gebhart/patrepeval huggingface dataset:
Characteristics of a Very Virulent Infectious Bursal Disease Virus from California (2009)

An outbreak of infectious bursal disease (IBD) in two California layer flocks resulted in the isolation of two infectious bursal disease viruses designated rA and rB. Increased mortality plus gross and histopathology in the layer flocks suggested rA and rB could be very virulent infectious bursal disease virus (vvIBDV). Preliminary studies indicated that high mortality resulted when bursa homogenates from the layer farms were used to inoculate specific-pathogen-free (SPF) chicks. In addition, rA and rB contained VP2 amino acid sequences typically seen in vvIBDV. Molecular and in vivo studies were conducted to more thoroughly identify and characterize the rA and rB viruses. Nucleotide sequence analysis demonstrated that rA and rB had identical sequences across the hypervariable VP2 (hvVP2) and segment B regions examined, and their amino acid sequences in the hvVP2 region were identical to the vvwIBDV type strains UK 661, OKYM, and Harbin. Furthermore, the genome segment B nucleotide sequences examined for rA and rB were a 98.1% match with vvIBDV and only an 88.0% match with classic IBDV strains. Phylogenetic analysis placed the rA and rB viruses with other vvIBDV and confirmed these viruses were close genetic descendants of vvIBDV seen around the world. Pathogenicity studies in 4-wk-old SPF chicks demonstrated that at a high dose (105.5 50% egg infective dose [EID50]) and a low dose (102.0 EID50) of rA and rB, mortality ranged from 91% to 100%. A pathogenic classic virus, standard challenge (STC), at similar doses did not cause mortality in the SPF chicks. In addition, mortality occurred in three out of four SPF birds exposed by direct contact to rA and rB inoculated chicks. Serum from convalescent birds inoculated with rA had high titers to IBDV but were negative for antibodies to infectious bronchitis virus, avian influenza virus, chicken anemia virus, Newcastle disease virus, Mycoplasma gallisepticum, and Mycoplasma synoviae. Virus isolation attempts on the rA and rB bursa homogenate inocula also indicated that no contaminating microorganisms contributed to the high mortality and pathology observed in the SPF chicks. In one experiment, broilers with maternal immunity to IBDV were protected from infection and disease when they were challenged with 10(2) EID50 and 10(5) EID50 of the STC virus. When challenged with 10(2) EID50 of the rA virus, the maternally immune broilers were protected from disease but not infection as evidenced by a positive reverse transcription-polymerase chain reaction (RT-PCR) assay for the virus. When the broilers were challenged with 10(5) EID50 of the rA virus, they had typical gross and histopathologic signs of IBD but no mortality by 7 days postinoculation. It was concluded that the rA and rB viruses meet the genotypic and phenotypic characteristics of a vvIBDV.
Tolerance Induction for Xenotransplantation (1997)

The transplantation of donor hematopoietic tissue prior to organ xenografting has the potential to induce lasting T cell tolerance and, possibly, tolerance of natural antibody-producing B cells. However, the development of specific and nontoxic methods of overcoming the immunologic and physiologic barriers to xenogeneic marrow engraftment is a major challenge that must be met before this goal can be achieved. A greater understanding of the species specificity of molecular interactions important for hematopoiesis and cell homing is a first step toward transcending these physiologic barriers. Perhaps most promising is the potential associated with the use of nonprimate xenogeneic donors genetically engineered to make donor tissues more readily capable of surviving and, in the case of hematopoietic cells, competing with host tissues for survival in a human environment.
Inter-laboratory comparison of plasma catecholamine determinations using several different assays. (1984)

Thirty-four laboratories performed altogether 41 plasma catecholamine assays on each of four samples. Various radioenzymatic assays, high performance liquid chromatographic (HPLC) assays with electrochemical detection and fluorimetric assays were used. There was reasonable agreement that the levels of adrenaline and noradrenaline in a basal plasma pool were about 0.2 and 1.8 nM, respectively. The levels in a pool of plasma obtained after exercise were about 0.7 and 11 nM, respectively. The study, however, revealed a sometimes considerable variability between methods as well as between laboratories using the same method. Results from duplicate determinations of noradrenaline suggest frequent problems with intra-laboratory reproducibility. Results concerning the recoveries of 0.7 or 3.0 nM adrenaline or 2.0 nM noradrenaline (added to the basal plasma pool) showed a rather frequent need for improved precision. Fluorimetric assays gave unacceptable results. Plasma free dopamine measurements showed a basal level of 0.1-0.2 nM with most HPLC assays and a tendency towards higher levels and greater scatter with radioenzymatic methods. On the whole, reverse phase HPLC methods and an inhomogeneous group of single-isotope derivative radioenzymatic assays showed the largest variability. Less variability was found with the radioenzymatic assay of Peuler & Johnson (1977), provided that a few obviously erroneous results were excluded. The smallest variability was found with microparticulate cation exchange HPLC. It is concluded that plasma catecholamine assays would benefit from better standardization and a continuous quality control. Problems associated with validation of new assays, as well as modifications of old assays are discussed.
Urodilatin limits acute reperfusion injury in the isolated rat heart (2000)

These results indicate that reduced cGMP concentration may impair myocyte survival during reperfusion. Stimulation of particulate guanylyl cyclase may appear as a new strategy to prevent immediate lethal reperfusion injury.
Energy Issues in Desalination Processes (2008)

Water, energy, and environmental issues are closely related. New water techniques consume energy, and innovative renewable energy techniques using biofuels and biodiesel consume an incredible amount of water. Different desalination techniques that consume different energy levels from different sources are in use today. Some people, environmentalists, decision makers, and even scientists, mainly in nonscientific publications, consider energy consumption in desalination to be too high and are seeking new ways of reducing it, which often involves increasing capital investment. Efforts should be directed at reducing not only energy consumption but also total water cost. A competent grasp of thermodynamics and heat and mass transfer theory, as well as a proper understanding of current desalination processes, is essential for ensuring beneficial improvements in desalination processes. Thermodynamics sets the absolute minimum limit of the work energy required to separate water from a salt solution. Unavoidable irreversibilities augment the actual energy consumption, yet modern desalination techniques have succeeded in considerably narrowing the gap between actual and limiting energy levels. The implication of this smaller gap is that only marginal energy reductions are possible. The current energy consumption of different desalination processes is reviewed in this paper. A comparison with other common energy-consuming ventures leads to some interesting conclusions.
Comprobación experimental de la importancia relativa de las vías superficial y subterránea de inundación en la liberación de sales de sedimentos desecados (1990)

espanolEl efecto de las inundaciones subterranea y superficial de sedimentos desecados en la liberacion de sales a la columna de agua durante las primeras fases de inundacion se ha estudiado en laboratorio con sedimento de la laguna de Gallocanta. Los iones mayoritarios se liberan mas rapidamente y en mayor cantidad en la inundacion subterranea. EI patron de variacion de las concentraciones es irregular en la inundacion subterranea y mas uniforme en la superficial. Los micronutrientes se observan en mayor cantidad en la inundacon subterranea, excepto en el caso del fosforo particulado. El nitrato inorganico disuelto es la fraccion rnas abundante y el fosforo reactivo soluble es la menos abundante (10% del fosforo total). EnglishThe relative importance of underground and surficial flooding of sediments on the release of mineral salts to the water column was tested in a laboratory experiment with sediment from Lake Gallocanta, a salt lake at 1,000 m.a.s.1. in NE. Spain (Zaragoza-Teruel). Homogenaized portions of sediment from the NW. shore of the lake were flooded independently surficially (up to down) and as groundwater (down to up). Eight samples from the water column were collected during the 48 hours experiment from different test tubes without disrupting the system. Major ions release from the sediment during the underground flooding faster and in a higher amount than in the surficial flooding. The pattem of the concentrations changes is very irregular in the first case, while it is very uniform during the second one. The relative amounts of major cations and anions keep the same order than in the lake waters (C1>S04, Na>Mg>Ca>K). Micronutrient concentrations are also higher in the underground than in the surficial flooding, but particulate phosphorus. Dissolved inorganic nitrogen as nitrate has the highest concentrations between the different orms. Total phosphorus release from the sediment in a lower amount (only 10% as compared to total nitrogen). Soluble reactive phosphorus is only 10% of the total phosphorus released. Under the experimental conditions mineral salts release from the sediment seems to be dominated by chemical and physical processes and not by biological ones catalaL'efecte de les inundacions subterranies i superficials de sediments dessecats en la lliberacio de sa!s a la columna d'aigua durant les primeres fases de la inundacio s'ha estudiat en el laboratori amb sediment de la llacuna de Gallocanta. Els ions majoritaris s'alliberen mes rapidament i en major quantitat en la inundacio subterrania. El patro de variacio de les concentracions es irregular en la inundacio subterrania i mes uniforme en la superficial. Els micronutrientes s'observen en major quantitat en la inundacio subterrania, exceptuant el cas del fosfor particulat. El nitrat inorganic disolt es la fraccio mes abundant i el fosfor reactiu soluble es la menys abundant (10% del fosfor total).
An Analysis of Deep Neural Network Models for Practical Applications (2016)

Since the emergence of Deep Neural Networks (DNNs) as a prominent technique in the field of computer vision, the ImageNet classification challenge has played a major role in advancing the state-of-the-art. While accuracy figures have steadily increased, the resource utilisation of winning models has not been properly taken into account. In this work, we present a comprehensive analysis of important metrics in practical applications: accuracy, memory footprint, parameters, operations count, inference time and power consumption. Key findings are: (1) power consumption is independent of batch size and architecture; (2) accuracy and inference time are in a hyperbolic relationship; (3) energy constraint is an upper bound on the maximum achievable accuracy and model complexity; (4) the number of operations is a reliable estimate of the inference time. We believe our analysis provides a compelling set of information that helps design and engineer efficient DNNs.
High frequency photonic microwave oscillators based on WGM resonators (2005)

This paper studies the applications of novel photonic microwave oscillators containing high-Q whispering gallery mode (WGM) resonators intended to produce low noise high frequency MW signals ranging from X-band to W-band. We theoretically compare the fundamental as well as practical restrictions on the performance of both an optical hyper-parametric oscillator based on a nonlinear high-Q WGM resonator and an "oscillator" based on two lasers locked to the same linear WGM resonator to produce stable MW beat signals. Finally, we report on a proof of the principle experiment where we realized the hyper-parametric oscillator generating /spl sim/ 10 GHz signals with 200 Hz linewidth and -110 dBc/Hz noise floor at 1 MHz from /spl sim/ 10 GHz carrier.
Complex genome-wide transcription dynamics orchestrated by Blimp1 for the specification of the germ cell lineage in mice (2008)

Specification of germ cell fate is fundamental in development. With a highly representative single-cell microarray and rigorous quantitative PCR analysis, we defined the genome-wide transcription dynamics that create primordial germ cells (PGCs) from the epiblast, a process that exclusively segregates them from their somatic neighbors. We also analyzed the effect of the loss of Blimp1, a key transcriptional regulator, on these dynamics. Our analysis revealed that PGC specification involves complex, yet highly ordered regulation of a large number of genes, proceeding under the strong influence of mesoderm induction but specifically avoiding developmental programs such as the epithelial-mesenchymal transition, Hox cluster activation, cell cycle progression, and DNA methyltransferase machinery. Remarkably, Blimp1 is essential for repressing nearly all the genes normally down-regulated in PGCs relative to their somatic neighbors. In contrast, it is dispensable for the activation of approximately half of the genes up-regulated in PGCs, uncovering the Blimp1-independent events for PGC specification. Notably, however, highly PGC-specific genes exhibited distinct correlations to Blimp1 in wild-type embryos, and these correlations faithfully predicted their expression impairments in Blimp1 mutants. Moreover, their expression overlaps within single cells were severely damaged without Blimp1, demonstrating that Blimp1 exerts positive influence on their concerted activation. Thus, Blimp1 is not a single initiator but a dominant coordinator of the transcriptional program for the establishment of the germ cell fate in mice.
Bone marrow mesenchymal stem cells from leukemia patients inhibit growth and apoptosis in serum-deprived K562 cells (2009)

Leukemic MSCs can inhibit K562 cell expansion and modulate the cell cycle to a state of relative quiescence. This allows the K562 cells to endure adverse conditions such as serum starvation. The PI3K-Akt-Bad signaling pathway may be involved in this antiapoptotic process via phosphorylation of the Akt and Bad proteins. Blocking MSC-induced transduction of the PI3K-Akt-Bad pathway may be a potential strategy for a targeted therapy to combat leukemia.
Bioinformatics : a practical guide to the analysis of genes andproteins (1998)

Foreword (Lee Hood). Preface. Contributors. PART ONE: BIOLOGICAL DATABASES. 1. Sequence Databases (Rolf Apweiler). 2. Mapping Databases (Peter S. White and Tara C. Matise). 3. Information Retrieval from Biological Databases (Andreas D. Baxevanis). 4. Genomic Databases (Tyra G. Wolfsberg). PART TWO: ANALYSIS AT THE NUCLEOTIDE LEVEL. 5. Predictive Methods Using DNA Sequences (Enrique Blanco and Roderic Guigo). 6. Predictive Methods Using RNA Sequences (David Mathews and Michael Zuker). 7. Sequence Polymorphisms (James C. Mullikin and Stephen T. Sherry). PART THREE: ANALYSIS AT THE PROTEIN LEVEL. 8. Predictive Methods Using Protein Sequences (Yanay Ofran and Burkhard Rost). 9. Protein Structure Prediction and Analysis (David Wishart). 10. Intermolecular Interactions and Biological Pathways (Gary D. Bader and Anton J. Enright). PART FOUR: INFERRING RELATIONSHIPS. 11. Assessing Pairwise Sequence Similarity: BLAST and FASTA (Andreas D. Baxevanis). 12. Creation and Analysis of Protein Multiple Sequence Alignments (Geoffrey J. Barton). 13. Sequence Assembly and Finishing Methods (Nancy F. Hansen, Pamela Jacques Thomas and Gerard G. Bouffard). 14. Phylogenetic Analysis (Fiona S. L. Brinkman). 15. Computational Approaches in Comparative Genomics (Andreas D. Baxevanis). 16. Using DNA Microarrays to Assay Gene Expression (John Quackenbush). 17. Proteomics and Protein Identification (Mark R. Holmes, Kevin R. Ramkissoon and Morgan C. Giddings). PART FIVE: DEVELOPING TOOLS. 18. Using Perl to Facilitate Biological Analysis (Lincoln D. Stein). Appendices. Glossary. Index.
Grain Boundary Defect Elimination in a Zeolite Membrane by Rapid Thermal Processing (2009)

Microporous molecular sieve catalysts and adsorbents discriminate molecules on the basis of size and shape. Interest in molecular sieve films stems from their potential for energy-efficient membrane separations. However, grain boundary defects, formed in response to stresses induced by heat treatment, compromise their selectivity by creating nonselective transport pathways for permeating molecules. We show that rapid thermal processing can improve the separation performance of thick columnar films of a certain zeolite (silicalite-1) by eliminating grain boundary defects, possibly by strengthening grain bonding at the grain boundaries. This methodology enables the preparation of silicalite-1 membranes with high separation performance for aromatic and linear versus branched hydrocarbon isomers and holds promise for realizing high-throughput and scalable production of these zeolite membranes with improved energy efficiency.
Weakest-precondition of unstructured programs (2005)

Program verification systems typically transform a program into a logical expression which is then fed to a theorem prover. The logical expression represents the weakest precondition of the program relative to its specification; when (and if!) the theorem prover is able to prove the expression, then the program is considered correct. Computing such a logical expression for an imperative, structured program is straightforward, although there are issues having to do with loops and the efficiency both of the computation and of the complexity of the formula with respect to the theorem prover. This paper presents a novel approach for computing the weakest precondition of an unstructured program that is sound even in the presence of loops. The computation is efficient and the resulting logical expression provides more leeway for the theorem prover efficiently to attack the proof.
Regulation of connective tissue growth factor expression in the aqueous humor outflow pathway. (2006)

This study demonstrates that CTGF expression in TM cells is modulated by several physiological agonists and by increased ocular pressure and mechanical stretch. These results suggest that the regulation of CTGF expression within tissues of the outflow pathway may play a role in the homeostasis of intraocular pressure, possibly by modulation of ECM production in these tissues.
Role of cytokines in rheumatoid arthritis: an education in pathophysiology and therapeutics (2008)

Advances in cDNA and monoclonal antibody technology in the 1980s fuelled the discovery and characterization of the properties of cytokines. It became apparent that because cytokines were expressed in tissues derived from autoimmune diseases, they were likely to be of fundamental importance in disease pathogenesis and developing a new class of biological therapeutics. In this review, we describe the history of bench to bedside translation of work that led to the identification of tumor necrosis factor (TNF) as a key regulator of the loss of homeostatic immune-inflammatory responses in rheumatoid arthritis (RA) and a good therapeutic target. First in human clinical trials in collaboration with a biotechnology company, the safety and efficacy of TNF blockade with a chimeric monoclonal antibody was substantiated in patients refractory to standard anti-rheumatoid drugs. Abnormal immune-inflammatory responses after therapy showed improvement and remain a focus of ongoing research in many laboratories. Longer term multi-center studies that followed with several anti-TNF biologicals have demonstrated the augmented efficacy, including inducing clinical remission, of low dose methotrexate and anti-TNF therapy co-therapy, but serious infections and lymphomas in a low frequency have been observed. In the course of the past decades, three 'blockbuster' anti-TNF biologicals are in the clinic. Over a million patients with RA and other immune-mediated diseases have been successfully treated, and a better perspective on the risk of harm and its management has become part of good clinical practice. This success has encouraged a burgeoning industry of biologicals for chronic diseases.
Disruption of Glial Glutamate Transport by Reactive Oxygen Species Produced in Motor Neurons (2003)

Observations of elevated CSF glutamate in amyotrophic lateral sclerosis (ALS), together with findings that motor neurons are selectively vulnerable to glutamate receptor-mediated ("excitotoxic") injury, support an excitotoxic contribution to the motor neuron loss in the disease. However, the basis of the apparent loss of astrocytic glutamate transport capacity in affected areas of motor cortex and spinal cord, which probably underlies the extracellular glutamate elevations, is unexplained. Here, we find that glutamate induces far greater reactive oxygen species (ROS) generation in cultured motor neurons than in other spinal neurons. In addition, we found that the ROS seem to be able to leave the motor neurons and induce oxidation and disruption of glutamate uptake in neighboring astrocytes. Correspondingly, in a transgenic mouse model of ALS, protein oxidation was increased in regions immediately surrounding motor neurons. These results provide a mechanism that can account for the localized loss of glial glutamate transport seen in the disease. Furthermore, the observations lend support for a feedforward model involving reciprocal interactions between motor neurons and glia, which may prove useful in understanding ALS pathogenesis.
Quantitative evaluation of congo red binding to amyloid-like proteins with a beta-pleated sheet conformation. (1989)

The binding of Congo red to several purified amyloid-like peptides having a beta-pleated sheet conformation was quantitatively examined. Congo red binds preferentially to the beta-pleated sheet conformation of both insulin fibrils and poly-L-lysine. Congo red does not bind nearly so well to poly-L-serine or polyglycine, despite the fact that these peptides also have a beta-pleated sheet conformation. Binding to insulin fibrils was saturable with an apparent Bmax of 2 moles of Congo red per mole of insulin fibrils and an apparent KD of 1.75 x 10(-7) M. Binding to beta-poly-L-lysine was similar but had a much higher apparent Bmax of 43. Binding of Congo red to beta-poly-L-lysine was pH dependent and appeared to be determined by the number of protonated lysine residues in the 250 amino acid peptide. We present a new hypothesis in which Congo red binds to amyloid-like proteins via bonds between the two negatively charged sulfonic acid groups of Congo red and two positively charged amino acid residues of two separate protein molecules which are properly oriented by virtue of the beta-pleated sheet conformation of the peptide backbone.