gebhart/patrepeval huggingface dataset:
Proline-Dependent Structural and Biological Properties of Peptides and Proteins (1993)

Proline residues confer unique structural constraints on peptide chains and markedly influence the susceptibility of proximal peptide bonds to protease activity. This review presents a critical analysis of peptidases involved in the cleavage of proline-containing peptide bonds, with particular attention to the role of proline peptidases in the regulation of the lifetime of biologically active peptides. Peptidases discussed include aminopeptidase P, prolidase, dipeptidyl peptidase IV, prolyl endopeptidase, and prolyl iminopeptidase. Attention is also given to HIV-1 protease, because this key enzyme processes an Xaa-Pro peptide bond. Analysis of the above enzymes reveals that they may function as key pacemakers in the control of the activity of many peptide hormones and that they are involved in a variety of immunological processes, including T-cell-mediated immune response. The novel occurrence of cis-trans isomerization about Xaa-Pro bonds and the biological function of peptidyl-prolyl cis-trans isomerases (immunophilins) are reviewed.
Vaccines Against Fungal Infections (1987)

The state-of-the-art reached in developing protective immunity against fungal infections through vaccination makes a survey of methodologies and results timely. This review describes experimental vaccinations against dermatophytes, pathogenic yeasts, and dimorphic fungi with special attention to the anti-Coccidioides immitis vaccine, which has reached clinical trials, and to the anti-Candida albicans and anti-Histoplasma capsulatum ribosomal vaccines. Also covered are vaccination experiments in compromised hosts aimed at eliciting acquired resistance to opportunistic fungal infections which constitute risk factors for these hosts. Immunization procedures include live, killed, and attenuated organisms, as well as different subcellular fractions such as cytoplasmic extracts, fungal culture filtrates, cell walls, or ribosomal fractions. A variety of experimental animal models and isolated human trials constitute the subjects in these studies. Acquired immunity has been evaluated through assessment of resistance to infection and determination of specific immune responses. It has been demonstrated that fungal vaccines do elicit both humoral and cell-mediated immunity in the immunized host. For some vaccines (e.g., H. capsulatum), a correlation between the induced immunity and protection was observed and the immunity could be adoptively transferred. In view of the potential of vaccines against fungal infections, a perspective on their applicability, significance, and value for human use is discussed.
Physical modeling of spiral inductors on silicon (2000)

This paper presents a physical model for planar spiral inductors on silicon, which accounts for eddy current effect in the conductor, crossover capacitance between the spiral and center-tap, capacitance between the spiral and substrate, substrate ohmic loss, and substrate capacitance. The model has been confirmed with measured results of inductors having a wide range of layout and process parameters. This scalable inductor model enables the prediction and optimization of inductor performance.
Abstract 817: Unbiased discovery of exosome-associated biomarkers using xenograft models (2017)

Abstract We developed a novel, genome-wide method for biomarker discovery that is able to separate intrinsic markers of disease from markers of host response. Specifically, we implanted cell lines derived from two primary canine osteosarcoma tumors with different biological behavior into the tibiae of athymic nude mice. Both cell lines formed orthotopic tumors, and each recapitulated the biological behavior of the original primary tumor in terms of growth rate and metastatic potential (1,2). We also developed a cross-species hybrid genome that allowed us to identify separate canine and mouse transcripts in tumor xenografts (2). In other words, we were able to determine the contribution of canine mRNA sequences (derived from the implanted tumor cells) and mouse mRNA sequences (derived from infiltrating stroma) to define tumor-intrinsic features and host-specific features that contribute to osteosarcoma progression. When we applied this analysis method to exosome-derived mRNAs, we found canine-derived transcripts that were only present in exosomes of tumor-bearing mice that were associated with functions such as protein kinase A (PKA) and actin cytoskeleton signaling, and with upstream transcriptional regulators such as FOXF1, ESR1, and TP53. We also found tumor-specific, canine-derived transcripts that were associated with functions such as caveolae-derived endocytosis, energy utilization and metabolism, immune interactions, and G-coupled receptor signaling, and with upstream transcriptional regulators such as HNF1A, ESR1, NIPR1, and HNF4A. This method has the potential to reduce the statistical uncertainty that arises from the use of pre-selected molecules among the background of thousands of genomic features in patient samples. Using genome-wide analyses, we are able to combine multiple, highly correlated genes to manage this problem, increase markers' robustness, and avoid random correlations. In conclusion, this technology is useful to identify nucleic acids that serve as cancer biomarkers with high precision, and inter-species sequence conservation can be used to further improve its predictions. References 1. Scott MC, Sarver AL, Tomiyasu H, Cornax I, Van Etten J, Varshney J, et al. Aberrant Retinoblastoma (RB)-E2F Transcriptional Regulation Defines Molecular Phenotypes of Osteosarcoma. J Biol Chem 2015;290(47):28070-83. 2. Scott MC, Tomiyasu H, Garbe JR, Cornax I, Amaya C, O'Sullivan MG, et al. Heterotypic models of osteosarcoma recapitulate tumor heterogeneity and biological behavior. Disease Models &amp; Mechanisms 2016, doi: 10.1242/dmm.026849. Citation Format: Milcah C. Scott, John R. Garbe, Hirotaka Tomiyasu, Alicia Donnelly, Brad A. Bryan, Subbaya Subramanian, Jaime F. Modiano. Unbiased discovery of exosome-associated biomarkers using xenograft models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 817. doi:10.1158/1538-7445.AM2017-817
A Cabled Acoustic Telemetry System for Detecting and Tracking Juvenile Salmon: Part 2. Three-Dimensional Tracking and Passage Outcomes (2011)

In Part 1 of this paper, we presented the engineering design and instrumentation of the Juvenile Salmon Acoustic Telemetry System (JSATS) cabled system, a nonproprietary sensing technology developed by the U.S. Army Corps of Engineers, Portland District (Oregon, USA) to meet the needs for monitoring the survival of juvenile salmonids through the hydroelectric facilities within the Federal Columbia River Power System. Here in Part 2, we describe how the JSATS cabled system was employed as a reference sensor network for detecting and tracking juvenile salmon. Time-of-arrival data for valid detections on four hydrophones were used to solve for the three-dimensional (3D) position of fish surgically implanted with JSATS acoustic transmitters. Validation tests demonstrated high accuracy of 3D tracking up to 100 m upstream from the John Day Dam spillway. The along-dam component, used for assigning the route of fish passage, had the highest accuracy; the median errors ranged from 0.02 to 0.22 m, and root mean square errors ranged from 0.07 to 0.56 m at distances up to 100 m. For the 2008 case study at John Day Dam, the range for 3D tracking was more than 100 m upstream of the dam face where hydrophones were deployed, and detection and tracking probabilities of fish tagged with JSATS acoustic transmitters were higher than 98%. JSATS cabled systems have been successfully deployed on several major dams to acquire information for salmon protection and for development of more "fish-friendly" hydroelectric facilities.
BINDER CHARACTERIZATION AND EVALUATION. VOLUME 3: PHYSICAL CHARACTERIZATION (1994)

The research results in this report concern the characterization of physical properties of asphalt binders and the development of test procedures for aging and adhesion. Asphalt binders were shown to be linear viscoelastic materials at expected pavement strains. Test methods and models describing rheological behavior were developed with the assumption of linear behavior. A mathematical model that contains parameters that can be used to relate physical and chemical parameters was developed. The test methods and models allow the stiffness of asphalt binders to be characterized as a function of loading time and temperature with the dynamic shear rheometer at intermediate to upper pavement surface temperatures and with a newly developed bending beam rheometer at low temperatures, where thermal cracking is important. To characterize fracture properties, the project developed a direct tension test, in which failure strain, stress, and energy are determined as functions of loading time and temperature. Limited work on fatigue properties at low temperatures successfully related them to tensile properties. A new phenomenon, low-temperature physical hardening, was identified during the project. This phenomenon results in increased stiffness of the binder when it is held at a constant temperature at room temperature or below. The blister test for quantitative measurement of adhesion between asphalt binder and aggregate surfaces was found to be impractical. The investigation of various factors, including film thickness, aging temperature, the effect of oxygen versus air, and the effect of mineral surfaces, led to a new aging procedure for simulating in-service oxidative hardening of asphalt binders, which was adopted as part of the new Strategic Highway Research program (SHRP) binder specification.
Synthesis, Characterization, and Polymerization Studies of Ethylenebis(hexamethylindenyl) Complexes of Zirconium and Hafnium (2011)

The chemistry of a series of ansa-bridged ethylene-bis(hexamethylindenyl)zirconium and hafnium complexes has been explored. Treatment of EBI*Li2·THF0.38 with MCl4·THF2 (M = Zr, Hf) gives rac-EBI*MCl2 (rac-2, rac-3) and meso-EBI*MCl2 (meso-2, meso-3) (M = Zr and Hf), respectively. The rac- and meso- isomers can be separated by fractional crystallization. meso-EBI*ZrMe2 (meso-4) can be prepared by alkylation of meso-2 with MeLi·LiBr. The molecular structures of rac- and meso-2 and rac- and meso-3 have been determined by single-crystal X-ray crystallography. A comprehensive structural comparison between these compounds and related ansa metallocenes has been carried out. rac- and meso-2 and rac- and meso-3 in the presence of modified methylaluminoxane (MMAO) are very active catalyst precursors for the polymerization of ethene to give high-density polyethene (HDPE) with molecular weights (Mw) in the range 100 000−220 000 and polydispersities (Mw/Mn) of ca. 2.6. The activities of both catalyst precursors rac- and meso-2 are some of the highest reported in the literature, at 61 800 and 38 200 kgPE/mol met/h/bar, respectively.
Cyanovirin-N Inhibits AIDS Virus Infections in Vaginal Transmission Models (2004)

The cyanobacterial protein cyanovirin-N (CV-N) potently inactivates diverse strains of HIV-1 and other lentiviruses due to irreversible binding of CV-N to the viral envelope glycoprotein gp120. In this study, we show that recombinant CV-N effectively blocks HIV-1(Ba-L) infection of human ectocervical explants. Furthermore, we demonstrate the in vivo efficacy of CV-N gel in a vaginal challenge model by exposing CV-N-treated female macaques (Macaca fascicularis) to a pathogenic chimeric SIV/HIV-1 virus, SHIV89.6P. All of the placebo-treated and untreated control macaques (8 of 8) became infected. In contrast, 15 of 18 CV-N-treated macaques showed no evidence of SHIV infection. Further, CV-N produced no cytotoxic or clinical adverse effects in either the in vitro or in vivo model systems. Together these studies suggest that CV-N is a good candidate for testing in humans as an anti-HIV topical microbicide.
Expression, Localization, and Thyrotropin Regulation of Cathepsin D in Human Thyroid Tissues (1997)

Enzymatic activity and isoform expression of cathepsin D (cath D) were studied in 107 cytosols from various human thyroid tissues including 21 normal tissues, 12 cold benign nodules, 17 toxic adenomas, 22 samples from Graves' disease patients, and 35 thyroid carcinomas. Cath D assay was optimized for human thyroid tissues. We found that mean cath D specific activities, expressed as units per milligrams protein minus thyroglobulin, were higher in carcinomas (P = 0.0001), toxic adenomas (P = 0.0001), and specimens from Graves' disease patients (P = 0.0001) than in normal thyroid tissues. Mean cath D activity in carcinomas was also significantly different from that in cold benign nodules (P < 0.001) and Graves' disease tissues (P < 0.05) but not from that of toxic adenomas. To determine possible mechanisms by which the observed increase in cath D activity might be regulated, we used Western blotting to measure relative amounts of cath D isoforms in the various thyroid tissues. We found that the 31-kDa major processing form of cath D was significantly increased in carcinomas and toxic adenomas compared with normal tissues (P < 0.01), cold benign nodules (P < 0.05), and Graves' disease tissues (P < 0.05). A positive correlation of cath D activity with relative expression of the 31-kDa form (r = 0.67, P = 0.0001) was observed in 104 thyroid cytosols. These data demonstrate a deregulation at the protein level, with resulting increases in cath D activity. Immunogold labeling of cath D showed particle concentration in lysosomes or phagosomes in both normal follicles and papillary carcinoma cells, indicating that cath D localization was not altered by malignant transformation in human thyroid cells. TSH induced cath D synthesis and secretion in extracellular fluid of normal human thyroid cells in primary culture; TSH had little effect on intracellular cath D level. In conclusion, TSH-induced cath D synthesis may explain high cath D levels in Graves' disease tissues and toxic adenomas, because these tissues possess a permanently stimulated cAMP transduction pathway. Furthermore, the overexpression of cath D in thyroid carcinomas in comparison with normal controls adds further arguments for the potential role of cath D in tumor growth and metastasis.
Promoter Analysis of the Barley Pht1;1 Phosphate Transporter Gene Identifies Regions Controlling Root Expression and Responsiveness to Phosphate Deprivation (2004)

Previous studies have shown that the promoter from the barley (Hordeum vulgare) phosphate transporter gene, HvPht1;1, activates high levels of expression in rice (Oryza sativa) roots and that the expression level was induced by up to 4-fold in response to phosphorus (P) deprivation. To identify promoter regions controlling gene regulation specificities, successive promoter truncations were made and attached to reporter genes. Promoters of between 856 and 1,400 nucleotides activated gene expression in a number of cell types but with maximal expression in trichoblast (root hair) cells. For shorter promoters the trichoblast specificity was lost, but in other tissues the distribution pattern was unchanged. The low P induction response was unaffected by promoter length. Domain exchange experiments subsequently identified that the region between -856 and -547 nucleotides (relative to the translational start) is required for epidermal cell expression. A second region located between 0 and -195 nucleotides controls root-tip expression. The HvPht1;1 promoter contains one PHO-like motif and three motifs similar to the dicot P1BS element. Analysis of promoters from which the PHO-like element was eliminated (by truncation) showed no change in the gene induction response to P deficiency. In contrast, mutation of the P1BS elements eliminated any induction of gene expression in response to low P. An internal HvPht1;1 promoter fragment, incorporating a single P1BS element, had an increased response to P deprivation in comparison with the unmodified promoter (containing three elements). Together these findings further our understanding of the regulation of the HvPht1;1 gene and provide direct evidence for a functional role of the P1BS element in the expression of P-regulated genes.
Multilevel reduced controlled switches AC-DC power conversion cells (2015)

This paper presents multilevel AC-DC single-phase power conversion cells for applications in which the regenerative operation is either not required or prohibited. The AC primary power source is a single phase from a permanent magnet (PM) generator or from an electrical grid. The cells are composed of two H-bridges in cascade: a unidirectional high-voltage H-bridge with two controlled switches and two power diodes, processing the active power, and a low-voltage H-bridge with four controlled switches and a floating capacitor. These cells can be part of multi-phase systems, in which it is required one cell for each phase. In this paper, some examples of application for three-phase systems are going to be given, exploring different ways of connection between the single-phase cells. Simulation and experimental results regarding the proposed cells will be shown for validation and comparison purposes.
Serial analysis of V6 ribosomal sequence tags (SARST‐V6): a method for efficient, high‐throughput analysis of microbial community composition (2005)

Serial analysis of ribosomal sequence tags (SARST) is a novel technique for characterizing microbial community composition. The SARST method captures sequence information from concatemers of short 16S rDNA polymerase chain reaction (PCR) amplicons from complex populations of DNA. Here, we describe a similar method, serial analysis of V6 ribosomal sequence tags (SARST-V6), which targets the V6 hypervariable region of bacterial 16S rRNA genes. The SARST-V6 technique exploits internal primer sequences to generate compatible restriction digest overhangs, thereby improving upon the efficiency of SARST. Serial analysis of V6 ribosomal sequence tags of bacterial community composition in hydrothermal marine sediments from Guaymas Basin resembled results of cloning and sequencing of single, full-length PCR products from ribosomal RNA genes of the same microbial community. Both methods identified the same major bacterial groups, but only SARST-V6 recovered thermodesulfobacteria and gamma-proteobacteria sequences, while only full-length PCR product cloning recovered candidate division OP11 se-quences. There were differences in the relative frequencies of some phylotypes. The disparities reflect differences in the amplicon pool obtained during initial amplification that may result from different primer affinities or DNA degradation. These results demonstrate the utility of SARST-V6 in collecting taxonomically informative data for high-throughput analysis of microbial communities.
Optimising the methods of evaluation of the effectiveness of botulinum toxin treatment of post-stroke muscle spasticity (2004)

The correct research design is crucial in establishing whether treatments for complex neurological disorders are effective

The effectiveness of botulinum toxin type A (BtxA) in reducing post-stroke muscle hypertonia and its complications has been demonstrated in adult patients in at least eight large randomised controlled trials (RCTs).1–8 The clinical benefits were reported when diverse treatment protocols and different dose schedules and injection techniques were used for the management of the same clinical indication. Nonetheless, some doubt as to the value of this treatment remain.9 What is the explanation for this apparent paradox? The contradiction may be explained by the inadequate design of these studies and the inherent difficulties with the interpretation of the results of RCTs of a drug treatment that is carried out in the context of rehabilitation for a person with chronic neurological disability. The WHO classification of functioning, disability, and health10 provides a useful framework for understanding the complex relation between the statistical significance and the clinical significance of a given treatment and helps to explain the complexity of rehabilitation research. A statistically significant change at the level of impairment (as a result of the intervention) may not alter the subject’s functional abilities or potential for social participation. The outcome of treatment with BtxA is clinically significant only if it results in the full or partial attainment of functional goals that are meaningful to the recipient of this treatment. An example of such outcomes is the achievement of safe walking and prevention of falls in a patient with dynamic foot equinus after BtxA injections into the calf muscles. Successful treatment reduces muscle …
Flip-chip assembly for photonic circuits (2004)

When tackling the issue of low cost and enabled mass production for photonic circuits, the application of flip-chip technology creates huge expectations. We report on the results of a European project, in which it was the goal to demonstrate standard packaging technology in combination with specific integrated optics devices, entailing demands and limitations different from IC technology. In integrated optics devices, mainly the fiber attachment, but also some special features as the accessibility of windows at the top-side of the chip (e.g. sensing devices) are prohibiting the positioning of the optical layer stack and the solder pads for the flip-chip processing at the same side of the silicon wafer. Therefore, a feed through technology for the electrical wiring had to be included. Compatibility issues in combining the feed through technology with integrated optics processing have been solved. In this paper, we will demonstrate the successful feed-through metallization and flip-chip assembly in combination with an integrated optical sensor. The sensor, which has been designed for the measurement of relative humidity from 0-100 %RH, has been realized and packaged according to this technology. The feed-through metallization, solder type and chip carrier material have been chosen in a way that the demands of the demonstrator device are fulfilled according to a given specification.
Ligar e desligar: um estudo exegético de Mateus 18:18 (2007)

In Matthew 18:18, Jesus said that all that the Church would “bind” or “loose” in Earth would be equally done in Heaven. This authority given to the Church, in this text, has been the object of many interpretations: (1) this is an authority to establish doctrines; (2) to forgive sins; or (3) to exercise ecclesiastic discipline. This research had the goal of searching for the best understanding of this text by meanings of a contextual and lexical-grammatical study of the main words in the text. The conclusion reached is that the text deals with the question of ecclesiastic discipline.
Phosphatidylinositol 3′-Kinase/AKT Signaling Is Activated in Medulloblastoma Cell Proliferation and Is Associated with Reduced Expression of PTEN (2006)

We conclude that activation of the PI3K/AKT pathway constitutes an important step in the molecular pathogenesis of medulloblastoma and that dysregulation of PTEN may play a significant role in this context.