Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Basis of the Interactions of the Nogo-66 Receptor and Its Homolog NgR2 with Myelin-Associated Glycoprotein: Development of NgROMNI-Fc, a Novel Antagonist of CNS Myelin Inhibition

Myelin-associated glycoprotein (MAG) is a sialic acid-binding Ig-family lectin that functions in neuronal growth inhibition and stabilization of axon–glia interactions. The ectodomain of MAG is comprised of five Ig-like domains and uses neuronal cell-type-specific mechanisms to signal growth inhibition. We show that the first three Ig-like domains of MAG bind with high affinity and in a sialic acid-dependent manner to the Nogo-66 receptor-1 (NgR1) and its homolog NgR2. Domains Ig3–Ig5 of MAG are sufficient to inhibit neurite outgrowth but fail to associate with NgR1 or NgR2. Nogo receptors are sialoglycoproteins comprised of 8.5 canonical leucine-rich repeats (LRR) flanked by LRR N-terminal (NT) and C-terminal (CT)-cap domains. The LRR cluster is connected through a stalk region to a membrane lipid anchor. The CT-cap domain and stalk region of NgR2, but not NgR1, are sufficient for MAG binding, and when expressed in neurons, exhibit constitutive growth inhibitory activity. The LRR cluster of NgR1 supports binding of Nogo-66, OMgp, and MAG. Deletion of disulfide loop Cys309–Cys336 of NgR1 selectively increases its affinity for Nogo-66 and OMgp. A chimeric Nogo receptor variant (NgROMNI) in which Cys309–Cys336 is deleted and followed by a 13 aa MAG-binding motif of the NgR2 stalk, shows superior binding of OMgp, Nogo-66, and MAG compared with wild-type NgR1 or NgR2. Soluble NgROMNI (NgROMNI-Fc) binds strongly to membrane-bound inhibitors and promotes neurite outgrowth on both MAG and CNS myelin substrates. Thus, NgROMNI-Fc may offer therapeutic opportunities following nervous system injury or disease where myelin inhibits neuronal regeneration.
Classification of Ovarian Cancer based on Intelligent Systems with Microarray Data

This paper studies an intelligent system, including a support vector regression (SVR) and a similar analysis, for the classification of the ovarian cancer with microarray data. That is, steps in the classification include a feature selection step and a distance measure step. Firstly, the SVR is used to do the feature selection. That is, the SVR is applied to obtain the important genes of ovarian cancer for all samples of microarray data. At the same time, we can compute the frequency of the gene selection based on the results of SVR for all samples to determine the target genes of ovarian cancer. Secondly, the distance under the similar analysis between target data and test data can be determined. From the distance results, the classification of ovarian cancer can easy to determine
Comparative genomic analysis of duplicated homoeologous regions involved in the resistance of Brassica napus to stem canker

All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.
Kinetic energy of vortex knots and unknots

New results on the kinetic energy of ideal vortex filaments in the shape of torus knots and unknots are presented. These knots are given by small-amplitude torus knot solutions (Ricca, 1993) to the Localized Induction Approximation (LIA) law. The kinetic energy of different knot and unknot types is calculated and presented for comparison. These results provide new information on relationships between geometry, topology and dynamics of complex vortex systems and help to establish possible connections between aspects of structural complexity of dynamical systems and vortical flows.
Multimodal Reranking of Content-based Recommendations for Hyperlinking Video Snippets

In this paper, we present an approach for topic-level search and hyperlinking of video snippets, which relies on content-based recommendation and multimodal re-ranking techniques. We identify topic-level segments using transcripts or subtitles and enrich them with other metadata. Segments are indexed in a word vector space. Given a text query or an anchor, the most similar segments are retrieved using cosine similarity scores, which are then combined with visual similarity scores, computed as the distance from the anchor's visual concept vector. This approach has performed well on the MediaEval 2013 Search and Hyperlinking task, evaluated over 1260 hours of BBC TV broadcast, in terms of overall mean average precision. Experiments showed that topic-segments based on transcripts from automatic speech recognition level systems (ASR) led to better performance than the ones based on subtitles for both search and hyperlinking. Moreover, by analyzing the effect of multimodal re-ranking on hyperlinking performance, we emphasize the merits of rich visual information available in the anchors for the hyperlinking task, and the merits of ASR for large-scale search and hyperlinking.
Children with life-limiting conditions in paediatric intensive care units: a national cohort, data linkage study

Objective To determine how many children are admitted to paediatric intensive care unit (PICU) with life-limiting conditions (LLCs) and their outcomes. Design National cohort, data-linkage study. Setting PICUs in England. Patients Children admitted to a UK PICU (1 January 2004 and 31 March 2015) were identified in the Paediatric Intensive Care Audit Network dataset. Linkage to hospital episodes statistics enabled identification of children with a LLC using an International Classification of Diseases (ICD10) code list. Main outcome measures Random-effects logistic regression was undertaken to assess risk of death in PICU. Flexible parametric survival modelling was used to assess survival in the year after discharge. Results Overall, 57.6% (n=89 127) of PICU admissions and 72.90% (n=4821) of deaths in PICU were for an individual with a LLC. The crude mortality rate in PICU was 5.4% for those with a LLC and 2.7% of those without a LLC. In the fully adjusted model, children with a LLC were 75% more likely than those without a LLC to die in PICU (OR 1.75 (95% CI 1.64 to 1.87)). Although overall survival to 1 year postdischarge was 96%, children with a LLC were 2.5 times more likely to die in that year than children without a LLC (OR 2.59 (95% CI 2.47 to 2.71)). Conclusions Children with a LLC accounted for a large proportion of the PICU population. There is an opportunity to integrate specialist paediatric palliative care services with paediatric critical care to enable choice around place of care for these children and families.
An approach to call-by-name delimited continuations

We show that a variant of Parigot's λμ-calculus, originally due to de Groote and proved to satisfy Boehm's theorem by Saurin, is canonically interpretable as a call-by-name calculus of delimited control. This observation is expressed using Ariola et al's call-by-value calculus of delimited control, an extension of λμ-calculus with delimited control known to be equationally equivalent to Danvy and Filinski's calculus with shift and reset. Our main result then is that de Groote and Saurin's variant of λμ-calculus is equivalent to a canonical call-by-name variant of Ariola et al's calculus. The rest of the paper is devoted to a comparative study of the call-by-name and call-by-value variants of Ariola et al's calculus, covering in particular the questions of simple typing, operational semantics, and continuation-passing-style semantics. Finally, we discuss the relevance of Ariola et al's calculus as a uniform framework for representing different calculi of delimited continuations, including "lazy" variants such as Sabry's shift and lazy reset calculus.
Architectural Exploration of Per-Core DVFS for Energy-Constrained On-Chip Networks

A feasible and scalable per-core DVFS architecture for on-chip network is presented. The supplies are dynamically adjusted at a very fine granularity based on the local traffic status. The adoption of multiple voltage supply networks and power selecting transistors provides the architecture with scala- bility and feasibility superior to existing similar techniques. With high-level simulation using 65nm power model obtained from widely-acknowledged tools, the effectiveness of the technique is demonstrated with quantitative analysis of energy overhead and latency penalty. Under various traffic patterns, the average flit energy is reduced considerably, ranging from 45% to 60%, with moderately increased but stable transmission latency.
Influence of the Micromechanics Models and Volume Fraction Distribution on the Overall Behavior of SiC/Al Functionally Graded Pressurized Cylinders

The assessment of the differences in results obtained from various micromechanics homogenization schemes, as well as the implications of assuming different volume fraction profiles was carried out in the present work. The functionally graded composite chosen for the analysis was Al-SiC and comparisons were made in terms of stress and strain distributions along the wall of an internally pressurized hollow cylinder. Different micromechanics homogenization schemes were implemented into Abaqus as user-defined subroutines (UMAT). The numerical simulations were compared to a set of analytical solutions available on the literature. The obtained results varied substantially according to the homogenization scheme employed. It was also found that the type of function chosen to describe the volume fraction distribution plays a major role on the development of the hoop stresses. Additionally, the finite element analysis showed significant stress variation when the actual volume fraction distribution was used. These gradients did not appear when the same profile was approximated by smooth exponential functions. This paper points out some important issues related to common practices associated with the analysis of FGM composites and serves as an overture to a more in-depth discussion of such problems.
The effects of food components on the digestion of DNA by pepsin

Abstract Recently, our study found that naked nucleic acids (NAs) can be digested by pepsin. To better understand the fate of dietary DNA in the digestive tract, in this study we investigated the effects of several food compositions on its digestion. The results showed that protein inhibited the digestion of DNA when the protein:DNA ratio was higher than 80:1 (m/m). DNA found in nucleoprotein (NA), which more closely resembles the state of DNA in food, was as efficiently digested as naked DNA. When the carbohydrate:DNA ratio was 50:1–140:1 (m/m), mono-, di- and polysaccharides did not inhibit DNA digestion. NaCl exhibited an inhibitory effect at 300 mM, whereas divalent cations (Ca2+ and Mg2+) exerted a much stronger inhibitory effect even at 50 mM. The polycation compounds (e.g. chitosan and spermine) showed a significant inhibitory effect at N/P (NH3+/PO4−) = 10:1. The close relationship between food composition and DNA digestion suggests that dietary habits and food complexes are important for understanding the in vivo fate of the ingested DNA in the digestive tract.
Computational Mass Spectrometry–Based Proteomics

Proteomics is defined as the system-widecharacterization of all the proteins in anorganism in terms of their sequence,localization, abundance, post-translationalmodifications, and biomolecular interac-tions. Modern proteomic investigationsare increasingly quantitative and compre-hensive [1]. Examples include the relativequantification of over 4,000 proteins inhaploid and diploid yeast, which identifiedthe pheromone signaling pathway asenriched in differential abundance [2];determination of site- and time-specificdynamics of more than 6,000 phosphory-lation sites of HeLa cells stimulated withepidermal growth factor [3]; and charac-terization of 232 multiprotein complexesin Saccharomyces cerevisiae, which proposednew cellular roles for 344 proteins [4]. Such investigations are now successfullyutilized in functional biology [5,6], geno-mics [7,8], and biomedical research [9]. Challenges of proteomic studies stemfrom the complexity of the proteome andto its broad dynamic range. For example,the human genome contains around20,000 protein coding genes. Their trans-lation, combined with splicing or proteol-ysis, yields an estimated 50,000–500,000proteins, and over 10 million differentprotein forms can be derived by somaticDNA rearrangements and post-transla-tional modifications [10]. The abundanceof protein species in human plasma spansmore than 10 orders of magnitude [11]. Unlike oligonucleotides, proteins cannotbe amplified, and therefore the objectivesof proteomics are achieved by sensitiveand scalable technologies identifying andquantifying proteins [12]. The overallmass spectrometry–based proteomic work-flow is summarized in Figure 1.
Robust asynchronous indoor localization using LED lighting

We propose a low-cost system for indoor self-localization of mobile devices using modulated LED ceiling lamps that are fully autonomous and broadcast their identifiers without any synchronization. The proposed self-localization method is designed to handle this lack of synchronization as well as the possibility of blocked line-of-sight connections or severe attenuation in real-world environments. This robustness is achieved by applying a suitable Bayesian signal model and by taking into account the inherent sparsity in detecting the concurrently visible lamps. The proposed estimator of the location approximates optimal Bayesian estimation while maintaining low complexity. Simulation results confirm a significant gain in performance compared to a classical matched-filter approach.
Sparse representations for text categorization

Sparse representations (SRs) are often used to characterize a test signal using few support training examples, and allow the number of supports to be adapted to the specific signal being categorized. Given the good performance of SRs compared to other classifiers for both image classification and phonetic classification, in this paper, we extended the use of SRs for text classification, a method which has thus far not been explored for this domain. Specifically, we demonstrate how sparse representations can be used for text classification and how their performance varies with the vocabulary size of the documents. In addition, we also show that this method offers promising results over the Naive Bayes (NB) classifier, a standard baseline classifier used for text categorization, thus introducing an alternative class of methods for text categorization.
Forcible destruction of severely misfolded mammalian glycoproteins by the non-glycoprotein ERAD pathway

Higher eukaryotes, but not yeast, are able to extract severely misfolded glycoproteins from the endoplasmic reticulum–associated degradation (ERAD) pathway for glycoproteins and target them to the ERAD pathway for non-glycoproteins to maintain the homeostasis of the ER.
The interaction between perceptual grouping and attention

I investigated the interaction between perceptual grouping and attention, focusing specifically on distracter rejection. The novelty of the thesis lies in the study of different configural types and their effect on search across space and time. Grouping by configuration is likely to facilitate search by making distracter rejection easier. Grouping can be based on the regular locations of elements, the similarity of elements and whether the elements form a closed shape. The effects of grouping occurred under conditions in which the groups never contained the target, although detection was faster if the target fell internal to the group relative to when it fell outside the group. These results, together with those from neuropsychological studies reported here, are consistent with rapid suppression of irrelevant distractor groups. Primitive grouping, apparently based on clusters of similar proximal elements, took place even when attention was reduced in patients with chronic spatial biases in visual selection. However, neurological damage to attention-related brain regions did disrupt grouping effects dependent on element shape. Attention may, therefore, be more critical for some forms of grouping. Grouping interacts with attention to determine perceptual performance. This operates in a graded manner, determined by the type of grouping.
Therapy of gastric mucosa-associated lymphoid tissue lymphoma

Mucosa-associated lymphoid tissue (MALT) lymphoma is a relatively common lymphoma and comprises ∼ 7% of all newly diagnosed non-Hodgkin’s lymphoma. It is mainly located in the stomach and has become a focus of interest due to its unique pathophysiological link with Helicobacter pylori (HP) and the consecutive response to HP eradication therapy. In view of this, HP eradication has become standard treatment for patients with localised disease, and recent data have suggested that HP-negative patients might benefit from antibiotic treatment. In case of non-response, however, the standard approach in such patients is unclear. Both radiation and chemotherapy have shown promising results, and at present there is only one randomised study, which nevertheless suggests chemotherapy as management of choice. The objective of this review is, therefore, to summarise and evaluate the data available for treatment of gastric MALT lymphoma and to highlight potential focus for further research.
Induced expression of Fndc 5 signi fi cantly increased cardiomyocyte differentiation rate of mouse embryonic stem cells

a Department of Biology, School of Sciences, University of Isfahan, Isfahan, Iran b Department of Cellular Biotechnology at Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran c Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran d Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
Sociomoral Reasoning and Antisocial Behaviors among Normal Sixth Graders.

Research has linked juvenile delinquency to immature sociomoral reasoning, but few studies have examined the kinds of behavior problems that are related to sociomoral reasoning among normal students. Sixth graders (N = 77) attending regular classrooms were administered a sociomoral reasoning preference task, and 19 of these children also received the Kohlberg moral judgment interview. Behavior problems were assessed by self-ratings on five scales of the Revised Behavior Problem Checklist. Maturity of sociomoral reasoning was found to be marginally associated with scores on the Socialized Aggression and Conduct Dis order scales (—.43 and —.28, respectively), but only among boys. Stronger asso ciations between sociomoral reasoning and socialized aggressive behaviors (-.47) and conduct disorder behaviors (-.43) became evident when vocabulary and SES were controlled through covariation. Results concur with those of other recent studies in indicating that the quality, or content, of social cognitions is re lated to children's behavior.
Estimating and Exploiting the Entropy of Sense Distributions

Word sense distributions are usually skewed. Predicting the extent of the skew can help a word sense disambiguation (WSD) system determine whether to consider evidence from the local context or apply the simple yet effective heuristic of using the first (most frequent) sense. In this paper, we propose a method to estimate the entropy of a sense distribution to boost the precision of a first sense heuristic by restricting its application to words with lower entropy. We show on two standard datasets that automatic prediction of entropy can increase the performance of an automatic first sense heuristic.
Functional bacterial amyloid increases Pseudomonas biofilm hydrophobicity and stiffness

The success of Pseudomonas species as opportunistic pathogens derives in great part from their ability to form stable biofilms that offer protection against chemical and mechanical attack. The extracellular matrix of biofilms contains numerous biomolecules, and it has recently been discovered that in Pseudomonas one of the components includes β-sheet rich amyloid fibrils (functional amyloid) produced by the fap operon. However, the role of the functional amyloid within the biofilm has not yet been investigated in detail. Here we investigate how the fap-based amyloid produced by Pseudomonas affects biofilm hydrophobicity and mechanical properties. Using atomic force microscopy imaging and force spectroscopy, we show that the amyloid renders individual cells more resistant to drying and alters their interactions with hydrophobic probes. Importantly, amyloid makes Pseudomonas more hydrophobic and increases biofilm stiffness 20-fold. Deletion of any one of the individual members of in the fap operon (except the putative chaperone FapA) abolishes this ability to increase biofilm stiffness and correlates with the loss of amyloid. We conclude that amyloid makes major contributions to biofilm mechanical robustness.
Dorsal vs. ventral differences in fast Up-state-associated oscillations in the medial prefrontal cortex of the urethane-anesthetized rat

We demonstrate, in the urethane-anesthetized rat, that within the medial prefrontal cortex (mPFC) there are clear subregional differences in the fast network oscillations associated with the slow oscillation Up-state. These differences, particularly between the dorsal and ventral subregions of the mPFC, may reflect the different functions and connectivity of these subregions.