gebhart/patrepeval huggingface dataset:
Modulation of the JNK Pathway in Liver Affects Insulin Resistance Status (2004)

The c-Jun N-terminal kinase (JNK) pathway is known to be activated under diabetic conditions and to possibly be involved in the progression of insulin resistance. In this study, we examined the effects of modulation of the JNK pathway in liver on insulin resistance and glucose tolerance. Overexpression of dominant-negative type JNK in the liver of obese diabetic mice dramatically improved insulin resistance and markedly decreased blood glucose levels. Conversely, expression of wild type JNK in the liver of normal mice decreased insulin sensitivity. The phosphorylation state of crucial molecules for insulin signaling was altered upon modification of the JNK pathway. Furthermore, suppression of the JNK pathway resulted in a dramatic decrease in the expression levels of the key gluconeogenic enzymes, and endogenous hepatic glucose production was also greatly reduced. Similar effects were observed in high fat, high sucrose diet-induced diabetic mice. Taken together, these findings suggest that suppression of the JNK pathway in liver exerts greatly beneficial effects on insulin resistance status and glucose tolerance in both genetic and dietary models of diabetes.
Seed Concentration Control of Metal Nanowire Diameter (2012)

Gold/silver nanowires (NWs) of controlled diameters were synthesized from catalytic metal seed particles at the substrate/solution interface. Small seed nanoparticles of three different sizes: ~1 nm (11 gold atoms), ~1.4 nm (~55 gold atoms), and homemade nanoparticles of ~2 nm were used. By varying a single type of seed particle concentration in the growth solution, the NW diameters and morphology could be controlled, between bundles of ultrathin NWs of ~2-3 nm diameter to thicker isolated single NWs with a mean diameter of ~16 nm. In addition, the catalytic reduction rate leading to NW growth was found to be seed size dependent at small seed sizes (<2 nm). The two types of metallic NW films were tested for their performance as transparent electrodes after additional metal deposition for their stabilization and conductivity enhancement. The thin NW bundles exhibit superior transparent conductor properties.
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models (2017)

Colorectal cancers (CRCs) can be divided into four gene expression-based biologically distinct consensus molecular subtypes (CMS). This classification provides a potential framework for stratified treatment, but to identify novel CMS-drug associations, translation of the subtypes to pre-clinical models is essential. The currently available classifier is dependent on gene expression signals from the immune and stromal compartments of tumors and fails to identify the poor-prognostic CMS4-mesenchymal group in immortalized cell lines, patient-derived organoids and xenografts. To address this, we present a novel CMS classifier based on a filtered set of cancer cell-intrinsic, subtype-enriched gene expression markers. This new classifier, referred to as CMScaller, recapitulated the subtypes in both in vitro and in vivo models (551 in total). Importantly, by analyzing public drug response data from patient-derived xenografts and cell lines, we show that the subtypes are predictive of response to standard CRC drugs. CMScaller is available as an R package.
A Huffman-Shannon-Fano code (1973)

A variable-word-length minimum-redundant code is described. It has the advantages of both the Huffman and Shannon-Fano codes in that it reduces transmission time, storage space, translation table space, and encoding and decoding times.
Graphics processing with the 88110 RISC microprocessor (2003)

The author presents details of the instructions and data types provided by the 88110's graphics unit. She also gives several graphics processing examples using both floating point and graphics instructions to achieve high performance. She points out that the 88110 combines sustained high performance general processor, graphics support, and floating point performance together on one chip. The graphics unit is flexible in supporting floating point, fixed point, and packed pixels. Pixel packing and unpacking are supported for manipulation of color intensity data types and packed pixel data types. A compare instruction can perform two Z-buffer compares in parallel. Pixel multiply is supported for compositing images together. A pixel rotate and all the other bit field instructions supported by the 88000 architecture provide a powerful means of manipulating data. The 88110 also maintains high bus bandwidth and has on chip multiprocessor support. All of these features combined make the 88110 well suited for central processing and graphics processing. This can eliminate the need for a secondary processor in a graphics system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
PHASE BEHAVIOR OF THE ETHANOL-BIODIESEL-DIESEL MICRO-EMULSION SYSTEM (2005)

The use of ethanol blended with regular diesel fuel was a subject of research in the 1980s. It was shown that suchblends were technically acceptable for existing diesel engines without modifications. Biodiesel as well as ethanol-blendedE-diesel yielded substantial reductions in urban emissions of carbon monoxide (CO), greenhouse gases (primarily CO2),sulfur oxides (SOx), and particulate matter (PM). The major drawback of E-diesel is that ethanol is immiscible in diesel overa wide range of temperatures. This study attempts to use biodiesel as a potential amphiphile in the ethanol-biodiesel system.The study looks into the phase behavior of the ethanol-biodiesel-diesel ternary system in order to identify key areas withinthe phase diagram that are stable isotropic micro-emulsions that could be used as potential biofuels for compression-ignitionengines. The instantaneous phase behavior indicated that the system formulates stable micro-emulsions over a fairly largeregion of the phase triangle, depending on the concentrations of different components. The single-phase area of thethree-component system was widest at higher biodiesel concentrations. The phase diagram indicated that at higher dieselconcentrations, in order to formulate a stable micro-emulsion, the ratio of biodiesel to ethanol in the system should be greaterthan 1:1. The results of the study suggested that biodiesel could be effectively used as an amphiphile in an ethanol-dieselblend.
Microbes inside—from diversity to function: the case of Akkermansia (2012)

The human intestinal tract is colonized by a myriad of microbes that have developed intimate interactions with the host. In healthy individuals, this complex ecosystem remains stable and resilient to stressors. There is significant attention on the understanding of the composition and function of this intestinal microbiota in health and disease. Current developments in metaomics and systems biology approaches allow to probe the functional potential and activity of the intestinal microbiota. However, all these approaches inherently suffer from the fact that the information on macromolecules (DNA, RNA and protein) is collected at the ecosystem level. Similarly, all physiological and other information collected from isolated strains relates to pure cultures grown in vitro or in gnotobiotic systems. It is essential to integrate these two worlds of predominantly chemistry and biology by linking the molecules to the cells. Here, we will address the integration of omics- and culture-based approaches with the complexity of the human intestinal microbiota in mind and the mucus-degrading bacteria Akkermansia spp. as a paradigm.
Chemical and Structural Insights into the Regioversatility of the Aminoglycoside Acetyltransferase Eis (2013)

A recently discovered cause of tuberculosis resistance to a drug of last resort, the aminoglycoside kanamycin, results from modification of this drug by the enhanced intracellular survival (Eis) protein. Eis is a structurally and functionally unique acetyltransferase with an unusual capability of acetylating aminoglycosides at multiple positions. The extent of this regioversatility and its defining protein features are unclear. Herein, we determined the positions and order of acetylation of five aminoglycosides by NMR spectroscopy. This analysis revealed unprecedented acetylation of the 3''-amine of kanamycin, amikacin, and tobramycin, and the γ-amine of the 4-amino-2-hydroxybutyryl group of amikacin. A crystal structure of Eis in complex with coenzyme A and tobramycin revealed how tobramycin can be accommodated in the Eis active site in two binding modes, consistent with its diacetylation. These studies, describing chemical and structural details of acetylation, will guide future efforts towards designing aminoglycosides and Eis inhibitors to overcome resistance in tuberculosis.
Nitroreductase-based GDEPT (2002)

Nitroreductases that metabolise aromatic nitro groups to hydroxylamines are attractive as enzymes for GDEPT because of the very large electronic change that this metabolism generates, providing an efficient switch that can be exploited to generate potent cytotoxins. While nitroreductase enzymes are widespread, nearly all the work using these in GDEPT has been with the nfsB gene product of Escherichia coli, an oxygen-insensitive flavin mononucleotide nitroreductase (NTR). Four classes of prodrugs for NTR have been described; dinitroaziridinylbenzamides, dinitrobenzamide mustards, 4-nitrobenzylcarbamates and nitroindolines. While some quinones are excellent substrates for NTR, none have been identified as potential GDEPT prodrugs. The most widely studied prodrug used for GDEPT in conjunction with NTR is the dinitroaziridinylbenzamide CB 1954. This shows high selectivity (>1000-fold) in cell lines transfected with NTR, has potent and long-lasting inhibition of NTR-transfected tumours in mice, and is in Phase I trial in conjunction with virally-delivered NTR enzyme. The related mustard SN 23862 has similar selectivity and superior bystander effects in animal models. Nitrobenzyl carbamates of a variety of cytotoxic amines (including aniline mustards, enediynes, duocarmycin analogues, pyrrolobenzodiazepines and the antitumour antibiotics doxorubicin, actinomycin D and mitomcyin C) are metabolised efficiently by NTR to the hydroxylamines, that fragment to release the amines. Nitroindoline derivatives of duocarmycins also show moderate selectivity for NTR-transfected cell lines in culture.
IL-12 stimulates the development of acute graft-versus-host disease in mice that normally would develop chronic, autoimmune graft-versus-host disease. (1994)

The injection of DBA/2 (D2) spleen cells into (C57BL/6 x DBA/2)F1 mice (BDF1) induces a chronic, autoimmune graft-vs-host disease (GVHD) that is characterized by: increased production of Th2-associated cytokines; increased levels of serum Ig, including IgE; increased production of IgG anti-DNA Abs; and no detectable antihost CTL activity. Experiments were performed to determine if treatment with the cytokine IL-12, which stimulates the production of Th1-associated cytokines and inhibits Th2-associated cytokine production, would inhibit humoral autoimmunity in this system. Treatment of mice with 100 ng IL-12 per day for 5 days, starting on the day of cell transfer, resulted in: 1) near complete suppression of autoantibody production; 2) decreased serum Ig levels; 3) detectable donor antihost CTL activity; and 4) greatly reduced numbers of host splenic B and T cells. Treatment of mice with a neutralizing anti-IFN-gamma mAb did not reverse these effects of IL-12. Thirty nanograms per day resulted in reduced numbers of host B cells and reduced serum anti-DNA levels, but no detectable antihost CTL activity. IL-12 treatment initiated 7 days after cell transfer had little effect on the development of autoimmune GVHD. These observations suggest the following: 1) IL-12 inhibits humoral autoimmunity in a murine parent-->F1 GVHD model by inducing the activation of host-reactive CTLs that reject the host immune system. 2) This effect is IFN-gamma-independent. 3) IL-12 needs to be present during the initial differentiation of T cells in this system to have this effect.
A wireless magnetoelastic micro-sensor array for simultaneous measurement of temperature and pressure (2001)

Magnetoelastic thick film sensors mechanically deform when subjected to a magnetic field impulse, launching elastic waves within the sensor the magnitude of which is greatest at the mechanical resonant frequency. As the sensors are magnetostrictive, the mechanical deformations launch magnetic flux that can be detected remotely. The characteristic resonant frequency of a magnetoelastic sensor, which is a function of the length, density, elasticity and Poisson's ratio of the sensor material, changes in response to temperature, pressure, ambient flow rate and, in combination with a mass changing, chemically responsive layer different analyte concentrations. By using an array of such sensors different environmental parameters can be simultaneously determined in a complex environment; we have designed and fabricated such an array for the simultaneous measurement of temperature and pressure.
Camptothecin: Roles of the D and E Rings in Binding to the Topoisomerase I-DNA Covalent Binary Complex (2005)

The alkaloid camptothecin is the prototypical DNA topoisomerase I poison. This core structure has formed the basis for two marketed antitumor agents and numerous clinical candidates, and has been the focus of many synthetic and medicinal chemistry studies. Recent reports have furthered our understanding of the roles played by the D and E rings of camptothecin in stabilization of the enzyme-DNA-camptothecin ternary complex. Important parameters for further study and optimization include the facility of E-ring lactone hydrolysis and the prospects for replacing the E ring with more stable structures, the role of the 14-CH group in binary complex binding, and the effect of ternary complex dynamics on the expression of cytotoxicity by the camptothecins.
Gene expression profiling of malignant mesothelioma cell lines: cDNA array study (2001)

To reveal genes relevant for malignant mesothelioma (MM), we carried out cDNA array experiments on 4 MM cell lines and 2 primary mesothelial cell cultures established from pleural fluid of non-cancer patients. Human cancer gene filters including 588 genes were used for the cDNA array experiments. Our study revealed 26 over-expressed genes that play a role in the regulation of cell fate, cell cycle, cell growth and DNA damage repair and 13 under-expressed genes encoding growth factors, receptors and proteins involved in cell adhesion, motility and invasion to be common to 3 or 4 MM cell lines. We confirmed the cDNA array results using RT-PCR for 5 of the over-expressed genes and for 3 of the under-expressed genes. Our study presents gene expression profiles in MM cell lines and shows the involvement of several genes, such as those encoding JAGGED1, ser/thr protein kinase NIK, Ku80 and cyclin D2, novel in MM.
Study of pulse compression from 1.5 μm distributed feedback lasers by a gires-tournois interferometer (1994)

Abstract In this paper, the compression experiments of picosecond optical pulses from a gain-switched InGaAsP distributed feedback (DFB) laser at a 1.5 μm wavelength range using a Gires-Tournois (G-T) interferometer are reported. Ultrashort optical pulses with a pulsewidth of 6.6 ps, repetition rate of 2.4 GHz, and peak power in excess of 200 mW are obtained. The compression ratio is close to 5. The explanation for the experimental results is given, and the pulse's compression characteristics of a G-T inteferometer are discussed by a computer simulation analysis.
Induction of tumour-specific immunity by manipulating the expression of major histocompatibility complex molecules on tumour cells (1990)

Class I major histocompatibility complex (MHC) molecules form part of the target structure recognized by the host cytotoxic T cells (CTL) to reject tumour cells. Many types of malignant tumour cells are reported in which expression of class I MHC genes is down-regulated. By DNA-mediated gene transfer, it is possible to re-express the 'missing' syngeneic (genetically identical) or to introduce 'new' allogeneic (genetically dissimilar) class I MHC genes into these MHC-deficient tumours. In both instances, the immunogenicity of the transfected tumour cells is greatly enhanced and results in their rejection in vivo. More importantly, these 'modified' tumour cells, which are positive for class I MHC molecules, can simultaneously generate an immunity against the 'wild-type' tumour cells which do not express these molecules. These observations suggest the distinct possibility of using gene transfer as a molecular immunotherapeutic approach to abrogate tumour growth.
Printing Processes (2000)

Abstract The role of chemical technology in printing processes is changing. These changes are driven by cost, convenience, and environmental pressures. Rapid advances in alternative media and computer technology are enabling the incorporation of electronic processes into the printing workflow to meet industry cost and performance needs. Elements of the printing process from image creation, capture, assembly, storage, movement, approval, duplication, output, and distribution are examined. The continuing role of chemical printing processes such as lithography, flexography, letterpress, screen printing, and thermal printing, as well as the various media and inks employed, is described. The opportunities provided by electronic technology are also presented. The newer electronic digital processes involve consumable materials that are based on chemical systems more suited to the changing needs of the printing industry. The new digital systems capabilities are discussed in terms of their impact on industry practices and workflow. Technologies that are changing the nature of the printing industry include thermal imaging, electrophotography, and ink‐jet printing.
Continuous sedation during spinal anaesthesia: gamma-hydroxybutyrate vs. propofol (1999)

Gamma-hydroxybutyrate (GHB) may well be developed as an alternative for optional sedation during spinal anaesthesia. As in the case of propofol (PRO), GHB has good sedative properties associated with cardiovascular and respiratory stability. When used as a narcotic agent, recovery times are variable (e.g. > 30 min); in contrast, sedative dosages, as used in intensive care patients (e.g. 10-20 mg kg−1 h−1), result in adequate clinical recovery. The goal of the present study was to compare the clinical properties of GHB and PRO after continuous administration during spinal anaesthesia (SPA). Thirty patients (ASA I and II) received either GHB (n = 15) or PRO (n = 15) at random. Patients refusing sedation (n = 15) received 0.9% saline (control). At eight defined time points, haemodynamic (BP, HR), respiratory (RR, RMV, PaO2, SpO2, PETO2, PETCO2, JOURNAL/ejanet/04.03/00003643-199901000-00006/OV0312_1/v/2021-02-06T021411Z/r/image-pngO2, JOURNAL/ejanet/04.03/00003643-199901000-00006/OV0312_1/v/2021-02-06T021411Z/r/image-pngCO2) and endocrinological parameters (plasma concentrations of noradrenaline and adrenaline) as well as the clinical side-effects were assessed simultaneously. With both sedatives, the desired level of sedation was achieved. Recovery times ranged between 1.7 ± 0.9 min with PRO and 6.1 ± 4.9 min with GHB. GHB provided stable haemodynamic conditions without clinically relevant respiratory depression. In contrast, PRO caused a decrease in mean arterial pressue (MAP) of 15%, whereas respiratory minute volume was decreased by 53% (with periods of apnoea, SpO2<90%). JOURNAL/ejanet/04.03/00003643-199901000-00006/OV0312_1/v/2021-02-06T021411Z/r/image-pngO2 and JOURNAL/ejanet/04.03/00003643-199901000-00006/OV0312_1/v/2021-02-06T021411Z/r/image-pngCO2 correlated with respiratory minute volume (GHB, PRO, control). Plasma noradrenaline and adrenaline concentrations remained nearly constant in the GHB and control groups and declined during sedation with PRO. Both GHB and PRO are suitable for optional sedation during spinal anaesthesia. Control and recovery are acceptable for clinical purposes. It seems that GHB and PRO have similar haemodynamic, respiratory and endocrinological characteristics. Therefore, GHB may serve as an alternative for the established management of continuous sedation during SPA with PRO.
FATAL ACUTE MYOCARDIAL INFARCTION AFTER INTRAVENOUS FLUORESCEIN ANGIOGRAPHY (1993)

Since its introduction, fluorescein angiography has been widely used to investigate diseases of the ocular fundus. A case of fatal acute myocardial infarction after intravenous fluorescein angiography is presented. This appears to be the first case documented by autopsy in which the findings are compatible with myocardial infarction as the cause of death. Although there are no known contraindications for fluorescein angiography in patients with a history of cardiovascular disease, the indications for this elective procedure should be carefully reviewed in such patients. Adequate emergency resuscitation equipment should be available in the fluorescein angiography suite.
Ozone, Hydrogen Peroxide/Ozone And UV/Ozone Treatment Of Chromium- And Copper-Complex Dyes: Decolorization And Metal Release (1995)

Metal-complex azo dyes constitute a significant fraction of the dyes used in the textile industry and exhibit properties such as superior light- and wash-fastness. While effluent color is not always regulated, the textile finishing industry often decolorizes wastewater using processes including chemical oxidation. In this study, the use of ozone, hydrogen peroxide/ozone and UV/ozone oxidant systems was examined for treatment of two common metal-complex (premetalized) dyes, Acid Black 52 (chromium) and Direct Blue 80 (copper). Oxidant dosages required for decolorization of these dyes were determined. The effect of bicarbonate alkalinity on the ozonation and the hydrogen peroxide/ozone processes also was examined.
RNA viruses in the sea (2008)

Viruses are ubiquitous in the sea and appear to outnumber all other forms of marine life by at least an order of magnitude. Through selective infection, viruses influence nutrient cycling, community structure, and evolution in the ocean. Over the past 20 years we have learned a great deal about the diversity and ecology of the viruses that constitute the marine virioplankton, but until recently the emphasis has been on DNA viruses. Along with expanding knowledge about RNA viruses that infect important marine animals, recent isolations of RNA viruses that infect single-celled eukaryotes and molecular analyses of the RNA virioplankton have revealed that marine RNA viruses are novel, widespread, and genetically diverse. Discoveries in marine RNA virology are broadening our understanding of the biology, ecology, and evolution of viruses, and the epidemiology of viral diseases, but there is still much that we need to learn about the ecology and diversity of RNA viruses before we can fully appreciate their contributions to the dynamics of marine ecosystems. As a step toward making sense of how RNA viruses contribute to the extraordinary viral diversity in the sea, we summarize in this review what is currently known about RNA viruses that infect marine organisms.