gebhart/patrepeval huggingface dataset:
Microbial Synthesis and Properties of Poly3-hydroxybutyrateco- 4-hydroxybutyrate (1996)

Microbial synthesis of copolymers of [R]-3-hydroxybutyrate (3HB) and 4-hydroxybutyrate (4HB), P(3HB-co-4HB), by Alcaligenes eutrophus, Alcaligenes latus, and Comamonas acidovorans from various carbon sources has been studied. The copolyester compositions varied from 0 to 100 mol% 4HB, depending on the microorganism and the combination of carbon substrates supplied. The thermal and physical properties of compositions with 0–100 mol% 4HB were investigated. The copolyesters represented a wide variety of polymeric materials, from hard crystalline plastic to very elastic rubbers, depending on composition. The copolyester films with high 4HB fractions (64–100 mol% 4HB) exhibited the characteristics of a thermoplastic elastomer, and the tensile strength increased from 17 to 104 MPa as the 4HB fraction increased. The enzymatic degradation of P(3HB-co-4HB) films was studied in an aqueous solution of extracellular polyhydroxybutyrate (PHB) depolymerase from Alcaligenes faecalis or lipase from Rhizopus delemer. The erosion rate of P(3HB-co-4HB) films was strongly dependent on the copolymer composition. In addition, environmental degradation of P(3HB-co-4HB) films in sea water was investigated.
Kistler launch assist platform return burn control (1999)

The thrust vector control (TVC) design for the Return Burn segment of the Kistler K-l Launch Assist Platform (LAP) is presented. The design features a two mode controller that initially provides state dependent pre-ignition orientation of the rocket engine, and upon ignition, rapid. reorientation of the vehicle x-axis back towards the launch zone. Following this pitch reversal, the controller seamlessly .switches to a second mode that features integral control with acceleration direction estimation. This second mode provides the fine pointing required by guidance to ballistically loft the .LAP back to the launch zone. Control gains for the design are pre-computed prior to launch through an automated design procedure that searches over a broad family of gains. The automated design tool simultaneously applies frequency domain and time domain constraints, which results in a controller that achieves, stable response with adequate margin and minimal settling time.
Bulk acoustic wave coupled resonator filters (2003)

Coupled resonator filters (CRF) are a new form of bulk acoustic wave device that involves the vertical stacking of resonators. In that regard, the CRF can be thought of as a variation on the better known stacked crystal filter (SCF). However, the CRF is actually somewhat more analogous to the monolithic crystal filter (MCF) that was a mainstay in filters for low frequency applications. This paper reviews coupled resonator concepts, briefly including the MCF, describes the design and modeling of CRFs, and presents representative experimental results.
Pathogenesis‐related proteins of plants (1991)

Abstract Infection of plants with pathogens like viruses or fungi often leads to a response of the host ranging from very mild to very severe. A very mild response usually does not result in considerable changes in the patterns of gene expression of the plant. However, a hypersensitive reaction, e.g., in the case of infection of Samsun NN tobacco with tobacco mosaic virus, is accompanied by a massive increase in the amounts of a large number of different proteins. Among these induced proteins are members of a group of so‐called pathogenesis‐related (PR) proteins. Frequently, the hypersensitively reacting host becomes resistant to subsequent pathogenic attack. The correlation of this phenomenon of acquired resistance and the induced protein synthesis suggests a direct involvement of these proteins in the observed replication deficiency of the pathogen. This has initiated studies by several research groups toward a better understanding of the role of these PR‐proteins in the hypersensitively reacting plant. This review deals with the progress that has been made with the analysis of the host response and the function of the PR proteins in the acquired resistance.
Involvement of the ALL-1 gene in a solid tumor. (1995)

Translocations involving chromosome band 11q23, found in 5-10% of human acute leukemias, disrupt the ALL-1 gene. This gene is fused by reciprocal translocation with a variety of other genes in acute lymphoblastic and myelogenous leukemias, and it undergoes self-fusion in acute myeloid leukemias with normal karyotype or trisomy 11. Here we report an alteration of the ALL-1 gene in a gastric carcinoma cell line (Mgc80-3). Characterization of this rearrangement revealed a three-way complex translocation, involving chromosomes 1 and 11, resulting in a partial duplication of the ALL-1 gene. Sequencing of reverse transcription-PCR products and Northern blot analysis showed that only the partially duplicated ALL-1 gene was transcribed, producing an mRNA with exon 8 fused to exon 2. This report of ALL-1 gene rearrangement in a solid tumor suggests that ALL-1 plays a role in the pathogenesis of some solid malignancies. The absence of the normal transcript in this cell line, in association with the loss-of-heterozygosity studies on chromosome 11q23 seen in solid tumors, suggests that ALL-1 is involved in tumorigenesis by a loss-of-function mechanism.
Automatic extraction of biological information from scientific text: protein-protein interactions. (1999)

We describe the basic design of a system for automatic detection of protein-protein interactions extracted from scientific abstracts. By restricting the problem domain and imposing a number of strong assumptions which include pre-specified protein names and a limited set of verbs that represent actions, we show that it is possible to perform accurate information extraction. The performance of the system is evaluated with different cases of real-world interaction networks, including the Drosophila cell cycle control. The results obtained computationally are in good agreement with current biological knowledge and demonstrate the feasibility of developing a fully automated system able to describe networks of protein interactions with sufficient accuracy.
Purification, Properties, and Function of Flavokinase from Rat Intestinal Mucosa (1990)

Flavokinase (ATP:riboflavin 5'-phosphotransferase) [EC 2.7.1.26] was purified to apparent homogeneity from rat intestinal mucosa by fractionation with ammonium sulfate, gel filtration, and flavin affinity chromatography. The addition of ATP to the enzyme solution was necessary for its binding to the affinity gel. The apparent molecular weight of the enzyme was estimated to be 13,500 by gel filtration on Sephadex G-100 and by SDS-PAGE. The properties of the enzyme, including its flavin specificity, were studied. Three types of riboflavin analogues were used for the flavin specificity study; namely, ones modified at the ribityl group, and at positions 3 and 8 of the isoalloxazine ring. Of the analogues modified at the ribityl group or position 3 of the isoalloxazine ring, only 2'-deoxyriboflavin was phosphorylated and then only weakly. On the other hand, most analogues modified at position 8 of the isoalloxazine ring were good substrates for the kinase, an appropriate increase in the substituent volume at position 8 of the isoalloxazine ring resulting in an increase in the Vmax value. In a previous paper on the mechanism of intestinal absorption of riboflavin, we proposed that one of the specific processes for the absorption of riboflavin is phosphorylation by flavokinase [Kasai, S. et al. (1988) J. Nutr. Sci. Vitaminol. 34, 265-280]. The present results support this conclusion because analogues that were absorbed at low concentrations through a process specific for riboflavin in our previous study were phosphorylated effectively by the enzyme, whereas those that were absorbed solely through simple diffusion at all concentrations were not phosphorylated or only phosphorylated weakly. The properties of the flavokinases from intestinal mucosa and liver were compared.
Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors (2014)

The conversion of somatic cells into pluripotent stem cells via overexpression of reprogramming factors involves epigenetic remodeling. DNA methylation at a significant proportion of CpG sites in induced pluripotent stem cells (iPSCs) differs from that of embryonic stem cells (ESCs). Whether different sets of reprogramming factors influence the type and extent of aberrant DNA methylation in iPSCs differently remains unknown. In order to help resolve this critical question, we generated human iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and cMYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28), and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identified Yamanaka-iPSC (Y-iPSC)-specific and Thomson-iPSC (T-iPSC)-specific recurrent aberrations. Strikingly, not only were the genomic locations of the aberrations different but also their types: reprogramming with Yamanaka factors mainly resulted in failure to demethylate CpGs, whereas reprogramming with Thomson factors mainly resulted in failure to methylate CpGs. Differences in the level of transcripts encoding DNMT3b and TET3 between Y-iPSCs and T-iPSCs may contribute partially to the distinct types of aberrations. Finally, de novo aberrantly methylated genes in Y-iPSCs were enriched for NANOG targets that are also aberrantly methylated in some cancers. Our study thus reveals that the choice of reprogramming factors influences the amount, location, and class of DNA methylation aberrations in iPSCs. These findings may provide clues into how to produce human iPSCs with fewer DNA methylation abnormalities.
High Throughput Protein Nanocrystal Fractionation in a Microfluidic Sorter (2015)

Protein crystallography is transitioning into a new generation with the introduction of the X-ray free electron laser, which can be used to solve the structures of complex proteins via serial femtosecond crystallography. Sample characteristics play a critical role in successful implementation of this new technology, whereby a small, narrow protein crystal size distribution is desired to provide high quality diffraction data. To provide such a sample, we developed a microfluidic device that facilitates dielectrophoretic sorting of heterogeneous particle mixtures into various size fractions. The first generation device demonstrated great potential and success toward this endeavor; thus, in this work, we present a comprehensive optimization study to improve throughput and control over sorting outcomes. First, device geometry was designed considering a variety of criteria, and applied potentials were modeled to determine the scheme achieving the largest sorting efficiency for isolating nanoparticles from microparticles. Further, to investigate sorting efficiency within the nanoparticle regime, critical geometrical dimensions and input parameters were optimized to achieve high sorting efficiencies. Experiments revealed fractionation of nanobeads from microbeads in the optimized device with high sorting efficiencies, and protein crystals were sorted into submicrometer size fractions as desired for future serial femtosecond crystallography experiments.
The role of the ubiquitination-proteasome pathway in breast cancer: Applying drugs that affect the ubiquitin-proteasome pathway to the therapy of breast cancer (2002)

The ubiquitin-proteasome pathway is responsible for most eukaryotic intracellular protein degradation. This pathway has been validated as a target for antineoplastic therapy using both in vitro and preclinical models of human malignancies, and is influenced as part of the mechanism of action of certain chemotherapeutic agents. Drugs whose primary action involves modulation of ubiquitin-proteasome activity, most notably the proteasome inhibitor PS-341, are currently being evaluated in clinical trials, and have already been found to have significant antitumor efficacy. On the basis of the known mechanisms by which these agents work, and the available clinical data, they would seem to be well suited for the treatment of breast neoplasms. Such drugs, alone and especially in combination with current chemotherapeutics, may well represent important advances in the therapy of patients with breast cancer.
Hepatitis C virus and the threshold of natural killer cell inhibition† (2005)

Natural killer (NK) cells provide a central defense against viral infection by using inhibitory and activation receptors for major histocompatibility complex class I molecules as a means of controlling their activity. We show that genes encoding the inhibitory NK cell receptor KIR2DL3 and its human leukocyte antigen C group 1 (HLA-C1) ligand directly influence resolution of hepatitis C virus (HCV) infection. This effect was observed in Caucasians and African Americans with expected low infectious doses of HCV but not in those with high-dose exposure, in whom the innate immune response is likely overwhelmed. The data strongly suggest that inhibitory NK cell interactions are important in determining antiviral immunity and that diminished inhibitory responses confer protection against HCV.
T-Regulatory Cells: Key Players in Tumor Immune Escape and Angiogenesis (2012)

T-regulatory cells (Tregs) are found infiltrating tumors in a vast array of tumor types, and tumor-infiltrating Tregs are often associated with a poor clinical outcome. Tregs are potent immunosuppressive cells of the immune system that promote progression of cancer through their ability to limit antitumor immunity and promote angiogenesis. Here, we discuss the ways in which Tregs suppress the antitumor immune response and elaborate on our recent discovery that Tregs make significant direct contributions to tumor angiogenesis. Further, we highlight several current therapies aimed at eliminating Tregs in cancer patients. Given the multifaceted role of Tregs in cancer, a greater understanding of their functions will ultimately strengthen future therapies.
Hypertensive disorders in pregnancy: screening by biophysical and biochemical markers at 11–13 weeks (2010)

Combined biophysical and biochemical testing at 11-13 weeks could effectively identify women at high risk for subsequent development of hypertensive disorders in pregnancy.
Buoyant density of hepatitis C virus recovered from infected hosts: two different features in sucrose equilibrium density-gradient centrifugation related to degree of liver inflammation. (1994)

Hepatitis C virus is reported to have a low buoyant density in sucrose. To determine the density of hepatitis C virus in the circulation of infected hosts and its association with the degree of liver inflammation, we examined serum samples from 10 patients who were positive for both hepatitis C virus antibody (C100 antigen) antibody and serum hepatitis C virus RNA. After the serum was ultracentrifuged in sucrose density gradient (10% to 60%), the hepatitis C virus RNA titer in each collected fraction was quantified by means of competitive reverse transcription-polymerase chain reaction. In samples from five blood donors, the hepatitis C virus RNA titer had a single peak at fractions with densities of 1.08 to 1.11 gm/ml. In samples from five patients with ALT abnormalities, the titer had two peaks at fractions with 1.09 to 1.10 gm/ml and 1.22 to 1.25 gm/ml. After the selected samples were treated with detergents and ultracentrifuged, the titer in the 1.08 to 1.11 gm/ml fractions decreased and that in the 1.22 to 1.25 gm fractions increased. This result implied that the hepatitis C virus density changed with removal of the viral envelope by lipid solvents. Thus the buoyant density of hepatitis C virus in sucrose was 1.08 to 1.11 gm/ml for an intact virion and 1.22 to 1.25 gm/ml for what was presumed to be a nucleocapsid. These results demonstrated that HCV virion is a dominant form in the circulation of blood donors without ALT abnormalities. In patients with liver inflammation HCV particles with higher densities of 1.22 to 1.25 gm/ml coexist with virion in the circulation, which might be presumed nucleocapsids.
Hyaluronidase in the Prevention of Sclerotherapy-induced Extravasation Necrosis (1996)

In the event of extravasation with 23.4% sodium chloride, in the model studied, one can expect maximal protection with a dose of 75 units of hyaluronidase.
Biological Significance of Unwinding Capability of Nuclear Matrix-Associating DNAs (1992)

Matrix attachment regions (MARs) are thought to separate chromatin into topologically constrained loop domains. A MAR located 5' of the human beta-interferon gene becomes stably base-unpaired under superhelical strain, as do the MARs flanking the immunoglobulin heavy chain gene enhancer; in both cases a nucleation site exists for DNA unwinding. Concatemerized oligonucleotides containing the unwinding nucleation site exhibited a strong affinity for the nuclear scaffold and augmented SV40 promoter activity in stable transformants. Mutated concatemerized oligonucleotides resisted unwinding, showed weak affinity for the nuclear scaffold, and did not enhance promoter activity. These results suggest that the DNA feature capable of relieving superhelical strain is important for MAR functions.
Macrophage inflammatory proteins 1 and 2: members of a novel superfamily of cytokines (1989)

A number of studies of inflammation and of cell growth and transformation have recently converged by defining two related families of cytokines. The first, represented by macrophage inflammatory protein 1, is composed of several gene products that have been identified in activated T cells, macrophages, and fibroblasts. The biological activities of this family are still being characterized but so far include effects on neutrophils, monocytes, and hematopoietic cells. The second, represented by macrophage inflammatory protein 2, includes platelet products such as platelet factor 4 and beta-thromboglobulin as well as several other recently described gene products that have effects on a number of cell types including neutrophils, fibroblasts, hematopoietic cells, and melanoma cells. The two families are structurally related and may have evolved from a common ancestral gene that duplicated and then diverged. Their differential control and expression in a wide variety of cell types suggests that they may have multiple functions in regulating inflammation and cell growth.
A response to Cheriton and Skeen's criticism of causal and totally ordered communication (1994)

In a paper to be presented at the 1993 ACM Symposium on Operating Systems Principles, Cheriton and Skeen offer their understanding of causal and total ordering as a communication property. In this brief rebuttal. I present some responses to their criticism, and also explain why I find their discussion of causal and total communication ordering to be narrow and incomplete.
New Proof-of-Concept in Viral Inactivation: Virucidal Efficacy of 405 nm Light Against Feline Calicivirus as a Model for Norovirus Decontamination (2016)

The requirement for novel decontamination technologies for use in hospitals is ever present. One such system uses 405 nm visible light to inactivate microorganisms via ROS-generated oxidative damage. Although effective for bacterial and fungal inactivation, little is known about the virucidal effects of 405 nm light. Norovirus (NoV) gastroenteritis outbreaks often occur in the clinical setting, and this study was designed to investigate potential inactivation effects of 405 nm light on the NoV surrogate, feline calicivirus (FCV). FCV was exposed to 405 nm light whilst suspended in minimal and organically-rich media to establish the virucidal efficacy and the effect biologically-relevant material may play in viral susceptibility. Antiviral activity was successfully demonstrated with a 4 Log<sub>10</sub> (99.99%) reduction in infectivity when suspended in minimal media evident after a dose of 2.8 kJ cm<sup>-2</sup>. FCV exposed in artificial faeces, artificial saliva, blood plasma and other organically rich media exhibited an equivalent level of inactivation using between 50-85% less dose of the light, indicating enhanced inactivation when the virus is present in organically-rich biologically-relevant media. Further research in this area could aid in the development of 405 nm light technology for effective NoV decontamination within the hospital environment.
High-density lipoprotein metabolism and progression of atherosclerosis: new insights from the HDL Atherosclerosis Treatment Study (2004)

The diverse action of high-density lipoprotein observed could be explained by the heterogeneity of high-density lipoprotein particles with completely different composition and properties. The modification of specific high-density lipoprotein subpopulations to reach the maximum atheroprotective effects under various pathologic conditions bears great potential in lipid research.
PulseCam: High-resolution blood perfusion imaging using a camera and a pulse oximeter (2016)

Measuring blood perfusion is important in medical care as an indicator of injury and disease. However, currently available devices to measure blood perfusion like laser Doppler flowmetry are bulky, expensive, and cumbersome to use. An alternative low-cost and portable camera-based blood perfusion measurement system has recently been proposed, but such camera-only system produces noisy low-resolution blood perfusion maps. In this paper, we propose a new multi-sensor modality, named PulseCam, for measuring blood perfusion by combining a traditional pulse oximeter with a video camera in a unique way to provide low noise and high-resolution blood perfusion maps. Our proposed multi-sensor modality improves per pixel signal to noise ratio of measured perfusion map by up to 3 dB and improves the spatial resolution by 2 - 3 times compared to best known camera-only methods. Blood perfusion measured in the palm using our PulseCam setup during a post-occlusive reactive hyperemia (PORH) test replicates standard PORH response curve measured using laser Doppler flowmetry device but with much lower cost and a portable setup making it suitable for further development as a clinical device.
Rapid induction of orthotopic hepatocellular carcinoma in immune-competent rats by non-invasive ultrasound-guided cells implantation (2010)

Ultrasound-guided implantation of Novikoff hepatoma cells is an effective means of establishing orthotopic hepatocellular carcinoma in Sprague-Dawley rats. Short-term and low-dose epirubicin chemotherapy had perturbed tumor progression by inducing apoptosis and neovascularization blockade.
Clinically relevant oral cancer model for serum proteomic eavesdropping on the tumour microenvironment. (2006)

Both RAG2/gamma(c) KO and SCID mouse are able to reliably engraft human oral cancer. Engraftment of normal oral tissue was less reliable. This is the first in vivo model allowing identification of proteins released from the tumour microenvironment.