Miracle-dz/UniFAR-FTUs huggingface dataset:
Epitope Fingerprinting for Recognition of the Polyclonal Serum Autoantibodies of Alzheimer's Disease

Autoantibodies (aAb) associated with Alzheimer's disease (AD) have not been sufficiently characterized and their exact involvement is undefined. The use of information technology and computerized analysis with phage display technology was used, in the present research, to map the epitope of putative self-antigens in AD patients. A 12-mer random peptide library, displayed on M13 phages, was screened using IgG from AD patients with two repetitions. Seventy-one peptides were isolated; however, only 10 were positive using the Elisa assay technique (Elisa Index > 1). The results showed that the epitope regions of the immunoreactive peptides, identified by phage display analysis, were on the exposed surfaces of the proteins. The putative antigens MAST1, Enah, MAO-A, X11/MINT1, HGF, SNX14, ARHGAP 11A, APC, and CENTG3, which have been associated with AD or have functions in neural tissue, may indicate possible therapeutic targets.
Supplementary Material for the Paper “Estimating the Aspect Layout of Object Categories”

We present detailed experimental results in this supplementary material for our paper “Estimating the Aspect Layout of Object Categories”. 1. 3DObject Dataset Fig. 1 shows the viewpoint confusion matrices of the eight categories in the 3DObject dataset obtained by our Aspect Layout Model (ALM). The viewpoint accuracy is computed among all the true positive detections. To see how the viewpoint estimation is related to detection, we report viewpoint accuracy as a function of recall. We plot the accuracy-recall curves for the eight categories in the 3DObject dataset in Fig. 2, where we compare our full model with our root model and DPM [1]. The area under the accuracy-recall curve is used as a quantitative measure for viewpoint estimation. Our full model achieves the best overall performance among the three models. Detailed detection results on the 3DObject dataset are presented in Table 1. Some aspect layout estimation results of the eight categories obtained by our full model are show in Fig.7-14.
Communications dans les réseaux fortement dynamiques

Les reseaux de vehicules sont une technologie emergente integrant les dernieres techniques de communication. Sans infrastructure, le reseau est un reseau dit ad hoc, un protocole de routage doit donc etre utilise pour assurer les communications inter-vehiculaires. Nous appelons ce type de reseau, un reseau ad hoc de vehicules. Nos travaux s'articulent autour de deux axes : le passage a l'echelle et la gestion de la mobilite dans un contexte autoroutier. Pour cela, nous avons propose une extension du protocole de routage ad hoc DSR pour les reseaux ad hoc hybride (comportant une infrastructure fixe). Des simulations a l'aide de JiST/SWANS ont montre une amelioration des performances en terme de passage a l'echelle, connectivite et capacite du reseau. Nous avons egalement etabli un modele analytique pour comparer le passage a l'echelle de deux classes de protocoles de routage : reactif et geographique. Nous concluons que l'utilisation d'un protocole geographique et ses optimisations ameliore de maniere significative le passage a l'echelle. Enfin, nous proposons un algorithme repartie de formation de convois de vehicules afin d'ameliorer la gestion de la mobilite dans un contexte de reseau ad hoc hybride de vehicules sur autoroute. Nous avons evalue cet algorithme a l'aide de simulations et conclu a une bonne qualite de formation des convois.
Discovery of Novel Irreversible Inhibitors of Interleukin (IL)-2-inducible Tyrosine Kinase (Itk) by Targeting Cysteine 442 in the ATP Pocket

Background: Itk is considered an important target for anti-inflammatory drug discovery, particularly asthma. Results: We have designed an irreversible covalent inhibitor of the kinase by targeting Cys-442 in the ATP pocket. Conclusion: We have produced a potent, selective inhibitor with a long duration of action. Significance: We describe a novel drug discovery strategy with specific design features for inhaled delivery. IL-2-inducible tyrosine kinase (Itk) plays a key role in antigen receptor signaling in T cells and is considered an important target for anti-inflammatory drug discovery. In order to generate inhibitors with the necessary potency and selectivity, a compound that targeted cysteine 442 in the ATP binding pocket and with an envisaged irreversible mode of action was designed. We incorporated a high degree of molecular recognition and specific design features making the compound suitable for inhaled delivery. This study confirms the irreversible covalent binding of the inhibitor to the kinase by x-ray crystallography and enzymology while demonstrating potency, selectivity, and prolonged duration of action in in vitro biological assays. The biosynthetic turnover of the kinase was also examined as a critical factor when designing irreversible inhibitors for extended duration of action. The exemplified Itk inhibitor demonstrated inhibition of both TH1 and TH2 cytokines, was additive with fluticasone propionate, and inhibited cytokine release from human lung fragments. Finally, we describe an in vivo pharmacodynamic assay that allows rapid preclinical development without animal efficacy models.
Expression of Vascular Endothelial Growth Factor Receptor-2 or Tie-2 on Peripheral Blood Cells Defines Functionally Competent Cell Populations Capable of Reendothelialization

Background—Receptor tyrosine kinases that include vascular endothelial growth factor (VEGFR)-1, VEGFR-2, and Tie-2 regulate cardiovascular development and physiological and pathological angiogenesis. We were interested in the phenotypic and functional characterization of peripheral blood cells expressing these receptors and their therapeutic potential in vascular injury. Methods and Results—VEGFR-1+, VEGFR-2+, and Tie-2+ cells constituted ≈3.0±0.2%, 0.8±0.5%, and 2.0±0.3%, respectively, of the total population of mononuclear cells in blood. Phenotypic analysis demonstrated that all 3 cell populations mainly expressed markers of monocytic/macrophage lineage. Only VEGFR-2+ and Tie-2+ cells phenotypically, morphologically, and functionally differentiated to endothelial cells after culture, whereas VEGFR-1+ cells did not. None of the cell types proliferated in vitro. Only freshly isolated VEGFR-2+ or Tie-2+ cells but not VEGFR-2− or Tie-2− cell populations significantly contributed to efficient endothelialization of balloon-injured femoral arteries of nude mice. Furthermore, these cells also differentiated into &agr;-actin–positive smooth muscle cells. Administration of bromodeoxyuridine to animals transplanted with human endothelial progenitor cells showed that VEGFR-2+ and Tie-2+ cells proliferated in vivo. Conclusions—These data demonstrate that expression of VEGFR-2 and/or Tie-2 on peripheral blood cells defines functionally competent cell populations that proliferate in vivo and that contribute to reendothelialization. These findings may have implications for a cell-based approach in vascular diseases.
Two-Microphone Adaptive Array Hearing Aids With Monaural And Binaural Outputs

Traditional two-microphone array processors applied to hearing aids require binaural inputs and produce a monaural output with improved target-to-jammer ratio (TJR), but no binaural cues. Previous work with normal-hearing listeners has demonstrated the potential to obtain a tradeo between localization and intelligibility with a lowpass/highpass system that splits the signal into two frequency bands, preserving binaural cues at low frequencies while improving TJR at high frequencies. In this work, the lowpass/highpass system and a conventional broadband array processor were evaluated with hearing-impaired subjects. The broadband array processor improved speech reception thresholds (SRTs) by an average of 10 dB relative to a binaural reference condition, while the lowpass/highpass method provided an average SRT improvement of 2 dB. Physical measurements show 20 dB of jammer attenuation over much of the frequency range where array processing is applied. These results suggest that hearingimpaired subjects rely on low frequency information more than normal-hearing listeners, and that e ective array processing hearing aids must operate over the entire frequency range.
Epigenetic contributions to cognitive aging: disentangling mindspan and lifespan

Epigenetic modifications of chromatin structure provide a mechanistic interface for gene–environment interactions that impact the individualization of health trajectories across the lifespan. A growing body of research indicates that dysfunctional epigenetic regulation contributes to poor cognitive outcomes among aged populations. Here we review neuroepigenetic research as it relates to cognitive aging, focusing specifically on memory function mediated by the hippocampal system. Recent work that differentiates epigenetic contributions to chronological aging from influences on mindspan, or the preservation of normal cognitive abilities across the lifespan, is also highlighted. Together, current evidence indicates that while age-related memory impairment is associated with dysfunction in the coordinated regulation of chromatin modification, animal models that show individual differences in cognitive outcome underscore the enormous mechanistic complexity that surrounds epigenetic dynamics in the aged hippocampus.
Identification and partial characterization of mitotic centromere- associated kinesin, a kinesin-related protein that associates with centromeres during mitosis

Using antipeptide antibodies to conserved regions of the kinesin motor domain, we cloned a kinesin-related protein that associates with the centromere region of mitotic chromosomes. We call the protein MCAK, for mitotic centromere-associated kinesin. MCAK appears concentrated on centromeres at prophase and persists until telophase, after which time the localization disperses. It is found throughout the centromere region and between the kinetochore plates of isolated mitotic CHO chromosomes, in contrast to two other kinetochore-associated microtubule motors: cytoplasmic dynein and CENP-E (Yen et al., 1992), which are closer to the outer surface of the kinetochore plates. Sequence analysis shows MCAK to be a kinesin-related protein with the motor domain located in the center of the protein. It is 60-70% similar to kif2, a kinesin-related protein originally cloned from mouse brain with a centrally located motor domain (Aizawa et al., 1992). MCAK protein is present in interphase and mitotic CHO cells and is transcribed as a single 3.4-kb message.
Unsupervised Estimation of Word Usage Similarity

We present a method to estimate word use similarity independent of an external sense inventory. This method utilizes a topicmodelling approach to compute the similarity in usage of a single word across a pair of sentences, and we evaluate our method in terms of its ability to reproduce a humanannotated ranking over sentence pairs. We find that our method outperforms a bag-ofwords baseline, and that for certain words there is very strong correlation between our method and human annotators. We also find that lemma-specific models do not outperform general topic models, despite the fact that results with the general model vary substantially by lemma. We provide a detailed analysis of the result, and identify open issues for future research.
Ocotillol Enhanced the Antitumor Activity of Doxorubicin via p53-Dependent Apoptosis

The use of doxorubicin (Dox) was severely constrained by dose-dependent side effects, which might be attenuated by combining a “sensitizer” to decrease its cumulative dosage. In this study, it was investigated whether ocotillol could enhance the antiproliferation activity of Dox. MTT assays and xenograft tumor model were firstly conducted to evaluate the effect of ocotillol on the antitumor activity of Dox. Flow cytometry and Hoechst staining assays were then performed to assess cell apoptosis. Western blot and real-time PCR were finally used to detect the expression of p53 and its target genes. Our results showed ocotillol to enhance Dox-induced cell death in p53 wild-type cancer cells. Compared with Dox alone, Dox with ocotillol (Dox-O) could induce much more cell apoptosis and activate p53 to a much greater degree, which in turn markedly increased expression of proapoptosis genes. The enhanced cytotoxic activity was partially blocked by pifithrin-α, which might be through attenuating the increased apoptosis. Furthermore, ocotillol significantly increased the antitumor activity of Dox in A549 xenograft tumor in nude mice. These findings indicated that ocotillol could potentiate the cytotoxic effect of Dox through p53-dependent apoptosis and suggested that coadministration of ocotillol with Dox might be a potential therapeutic strategy.
A comprehensive review of recursive Naïve Bayes Classifiers

In this paper we provide a comprehensive empirical review of a variant of the Recursive Naive Baye Classifier (RNBC*) in comparison to simple Naive Bayes and C4.5. We show that in terms of a zero one loss cost function for classification accuracy, RNBC* outperformed Naive Bayes and was comparable to C4.5, for the range of data-sets tested. As the Naive Bayes classifier has been shown to be a robust classifier in many domains, this is a significant result. We estimate the bias variance decomposition of RNBC* and show that the bias-variance profile of RNBC* is more similar to that of decision trees than Naive Bayes. We demonstrate how variance reducing ensemble techniques such as Bagging and Boosting can be effective in increasing the classification accuracy of RNBC*.
Paralysis and killing of Caenorhabditis elegans by enteropathogenic Escherichia coli requires the bacterial tryptophanase gene

Pathogenic Escherichia coli, including enteropathogenic E. coli (EPEC), enterohaemorrhagic E. coli (EHEC), enteroinvasive E. coli (EIEC) and enterotoxigenic E. coli (ETEC) are major causes of food and water‐borne disease. We have developed a genetically tractable model of pathogenic E. coli virulence based on our observation that these bacteria paralyse and kill the nematode Caenorhabditis elegans. Paralysis and killing of C. elegans by EPEC did not require direct contact, suggesting that a secreted toxin mediates the effect. Virulence against C. elegans required tryptophan and bacterial tryptophanase, the enzyme catalysing the production of indole and other molecules from tryptophan. Thus, lack of tryptophan in growth media or deletion of tryptophanase gene failed to paralyse or kill C. elegans. While known tryptophan metabolites failed to complement an EPEC tryptophanase mutant when presented extracellularly, complementation was achieved with the enzyme itself expressed either within the pathogen or within a cocultured K12 strains. Thus, an unknown metabolite of tryptophanase, derived from EPEC or from commensal non‐pathogenic strains, appears to directly or indirectly regulate toxin production within EPEC. EPEC strains containing mutations in the locus of enterocyte effacement (LEE), a pathogenicity island required for virulence in humans, also displayed attenuated capacity to paralyse and kill nematodes. Furthermore, tryptophanase activity was required for full activation of the LEE1 promoter, and for efficient formation of actin‐filled membranous protrusions (attaching and effacing lesions) that form on the surface of mammalian epithelial cells following attachment and which depends on LEE genes. Finally, several C. elegans genes, including hif‐1 and egl‐9, rendered C. elegans less susceptible to EPEC when mutated, suggesting their involvement in mediating toxin effects. Other genes including sek‐1, mek‐1, mev‐1, pgp‐1,3 and vhl‐1, rendered C. elegans more susceptible to EPEC effects when mutated, suggesting their involvement in protecting the worms. Moreover we have found that C. elegans genes controlling lifespan (daf‐2, age‐1 and daf‐16), also mediate susceptibility to EPEC. Together, these data suggest that this C. elegans/EPEC system will be valuable in elucidating novel factors relevant to human disease that regulate virulence in the pathogen or susceptibility to infection in the host.
Brain Tumor Signs and Symptoms: Analysis of Primary Health Care Records From the UKCCS

OBJECTIVE: To compare the frequency of brain tumor signs and symptoms in children with and without brain tumors. METHODS: This was a UK population-based retrospective analysis of primary care records. Participants were 195 children (1–14 years) newly diagnosed with brain tumors and 285 controls matched by age, gender, and region. Comparisons included total number of prediagnosis consultations, number with ≥1 symptom suggestive of a brain tumor, total number of symptoms, number of different symptoms, and number of visits with specific combinations of symptoms. RESULTS: On average, cases consulted more often than controls between birth and diagnosis/pseudodiagnosis with brain tumor signs and symptoms. Their consultation rate with ≥1 suggestive symptom escalated in the 2 years before diagnosis. Symptom prevalence was higher among cases than controls, a relative difference of 3.29 times as many consultations with ≥1 suggestive symptom (95% confidence interval [CI]: 2.82–3.83) and 7.01 as many with more than 1 (95% CI: 5.38–9.13). In each 6-month period in the 4 years before diagnosis, cases had at least twice as many consultations with ≥1 suggestive symptom (20.81 times as many in the 6 months before diagnosis [95% CI: 14.29–30.30]) and 2–3 times more records of suggestive symptoms (28.35 times more in the 6 months before diagnosis [95% CI: 19.05–42.19]). Symptoms rarely or not observed among control children included head tilt, odd head movements, odd posture, back or neck stiffness, and unsteadiness without obvious cause. CONCLUSION Key to identifying the 1 child among many who merits prompt investigation is recognition of unusual symptoms, or specific symptom patterns.
In Silico Systems Biology Analysis of Variants of Uncertain Significance in Lynch Syndrome Supports the Prioritization of Functional Molecular Validation

Lynch syndrome (LS) is a genetic condition secondary to germline alterations in the DNA mismatch repair (MMR) genes with 30% of changes being variants of uncertain significance (VUS). Our aim was to perform an in silico reclassification of VUS from a large single institutional cohort that will help prioritizing functional validation. A total of 54 VUS were detected with 33 (61%) novel variants. We integrated family history, pathology, and genetic information along with supporting evidence from eight different in silico tools at the RNA and protein level. Our assessment allowed us to reclassify 54% (29/54) of the VUS as probably damaging, 13% (7/54) as possibly damaging, and 28% (15/54) as probably neutral. There are more than 1,000 VUS reported in MMR genes and our approach facilitates the prioritization of further functional efforts to assess the pathogenicity to those classified as probably damaging. Cancer Prev Res; 10(10); 580–7. ©2017 AACR.
An interaction model for mobile agent services using social networks

Computer networks have been experiencing dramatic changes in their nature over the past few years. Traditionally, network services have been provided through simple interactions between a service provider and service consumers (e.g., web server and clients). For example, CNN's web server provides its clients with news through HTTP (Hyper Text Transfer Protocol). Recent distributed networks, on the other hand, provide network services in a more complex manner involving a greater degree of interaction among service components [1]. Examples of this include mobile agent services [2, 6, 8] where a number of virtual software entities, called agents, migrate over networks to interact with each other and provide network services.
Gabor-LBP Based Region Covariance Descriptor for Person Re-identification

Person re-identification is an important problem in computer vision, which involves matching appearance of individuals between non-overlapping camera views. In this paper we present a novel appearance-based method for person re-identification problem. Color feature, Gabor, local binary pattern (LBP) are utilized to form a covariance descriptor to handle the difficulties such as varying illumination, viewpoint angle and non-rigid body, then distances of these features are computed to match these individuals. Experimental results over the challenging dataset VIPeR demonstrate that our method obtains competitive performance.
Get along with quantitative research process

The world progresses through research.Empirical research relies on scientific procedures and uses a systematic approach to find answers to research problems.Every research is inherently ambiguous and requires extreme delicacy on the part of researcher for its execution.For the research results to be accepted, a research project requires disciplined approach towards an enquiry into the research problem. It demands extreme dedication, skilfulness, mastery and temperament from the researcher. It is generally observed that the researchers fall short of application of research methodology, whether it is qualitative or quantitative, when they write their research papers and working papers.This article is an attempt to understand the basic process of conducting research particularly quantitative research and to discuss considerations a researcher must be bearing in mind while undertaking quantitative research.
Cost-efficient negotiation over multiple resources with reinforcement learning

Cloud applications can achieve similar performance with diverse multi-resource configurations, allowing cloud service providers to benefit from optimal resource allocation for reducing their operation cost. This paper aims to solve the problem of multi-resource negotiation with considerations of both the service-level agreement (SLA) and the cost efficiency. The performance and resource demand are usually application-dependent, making the optimization problem complicated, especially when the dimension of multi-resource configuration is large. To this end, we use reinforcement learning to solve the optimization problem of multi-resource configuration with simultaneous optimization of the learning efficiency and performance guarantee. The developed prototype named SmartYARN is extended Apache YARN equipped with our learning algorithm which can enable cloud applications to negotiate multiple resources cost-effectively. The extensive evaluations show that SmartYARN performs well in reducing the cost of resource usage while maintaining compliance with the SLA constraints of cloud service simultaneously.
Multiclass Linear Dimension Reduction by Weighted Pairwise Fisher Criteria

We derive a class of computationally inexpensive linear dimension reduction criteria by introducing a weighted variant of the well-known K-class Fisher criterion associated with linear discriminant analysis (LDA). It can be seen that LDA weights contributions of individual class pairs according to the Euclidean distance of the respective class means. We generalize upon LDA by introducing a different weighting function.