gebhart/patrepeval huggingface dataset:
ControlShell: component-based real-time programming (2002)

Real-time system software is notoriously hard to share and reuse. The paper walks through the methodology and application of ControlShell, a component-based programming system real-time system software development. ControlShell combines graphical system-building tools, an execution-time configuration manager, a real-time matrix package, and an object name service into an integrated development environment. It targets complex systems that require on-line reconfiguration and strategic control. ControlShell takes advantage of functional object hierarchies to enable code sharing and reuse. It gains flexibility by supporting easy interconnectivity of these objects. It features a unique configuration control system for changing operating modes.
Mi2β-mediated silencing of the fetal γ-globin gene in adult erythroid cells (2013)

An understanding of the human fetal to adult hemoglobin switch offers the potential to ameliorate β-type globin gene disorders such as sickle cell anemia and β-thalassemia through activation of the fetal γ-globin gene. Chromatin modifying complexes, including MBD2-NuRD and GATA-1/FOG-1/NuRD, play a role in γ-globin gene silencing, and Mi2β (CHD4) is a critical component of NuRD complexes. We observed that knockdown of Mi2β relieves γ-globin gene silencing in β-YAC transgenic murine chemical inducer of dimerization hematopoietic cells and in CD34(+) progenitor-derived human primary adult erythroid cells. We show that independent of MBD2-NuRD and GATA-1/FOG-1/NuRD, Mi2β binds directly to and positively regulates both the KLF1 and BCL11A genes, which encode transcription factors critical for γ-globin gene silencing during β-type globin gene switching. Remarkably, <50% knockdown of Mi2β is sufficient to significantly induce γ-globin gene expression without disrupting erythroid differentiation of primary human CD34(+) progenitors. These results indicate that Mi2β is a potential target for therapeutic induction of fetal hemoglobin.
Abstraction and Control for Groups of Robots (2004)

This paper addresses the general problem of controlling a large number of robots required to move as a group. We propose an abstraction based on the definition of a map from the configuration space Q of the robots to a lower dimensional manifold A, whose dimension is independent of the number of robots. In this paper, we focus on planar fully actuated robots. We require that the manifold A has a product structure A=G/spl times/S, where G is a Lie group, which captures the position and orientation of the ensemble in the chosen world coordinate frame, and S is a shape manifold, which is an intrinsic characterization of the team describing the "shape" as the area spanned by the robots. We design decoupled controllers for the group and shape variables. We derive controllers for individual robots that guarantee the desired behavior on A. These controllers can be realized by feedback that depends only on the current state of the robot and the state of the manifold A. This has the practical advantage of reducing the communication and sensing that is required and limiting the complexity of individual robot controllers, even for large numbers of robots.
Asparagine-linked oligosaccharides on lutropin, follitropin, and thyrotropin. II. Distributions of sulfated and sialylated oligosaccharides on bovine, ovine, and human pituitary glycoprotein hormones. (1988)

The asparagine-linked oligosaccharides on the pitui-
Human non-synonymous SNPs: server and survey (2002)

Human single nucleotide polymorphisms (SNPs) represent the most frequent type of human population DNA variation. One of the main goals of SNP research is to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases. Non-synonymous coding SNPs (nsSNPs) comprise a group of SNPs that, together with SNPs in regulatory regions, are believed to have the highest impact on phenotype. Here we present a World Wide Web server to predict the effect of an nsSNP on protein structure and function. The prediction method enabled analysis of the publicly available SNP database HGVbase, which gave rise to a dataset of nsSNPs with predicted functionality. The dataset was further used to compare the effect of various structural and functional characteristics of amino acid substitutions responsible for phenotypic display of nsSNPs. We also studied the dependence of selective pressure on the structural and functional properties of proteins. We found that in our dataset the selection pressure against deleterious SNPs depends on the molecular function of the protein, although it is insensitive to several other protein features considered. The strongest selective pressure was detected for proteins involved in transcription regulation.
<title>Three-dimensional surface measurement using grating projection method by detecting phase and contrast</title> (1999)

A grating projection method using a stereomicroscope is developed to provide a surface profile measurement. The phase shifting technique is applied for high accuracy detection of the projected fringe. To overcome 2(pi) phase jump caused by large step in height and to detect absolute height from the fringe number, contrast detection of the projected pattern is available. The contrast varies in relation with the distance between the sample and the objective lens. This variation is almost as same as optical sectioning that is usually used in confocal microscopy. The fast reconstruction procedure is proposed to analyze the focal point from a few images. This method is demonstrated and conformed to measure the steep surface profile of a test sample.
Medical aspects of ketone body metabolism. (1995)

Ketone bodies are produced in the liver, mainly from the oxidation of fatty acids, and are exported to peripheral tissues for use as an energy source. They are particularly important for the brain, which has no other substantial non-glucose-derived energy source. The 2 main ketone bodies are 3-hydroxybutyrate (3HB) and acetoacetate (AcAc). Biochemically, abnormalities of ketone body metabolism can present in 3 fashions: ketosis, hypoketotic hypoglycemia, and abnormalities of the 3HB/AcAc ratio. Normally, the presence of ketosis implies 2 things: that lipid energy metabolism has been activated and that the entire pathway of lipid degradation is intact. In rare patients, ketosis reflects an inability to utilize ketone bodies. Ketosis is normal during fasting, after prolonged exercise, and when a high-fat diet is consumed. During the neonatal period, infancy and pregnancy, times at which lipid energy metabolism is particularly active, ketosis develops readily. Pathologic causes of ketosis include diabetes, ketotic hypoglycemia of childhood, corticosteroid or growth hormone deficiency, intoxication with alcohol or salicylates, and several inborn errors of metabolism. The absence of ketosis in a patient with hypoglycemia is abnormal and suggests the diagnosis of either hyperinsulinism or an inborn error of fat energy metabolism. An abnormal elevation of the 3HB/AcAc ratio usually implies a non-oxidized state of the hepatocyte mitochondrial matrix resulting from hypoxia-ischemia or other causes. We summarize the differential diagnosis of abnormalities of ketone body metabolism, as well as pertinent recent advances in research.
A Protecting Group for Carboxylic Acids That Can Be Photolyzed by Visible Light (2005)

We report on a photolabile protecting (caging) group that is new for carboxylic acids. Unlike previously used caging groups for carboxylic acids, it can be photolyzed rapidly and efficiently in the visible wavelength region. The caging group 7-N,N-diethyl aminocoumarin (DECM) was used to cage the gamma-carboxyl group of glutamic acid, which is also a neurotransmitter. The caged compound has a major absorption band with a maximum at 390 nm (epsilon(390) = 13651 M(-)(1) cm(-)(1)). Experiments are performed at 400 nm (epsilon(400) = 12232 M(-)(1) cm(-)(1)) and longer wavelengths. DECM-caged glutamate is water soluble and stable at pH 7.4 and 22 degrees C. It photolyzes rapidly in aqueous solution to release glutamic acid within 3 micros with a quantum yield of 0.11 +/- 0.008 in the visible region. In whole-cell current-recording experiments, using HEK-293 cells expressing glutamate receptors and visible light for photolysis, DECM-caged glutamate and its photolytic byproducts were found to be biologically inert. Neurotransmitter receptors that are activated by various carboxyl-group-containing compounds play a central role in signal transmission between approximately 10(12) neurons of the nervous system. Caged neurotransmitters have become an essential tool in transient kinetic investigations of the mechanism of action of neurotransmitter receptors. Previously uncaging the compounds suitable for transient kinetic investigations required ultraviolet light and expensive lasers, and, therefore, special precautions. The availability of caged neurotransmitters suitable for transient kinetic investigations that can be photolyzed by visible light allows the use of simple-to-use, readily available inexpensive light sources, thereby opening up this important field to an increasing number of investigators.
Simulation optimization (1997)

Simulation optimization can be defined as the process of finding the best input variable values from among all possibilities without explicitly evaluating each possibility. The objective of simulation optimization is to minimize the resources spent while maximizing the information obtained in a simulation experiment. The purpose of this paper is to review the area of simulation optimization. A critical review of the methods employed and applications developed in this relatively new area are presented and notable successes are highlighted. Simulation optimization software tools are discussed. The intended audience is simulation practitioners and theoreticians as well as beginners in the field of simulation.
Generation of coherent confined acoustic phonons by drifting electrons in quantum wire (2000)

We developed a quantum theory of generation of coherent confined acoustic phonons by one-dimensional electrons drifting in a quantum wire. A general formula for the factor of amplification of the phonon flux, , is derived. When the electron drift velocity, V d , is greater than the sound phase velocity, S, then at low temperatures the above generation occurs only in a narrow range of phonon wave vectors,
A monoclonal antibody specific for the Thomsen-Friedenreich cryptic T antigen. (1982)

A monoclonal antibody (49H.24) is described that was made after immunization of BALB/c mice with human neuraminidase-treated erythrocytes (NE-RBC). 49H.24 is an IgM and reacts with NE-RBC but not untreated, normal human RBC. As little as 100 pg of antibody protein produced detectable direct agglutination of, or binding to, NE-RBC. The fine specificity of 49H.24 was determined by using a series of synthetic sugar haptens as inhibitors of agglutination or binding of 49H.24 to NE-RBC. Only synthetic T hapten (beta Gal(1 leads to 3)alpha GalNAc) produced complete inhibition of agglutination or binding, and no inhibition was produced by several other closely related haptens. Synthetic T hapten-coated silica beads (Synsorb) were used to affinity purify 49H.24. Affinity-purified antibody was radiolabeled with 125I and used in a sensitive competition assay to detect natural T antigen associated with cell membranes or in soluble form. The potential use of this or similar monoclonal antibodies as probes for an important human tumor marker is discussed.
The channel capacity of hybrid fiber/coax (HFC) networks (2002)

The hybrid fiber/coax (HFC) is emerging as an inexpensive architecture for providing broadband services to residences. It has optical fibers extending from the central office or headend to remote fiber nodes. Extending from the fiber nodes to the residences is a coaxial cable distribution bus. Multiplexing allows 100 to 500 users to share the bandwidth of each coax distribution bus. This architecture advantageously combines the long range of optical fiber with the high bandwidth and simple electrical interfaces of the coaxial cable. HFC will initially provide telephony and cable TV, but it also has sufficient bandwidth for future interactive and multimedia services. Many regional telephone companies, and most cable TV companies, in the US have committed to HFC. This architecture will be widely deployed well into the future, while the demand for residential bandwidth will increase. To meet this demand, there will be an increasing need for multi-user information theory and communication techniques to maximize the bandwidth and fully exploit the potential of this unique medium. This paper initializes exploration into maximizing the channel capacity of HFC.
The tandemly repeated sequences of cartilage link protein contain the sites for interaction with hyaluronic acid. (1987)

The ternary complex involving link protein (LP), proteoglycan monomer, and hyaluronic acid (HA) is an important component of the extracellular matrix of cartilage. LP contains tandemly repeated sequences that were tested for their ability to interact with HA. A solid-phase assay was developed in which LP could specifically bind to immobilized HA. Detection of LP was by means of an antiserum directed against a peptide from the NH2-terminal half of LP. LP binding to HA could be inhibited with mAb 8A4 (Caterson, B., J. R. Baker, J. E. Christner, Y. Lee, and M. Lentz. 1985. J. Biol. Chem. 260:11348-11356). Using synthetic peptides that correspond to specific amino acid sequences of chicken LP (Deák, F., I. Kiss, K. J. Sparks, W. S. Argraves, G. Hampikian, and P. F. Goetinck. 1986. Proc. Natl. Acad. Sci. USA. 83:3766-3770) the epitopes for mAb 8A4 were determined to reside in peptides Gly217-Pro226 and Arg316-Arg325. These two peptides were also capable of inhibiting the interaction between LP and HA. The peptide Trp242-Val251 and Pro339-Val348 could also inhibit the interaction between LP and HA. All four peptides reside in the tandemly repeated domains of LP and they contain clusters of positively charged amino acids. Polylysine could not inhibit the interaction of LP with HA. The results indicate that the sites for interaction with HA are in the tandemly repeated sequences of LP and that there are four potential sites available for that interaction.
Synergistic Interaction of CLAVATA1, CLAVATA2, and RECEPTOR-LIKE PROTEIN KINASE 2 in Cyst Nematode Parasitism of Arabidopsis (2012)

Plant-parasitic cyst nematodes secrete CLAVATA3 (CLV3)/ENDOSPERM SURROUNDING REGION (CLE)-like effector proteins. These proteins act as ligand mimics of plant CLE peptides and are required for successful nematode infection. Previously, we showed that the CLV2/CORYNE (CRN) heterodimer receptor complex is required for nematode CLE signaling. However, there was only a partial reduction in nematode infection when this signaling was disrupted, indicating that there might be additional nematode CLE receptors. In this study, we demonstrate that CLV1 and RECEPTOR-LIKE PROTEIN KINASE 2/TOADSTOOL2 (RPK2), two additional receptors that can transmit the CLV3 signal independent of CLV2/CRN for shoot apical meristem maintenance, also play a role in nematode CLE perception. Localization studies showed that both receptors are expressed in nematode-induced syncytia. Infection assays with clv1 and rpk2 single mutants revealed a decrease in both nematode infection and syncytium size. Significantly, further reduction in nematode infection was observed when rpk2 was combined with clv1 and clv2 mutants. Taken together, our results indicate that parallel signaling pathways involving CLV1, CLV2, and RPK2 are important for nematode parasitism.
Dietary gangliosides positively modulate the percentages of Th1 and Th2 lymphocyte subsets in small intestine of mice at weaning (2001)

We studied the influence of dietary gangliosides on the number of spontaneous cytokine-secreting cells from two intestinal lymphocyte populations: lamina propria lymphocytes and Peyer's patches lymphocytes in Balb/c mice for 28 days after weaning. Weanling mice were separated into two groups, designated as Control and BG. The Control group was fed with a semipurified diet without gangliosides and the BG group was fed with the semipurified diet supplemented with 47 mg/kg of a mixture of bovine brain gangliosides. Intestinal lymphocytes were isolated from mice killed at 3, 7, 14 and 28 days after weaning, and the percentages of spontaneous Th1 as well as Th2 cytokine-secreting lymphocytes were determined using the ELISPOT assay. The BG group animals showed an earlier development in the number of cytokine-secreting cells, which appeared one week later in Control animals. In addition, mice fed with the ganglioside-supplemented diet showed a significantly higher number of Th1 and Th2 cytokine-secreting lymphocytes than Control mice in lamina propria and Peyer's patches lymphocytes at the end of the experimental period (28 days). Our results suggest that dietary gangliosides influence the maturation process of the intestinal immune system that take place during weaning.
Delta‐6‐desaturase activity and arachidonic acid synthesis are increased in human breast cancer tissue (2013)

Omega-6 (n-6) arachidonic acid (AA) and its pro-inflammatory metabolites, including prostaglandin E2 (PGE(2)), are known to promote tumorigenesis. Delta-6 desaturase (D6D) is the rate-limiting enzyme for converting n-6 linoleic acid (LA) to AA. Our objective was to determine if AA synthesis, specifically D6D activity, and PGE(2) levels are increased in cancerous breast tissue, and whether these variables differ between estrogen receptor positive (ER+) and negative (ER-) breast cancers. Gas chromatography was performed on surgical breast tissue samples collected from 69 women with breast cancer. Fifty-four had ER+ breast cancer, and 15 had ER- breast cancer. Liquid chromatography-mass spectrometry was used to determine PGE(2) levels. Lipid analysis revealed higher levels of LA metabolites (C18:3 n-6, C20:3 n-6, and AA) in cancerous tissue than in adjacent noncancerous tissue (P < 0.01). The ratio of LA metabolites to LA, a measure of D6D activity, was increased in cancerous tissue, suggesting greater conversion of LA to AA (P < 0.001), and was higher in ER- than in ER+ patients, indicating genotype-related trends. Similarly, PGE(2) levels were increased in cancerous tissue, particularly in ER- patients. The results showed that the endogenous AA synthetic pathway, D6D activity, and PGE(2) levels are increased in breast tumors, particularly those of the ER- genotype. These findings suggest that the AA synthetic pathway and the D6D enzyme in particular may be involved in the pathogenesis of breast cancer. The development of drugs and nutritional interventions to alter this pathway may provide new strategies for breast cancer prevention and treatment.
Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination (2006)

The 3D structures of human therapeutic targets are enabling for drug discovery. However, their purification and crystallization remain rate determining. In individual cases, ligands have been used to increase the success rate of protein purification and crystallization, but the broad applicability of this approach is unknown. We implemented two screening platforms, based on either fluorimetry or static light scattering, to measure the increase in protein thermal stability upon binding of a ligand without the need to monitor enzyme activity. In total, 221 different proteins from humans and human parasites were screened against one or both of two sorts of small-molecule libraries. The first library comprised different salts, pH conditions, and commonly found small molecules and was applicable to all proteins. The second comprised compounds specific for protein families of particular interest (e.g., protein kinases). In 20 cases, including nine unique human protein kinases, a small molecule was identified that stabilized the proteins and promoted structure determination. The methods are cost-effective, can be implemented in any laboratory, promise to increase the success rates of purifying and crystallizing human proteins significantly, and identify new ligands for these proteins.
Intraoperative optical refractive biometry for intraocular lens power estimation without axial length and keratometry measurements (2005)

A new model for IOL power calculation was derived based on an optical refractive methodology that breaks away from the conventional art introduced by Fyodorov in the 1960s. A purely refractive algorithm is used to predict the power of the IOL at the time of surgery without the need for axial length and keratometry measurements. This method bypasses some limitations of conventional biometry and shows promise in the post-refractive cataract cases.
Protection from Alzheimer's-like disease in the mouse by genetic ablation of inducible nitric oxide synthase (2005)

Brains from subjects who have Alzheimer's disease (AD) express inducible nitric oxide synthase (iNOS). We tested the hypothesis that iNOS contributes to AD pathogenesis. Immunoreactive iNOS was detected in brains of mice with AD-like disease resulting from transgenic expression of mutant human beta-amyloid precursor protein (hAPP) and presenilin-1 (hPS1). We bred hAPP-, hPS1-double transgenic mice to be iNOS(+/+) or iNOS(-/-), and compared them with a congenic WT strain. Deficiency of iNOS substantially protected the AD-like mice from premature mortality, cerebral plaque formation, increased beta-amyloid levels, protein tyrosine nitration, astrocytosis, and microgliosis. Thus, iNOS seems to be a major instigator of beta-amyloid deposition and disease progression. Inhibition of iNOS may be a therapeutic option in AD.
The Human ATP-Binding Cassette (ABC) Transporter Superfamily (2001)

The ATP-binding cassette (ABC) transporter superfamily contains membrane proteins that translocate a variety of substrates across extra- and intra-cellular membranes. Genetic variation in these genes is the cause of or contributor to a wide variety of human disorders with Mendelian and complex inheritance, including cystic fibrosis, neurological disease, retinal degeneration, cholesterol and bile transport defects, anemia, and drug response. Conservation of the ATP-binding domains of these genes has allowed the identification of new members of the superfamily based on nucleotide and protein sequence homology. Phylogenetic analysis is used to divide all 48 known ABC transporters into seven distinct subfamilies of proteins. For each gene, the precise map location on human chromosomes, expression data, and localization within the superfamily has been determined. These data allow predictions to be made as to potential functions or disease phenotypes associated with each protein. In this paper, we review the current state of knowledge on all human ABC genes in inherited disease and drug resistance. In addition, the availability of the complete Drosophila genome sequence allows the comparison of the known human ABC genes with those in the fly genome. The combined data enable an evolutionary analysis of the superfamily. Complete characterization of all ABC from the human genome and from model organisms will lead to important insights into the physiology and the molecular basis of many human disorders.