gebhart/patrepeval huggingface dataset:
Model of extreme hypoglycemia in dogs made ketotic with (R,S)-1,3-butanediol acetoacetate esters (1995)

The rationale behind this study is that controlled starvation of poorly differentiated (anaplastic) fast-growing tumor cells, but not host cells, might be possible in vivo. The energy metabolism of anaplastic tumor cells, but not host cells, is largely dependent on carbohydrate metabolism at all times. Therefore depleting plasma of carbohydrate fuels could place these tumor cells at a significant metabolic disadvantage. Hence an animal model was developed in which all cells would be required to oxidize fatty acids, ketoacids, and/or 1,3-butanediol to satisfy their energy needs. To achieve this aim, one would need ketosis, severe hypoglycemia, and low lactatemia. Anesthetized normal dogs were infused with somatostatin and a mixture of (R,S)-1,3-butanediol monoacetoacetate and (R,S)-1,3-butanediol diacetoacetate; these latter compounds are nonionized precursors of ketoacids. They were infused at 90% of the dog's caloric requirement. After establishment of a moderate ketosis (2-3 mM) over < 100 min, a severe degree of hypoglycemia (close to 0.5 mM) without rebound and without hyperlactatemia was induced by infusing insulin and dichloroacetate. Tracer kinetic measurements showed 1) a 20% decrease in the rate of appearance of glucose, 2) 50 and 62% increases in glycerol and nonesterified fatty acid rates of appearance, reflecting stimulation of lipolysis, and 3) no change in the rate of glutamine appearance. We suggest that this model may prove useful for selectively starving those cancer cells that are unable to utilize fat-derived fuels while preserving nutrient supply to vital organs.
Vasopressin Deficiency Contributes to the Vasodilation of Septic Shock (1997)

Vasopressin plasma levels are inappropriately low in vasodilatory shock, most likely because of impaired baroreflex-mediated secretion. The deficiency in vasopressin contributes to the hypotension of vasodilatory septic shock.
Expression, Purification and Transduction of PEP-1-Botulinum Neurotoxin Type A (PEP-1-BoNT/A) into Skin (2006)

Botulinum neurotoxin A (BoNT/A) has been used therapeutically to treat muscular hypercontractions and sudomotor hyperactivity and it has been reported that BoNT/A might have analgesic properties in headache. PEP-1 peptide is a known carrier peptide that delivers full-length native proteins in vitro and in vivo. In this study, a BoNT/A gene were fused with PEP-1 peptide in a bacterial expression vector to produce a genetic in-frame PEP-1-BoNT/A fusion protein. The expressed and purified PEP-1-BoNT/A fusion proteins were efficiently transduced into cells in a time- and dose-dependent manner when added exogenously in a culture medium. In addition, immunohistochemical analysis revealed that PEP-1-BoNT/A fusion protein efficiently penetrated into the epidermis as well as the dermis of the subcutaneous layer, when sprayed on mice skin. These results suggest that PEP-1-BoNT/A fusion protein provide an efficient strategy for therapeutic delivery in various human diseases related to this protein.
Automatic tiling of iterative stencil loops (2004)

Iterative stencil loops are used in scientific programs to implement relaxation methods for numerical simulation and signal processing. Such loops iteratively modify the same array elements over different time steps, which presents opportunities for the compiler to improve the temporal data locality through loop tiling. This article presents a compiler framework for automatic tiling of iterative stencil loops, with the objective of improving the cache performance. The article first presents a technique which allows loop tiling to satisfy data dependences in spite of the difficulty created by imperfectly nested inner loops. It does so by skewing the inner loops over the time steps and by applying a uniform skew factor to all loops at the same nesting level. Based on a memory cost analysis, the article shows that the skew factor must be minimized at every loop level in order to minimize cache misses. A graph-theoretical algorithm, which takes polynomial time, is presented to determine the minimum skew factor. Furthermore, the memory-cost analysis derives the tile size which minimizes capacity misses. Given the tile size, an efficient and general &lt;i&gt;array-padding&lt;/i&gt; scheme is applied to remove conflict misses. Experiments were conducted on 16 test programs and preliminary results showed an average speedup of 1.58 and a maximum speedup of 5.06 across those test programs.
The temporal relationship between glycogen phosphorylase and activation of the pyruvate dehydrogenase complex during adrenaline infusion in resting canine skeletal muscle (2002)

The present study examined the effect of adrenaline infusion on the activation status of glycogen phosphorylase and the pyruvate dehydrogenase complex (PDC) and on the accumulation of glucose-6-phosphate (G-6-P) and acetylcarnitine in resting canine skeletal muscle. The study was performed in an effort to gain some insight into the temporal relationship between glycogen phosphorylase and PDC activation in vivo in skeletal muscle, which is currently unresolved. Multiple muscle samples were obtained from canine brachial muscle (n = 10) before and during (1, 3, 7 and 15 min) adrenaline infusion (0.14 microg (kg body mass)(-1) min(-1), I.V.). Adrenaline infusion increased glycogen phosphorylase "a" by > 2-fold above basal levels after 3 min (pre-infusion = 9.2 +/- 1.1 vs. 3 min = 22.3 +/- 4.0 mmol glucosyl units (kg dry muscle)(-1) min(-1), P < 0.05). The concentration of G-6-P increased transiently from its basal concentration at 1 min (pre-infusion = 1.5 +/- 0.2 vs. 1 min = 4.4 +/- 0.9 mmol kg dry muscle)(-1), P < 0.01), declined to its pre-infusion concentration at 3 min (P < 0.05), and then increased again after 7 min of infusion (P < 0.05). The PDC was activated following 7 min of adrenaline infusion (pre-infusion = 0.22 +/- 0.04 vs. 7 min = 1.04 +/- 0.15 mmol acetyl-CoA (kg wet muscle)(-1) min(-1), P < 0.01), and this degree of activation was maintained for the duration of infusion. During the first 3 min of infusion, the concentration of acetylcarnitine declined (pre-infusion = 3.8 +/- 0.3 vs. 3 min = 1.6 +/- 0.2 mmol (kg dry muscle)(-1), P < 0.05), before transiently increasing at 7 min above the 3 min concentration (3 min = 1.6 +/- 0.2 vs. 7 min = 5.1 +/- 1.0 mmol (kg dry muscle)(-1), P < 0.01). This is the first study to demonstrate that adrenaline can indirectly activate the PDC in skeletal muscle in vivo at rest. The results demonstrate that adrenaline increased glycogen phosphorylase activation and glycolytic flux within 3 min of infusion, but took several more minutes to activate the PDC. This temporal relationship, combined with a probable adrenaline-induced increase in metabolic rate (and thereby resting ATP demand), resulted in the biphasic changes in G-6-P and acetylcarnitine with infusion time.
Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI (2001)

Crystallization is a unique process that occurs at the expense of entropy, including the conformational entropy of surface residues, which become ordered in crystal lattices during formation of crystal contacts. It could therefore be argued that epitopes free of amino acids with high conformational entropy are more thermodynamically favorable for crystal formation. For a protein recalcitrant to crystallization, mutation of such surface amino acids to residues with no conformational entropy might lead to enhancement of crystallization. This paper reports the results of experiments with an important cytosolic regulator of GTPases, human RhoGDI, in which lysine residues were systematically mutated to alanines. Single and multiple mutations were introduced into two different variants of RhoGDI, NDelta23 and NDelta66, in which the first 23 and 66 residues, respectively, were removed by recombinant methods. In total, 13 single and multiple mutants were prepared and assessed for crystallization and all were shown to crystallize using the Hampton Research Crystal Screens I and II, in contrast to wild-type NDelta23 and NDelta66 RhoGDI which did not crystallize. Four crystal structures were solved (the triple mutants NDelta23:K135,138,141A and NDelta66:K135,138,141A, and two single mutants NDelta66:K113A and NDelta66:K141A) and in three cases the crystal contacts of the new lattices were found precisely at the sites of mutations. These results support the notion that it is, in principle, possible to rationally design mutations which systematically enhance proteins' ability to crystallize.
From ORFeome to Biology: A Functional Genomics Pipeline (2004)

As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a human ORFeome resource and established a functional genomics and proteomics analysis pipeline to address the major topics in the post-genome-sequencing era: the identification of human genes and splice forms, and the determination of protein localization, activity, and interaction. Combined with the understanding of when and where gene products are expressed in normal and diseased conditions, we create information that is essential for understanding the interplay of genes and proteins in the complex biological network. We have implemented bioinformatics tools and databases that are suitable to store, analyze, and integrate the different types of data from high-throughput experiments and to include further annotation that is based on external information. All information is presented in a Web database (http://www.dkfz.de/LIFEdb). It is exploited for the identification of disease-relevant genes and proteins for diagnosis and therapy.
TarO-specific inhibitors of wall teichoic acid biosynthesis restore β-lactam efficacy against methicillin-resistant staphylococci (2016)

The widespread emergence of methicillin-resistant Staphylococcus aureus (MRSA) has dramatically eroded the efficacy of current β-lactam antibiotics and created an urgent need for new treatment options. We report an S. aureus phenotypic screening strategy involving chemical suppression of the growth inhibitory consequences of depleting late-stage wall teichoic acid biosynthesis. This enabled us to identify early-stage pathway-specific inhibitors of wall teichoic acid biosynthesis predicted to be chemically synergistic with β-lactams. We demonstrated by genetic and biochemical means that each of the new chemical series discovered, herein named tarocin A and tarocin B, inhibited the first step in wall teichoic acid biosynthesis (TarO). Tarocins do not have intrinsic bioactivity but rather demonstrated potent bactericidal synergy in combination with broad-spectrum β-lactam antibiotics against diverse clinical isolates of methicillin-resistant staphylococci as well as robust efficacy in a murine infection model of MRSA. Tarocins and other inhibitors of wall teichoic acid biosynthesis may provide a rational strategy to develop Gram-positive bactericidal β-lactam combination agents active against methicillin-resistant staphylococci.
Asymptotic properties of black-box identification of transfer functions (1985)

The problem of estimating the transfer function of a linear, stochastic system is considered. The transfer function is parametrized as a black box and no given order is chosen a priori. This means that the model orders may increase to infinity when the number of observed data tends to infinity. The consistency and convergence properties of the resulting transfer function estimates are investigated. Asymptotic expressions for the variances and distributions of these estimates are also derived for the case that the model orders increase. It is shown that the variance of the transfer function estimate at a certain frequency is asymptotically given by the noise-to-signal ratio at that frequency mulliplied by the model-order-to-number-of-data-points ratio.
Magnetic particles in ultrasensitive biomarker protein measurements for cancer detection and monitoring (2011)

IMPORTANCE OF THE FIELD: Devices for the reliable detection of panels of biomarker proteins facilitated by magnetic bead-based technologies have the potential to greatly improve future cancer diagnostics. The reason for this review is to highlight promising research on emerging procedures for protein capture, transport and detection featuring magnetic particles. AREAS COVERED IN THIS REVIEW: The review covers applications of magnetic particles in protein immunoassays in emerging research and commercial methods, and stresses multiplexed protein assays for reliable future cancer diagnostics. Research literature over the past dozen years has been surveyed and specific examples are presented in detail. EXPERT OPINION: Magnetic particles are important components of emerging protein detection systems. They need to be integrated into simple inexpensive systems for accurate, sensitive detection of fully validated panels of biomarker proteins to be widely useful in clinical cancer diagnostics.
Modified gateway system for double shRNA expression and Cre/lox based gene expression (2011)

Our system is a valuable addition to already existing library of Gateway based vectors and can be an essential tool for many aspects of gene functional studies.
IL-33–Responsive Lineage−CD25+CD44hi Lymphoid Cells Mediate Innate Type 2 Immunity and Allergic Inflammation in the Lungs (2011)

Innate immunity provides the first line of response to invading pathogens and a variety of environmental insults. Recent studies identified novel subsets of innate lymphoid cells that are capable of mediating immune responses in mucosal organs. In this paper, we describe a subset of lymphoid cells that is involved in innate type 2 immunity in the lungs. Airway exposure of naive BALB/c or C57BL/6J mice to IL-33 results in a rapid (<12 h) production of IL-5 and IL-13 and marked airway eosinophilia independently of adaptive immunity. In the lungs of nonsensitized naive mice, IL-33-responsive cells were identified that have a lymphoid morphology, lack lineage markers, highly express CD25, CD44, Thy1.2, ICOS, Sca-1, and IL-7Rα (i.e., Lin(-)CD25(+)CD44(hi) lymphoid cells), and require IL-7Rα for their development. Airway exposure of naive mice to a clinically relevant ubiquitous fungal allergen, Alternaria alternata, increases bronchoalveolar lavage levels of IL-33, followed by IL-5 and IL-13 production and airway eosinophilia without T or B cells. This innate type 2 response to the allergen is nearly abolished in mice deficient in IL-33R (i.e., ST2), and the Lin(-)CD25(+)CD44(hi) lymphoid cells in the lungs are required and sufficient to mediate the response. Thus, a subset of innate immune cells that responds to IL-33 and vigorously produces Th2-type cytokines is present in mouse lungs. These cells may provide a novel mechanism for type 2 immunity in the airways and induction of allergic airway diseases such as asthma.
The Use of Virtual Fixtures as Perceptual Overlays to Enhance Operator Performance in Remote Environments. (1992)

Abstract : This report introduces the notion of virtual fixtures for use in telepresence systems. Tools and fixtures in the real world (e.g., a ruler guiding a pencil) enhance human performance by guiding manual operations, providing localizing references, reducing mental workload, and increasing precision. Virtual fixtures are computer-generated percepts overlaid on top of the reflection of a remote workspace which can provide similar benefits. Because such perceptual overlays are virtual constructions they can be diverse in modality, abstract in form, and custom tailored to individual situations. This study investigates the potential of virtual fixtures by implementing simple combinations of haptic surfaces and auditory sensations as virtual perceptual aids in a standardized telemanipulation task. Subjects viewed the remote environment through a vision system while wearing an upper-body exoskeleton. Eight subjects controlled a slave robot arm to perform standard Fitts' law peg-insertion tasks with and without the aid of a variety of virtual fixtures. Fixtures composed of haptic and auditory perceptual overlays increased operator performance up to 70%. Simple fixtures devised from basic elements can be powerful perceptual aids; a workstation environment might be developed to allow a teleoperator to design and implement virtual fixtures interactively.
Effects of taxol on the human NCI-H295 adrenocortical carcinoma cell line (1996)

We investigated the effects of taxol, an antimicrotubule agent active in different cancers, on the human NCI-H295 steroid-secreting adrenocortical carcinoma cell line. Cells were incubated for 48, 72 or 96 h with taxol 10(-10)-10(-4) M. Cell viability was evaluated by MTT assay with IC50 calculation. Apoptosis was investigated by measuring DNA fragmentation with ELISA assay after cell exposure to taxol at IC50 for 24 h. For secretion studies, aldosterone, cortisol, testosterone and dehydroepiandrosterone-sulphate (DHEA-S) were measured by RIA in the conditioned medium after 96 h exposure to taxol 10(-10)-10(-6) M, and expressed as percentage of steroid production by control cells. By MTT, taxol induced a dose-dependent inhibition of cell proliferation, with ICs50 at 72-96 h corresponding to blood levels achieved in vivo in patients with other types of cancer. Nuclear fragmentation, morphologically confirmed at electron microscopy, showed a 4-fold increase after exposure to taxol. With 10(-6) M taxol, aldosterone decreased to 48%, cortisol to 61%, testosterone to 76% and DHEA-S to 89% of steroid production by control cells. Taxol is an effective cytotoxic and antiproliferative agent in a human adrenocortical steroid-secreting carcinoma cell line. Apoptosis induced by the drug is involved in neoplastic cell death.
A biochemical analysis of human periodontal tissue proteoglycans (1992)

Proteoglycans synthesized by periodontal (gingival, periodontal ligament, dental follicle) fibroblasts were analysed by SDS/polyacrylamide and agarose gel electrophoresis after being labelled with radioactive sulphate. Medium, cell membrane and extracellular matrix fractions were analysed separately. Samples were treated with chondroitinase AC, chondroitinase ABC, heparitinase or a combination of chondroitinase ABC and heparitinase before electrophoretic separation of proteoglycans. Antibodies to versican and decorin were used to identify these molecules by Western immunoblots. For steady-state metabolic radiolabelling of fibroblasts, medium and cell membrane fractions contained about equal proportions of radiolabelled proteoglycans (about 43%), whereas less radioactivity (about 14%) was found in proteoglycans of the matrix fraction. Periodontal fibroblasts produce six major proteoglycans: versican, a high-molecular-mass chondroitin sulphate proteoglycan (CSPG); decorin, a dermatan sulphate proteoglycan (DSPG); a membrane-associated heparan sulphate proteoglycan (HSPG); two medium- or matrix-associated HSPGs; and a 91 kDa membrane-associated CSPG. Variation in decorin molecular size was observed in mass cultures of fibroblasts. Similar polydispersity in molecular size of decorin was seen in several clones established from one mass culture.
Deletion of the gene encoding the adenovirus 5 early region 1b 21,000-molecular-weight polypeptide leads to degradation of viral and host cell DNA (1984)

The adenovirus 5 mutant H5dl337 lacks 146 base pairs within early region 1B. The deletion removes a portion of the region encoding the E1B 21,000-molecular-weight (21K) polypeptide, but does not disturb the E1B-55K/17K coding region. The virus is slightly defective for growth in cultured HeLa cells, in which its final yield is reduced ca. 10-fold compared with wild-type virus. The mutant displays a striking phenotype in HeLa cells. The onset of cytopathic effect is dramatically accelerated, and both host cell and viral DNAs are extensively degraded late after infection. This defect has been described previously for a variety of adenovirus mutants and has been termed a cytocidal (cyt) phenotype. H5dl337 serves to map this defect to the loss of E1B-21K polypeptide function. In addition to its defect in the productive growth cycle, H5dl337 is unable to transform rat cells at normal efficiency.
Enterprise expert and knowledge discovery (1999)

In this paper we describe two systems designed to connect users to distributed, continuously changing experts and their knowledge. Using information retrieval, information extraction, and collaborative filtering techniques, these systems are able to enhance corporate knowledge management by overcoming traditional problems of knowledge acquisition and maintenance and associated (human and financial) costs. We describe the purpose of these two systems, how they work, and current deployment in a global corporate environment to enable end users to directly discover experts and their knowledge.
RF over Fibre Networks (2006)

In recent years there have been considerable advances in the transmission of RF signals over optical fibre links. However as wireless services themselves have advanced there is now a greater need for systems which can select and route RF signals over optical fibre networks. This paper will report some recent advances in the routing of RF services over optical amplifier based switches, indicating the potential scale of networks that can be envisaged in the future
Heparin, sulfated heparinoids, and lipoteichoic acids bind to the 70-kDa peptidoglycan/lipopolysaccharide receptor protein on lymphocytes. (1994)

The same 70-kDa protein, present on the surface of mouse lymphocytes, served as the predominant binding site for heparin, heparinoids, and bacterial lipoteichoic acids, as well as peptidoglycan and lipopolysaccharides. This conclusion was supported by the following results: (a) all of these compounds photoaffinity cross-linked to one major 70-kDa 6.5-7.0 pI protein that co-migrated on two-dimensional polyacrylamide gel electrophoresis; (b) peptide maps of the 70-kDa proteins digested with chymotrypsin, subtilisin, protease V, or papain yielded the same peptides for heparin-, lipoteichoic acid-, peptidoglycan-, and lipopolysaccharide-binding proteins; (c) cross-linking of peptidoglycan, lipopolysaccharide, lipoteichoic acid, and heparin was competitively inhibited by the same compounds with the same order of potency, i.e. carboxyl-reduced sulfated heparin > peptidoglycan > pentosan polysulfate > heparin > chitin > dextran sulfate > trestatin sulfate > polyanetholesulfonate > fucoidan > beta-cyclodextrin tetradecasulfate > heparan sulfate > carrageenan lambda > lipoteichoic acids > Re-lipopolysaccharide > lipopolysaccharide > lipid A > polygalacturonic acid; and (d) cross-linking of each of these ligands was not inhibited by carboxyl-reduced heparin, dextran, beta-cyclodextrin, trestatin, carrageenan kappa, chondroitin 4-sulfate, chondroitin 6-sulfate, beta-D-glucan, carboxy-methylcellulose, levan, alpha-D-mannan, and glycogen. The minimum size of the molecule that bound was 7-9 glycan residues, whereas, di- and trisaccharides did not bind. There was a logarithmic linear relationship between the strength of the binding and the length of the polymer (up to > 1500 glycan residues), which indicates an avidity effect of the cooperative binding of one polymeric molecule to several receptor molecules on the cell surface. The 70-kDa receptor, therefore, has a broad, but limited specificity of binding for non-charged (peptidoglycan and chitin), highly negatively charged (heparin and heparinoids), and weakly negatively charged (lipoteichoic acids, lipopolysaccharides, and lipid A) ligands.