Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Studies on Suspect Very Virulent Infectious Bursal Disease Virus Genomic RNA Samples

Abstract Infectious bursal disease (IBD) associated with high mortality was first observed in Europe in the mid-1980s. The viruses identified in those outbreaks were described as being very virulent infectious bursal disease virus (vvIBDV) strains. These viruses have spread to nearly every continent but have not yet been identified in North America, Australia, and New Zealand. There is a real and immediate concern that the very virulent form of IBDV will continue to spread until it is present on every continent. Genomic RNA samples from IBDV strains suspected of being very virulent were submitted to our laboratory for molecular analysis. Nucleotide sequences of the VP2gene hypervariable sequence region were determined for 18 of these viruses. A comparison with published vvIBDV sequences indicated that all but one sample (Thai 4) had nucleotide and predicted amino acid sequences consistent with vvIBDV strains. Published sequences and the nucleotide sequences of our 17 putative vvIBDV strains were used to identify unique nucleotides in the VP2 gene. Probe pairs for a real-time reverse transcriptase–polymerase chain reaction (RT-PCR) assay were designed based on these unique sequences and then used to test the 17 genomic samples that were identified by nucleotide sequencing to be consistent with vvIBDV, plus the one Thai 4 sample that was not consistent with vvIBDV. Using melting temperature (Tm) analysis following real-time RT-PCR, two probe pairs (vv232 and vv256) successfully identified the 17 putative vvIBDV strains and distinguished them from the Thai 4 sample. An additional 26 genomic RNA samples submitted as suspect vvIBDV strains were then tested using the vv232 and vv256 probes. Based on the melting point analysis of these two probes, all 26 samples contained nucleotide sequences consistent with vvIBDV strains. The specificity of the vv232 and vv256 probe pairs was evaluated using 19 non-vvIBDV strains. In every case, the probes distinguished the 19 classic and variant (non-vvIBDV) strains from the putative vvIBDV strains. Diagnostic assays that can reliably identify vvIBDV strains are needed for surveillance programs designed to monitor the spread of these viruses.
Amino Acids of Conserved Kinase Motifs of Cytomegalovirus Protein UL97 Are Essential for Autophosphorylation

ABSTRACT Thirteen point mutations targeting predicted domains conserved in homologous protein kinases were introduced into the UL97 coding region of the human cytomegalovirus. All mutagenized proteins were expressed in cells infected with recombinant vaccinia viruses (rVV). Several mutations drastically reduced ganciclovir (GCV) phosphorylation. Mutations at amino acids G340, A442, L446, and F523 resulted in a complete loss of pUL97 phosphorylation, which was strictly associated with a loss of GCV phosphorylation. Our results confirm that in rVV-infected cells pUL97 phosphorylation is due to autophosphorylation and show that several amino acids conserved within domains of protein kinases are essential for this pUL97 phosphorylation. GCV phosphorylation is dependent on pUL97 phosphorylation.
Gender Difference in HIV RNA Levels: A Meta‐Analysis of Published Studies

&NA; Plasma HIV RNA copy number is a strong prognostic marker of progression to AIDS in antiretroviral‐naive persons. Recent research suggests women have lower HIV RNA levels than comparable men. Because clinical care recommendations currently include HIV RNA thresholds as a guide to initiating antiretroviral therapy (ART), the authors undertook the present quantitative meta‐analysis to explore the relation between gender and plasma HIV RNA levels. A gender difference in HIV RNA levels was observed in the CD4‐unadjusted and ‐adjusted analyses. The summary estimate including only CD4‐adjusted results with the lowest heterogeneity indicated that on average, women have 41% lower plasma HIV RNA levels than men (‐.23 log10; 95% confidence interval [CI], ‐.16 to ‐.31 log10). Because numerous studies have found similar HIV disease progression rates in men and women, adjusted for CD4 but not HIV RNA, the present meta‐analysis supports the use of lower HIV RNA thresholds in women than in men to guide initiation of ART. Given the patient characteristics in the original studies used in this meta‐analysis, the results are most likely to apply to therapy‐naive persons with CD4 lymphocyte counts >200 cells/mm3, a subgroup for whom HIV RNA levels may strongly influence the decision to initiate therapy.
Terrain based navigation tools for underwater vehicles using eigen analysis

Abstract The development of tools for Terrain Based Navigation of Underwater Vehicles rooted on Principal Component Analysis are proposed and discussed in detail. Resorting to a nonlinear Lyapunov transformation, the synthesis and analysis of a nonlinear multirate H2 estimator is presented with guaranteed stability and optimal performance on equilibrium trajectories. Post-processing techniques using a fixed interval non-causal smoother are outlined to improve the performance of the overall framework. Results from Monte Carlo simulation techniques to assess the performance of the proposed tools are included.
SOCIOECONOMIC STATUS DURING CHILDHOOD AND HEALTH STATUS IN ADULTHOOD: THE WROCŁAW GROWTH STUDY

Summary It has been widely observed that socioeconomic status (SES) is associated with frequency of cardiovascular disease. Both men and women of low socioeconomic position have increased risk of cardiovascular disease morbidity and premature death. In this study the relationship between SES in childhood, and health status at the age of 50 years was examined. Socioeconomic status in childhood was measured using objective (father’s educational level and number of children in the family) and subjective (self-assessed SES in childhood declared in early adulthood) indicators. Data from the Wrocław Growth Study were completed when subjects were 50 years old, and information concerning health status was added. The results indicated that the objective, universally used measures of SES in childhood such as father’s educational level and size of family did not show any essential relationships with health outcomes in adulthood, both for men and women. By contrast, retrospective, self-assessed SES (as better, average or worse as compared with peers) in childhood was significantly associated with the appearance of cardiovascular disease among women aged 50 years. Women who at the beginning of their adult life declared better socioeconomic condition in childhood were significantly healthier at the age of 50 years (OR=3·43; p=0·02). Moreover, this appeared to be independent of BMI, SES and life-style in adulthood. For men, retrospective self-assessed SES showed no relation to health status at the age of 50 years. The gender differences in the relationships between self-assessed SES in childhood and health status in adulthood are explained by possible selective premature mortality among men from lower childhood SES and/or sex differences in cognitive abilities.
The -308 tumour necrosis factor-alpha gene polymorphism predicts therapeutic response to TNFalpha-blockers in rheumatoid arthritis and spondyloarthritis patients.

OBJECTIVE To examine whether the G-to-A polymorphism at position -308 in the promoter of the tumour necrosis factor-alpha (TNFalpha) gene influences the therapeutic response to TNFalpha-blockers in patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) and ankylosing spondylitis (AS). METHODS A total of 54 patients with RA, 10 with PsA and 22 with AS were genotyped by polymerase chain reaction for the -308 TNFalpha promoter polymorphism. They were treated with infliximab (n = 63), adalimumab (n = 10) or etanercept (n = 13). Clinical response was assessed after 24 weeks by the Disease Activity Score in 28 joints (DAS28) for RA and PsA, and the Bath Ankylosing Spondylitis Activity Index (BASDAI) for AS patients. RESULTS All patients with the A/A genotype (n = 3, all RA) and two patients with the A/G genotype (AS) failed to respond to anti-TNF treatment. Irrespective of the underlying disease, moderate response (n = 44) was predominantly associated with the A/G genotype (A/G 18/22, G/G 4/22), whereas good response (n = 59) was exclusively seen in patients with the G/G genotype. The average improvement in the DAS28 score was 0.83 in the A/A, 1.50 in the A/G and 2.64 in the G/G group of RA and PsA patients (P < 0.0001). The BASDAI score in AS improved on average by 1.21 in the A/G and by 3.30 in the G/G group (P < 0.005). CONCLUSIONS The data suggest that humans with a TNFalpha -308 G/G genotype are better responders to anti-TNFalpha treatment than those with A/A or A/G genotypes independent of the treated rheumatic disease (RA, PsA or AS).
How soil moisture, rain pulses, and growth alter the response of ecosystem respiration to temperature

In this paper, we analyzed 3 years of carbon flux data from continuous eddy covariance measurements to investigate how soil moisture, rain pulses, and growth alter the response of ecosystem respiration to temperature. The data were acquired over an annual grassland and from the grass understory of an oak/grass savanna ecosystem in California. We observed that ecosystem respiration was an exponential function of soil temperature during the winter wet season and a jump in ecosystem respiration occurred, at comparable temperatures, during the spring growth period. The depletion of the moisture from the soil reservoir, during spring, limited ecosystem respiration after its volumetric water content dropped below a threshold of 0.15 m3 m−3. The senescence of grass during the summer switched the source of ecosystem respiration to heterotrophic bacteria and fungi. During the summer, respiration proceeded at a low basal rate (about 0.10 to 0.3 g C m−2 d−1), except when summer rain events stimulated large dynamic pulses in heterotrophic respiration. Peak respiratory pulses were on the order of 60–80 times baseline and could not be explained by functions that depend on mean soil moisture and temperature. We found that the magnitude of the respiratory pulses was inversely related to its prerain value and that the time constant, describing the exponential decay of the respiratory pulses after the rain event, was a function of the amount of rainfall. The amount of carbon lost, in association with a few summer rain events, was greater at the site with higher primary productivity and soil carbon content.
Stress Testing With and Without Imaging Perspective

Over the past 30 years, there have been great advances in cardiovascular imaging and treatment. Early in this period, new techniques were usually investigated on a limited research basis before widespread adoption. This research helped to develop evidence to define proper application in clinical practice. Sometimes, this evidence did not support the initial promising reports. Pulmonary blood volume measurements, regional ejection fraction images, digital subtraction angiography, stress echocardiography using transesophageal pacing, pacemaker therapy for hypertrophic cardiomyopathy, laser coronary angiography, and aortic valvuloplasty were all appropriately tested on a limited scale and abandoned. Response by Min and Shaw see p 257 In the past 15 years, declining Medicare reimbursements have contributed to a “make it up on volume/grow the business” mentality in medicine that often embraces a broader application of new technology before it has been adequately studied to establish its correct role. Many observers have commented that clinical practice often now “runs ahead of” guidelines. Should this pattern continue with respect to newer technology, eg, computed tomographic (CT) angiography, for the diagnostic and prognostic assessment of chronic coronary artery disease (CAD)? To answer this question, the reader must understand the current health-care crisis, the overwhelming evidence supporting the current use of stress imaging with or without imaging, and the limited evidence for CT angiography. The need for fundamental health-care reform is increasingly recognized. For the past 2 years, all the major presidential candidates have defined positions on health-care reform. A prominent 2-page advertisement in the Sunday New York Times signed by 10 past political leaders, including a former chairman of the Federal Reserve Board, summarized it well: “Mounting healthcare costs…threaten American competitiveness, and, if they remain unchecked, could even bankrupt the country. …The prognosis for our nation’s health is beyond unacceptable—it is inconsistent with America’s long-standing tradition of stewardship. ”1 …
Parentage of low‐grade metasediments in the Sanbagawa belt, eastern Shikoku, Southwest Japan, and its geotectonic implications

This study examines the geology of low‐grade (chlorite zone) metamorphic rocks in the Sanbagawa belt and of a Jurassic accretionary complex in the Northern Chichibu belt, eastern Shikoku, Japan. The bulk chemistries of metasandstones and metapelites in the Sanbagawa belt of eastern Shikoku are examined in order to determine their parentage. The Sanbagawa belt can be divided into northern and southern parts based on lithology and geologic structure. Geochemical data indicate that metasediments in the northern and southern parts are the metamorphic equivalents of the KS‐II (Coniacian–Campanian) and KS‐I (late Albian–early Coniacian) units of the Shimanto belt, respectively. The depositional ages of the parent sediments of low‐grade metamorphic rocks found in the Sanbagawa belt and the Jurassic Northern Chichibu belt, indicate a north‐younging polarity. In contrast, sedimentological evidence indicates younging to the south. These observations suggest that a tectonic event has resulted in a change from a northerly to southerly dip direction for schistosity and bedding in the Sanbagawa and Northern Chichibu belts of eastern Shikoku. The younging polarity observed in the Sanbagawa and Northern Chichibu belts, together with previously reported data on vitrinite reflectance and geological structure, indicate that the Northern Chichibu belt was part of the overburden formerly lying on top of the Sanbagawa low‐grade metamorphic rocks.
Multiparametric Renal Magnetic Resonance Imaging: Validation, Interventions, and Alterations in Chronic Kidney Disease

Background: This paper outlines a multiparametric renal MRI acquisition and analysis protocol to allow non-invasive assessment of hemodynamics (renal artery blood flow and perfusion), oxygenation (BOLD T2*), and microstructure (diffusion, T1 mapping). Methods: We use our multiparametric renal MRI protocol to provide (1) a comprehensive set of MRI parameters [renal artery and vein blood flow, perfusion, T1, T2*, diffusion (ADC, D, D*, fp), and total kidney volume] in a large cohort of healthy participants (127 participants with mean age of 41 ± 19 years) and show the MR field strength (1.5 T vs. 3 T) dependence of T1 and T2* relaxation times; (2) the repeatability of multiparametric MRI measures in 11 healthy participants; (3) changes in MRI measures in response to hypercapnic and hyperoxic modulations in six healthy participants; and (4) pilot data showing the application of the multiparametric protocol in 11 patients with Chronic Kidney Disease (CKD). Results: Baseline measures were in-line with literature values, and as expected, T1-values were longer at 3 T compared with 1.5 T, with increased T1 corticomedullary differentiation at 3 T. Conversely, T2* was longer at 1.5 T. Inter-scan coefficients of variation (CoVs) of T1 mapping and ADC were very good at <2.9%. Intra class correlations (ICCs) were high for cortex perfusion (0.801), cortex and medulla T1 (0.848 and 0.997 using SE-EPI), and renal artery flow (0.844). In response to hypercapnia, a decrease in cortex T2* was observed, whilst no significant effect of hyperoxia on T2* was found. In CKD patients, renal artery and vein blood flow, and renal perfusion was lower than for healthy participants. Renal cortex and medulla T1 was significantly higher in CKD patients compared to healthy participants, with corticomedullary T1 differentiation reduced in CKD patients compared to healthy participants. No significant difference was found in renal T2*. Conclusions: Multiparametric MRI is a powerful technique for the assessment of changes in structure, hemodynamics, and oxygenation in a single scan session. This protocol provides the potential to assess the pathophysiological mechanisms in various etiologies of renal disease, and to assess the efficacy of drug treatments.
Efficiency of Recombination Reactions Catalyzed by Class 1 Integron Integrase IntI1

ABSTRACT The class 1 integron integrase, IntI1, recognizes two distinct types of recombination sites, attI sites, found in integrons, and members of the 59-be family, found in gene cassettes. The efficiencies of the integrative version of the three possible reactions, i.e., between two 59-be, between attI1 and a 59-be, or between two attI1 sites, were compared. Recombination events involving two attI1 sites were significantly less efficient than the reactions in which a 59-be participated, and the attI1 × 59-be reaction was generally preferred over the 59-be × 59-be reaction. Recombination of attI1 with secondary sites was less efficient than the 59-be × secondary site reaction.
Extranjería y diferenciación residencial en Canarias: la perspectiva del microanálisis espacial

Este texto adelanta algunos resultados del proyecto de investigacion: «Repercusiones socioeconomicas y territoriales de la vivienda de la poblacion extranjera en Canarias» (PI042005/127), dirigido por Josefina Dominguez Mujica y financiado por la Direccion General de Universidades e Investigacion de la Consejeria de Educacion, Cultura y Deportes del Gobierno de Canarias.
Interactive graphical querying of time series and linear sequence data sets

Numerous analytic domains involve the study of measurable quantities that change over time. This widespread interest in time series data sets has led to substantial work in algorithmic strategies for querying and indexing data. Much less work has been done in the development of interactive tools for identifying patterns in these data sets. This dissertation uses a graphical mechanism for specifying queries on time series data to provide the basis for an exploration of the algorithmic and semantic issues surrounding interactive querying of time series data. Contributions of this dissertation include: (1) The definition of timeboxes—rectangular widgets that can be used in direct-manipulation Graphical User Interfaces (GUIs) to specify query constraints on time series data sets. Timeboxes are used to simultaneously specify two sets of constraints: given a set of N time series profiles, a timebox covering time periods x1…x2 (x 1 ≤ x2) and values y 1…y2 (y1 ≤ y2) will retrieve only those n ∈ N that have values y1 ≤ y ≤ y2 during all times x 1 ≤ x ≤ x2. (2) The TimeSearcher information visualization tool, which is based on the time-box query model. TimeSearcher's object-oriented architecture can easily be extended to support variants of the timebox model that provide additional expressive power. (3) The design and implementation of query models and widgets that extend the timebox model, including variable-time timeboxes (VTTs), angular queries, leaders & laggards queries, multiple search attributes, and query inversion. (4) Analysis of algorithmic issues: A comparison of multiple alternative search algorithms found that simple sequential scans outperformed geometric indices for processing timebox queries. (5) Empirical evaluation of timeboxes: Two empirical studies, each with 12 subjects, provided preliminary insight into the utility of timeboxes and led to design improvements for input and display. (6) Validation through case studies: TimeSearcher has been used by molecular biologists to explore gene expression data and nucleotide frequencies. This work has validated the utility of the tool and identified design suggestions and opportunities. (7) A framework for extending the timebox model, including the description of numerous possible extensions.
3‐D structure, volume, and DNA content of erythrocyte nuclei of polyploid fish

We have explored the potential relationship between ploidy level, DNA content (pg DNA nucleus−1), and dimensional characteristics, such as volume (μm3), surface area (μm2), and 3‐D structure of erythrocyte nuclei in a series of fish ploidy level models using Feulgen image analysis densitometry, flow cytometry, and confocal laser scanning microscopy. The species were diploid tench (Tinca tinca) (2n), Cuban gar (Atractosteus tristoechus) (2n), triploid tench (3n), evolutionary tetraploid sterlet (Acipenser ruthenus) (4n), evolutionary octaploid Siberian sturgeon (A. baerii) (8n), triploid Siberian sturgeon exhibiting dodecaploidy (12n), evolutionary 12n shortnose sturgeon (A. brevirostrum), and experimentally obtained sturgeon hybrids that were tetraploid, hexaploid (6n), heptaploid (7n), octaploid, decaploid (10n), dodecaploid and/or tetradecaploid (14n). Increase in ploidy was accompanied by growth of the nucleus and an increase in the number of flattened ellipsoid nuclei with increased transverse diameter. The volume (Vvoxel) of erythrocyte nuclei, as the sum of voxels calculated from live cells, seems more accurate than volume (Vaxis) calculated from measuring the major and minor axis, especially at higher and odd ploidy levels. Data of absolute and relative DNA content were in agreement with previously published reports. Species of the same ploidy level, but differing in DNA content, had a similar mean erythrocyte nuclear volume (Vvoxel), as demonstrated in sterlet and a hybrid of sterlet and beluga (48.3 and 48.9 μm3, respectively), with a respective mean DNA content of 3.74 and 3.10 pg DNA nucleus−1. A similar relationship was found for the ploidy 6n, 10n, 12n. The surface‐to‐volume ratio decreased non‐linearly with increasing ploidy. The DNA in erythrocyte nuclei appeared to be more densely packed with increase in ploidy level.
Multipoint Binding of the SLP-76 SH2 Domain to ADAP Is Critical for Oligomerization of SLP-76 Signaling Complexes in Stimulated T Cells

ABSTRACT The adapter molecules SLP-76 and LAT play central roles in T cell activation by recruiting enzymes and other adapters into multiprotein complexes that coordinate highly regulated signal transduction pathways. While many of the associated proteins have been characterized, less is known concerning the mechanisms of assembly for these dynamic and potentially heterogeneous signaling complexes. Following T cell receptor (TCR) stimulation, SLP-76 is found in structures called microclusters, which contain many signaling complexes. Previous studies showed that a mutation to the SLP-76 C-terminal SH2 domain nearly abolished SLP-76 microclusters, suggesting that the SH2 domain facilitates incorporation of signaling complexes into microclusters. S. C. Bunnell, A. L. Singer, D. I. Hong, B. H. Jacque, M. S. Jordan, M. C. Seminario, V. A. Barr, G. A. Koretzky, and L. E. Samelson, Mol. Cell. Biol., 26:7155–7166, 2006). Using biophysical methods, we demonstrate that the adapter, ADAP, contains three binding sites for SLP-76, and that multipoint binding to ADAP fragments oligomerizes the SLP-76 SH2 domain in vitro. These results were complemented with confocal imaging and functional studies of cells expressing ADAP with various mutations. Our results demonstrate that all three binding sites are critical for SLP-76 microcluster assembly, but any combination of two sites will partially induce microclusters. These data support a model whereby multipoint binding of SLP-76 to ADAP facilitates the assembly of SLP-76 microclusters. This model has implications for the regulation of SLP-76 and LAT microclusters and, as a result, T cell signaling.