gebhart/patrepeval huggingface dataset:
Dendritic Cells as Antigen Presenting Cellsin Vivo (1990)

The biology of antigen presenting cells (APC) traditionally is studied in tissue culture systems using T cells that have been expanded beforehand by stimulation with antigen. Here we consider the distinctive roles of dendritic cells for sensitizing or priming T cells both in vitro and in vivo. Several functions of dendritic cells have been identified in tissue culture that are pertinent to T cell sensitization. These include the ability to a) capture and retain foreign antigens in an immunogenic form, b) bind antigen-specific resting lymphocytes, and c) activate T cells to produce lymphokines and undergo long term clonal growth. Dendritic cells have several properties in vivo that also would contribute to APC function. These are a) their widespread tissue distribution permitting access to antigens in most organs, b) the capacity to home via the blood stream and afferent lymph to the T-dependent areas of spleen and lymph node, and c) the ability to capture antigen in antigen-pulsed animals. Dendritic cells bearing antigen have been administered in situ to initiate responses like contact sensitivity, graft rejection, and antibody formation. A most striking recent example is that, when dendritic cells are pulsed with protein antigens in vitro and administered to immunologically naive mice, there is direct priming of antigen-specific T cells that are restricted to the MHC of the injected APC.
Biological liquid crystal elastomers (2002)

Liquid crystal elastomers (LCEs) have recently been described as a new class of matter. Here we review the evidence for the novel conclusion that the fibrillar collagens and the dragline silks of orb web spiders belong to this remarkable class of materials. Unlike conventional rubbers, LCEs are ordered, rather than disordered, at rest. The identification of these biopolymers as LCEs may have a predictive value. It may explain how collagens and spider dragline silks are assembled. It may provide a detailed explanation for their mechanical properties, accounting for the variation between different members of the collagen family and between the draglines in different spider species. It may provide a basis for the design of biomimetic collagen and dragline silk analogues by genetic engineering, peptide- or classical polymer synthesis. Biological LCEs may exhibit a range of exotic properties already identified in other members of this remarkable class of materials. In this paper, the possibility that other transversely banded fibrillar proteins are also LCEs is discussed.
Patterns of Colorectal Cancer Care in the United States: 1990–2010 (2015)

Our findings demonstrate increased adoption of chemotherapy and radiation therapy for colon and rectal cancer patients and differences in therapy by age, comorbidity, and diagnosis year. Increased receipt of these therapies in the community may further reduce CRC mortality.
A survey of base sequences, disjoint complementary sequences and OD(4t; t, t, t, t) (1989)

We survey the existence of base sequences, that is four sequences of lengths m + p, m + p, m, m, p odd with zero auto correlation function which can be used with Yang numbers and four disjoint complementary sequences (and matrices) with zero non-periodic (periodic) autocorrelation function to form longer sequences. We survey their application to make orthogonal designs OD(4t; t, t, t, t). We give the method of construction of OD(4t; t, t, t, t) for t = 1,3,..., 41, 45,...,65, 67, 69, 75, 77, 81, 85, 87, 91, 93, 95, 99, 101, 105, 111, 115, 117, 119, 123, 125, 129, 133, 141,..., 147, 153, 155, 159, 161, 165, 169, 171, 175, 177, 183, 185, 189, 195, 201, 203, 205, 209.
FAXING—150 YEARS OLD! (1994)

Although the office fax machine has only become popular in the past decade, this year sees its 150th anniversary. It was patented on 27 May 1843, 30 years even before the telephone. But whereas the telephone quickly established itself as an essential tool for business, commercial success has been much longer coming for a machine that could transmit pictures and documents, within seconds, from one office to another. The inventor of the idea was Alexander Bain, who was born in 1810. Bain, a Scotsman from a remote croft in Caithness, is reputed to have performed his early experiments using cattle jawbones for hinges, heather for springs and metal plates buried in the earth for batteries. He was apprenticed to a clockmaker in Wick and invented the first electric clock, which used electromagnetism to pull a pendulum from side to side. He then moved to London and patented his fax machine.
Optical measurement of cycle-dependent cell growth (2011)

Determining the growth patterns of single cells offers answers to some of the most elusive questions in contemporary cell biology: how cell growth is regulated and how cell size distributions are maintained. For example, a linear growth in time implies that there is no regulation required to maintain homeostasis; an exponential pattern indicates the opposite. Recently, there has been great effort to measure single cells using microelectromechanical systems technology, and several important questions have been explored. However, a unified, easy-to-use methodology to measure the growth rate of individual adherent cells of various sizes has been lacking. Here we demonstrate that a newly developed optical interferometric technique, known as spatial light interference microscopy, can measure the cell dry mass of many individual adherent cells in various conditions, over spatial scales from micrometers to millimeters, temporal scales ranging from seconds to days, and cell types ranging from bacteria to mammalian cells. We found evidence of exponential growth in Escherichia coli, which agrees very well with other recent reports. Perhaps most importantly, combining spatial light interference microscopy with fluorescence imaging provides a unique method for studying cell cycle-dependent growth. Thus, by using a fluorescent reporter for the S phase, we measured single cell growth over each phase of the cell cycle in human osteosarcoma U2OS cells and found that the G2 phase exhibits the highest growth rate, which is mass-dependent and can be approximated by an exponential.
Counting and Sizing of Submicron Particles by the Resistive Pulse Technique (1970)

The resistive (Coulter) method of counting and sizing particles in a conducting fluid has been extended to polystyrene spheres 900 Å in diameter, with a present detection limit near 600 Å, through the use of individual submicron pores etched in irradiated plastic sheet. The use of a nonionic surfactant and ultrasonic cleaning effectively relieves the problem of plugging. The particles may be driven through the pore by the electric field, without the use of pressure, to yield the vector sum of the electrophoretic and electro-osmotic velocities. A new theory, yielding an upper limit to the resistive pulse on passage of a sphere, agrees well with data for spheres with diameters d&amp;lt;0.4D, where D is the pore diameter, and complements a previous theory that gives a lower limit, valid for d&amp;gt;0.9D. We estimate that a detection limit near 250 Å will be attainable with the further development of current techniques.
d -β-Hydroxybutyrate protects neurons in models of Alzheimer's and Parkinson's disease (2000)

The heroin analogue 1-methyl-4-phenylpyridinium, MPP(+), both in vitro and in vivo, produces death of dopaminergic substantia nigral cells by inhibiting the mitochondrial NADH dehydrogenase multienzyme complex, producing a syndrome indistinguishable from Parkinson's disease. Similarly, a fragment of amyloid protein, Abeta(1-42), is lethal to hippocampal cells, producing recent memory deficits characteristic of Alzheimer's disease. Here we show that addition of 4 mM d-beta-hydroxybutyrate protected cultured mesencephalic neurons from MPP(+) toxicity and hippocampal neurons from Abeta(1-42) toxicity. Our previous work in heart showed that ketone bodies, normal metabolites, can correct defects in mitochondrial energy generation. The ability of ketone bodies to protect neurons in culture suggests that defects in mitochondrial energy generation contribute to the pathophysiology of both brain diseases. These findings further suggest that ketone bodies may play a therapeutic role in these most common forms of human neurodegeneration.
Fatty Acid Transduction of Nitric Oxide Signaling (2005)

Mass spectrometric analysis of human plasma and urine revealed abundant nitrated derivatives of all principal unsaturated fatty acids. Nitrated palmitoleic, oleic, linoleic, linolenic, arachidonic and eicosapentaenoic acids were detected in concert with their nitrohydroxy derivatives. Two nitroalkene derivatives of the most prevalent fatty acid, oleic acid, were synthesized (9- and 10-nitro-9-cis-octadecenoic acid; OA-NO2), structurally characterized and determined to be identical to OA-NO2 found in plasma, red cells, and urine of healthy humans. These regioisomers of OA-NO2 were quantified in clinical samples using 13C isotope dilution. Plasma free and esterified OA-NO2 concentrations were 619 +/- 52 and 302 +/- 369 nm, respectively, and packed red blood cell free and esterified OA-NO2 was 59 +/- 11 and 155 +/- 65 nm. The OA-NO2 concentration of blood is approximately 50% greater than that of nitrated linoleic acid, with the combined free and esterified blood levels of these two fatty acid derivatives exceeding 1 microm. OA-NO2 is a potent ligand for peroxisome proliferator activated receptors at physiological concentrations. CV-1 cells co-transfected with the luciferase gene under peroxisome proliferator-activated receptor (PPAR) response element regulation, in concert with PPARgamma, PPARalpha, or PPARdelta expression plasmids, showed dose-dependent activation of all PPARs by OA-NO2. PPARgamma showed the greatest response, with significant activation at 100 nm, while PPARalpha and PPARdelta were activated at approximately 300 nm OA-NO2. OA-NO2 also induced PPAR gamma-dependent adipogenesis and deoxyglucose uptake in 3T3-L1 preadipocytes at a potency exceeding nitrolinoleic acid and rivaling synthetic thiazo-lidinediones. These data reveal that nitrated fatty acids comprise a class of nitric oxide-derived, receptor-dependent, cell signaling mediators that act within physiological concentration ranges.
Optimizing Greenhouse Corn Production: Summary (2012)

This publication provides a summary of the goals and scope of our studies to optimize greenhouse corn production, as well as a single-page chart of all the recommendations. The chart includes recommendations for substrate, container, irrigation, fertilization, spacing and lighting. In this version, we updated the pot size recommendation. This document is one entry in a series of questions and answers originally posted to the Purdue University Department of Horticulture & Landscape Architecture’s Plant Growth Facility Web site (http://www.hort.purdue.edu/hort/facilities/greenhouse/CornMethod.shtml) regarding best practices for corn plant growth in a greenhouse. Controlled studies were conducted with the goals of optimizing growth and yield; developing standardized methodology using readily available commercial materials; and providing recommendations for both high-tech and low-tech facilities. Digital images showing treatment differences are included, as well as statistical analysis of data. A summary of recommendations; materials and methods description; and a reference list are available in separate documents.
Elimination of electrooxidizable interferant-produced currents in amperometric biosensors (1992)

Electrooxidizable ascorbate, urate, and acetaminophen that interfere with amperometric glucose assays are completely and rapidly oxidized by hydrogen peroxide in a multilayer electrode. The multilayer electrode is composed of an immobilized, but not electrically "wired", horseradish peroxidase (HRP) film coated onto a film of electrically "wired" glucose oxidase (GO). The "wired" enzyme is connected by a redox epoxy network to a vitreous carbon electrode. The current from the electrooxidizable interferants is decreased by their peroxidase-catalyzed preoxidation by a factor of 2500, and the glucose/interferant current ratio is increased 10(3)-fold. Undesired electroreduction of hydrogen peroxide can result when HRP is also "wired" to the electrode. Such unwanted "wiring" is prevented by incorporating an electrically insulating barrier layer between the wired GO film and the HRP film. The hydrogen peroxide necessary for elimination of interferants can be added externally, or when this is not possible, it can be generated in situ by means of a coupled enzyme reaction.
Elucidation of monoclonal antibody polyspecificity using a synthetic combinatorial library. (1996)

The potential polyspecificity of an antipeptide monoclonal antibody was systematically examined using a soluble synthetic combinatorial library (SCL). This SCL was composed of 400 different hexapeptide mixtures, each of which consisted of more than 130,000 peptides totalling 50 million individual sequences in approximately equimolar concentration. The 400 peptide mixtures making up this SCL were screened by competitive enzyme-linked immunosorbent assay (ELISA) for their ability to inhibit monoclonal antibody binding to the original immunizing peptide. Individual peptides were derived from three different peptide mixtures of the peptide library through an iterative screening and selection process. In addition to the identification of the six-residue antigenic determinant recognized by this monoclonal antibody, two other hexapeptides were found to have binding affinities 5- to 10-fold higher than the original antigenic determinant sequence. These peptide sequences represent analogs in which a polar amino acid (threonine) in the original antigenic determinant was substituted with a large, aromatic amino acid (either tryptophan or tyrosine). Peptide analogs of the antigenic determinant, ranging from single to multiple substitutions, as well as peptide sequences completely unrelated to the immunizing peptide, were also identified having binding affinities comparable to the original immunogen. The present study illustrates the power of SCLs for the determination of alternative binding motifs for antigen antibody interactions. The use of SCLs in this manner may help to elucidate the extent of cross-reactivity, polyspecificity and molecular mimicry found in antigen-antibody interactions.
Double long‐chain amidine liposome‐mediated self replicating DNA transfection (1996)

We present experimental evidence that a complex made of a double long chain cationic amphiphile and recombinant mRNA facilitates the entry and expression of genetic material into cells. Combining the properties of the self replicating recombinant mRNA driven by the Semliki Forest Virus (SFV) replicon and the transfection potentialities of a new cationic amphiphile (N-t-butyl-N'-tetradecyl-3-tetradecylaminopropionamidine) yields a highly efficient mRNA transfection system conferring up to 100% infectivity. The preparation and characterization of the long chain amidine cationic amphiphile-mRNA complex as well as the influence of the diC14-amidine/RNA ratio on the infective activity are described.
TRON: process-specific file protection for the UNIX operating system (1995)

The file protection mechanism provided in UNIX is insufficient for current computing environments. While the UNIX file protection system attempts to protect users from attacks by other users, it does not directly address the agents of destruction--- executing processes. As computing environments become more interconnected and interdependent, there is increasing pressure and opportunity for users to acquire and test non--secure, and possibly malicious, software. We introduce TRON, a process--level discretionary access control system for UNIX. TRON allows users to specify capabilities for a process&amp;apos; access to individual files, directories, and directory trees. These capabilities are enforced by system call wrappers compiled into the operating system kernel. No privileged system calls, special files, system administrator intervention, or changes to the file system are required. Existing UNIX programs can be run without recompilation under TRON--enhanced UNIX. Thus, TRON improves UNIX secu...
Kinetics of Decarburization of Liquid Iron in Ar-CO-CO<SUB>2</SUB> Atmospheres (1974)

The present paper deals with a kinetic study of decarburization of liquid iron in Ar-CO-CO2atmospheres at 1600°C. The study has been especially devoted to determining therate-controlling step at low carbon contents of the melt.At concentrations of carbon highr than 0.02-0.05 %, the rate of decarburization is controlled primarily by gaseous mass transfer.At concentrations of carbon lower than 0.02-0.05 %, the rate of decarburization no longer depends on the gas flow rate, if it is higher than 1300cc/min. The rate-co, ntrolling step of decarburization under this condition varies according to the composition of Ar-CO-CO2.Chemical reaction becomes important in rate-controlling mechanism as the partial pressure of Ar or CO in the gas mixture increases, while mass transfer of carbon becomes important as the partial pressure of CO2 increases.In the range of chemical reaction control, the experimental reasults are explained reasonably by the model based on the simultaneous reactions: CO2+C←/→2CO, CO2←/→CO+O, C+O←/→CO.In the range of mass transfer control, the value of mass transfer coefficient of carbon is the same as that for the decarburization by CO-CO2 and Ar-CO2.It is concluded that the mechanism of decarburization by CO-CO2 and Ar-CO2, previously studied, can be explained on the basis of the present study.
Integrated Microfluidic Systems (2003)

Microchips: Multistep reactions may be catalyzed by enzymes immobilized on microbeads trapped inside microfluidic channels. Large integrated microfluidic circuits can be created by using multilayer soft lithography in poly(dimethylsiloxane). These circuits (see schematic representation) can be used to perform hundreds of different reactions simultaneously, and can be applied to a range of problems, from enzymatic assays to crystallization of proteins.
Universal approximation using feedforward networks with non-sigmoid hidden layer activation functions (1989)

K.M. Hornik, M. Stinchcombe, and H. White (Univ. of California at San Diego, Dept. of Economics Discussion Paper, June 1988; to appear in Neural Networks) showed that multilayer feedforward networks with as few as one hidden layer, no squashing at the output layer, and arbitrary sigmoid activation function at the hidden layer are universal approximators: they are capable of arbitrarily accurate approximation to arbitrary mappings, provided sufficiently many hidden units are available. The present authors obtain identical conclusions but do not require the hidden-unit activation to be sigmoid. Instead, it can be a rather general nonlinear function. Thus, multilayer feedforward networks possess universal approximation capabilities by virtue of the presence of intermediate layers with sufficiently many parallel processors; the properties of the intermediate-layer activation function are not so crucial. In particular, sigmoid activation functions are not necessary for universal approximation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cellular Polymers for Medical Use: The Vital Role of Porosity and Permeability (1984)

Cellular polymers have played a significant role in the development of a base of knowledge for the safe and efficacious use of surgically implantable biomaterials. Inherent compatibility and properties of porosity and permeability are vital attributes for the ingrowth of soft and rigid tissues into select indwelling devices. Such characteristics are necessary for long-term physiological acceptability of vascular grafts and for permanent bone attachment of dental and orthopedic appliances, and for controlled drug release implants. Early experience with sponges of polyvinyl alcohol denatured gelatin collagen and silicone rubber has aided in the establishment of criteria for pore size which have carried over to more recently used foams of polyurethane, polytetrafluoroethylene and polyethylene. Cellular polymers and their composites promise to play an even larger role in health care delivery of the future.
Immunization of Owl Monkeys with a Combination of Plasmodium Falciparum Asexual Blood-Stage Synthetic Peptide Antigens (1990)

A mixture of 3 synthetic peptides (35.1, 55.1, and 83.1) corresponding to portions of the 35 kDa, 55 kDa, and 83 kDa proteins from the asexual blood stages of Plasmodium falciparum and a polymer of a syntheic peptide incorporating the 3 individual peptides (SPf66) were tested as candidate malaria vaccine antigens in Aotus nancymai. Monkeys were immunized with combinations of the 3 peptides from 2 separate sources (Centers for Disease Control [CDC], Atlanta, GA or Colombia) or with the synthetic polymer. Animals immunized with a combination of the 3 peptides from CDC had higher antibody titers to the 35.1 and 55.1 peptides than to the 83.1 peptide. Monkeys immunized with a combination of the 3 peptides produced in Colombia developed higher levels of antibody to the 55.1 than to the 83.1 and 35.1 peptides. Animals immunized with the polymer produced detectable antibodies to the 55.1 peptide alone. Following challenge with P. falciparum, no differences were observed between the 3 vaccine groups and 2 control groups with respect to the number of animals with parasitemias greater than or equal to 10%. The inconsistency of serologic response to all 3 peptides in these animals contrasted with previous trials performed in Colombia where the monkeys developed high antibody titers against the 3 peptides and were protected against the experimental infection.
Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations (2009)

As the cost of DNA sequencing drops, we are moving beyond one genome per species to one genome per individual to improve prevention, diagnosis, and treatment of disease by using personal genotypes. Computational methods are frequently applied to predict impairment of gene function by nonsynonymous mutations in individual genomes and single nucleotide polymorphisms (nSNPs) in populations. These computational tools are, however, known to fail 15%-40% of the time. We find that accurate discrimination between benign and deleterious mutations is strongly influenced by the long-term (among species) history of positions that harbor those mutations. Successful prediction of known disease-associated mutations (DAMs) is much higher for evolutionarily conserved positions and for original-mutant amino acid pairs that are rarely seen among species. Prediction accuracies for nSNPs show opposite patterns, forecasting impediments to building diagnostic tools aiming to simultaneously reduce both false-positive and false-negative errors. The relative allele frequencies of mutations diagnosed as benign and damaging are predicted by positional evolutionary rates. These allele frequencies are modulated by the relative preponderance of the mutant allele in the set of amino acids found at homologous sites in other species (evolutionarily permissible alleles [EPAs]). The nSNPs found in EPAs are biochemically less severe than those missing from EPAs across all allele frequency categories. Therefore, it is important to consider position evolutionary rates and EPAs when interpreting the consequences and population frequencies of human mutations. The impending sequencing of thousands of human and many more vertebrate genomes will lead to more accurate classifiers needed in real-world applications.