Miracle-dz/UniFAR-FTUs huggingface dataset:
UM AMBIENTE DE CONTEXTO PERSONALIZADO E ORIENTADO ATAREFAS NA ARQUITETURA CLINICSPACE

O projeto ClinicSpace tem por objetivo preencher as lacunas existentes nos sistemas clinicos atuais, no que tange as caracteristicas de pervasividade e apoio de tarefas computacionais as atividades clinicas que o usuario (medico) realiza. A arquitetura do modelo ClinicSpace, construida a partir da perspectiva dada pela teoria da atividade, e composta por varios modulos que interligados oferecem as caracteristicas necessarias a um sistema clinico pervasivo orientado ao usuario-final. Um desses modulos e o tratamento de contexto das tarefas clinicas. Esse trabalho realiza uma discussao sobre os requisitos presentes para o tratamento de contexto das tarefas clinicas, definindo uma arquitetura para associa-los as tarefas do usuario, permitindo personalizacao de contexto e entrada automatica de dados. A personalizacao e obtida atraves da utilizacao de Elementos Programaveis de Contexto, que sao representados por atuadores, fisicos ou logicos, responsaveis por dotar o sistema de capacidade de execucoes automaticas, baseadas em parâmetros de contexto especificados pelo usuario. Ja a entrada automatica de dados trata da obtencao destes de maneira implicita, obtendo as informacoes utilizadas pelas aplicacoes que o usuario executa, no decorrer de suas tarefas. Para isso, definiu-se uma arquitetura com suporte a personalizacao e especificacao semântica dos dados nela utilizados. Para construir tais funcionalidades, estendeu-se o middleware pervasivo EXEHDA, modificando servicos existentes e agregando novos servicos. A principal contribuicao do trabalho esta na interligacao existente entre os componentes que integram a arquitetura, construindo uma visao unica do contexto de uma tarefa sob a perspectiva dos dados necessarios a ela e da capacidade de personalizacao pelo usuario. Dessa forma, reduz-se a necessidade da entrada explicita de dados, e contribui-se para a reducao da rejeicao da adocao dos sistemas clinicos em ambientes altamente dinâmicos, como os hospitalares.
On the Number of Edges in Random Planar Graphs

We consider random planar graphs on $n$ labelled nodes, and show in particular that if the graph is picked uniformly at random then the expected number of edges is at least $\frac{13}{7}n +o(n)$. To prove this result we give a lower bound on the size of the set of edges that can be added to a planar graph on $n$ nodes and $m$ edges while keeping it planar, and in particular we see that if $m$ is at most $\frac{13}{7}n - c$ (for a suitable constant~$c$) then at least this number of edges can be added.
Roles for the C-terminal Region of Sigma 54 in Transcriptional Silencing and DNA Binding*

Twenty-one conserved positively charged and aromatic amino acids between residues 331 and 462 of sigma 54 were changed to alanine, and the mutant proteins were studied by transcription, band shift analysis, and footprinting in vitro. A small segment corresponding to the rpoN box was found to be most important for binding duplex DNA. Two amino acids, 52 residues apart, were found to be critical for maintaining transcriptional silencing in the absence of activator. These two activator bypass mutants and several other mutants failed to bind the type of fork junction DNA thought to be required to maintain silencing. The two bypass mutants showed a binding pattern to DNA probes that was unique, both in comparison to other C-terminal mutants and to previously known N-terminal bypass mutants. On this basis, a model is proposed for the role of the C terminus and the N terminus of sigma 54 in enhancer-dependent transcription.
Charge and magnetic order in La0.5Sr1.5MnO4.

Elastic neutron scattering measurements characterizing the charge and magnetic order in La{sub 0.5}Sr{sub 1.5}MnO{sub 4} are presented. Superlattice reflections corresponding to an alternating Mn{sup +3}/Mn{sup +4} pattern with wave vector {ital q}{sub co}=(1/2,1/2,0) are observed below the charge ordering temperature, {ital T}{sub co}{approx_equal}217 K. Below the N{acute e}el temperature, {ital T}{sub {ital N}}{approx_equal}110 K, the magnetic moments associated with these ions form an ordered structure with dimensions 2{radical}2{ital a}{times}2{radical}2{ital a}{times}2{ital c} relative to the underlying chemical cell. {copyright} {ital 1996 The American Physical Society. }
Hepatocellular carcinoma in Lebanon: Etiology and prognostic factors associated with short-term survival.

AIM To study the epidemiology of HCC in Lebanon and prognostic factors predictive of early mortality. METHODS An observational follow-up cohort study of HCC cases diagnosed over a five-year period was carried out. Multivariate analysis was conducted to identify prognostic factors in comparison to Cancer of the Liver Italian Program (CLIP) score. Multiple variables including the etiology of underlying liver disease, the demographic characteristics of patients, and the severity of liver disease evaluated by the Child-Pugh score were studied. Tumor parameters included the time of diagnosis of HCC, alpha-fetoprotein level, number and size of nodules, presence of portal vein thrombosis, and treatment modalities. Death or loss of follow-up was considered as an end-point event. RESULTS Ninety-two patients (mean 60.5 +/- 22.3 years) were included. Etiology of underlying disease was hepatitis B, C, and alcohol in 67%, 20%, and 23.5% respectively. Child-Pugh class at diagnosis was A, B, and C in 34.8%, 39.3% and 25.8% respectively. Overall survival was 44.8%, 32.8% and 17.6% at 1, 2 and 3 years respectively (mean F/U 40.2 +/- 23.5 mo). Multivariate analysis identified three predictors of early mortality (< 6 mo): bilirubin > 3.2 mg/dL (P < 0.01), HCC as first presentation of liver disease (P = 0.035), and creatinine > 1 mg/dL (P = 0.017). A score based on these variables outperformed the CLIP score by Cox proportional hazard. ROC curve showed both models to be equivalent and moderately accurate. CONCLUSION HBV is the leading cause of HCC in Lebanon. Independent predictors of early mortality are elevated bilirubin, creatinine and HCC as first manifestation of disease. Prospective validation of a score based on these clinical parameters in predicting short-term survival is needed.
Phylogenetic Analysis of Chromosomally Determined Qnr and Related Proteins

ABSTRACT qnr genes were discovered on plasmids by their ability to reduce quinolone susceptibility, but homologs can be found in the genomes of at least 92 Gram-negative, Gram-positive, and strictly anaerobic bacterial species. The related pentapeptide repeat protein-encoding mfpA gene is present in the genome of at least 19 species of Mycobacterium and 10 other Actinobacteria species. The native function of these genes is not yet known.
Plankton food webs of the Gulf of Mexico spawning grounds of Atlantic Bluefin tuna

We used linear inverse ecosystem modeling techniques to assimilate data from extensive Lagrangian field experiments into a mass-balance constrained food web for the Gulf of Mexico open-ocean ecosystem. This region is highly oligotrophic, yet Atlantic Bluefin Tuna (ABT) travel long distances from feeding grounds in the North Atlantic to spawn there. Our results show that the food web is dominated by the microbial loop (>80% of net primary productivity is respired by heterotrophic bacteria and protists that feed on them). In contrast, herbivorous food web pathways from phytoplankton to metazoan zooplankton process <4% of net primary production in the mixed layer. Nevertheless, ABT larvae feed preferentially on calanoid copepods and other suspension-feeding zooplankton that in turn derive much of their nutrition from diatoms and mixotrophic flagellates. This allows ABT larvae to maintain a comparatively low trophic level (∼4.0 for pre-flexion larvae; ∼4.2 for post-flexion larvae) that increases trophic transfer from phytoplankton to larval fish.
Single-Cell Transcriptomics Identifies Dysregulated Metabolic Programs of Aging Alveolar Progenitor Cells in Lung Fibrosis

Aging is a critical risk factor in progressive lung fibrotic diseases such as idiopathic pulmonary fibrosis (IPF). Loss of integrity of type 2 alveolar epithelial cells (AEC2s) is the main causal event in the pathogenesis of IPF. To systematically examine the genomic program changes of AEC2s with aging and lung injury, we performed unbiased single cell RNA-seq analyses of lung epithelial cells from either uninjured or bleomycin-injured young and old mice. Major lung epithelial cell types were readily identified with canonical cell markers in our dataset. Heterogenecity of AEC2s was apparent, and AEC2s were then classified into three subsets according to their gene signatures. Genes related to lipid metabolism and glycolysis were significantly altered within these three clusters of AEC2s, and also affected by aging and lung injury. Importantly, IPF AEC2s showed similar genomic programming and metabolic changes as that of AEC2s from bleomycin injured old mouse lungs relative to controls. Furthermore, perturbation of both lipid metabolism and glycolysis significantly changed progenitor renewal capacity in 3-Demensional organoid culture of AEC2s. Taken togather, this work identified metabolic defects of AEC2s in aging and during lung injury. Strategies to rectify these altered programs would promote AEC2 renewal which in turn improves lung repair. One sentence summary Metabolic defects of alveolar progenitors in aging and during lung injury impair their renewal.
Potential Intervention by Vaccinia Virus Complement Control Protein of the Signals Contributing to the Progression of Central Nervous System Injury to Alzheimer's Disease

Abstract: Traumatic brain injury (TBI) is one of the few known risk factors for Alzheimers disease (AD) and for depression. The mechanisms by which trauma causes delayed cognitive deficits are largely unknown. In recent studies, it was demonstrated that the complement system (an important component of the immune system and a mediator of inflammation) is activated both in human AD and following experimental TBI in rats. Amyloid proteins are also present in AD and following TBI, and are known to activate complement in vitro. Based on these and other previous studies, it was hypothesized that regulation of the complement system will attenuate the long‐term consequences of TBI. Vaccinia virus complement control protein (VCP) is a protein encoded by vaccinia virus. It blocks both the classic and alternative pathways of complement activation in vitro, and by doings so prevents the generation of proinflammatory chemotactic factors. Based on in vitro studies VCP can block the complement activation by the amyloid beta peptide. Using a fluid percussion rat model that causes traumatic brain injury (TBI), it was found that VCP significantly enhances functional recovery as determined by the Morris Water Maze test. Taken togther these studies indicate that potentially VCP could block molecular signals such as the formation of amyloid beta or the activation of complement to inhibit formation of AD following TBI.
STAT1-induced Apoptosis Is Mediated by Caspases 2, 3, and 7*

STAT1 (signal transducer and activator of transcription 1) has been implicated as a mediator of a variety of biological responses in response to stimulation by specific growth factors and cytokines. To understand better the role of STAT1 in the interferon-γ (IFN-γ)-induced phenotype, we generated an active form of STAT1 (STAT1C) by substituting Cys residues for both Arg-656 and Asn-658 within the C-terminal loop of the STAT1 SH2 domain. The IFN-γ activation site element was stimulated and bound efficiently by STAT1C without IFN-γ treatment. STAT1C was found to be tyrosine-phosphorylated in the nucleus for more than 30 h after IFN-γ stimulation. STAT1-negative U3A cells reexpressing STAT1C showed retarded cell growth and underwent apoptosis when treated with IFN-γ. Further analysis demonstrated that apoptosis was preceded by proteolytic cleavage of caspases 2, 3, and 7, and wild type STAT1 also induced cleavage of caspase 7 when expressed in STAT1-negative U3A cells, indicating that STAT1C augments potential activity of wild type STAT1. Studies with cycloheximide treatment showed that protein synthesis induced in the first 24 h after IFN-γ treatment was required for apoptosis under these conditions. Finally, we found that STAT1C-induced apoptosis was, in part, mediated by caspase 2, 3, and 7 because benzyloxycarbonyl-valyl-aspartyl-valyl-alanyl-aspartic acid fluoromethyl ketone (Z-VDVAD-FMK) treatment partially blocked apoptosis. These results suggest that prolonged nuclear localization of activated STAT1 results in apoptosis involving specific regulation of caspase pathway.
Lattice Boltzmann model for simulating flows with multiple phases and components.

A lattice Boltzmann model is developed which has the ability to simulate flows containing multiple phases and components. Each of the components can be immiscible with the others and can have different mass values. The equilibrium state of each component can have a nonideal gas equation of state at a prescribed temperature exhibiting thermodynamic phase transitions. The scheme incorporated in this model is the introduction of an interparticle potential. The dynamical rules in this model are local so it is highly efficient to compute on massively parallel computers. This model has many applications in large-scale numerical simulations of various types of fluid flows.
Designing messages with high sensation value: When activation meets reactance

Objective: Based on two theoretical models – activation model of information exposure and psychological reactance theory – this study examined the individual and combined effects of message sensation value (MSV) and controlling language on young adults’ information processing. Method: Two experimental studies on anti-drunken driving and anti-smoking public service announcements were conducted that were conceptual replications of one another. The measures included perceived threat to freedom, sensation seeking, perceived ad effectiveness and state reactance (anger). Results: Across the two studies, MSV was found to advance the perceived ad effectiveness, and controlling language contributed to anger. A consistent interaction was revealed, such that participants responded positively to the high sensation value messages when presented with low controlling language. The effect of high sensation value anti-smoking ads to advance persuasiveness particularly under the condition of low controlling language was more influential to low sensation seekers. Implication: This study suggests that increasing MSV coupled with high controlling language can backfire, especially when targeting young adults. The implications for persuasion in general are considered, as well as the specific findings for drunken driving and smoking.
Cyber Security, Cyber Crime and Cyber Forensics - Applications and Perspectives

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Insights into HER2 signaling from step-by-step optimization of anti-HER2 antibodies

HER2, a ligand-free tyrosine kinase receptor of the HER family, is frequently overexpressed in breast cancer. The anti-HER2 antibody trastuzumab has shown significant clinical benefits in metastatic breast cancer; however, resistance to trastuzumab is common. The development of monoclonal antibodies that have complementary mechanisms of action results in a more comprehensive blockade of ErbB2 signaling, especially HER2/HER3 signaling. Use of such antibodies may have clinical benefits if these antibodies can become widely accepted. Here, we describe a novel anti-HER2 antibody, hHERmAb-F0178C1, which was isolated from a screen of a phage display library. A step-by-step optimization method was employed to maximize the inhibitory effect of this anti-HER2 antibody. Crystallographic analysis was used to determine the three-dimensional structure to 3.5 Å resolution, confirming that the epitope of this antibody is in domain III of HER2. Moreover, this novel anti-HER2 antibody exhibits superior efficacy in blocking HER2/HER3 heterodimerization and signaling, and its use in combination with pertuzumab has a synergistic effect. Characterization of this antibody revealed the important role of a ligand binding site within domain III of HER2. The results of this study clearly indicate the unique potential of hHERmAb-F0178C1, and its complementary inhibition effect on HER2/HER3 signaling warrants its consideration as a promising clinical treatment.
Deep gray matter T2 hypointensity is present in patients with clinically isolated syndromes suggestive of multiple sclerosis

Gray matter (GM) magnetic resonance imaging (MRI) T2 hypointensity, a putative marker of iron deposition, is a frequent finding in patients with clinically definite (CD) multiple sclerosis (MS). The objective of this study was to assess: (a) how early deep GM T2 hypointensity occurs in MS, by studying patients with clinically isolated syndromes (CIS) suggestive of MS, and (b) whether they contribute to predict subsequent evolution to CDMS. Dual-echo scans using two different acquisition protocols were acquired from 47 CIS patients and 13 healthy controls (HC). Normalized T2-intensity of the basal ganglia and thalamus was quantified. Patients were assessed clinically at the time of MRI acquisition and after three years. During the observation period, 18 patients (38%) evolved to CDMS. At the baseline, only the GM T2-intensity of the left caudate nucleus was significantly reduced in CIS patients in comparison with the HC (p = 0.04). At the baseline, the T2 intensity of the left caudate nucleus was significantly lower (p = 0.01) in CIS patients with disease dissemination in space (DIS), but not in those without DIS, compared to the HC. The baseline T2 lesion volume, but not GM T2 hypointensity, was associated with evolution to CDMS (hazard ratio = 1.60, 95% confidence interval (CI) = 1.05—2.42; p = 0.02). In CIS patients, deep GM is not spared, suggesting that iron-related changes and neurodegeneration occurs early. The magnitude of such damage is only minor and not associated with an increased risk of evolution to CDMS.
A pharmacologic examination of receptors mediating serotonin-induced bronchoconstriction in the anesthetized guinea pig.

The receptors involved in the bronchoconstriction evoked in vivo by intravenous administration to the anesthetized guinea pig of serotonin and serotonin-related agonists have been examined in this study. Animals were pretreated with indomethacin and (+/-)-propranolol to inhibit cyclooxygenase and beta adrenergic receptors, respectively, and pulmonary parameters were obtained with a Buxco pulmonary mechanics computer. Dose-dependent increases in pulmonary resistance and decreases in dynamic lung compliance were produced by serotonin, 2-methyl-serotonin, 5-methoxy-tryptamine, alpha-methyl-serotonin, 5-carboxamidotryptamine, and m-trifluoromethylphenylpiperazine (TFMPP). Responses to all agonists except 2-methyl-serotonin, a selective 5-hydroxytryptamine3 (5-HT3) agonist, were antagonized by the 5-HT2 antagonists, LY53857 and ketanserin. Zaclopride, 1 and 10 mg/kg, a selective 5-HT3 antagonist, blocked responses to 2-methyl-serotonin. A maximally effective dose of LY53857 (1 mg/kg) produced larger shifts of the dose-response curves to serotonin, 5-methoxytryptamine and alpha-methyl-serotonin than did a maximally effective dose of ketanserin (1 mg/kg). Thiorphan, 10 mg/kg, an inhibitor of neutral endopeptidase, potentiated 2-methyl-serotonin and, when studied in the presence of LY53857, also potentiated serotonin, 5-methoxytryptamine and TFMPP. After thiorphan and LY53857, responses to serotonin, but not 5-methoxytryptamine or TFMPP, were blocked by zaclopride. Capsaicin pretreatment of the animals resulted in rightward shifts of the dose-response curves to serotonin, 2-methyl-serotonin and TFMPP, but not to 5-methoxytryptamine or alpha-methyl-serotonin. Potentiation by thiorphan and antagonism by zaclopride of responses to serotonin were still evident after capsaicin pretreatment. (ABSTRACT TRUNCATED AT 250 WORDS)
Evolution of Trophic Transmission in Parasites: Why Add Intermediate Hosts?

Although multihost complex life cycles (CLCs) are common in several distantly related groups of parasites, their evolution remains poorly understood. In this article, we argue that under particular circumstances, adding a second host to a single‐host life cycle is likely to enhance transmission (i.e., reaching the target host). For instance, in several situations, the propagules of a parasite exploiting a predator species will achieve a higher host‐finding success by encysting in a prey of the target predator than by other dispersal modes. In such a case, selection should favor the transition from a single‐ to a two‐host life cycle that includes the prey species as an intermediate host. We use an optimality model to explore this idea, and we discuss it in relation to dispersal strategies known among free‐living species, especially animal dispersal. The model found that selection favored a complex life cycle only if intermediate hosts were more abundant than definitive hosts. The selective value of a complex life cycle increased with predation rates by definitive hosts on intermediate hosts. In exploring trade‐offs between transmission strategies, we found that more costly trade‐offs made it more difficult to evolve a CLC while less costly trade‐offs between traits could favor a mixed strategy.
New patented histone deacetylase inhibitors

Importance of the field: Following FDA approval of vorinostat in 2006, several novel HDAC inhibitors (HDACis) have entered clinical trials, and there are numerous published patent applications claiming novel HDACis which were optimized as potential drug candidates, designed for regional or systemic release, and created as dual or multifunctional inhibitors. Given the breadth and depth of recent reporting of novel HDACis, there has emerged a need to review the field from a chemist's perspective in one compact article. Areas covered in this review: This review provides a summary of published patent applications claiming novel HDACis from 2007 until mid-2009, covering mainly classes I, II and IV anticancer HDACis including those that have recently advanced to the clinic. What the reader will gain: Readers will rapidly gain an overview of the majority of HDACi scaffolds with representative structure–activity relationships; they will learn how these new compounds were created, how their drug like properties were improved and which companies are the main players in the field. Take home message: Although competition in this field is intense, the future application of HDACis to treat human disease either as single agents or in combination with existing drugs holds real promise.