Miracle-dz/UniFAR-FTUs huggingface dataset:
Herpes Simplex Virus Type 1 Infection Leads to Loss of Serine-2 Phosphorylation on the Carboxyl-Terminal Domain of RNA Polymerase II

ABSTRACT Previous studies have shown that herpes simplex virus type 1 (HSV-1) infection alters the phosphorylation of the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAP II), creating a new form of the enzyme known as RNAP III. However, the specific phosphorylation changes induced by HSV-1 have not been characterized. In this study, we used phospho-specific anti-CTD antibodies to probe the structure of the postinfection RNAP II. We find that RNAP III is phosphorylated on serine-5 (Ser-5) of the CTD consensus repeat but generally lacks phosphorylation on serine-2 (Ser-2). Since Ser-2 phosphorylation is normally associated with efficient transcriptional elongation and the recruitment of pre-mRNA processing factors, our results suggest that RNAP III may have altered elongation properties and decreased interactions with the mRNA processing machinery. The viral factors responsible for the reduction in Ser-2 CTD phosphorylation were studied. We found that viral immediate-early (IE) gene expression is required and sufficient, in the context of infection, for loss of Ser-2 phosphorylation. However, studies with viral mutants failed to implicate a single IE protein (among ICP0, ICP4, ICP22, and ICP27) in this process. Although most Ser-2-phosphorylated RNAP II is lost after infection, our immunofluorescence analyses identified a small subfraction that escapes loss and relocalizes to splicing antigen-rich nuclear speckles. A similar phenomenon is seen in uninfected cells after various treatments that inhibit RNAP II transcription. We hypothesize that the HSV-1-induced relocalization of residual Ser-2-phosphorylated RNAP II to nuclear speckles reflects a host response to the inhibition of cellular gene transcription.
Systematic Reviews and Meta-and Pooled Analyses Breastfeeding and Childhood Asthma : Systematic Review and Meta-Analysis

Asthma and wheezing disorders are common chronic health problems in childhood. Breastfeeding provides health benefits, but it is not known whether or how breastfeeding decreases the risk of developing asthma. We performed a systematic review and meta-analysis of studies published between 1983 and 2012 on breastfeeding and asthma in children from the general population.We searched the PubMed and Embase databases for cohort, crosssectional, and case-control studies.We grouped the outcomes into asthma ever, recent asthma, or recent wheezing illness (recent asthma or recent wheeze). Using random-effects meta-analyses, we estimated pooled odds ratios of the association of breastfeeding with the risk for each of these outcomes.We performedmeta-regression and stratified meta-analyses. We included 117 of 1,464 titles identified by our search. The pooled odds ratios were 0.78 (95% confidence interval: 0.74, 0.84) for 75 studies analyzing “asthma ever,” 0.76 (95% confidence interval: 0.67, 0.86) for 46 studies analyzing “recent asthma,” and 0.81 (95% confidence interval: 0.76, 0.87) for 94 studies analyzing recent wheezing illness. After stratification by age, the strong protective association found at ages 0–2 years diminished over time. We found no evidence for differences by study design or study quality or between studies in Western and non-Western countries. A positive association of breastfeeding with reduced asthma/wheezing is supported by the combined evidence of existing studies.
Beliefs and Communication, The Basis of Collaborative Agents

Nowadays, simulation scenarios require enhanced agents being capable of communication, learning and having beliefs about their self or about their world. The distinction between facts and (possible false) beliefs is part of the requirements in order to describe scenarios closer to real world. This work proposes a solution which allows information exchange between agents, making use of generic/standard and ad-hoc message types, involving their self beliefs and their beliefs about the world where they act. Standard agent types being capable of automatic management of standard message types are defined. SPARQL, a standard RDF based query language, is used as part of the communication protocol. The paper is build around a social simulation scenario that provides the possibility of testing and describing the benefices of this work.
Fiscal Decentralization in Mexico: The Bailout Problem

The purpose of this paper is to identify and analyze the determinants and consequences of bailing out states, in particular, those observed in Mexico. This work suggests that the explicit generalized bailout carried out by the federal government in Mexico in 1995 created a moral hazard problem. Another result of the analysis is that the existing institutional-legal framework is not adequate, since it provides incentives for states to borrow and for banks to lend without evaluating the risk of the project. Likewise, the importance of the state is a major determinant in providing bailout transfers. Also, the more fiscal need a state government has when the state government is incapable of adjusting its expenditure, the more likely the state to get an extraordinary transfer during the period of study. On the other hand, political variables are not an important determinant of a bailout, except, perhaps, when there are state elections. It is also shown that excessive indebtedness of local states may have equity implications as well: bailouts tend to be highly regressive, as the poorer—and less indebted—states receive much less in extraordinary resources.
Identification and Characterization of the DNA Binding Domain of CpG-binding Protein*

CpG-binding protein is a transcriptional activator that exhibits a unique DNA binding specificity for unmethylated CpG motifs. CpG-binding protein contains a cysteine-rich CXXC domain that is conserved in DNA methyltransferase 1, methyl binding domain protein 1, and human trithorax. In vitro DNA binding assays reveal that CpG-binding protein contains a single DNA binding domain comprised of the CXXC domain and a short carboxyl extension. Specific mutation to alanine of individual conserved cysteine residues within the CXXC domain abolishes DNA binding activity. Denaturation/renaturation experiments in the presence of various metal cations demonstrate that the CXXC domain requires zinc for efficient DNA binding activity. Ligand selection of high affinity binding sites from a pool of degenerate oligonucleotides reveals that CpG-binding protein interacts with a variety of sequences that contains the CpG dinucleotide with a consensus binding site of (A/C)CpG(A/C). Mutation of the CpG motif(s) present within ligand-selected oligonucleotides ablates the interaction with CpG-binding protein, and mutation to thymine of the nucleotides flanking the CpG motifs reduces the affinity of CpG-binding protein. Hence, a CpG motif is necessary and sufficient to comprise a binding site for CpG-binding protein, although the immediate flanking sequence affects binding affinity.
Peritoneal macrophage cholesteryl ester content as a function of plasma cholesterol in rats.

Cholesterol accumulation in macrophages that have migrated in the subintimal space leads to foam cell formation, which is believed to be one of the initiating events in atherosclerosis. In this study we investigated the effect of cholesterol feeding on peritoneal monocyte/macrophage cholesterol content and peritoneal cavity lipoprotein composition in rats. A cholesterol (2%) and cholic acid (1%) diet caused significant hypercholesterolemia in plasma, and at the same time the cholesterol content of peritoneal monocytes/macrophages was increased. At day 7, the cellular cholesteryl ester content had risen to 30.1 micrograms/mg cellular protein from a baseline value of 9.2 micrograms/mg. The unesterified cholesterol content also increased by 56%. At this time, acyl-coenzyme A:cholesterol acyltransferase (ACAT) activity was doubled, whereas neutral and acidic cholesteryl ester hydrolase activities were unchanged. Reversal to the regular chow diet after 7 days of the cholesterol-enriched diet normalized plasma cholesterol levels as well as peritoneal monocyte/macrophage cholesteryl ester content. ACAT activity also decreased toward normal levels. Analysis of the d less than 1.21 g/ml peritoneal lipoproteins isolated by ultracentrifugation revealed the presence, in both normal and hypercholesterolemic rats, of apolipoprotein A-I-rich lipid complexes with pre-beta mobility on agarose gel electrophoresis. The size of the peritoneal lipoproteins was smaller than that of plasmatic high density lipoproteins, and their chemical composition was also different from that of the major plasma lipoproteins. The cholesteryl ester content of peritoneal lipoproteins increased after feeding of the cholesterol-enriched diet. In conclusion, our results show that cholesterol feeding leads to rapid accumulation of cholesteryl esters in monocytes/macrophages. As soon as plasma cholesterol levels are returned to normal, cellular cholesterol content is also normalized. (ABSTRACT TRUNCATED AT 250 WORDS)
Mining sequential patterns with extensible knowledge representation

Mining sequential patterns is an important activity in computerized data analysis, and further analysis of discovered patterns can lead to more important findings in a post mining stage. Methods that integrate the traditional mining tasks with a knowledge representation facilitating such as post pruning are therefore needed. In this paper a set-based approach to mining frequent sequential patterns in customer transactional databases is described which includes an extensible knowledge representation. This knowledge representation is a byproduct of the set-based approach which contributes to facilitate post data mining and analysis. The proposed approach employs a set based knowledge representation and improves the performance of Apriori based algorithms while preserving a complete set of sequential patterns. It takes advantage of an incremental mining methodology and provides a rich knowledge representation. Performance results of the proposed approach are compared to the performance of existing sequential pattern mining algorithms including GSP Generalized Sequential Pattern and PrefixSpan. The effective knowledge representation inferred from the set based approach can be extended to other data mining tasks and data analysis models. Such extension is demonstrated by two instances of enriched knowledge representations in sequential databases, namely Set Occurrence Tables and Set Distance computations, along with their use of association rules generation, feature selection and ad hoc analysis in the post mining stage.
Patellar sleeve fracture: demonstration with MR imaging.

PURPOSE To demonstrate the magnetic resonance (MR) imaging characteristics of patellar sleeve fracture, a cartilaginous avulsion from the lower pole of the patella occurring during forceful contraction of the quadriceps muscle against a partially flexed knee. MATERIALS AND METHODS The authors evaluated radiographs and MR images from three children with suspected sleeve fractures. RESULTS Radiographs showed small bone fragments avulsed from the lower patella in two children and no bone abnormality in one. MR imaging demonstrated separation of most of the cartilaginous lower patella in all children, definite intraarticular extension in one, and possible intraarticular extension in another. CONCLUSION MR imaging can help determine the need for surgery by depicting the extent of cartilaginous injury and displacement of fracture fragments.
Functional Characterization of pH-Sensitive Organic Anion Transporting Polypeptide OATP-B in Human

The pH-sensitive activity of human organic anion transporting polypeptide OATP-B, which is expressed at the apical membrane of human small intestinal epithelial cells, was functionally characterized. When initial uptake of estrone-3-sulfate, a typical substrate of OATP, was studied kinetically, we observed an increase in Vmax with decrease of pH from 7.4 to 5.0, whereas the change in Km was negligible. OATP-B-mediated uptake of estrone-3-sulfate was independent of sodium, chloride, bicarbonate, or glutathione, whereas the proton ionophore carbonylcyanide p-trifluoromethoxyphenylhydrazone exhibited a pH-dependent inhibitory effect, suggesting that a proton gradient is a driving force for OATP-B. When OATP-B was expressed in human embryonic kidney 293 cells, uptake activities for anionic compounds showed various kinds of pH sensitivity. Dehydroepiandrosterone-sulfate, estrone-3-sulfate, and fexofenadine were transported by OATP-B at both neutral and acidic pH, whereas estradiol-17β-glucuronide, acetic acid, and lactic acid were not transported at all. Transport of taurocholic acid and pravastatin by OATP-B was observed only at acidic pH, demonstrating a pH-sensitive substrate specificity of OATP-B. Because the physiological pH close to the surface of intestinal epithelial cells is acidic, the roles of OATP-B in the small intestine might be different from those in other tissues, such as liver basolateral membrane. Although the driving force for OATP-B has not been fully established, the clarification of factors, such as pH, that affect the OATP-B-activity is essential for an understanding of the physiological and pharmacological relevance of the transporter in the small intestine.
UNDERSTANDING THE PERCEPTUAL AND COGNITIVE PRECURSORS TO THE ACQUISITION OF LANGUAGE: AN EXAMINATION OF INFANTS? PERCEPTION AND USE OF MANUAL GESTURES AND SIGNS

We tested hearing 6and 10-month-olds’ ability to discriminate among three American Sign Language (ASL) parameters (location, handshape, and movement) as well as a grammatical marker (facial expression). ASL-naïve infants were habituated to a signer articulating a two-handed symmetrical sign in neutral space. During test, infants viewed novel two-handed signs that varied in only one parameter or in facial expression. Infants detected changes in the signer’s facial expression and in the location of the sign but provided no evidence of detecting the changes in handshape or movement. These findings are consistent with children’s production errors in ASL and reveal that infants can distinguish among some parameters of ASL more easily than others.
Interface-Walkthroughs: efficient collaborative testing

A walkthrough facility for testing the usability of a user interface design before the software is written or a prototype is built is described. The use of this method to evaluate screen panels, which may include pull-down menus, dialogue boxes, palettes, and other interface elements, is reported. These pluralistic usability walkthroughs have four characteristics. First, three types of people participate in the walkthrough: representatives of the expected user population, product developers, and human factors professionals. Second, the user interface panels are presented in the same order they would be confronted online. Third, participants write down their responses on each panel before there is any discussion. Finally, the representative users speak first when discussing the panels and the experts speak only when the users have exhausted their comments. The limitations and benefits of the walkthrough approach are examined. <<ETX>>
The use of distributed network-based IDS systems in detection of evasion attacks

The paper discusses some problems in the use of intrusion detection systems (IDS), especially related to evasion attacks. Important characteristics of this type of attack are presented, and the possibilities for attack analyzed. Characteristics of network and host based IDS systems are compared, and some aspects of a distributed approach to the architecture of IDS are analyzed. On the basis of such discussion, the paper proposes the use of distributed network based IDS systems, which are client based, in the detection of evasion attacks. The proposed model is compared to host based intrusion prevention systems (HIPS). Important characteristics of the model are discussed. Some implementation issues are presented.
Biomarkers of Ovarian Reserve

The primary function of the female ovary is the production of a mature and viable oocyte capable of fertilization and subsequent embryo development and implantation. At birth, the ovary contains a finite number of oocytes available for folliculogenesis. This finite number of available oocytes is termed “the ovarian reserve”. The determination of ovarian reserve is important in the assessment and treatment of infertility. As the ovary ages, the ovarian reserve will decline. Infertility affects approximately 15%–20% of reproductive aged couples. The most commonly used biomarker assay to assess ovarian reserve is the measurement of follicle stimulating hormone (FSH) on day 3 of the menstrual cycle. However, anti-müllerian hormone and inhibin-B are other biomarkers of ovarian reserve that are gaining in popularity since they provide direct determination of ovarian status, whereas day 3 FSH is an indirect measurement. This review examines the physical tools and the hormone biomarkers used to evaluate ovarian reserve.
Probabilistic Partial Evaluation: Exploiting Rule Structure in Probabilistic Inference

Bayesian belief networks have grown to prominence because they provide compact representations of many domains, and there are algorithms to exploit this compactness. The next step is to allow compact representations of the conditional probability tables of a variable given its parents. In this paper we present such a representation in terms of parent contexts and provide an algorithm that exploits this compactness. The representation is in terms of rules that provide conditional probabilities in different contexts. The algorithm is based on eliminating the variables not needed in an answer in turn. The operations for eliminating a variable correspond to a form of partial evaluation, where we are careful to maintain the probabilistic dependencies necessary for correct probabilistic inference. We show how this new method can exploit more structure than previous methods for structured belief network inference.
Methylenedioxymethamphetamine (MDMA, ‘Ecstasy’): Neurodegeneration versus Neuromodulation

The amphetamine analogue 3,4-methylenedioxymethamphetamine (MDMA, ‘ecstasy’) is widely abused as a recreational drug due to its unique psychological effects. Of interest, MDMA causes long-lasting deficits in neurochemical and histological markers of the serotonergic neurons in the brain of different animal species. Such deficits include the decline in the activity of tryptophan hydroxylase in parallel with the loss of 5-HT and its main metabolite 5-hydoxyindoleacetic acid (5-HIAA) along with a lower binding of specific ligands to the 5-HT transporters (SERT). Of concern, reduced 5-HIAA levels in the CSF and SERT density have also been reported in human ecstasy users, what has been interpreted to reflect the loss of serotonergic fibers and terminals. The neurotoxic potential of MDMA has been questioned in recent years based on studies that failed to show the loss of the SERT protein by western blot or the lack of reactive astrogliosis after MDMA exposure. In addition, MDMA produces a long-lasting down-regulation of SERT gene expression; which, on the whole, has been used to invoke neuromodulatory mechanisms as an explanation to MDMA-induced 5-HT deficits. While decreased protein levels do not necessarily reflect neurodegeneration, the opposite is also true, that is, neuroregulatory mechanisms do not preclude the existence of 5-HT terminal degeneration.
Learning Abilities and Disabilities: Generalist Genes, Specialist Environments

Twin studies comparing identical and fraternal twins consistently show substantial genetic influence on individual differences in learning abilities such as reading and mathematics, as well as in other cognitive abilities such as spatial ability and memory. Multivariate genetic research has shown that the same set of genes is largely responsible for genetic influence on these diverse cognitive areas. We call these “generalist genes. ” What differentiates these abilities is largely the environment, especially nonshared environments that make children growing up in the same family different from one another. These multivariate genetic findings of generalist genes and specialist environments have far-reaching implications for diagnosis and treatment of learning disabilities and for understanding the brain mechanisms that mediate these effects.
A reconstrução do sentido de comunidade : implicações teórico-metodológicas no trabalho sobre a experiência de sentido de comunidade

This project aims to give a contribute looking at the Experience of Sense of Community as well as its’ possibility of reconstruction. Based on McMillan and Chavis (1986) and McMillan (1996) Theory of the Sense of Community, we adapted a first version of the Brief Sense of Community Scale (BSCS; Peterson, Speer & McMillan, 2008) for the portuguese population, taking as referent geographical communities. Departing from psychometric analysis, we explore the issue of one or multiple dimensions of the BSCS. We attain two dimensions from the data: Involvement (including the original theoretical dimensions Membership, Influence and Shared Emotional Connections) and also Fulfillment of Needs. Inclusion of the Importance of the Community Scale, that considers both personal and social fields, is also analyzed with the BSCS. We observed a stronger relation between Importance of the Community and Involvement than between the two dimensions of the Sense of Community. Therefore, we suggest that the Importance of the Community might have a renewal effect on the Sense of Community by serving as a regulator of the Involvement and the degree of investment in the community. This relation imply that the meaning and identity, that the community holds for the individual, will be more important than the Satisfaction of individual’s Needs. Considering the relation between socio-demographic variables, we observed statistically significant data, related to professional qualification, dimension of family household, residence area, work in the area of residence, time of residence, practice of religion and joining community activities. Finally, some implications are reflected on the methodological decisions considering relevant conditions for the Rebuilding of Sense of Community. Key-Words: Sense of Community; Importance of the Community.
Cardiac autonomic function in patients with rheumatoid arthritis: heart rate turbulence analysis.

OBJECTIVE Rheumatoid arthritis (RA) is a chronic systemic disease. The risk of cardiovascular morbidity and mortality is high in patients with RA. Heart rate turbulence (HRT) expresses ventriculophasic sinus arrhythmia and has been considered to reflect cardiac autonomic activity. It has been shown that HRT is an independent and powerful predictor of mortality. The aim of this study is to determine if HRT changes in patients with RA in comparison with the healthy controls. METHODS The study was performed as a cross-sectional study. Twenty-six patients with RA (mean age 56 ± 10 years, 18 women) and 26 healthy controls (mean age 55 ± 9 years, 18 women) were enrolled in this study. All participants underwent 24 hours Holter electrocardiogram monitoring. HRT measurements, turbulence onset (TO) and turbulence slope (TS), were calculated in patients and healthy controls that have at least one ventricular premature complex (VPC) in their Holter recordings. TO is a measure of the early sinus acceleration and TS is the measure of the rate of sinus deceleration that follows the sinus acceleration after a VPC. Mann-Whitney U test was used for comparison of continuous variables and the Chi-square test for comparison of categorical variables. RESULTS There were no statistically significant differences in TO and TS between the RA and control groups (TO: -2.2 ± 3.1% vs -2.8 ± 2.5%, p=0.25; TS: 11.5 ± 9.7 ms/RR vs 15.5 ± 10.9 ms/RR, p=0.10). CONCLUSION HRT parameters, which determine the autonomic dysfunction, did not seem to be altered in patients with RA.