Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the Fitness Landscape of an RNA Virus by Using a Universal Barcode Microarray

ABSTRACT Studies of viral pathogenesis have relied heavily on analyses of specific clones and their genetic determinants of virulence. It is sometimes difficult to apply this reductionist approach to the study of RNA viruses, which by virtue of their very high mutation rates, exist as a complex mixture of mutants. While quasispecies theory has provided an intellectual framework for exploring the relationship between the viral population structure and phenotype, experimental studies have been limited by the relatively poor resolution of traditional sequencing-based approaches. We have addressed this problem by developing a molecular barcoding strategy in which viral subpopulations are tagged with unique 20-nucleotide sequences. The behavior of these subpopulations can be monitored using a universal barcode microarray. We demonstrate the performance of our barcode microarray platform using poliovirus, a model RNA virus. Using this platform, we explored the fitness landscape occupied by an artificial quasispecies consisting of 48 randomly mutagenized clones. We were able to rapidly derive precise fitness measurements for a majority of these clones and identified a neutral space surrounding the wild type. The experimental paradigm presented here is readily adaptable to other viral systems and can potentially be used to track thousands of variants in a cost-effective manner.
Clinical and pathological features of nodular gastritis in adults

Nodular gastritis (NG) is an unusual type of gastritis in children and it is frequently found in association with Helicobacter pylori infection (1). On the other hand, data on antral nodularity in adults are sparse. NG is not classified as endoscopic gastritis according to the Sydney classification system but it is increasingly used as a descriptive term (2). Some authors also attribute a pathologic
Detection of Mycoplasma pulmonis in Laboratory Rats and Technicians

Five species of mycoplasma are associated with several rat diseases. Mycoplasma pulmonis is the most important and most studied, possibly causing disease in rats and undermining the validity of laboratory experiments. M. pulmonis was isolated in 144/240 laboratory rats and identified by PCR in 155/240. This species was also detected in 12 human individuals (technicians of a laboratory animal house hold) in contact with these rats. The results were confirmed by sequencing of DNA products. Mycoplasma species are host specific; however, M. pulmonis was identified in humans, suggesting a case of unspecific colonization. Statistical analysis shows a greater risk for M. pulmonis colonizing individuals who are exposed to infected rats in animal facilities than individuals who do not. The detection of M. pulmonis in humans indicates a new status for this mollicute mycoplasmas in animal‐holding facilities.
Aggravated Lyme Carditis in CD 11 a / and CD 11 c / Mice

CD18 hypomorph mice expressing reduced levels of the common 2 integrin chain develop aggravated Lyme carditis, compared to that developed by wild-type (WT) mice, upon infection with the spirochete Borrelia burgdorferi. The enhancement of Lyme carditis in these mice is characterized by increased macrophage infiltration, correlating with augmented expression of the monocyte/macrophage chemoattractant protein 1 (MCP-1). The lack of CD18 results in the deficiency of all 2 integrins, i.e., CD11a/CD18 (LFA-1), CD11b/ CD18 (Mac-1/CR3), CD11c/CD18 (p150,95/CR4), and CD11d/CD18. To determine the roles of the various 2 integrins in controlling the development of aggravated Lyme carditis, disease induction was analyzed in CD11a / , CD11b / , and CD11c / mice. CD11a / and CD11c / mice, but not CD11b / mice, developed aggravated Lyme carditis after exposure to B. burgdorferi. Similarly to CD18 hypomorph mice, CD11c / mice expressed higher levels of MCP-1, compared to both WT and CD11a / mice, as determined by in vitro analysis of MCP-1 secretion by bone marrow-derived dendritic cells and in vivo analysis of MCP-1 mRNA expression in B. burgdorferi-infected hearts. On the other hand, CD11a deficiency was associated with heightened heart B. burgdorferi burden relative to that of WT mice. Overall, our results suggest that the increased severity of Lyme carditis in CD18 hypomorph mice is caused by deficiency in CD11a or CD11c, possibly via different mechanisms.
A QUALITATIVE STUDY OF URBAN AND SUBURBAN ELEMENTARY STUDENT UNDERSTANDINGS OF PEST-RELATED SCIENCE AND AGRICULTURAL EDUCATION BENCHMARKS

The purpose of this qualitative study was to determine the understandings of pest-related science by elementary students f (N = 9). Guided by theoretical frameworks for science education and studies on agricultural literacy, clinical interviews were used to surface fifth graders thinking about three benchmarks for the concept of human management of crop growth. Data analysis included validating benchmarks and language to guide the discourse, generating conceptual proposition maps, coding student responses for comparison with expert propositions, and confirming or disconfirming patterns among students. Out-of-school experiences were the strongest determinant of student ability to engage in discourse that was compatible with experts. Students held incomplete understanding of pest-related benchmarks as indicated in their lack of ability to make connections between scientific, societal, and technological concepts. Informants lacked language to accurately articulate an understanding of the pest-related benchmarks. Most informants, especially urban, nongardening students lacked an understanding of pests and their control in the growth of plants for food. Core biological concepts, e. g. plant growth needs, may provide a structure for integrating agri-food system principles into the elementary school curriculum.
Wavelength and mode stabilization of widely tunable SG-DBR and SSG-DBR lasers

A novel mode stabilization scheme for widely tunable SG-DBR and SSG-DBR lasers is demonstrated. It is shown that a minimum in active section voltage is obtained when a cavity mode and a reflection peak of each DBR mirror are aligned. Locking the laser to such a local minimum in active section voltage therefore ensures stable single-mode operation.
Quantifying Isentropic Mixing in a Modified Lagrangian Coordinate : 1 Applications to Rossby Wave Breaking

Isentropic mixing is an important process for the distribution of chemical constituents in the mid-to-high latitudes. A new framework is introduced to quantify both symmetric and asymmetric isentropic mixing in a modified Lagrangian coordinate. The framework is applied to quantify the mixing associated with the two types of Rossby wave breaking (i.e. cyclonic and anticyclonic) in two sets of idealized numerical simulations – eddy lifecycle simulations and a long climate simulation. In both sets of simulations, cyclonic wave breaking (CWB) exhibits either comparable or stronger mixing than anticyclonic wave breaking (AWB). Since CWB occurs less frequently while AWB occurs more frequently when the jet shifts poleward, this difference in mixing strength between the two types of Rossby wave breaking translates into a change in total isentropic mixing when the jet shifts. Specifically, it is found in the climate simulation that as the jet shifts poleward, symmetric mixing is weakened in the underworld and both symmetric and asymmetric mixing across the tropopause is weakened in the mid-to-high latitudes. The dynamical relationship above is relevant not only for internal climate variability such as the El-Niño Southern Oscillation (ENSO) and the annular modes, but also, for future climate change that may drive changes in the jet position. 8
Effect of Learning "Outdoor Study" Ability to Communicate in Writing and Social-Geography Student Learning Outcomes at "Mataraman" East Java-The Republic of Indonesia*

This study aims to explain the influence of the learning model "outdoor study" of the ability to communicate through writing or "paper" and the result of learning social-geography students. Learning model "outdoor study" done by the students conduct field observations and interviews. The ability to communicate through writing is measured based on the task of making “paper”. Learning outcomes are measured through the pre-test and post-test. This study was designed using quasi experiment with non-equivalent patterns of pre-post test control group desaign. The research location in the Midle Junior School in the area "Mataraman" East Java Province. Area "Mataraman" is Blitar, Tulungagung, and Bojonegoro. Analysis of data using test scores and gain one-way ANOVA with a confidence level of 0.05. The results showed that the learning model "outdoor study" effect on the ability to communicate through writing or paper with a score of F calculate equal to 6.410. Furthermore, also affects the learning outcomes geography scores F calculate equal to 7.114. In which both scores indicate greater than the value of F table 4.00. Thus, it can be concluded that the study "outdoor study" through observation and field interviews, not only can improve learning outcomes, but also can improve students' skills in writing papers in the field of geography. Such learning is necessary implemented in Junior Midle School since been shown to improve the ability to write "paper" and student learning outcomes. DOI: 10.5901/mjss.2016. v7n3p429
Topical timolol gel for infantile hemangiomas: a pilot study.

I nfantile hemangiomas (IHs) affect approximately 5% to 10% of white children. Most IHs undergo spontaneous involution, with only a small proportion requiring systemic intervention. For these, propranolol, a nonselective -blocker, has emerged as an alternative systemic treatment to corticosteroids. The proposed therapeutic effects of propranolol on IHs are vasoconstriction; decreased expression of vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) genes through downregulation of the RAF/mitogen–activated protein kinase pathway; and apoptosis of capillary endothelial cells. Superficial IHs, particularly facial IHs, are associated with substantial parental distress, and we currently have a limited therapeutic repertoire. Timolol, a nonselective -blocker similar to propranolol, is available in a topical gel formulation for treatment of glaucoma. We describe herein a series of 6 patients with superficial head and neck IHs treated with timolol maleate, 0.5%, gel.
Determinants of depression and anxiety in patients with refractory epilepsy and cognitive problems

800x600 Background and Purpose: Few studies of psychopathology in patients with cognitive problems and refractory epilepsy (RE) have been performed . We aimed to assess depression, anxiety, and their determining factors in Bulgarian patients with RE and cognitive problems. Method s: We conduct ed a study based on questionnaires designed for people with intellectual disability (stigma scale, Glasgow Depression Scale, Glasgow Anxiety Scale) and a purposeful interview on clinical and social factors of 6 4 patients with RE and cognitive problems . Results : We found depression in 40.63% and anxiety in 71.43% of study participants. Depression correlated with female gender P < 0.01 ( c 2 = 6.48), seizure type P < 0.05 ( c 2 = 7.68), seizure severity P < 0.05 ( c 2 = 9.04), educational level P < 0.05 ( c 2 = 3.86), and stigma P < 0.01 ( c 2 = 12.57). Seizure severity, gender, stigma, and educational level proved to be predictors of depression on multivariate regression analysis P < 0.001 (F = 12.08). Anxiety correlated with seizure severity P < 0.05 ( c 2 = 8.65), focal neurological deficit P < 0.05 ( c 2 = 5.91), stigma P < 0.05 ( c 2 = 7.01), and depression P < 0.05 ( c 2 = 5.31). Seizure severity and focal neurological deficit were the only predictors of anxiety on multivariate regression analysis P < 0.001 (F = 6.35). Conclusions : W e have affirmed frequent anxiety and depression in patients with RE and cognitive problems and their clinical, social, and demographic determinants. The results from our study prove the necessity of a multidisciplinary approach to these patients. Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:. 0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman","serif";}
Somatic Treatment of Catatonia

Objective: The authors reviewed the recent literature regarding the treatment of catatonia as a syndrome of multiple etiologies. Given the historical and clinical association of catatonia with schizophrenia, the authors' examined the assumption that the first-line treatment of catatonia is antipsychotic medication. Methods: Articles published between January 1, 1985 and December 31, 1994 were located using the Paperchase® medical literature search system. Additionally, references from those identified articles were examined for possible inclusion in this review. To be included in this review, articles had to be written in English and report specific symptoms of catatonia to determine, retrospectively, if DSM-IV criteria for catatonia were met. Results: Seventy publications met inclusion criteria and reported on a total of 178 patients and included 270 separate treatment episodes. Most of the articles were case-reports, although a few case-series were identified. Multiple causes of catatonia were identified in these reports. The most commonly reported treatment for catatonia was with benzodiazepines which were effective in 70 percent of the cases, with lorazepam demonstrating the highest frequency of use and a 79 percent complete response rate. Electroconvulsive therapy (ECT) was also efficacious (85%) and was more likely to provide a positive outcome in cases of malignant catatonia. Antipsychotics demonstrated poor efficacy. Conclusions: Catatonia is a nonspecific syndrome with multiple etiologies. Treatment of catatonia should be based on the underlying cause when it is identifiable. Lorazepam appears to offer a safe, effective first-line treatment of catatonia. ECT should be considered when rapid resolution is necessary (e.g., malignant catatonia) or when an initial lorazepam trial fails.
Hyaluronan Oligosaccharides Induce Matrix Metalloproteinase 13 via Transcriptional Activation of NFκB and p38 MAP Kinase in Articular Chondrocytes*

Hyaluronan exerts a variety of biological effects on cells including changes in cell migration, proliferation, and matrix metabolism. However, the signaling pathways associated with the action of hyaluronan on cells have not been clearly defined. In some cells, signaling is induced by the loss of cell-hyaluronan interactions. The goal of this study was to use hyaluronan oligosaccharides as a molecular tool to explore the effects of changes in cell-hyaluronan interactions and determine the underlying molecular events that become activated. In this study, hyaluronan oligosaccharides induced the loss of extracellular matrix proteoglycan and collagen from cultured slices of normal adult human articular cartilage. This loss was coincident with an increased expression of matrix metalloproteinase (MMP)-13. MMP-13 expression was also induced in articular chondrocytes by hyaluronan (HA) hexasaccharides but not by HA tetrasaccharides nor high molecular weight hyaluronan. MMP-13 promoter-reporter constructs in CD44-null COS-7 cells revealed that both CD44-dependent and CD44-independent events mediate the induction of MMP-13 by hyaluronan oligosaccharides. Electromobility gel shift assays demonstrated the activation of chondrocyte NFκB by hyaluronan oligosaccharides. NFκB activation was also documented in C-28/I2 immortalized human chondrocytes by luciferase promoter assays and phosphorylation of IKK-α/β. The link between activation of NFκB and MMP-13 induction by HA oligosaccharides was further confirmed through the use of the NFκB inhibitor helenalin. Inhibition of MAP kinases also demonstrated the involvement of p38 MAP kinase in the hyaluronan oligosaccharide induction of MMP-13. Our findings suggest that hyaluronan-CD44 interactions affect matrix metabolism via activation of NFκB and p38 MAP kinase.
Alterations in coronary sinus pO2 and O2 saturation resulting from pCO2 changes.

The ability of coronary sinus pO2 to remain constant in the face of a shift in the O2 dissociation curve was tested in a series of anaesthetized dogs during respiratory-induced alterations in blood pH, resulting from either hyperventilation or CO2 inhalation. Coronary sinus pO2 was not constant, but varied from 8.2 to 96 mm Hg (1.09 to 12.8 kPa) as coronary sinus pH was altered from 6.97 to 7.71 and coronary sinus pCO2 was varied from 16 to 96 mm Hg (2.13 to 12.8 kPa). The coronary sinus pO2 was logarithmically related to coronary sinus pCOa. Myocardial O2 extraction varied from 13 to 87%. The low coronary sinus pO2 reached during hypocapnia suggests that O2 delivery to the myocardium is impaired at this time. The hypothesis is presented that myocardial pCO2 is a primary agent controlling coronary flow.
Financial Constraints, Investment, and the Value of Cash Holdings

Previous studies report that cash holdings are more valuable for financially constrained firms than for unconstrained firms. We examine (i) why this is so and (ii) why some constrained firms appear to hold too little cash. Our results indicate that greater cash holdings are associated with higher levels of investment for constrained firms with high hedging needs and that the association between investment and value is stronger for constrained firms than for unconstrained firms. These findings imply that higher cash holdings allow constrained firms to undertake value-increasing projects that might otherwise be bypassed. We further find that some constrained firms exhibit low cash holdings because of persistently low cash flows. Overall, our findings support the view that greater cash holdings of constrained firms are a value-increasing response to costly external financing. The Author 2009. Published by Oxford University Press on behalf of The Society for Financial Studies. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org. , Oxford University Press.
Pseudomonas Vaccine I. Preparation and Assay

were required to kill 100% of the mice in 24 to 48 hr; the concentration of this LD100 was determined by plate count. Pseudomonas for vaccine preparation was grown on nutrient agar (Difco) for 24 hr at 37 C; the colonies were then suspended in 0.5% phenolsaline. After standing overnight at 37 C (temperatures of 60 and 65 C were tried with negative results), the suspension was tested for sterility, and the bacterial density was adjusted to approximately 9 X 108 cells per milliliter. Neither pathological symptoms (including pyrogenicity)
Intrinsic Randomness Problem in the Framework of Slepian-Wolf Separate Coding System

This paper deals with the random number generation problem under the framework of a separate coding system for correlated memoryless sources posed and investigated by Slepian and Wolf. Two correlated data sequences with length n are separately encoded to nR1, nR2 bit messages at each location and those are sent to the information processing center where the encoder wish to generate an approximation of the sequence of independent uniformly distributed random variables with length nR3 from two received random messages. The admissible rate region is defined by the set of all the triples (R1,R2,R3) for which the approximation error goes to zero as n tends to infinity. In this paper we examine the asymptotic behavior of the approximation error inside and outside the admissible rate region. We derive an explicit lower bound of the optimal exponent for the approximation error to vanish and show that it can be attained by the universal codes. Furthermore, we derive an explicit lower bound of the optimal exponent for the approximation error to tend to 2 as n goes to infinity outside the admissible rate region.
Expressão da proteina erbB-2 e dos receptores de esteroides na transição das frações in situ e invasora de neoplasias de mama

Introducao: Ha evidencias indicando que a transicao de carcinoma ductal in situ (CDIS) para carcinoma ductal invasivo (CDI) e regulada por um numero restrito de genes. Ainda permanece obscuro se a expressao do receptor erbB-2 e dos receptores hormonais predizem o potencial invasivo dos CDIS. Objetivos: Avaliar a expressao dos receptores de estrogeno e progesterona (RE/RP) e da proteina erbB-2 em areas especificas em tumores que apresentem componentes de CDIS e CDI concomitantemente, indicando uma possivel transicao. Materiais e Metodos: Foram selecionados 85 casos de carcinomas da mama apresentando regioes contiguas de CDIS e CDI e obtidas amostras histologicas separadas, uma da regiao CDIS e outra da regiao CDI, do bloco de parafina original do diagnostico, para montagem de um TMA (tissue microarray). A expressao das proteinas erbB-2, RE e RP foram verificadas atraves da tecnica convencional de imuno-histoquimica. Os dados clinicos das pacientes foram coletados por consulta ao prontuario. Resultados: Aproximadamente 35% das areas invasivas foram classificadas como 2+ ou 3+ para o erbB-2, em contraste a 47% no componente invasivo correspondente. A expressao de erbB-2 nao se mostrou diferente nos componentes in situ e invasivo (p=0,12). A expressao de RP nao foi estatisticamente diferente comparando-se regioes in situ e invasivas do tumor (p=0,06). Em contraste, houve uma discreta mudanca na expressao de RE (p=0,04). O coeficiente de concordância intraclasse (ICC) revelou forte concordância nas comparacoes entre as amostras de erbB-2 (ICC=0,61), RP (ICC=0,61) e RE (ICC=0,70), nos componentes in situ e invasivo. Conclusao: Os achados sugerem que a expressao de erbB-2, RE e RP nao diferem entre os componentes in situ e invasivo do carcinoma da mama, especialmente nas regioes de transicao de um componente a outro. Espera-se que as alteracoes moleculares ocorridas antes da mudanca morfologica do tecido persistam na forma invasiva do tumor. A concomitância da atuacao de fatores epigeneticos pode explicar porque alguns tumores in situ evoluem para invasivos, enquanto outros tumores in situ com caracteristicas moleculares semelhantes nao apresentam a mesma evolucao, suportando a hipotese de uma base multifatorial para a progressao da doenca Abstract