gebhart/patrepeval huggingface dataset:
Identification of hyaluronic acid binding sites in the extracellular domain of CD44 (1993)

CD44 is a polymorphic glycoprotein expressed on the surface of many tissues and cell lines which has been implicated in a number of cellular functions including lymphocyte homing to mucosal lymphoid tissue (Peyers patches), leukocyte activation, lymphopoiesis, and tumor metastasis. The predominant isoform found on human leukocytes, CD44H, is a receptor for hyaluronic acid. Because of the prominent role CD44 plays in diverse biological processes, we set out to identify the hyaluronic acid binding site(s) in the extracellular domain of CD44H. Using truncation and site-directed mutagenesis we identified two regions containing clusters of conserved basic residues which are important in hyaluronic acid binding. One of these regions is situated near the NH2 terminus and is homologous to other hyaluronic acid binding proteins including cartilage link protein. The other more membrane proximal region lies outside the link protein homologous domain. Mutagenesis of basic residues within these regions established their role as determinants in hyaluronic acid binding. Mutation of Arg 41, a position where a basic residue is conserved in all hyaluronic acid binding proteins, completely abolished binding suggesting that this residue plays a critical role in hyaluronic acid binding.
Pharmacokinetics, tissue distribution, and stability of antisense oligodeoxynucleotide phosphorothioate ISIS 3466 in mice. (1994)

Phosphorothioate oligonucleotides have a potential as therapeutic agents. The pharmacokinetics, tissue distribution, stability, and cellular uptake by LOX ascites tumor of p120 antisense phosphorothioate oligonucleotide, ISIS 3466, were studied in vivo. The oligonucleotide, which was quickly cleared from the circulation in the normal mice after IV injection, was readily absorbed into the systemic circulation from the peritoneum. The oligonucleotide was found in most tissues 48 h after IP administration. The highest concentrations were in kidney and liver, but the brain had a very low concentration. The phosphorothioate oligonucleotide was intact even after 48 h. When the oligonucleotide was complexed with cationic lipid DOTMA, the DOTMA did not affect the oligonucleotide uptake or tissue distribution in normal mice. However, DOTMA significantly increased the oligonucleotide cellular uptake (4-10 times) in LOX ascites tumors in an IP/IP model. These results indicate that the phosphorothioate oligonucleotide is stable, has favourable kinetics for use as an therapeutic agent, and that DOTMA could be useful in local delivery of the oligonucleotide in vivo.
Sequence-Independent and Linear Variation of Oligonucleotide DNA Binding Stabilities (1996)

The ability to equalize the DNA binding stability of comprehensive sets of oligonucleotides is imperative for the application of sequencing by hybridization technology. By substitution of ribonucleotides into an oligonucleotide composed of deoxyribonucleotides, and vice versa, the duplex stability of the oligonucleotide is changed linearly with the number of serial alternations of sugar configurations within the molecule. Since this effort occurs independently of the actual base sequence, any set of oligonucleotides could be adjusted to a defined level of binding stability.
Test Results of Air-Permeable Charcoal Impregnated Suits to Challenge by Chemical and Biological Warfare Agents and Simulants. Executive Summary and Summary Report (2003)

Abstract : Swatches from five commercially available air-permeable charcoal impregnated protective suits were challenged with liquid droplets of Sarin (GB) and mustard (HD), using modifications of the convective permeation test procedure described in TOP 8-2-501. The cumulative mass of each agent that permeated each swatch was determined over time. and the results for all swatches were used to determine a weighted-average cumulative mass for each suit. From these data a physiologically derived breakthrough time was calculated for each suit for the purpose of comparison. In addition, intact suits were challenged with corn-oil aerosol to simulate a biological or chemical aerosol. Protection factors were determined for each suit.
Volumetric acoustic vector intensity imager (2006)

A new measurement system, consisting of a mobile array of 50 microphones that form a spherical surface of radius 0.2m, that images the acoustic intensity vector throughout a large volume is discussed. A simultaneous measurement of the pressure field across all the microphones provides time-domain holograms. Spherical harmonic expansions are used to convert the measured pressure into a volumetric vector intensity field on a grid of points ranging from the origin to a maximum radius of 0.4m. Displays of the volumetric intensity image are used to locate noise sources outside the volume. There is no restriction on the type of noise source that can be studied. An experiment inside a Boeing 757 aircraft in flight successfully tested the ability of the array to locate flow-noise-excited sources on the fuselage. Reference transducers located on suspected noise source locations can also be used to increase the ability of this device to separate and identify multiple noise sources at a given frequency by using the theory of partial field decompositions. The frequency range of operation is 0to1400Hz. This device is ideal for the diagnostic analysis of noise sources in commercial and military transportation vehicles in air, on land, and underwater.
Proliferation and Expression of Progenitor and Mature Retinal Phenotypes in the Adult Mammalian Ciliary Body after Retinal Ganglion Cell Injury (2007)

Together, these results suggest that progenitorlike cells of the CB respond to cues associated with the loss of a single retinal cell type and that a subpopulation of those cells may differentiate into a cell that bears phenotypic resemblance to those seen in the retina.
Chemical characterization of iron (III)-hydroxide-dextrin complexes. A comparative study of commercial preparations with alleged reproductions used in the examination of bioavailability. (1984)

The iron (III)-hydroxide-dextrin complexes in two commercial preparations were compared with alleged reproduction which have been prepared for bioavailability studies published recently. Precipitation behaviour in chloride media, kinetics of reduction by ascorbic acid, magnetic susceptibility and laser light scattering data reveal that the original preparations and the alleged reproductions are neither identical nor equivalent in chemical properties. The historical controversy about iron(II) versus iron(III) preparations in oral therapy should be dropped because, on chemical grounds, iron(II) salts are sources of iron(III) species appearing in the gastro-intestinal tract.
Tumor necrosis factor-mediated release of platelet-derived growth factor from cultured endothelial cells. (1987)

Platelet-derived growth factor (PDGF) is a 30,000-Mr glycoprotein that is chemotactic and mitogenic for vascular smooth muscle cells (SMC). It is also a potent vasoconstrictor. In the present study, we found that the macrophage-derived polypeptide, tumor necrosis factor (TNF), releases a factor from human umbilical vein endothelial cells (EC) that is mitogenic for SMC. Postculture medium from TNF-stimulated EC induced a 90% increase in mitogenesis is compared with controls. This effect was half-maximal at a TNF dose of 114 pM, reflected a 2.5-fold increase in PDGF-specific mRNA synthesis, and peaked at 15 h of TNF stimulation. Mitogenic activity was completely abrogated by preincubation of postculture medium with antibody to platelet PDGF. Stimulation of EC with IL-1 (60-240 pM) led to the release of similar mitogenic activity. Thus, in addition to its effects on the hemostatic and adhesive properties of EC, TNF also promotes release of PDGF, which may serve to modulate proliferation of vascular SMC during wound healing, inflammation, and atherogenesis.
A Scalable and Programmable Simplicial CNN Digital Pixel Processor Architecture (2004)

We propose a programmable architecture for a single instruction multiple data image processor that has its foundation on the mathematical framework of a simplicial cellular neural networks. We develop instruction primitives for basic image processing operations and show examples of processing binary and gray scale images. Fabricated in deep submicron CMOS technologies, the complexity of the digital circuits and wiring in each cell is commensurate with pixel level processing.
The LFA-1, Mac-1 glycoprotein family and its deficiency in an inherited disease. (1985)

A family of functionally important, high-molecular-weight glycoproteins with identical beta subunits has recently been defined on leukocyte cell surfaces. Soon after these molecules and at least some of their functions had been defined with monoclonal antibodies, an inherited disease, LFA-1, Mac-1 deficiency, was discovered in humans. This deficiency has confirmed that this glycoprotein family is of central importance in leukocyte cell surface adhesion reactions.
In Vivo Consequences of Putative Active Site Mutations in Yeast DNA Polymerases α, ε, δ, and ζ (2001)

Several amino acids in the active site of family A DNA polymerases contribute to accurate DNA synthesis. For two of these residues, family B DNA polymerases have conserved tyrosine residues in regions II and III that are suggested to have similar functions. Here we replaced each tyrosine with alanine in the catalytic subunits of yeast DNA polymerases alpha, delta, epsilon, and zeta and examined the consequences in vivo. Strains with the tyrosine substitution in the conserved SL/MYPS/N motif in region II in Pol delta or Pol epsilon are inviable. Strains with same substitution in Rev3, the catalytic subunit of Pol zeta, are nearly UV immutable, suggesting severe loss of function. A strain with this substitution in Pol alpha (pol1-Y869A) is viable, but it exhibits slow growth, sensitivity to hydroxyurea, and a spontaneous mutator phenotype for frameshifts and base substitutions. The pol1-Y869A/pol1-Y869A diploid exhibits aberrant growth. Thus, this tyrosine is critical for the function of all four eukaryotic family B DNA polymerases. Strains with a tyrosine substitution in the conserved NS/VxYG motif in region III in Pol alpha, -delta, or -epsilon are viable and a strain with the homologous substitution in Rev3 is UV mutable. The Pol alpha mutant has no obvious phenotype. The Pol epsilon (pol2-Y831A) mutant is slightly sensitive to hydroxyurea and is a semidominant mutator for spontaneous base substitutions and frameshifts. The Pol delta mutant (pol3-Y708A) grows slowly, is sensitive to hydroxyurea and methyl methanesulfonate, and is a strong base substitution and frameshift mutator. The pol3-Y708A/pol3-Y708A diploid grows slowly and aberrantly. Mutation rates in the Pol alpha, -delta, and -epsilon mutant strains are increased in a locus-specific manner by inactivation of PMS1-dependent DNA mismatch repair, suggesting that the mutator effects are due to reduced fidelity of chromosomal DNA replication. This could result directly from relaxed base selectivity of the mutant polymerases due to the amino acid changes in the polymerase active site. In addition, the alanine substitutions may impair catalytic function to allow a different polymerase to compete at the replication fork. This is supported by the observation that the pol3-Y708A mutation is recessive and its mutator effect is partially suppressed by disruption of the REV3 gene.
The Lifetime Risk of Stroke (2006)

The LTR of stroke in middle-aged adults is 1 in 6 or more, which is equal to or greater than the LTR of AD. Women had a higher risk because of longer life expectancy. BP is a significant determinant of the LTR of stroke, and promotion of normal BP levels in the community might be expected to substantially reduce this risk.
Gene and alternative splicing annotation with AIR (2005)

Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts.
Evaluation of stereo vision obstacle detection algorithms for off-road autonomous navigation (2005)

Reliable detection of non-traversable hazards is a key requirement for off-road autonomous navigation. Under the Army Research Laboratory (ARL) Collaborative Technology Alliances (CTA) program, JPL has evaluated the performance of seven obstacle detection algorithms on a General Dynamics Robotic Systems (GDRS) surveyed obstacle course containing 21 obstacles. Stereo imagery was collected from a GDRS instrumented train traveling at 1m/s, and processed off-line with run-time passive perception software that includes: a positive obstacle detector, a negative obstacle detector, a non-traversable tree trunk detector, an excessive slope detector, a range density based obstacle detector, a multi-cue water detector, and a low-overhang detector. On the 170m course, 20 of the 21 obstacles were detected, there was complementary detection of several obstacles by multiple detectors, and there were no false obstacle detections. A detailed description of each obstacle detection algorithm and their performance on the surveyed obstacle course is presented in this paper.
Materials-Related Aspects of Thermochemical Water and Carbon Dioxide Splitting: A Review (2012)

Thermochemical multistep water- and CO2-splitting processes are promising options to face future energy problems. Particularly, the possible incorporation of solar power makes these processes sustainable and environmentally attractive since only water, CO2 and solar power are used; the concentrated solar energy is converted into storable and transportable fuels. One of the major barriers to technological success is the identification of suitable active materials like catalysts and redox materials exhibiting satisfactory durability, reactivity and efficiencies. Moreover, materials play an important role in the construction of key components and for the implementation in commercial solar plants. The most promising thermochemical water- and CO2-splitting processes are being described and discussed with respect to further development and future potential. The main materials-related challenges of those processes are being analyzed. Technical approaches and development progress in terms of solving them are addressed and assessed in this review.
PCR-aided DNasel footprinting of single copy gene sequences in permeabilized cells (1990)

Journal Article PCR-aided DNasel footprinting of single copy gene sequences in permeabilized cells Get access R.L. Tanguay, R.L. Tanguay Beckman Research Institute of the City of Hope, Department of BiologyDuarte, CA 91010, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar G.P. Pfeifer, G.P. Pfeifer Beckman Research Institute of the City of Hope, Department of BiologyDuarte, CA 91010, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar A.D. Riggs A.D. Riggs * Beckman Research Institute of the City of Hope, Department of BiologyDuarte, CA 91010, USA *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 19, 11 October 1990, Page 5902, https://doi.org/10.1093/nar/18.19.5902 Published: 11 October 1990 Article history Received: 31 August 1990 Published: 11 October 1990
A Controlled Subatmospheric Pressure Dressing Increases the Rate of Skin Graft Donor Site Reepithelialization (1998)

The ability to increase the rate of skin graft donor site reepithelialization significantly in a cost-effective manner has important implications for the patient undergoing major reconstructive procedures. In this study the effect of externally applied reduced pressure (the V.A.C.) on the rate of healing of donor site wounds was initially investigated using a porcine model (N = 4), then repeated on humans (N = 10). Split-thickness skin grafts were harvested from the backs of pigs using standard technique. Half of the donor sites were treated with subatmospheric pressure (125 mmHg) and half were treated with an OpSite dressing. Biopsies taken every 48 hours demonstrated that sites exposed to reduced pressure healed at a much faster rate than sites treated with a standard occlusive dressing. Similarly, donor sites in humans reepithelialized faster in 7 of 10 patients, the rate was the same in 2 of 10 patients, and OpSite was faster in 1 of 10 patients. We believe this technology has the potential to be a relatively simple and cost-efficient method for increasing the rate of donor site healing.
Cardiosphere-Derived Cells Improve Function in the Infarcted Rat Heart for at Least 16 Weeks – an MRI Study (2011)

CDCs were retained in the infarcted rat heart for 16 weeks and improved cardiac function.
Extension of the bi-epitaxial Josephson junction process to various substrates (1991)

We report an extension of the bi-epitaxial Josephson junction process that permits the use of a variety of substrate materials and allows junctions to be placed at any level of a multilayer structure. The new materials, SrTiO3, MgO, and CeO2, serve as a base layer, a seed layer, and a buffer layer, respectively, and replace Al2O3, MgO, and SrTiO3 in the original bi-epitaxial process. This new process offers much more flexibility in designing a circuit. Bi-epitaxial junctions made with the new set of materials show much improved electrical properties, especially at 77 K. We attribute the improved electrical characteristics to a better thermal expansion match between the substrate and the thin-film layers. Important junction properties such as critical currents and junction resistances are compared to other types of grain boundary junctions.
Combination of antiangiogenesis with chemotherapy for more effective cancer treatment (2008)

Angiogenesis is a hallmark of tumor development and metastasis and is now a validated target for cancer treatment. However, the survival benefits of antiangiogenic drugs have thus far been rather modest, stimulating interest in developing more effective ways to combine antiangiogenic drugs with established chemotherapies. This review discusses recent progress and emerging challenges in this field; interactions between antiangiogenic drugs and conventional chemotherapeutic agents are examined, and strategies for the optimization of combination therapies are discussed. Antiangiogenic drugs such as the anti-vascular endothelial growth factor antibody bevacizumab can induce a functional normalization of the tumor vasculature that is transient and can potentiate the activity of coadministered chemoradiotherapies. However, chronic angiogenesis inhibition typically reduces tumor uptake of coadministered chemotherapeutics, indicating a need to explore new approaches, including intermittent treatment schedules and provascular strategies to increase chemotherapeutic drug exposure. In cases where antiangiogenesis-induced tumor cell starvation augments the intrinsic cytotoxic effects of a conventional chemotherapeutic drug, combination therapy may increase antitumor activity despite a decrease in cytotoxic drug exposure. As new angiogenesis inhibitors enter the clinic, reliable surrogate markers are needed to monitor the progress of antiangiogenic therapies and to identify responsive patients. New targets for antiangiogenesis continue to be discovered, increasing the opportunities to interdict tumor angiogenesis and circumvent resistance mechanisms that may emerge with chronic use of these drugs.
Allelic loss in locally metastatic, multisampled prostate cancer. (1994)

In order to determine whether retention or loss of potential tumor suppressor loci that map to 8p, 10q, or 16q reflect genetic relationships among prostatic intraepithelial neoplasias (PINs), multicentric primary prostatic cancers, and regional lymph node metastases or are associated with the metastatic phenotype, we analyzed 19 cases of locally metastatic prostate carcinoma (stage D1) utilizing polymerase chain reaction techniques. In each case, tissue samples from metastatic tumor, the (dominant) primary tumor, and nonneoplastic prostatic tissue were examined. In selected cases, allelic loss in additional tumor foci, separate from the dominant tumor nodule, and areas of PIN were examined. Allelic loss of sequences on 8p, 10q, and 16q were observed in 20-29% of PINs, 18-42% of primary tumors, and 8-25% of metastatic tumors. Discrepancies in sequence dosage between histological components were most pronounced for 8p sequences, especially between the dominant tumor nodule and metastatic deposits in cases in which > or = 3 separate tumor foci/gland were identified. These results suggest that putative premalignant lesions, moderately or poorly differentiated, geographically separate primary tumor foci, and metastases within morphologically "complex" prostates (those with > or = 3 foci/gland) are likely to be more discordant for sequence dosage at 8p than those within "simpler" glands (< 3 foci/gland). Also, our results suggest that lymph node metastases may be genetically related to either the dominant or additional primary tumor foci in more complex prostates and that accumulation of genetic aberration may differ in primary and metastatic lesions.