Miracle-dz/UniFAR-FTUs huggingface dataset:
Replication of Subgenomic Hepatitis A Virus RNAs Expressing Firefly Luciferase Is Enhanced by Mutations Associated with Adaptation of Virus to Growth in Cultured Cells

ABSTRACT Replication of hepatitis A virus (HAV) in cultured cells is inefficient and difficult to study due to its protracted and generally noncytopathic cycle. To gain a better understanding of the mechanisms involved, we constructed a subgenomic HAV replicon by replacing most of the P1 capsid-coding sequence from an infectious cDNA copy of the cell culture-adapted HM175/18f virus genome with sequence encoding firefly luciferase. Replication of this RNA in transfected Huh-7 cells (derived from a human hepatocellular carcinoma) led to increased expression of luciferase relative to that in cells transfected with similar RNA transcripts containing a lethal premature termination mutation in 3Dpol (RNA polymerase). However, replication could not be confirmed in either FrhK4 cells or BSC-1 cells, cells that are typically used for propagation of HAV. Replication was substantially slower than that observed with replicons derived from other picornaviruses, as the basal luciferase activity produced by translation of input RNA did not begin to increase until 24 to 48 h after transfection. Replication of the RNA was reversibly inhibited by guanidine. The inclusion of VP4 sequence downstream of the viral internal ribosomal entry site had no effect on the basal level of luciferase or subsequent increases in luciferase related to its amplification. Thus, in this system this sequence does not contribute to viral translation or replication, as suggested previously. Amplification of the replicon RNA was profoundly enhanced by the inclusion of P2 (but not 5′ noncoding sequence or P3) segment mutations associated with adaptation of wild-type virus to growth in cell culture. These results provide a simple reporter system for monitoring the translation and replication of HAV RNA and show that critical mutations that enhance the growth of virus in cultured cells do so by promoting replication of viral RNA in the absence of encapsidation, packaging, and cellular export of the viral genome.
Quality of health care for children: role of health and chronic illness in inpatient care experiences.

OBJECTIVE To assess how parent reports about the inpatient care of their children vary according to the health status of children with and without chronic conditions. DESIGN We analyzed parent responses to the Picker Institute Pediatric Inpatient Survey. SETTING Thirty-nine hospitals between January 1, 1997, and December 31, 1999. PARTICIPANTS Overall, 12 562 parents of children who received inpatient care at participating hospitals. Main Outcome Measure Parent rating of overall quality of care. RESULTS Fifty-one percent of parents reported that their child had a chronic condition. Quality-of-care ratings varied according to health status and the presence of chronic conditions. Parents of children in the worst (fair or poor) health without chronic conditions reported lower quality of care (P < .001) and more care problems (P < .001) than did those with chronic conditions. Parents of children in the best (excellent, very good, or good) health tended to rate care highly, whether or not their children had chronic conditions. In a multivariable model, the decrement in perceived quality of care associated with poorer health was greater for those without than for those with chronic conditions (P < .001). CONCLUSIONS Although children in poor health are at risk for experiencing a lower quality of health care, parents of such children who have chronic conditions report fewer care-related problems. This may be owing to the more frequent health care interactions and better continuity of care for children with chronic conditions.
Studies of the immunology of the newborn infant. VI. Bacteriostatic and complement activity of the serum.

Twenty-three infants from 2 weeks to 6 months old, all of whom had measurable titers of transplacentally-received diphtheria antitoxin, were immunized with a single injection of diphtheria toxoid on alum. Infants with a low level of passive transplacental antibody were able to respond as well or almost as well as infants who had no passive transfer. The formation of circulating antibody was depressed in infants with a high titer of passively received antibody. It is suggested that the amount of interference with active immunization is dependent on the relation of the titer of passive transfer and the potency of the antigen. The application of this principle is indicated.
Maternal Executive Function, Heart Rate, and EEG Alpha Reactivity Interact in the Prediction of Harsh Parenting

Do physiological and behavioral performance indicators of effortful cognitive self-regulation converge additively or interactively in their statistical prediction of individual differences in harsh parenting? To answer this question, we examined heart rate (HR) and electroencephalography alpha (&agr;) reactivity during executive function (EF) tasks, along with observed and self-reported indicators of harsh parenting. A socioeconomically diverse sample of 115 mothers with 3- to 7-year-old children completed questionnaires and a laboratory visit. Three quarters of the mothers showed typical patterns of task reactivity that were interpretable (i.e., increases in HR and decreases in &agr;). Among them, we found no evidence to suggest that variance in harsh parenting was associated with magnitude of HR or &agr; reactivity independently. Instead, the physiological variables interacted to enhance the EF statistical effect. EF explained one third of the variance in harsh parenting among mothers showing the largest &agr; decreases when accompanied by modest to moderate (rather than substantial) HR increases. Physiological indicators can clarify the role and estimation of the strength of the effect of direct behavioral measures of cognitive regulation in the etiology of harsh parenting behaviors.
Racionalizando a utilização do algoritmo PHRED para a análise de seqüências de DNA

A ciencia e, por vezes, dogmatica. Mesmo o cientista questionador as vezes e obrigado a tomar como verdade algo que se acredita na comunidade de forma a realizar suas pesquisas em busca do conhecimento. Na area da genomica, alguns dogmas estao ainda arraigados a cultura cientifica e o objetivo principal da presente tese foi tentar, na medida do possivel, questionar e testar alguns desses dogmas com a intencao de trazer a luz da razao um conhecimento mais solido sobre alguns limitados aspectos relacionados, principalmente, ao processo de nomeacao das bases (base-calling). Para avaliar, portanto, a utilizacao do algoritmo PHRED, o principal nomeador de bases utilizado em projetos genoma, desenvolvemos primeiro uma metodologia solida de analise. Tal metodologia tentou diminuir o numero de variaveis a se analisar em uma corrida de sequenciamento para que nossas analises nao levassem em consideracao peculiaridades especificas de uma ou outra reacao produzida. Dessa forma, realizamos o sequenciamento de um vetor de clonagem bastante conhecido (pUC18) em um unico conjunto, homogeneizando as amostras de forma que a unica variavel possivel fosse a separacao eletroforetica e o padrao de nomeacao de bases. Produzimos, portanto, 846 sequencias do vetor pUC18 que foram comparadas, atraves de alinhamentos locais, com um controle positivo: a sequencia ja publicada para esta molecula. Dessa forma, pudemos identificar os erros do sequenciamento / nomeacao de bases e avaliar diferentes parâmetros de utilizacao do algoritmo PHRED. Verificamos que o padrao de erros observado era relativamente igual ao esperado, que as bases incorretas nao podiam ser previstas atraves da observacao dos valores de qualidade de sua vizinhanca e que as trocas (mismatches) sao mais comuns quando associadas a valores baixos de qualidade, enquanto se nota a presenca de erros relacionados a indels de alta qualidade. Percebemos tambem uma aplicacao desta abordagem para o processo de desenho de iniciadores de sequenciamento e realizamos um estudo avaliando este topico, o qual mostra que a leitura de boa qualidade e iniciada a uma distância mensuravel a jusante do iniciador de sequenciamento. Com o objetivo de tentar mascarar as bases incorretas em letras minusculas, observamos que o valor de qualidade 7 parece ser o mais adequado para utilizar nesses casos, em boa parte das situacoes. Alem disso, calibramos o programa PHRED para funcionar de forma a apresentar apenas a informacao nao-ruidosa, biologicamente relevante. Por ultimo, analisamos ainda a formacao de consensos a partir dessas sequencias e mostramos a surpreendente ineficiencia do re-sequenciamento de forma a produzir sequencias fieis a molecula molde. %%%%Science is sometimes dogmatic. Even the very thinker scientists are sometimes forced to accept as true something believed by the community in order to advance their research. In the genomic research field, some dogmas are still attached to scientific culture and the main goal of this thesis is the tentative to question some of these dogmas and bring to…
Neurotrophins and Trk receptors in primitive neuroectodermal tumor cell lines.

OBJECTIVE Primitive neuroectodermal tumors (PNETs) are thought to be derived from early central nervous system precursors. Therefore, we hypothesized that the neurotrophins (nerve growth factor, brain-derived neurotrophic factor, and neurotrophin-3) and their receptors (TrkA, TrkB, and TrkC), which are involved in the proliferation, differentiation, and survival of neuronal cells, might be important in regulating tumor growth. METHODS Using ribonucleic acid (RNA) blotting and reverse transcription-polymerase chain reaction analysis, we investigated the expression of these ligands and their receptors in six PNET cell lines (Daoy, PFSK, D283 Med, UW288-1, CHP707m, and D341 Med). Neurotrophin protein levels were measured using enzyme-linked immunosorbent assay procedures. Receptor function was demonstrated by autophosphorylation. Induction of c-Fos expression and effects on cell proliferation were assessed after the addition of exogenous neurotrophin. RESULTS Three cell lines expressed messenger RNA for all neurotrophins, whereas the other three expressed two of the three neurotrophins. Neurotrophin protein levels were low. All cell lines expressed trkA messenger RNA. Five expressed the amino terminus of trkB, but three of these did not express the carboxyl terminus. All cell lines contained trkC messenger RNA, but the receptor was truncated in two cell lines. No cell line contained message for a receptor containing an insertion in the tyrosine kinase domain. The addition of neurotrophin to PNET cells resulted in phosphorylation of a protein that was immunoprecipitated with an anti-pan-Trk antibody. c-Fos expression and cell growth were increased by preincubation with neurotrophins, but only in the cell lines expressing the relevant full-length receptors. CONCLUSION The expression of neurotrophins and neurotrophin receptors by PNET cell lines is variable. The presence of activated Trk receptors in these cell lines may be required for rapid growth, via an autocrine loop mechanism. This will require further investigation.
Paired Indices for Clustering Evaluation - Correction for Agreement by Chance

In the present paper we focus on the performance of clustering algorithms recurring to indices of paired agreement to measure the accordance between clusters and an a priori known structure. We specifically propose a method to correct all indices considered for agreement by chance â the adjusted indices are meant to provide a realistic measure of clustering performance. The proposed method enables the correction of virtually any index â overcoming previous limitations known in the literature - and provides very precise results. We use simulated datasets under diverse scenarios and discuss the pertinence of our proposal which is particularly relevant when poorly separated clusters are considered. Finally we compare the performance of EM and K-Means algorithms, within each of the simulated scenarios and generally conclude that EM generally yields best results.
An Almost m-wise Independent Random Permutation of the Cube

We describe a very simple method of randomly permuting the cube {0, 1}n such that the sample space is very small, but, given any m distinct points in {0, 1}n, the images of those points under the random permutation are approximately uniformly distributed over all sequences of m distinct points.
Apoptotic and Inflammatory Effects Induced by Different Particles in Human Alveolar Macrophages

Pollutant particles induce apoptosis and inflammation, but the relationship between these two biological processes is not entirely clear. In this study, we compared the proapoptotic and proinflammatory effects of four particles: residual oil fly ash (ROFA), St. Louis particles SRM 1648 (SL), Chapel Hill PM10 (CHP), and Mount St. Helens dust (MSH). Human alveolar macrophages (AM) were incubated with these particles at 100 μg/ml. Cell death was assessed by annexin V (AV) expression, histone release, nuclear morphology, caspase 3-like activity and release of caspase 1 for apoptosis, and propidium iodide (PI) for necrosis, and inflammation was measured by interleukin (IL)-1β and IL-6. We found that particle effects on these cell death measurements varied, and ROFA affected most (four out of five) endpoints, including nuclear morphological changes. CHP and SL also caused necrosis. For cytokine release, the potency was CHP > SL > ROFA > MSH. The proapoptotic and proinflammatory effects induced by the whole particles were unaltered after the particles were washed with water. The water-soluble fraction was relatively inactive, as were individual soluble metals (V, Ni, Fe). ROFA-induced nuclear fragmentation was associated with upregulation and mitochondrial release of apoptosis-inducing factor (AIF), a caspase-independent chromatin condensation factor, and upregulation of DNase II, a lysosomal acid endonuclease. These results indicate that the potential for particles to induce apoptosis does not correlate with their proinflammatory properties, although active components for both processes reside in the water-insoluble core. Both apoptosis and inflammatory endpoints should be included when the toxicity of different pollutant particles is assessed.
Icon, index, symbol and denotation, connotation, metasign

Abstract We discuss how Hjelmslev's denotation, connotation, and metasign could correspond to Peirce's icon, index, and symbol. Our argument is based on the application of both theories to the programming language problem of confusion as to whether a sign signifies a value, reference, or type.
THE DISTRIBUTION OF HISTOCOMPATIBILITY ANTIGENS ON T AND B CELLS IN THE GUINEA PIG

SUMMARY The distribution of histocompatibility (H) antigens on different lymphocyte populations in the guinea pig was examined with alloantisera prepared by cross immunizing strain 2 and strain 13 animals. These alloantisera killed only 30-40% of lymph node cells, and those cells that remain alive after killing by the alloantisera are markedly depleted in immunoglobulin-bearing B lymphocytes. Absorption studies of the anti-2 serum demonstrated that the alloantigen content of lymph node cells was 7-8 times that of thymocytes, while the alloantigen content of L2C leukemia cells, a pure population of malignant B cells, was 25-30 times that of thymocytes. Furthermore, pure B lymph node cells, prepared by treating lymph node cells with an anti-T cell serum and C, were more efficient than normal lymph node cells in the absorption of the alloantisera. Finally, those lymph node cells which remain alive after treatment with the alloantisera and C failed to respond to endotoxin, a B cell mitogen, whereas these same cells responded normally to phytohemagglutinin, a T cell mitogen. These results demonstrate an increased content of H antigen on the B lymphocyte compared to the T lymphocyte. Since H antigens play a role in the cooperation between B and T cells, information as to the distribution of H antigens on these cells may have important implications for cell to cell interaction in the immune response.
Design Process of Interior PM Synchronous Motor for 42-V Electric Air-Conditioner System in Hybrid Electric Vehicle

This paper presents a design approach to an interior permanent magnetic synchronous motor (IPMSM) for the compressor of a hybrid electric vehicle operated in a 42-V battery system. The approach is to estimate the range of inductance and back-EMF to satisfy the required efficiency of IPMSM. Then, the preliminary geometry satisfying the region is decided by PM type, current density, fill factor, and so on. Last, the detailed design with optimization is performed to consider magnetic saturation and reduce cogging torque and torque ripple. At this time, the simulation results are obtained by finite element analysis and in consideration of operating temperature. In the end, the validity of the design process presented in this paper is verified by test.
Inflation Bets on the Long Bond

The liquidity premium theory of interest rates predicts that the Treasury yield curve steepens with inflation uncertainty as investors demand larger risk premia to hold long-term bonds. Using the dispersion of inflation forecasts to measure this uncertainty, we find the opposite. Since the prices of long-term bonds move more with inflation than short-term ones, investors also disagree and speculate more about long-maturity payoffs with greater uncertainty. Shorting frictions, measured using Treasury lending fees, then lead long maturities to become over-priced and the yield curve to flatten. We estimate this inflation-betting effect using time variation in inflation disagreement and Treasury supply.
POSTER: A new framework against privilege escalation attacks on android

The Android provides a permission-based security model to restrict the operations that each application can perform; however, it has been shown to be vulnerable to privilege escalation attacks. Applications can cooperate to perform operations that forbidden to perform separately which may lead to privacy leakage. In this poster, we present the design of a new policy-centered security framework against the application-level privilege escalation attacks. Different from previous policy-centered schemes, the communication content is also considered into the inspection besides the permissions. Specially, we allow the privacy information selectively to be passed in the middleware and deploy a mandatory access control at the kernel based on the dynamical taint tracking. Test results show that it can prevent known confused deputy attacks and is also flexible to prevent the unknowns; furthermore it can reduce the false positives of preventing colluding attacks compared to the previous work.
The Scielo Corpus: a Parallel Corpus of Scientific Publications for Biomedicine

The biomedical scientific literature is a rich source of information not only in the English language, for which it is more abundant, but also in other languages, such as Portuguese, Spanish and French. We present the first freely available parallel corpus of scientific publications for the biomedical domain. Documents from the ”Biological Sciences” and ”Health Sciences” categories were retrieved from the Scielo database and parallel titles and abstracts are available for the following language pairs: Portuguese/English (about 86,000 documents in total), Spanish/English (about 95,000 documents) and French/English (about 2,000 documents). Additionally, monolingual data was also collected for all four languages. Sentences in the parallel corpus were automatically aligned and a manual analysis of 200 documents by native experts found that a minimum of 79% of sentences were correctly aligned in all language pairs. We demonstrate the utility of the corpus by running baseline machine translation experiments. We show that for all language pairs, a statistical machine translation system trained on the parallel corpora achieves performance that rivals or exceeds the state of the art in the biomedical domain. Furthermore, the corpora are currently being used in the biomedical task in the First Conference on Machine Translation (WMT’16).
Emotional Intelligence via Wearables: A Method for Detecting Frustration

The research discussed in this paper is part of a pilot study in the use of wearable devices incorporating electroencephalogram (EEG) and heartrate sensors to sense for the emotional responses closely correlated to frustration when performing certain tasks. For this study the methodology used a combination of puzzle, arcade style game and a meditation apps to emulate a task based environment and detect frustration and satisfaction emotions. Preliminary results indicate that degree of task completion has an effect on emotions and can be detected by EEG and heartrate changes.
Empiric Vancomycin Use in Febrile Neutropenic Oncology Patients

Vancomycin is commonly added as empiric therapy for febrile neutropenia. A retrospective chart review was conducted at a large community teaching institution to evaluate vancomycin use in oncology patients. The results revealed that a majority of empiric vancomycin therapy was inappropriate, raising concern for antibiotic resistance and prompting opportunities for improvement.
Mimesis: Culture - Art - Society

Mimesis, the notion that art imitates reality, has long been recognized as one of the central ideas of Western aesthetics and has been most frequently associated with Aristotle. Less well documented is the great importance of mimetic theories of literature, theater, and the visual arts during the Renaissance and the Enlightenment. In this book, the most comprehensive overview of the theory of mimesis since Auerbach's monumental study, Gunter Gebauer and Christoph Wulf provide a thorough introduction to the complex and shifting meanings of the term. Beginning with the Platonic doctrine of imitation, they chart the concept's appropriation and significance in the aesthetic theories of Aristotle, Moliere, Shakespeare, Racine, Diderot, Lessing, and Rousseau. They examine the status of mimesis in the nineteenth-century novel and its reworking by such modern thinkers as Benjamin, Adorno, and Derrida. Widening the traditional understanding of mimesis to encompass the body and cultural practices of everyday life, their work suggests the continuing value of mimetic theory and will prove essential reading for scholars and students of literature, theater, and the visual arts.
What is an antique

Antiques are undoubtedly objects worthy of aesthetic appreciation, but do they have a distinctive aesthetic value in virtue of being antiques? In this article we give an account of what it is to be an antique that gives the thesis that they do have a distinctive aesthetic value a chance of being true and suggests what that distinctive value consists in. After introducing our topic in Section I, in Section II we develop and defend the Adjectival Thesis: the thesis that the concept of being an antique is an adjectival concept. This provides us with the means to formulate our definition, which we do in Section III. In Section IV we further explicate and defend our definition. In Section V we conclude by briefly saying where we think our definition could be improved, by making a few comments about the aesthetics of antiques and by stating an interesting consequence of our definition: that it is not analytic that antiques are old.