gebhart/patrepeval huggingface dataset:
High-density reachability analysis (1995)

We address the problem of reachability analysis for large finite state systems. Symbolic techniques have revolutionized reachability analysis but still have limitations in traversing large systems. We present techniques to improve the symbolic breadth-first traversal and compute a lower bound on the reachable states. We identify the problem as one of density during traversal and our techniques seek to improve the same. Our results show a marked improvement on the existing breadth-first traversal methods.
Three new isolates of porcine respiratory coronavirus with various pathogenicities and spike (S) gene deletions (1994)

Three new isolates of porcine respiratory coronavirus (PRCV) were isolated and partially characterized. These PRCV isolates showed a selective tropism for respiratory tissue and were antigenically related to transmissible gastroenteritis virus. PCR amplification of the 5' half of the spike (S) genes of the three PRCV isolates indicated that a large deletion, characteristic of PRCV, was present. By using cDNA probes specific for the transmissible gastroenteritis virus S gene, the PCR products were shown to be specific in a Southern blot. The three new PRCV isolates were shown to vary in S gene deletion size. In a separate study, these isolates have also been shown to vary in pathogenicity. These new PRCV isolates should serve as important tools in gaining a better understanding of the pathogenesis of coronavirus infections.
A new technique for fully autonomous and efficient 3D robotics hand/eye calibration (1989)

The authors describe a novel technique for computing position and orientation of a camera relative to the last joint of a robot manipulator in an eye-on-hand configuration. It takes only about 100+64N arithmetic operations to compute the hand/eye relationship after the robot finishes the movement, and incurs only additional 64 arithmetic operations for each additional station. The robot makes a series of automatically planned movements with a camera rigidly mounted at the gripper. At the end of each move, it takes a total of 90 ms to grab an image, extract image feature coordinates, and perform camera extrinsic calibration. After the robot finishes all the movements, it takes only a few milliseconds to do the calibration. A series of generic geometric properties or lemmas are presented, leading to the derivation of the final algorithms, which are aimed at simplicity, efficiency, and accuracy while giving ample geometric and algebraic insights. Critical factors influencing the accuracy are analyzed, and procedures for improving accuracy are introduced. Test results of both simulation and real experiments on an IBM Cartesian robot are reported and analyzed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthesis of [18F]3‐[1‐(3‐fluoropropyl)‐(S)‐pyrrolidin‐2‐ylmethoxy]pyridine ([18F]NicFP): a potential α4β2 nicotinic acetylcholine receptor radioligand for PET (2003)

Abstract Nicotinic acetylcholine receptors are widely distributed throughout the human brain and are believed to play a role in several neurological and psychiatric disorders. In order to identify an effective PET radioligand for in vivo assessment of the α 4 β 2 subtype of nicotinic receptor, we synthesized [ 18 F]3‐[1‐(3‐fluoropropyl)‐( S )‐pyrrolidin‐2‐ylmethoxy]pyridine (NicFP). The in vitro K D of NicFP was determined to be 1.1 nM, and the log P value obtained by HPLC analysis of the unlabelled standard was found to be 2.2. The radiosynthesis of [ 18 F]NicFP was carried out by a nucleophilic substitution reaction of anhydrous [ 18 F]fluoride and the corresponding mesylate precursor. After purification by HPLC, the radiochemical yield was determined to be 11.3±2.1% and the specific activity was 0.47±0.18 Ci/μmol (EOS, n = 3). The time of synthesis and purification was 99±2 min. The final product was prepared as a sterile saline solution suitable for in vivo use. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and Titanium amplicon pyrosequencing and metagenomic approaches (2009)

The polymicrobial nature of VLU and previous research on diabetic foot ulcers and surgical site infections suggest that the future of therapy for such wounds lies in the core of the logical and proven multiple concurrent strategy approach, which has been termed "biofilm-based wound care" and the use of individualized therapeutics rather than in a single treatment modality.
Protein Tyrosine Phosphatases: A Diverse Family of Intracellular and Transmembrane Enzymes (1991)

Protein tyrosine phosphatases (PTPs) represent a diverse family of enzymes that exist as integral membrane and nonreceptor forms. The PTPs, with specific activities in vitro 10 to 1000 times greater than those of the protein tyrosine kinases would be expected to effectively control the amount of phosphotyrosine in the cell. They dephosphorylate tyrosyl residues in vivo and take part in signal transduction and cell cycle regulation. Most of the transmembrane forms, such as the leukocyte common antigen (CD45), contain two conserved intracellular catalytic domains; but their external segments are highly variable. The structural features of the transmembrane forms suggest that these receptor-linked PTPs are capable of transducing external signals; however, the ligands remain unidentified. A hypothesis is proposed explaining how phosphatases might act synergistically with the kinases to elicit a full physiological response, without regard to the state of phosphorylation of the target proteins.
Bone Marrow and Recombinant Human Bone Morphogenetic Protein-2 in Osseous Repair (1999)

Bone marrow stem cells and recombinant human bone morphogenetic protein-2 each has the capacity to repair osseous defects. Recombinant human bone morphogenetic proteins require the presence of progenitor cells to function. It is hypothesized that a composite graft of recombinant human bone morphogenetic protein-2 and marrow would be synergistic and could result in superior grafting to autogenous bone graft. Syngeneic Lewis rats with a 5-mm critical sized femoral defect were grafted with recombinant human bone morphogenetic protein-2 and marrow, recombinant human bone morphogenetic protein-2, marrow, syngeneic cancellous bone graft, or carrier alone (control). Serial radiographs (3, 6, 9, 12 weeks) and torque testing (12 weeks) were performed. Bone formation and union were determined. The recombinant human bone morphogenetic protein-2 and marrow composite grafts achieved 100% union at 6 weeks. Recombinant human bone morphogenetic protein alone achieved 80% union by week 12. Both groups yielded a higher union rate and superior mechanical properties than did either syngeneic bone graft (38%) or marrow (47%) alone. The superior performance of recombinant human bone morphogenetic protein-2 combined with bone marrow in comparison with each component alone strongly supports a biologic synergism. This experimentation shows the clinical importance of establishing operative site proximity for the osteoinductive factors and responding progenitor cells.
Options for the control of influenza II : proceedings of the International Conference on Options for the Control of Influenza, Courchevel, 27 September-2 October, 1992 (1993)

Part 1 Introductory lecture - full papers: disease impact (4 papers) economics and policy of control programs (3 papers) community vaccine studies in children and adults (4 papers) vaccine studies in the US medicare population (9 papers) vaccine development (3 papers) evolution and ecology of influenza (6 papers) immunology (6 papers) molecular and cellular biology (8 papers) antivirals (3 papers). Part 2 Additional reports: surveillance (4 papers) vaccine trials (4 papers) vaccine policies and strategies (8 papers) vaccination of infants and children (4 papers). Part 3 Conference consensus on recommendations (4 papers).
Oxidative Thymine Dimer Repair in the DNA Helix (1997)

The metallointercalator Rh(phi)2DMB3+ (phi, 9,10-phenanthrenequinone diimine; DMB, 4,4'-dimethyl-2,2'-bipyridine) catalyzed the repair of a thymine dimer incorporated site-specifically in a 16-base pair DNA duplex by means of visible light. This repair could be accomplished with rhodium noncovalently bound to the duplex and at long range (16 to 26 angstroms), with the rhodium intercalator tethered to either end of the duplex assembly. This long-range repair was mediated by the DNA helix. Repair efficiency did not decrease with increasing distance between intercalated rhodium and the thymine dimer, but it diminished with disruption of the intervening pi-stack.
PROTEIN SPLICING ELEMENTS AND PLANTS: From Transgene Containment to Protein Purification (2005)

Protein splicing elements, termed inteins, have been discovered in all the domains of life. Basic research on inteins has led to a greater understanding of how they mediate the protein splicing process. Because inteins are natural protein engineering elements they have been harnessed for use in a number of applications, including protein purification, protein semisynthesis, and in vivo and in vitro protein modifications. This review focuses on the use of inteins in plants. A split-gene technique utilizes inteins to reconstitute the activity of a transgene product with the goal of limiting the spread of transgenes from a genetically modified plant to a weedy relative. Furthermore, merging the intein tag for protein purification with the large protein yields possible with plants has the potential to produce pharmaceutically important proteins. Finally, relevant techniques that may be used in plants in the future are discussed.
Purification of the Major Allergen of Red Soft Coral <i>(Dendronephthya nipponica)</i> (2001)

Red soft coral (RSC; Dendronephthya nipponica, a marine coelenterate) causes spiny lobster fishermen living along the Pacific coast of Miyazaki Prefecture in Japan to develop occupational allergies, such as conjunctivitis, rhinitis, dermatitis and bronchial asthma. The aim of this study was to purify and to characterize RSC allergen, which causes occupational asthma in spiny lobster fishermen. The allergic responsiveness of spiny lobster fishermen to RSC was examined. The examinations included specific IgE production, skin test responses, lymphocyte stimulation tests and specific IgG production. We found that RSC has a strong sensitizing activity in humans at a molecular weight of 10 kD or more, while it has no IgE-producing activity at a molecular weight of less than 10 kD. Neither the nonatopic controls nor the atopic non-coral-allergic controls exhibited any RAST-binding activity to any fraction. For the purification and the identification of this new allergen component, repeated gel filtration of the RSC extract was performed on a Sephacryl S-200 column, followed by gel filtration on a Superose-6 column. The purified major allergen component Den n 1, which is separated on a Mono-Q column, showed intradermal responses, lymphocyte stimulating activity and specific IgG-producing activity in RSC-induced bronchial asthma patients. The 53-kD component was electroblotted on a polyvinylidene difluoride membrane. The N-terminal amino acid sequence of this new allergen component (Den n 1) was determined as Asp-Asp-Ile-Asn-Arg-Tyr-Ala-Phe-Asp-Asn-Lys-Ile-Asn- Asp-Lys-Leu-Phe-Asp-His-Trp-Gln-Ser.
Sol–gel-derived nanocrystalline gold–silicate composite biosensor (1998)

A new class of sol–gel-derived electrochemical biosensors is introducted and demonstrated for glucose sensing. The electrode material comprises an interconnected dispersion of gold nanocrystals imbedded in a porous methyl silicate matrix. The gold nanoparticles provide electrocatalysis and electric conductivity; the methyl groups endow hydrophobicity and limit the active area of the exposed gold, thus decreasing the background current; the silicate provides a transparent and porous backbone; and the encapsulated glucose oxidase provides biocatalysis.
Iron Chelation: Inhibition of Key Signaling Pathways in the Induction of the Epithelial Mesenchymal Transition in Pancreatic Cancer and Other Tumors (2013)

Pancreatic cancer is the fourth leading cause of cancer-related deaths worldwide in both men and women. It presents late with non-specific symptoms, which makes it difficult to diagnose until the cancer has progressed and metastasized. Metastasis is facilitated by the epithelial-to-mes-enchymal transition (EMT), which is promoted via the oncogenic transforming growth factor beta (TGFβ), Wnt, and nuclear factor kappa B (NFκB) signaling pathways. However, recent studies have demonstrated that the EMT can be inhibited by novel anti-cancer agents known as thiosemicarbazone iron chelators. These novel agents also up-regulate the metastasis suppressor, N-myc downstream regulated gene 1 (NDRG1), which can restore normal signaling to the cell and suppresses metastasis via inhibition of the EMT. Through the ability of iron chelators to up-regulate NDRG1 expression and affect multiple molecular targets, these agents have the potential to maintain the epithelial phenotype of cancer cells and may lead to improved survival rates for patients with late-stage disease.
Next-generation optical storage area networks: the light-trails approach (2005)

Multiple architectures, technologies, and standards have been proposed for storage area networks, typically in the WAN environment. The transport aspect of storage signifies that optical communications is the key underlying technology. The contemporary SAN over optical network concept uses the optical layer for pure transport with minimal intelligence. This leads to high cost and overprovisioning. Future optical networks, however, can be expected to play a role in optimizing SAN extension into the WAN. An essential characteristic of SAN systems is tight coupling between nodes in a SAN network. Nodes in a SAN system have two critical functions that are presently emulated by data layers and can be offloaded to the optical layer. First, nodes need to signal among each other to achieve tasks such as synchronous and asynchronous storage. Second, to benefit from an optimized network, nodes need to allocate bandwidth dynamically in real time. In this article we show how the optical layer can be furthered from just pure transport to creating opportunities in provisioning as well as providing the mirroring function of SAN systems (multicasting) and consequently lead to reduction in cost. We demonstrate that the light-trail model is one way of efficiently utilizing the optical layer for SAN.
Immunomodulatory Effects of Hypertonic Resuscitation on the Development of Lung Inflammation Following Hemorrhagic Shock (1998)

Hypertonic resuscitation fluids are known to be effective in restoring circulating volume in the hypovolemic trauma patient. Previous studies have suggested that hypertonicity might exert effects on immune cells leading to an altered host response. The present studies evaluated the effect of hypertonic resuscitation on the development of lung injury in a hemorrhagic shock model in which antecedent shock primes for increased lung neutrophil sequestration in response to intratracheal LPS. Resuscitation with hypertonic saline significantly reduced albumin leak, bronchoalveolar lavage fluid neutrophil counts, and the degree of histopathologic injury compared with resuscitation with Ringer's lactate. Both in vivo and in vitro data suggest that this beneficial effect may be related to altered adhesion molecule expression by the neutrophil. Specifically, hypertonicity induced shedding of L-selectin and prevented LPS-stimulated expression and activation of CD11b, both of which might contribute to reduced sequestration in the lung. Impaired up-regulation of lung ICAM-1 may have also participated, although ex vivo studies suggest that alterations in neutrophils were sufficient to account for the effect. Lung cytokine-induced neutrophil chemoattractant did not differ between animals resuscitated with hypertonic saline vs Ringer's lactate. Considered together, these studies demonstrate a possible novel approach to inhibiting organ injury in disease processes characterized by neutrophil-mediated damage.
Positive regulation of the glucocorticoid receptor in human T-cells sensitive to the cytolytic effects of glucocorticoids. (1988)

Regulation of glucocorticoid receptor (GR) protein and mRNA were examined in the human leukemic T-cell line CEM-C7. Unlike other cells in which GR regulation has been examined, the growth of these cells is inhibited by glucocorticoids, leading to cell death. Treatment of glucocorticoid-sensitive CEM-C7 cells with 1 microM dexamethasone for 18 h resulted in an increase in both cytoplasmic and nuclear GR protein, as determined by immunoblotting with anti-human GR antisera. Analysis of GR mRNA levels by Northern blotting revealed a corresponding increase in mRNA in steroid-treated cells. An increase in GR mRNA was detectable after as little as 3 h of treatment with dexamethasone, and GR mRNA concentration continued to increase for at least 18 h, well before the onset of growth arrest or cell death. GR mRNA concentration was not altered after dexamethasone treatment of the glucocorticoid-resistant mutant cell line ICR27TK.3, which lacks functional GR. Thus, the increase in GR seen in glucocorticoid-sensitive cells is a GR-mediated response. These results are in sharp contrast to the down-regulation of GR reported in other cells and tissues, and suggest that regulation of the GR by its cognate ligand may be tissue-specific.
The synthesis of tris(perfluoroalkyl)phosphines (2005)

Tris(perfluoroalkyl)phosphines, of interest as tunable alternatives to the carbon monoxide ligand, can be synthesised by the nucleophile mediated reaction of perfluoroalkyltrimethylsilanes with triphenylphosphite; the method can be extended to diphosphines.
Transplantation of chromosomally marked syngeneic marrow cells into mice not subjected to hematopoietic stem cell depletion. (1984)

The percentage of donor-host chimerism was determined 4-6 weeks or six months after injection of normal bone marrow cells into normal syngeneic or coisogeneic recipient mice. Donor-recipient pairs had chromosome markers that provided easy identification of metaphase cells. The percentage of donor cells in marrow or spleen ranged from 0 to 16% and this percentage was independent of the age of recipient or attempts to stimulate hematopoiesis in donor and/or host mice. In adult C57BL/6 mice there was a roughly linear dose-response relationship between cell dose and percentage of chimerism. There was no apparent dose-response relationship for AKR mice. The percentage of donor cells in the spleen was correlated to that seen in the marrow of recipients. Neonatal mice given the same intraperitoneal marrow cell dose as weanlings, but a larger number of cells relative to their own marrow mass, did not show a larger percentage of chimerism than weanlings. Similarly, weanlings given the same intravenous dose as adults showed no greater degree of chimerism than adults. Temporary anemia, induced by bleeding donors prior to cell collection, or more chronic hemopoietic stimulus (produced by injecting recipients with phenylhydrazine prior to cell injection with subsequent bleeding at intervals) did not result in an increased percentage of chimerism. These results indicate that there are "empty" sites in bone marrow of normal mice in which injected hematopoietic stem cells can lodge and grow.
Reversal of age-related increase in brain protein oxidation, decrease in enzyme activity, and loss in temporal and spatial memory by chronic administration of the spin-trapping compound N-tert-butyl-alpha-phenylnitrone. (1991)

Oxygen free radicals and oxidative events have been implicated as playing a role in bringing about the changes in cellular function that occur during aging. Brain readily undergoes oxidative damage, so it is important to determine if aging-induced changes in brain may be associated with oxidative events. Previously we demonstrated that brain damage caused by an ischemia/reperfusion insult involved oxidative events. In addition, pretreatment with the spin-trapping compound N-tert-butyl-alpha-phenylnitrone (PBN) diminished the increase in oxidized protein and the loss of glutamine synthetase (GS) activity that accompanied ischemia/reperfusion injury in brain. We report here that aged gerbils had a significantly higher level of oxidized protein as assessed by carbonyl residues and decreased GS and neutral protease activities as compared to young adult gerbils. We also found that chronic treatment with the spin-trapping compound PBN caused a decrease in the level of oxidized protein and an increase in both GS and neutral protease activity in aged Mongolian gerbil brain. In contrast to aged gerbils, PBN treatment of young adult gerbils had no significant effect on brain oxidized protein content or GS activity. Male gerbils, young adults (3 months of age) and retired breeders (15-18 months of age), were treated with PBN for 14 days with twice daily dosages of 32 mg/kg. If PBN administration was ceased after 2 weeks, the significantly decreased level of oxidized protein and increased GS and neutral protease activities in old gerbils changed in a monotonic fashion back to the levels observed in aged gerbils prior to PBN administration. We also report that old gerbils make more errors than young animals and that older gerbils treated with PBN made fewer errors in a radial arm maze test for temporal and spatial memory than the untreated aged controls. These data can be interpreted to indicate that oxidation of cellular proteins may be a critical determinant of brain function. Moreover, it also implies that there is an age-related increase in vulnerability of tissue to oxidation that can be modified by free radical trapping compounds.
Comparison of Addition of Salmeterol to Inhaled Steroids With Doubling of the Dose of Inhaled Steroids (1996)

A study was done to compare the efficacy and safety of the coprescription of salmeterol 50 microgram twice daily or 100 microgram twice daily with beclomethasone dipropionate (BDP) 500 micrograms twice daily (SALM 50 and SALM 100) with BDP 1,000 microgram twice daily (BDP 1,000) in patients with asthma not controlled by BDP 500 microgram twice daily (or the equivalent). Following a run-in period, 738 patients at 72 centers were randomized to treatment for 24 wk in a double-blind, parallel-group study during which they maintained a daily record of peak expiratory flow rates (PEFRs) and symptom scores. At about 40 of the centers, bronchial hyperresponsiveness (BHR) to histamine was measured during and at 3 and 14 d after stopping treatment. Both groups taking salmeterol showed an improvement of more than 45 L/min in their morning PEFR and 30 L/min in their evening PEFR, compared with respective improvements of 16 L/min and 6 L/min in the group taking BDP 1,000. Both the SALM 50 and SALM 100 groups had a significantly increased percentage of symptom-free and rescue-free days and nights compared with the BDP 1,000 group, and there was no difference between the two salmeterol groups. None of the treatments altered BHR. Exacerbation rates did not differ among the three groups. We conclude that in this selected group of symptomatic patients taking BDP 500 micrograms twice daily, the addition of salmeterol provides better improvement in lung function and symptom control, without altering BHR or increasing exacerbation rates, than does doubling the dose of BDP.
Future Water Resources for Irrigation (Technology and Sustainability) (2004)

The study highlights novel ideas to manage urban and rural waste streams keeping in mind the maintenance and enhancement of the productive capacity of limited water resources. One such technique is stubble mulching and the need to recognize climate variability and change in all strategic and tactical planning and management of water.