Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and Cellular Pathobiology Human Glioma Growth Is Controlled by MicroRNA-10 b

MicroRNA (miRNA) expression profiling studies revealed a number of miRNAs dysregulated in the malignant brain tumor glioblastoma. Molecular functions of these miRNAs in gliomagenesis are mainly unknown. We show that inhibition of miR-10b, a miRNA not expressed in human brain and strongly upregulated in both lowgrade and high-grade gliomas, reduces glioma cell growth by cell-cycle arrest and apoptosis. These cellular responses are mediated by augmented expression of the direct targets of miR-10b, including BCL2L11/Bim, TFAP2C/AP-2g , CDKN1A/p21, and CDKN2A/p16, which normally protect cells from uncontrolled growth. Analysis of The Cancer Genome Atlas expression data set reveals a strong positive correlation between numerous genes sustaining cellular growth and miR-10b levels in human glioblastomas, while proapoptotic genes anticorrelate with the expression of miR-10b. Furthermore, survival of glioblastoma patients expressing high levels of miR-10 family members is significantly reduced in comparison to patients with low miR-10 levels, indicating that miR-10 may contribute to glioma growth in vivo. Finally, inhibition of miR-10b in a mouse model of human glioma results in significant reduction of tumor growth. Altogether, our experiments validate an important role of miR-10b in gliomagenesis, reveal a novel mechanism of miR-10b–mediated regulation, and suggest the possibility of its future use as a therapeutic target in gliomas. Cancer Res; 71(10); 1–10. 2011 AACR.
Relationship between the amplitude of &agr; waves and reaction time

The amplitude of &agr; waves in an ongoing electroencephalogram can be reduced by visual stimuli and by attention. We reduced &agr; amplitudes by presenting a short visual stimulus in the visual periphery, 10° apart from the fovea, and measured (i) the decrease of &agr; amplitudes as a function of time and (ii) delays in reaction to foveal stimuli presented at various intervals after the peripheral stimulus. It turned out that in the time window from 0 to 2 s after the peripheral stimulus, both responses decrease in parallel with a minimum at 350–500 ms. The close correspondence between &agr; amplitude and reaction time supports the view that &agr; waves are functionally relevant for this behaviour.
A 433 MHz 64 b quad issue RISC microprocessor

This 9.6 M transistor quad-issue RISC microprocessor achieves greater than 500 SPECint92 (estimated) at 433 MHz. The die measures 14.5/spl times/14.4 mm/sup 2/ fabricated in a 0.35 /spl mu/m CMOS process. The chip uses split-power supplies; the core operates at 2.0 V and the external interface at 3.3 V. The chip dissipates less than 25 W.
Effects of nitric oxide synthase inhibition on the pathophysiology observed in a model of chronic granulomatous colitis.

The objective of this study was to assess the role that nitric oxide (NO) may play in mediating the colonic inflammation observed in a model of chronic granulomatous colitis using two pharmacologically different inhibitors of nitric oxide synthase (NOS). The NOS inhibitors NG-nitro-L-arginine methyl ester (L-NAME; 15 mumol/kg/day) and aminoguanidine (AG; 15 mumol/kg/day) were administered to rats in their drinking water, beginning 3 days before the induction of colitis and continuing for the entire 3-week period. We found that chronic NOS inhibition by L-NAME or AG significantly attenuated the peptidoglycan/polysacchride (PG/PS)-induced increases in macroscopic colonic inflammation scores and colonic MPO activity. Only AG, and not L-NAME, attenuated the PG/PS-induced increases in colon dry weight. Both L-NAME and AG significantly attenuated the PG/PS-induced increases in spleen inflammation, whereas neither drug significantly attenuated the PG/PS-induced liver inflammation. Although both L-NAME and AG inhibited NO production in vivo, as measured by decreases in plasma nitrite and nitrate levels, only AG was found to attenuate these values significantly (38 +/- 3 vs. 83 +/- 8 microM, respectively; P < .05). Finally, administration of L-NAME, but not of AG, significantly increased mean arterial pressure from 83 mm Hg in colitic animals to 105 mm Hg in the PG/PS+L-NAME-treated animals (P < .05). We conclude that NO may play an important role in mediating some of the pathophysiology associated with this model of chronic granulomatous colitis.
Timing and Competence of Neural Crest Formation

Neural crest cells can be induced by an interaction between neural plate and ectoderm. To clarify the timing and nature of these inductive interactions, we have examined the time of competence of the neural plate to become neural crest as well as the time of neural fold specification. The neural plate is competent to respond to inductive interactions with the nonneural ectoderm for a limited period, rapidly losing its responsive ability after stage 10. In contrast, nonneural ectoderm from numerous stages retains the ability to induce neural crest cells from competent neural plate. When neural folds are explanted to test their ability to produce neural crest without further tissue interactions, we find that folds derived from all rostrocaudal levels of the open neural plate are already specified to express the neural crest marker Slug. However, additional signals may be required for maintenance of Slug expression, since the transcript is later down-regulated in vitro in the absence of tissue interactions. Taken together, these results suggest that there are multiple stages of neural crest induction. The earliest induction must have occurred by the end of gastrulation, since the newly formed neural fold population is already specified to form neural crest. However, isolated neural folds eventually down-regulate Slug, suggesting a second phase that maintains neural crest formation. Thus, induction of the neural crest may involve multiple and sustained tissue interactions.
A review of histomorphometric analysis techniques for assessing implant-soft tissue interface

Abstract The success of dental implant treatment depends on the healing of both hard and soft tissues. While osseointegration provides initial success, the biological seal of the peri-implant soft tissue is crucial for maintaining the long term success of implants. Most studies of the biological seal of peri-implant tissues are based on animal or monolayer cell culture models. To understand the mechanisms of soft tissue attachment and the factors affecting the integrity of the soft tissue around the implants, it is essential to obtain good quality histological sections for microscopic examination. The nature of the specimens, however, which consist of both metal implant and soft peri-implant tissues, poses difficulties in preparing the specimens for histomorphometric analysis of the implant-soft tissue interface. We review various methods that have been used for the implant-tissue interface investigation with particular focus on the soft tissue. The different methods are classified and the advantages and limitations of the different techniques are highlighted.
Fingerprint Matching Using an Orientation-Based Minutia Descriptor

We introduce a novel fingerprint representation scheme that relies on describing the orientation field of the fingerprint pattern with respect to each minutia detail. This representation allows the derivation of a similarity function between minutiae that is used to identify corresponding features and evaluate the resemblance between two fingerprint impressions. A fingerprint matching algorithm, based on the proposed representation, is developed and tested with a series of experiments conducted on two public domain collections of fingerprint images. The results reveal that our method can achieve good performance on these data collections and that it outperforms other alternative approaches implemented for comparison.
American tegumentary leishmaniasis: Is antimonial treatment outcome related to parasite drug susceptibility?

BACKGROUND Antimonials are the first drug of choice for the treatment of American tegumentary leishmaniasis (ATL); however, their efficacy is not predictable, and this may be linked to parasite drug resistance. We aimed to characterize the in vitro antimony susceptibility of clinical isolates of Peruvian patients with ATL who were treated with sodium stibogluconate and to correlate this in vitro phenotype with different treatment outcomes. METHODS Thirty-seven clinical isolates were obtained from patients with known disease and treatment histories. These isolates were typed, and the susceptibility of intracellular amastigotes to pentavalent (SbV) and trivalent (SbIII) antimonials was determined. RESULTS We observed 29 SbV-resistant isolates among 4 species of subgenus Viannia, most of which exhibited primary resistance; isolates resistant only to SbIII; and 3 combinations of in vitro phenotypes: (1) parasites sensitive to both drugs, (2) parasites resistant to both drugs, and (3) parasites resistant to SbV only (the majority of isolates fell into this category). There was no correlation between in vitro susceptibility to both antimonials and the clinical outcome of therapy. CONCLUSION Antimony insensitivity might occur in a stepwise fashion (first to SbV and then to SbIII). Our data question the definition of true parasite resistance to antimonials. Further studies of treatment efficacy should apply standardized protocols and definitions and should also consider host factors.
Pros and cons of quitting, self-efficacy, and the stages of change in smoking cessation.

In The Netherlands, 34% of the population smoke, and 70% of these smokers are not planning to quit. The lower percentages in the U.S. population seem to reflect a difference in smoking culture. This study analyzes the pros and cons of quitting and self-efficacy expectation in the 5 stages of change in the Dutch population. The results are compared with the pattern of the pros and cons of smoking and self-efficacy expectations found in U.S. samples. The data show the hypothesized pattern: In the first 2 stages, the expected positive outcomes of quitting discriminated better between the stages than self-efficacy, whereas for later stages, self-efficacy was the better discriminator. This study shows that the stage typology is applicable to the Dutch population and that the pattern of the pros, cons, and self-efficacy is very similar to the pattern found in the U.S. populations.
Studies on toxoplasmosis. I. Isolation of Toxoplasma from muscles of human, dogs, and cats.

Diaphragm muscle specimens from 53 humans who died of various diseases unrelated to toxoplasmosis, and from 87 healthy dogs, and mixed specimens of diaphragm and abdominal muscles from 25 healthy cats were examined for the presence of Toxoplasma. The muscle specimens were digested with trypsin, and the digested materials were inoculated into the peritoneal cavity of mice (gpc strain). Toxoplasma was isolated from 2 (3.8 %) out of 53 humans, 11 (12.6 %) out of 87 dogs, and 17 (68.0 %) out of 25 cat muscle specimens. Eight (15.7 %) out of 51 humans, 15 (17.2 %) out of 87 dogs, and 15 (60.0 %) out of 25 cats were HA test (Hanaki et al. 1964) positive at titers of 1: 64 or higher. The human cases, from which Toxoplasma was isolated, showed negative HA. In the cases of cats, the results of isolation of the parasite and the HA test were roughly correlated, but this was not the case in humans or dogs.
Discrete element method (DEM) and its possible application

In this paper, an outline of the discrete element method (DEM) which had been popular as a tool for solving dynamics of granular media was summarized in terms of its formulation. Successively, some examples of DEM application in terramechanics, where interactions between terrain and machine are the main subject of study, were introduced. Lastly, an attempt of DEM application to plant root-soil interaction was discussed.
Multi-criteria optimization of neural networks using multi-objective genetic algorithm

This paper propose a new multi-objective model optimization allow training the multi-layer perceptron neural network (MLPNN) and optimizing its architecture. More precisely, this model aims to satisfy two objectives: the first one is minimizing the perceptron error (training objective) and the second one is minimizing the sum of the absolute weights (optimizing architecture objective). As known, a multi-objective problem's optimal solution is a set called Pareto set, from which a single weight vector with best performance will correspond to a reduced number of weights; this set is a compromise between the two objectives. To solve the proposed model, we have chosen the NSGA II algorithm (Non-Dominated Sorting Genetic Algorithm II). This algorithm has shown to be very powerful for multi-objective optimization, thus for multi-objective learning.
Dynamic interactions of proteins in complex networks: identifying the complete set of interacting E2s for functional investigation of E3‐dependent protein ubiquitination

A ubiquitin ligase (E3) functions at the crossroad between ubiquitin activation and the attachment of ubiquitin to protein substrates. During this process, the E3 interacts with both a substrate and a ubiquitin‐conjugating enzyme (E2). Although a major goal when investigating an E3 is to identify its substrates, recent evidence indicates that the E2 dictates the type of ubiquitin modification that will occur on the substrate. There are ∼ 30 E2s identified in the human genome, many of which remain to be characterized. We found that the RING E3 BRCA1/BARD1 can interact with 10 different E2s. The ability of BRCA1 to interact with multiple E2s is likely to be a common feature among other RING and U‐box E3s. We and others have also found that certain E2s show a preference for attaching either the first ubiquitin to a substrate lysine or ubiquitin to itself (chain building), suggesting that E2s may play a role in dictating product formation. Therefore, when investigating the functions of an E3 it is advisable to identify all E2s that interact with the E3 so that these can be used in E3‐dependent substrate‐ubiquitination assays. We describe a method used to identify all the E2s that interact with BRCA1. Defining the set of E2s that interact with other RING and U‐box E3s will open the door for predictive models and lead to a better understand of substrate ubiquitination.
Who should robots adapt to within a multi-party interaction in a public space?

Robots in public environments are challenged with socially appropriate interactions with previously unseen users: they need to offer appropriate services and shape their interaction style according to the particular individual's needs and preferences, for example the elderly and children. In addition, interactions in public spaces are not limited to merely two parties, but often involve multi-party situations with changing numbers of participants. The research question of this work is to investigate what rules should a socially competent robot follow in order to adapt to such complex social situations in real-world scenarios.
Molecular Interactions Involved in the Transactivation of the Human T-Cell Leukemia Virus Type 1 Promoter Mediated by Tax and CREB-2 (ATF-4)

ABSTRACT The human T-cell leukemia virus type 1 (HTLV-1) Tax protein activates viral transcription through three 21-bp repeats located in the U3 region of the HTLV-1 long terminal repeat and called Tax-responsive elements (TxREs). Each TxRE contains nucleotide sequences corresponding to imperfect cyclic AMP response elements (CRE). In this study, we demonstrate that the bZIP transcriptional factor CREB-2 is able to bind in vitro to the TxREs and that CREB-2 binding to each of the 21-bp motifs is enhanced by Tax. We also demonstrate that Tax can weakly interact with CREB-2 bound to a cellular palindromic CRE motif such as that found in the somatostatin promoter. Mutagenesis of Tax and CREB-2 demonstrates that both N- and C-terminal domains of Tax and the C-terminal region of CREB-2 are required for direct interaction between the two proteins. In addition, the Tax mutant M47, defective for HTLV-1 activation, is unable to form in vitro a ternary complex with CREB-2 and TxRE. In agreement with recent results suggesting that Tax can recruit the coactivator CREB-binding protein (CBP) on the HTLV-1 promoter, we provide evidence that Tax, CREB-2, and CBP are capable of cooperating to stimulate viral transcription. Taken together, our data highlight the major role played by CREB-2 in Tax-mediated transactivation.
Semantic Knowledge Graph Network Features for Drug Repurposing

Given the significant time and financial costs of developing a commercial drug, it remains important to constantly reform the drug discovery pipeline with novel technologies that can narrow the candidates down to the most promising lead compounds for clinical testing. Computational approaches are used to expedite the drug discovery processes. Semantic knowledge graphs can assist these computational approaches, because they connect different biological databases and reflect the relationships between genes, pathways and diseases. Here, we took advantage of the Euretos Knowledge Platform (EKP), a commercial database that integrates more than 170 different biological resources including DrugBank, and evaluated the usefulness of the underlying semantic knowledge graphs to predict novel drug-disease associations. We extracted network-based features from the semantic knowledge graph and tested their ability to separate between the positive and negative data sets of drug-disease pairs. Our results showed that the extracted features such as the total number of intermediate concepts (count), the number of different semantic categories (diversity), and the predicates connecting a drug-disease pair were successful in separating the positive from the negative sets. These features provide a proof of concept for using semantic knowledge graphs for drug repurposing efforts. Our work reveals the added value of integrating different biological databases for solving complex biological questions.
The performance of control charts using transfer function

The procedure to accommodate continuous data with autocorrelation is to use control charts residuals which are adjusted by time series methods, and when we analyze discrete data with autocorrelation is analyzed, the Poisson distribution is often employed. This paper shows the application of statistic quality control (SQC) to the sand foundry in the Industry FUNDIMISA, in Santo Angelo (RS/Brasil). The variable plasticity of the sand was analyzed before the elaboration of the broken casts, and verified its relation with the non conformity of those broken casts. The objective of this paper is to investigate the performance and adequacy of the traditional use of control charts with autocorrelated data, and to motivate the use of Time Series methodologies to fit the correlated continuous variable; and the use of Poisson regression models to fit the correlated discrete variable, and to discuss the use of Transfer Function models in a productive process.
A comparison of heavy-tailed VaR estimates and Filtered Historical Simulation: Evidence from emerging markets

The purpose of this paper is to investigate relative performance of Value at Risk (VaR) models in forecasting risk of emerging markets financial series. Among well-known Value-at-Risk modelling techniques, we based our estimates on GARCH, Extereme Value Theory (EVT) and Filtered Historical Simulation (FHS). Risk estimates are then exposed to the backtesting models inorder to evaluating comparative accuracy of the VaR models. The results indicate that EVT-based VaR estimates provides us with more accurate estimation of VaR specially in higher quantiles.
An emergentist perspective on the origin of number sense

The finding that human infants and many other animal species are sensitive to numerical quantity has been widely interpreted as evidence for evolved, biologically determined numerical capacities across unrelated species, thereby supporting a ‘nativist’ stance on the origin of number sense. Here, we tackle this issue within the ‘emergentist’ perspective provided by artificial neural network models, and we build on computer simulations to discuss two different approaches to think about the innateness of number sense. The first, illustrated by artificial life simulations, shows that numerical abilities can be supported by domain-specific representations emerging from evolutionary pressure. The second assumes that numerical representations need not be genetically pre-determined but can emerge from the interplay between innate architectural constraints and domain-general learning mechanisms, instantiated in deep learning simulations. We show that deep neural networks endowed with basic visuospatial processing exhibit a remarkable performance in numerosity discrimination before any experience-dependent learning, whereas unsupervised sensory experience with visual sets leads to subsequent improvement of number acuity and reduces the influence of continuous visual cues. The emergent neuronal code for numbers in the model includes both numerosity-sensitive (summation coding) and numerosity-selective response profiles, closely mirroring those found in monkey intraparietal neurons. We conclude that a form of innatism based on architectural and learning biases is a fruitful approach to understanding the origin and development of number sense. This article is part of a discussion meeting issue ‘The origins of numerical abilities'.
Functional Identification of the Product of the Bacillus subtilis yvaL Gene as a SecG Homologue

ABSTRACT Protein export in Escherichia coli is mediated by translocase, a multisubunit membrane protein complex with SecA as the peripheral subunit and the SecY, SecE, and SecG proteins as the integral membrane domain. In the gram-positive bacterium Bacillus subtilis, SecA, SecY, and SecE have been identified through genetic analysis. Sequence comparison of the Bacilluschromosome identified a potential homologue of SecG, termed YvaL. A chromosomal disruption of the yvaL gene results in mild cold sensitivity and causes a β-lactamase secretion defect. The cold sensitivity is exacerbated by overexpression of the secretory protein α-amylase, whereas growth and β-lactamase secretion are restored by coexpression of yvaL or the E. coli secG gene. These results indicate that the yvaL gene codes for a protein that is functionally homologous to SecG.
Directional Modulation Based on 4-D Antenna Arrays

Four-dimensional (4-D) antenna arrays are formed by introducing a fourth dimension, time, into traditional antenna arrays. In this paper, a time-modulated 4-D array with constant instantaneous directivity is proposed for directional modulation. The main idea is that the 4-D array transmits correct signal without time modulation in the desired direction, while transmitting time-modulated signals in other directions. As longs as the time modulation frequency is less than the bandwidth of the transmitted signal, the time-modulated signals cannot be demodulated correctly due to the aliasing effect, implying that time-modulated signals go distorted. Thus, the 4-D array can be used to transmit direction-dependent signals in secure wireless communications. The proposed idea is verified by experiments based on AM signal transmission through the 4-D array. Moreover, BPSK signal transmission through the 4-D array is studied and the bit error rate (BER) performance is investigated. Simulation results show that the BERs of time-modulated BPSK (TM-BPSK) signals transmitted through the sidelobes of the 4-D array are much higher than those of BPSK signals and almost keep unchanged even under higher SNR. Finally, two enhanced methods are presented to improve the feasibility of directional modulation by using random time sequences and random time modulation frequency.