gebhart/patrepeval huggingface dataset:
Objective-type dark-field illumination for scattering from microbeads (2001)

We introduce a method for detecting and tracking small particles in a solution near a surface. The method is based on blocking the backreflected illumination beam in an objective-type total internal reflection microscope, leaving unhindered the light scattered by the particles and resulting in dark-field illumination. Using this method, we tracked the motion of 60-nm polystyrene beads with a signal-to-noise ratio of 6 and detected 20-nm gold particles with a signal-to-noise ratio of 5. We illustrate the method's use by following the Brownian motion of small beads attached by short DNA tethers to a substrate.
The sequence and reactive site of ecotin. A general inhibitor of pancreatic serine proteases from Escherichia coli. (1991)

Ecotin, a serine protease inhibitor found in the periplasm of Escherichia coli, is unusual in its ability to inhibit chymotrypsin, trypsin, and elastase. To address the structural basis of its broad specificity, the gene for ecotin has been cloned and its sequence determined. A promoter of the 17-base pair spacing class was identified, and the probable transcriptional start site lies 18 base pairs upstream from a ribosome binding locus. The gene is followed by a series of conserved repetitive extragenic palindromic sequences. Ecotin has a signal peptide of 20 amino acids which confirms its periplasmic localization. Sequence analyses by Edman degradation and mass spectrometry confirmed 71% of the deduced protein sequence of calculated monomeric molecular mass 16,096 Da. Comparisons of the primary structure for the 142-amino acid protein with the major classes of serine protease inhibitors suggest that ecotin is a novel inhibitor. The reactive site of ecotin was determined to be Met84 for its complexes with chymotrypsin, trypsin, and elastase. The scissile Met84-Met85 bond lies within a disulfide-bonded protein segment similar to other classes of inhibitors.
Targeting BCL1 lymphoma with anti‐idiotype antibodies: Biodistribution kinetics of directly labeled antibodies and bispecific antibody‐targeted bivalent haptens (1997)

The mouse BCL1 lymphoma model has been used for evaluating immunotherapy with anti-idiotype (anti-Id) antibodies, including Id immunisation, IgG therapy and bispecific (Bs) antibody-targeted cytotoxicity. Here, we provide quantitative data on the targeting of small (25 ± 12 mg) intrasplenic BCL1 tumours, using anti-Id IgG, F(ab')2 and anti-Id × anti-hapten BsF(ab')2 covalently labelled with 125iodine, as well as noncovalent complexes of BsF(ab')2 and 125 I-labelled bivalent hapten. The results are the following: 1) up to 115% of the injected dose per gram (% ID/g) of spleen can be localised in the first hour, corresponding to approximately 600% ID/g of tumour; 2) localisation is specific for cell-surface Id; 3) optimal doses can overcome circulating Id; 4) circulating Id markedly increases the catabolism of IgG, thus impairing tumour localisation; 5) bivalent reagents are internalised by the target cells; 6) iodine covalently bound to bivalent antibodies [IgG, F(ab')2]; is rapidly (T1/2: 6-9 hr) released from the tumour; in contrast, the bivalent hapten is retained for a longer time (T1/2: 25 hr); and 7) in the absence of bivalent hapten, the monovalent BsF(ab')2 is not rapidly internalised and dissociates from tumour cell-surface Id. Our results suggest that monovalent anti-Id, lacking Fc, can efficiently be targeted to the BCL1 tumour surface. For radioimmunotherapy, the intracellular targeting of catabolism-resistant 125I-labelled bivalent hapten provides optimal tissue selectivity. Int. J. Cancer 71: 1000-1009, 1997. © 1997 Wiley-Liss Inc.
Advanced Turbine Systems annual program review (1995)

Integrated High Performance Turbine Engine Technology (IHPTET) is a joint Air Force, Navy, Army, NASA, ARPA, and industry program focused on developing turbine engine technologies, with the goal of doubling propulsion capability by around the turn-of-the-century, and thus providing smaller, lighter, more durable, more affordable turbine engines in the future. IHPTET`s technology development plan for increasing propulsion capability with respect to time is divided into three phases. This phased approach reduces the technological risk of taking one giant leap, and also reduces the {open_quotes}political{close_quotes} risk of not delivering a product for an extended period of time, in that the phasing allows continuous transfer of IHPTET technologies to our warfighters and continuous transfer to the commercial sector (dual-use). The IHPTET program addresses the three major classes of engines: turbofan/turbojet, turboshaft/turboprop, and expendables.
Bioseparations: downstream processing for biotechnology (1988)

This book offers an introduction to the separation and purification of biochemicals. Bridges two scientific cultures, providing an introduction to bioseparations. The authors supplement the ideas by worked examples. Discusses removal of insolubles, product isolation, purification and polishing.
Molecular cloning of adeno-associated virus variant genomes and generation of infectious virus by recombination in mammalian cells. (1984)

Continued passage of the human parvovirus, adeno-associated virus (AAV), at high multiplicity of infection in human cells results in the accumulation of AAV particles containing variant genomes. We have analyzed the structure of individual variant AAV genomes by molecular cloning in the Escherichia coli plasmid, pBR328. Each of the AAV inserts in six individual recombinant plasmids contained a single internal deletion but in contrast to a previous model, the locations of the deletions were nonrandom. The molecular cloning protocol also generated recombinant plasmids containing the entire AAV2 DNA sequence which yielded infectious AAV particles when transfected into human 293 cells in the presence of helper adenovirus using a DEAE-transfection procedure. Infectious AAV genomes were also generated by recombination when cells were jointly transfected with a mixture of plasmids containing two different mutant AAV genomes. The efficiency of this recombination appear to be influenced by the degree of homology between the mutant AAV genomes.
Viral Escape from Dominant Simian Immunodeficiency Virus Epitope-Specific Cytotoxic T Lymphocytes in DNA-Vaccinated Rhesus Monkeys (2003)

Virus-specific cytotoxic T lymphocytes (CTL) are critical for control of human immunodeficiency virus type 1 replication. However, viral escape from CTL recognition can undermine this immune control. Here we demonstrate the high frequency and pattern of viral escape from dominant epitope-specific CTL in SIV gag DNA-vaccinated rhesus monkeys following a heterologous simian immunodeficiency virus (SIV) challenge. DNA-vaccinated monkeys exhibited initial effective control of the SIV challenge, but this early control was lost by serial breakthroughs of viral replication over a 3-year follow-up period. Increases in plasma viral RNA correlated temporally with declines of dominant SIV epitope-specific CD8(+) T-lymphocyte responses and the emergence of viral mutations that escaped recognition by dominant epitope-specific CTL. Viral escape from CTL occurred in a total of seven of nine vaccinated and control monkeys, including three animals that initially controlled viral replication to undetectable levels of plasma viral RNA. These data suggest that CTL exert selective pressure on viral replication and that viral escape from CTL may be a limitation of CTL-based AIDS vaccine strategies.
Size-induced transition-temperature reduction in nanoparticles of ZnS (1999)

X-ray-diffraction studies of nanometer-sized particles of zinc sulfide show a significant reduction in the zinc-blende-to-wurtzite phase transition temperature, as compared to the bulk value. Five nanoparticle samples were annealed in vacuum at temperatures increasing from room temperature (23 \ifmmode^\circ\else\textdegree\fi{}C) to 500 \ifmmode^\circ\else\textdegree\fi{}C. Post-anneal analyses revealed an increase of crystallite size, accompanied by a partial transformation from the cubic, zinc-blende structure to the hexagonal, wurtzite structure at temperatures as low as 400 \ifmmode^\circ\else\textdegree\fi{}C. This is significantly less than accepted bulk transition temperature of 1020 \ifmmode^\circ\else\textdegree\fi{}C. The particles also show some lattice distortion with decreasing particle size and there is a monotonic reduction in the specific volume of about 2.3% as the particle size decreases from about 240 to about 30 \AA{}.
Characterization of an Antisense Transcript Spanning the UL81-82 Locus of Human Cytomegalovirus (2005)

In this study we present the characterization of a novel transcript, UL81-82ast, UL81-82 antisense transcript, and its protein product. The transcript was initially found in a cDNA library of monocytes from a seropositive donor. mRNA was obtained from monocytes isolated from a healthy donor with a high antibody titer against human cytomegalovirus (HCMV). The mRNAs were cloned into a lambda phage-derived vector to create the cDNA library. Using PCR, UL81-82ast was amplified from the library. The library was tested for the presence of numerous HCMV genes. Neither structural genes nor immediate-early genes were found. UL81-82ast was detected in five bone marrow samples from healthy antibody-positive donors. This same transcript was also found in in vitro-infected human fibroblasts early after infection but disappears at the same time that UL82 transcription begins. Not only was the transcript amplified using reverse transcription-PCR and sequenced but its protein product (UL82as protein) was detected by both Western blot and immunofluorescence. Phylogenetic studies using UL82as protein were conducted, showing a high degree of conservation in clinical isolates, laboratory strains of HCMV, and even in chimpanzee CMV. The transcript could be involved in the posttranscriptional regulation of the UL82 gene, affecting its mRNA stability or translation. Since the UL82 product, pp71, functions as an immediate-early transactivator, its posttranscriptional control could have some effect over latency reactivation and lytic replication.
Contactless dielectrophoretic spectroscopy: Examination of the dielectric properties of cells found in blood (2011)

Abstract The use of non‐invasive methods to detect and enrich circulating tumor cells (CTCs) independent of their genotype is critical for early diagnostic and treatment purposes. The key to using CTCs as predictive clinical biomarkers is their separation and enrichment. This work presents the use of a contactless dielectrophoresis (cDEP) device to investigate the frequency response of cells and calculate their area‐specific membrane capacitance. This is the first demonstration of a cDEP device which is capable of operating between 10 and 100 kHz. Positive and negative dielectrophoretic responses were observed in red blood cells, macrophages, breast cancer, and leukemia cells. The area‐specific membrane capacitances of MDA‐MB231, THP‐1 and PC1 cells were determined to be 0.01518 ± 0.0013, 0.01719 ± 0.0020, 0.01275 ± 0.0018 (F/m 2 ), respectively. By first establishing the dielectrophoretic responses of cancerous cells within this cDEP device, conditions to detect and enrich tumor cells from mixtures with non‐transformed cells can be determined providing further information to develop methods to isolate these rare cells.
[Rapid identification of mycobacteria by combined method of polymerase chain reaction and the gen-probe DNA hybridization system]. (1994)

We developed the rapid detection and identification method of mycobacteria, involving amplification of mycobacterial 16S rRNA gene by nested PCR and identification of M. tuberculosis complex or M. avium-intracellulare complex (MAC) by hybridization protection assay (HPA) using the acridinium-ester (AE) labeled DNA probe. The specificity of the nested PCR combined with DNA probe test was excellent in terms of detection of mycobacterial organisms and identification of M. tuberculosis or MAC. The detection limits of the present method were 10 fg DNA for M. tuberculosis, and 100 fg DNA for MAC, respectively. We further investigated on the optimum temperature for hybridization in HPA with AE labeled DNA probe because there was the difference in the mode of DNA-RNA hybridization from that of DNA-DNA hybridization. In our method, the optimum temperature of hybridization was estimated as 55 +/- 1 degrees C. In preliminary experiments on two clinical cases, we practically detected and identified M. tuberculosis and MAC in clinical specimens, such as sputa, by using this newly devised method. We concluded that this method is useful for rapid detection and identification of M. tuberculosis and MAC in clinical specimens.
Hepatoprotective and Antioxidant Potential of Organic and Conventional Grape Juices in Rats Fed a High-Fat Diet (2014)

The objective of this study was to investigate the antioxidant and hepatoprotective effect of the chronic use of conventional (CGJ) or organic (OGJ) grape juice from the Bordeaux variety grape on oxidative stress and cytoarchitecture in the liver of rats supplemented with a high-fat diet (HFD) for three months. The results demonstrated that HFD induced an increase in thiobarbituric acid-reactive substances (TBARS), catalase (CAT) activity and 2',7'-dihydrodichlorofluorescein (DCFH) oxidation and a decrease in sulfhydryl content and superoxide dismutase (SOD) and glutathione peroxidase (GPx) activities. HFD also induced hepatocellular degeneration and steatosis. These alterations were prevented by CGJ and OGJ, where OGJ was more effective. Therefore, it was concluded that HFD induced oxidative stress and liver damage and that the chronic use of grape juice was able to prevent these alterations.
The Pathogenesis of Edema in Diabetic Maculopathy (1999)

Diabetic maculopathy is characterized by the accumulation of extracellular fluid in Henle's layer and the inner nuclear layer of the retina. The localization of the edema is likely to be due, in part, to the relative barrier properties of the inner and outer plexiform layers. The origin of the extracellular fluid is from the intravascular compartment. Although changes to retinal blood flow may partly explain the extravasation of fluid, the most important mechanism is breakdown of the blood retinal barriers. Both the inner blood retinal barrier formed by the retinal capillary endothelial cell tight junctions and the outer barrier formed by the retinal pigment epithelial cell tight junctions can be affected. The mechanism of breakdown of the blood retinal barriers is likely to be changes to the tight junction proteins including occludin and ZO-1. The biochemical messenger inducing these changes may be vascular endothelial growth factor. The origin of this or other cofactors may be the retinal glial cells. The underlying biochemical stimulus to the production of vascular endothelial growth factor is chronic hyperglycaemia, but it is uncertain by what pathway this is effected.
A novel cytarabine crystalline lipid prodrug: hexadecyloxypropyl cytarabine 3',5'-cyclic monophosphate for proliferative vitreoretinopathy. (2012)

The cyclic monophosphate prodrug, HDP-cP-Ara-C, was found to have physiochemical properties better suited for sustained delivery of cytarabine to posterior segments of the eye. These properties included limited aqueous solubility, in vitro antiproliferative activity, and good tolerability after injection into rabbit eyes.
Cytokine-independent growth and clonal expansion of a primary human CD8+ T-cell clone following retroviral transduction with the IL-15 gene (2007)

Malignancies arising from retrovirally transduced hematopoietic stem cells have been reported in animal models and human gene therapy trials. Whether mature lymphocytes are susceptible to insertional mutagenesis is unknown. We have characterized a primary human CD8(+) T-cell clone, which exhibited logarithmic ex vivo growth in the absence of exogenous cytokine support for more than 1 year after transduction with a murine leukemia virus-based vector encoding the T-cell growth factor IL-15. Phenotypically, the clone was CD28(-), CD45RA(-), CD45RO(+), and CD62L(-), a profile consistent with effector memory T lymphocytes. After gene transfer with tumor-antigen-specific T-cell receptors, the clone secreted IFN-gamma upon encountering tumor targets, providing further evidence that they derived from mature lymphocytes. Gene-expression analyses revealed no evidence of insertional activation of genes flanking the retroviral insertion sites. The clone exhibited constitutive telomerase activity, and the presence of autocrine loop was suggested by impaired cell proliferation following knockdown of IL-15R alpha expression. The generation of this cell line suggests that nonphysiologic expression of IL-15 can result in the long-term in vitro growth of mature human T lymphocytes. The cytokine-independent growth of this line was a rare event that has not been observed in other IL-15 vector transduction experiments or with any other integrating vector system. It does not appear that the retroviral vector integration sites played a role in the continuous growth of this cell clone, but this remains under investigation.
Neuronal And Axonal Injury During Functional Electrical Stimulation; A Review Of The Possible Mechanisms (2005)

The mechanisms by which neuronal or axonal injury may occur in the brain or in peripheral nerve during electrical stimulation are discussed in this review. The likely contributions of electrochemical processes at the electrode-tissue interface, and of factors related to the passage of the stimulus current, and to the induced neuronal activity itself, are considered. Evidence is cited linking Morphologic changes in these cells to the excitation of large numbers of neurons or axons, perhaps through the intermediary of inducing deleterious changes in the composition of the extracellular fluid.
Three-dimensional microfluidic devices fabricated in layered paper and tape (2008)

This article describes a method for fabricating 3D microfluidic devices by stacking layers of patterned paper and double-sided adhesive tape. Paper-based 3D microfluidic devices have capabilities in microfluidics that are difficult to achieve using conventional open-channel microsystems made from glass or polymers. In particular, 3D paper-based devices wick fluids and distribute microliter volumes of samples from single inlet points into arrays of detection zones (with numbers up to thousands). This capability makes it possible to carry out a range of new analytical protocols simply and inexpensively (all on a piece of paper) without external pumps. We demonstrate a prototype 3D device that tests 4 different samples for up to 4 different analytes and displays the results of the assays in a side-by-side configuration for easy comparison. Three-dimensional paper-based microfluidic devices are especially appropriate for use in distributed healthcare in the developing world and in environmental monitoring and water analysis.
Vaccines in the treatment of cancer (1995)

The development of vaccines for treating cancer is discussed. The central hypothesis behind active specific immunotherapy for cancer is that tumor cells express unique antigens that tell the immune system that something about these cells is foreign. A vaccine is a way of delivering an antigen to the immune system such that immune cells recognize the antigen as foreign and destroy any cells bearing that antigen. Early trials of vaccines for treating cancer were limited by technical problems related to poor knowledge of the immune system. Recent research has focused on expression on the surfaces of antigen-presenting cells of antigenic peptides bound to major histocompatibility complex (MHC) molecules, peptide recognition by cytotoxic T cells, and the requirement for a second signal, such as the costimulatory molecule B7, for T-cell activation. Antigenic peptides constitute the "keys" that open the "locks" of T cells; the problem is that researchers have difficulty choosing the right keys from among the myriad available. Administering an adjuvant enhances the immune response by making the antigen more recognizable as foreign. Vaccine preparation techniques include peptide pulsing (a method for bosting cell-surface expression of the antigenic peptide-MHC combinations), intramuscular injections of DNA plasmids encoding the desired antigen, and gene insertion into vaccinia virus by recombinant DNA technology. Cancer vaccines may be administered by scarification, by subcutaneous and intramuscular injection, and intranasally. Clinical trials of cancer vaccines continue to encounter problems because of the many variables in administration routes, dosages, patient populations, and methods for evaluating responses. There have been some promising results but also many treatment failures. Antigen targets in trials today include normal antigens that have a limited normal-tissue distribution or expression (e.g., carcinoembryonic antigen), viral proteins (e.g., E6 protein of human papillomavirus), and mutated oncogenes. Toxicities have been mild. Better understanding of the immune system and better technology have led to advances in the development of vaccines for treating cancer, but there is still much progress to achieve.
Harmonic distortion reduction in multi-level PWM modulators for audio power amplifiers (2003)

This paper presents a new methodology to reduce harmonic distortion in multilevel PWM modulators with uniform sampling. The proposed approach generates pulses with widths longer than a pre-determinate value. This ensures the needed time for the calculations and helps to reduce audio distortion introduced by the nonzero rise and fall time of the switches. Therefore the methodology allows smaller harmonic distortions than the inherent of uniform sampled PWM signals. Simulation results are presented.
The type I fatty acid and polyketide synthases: a tale of two megasynthases (2007)

This review chronicles the synergistic growth of the fields of fatty acid and polyketide synthesis over the last century. In both animal fatty acid synthases and modular polyketide synthases, similar catalytic elements are covalently linked in the same order in megasynthases. Whereas in fatty acid synthases the basic elements of the design remain immutable, guaranteeing the faithful production of saturated fatty acids, in the modular polyketide synthases, the potential of the basic design has been exploited to the full for the elaboration of a wide range of secondary metabolites of extraordinary structural diversity.
The design of history mechanisms and their use in collaborative educational simulations (1999)

Reviewing past events has been useful in many domains. Videotapes and flight data recorders provide invaluable technological help to sports coaches or aviation engineers. Similarly, providing learners with a readable recording of their actions may help them monitor their behavior, reflect on their progress, and experiment with revisions of their experiences. It may also facilitate active collaboration among dispersed learning communities. Learning histories can help students and professionals make more effective use of digital library searching, word processing tasks, computer-assisted design tools, electronic performance support systems, and web navigation.This paper describes the design space and discusses the challenges of implementing learning histories. It presents guidelines for creating effective implementations, and the design tradeoffs between sparse and dense history records. The paper also presents a first implementation of learning histories for a simulation-based engineering learning environment called SimPLE (Simulated Processes in a Learning Environment) for the case of a semiconductor fabrication module, and reports on early user evaluation of learning histories implemented within SimPLE.