gebhart/patrepeval huggingface dataset:
Sterilization of Aortic Valve Grafts for Transplantation (1970)

Valve graft sterility is a prerequisite for long term success in transplantation of homologous or heterologous aortic valves. Grafts obtained sterilely or unsterilely have been treated with β-propiolactone,<sup>1,2</sup>ethylene oxide,<sup>3</sup>irradiation,<sup>4,5</sup>4% buffered formaldehyde solution (formalin),<sup>6</sup>and antibiotic solutions.<sup>7</sup>These methods are generally considered effective in eliminating organisms from the tissue. However, the long-term resistance to infection of grafts so prepared is not known. Endocarditis involving the homograft has been reported by several investigators utilizing these techniques,<sup>4,6,8-11</sup>although the incidence is not particularly higher than prosthetic substitutes. Analysis of our own experience<sup>12</sup>with the β-propiolactone sterilized valve revealed late failure from infection in a high percentage of cases, but common bacteria were not responsible for failure in most patients. The relative importance of factors such as the type of bacteria present at the time of harvest, interval between donor's death and valve procurement,
Serum Levels of Tumor Necrosis Factor and Interleukin-13 Are Elevated in Patients with Localized Scleroderma (2003)

These results suggest that TNF and IL-13 may be associated with the development of LSc.
Orexin System: The Key for a Healthy Life (2017)

The orexin-A/hypocretin-1 and orexin-B/hypocretin-2 are neuropeptides synthesized by a cluster of neurons in the lateral hypothalamus and perifornical area. Orexin neurons receive a variety of signals related to environmental, physiological and emotional stimuli, and project broadly to the entire CNS. Orexin neurons are "multi-tasking" neurons regulating a set of vital body functions, including sleep/wake states, feeding behavior, energy homeostasis, reward systems, cognition and mood. Furthermore, a dysfunction of orexinergic system may underlie different pathological conditions. A selective loss orexin neurons was found in narcolepsia, supporting the crucial role of orexins in maintaining wakefulness. In animal models, orexin deficiency lead to obesity even if the consume of calories is lower than wildtype counterpart. Reduced physical activity appears the main cause of weight gain in these models resulting in energy imbalance. Orexin signaling promotes obesity resistance via enhanced spontaneous physical activity and energy expenditure regulation and the deficiency/dysfunction in orexins system lead to obesity in animal models despite of lower calories intake than wildtype associated with reduced physical activity. Interestingly, orexinergic neurons show connections to regions involved in cognition and mood regulation, including hippocampus. Orexins enhance hippocampal neurogenesis and improve spatial learning and memory abilities, and mood. Conversely, orexin deficiency results in learning and memory deficits, and depression.
1,2,4-Triazole Derivative as an Electron Transport Layer in Organic Electroluminescent Devices (1993)

Organic electroluminescent devices with multilayer structures were fabricated using a 1,2,4-triazole derivative as the carrier transport layer. 3-(4-Biphenylyl)-4-phenyl-5-(4- tert -butylphenyl)-1,2,4-triazole (TAZ) was found to be electron-transporting, and a cell with a structure of glass substrate/indium-tin oxide/triphenylamine derivative (TPD)/TAZ/Alq/Mg:Ag exhibited bright blue electroluminescence from the TPD layer. A luminance of 3700 cd/m 2 with an emission peak at 464 nm was achieved at a drive voltage of 16 V.
Directed-graph epidemiological models of computer viruses (2002)

The strong analogy between biological viruses and their computational counterparts has motivated the authors to adapt the techniques of mathematical epidemiology to the study of computer virus propagation. In order to allow for the most general patterns of program sharing, a standard epidemiological model is extended by placing it on a directed graph and a combination of analysis and simulation is used to study its behavior. The conditions under which epidemics are likely to occur are determined, and, in cases where they do, the dynamics of the expected number of infected individuals are examined as a function of time. It is concluded that an imperfect defense against computer viruses can still be highly effective in preventing their widespread proliferation, provided that the infection rate does not exceed a well-defined critical epidemic threshold.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Production of Optically Pure d -Lactic Acid in Mineral Salts Medium by Metabolically Engineered Escherichia coli W3110 (2003)

The resistance of polylactide to biodegradation and the physical properties of this polymer can be controlled by adjusting the ratio of L-lactic acid to D-lactic acid. Although the largest demand is for the L enantiomer, substantial amounts of both enantiomers are required for bioplastics. We constructed derivatives of Escherichia coli W3110 (prototrophic) as new biocatalysts for the production of D-lactic acid. These strains (SZ40, SZ58, and SZ63) require only mineral salts as nutrients and lack all plasmids and antibiotic resistance genes used during construction. D-Lactic acid production by these new strains approached the theoretical maximum yield of two molecules per glucose molecule. The chemical purity of this D-lactic acid was approximately 98% with respect to soluble organic compounds. The optical purity exceeded 99%. Competing pathways were eliminated by chromosomal inactivation of genes encoding fumarate reductase (frdABCD), alcohol/aldehyde dehydrogenase (adhE), and pyruvate formate lyase (pflB). The cell yield and lactate productivity were increased by a further mutation in the acetate kinase gene (ackA). Similar improvements could be achieved by addition of 10 mM acetate or by an initial period of aeration. All three approaches reduced the time required to complete the fermentation of 5% glucose. The use of mineral salts medium, the lack of antibiotic resistance genes or plasmids, the high yield of D-lactate, and the high product purity should reduce costs associated with nutrients, purification, containment, biological oxygen demand, and waste treatment.
Nuclear Phospholipase C in Biological Control and Cancer (2011)

Inositol lipids are key regulators of several cellular functions. The identification of an independent nuclear polyphosphoinositides signaling machinery has led the way to find new roles for these molecules. PI-PLC-β1 is the most extensively studied PLC isoform in the nuclear compartment and a key player in the regulation of nuclear lipid signaling. Nuclear PI-PLC-β1 is involved in cell cycle progression and differentiation in response to growth factor stimulation. A growing body of evidence has demonstrated that nuclear phosphoinositides are also involved in cancer cell generation, proliferation, and resistance to apoptosis. Evidence on ex vivo human cancer cells from patients with myelodysplastic syndromes (MDS) confirmed these observations, suggesting the involvement of PI-PLC-β1 both in the pathogenesis of the disease and in the progression of MDS to acute myeloid leukemia. These studies have offered new targets for the development of novel therapeutic strategies as well as new prognostic tools.
Grassystatins A−C from Marine Cyanobacteria, Potent Cathepsin E Inhibitors That Reduce Antigen Presentation (2009)

In our efforts to explore marine cyanobacteria as a source of novel bioactive compounds, we discovered a statine unit-containing linear decadepsipeptide, grassystatin A (1), which we screened against a diverse set of 59 proteases. We describe the structure determination of 1 and two natural analogues, grassystatins B (2) and C (3), using NMR, MS, and chiral HPLC techniques. Compound 1 selectively inhibited cathepsins D and E with IC(50)s of 26.5 nM and 886 pM, respectively. Compound 2 showed similar potency and selectivity against cathepsins D and E (IC(50)s of 7.27 nM and 354 pM, respectively), whereas the truncated peptide analogue grassystatin C (3), which consists of two fewer residues than 1 and 2, was less potent against both but still selective for cathepsin E. The selectivity of compounds 1-3 for cathepsin E over D (20-38-fold) suggests that these natural products may be useful tools to probe cathepsin E function. We investigated the structural basis of this selectivity using molecular docking. We also show that 1 can reduce antigen presentation by dendritic cells, a process thought to rely on cathepsin E.
Production of Monocyte Chemotactic Protein‐1 By Rat Brain Macrophages (1996)

In the present study, we show that cultured rat brain macrophages release a soluble factor that stimulates the migration of bone marrow-derived macrophages, as determined by an in vitro chemotaxis assay. A checkerboard analysis indicated that most of this effect resulted from a polarized migration of the cells (chemotactic phenomenon), rather than in an increase in cell motility (chemokinesis). This activity was significantly decreased by an immune serum directed against the rat monocyte chemoattractant protein-1 (chemokine MCP-1). Northern blot analysis demonstrated expression of the MCP-1 gene in cultured brain macrophages, but its absence in unstimulated bone marrow-derived macrophages. Up-regulation of MCP-1 expression was observed when lipopolysaccharide was added to cultured brain macrophages, a peak occurring after a 6 h period of stimulation. Also, inflammatory cytokines such as interleukin (IL)-1 beta, colony stimulating factor-1, tumour necrosis factor-alpha and IL-6 individually increased the basal level of MCP-1 mRNA. Subsequently, we demonstrated the in vivo production of MCP-1 in the adult rat brain following injury induced by a local injection of kainic acid. MCP-1 synthesis was localized in both astrocytes and brain macrophages. These results suggest that the activation of resting microglial cells into brain macrophages and their subsequent secretion of chemokines could contribute to the mechanism(s), leading to the infiltration of the CNS by blood-derived monocytes, as observed in several pathologies.
Modulation of γ-secretase specificity using small molecule allosteric inhibitors (2009)

gamma-Secretase cleaves multiple substrates within the transmembrane domain that include the amyloid precursor protein as well as the Notch family of receptors. These substrates are associated with Alzheimer disease and cancer. Despite extensive investigation of this protease, little is known regarding the regulation of gamma-secretase specificity. To discover selective inhibitors for drug development and for probing the mechanisms of gamma-secretase specificity, we screened chemical libraries and consequently developed a di-coumarin family of inhibitors that preferentially inhibit gamma-secretase-mediated production of Abeta42 over other cleavage activities. These coumarin dimer-based compounds interact with gamma-secretase by binding to an allosteric site. By developing a multiple photo-affinity probe approach, we demonstrate that this allosteric binding causes a conformational change within the active site of gamma-secretase at the S2 and S1 sub-sites that leads to selective inhibition of Abeta42. In conclusion, by using these di-coumarin compounds, we reveal a mechanism by which gamma-secretase specificity is regulated and provide insights into the molecular basis by which familial presenilin mutations may affect the active site and specificity of gamma-secretase. Furthermore, this class of selective inhibitors provides the basis for development of Alzheimer disease therapeutic agents.
Label-Free Detection of Peptide Nucleic Acid−DNA Hybridization Using Localized Surface Plasmon Resonance Based Optical Biosensor (2005)

The development of label-free optical biosensors for DNA and other biomolecules has the potential to impact life sciences as well as screening in medical and environmental applications. In this report, we developed a localized surface plasmon resonance (LSPR) based label-free optical biosensor based on a gold-capped nanoparticle layer substrate immobilized with peptide nucleic acids (PNAs). PNA probe was designed to recognize the target DNA related to tumor necrosis factor. The nanoparticle layer was formed on a gold-deposited glass substrate by the surface modified silica nanoparticles using silane-coupling reagent. The optical properties of gold-capped nanoparticle layer substrate were characterized through monitoring the changes in the absorbance strength, as the thickness of the biomolecular layer increased with hybridization. The detection of PNA-DNA hybridization with target oligonucleotides and PCR-amplified real samples were performed with a limit of detection value of 0.677 pM target DNA. Selective discrimination against a single-base mismatch was also achieved. Our LSPR-based biosensor with the gold-capped nanoparticle layer substrate is applicable to the design of biosensors for monitoring of the interaction of other biomolecules, such as proteins, whole cells, or receptors with a massively parallel detection capability in a highly miniaturized package.
Sigma‐1 receptor: a pivotal role in lens cell survival (2007)

Abstract Purpose: Sigma‐1 receptor (Sig‐1R) has no known homology with any other receptors. Natural ligands are yet to be identified. Sig‐1R appears to play a critical role in controlling cell proliferation. The human lens grows throughout life and uncontrolled growth after cataract surgery is responsible for Posterior Capsule Opacification (PCO). We have therefore investigated a possible role for Sig‐1R antagonists in controlling PCO. Methods: The human lens cell line FHL124 expresses the Sig‐1R and was employed for this study. Cells were maintained in EMEM or EMEM supplemented with 5% Serum (FCS) at 35°C in 5% CO2. Sig‐1R siRNA and scrambled siRNA were purchased from Ambion. Cell growth was assessed by measuring total protein and cell death by quantifying LDH leakage. mRNA level was assayed by RT‐PCR. Protein level was measured by western blotting. Results: A dose‐dependent effect of Sig‐1R antagonist (rimcazole or BD1047) on cell growth was observed. 72 hours of transfection with siRNAs directed against Sig‐1R reduced mRNA and protein levels by over 70 and 60% respectively. Subsequent incubation for 96 hours in 5%FCS gave a partial recovery of mRNA, but no significant increase in protein expression. LDH leakage assays showed that significant cell death occurred and was accompanied by an increased level of Caspase‐3. The increases of pERK and pAkt stimulated with 10nM thrombin were inhibited by silencing Sig‐1R, but not in cells exposed to scrambled siRNA. The recycling level of EGF receptor was significantly reduced by Sig‐1R antagonists compared with controls. Conclusions: This study establishes a central role for the Sig‐1R in lens cell survival through modulating the activity of growth factor receptor mediated cell signalling and growth factor receptor trafficking.
Activities of Bismuth Thiols against Staphylococci and Staphylococcal Biofilms (2001)

Indwelling medical devices are associated with infectious complications. Incorporating antimicrobials into indwelling materials may reduce bacterial colonization. Bismuth thiols are antibiofilm agents with up to 1,000-fold-greater antibacterial activity than other bismuth salts. Staphylococci are particularly sensitive, as determined by agar diffusion and broth dilution susceptibility testing. Bismuth-ethanedithiol inhibited 10 methicillin-resistant Staphylococcus epidermidis strains at 0.9 to 1.8, Staphylococcus aureus ATCC 25923 at 2.4, and S. epidermidis ATCC 12228 at 0.1 microM Bi(3+). Antiseptic-resistant S. aureus was sensitive to bismuth-2-3-dimercaptopropanol (BisBAL) at < or = 7 microM Bi(3+). Hydrogel-coated polyurethane rods soaked in BisBAL inhibited S. epidermidis for 39 days (inhibitory zone diameter in agar, > or = 30 mm for > 25 days). Slime from 16 slime-producing S. epidermidis strains was inhibited significantly by bismuth-3,4-dimercaptotoluene (BisTOL), but not by AgNO3, at subinhibitory concentrations. In conclusion, bismuth-thiols are bacteriostatic and bactericidal against staphylococci, including resistant organisms, but are also inhibitors of slime at subinhibitory concentrations. At subinhibitory concentrations, BisTOL may be useful in preventing the colonization and infection of indwelling intravascular lines, since staphylococci are important pathogens in this setting.
Gaze awareness for video-conferencing: a software approach (2000)

Previous attempts at bringing gaze awareness to desktop videoconferencing have relied on hardware solutions. In this article, the authors describe their software approach, which tracks participants' head and eye movements using vision techniques, then uses this information to graphically place the head and eyes in a 3D environment.
The plant alkaloid usambarensine intercalates into DNA and induces apoptosis in human HL60 leukemia cells. (2000)

Usambarensine is a plant alkaloid isolated from the roots of Strychnos usambarensis collected in Central Africa. This bis-indole compound displays potent antiamoebic activities and shows antigardial, antimalarial and cytotoxic effects. Usambarensine is highly toxic to B16 melanoma cells and inhibits the growth of leukemia and carcinoma cells. To date, the molecular basis for its diverse biological effects remains totally unknown. However, its capacity to inhibit nucleic acids synthesis in melanoma cells, on the one hand, and its structural analogy with DNA-binding pyridoindole plant alkaloids recently studied (cryptolepine and matadine), on the other hand, suggested that usambarensine could also bind to DNA. Consequently, we studied the strength and mode of binding to DNA of usambarensine by means of absorption, circular and linear dichroism. The results of the optical measurements indicate that the alkaloid effectively binds to DNA and behaves as a typical intercalating agent. Biochemical experiments indicated that, in contrast to cryptolepine and matadine, usambarensine does not interfere with the catalytic activity of topoisomerase II. Human HL60 leukemia cells were used to assess the cytotoxicity of the alkaloid and its effect on the cell cycle. Usambarensine treatment is associated with a loss of cells in the G1 phase accompanied with a large increase in the sub-G1 region which is characteristic of apoptotic cells. The DNA of usambarensine-treated cells was severely fragmented and the proteolytic activity of DEVD-caspases is enhanced. Usambarensine is thus characterized as DNA intercalator inducing apoptosis in leukemia cells.
A New Solution for Camera Calibration and Real-Time Image Distortion Correction in Medical Endoscopy–Initial Technical Evaluation (2011)

Medical endoscopy is used in a wide variety of diagnostic and surgical procedures. These procedures are renowned for the difficulty of orienting the camera and instruments inside the human body cavities. The small size of the lens causes radial distortion of the image, which hinders the navigation process and leads to errors in depth perception and object morphology. This article presents a complete software-based system to calibrate and correct the radial distortion in clinical endoscopy in real time. Our system can be used with any type of medical endoscopic technology, including oblique-viewing endoscopes and HD image acquisition. The initial camera calibration is performed in an unsupervised manner from a single checkerboard pattern image. For oblique-viewing endoscopes the changes in calibration during operation are handled by a new adaptive camera projection model and an algorithm that infer the rotation of the probe lens using only image information. The workload is distributed across the CPU and GPU through an optimized CPU+GPU hybrid solution. This enables real-time performance, even for HD video inputs. The system is evaluated for different technical aspects, including accuracy of modeling and calibration, overall robustness, and runtime profile. The contributions are highly relevant for applications in computer-aided surgery and image-guided intervention such as improved visualization by image warping, 3-D modeling, and visual SLAM.
Word sequence kernels (2003)

We address the problem of categorising documents using kernel-based methods such as Support Vector Machines. Since the work of Joachims (1998), there is ample experimental evidence that SVM using the standard word frequencies as features yield state-of-the-art performance on a number of benchmark problems. Recently, Lodhi et al. (2002) proposed the use of string kernels, a novel way of computing document similarity based of matching non-consecutive subsequences of characters. In this article, we propose the use of this technique with sequences of words rather than characters. This approach has several advantages, in particular it is more efficient computationally and it ties in closely with standard linguistic pre-processing techniques. We present some extensions to sequence kernels dealing with symbol-dependent and match-dependent decay factors, and present empirical evaluations of these extensions on the Reuters-21578 datasets.
Preventive effects of citrulline on Western diet-induced non-alcoholic fatty liver disease in rats (2016)

A Western diet induces insulin resistance, liver steatosis (non-alcoholic fatty liver disease (NAFLD)) and intestinal dysbiosis, leading to increased gut permeability and bacterial translocation, thus contributing to the progression of NAFLD to non-alcoholic steatohepatitis. In the present study, we sought, in a model of Western diet-induced NAFLD, to determine whether citrulline (Cit), an amino acid that regulates protein and energy metabolism, could decrease Western diet-induced liver injuries, as well as the mechanisms involved. Sprague-Dawley rats were fed a high-fat diet (45 %) and fructose (30 %) in drinking water or a control diet associated with water (group C) for 8 weeks. The high-fat, high-fructose diet (Western diet) was fed either alone (group WD) or with Cit (1 g/kg per d) (group WDC) or an isonitrogenous amount of non-essential amino acids (group WDA). We evaluated nutritional and metabolic status, liver function, intestinal barrier function, gut microbiota and splanchnic inflammatory status. Cit led to a lower level of hepatic TAG restricted to microvesicular lipid droplets and to a lower mRNA expression of CCAAT-enhancer-binding protein homologous protein, a marker of endoplasmic reticulum stress, of pro-inflammatory cytokines Il6 (P<0·05) and Tnfα, and of toll-like receptor 4 (Tlr4) (P<0·05). Cit also improved plasma TAG and insulin levels. In the colon, it decreased inflammation (Tnfα and Tlr4 expressions) and increased claudin-1 protein expression. This was associated with higher levels of Bacteroides/Prevotella compared with rats fed the Western diet alone. Cit improves Western diet-induced liver injuries via decreased lipid deposition, increased insulin sensitivity, lower inflammatory process and preserved antioxidant status. This may be related in part to its protective effects at the gut level.