We evaluate the performance of our model-based suggestion techniques with both synthetic and real users. Results show that such suggestions are highly attractive to users and can stimulate them to express more preferences to improve the chance of identifying their most preferred item by up to 78%.
Hippocampal, caudate, and ventricular changes in Parkinson's disease with and without dementia

Parkinson's disease (PD) has been associated with mild cognitive impairment (PDMCI) and with dementia (PDD). Using radial distance mapping, we studied the 3D structural and volumetric differences between the hippocampi, caudates, and lateral ventricles in 20 cognitively normal elderly (NC), 12 cognitively normal PD (PDND), 8 PDMCI, and 15 PDD subjects and examined the associations between these structures and Unified Parkinson's Disease Rating Scale (UPDRS) Part III:motor subscale and Mini‐Mental State Examination (MMSE) performance. There were no hippocampal differences between the groups. 3D caudate statistical maps demonstrated significant left medial and lateral and right medial atrophy in the PDD vs. NC, and right medial and lateral caudate atrophy in PDD vs. PDND. PDMCI showed trend‐level significant left lateral caudate atrophy vs. NC. Both left and right ventricles were significantly larger in PDD relative to the NC and PDND with posterior (body/occipital horn) predominance. The magnitude of regionally significant between‐group differences in radial distance ranged between 20–30% for caudate and 5–20% for ventricles. UPDRS Part III:motor subscale score correlated with ventricular enlargement. MMSE showed significant correlation with expansion of the posterior lateral ventricles and trend‐level significant correlation with caudate head atrophy. Cognitive decline in PD is associated with anterior caudate atrophy and ventricular enlargement. © 2010 Movement Disorder Society
Structure and function of the notochord: an essential organ for chordate development

The notochord is the defining structure of the chordates, and has essential roles in vertebrate development. It serves as a source of midline signals that pattern surrounding tissues and as a major skeletal element of the developing embryo. Genetic and embryological studies over the past decade have informed us about the development and function of the notochord. In this review, I discuss the embryonic origin, signalling roles and ultimate fate of the notochord, with an emphasis on structural aspects of notochord biology.
Regulation of cholesterol/lipid biosynthetic genes by Egr2/Krox20 during peripheral nerve myelination

Myelination of peripheral nerves by Schwann cells requires a large amount of lipid and cholesterol biosynthesis. To understand the transcriptional coordination of the myelination process, we have investigated the developmental relationship between early growth response 2 (Egr2)/Krox20 – a pivotal regulator of peripheral nerve myelination – and the sterol regulatory element binding protein (SREBP) pathway, which controls expression of cholesterol/lipid biosynthetic genes. During myelination of sciatic nerve, there is a very significant induction of SREBP1 and SREBP2, as well as their target genes, suggesting that the SREBP transactivators are important regulators in the myelination process. Egr2/Krox20 does not appear to directly regulate the levels of SREBP pathway components, but rather, we found that Egr2/Krox20 and SREBP transactivators can synergistically activate promoters of several SREBP target genes, indicating that direct induction of cholesterol/lipid biosynthetic genes by Egr2/Krox20 is a part of the myelination program regulated by this transactivator.
Identification of gene function using prediction by partial matching (PPM) language models

In this paper, we describe the utilization of text encoding and prediction by partial matching language modeling to identify gene functions within abstracts of biomedical papers. The National Center for Biotechnology Information has "GeneRIF" - a collection of the best possible functional representations for a subset of abstracts from PubMed. We use GeneRIF to test the efficiency of our technique. We discuss the methodology adopted to construct models necessary to enable the Text Mining Toolkit to distinguish between gene functions and the rest of the abstract (non gene functions). We also describe the similarity based approach we deploy on the list of automatically annotated functions to generate the most likely gene function representative of the paper. The results indicate that our combined approach to identify gene functions in scientific abstracts performs very well on both precision and recall, and therefore presents exciting opportunities for use in extracting other entities embedded in scientific text.
Acoustics Analysis of Differences across Formants of Four Chinese PUTONGHUA

This paper presents a preliminary analysis of differences of formants among Shanghai, Guangzhou, Chongqing and Xiamen dialectal Putonghua (PTH) in China. An improved formant model based on the linear prediction (LP) feature analysis and a two-dimensional(2D) hidden Markov model (HMM) of formants is employed for estimation of the formant frequencies of vowels and diphthongs. The experiments show Guangzhou dialectal PTH (GZPTH) has the highest average frequency in 1st formant(F1) while Shanghai PTH(SHPTH) has lowest of F1 among four dialectal PTHs. In contrast, Chongqing PTH (CQPTH) gives highest frequency in 2nd and 3rd formants (F2, F3) with a comparison of other dialectal PTHs. The formant spaces of four dialectal PTHs have also been investigated.
A Novel Vaccine Using Nanoparticle Platform to Present Immunogenic M2e against Avian Influenza Infection

Using peptide nanoparticle technology, we have designed two novel vaccine constructs representing M2e in monomeric (Mono-M2e) and tetrameric (Tetra-M2e) forms. Groups of specific pathogen free (SPF) chickens were immunized intramuscularly with Mono-M2e or Tetra-M2e with and without an adjuvant. Two weeks after the second boost, chickens were challenged with 107.2 EID50 of H5N2 low pathogenicity avian influenza (LPAI) virus. M2e-specific antibody responses to each of the vaccine constructs were tested by ELISA. Vaccinated chickens exhibited increased M2e-specific IgG responses for each of the constructs as compared to a non-vaccinated group. However, the vaccine construct Tetra-M2e elicited a significantly higher antibody response when it was used with an adjuvant. On the other hand, virus neutralization assays indicated that immune protection is not by way of neutralizing antibodies. The level of protection was evaluated using quantitative real time PCR at 4, 6, and 8 days post-challenge with H5N2 LPAI by measuring virus shedding from trachea and cloaca. The Tetra-M2e with adjuvant offered statistically significant (P < 0.05) protection against subtype H5N2 LPAI by reduction of the AI virus shedding. The results suggest that the self-assembling polypeptide nanoparticle shows promise as a potential platform for a development of a vaccine against AI.
Analysis of Public-Key Cryptography for Wireless Sensor Networks Security

With the widespread growth of applications of Wireless Sensor Networks (WSNs), the need for reliable security mechanisms these networks has increased manifold. Many security solutions have been proposed in the domain of WSN so far. These solutions are usually based on well-known cryptographic algorithms. In this paper, we have made an effort to survey well known security issues in WSNs and study the behavior of WSN nodes that perform public key cryptographic operations. We evaluate time and power consumption of public key cryptography algorithm for signature and key management by simulation. Keywords—Wireless Sensor Networks, Security, Public Key Cryptography, Key Management.
Association analysis of Cytochrome P 450 Polymorphisms in Phenytoin induced Severe-Cutaneous Adverse Reactions ( SCARS ) in Young Epileptic Patients

This study was aimed to examine the relationship between CYP2Cs genes on chromosome 10, which control the enzyme activities of cytochrome P450, and the occurrence of phenytoin induced severe cutaneous adverse reactions (SCARs) in Thai epilepsy children. DNA samples from SCARs and tolerances. Single Nucleotide polymorphisms (SNPs) composing of rs1592037 (CYP2C8), rs17110192 (CYP2C18), and rs3758581 (CYP2C19) were genotyped by allelespecific PCR. Significant associations were observed between heterozygous genotypes for mutant allele located on rs3758581 and rs17110192 and phenytoin-induced SCARs in Thai epilepsy pediatric patient (OR = 14.52; 95 % CI 1.18 – infinity, p value = 0.044).
Harmonic parameterization by electrostatics

In this article, we introduce a method to apply ideas from electrostatics to parameterize the open space around an object. By simulating the object as a virtually charged conductor, we can define an object-centric coordinate system which we call Electric Coordinates. It parameterizes the outer space of a reference object in a way analogous to polar coordinates. We also introduce a measure that quantifies the extent to which an object is wrapped by a surface. This measure can be computed as the electric flux through the wrapping surface due to the electric field around the charged conductor. The electrostatic parameters, which comprise the Electric Coordinates and flux, have several applications in computer graphics, including: texturing, morphing, meshing, path planning relative to a target object, mesh parameterization, designing deformable objects, and computing coverage. Our method works for objects of arbitrary geometry and topology, and thus is applicable in a wide variety of scenarios.
Progressive Aphasia with Lewy Bodies

Dementia with Lewy bodies (DLB) may include both Alzheimer and Lewy body pathology, but has never been reported to cause primary progressive aphasia. We report a 69-year-old woman who died 11 years after presenting with the syndrome of progressive aphasia. Six years after aphasia onset she developed visual hallucinations, and subsequently parkinsonism. Autopsy examination revealed Alzheimer’s disease (AD), cortical Lewy bodies, and depigmentation and Lewy bodies in the substantia nigra and locus ceruleus. The aphasia most likely reflected the initial onset of AD, and the psychosis and parkinsonism most likely reflected the subsequent onset of Lewy body pathology. This first reported case of progressive aphasia occurring within the context of AD and Lewy body pathology uniquely illustrates the clinical and pathological nosological relationships between these two disease processes, and demonstrates a limitation of the general term, ‘DLB’.
Guinea Worm (Dracunculus medinensis) Infection in a Wild-Caught Frog, Chad

A third-stage (infective) larva of Dracunculus medinensis, the causative agent of Guinea worm disease, was recovered from a wild-caught Phrynobatrachus francisci frog in Chad. Although green frogs (Lithobates clamitans) have been experimentally infected with D. medinensis worms, our findings prove that frogs can serve as natural paratenic hosts.