gebhart/patrepeval huggingface dataset:
THE SMALL NUCLEOLAR RNAs (1995)

The present review summarizes key progress made in characterizing the small nucleolar RNAs (snoRNAs) of eukaryotic cells. Recent studies have shown snoRNA populations to be substantially more complex than anticipated initially. Many newly discovered snoRNAs are synthesized by an intron-processing pathway, which provides a potential mechanism for coordinating nuclear RNA synthesis. Several snoRNAs and snoRNP proteins are known to be needed for processing of ribosomal RNA, but precise functions remain to be defined. In principle, snoRNAs could have several roles in ribosome synthesis including: folding of pre-rRNA, formation of rRNP substrates, catalyzing RNA cleavages, base modification, assembly of pre-ribosomal subunits, and export of product rRNP particles.
Stimulated Emission as a Result of Multiphoton Interference (2007)

By performing an experiment on stimulated emission by two photons in the parametric amplification process and comparing it to a three-photon interference scheme, we present evidence in support of the idea that the underlying physics of stimulated emission is simply the constructive interference due to photon indistinguishability. So the observed signal enhancement upon the input of photons can be interpreted as a result of multiphoton interference of the input photons and the otherwise spontaneously emitted photon from the amplifier.
Purification and properties of anionic glutathione S-transferase from bovine ciliary body (1986)

An anionic glutathione S-transferase was purified from bovine ciliary body by DEAE-agarose chromatography and affinity chromatography on GSH-agarose and Orange A. The enzyme accounts for about 25% of total soluble glutathione S-transferase activity of the tissue. The purified enzyme has a molecular mass of about 50,000 Da and is composed of two identical subunits of about 25,000 Da. The enzyme has a pI of 5.8. The enzyme conjugates GSH with 1-chloro-2,4-dinitrobenzene, p-nitrobenzyl chloride, 1,2-epoxy-3-(p-nitrophenyl)propane, 1,2-dinitrobenzene and 3,4-dinitrobenzoic acid. The Km values for 1-chloro-2,4-dinitrobenzene and GSH are 0.40 mM and 0.57 mM respectively. Haematin is a non-competitive inhibitor (Ki = 4.5 microM) when tested with various concentrations of 1-chloro-2,4-dinitrobenzene. The enzyme shows no glutathione peroxidase activity with either H2O2 or cumene peroxide as substrate. On the basis of substrate specificities, pI values, amino acid composition and peptide maps, it is concluded that the ciliary-body enzyme is probably identical with the anionic form of glutathione S-transferase from bovine lens and liver.
Serum Cytokine of IL-10 and IL-12 in Chronic Liver Disease: The Immune and Inflammatory Response (2015)

The current study was designed to investigate the potential association of serum interleukin-10 and interleukin-12 with HCV infection in chronic liver disease and to evaluate their possible role as new biomarkers in HCC development. Material and Methods. Forty-one patients suffering from chronic liver disease (33 patients harbor HCV infection and 8 are HCV-negative patients) were enrolled in the present study and histopathologically diagnosed into 15 patients with HCC, 16 patients with LC, and 10 patients with liver histology compatible with precirrhotic hepatitis (PCH). Ten patients complaining of cholecystitis were included as nondisease control. Serum levels of IL-10 and IL-12 were measured by enzyme linked immunosorbent assay (ELISA). Results. HCV-infected patients showed elevated expression of IL-10 and IL-12 compared to nondisease controls (P < 0.0001) but there is no significant difference with respect to their expression in HCV-negative patients. Serum IL-10 and IL-12 were elevated significantly with disease progression (P < 0.0001) and a positive correlation coefficient was detected between IL-10, IL-12 (r = 0.785, P < 0.0001), and transaminase values suggesting their possible role in chronic inflammation progression leading to HCC. Conclusion. IL-10 and IL-12 might be involved in chronic inflammation progression leading to HCC and their evaluation could be used as new biomarkers to reflect the degree of inflammation in HCC development.
M. Spriggs, ed., Marxist Perspectives in Archaeology (1985)

Hours Francis. M. Spriggs, ed., Marxist Perspectives in Archaeology. In: L'Homme, 1985, tome 25 n°95. pp. 200-201.
Identification of mildew resistance in wild and cultivated Central Asian grape germplasm (2013)

This study provides evidence that powdery mildew resistance is present in V. vinifera subsp. sylvestris, the dioecious wild progenitor of the cultivated grape. Four first-degree parent progeny relationships were discovered among the hermaphroditic powdery mildew resistant cultivars, supporting the existence of intentional grape breeding efforts. Although several Chinese grape species are resistant to powdery mildew, no direct genetic link to the resistance found in V. vinifera could be established.
Molecular Quantification ofGardnerella vaginalisandAtopobium vaginaeLoads to Predict Bacterial Vaginosis (2008)

We report a highly reproducible, quantitative tool to objectively analyze vaginal flora that uses cutoff values for the concentrations of A. vaginae and G. vaginalis to establish the molecular diagnosis of BV.
Nevirapine Bioactivation and Covalent Binding in the Skin (2013)

Nevirapine (NVP) treatment is associated with serious skin rashes that appear to be immune-mediated. We previously developed a rat model of this skin rash that is immune-mediated and is very similar to the rash in humans. Treatment of rats with the major NVP metabolite, 12-OH-NVP, also caused the rash. Most idiosyncratic drug reactions are caused by reactive metabolites; 12-OH-NVP forms a benzylic sulfate, which was detected in the blood of animals treated with NVP or 12-OH-NVP. This sulfate is presumably formed in the liver; however, the skin also has significant sulfotransferase activity. In this study, we used a serum against NVP to detect covalent binding in the skin of rats. There was a large artifact band in immunoblots of whole skin homogenates that interfered with detection of covalent binding; however, when the skin was separated into dermal and epidermal fractions, covalent binding was clearly present in the epidermis, which is also the location of sulfotransferases. In contrast to rats, treatment of mice with NVP did not result in covalent binding in the skin or skin rash. Although the reaction of 12-OH-NVP sulfate with nucleophiles such as glutathione is slow, incubation of this sulfate with homogenized human and rat skin led to extensive covalent binding. Incubations of 12-OH-NVP with the soluble fraction from a 9,000g centrifugation (S9) of rat or human skin homogenate in the presence of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) produced extensive covalent binding, but no covalent binding was detected with mouse skin S9, which suggests that the reason mice do not develop a rash is that they lack the required sulfotransferase. This is the first study to report covalent binding of NVP to rat and human skin. These data provide strong evidence that covalent binding of NVP in the skin is due to 12-OH-NVP sulfate, which is likely responsible for NVP-induced skin rash. Sulfation may represent a bioactivation pathway for other drugs that cause a skin rash.
Total plasma antioxidant capacity in cystic fibrosis (2000)

Several studies have demonstrated ongoing oxidative stress in cystic fibrosis (CF). With the complexity of the antioxidant network, measurement of individual antioxidants does not necessarily assess how they work in combination. One measure that has been proposed as a gauge of total plasma antioxidant capacity is the Trolox-equivalent antioxidant capacity (TEAC) of plasma. We decided to look at plasma TEAC levels in children with CF, and relate this measure to their nutritional status, lung function, and blood measurements of several known antioxidants. We hypothesized that values in general would be lower than healthy control values, especially during acute pulmonary exacerbations. Twenty-nine children were evaluated, five of whom were during an acute pulmonary exacerbation. Height and weight, expiratory spirometry, and lung volumes were assessed, as were serum concentrations of vitamins A and E, uric acid, albumin, and lymphocyte glutathione (GSH) concentrations. TEAC values for nonhospitalized patients (1.40 +/- 0. 20 mmol/L) were not different from laboratory control values (1.35 +/- 0.11 mmol/L), but greater than values for hospitalized patients (1.09 +/- 0.17 mmol/L). TEAC correlated with anthropometric values (height: r = 0.39, P < 0.03; weight: r = 0.50, P < 0.01; body mass index: r = 0.47, P < 0.01), and pulmonary function (forced expiratory volume in 1 sec: r = 0.43, P < 0.02; residual volume/total lung capacity: r = -0.42, P < 0.03), but not with age. Univariate correlation with blood measurements demonstrated a significant correlation of TEAC with uric acid (r = 0.49, P < 0.02), but not with albumin, vitamins A or E, or lymphocyte GSH. Multiple regression analysis demonstrated a correlation between TEAC and uric acid, albumin, and lymphocyte GSH in the non-hospitalized group (r(2) = 0.38, P < 0.03). We conclude that TEAC appears to represent a mixed antioxidant response, rather than response to a single antioxidant. While being responsive to oxidative stress, the mechanism of the response may differ between clinical situations, such that the clinical significance of changes in plasma TEAC remains to be defined.
[Neuromodulation as a treatment for overactive bladder syndrome]. (2012)

Neuromodulation is used as a treatment for overactive bladder syndrome, if conservative management is ineffective or only partially effective. Sacral neuromodulation is now a minimally invasive treatment as a result of improvements in surgical technique, and it has good long-term results. Nevertheless the risk of complications such as pain and decreasing effect is still present. Developments in alternative neuromodulation treatments, such as posterior tibial nerve stimulation, pudendal nerve stimulation and intravesical injection therapy with botulinum neurotoxin, have extended the role of neuromodulation. Intravesical injection therapy with botulinum toxin, along with sacral neuromodulation, has been included in the treatment algorithm of overactive bladder syndrome if this does not respond to conservative therapy. When choosing for a neuromodulation therapy, the side-effects and complications of the treatments should be considered alongside the specific patient situation and evidence for effectiveness and long-term effectiveness.
Enhanced acid stability of a reduced nicotinamide adenine dinucleotide (NADH) analogue (2001)

A methyl substituent at C-5 of the nicotinamide ring is found to confer increased acid stability in a reduced nicotinamide model (5-20 fold) and in a reduced dinucleotide coenzyme (2-3 fold), while retaining reactivity towards hydride transfer.
EFFECTS OF HEMATOPORPHYRIN DERIVATIVE ON THE CELLULAR ENERGY METABOLISM IN THE ABSENCE AND PRESENCE OF LIGHT (1989)

Effects of Photofrin II on energy metabolism and metabolic viability were studied in a mammalian transformed cell line (BHK-21) in dark and after photo-irradiation with visible light. Cells were allowed to accumulate Photofrin by incubating for 4 h in buffer containing Photofrin (5-60 micrograms/ml). The results show that Photofrin significantly affects the cellular energy metabolism even in the absence of light; activity of cytochrome c oxidase is decreased and glucose utilization and lactate production (glycolysis) are increased. Irradiation with light resulted in a significant decrease in the activity of cytochrome c oxidase, glycolysis, ATP content, energy charge, ratios of adenine nucleotides like ATP/ADP, ATP/AMP and cell viability (dye exclusion test). Presence of inhibitors of energy metabolism, potassium cyanide (respiration) and 2-deoxyglucose (glycolysis), further enhanced the cytotoxic effects induced by hematoporphyrin derivative and light.
公司治理结构和东亚:韩国、印尼、马来西亚、泰国 (1999)

从广义上讲，很明显，公司治理结构只是导致近两年东亚危机的原因之一。正如世界银行和国际货币基金组织报告所指出的，东亚危机的起源和发展涉及多种复杂的经济及社会因素的相互作用，但是有一个因素贯穿事件始终，那就是这些国家的大公司和银行不顾负债率过高的事实，大...
Expression of GTP-dependent and GTP-independent Tissue-type Transglutaminase in Cytokine-treated Rat Brain Astrocytes (1997)

Tissue-type transglutaminases (TGases) were recently shown to exert dual enzymatic activities; they catalyze the posttranslational modification of proteins by transamidation, and they also act as guanosine triphosphatase (GTPase). Here we show that a tissue-type TGase is expressed in rat brain astrocytes in vitro, and is induced by the inflammation-associated cytokines interleukin-1beta and to a lesser extent by tumor necrosis factor-alpha. Induction is accompanied by overexpression and appearance of an additional shorter clone, which does not contain the long 3'-untranslated region and encodes for a novel TGase enzyme whose C terminus lacks a site that affects the enzyme's interaction with guanosine triphosphate (GTP). Expression of two clones revealed that the long form is inhibited noncompetitively by GTP, but the short form significantly less so. The different affinities for GTP may account for the difference in physiological function between these two enzymes.
CCR2 chemokine receptor signaling mediates pain in experimental osteoarthritis (2012)

Osteoarthritis is one of the leading causes of chronic pain, but almost nothing is known about the mechanisms and molecules that mediate osteoarthritis-associated joint pain. Consequently, treatment options remain inadequate and joint replacement is often inevitable. Here, we use a surgical mouse model that captures the long-term progression of knee osteoarthritis to longitudinally assess pain-related behaviors and concomitant changes in the innervating dorsal root ganglia (DRG). We demonstrate that monocyte chemoattractant protein (MCP)-1 (CCL2) and its high-affinity receptor, chemokine (C-C motif) receptor 2 (CCR2), are central to the development of pain associated with knee osteoarthritis. After destabilization of the medial meniscus, mice developed early-onset secondary mechanical allodynia that was maintained for 16 wk. MCP-1 and CCR2 mRNA, protein, and signaling activity were temporarily up-regulated in the innervating DRG at 8 wk after surgery. This result correlated with the presentation of movement-provoked pain behaviors, which were maintained up to 16 wk. Mice that lack Ccr2 also developed mechanical allodynia, but this started to resolve from 8 wk onwards. Despite severe allodynia and structural knee joint damage equal to wild-type mice, Ccr2-null mice did not develop movement-provoked pain behaviors at 8 wk. In wild-type mice, macrophages infiltrated the DRG by 8 wk and this was maintained through 16 wk after surgery. In contrast, macrophage infiltration was not observed in Ccr2-null mice. These observations suggest a key role for the MCP-1/CCR2 pathway in establishing osteoarthritis pain.
Direct-touch vs. mouse input for tabletop displays (2007)

We investigate the differences -- in terms of bothquantitative performance and subjective preference -- between direct-touch and mouse input for unimanual andbimanual tasks on tabletop displays. The results of twoexperiments show that for bimanual tasks performed ontabletops, users benefit from direct-touch input. However,our results also indicate that mouse input may be moreappropriate for a single user working on tabletop tasksrequiring only single-point interaction.
Ventilation by high-frequency oscillation (1980)

The effect of applying a high-frequency small-volume sinusoidal oscillation at the airway was investigated in anesthetized apneic beagle dogs (mean wt 11 kg, mean VDphys 6.6 +/- 0.6 ml/kg). Oscillations generated by a piston in a cylinder were transmitter to the lungs through an uncuffed endotracheal tube (4.5 mm ID, 6.0 mm OD), which allowed a substantial leak back through the vocal cords. A bias flow of fresh gas presented inspired air to the midtracheal level. The minimum distal airway pressure (measured at the end of the endotracheal tube) was maintained between 0 and 2 cmH2O. Peak airway pressures were 4-8 cmH2O. The optimal frequency for CO2 elimination was 15 Hz. Using volumes of 1.9 ml/kg (range 1.7-2.3) at this frequency the mean PaCO2 was 33.1 +/- 0.5 Torr. In four dogs breathing 100% O2 the PaO2 was 594 +/- 9 Torr during spontaneous ventilation and 580 +/- 9 Torr after 5 h of uninterrupted oscillation. In four experiments using room air the PaO2 was 95 +/- 5 Torr during spontaneous respiration and 106 +/- 1 Torr after 5 h of oscillation. In an additional seven studies there was no difference in mean cardiac output between oscillation and conventional mechanical ventilation. This study demonstrates that high-frequency small-volume oscillations can maintain gas exchange for many hours presumably by markedly enhancing the diffusivity of gases in the lung.
DGR mutagenic transposition occurs via hypermutagenic reverse transcription primed by nicked template RNA (2017)

Diversity-generating retroelements (DGRs) are molecular evolution machines that facilitate microbial adaptation to environmental changes. Hypervariation occurs via a mutagenic retrotransposition process from a template repeat (<i>TR</i>) to a variable repeat (<i>VR</i>) that results in adenine-to-random nucleotide conversions. Here we show that reverse transcription of the <i>Bordetella</i> phage DGR is primed by an adenine residue in <i>TR</i> RNA and is dependent on the DGR-encoded reverse transcriptase (bRT) and accessory variability determinant (Avd ), but is <i>VR</i>-independent. We also find that the catalytic center of bRT plays an essential role in site-specific cleavage of <i>TR</i> RNA for cDNA priming. Adenine-specific mutagenesis occurs during reverse transcription and does not involve dUTP incorporation, indicating it results from bRT-catalyzed misincorporation of standard deoxyribonucleotides. In vivo assays show that this hybrid RNA-cDNA molecule is required for mutagenic transposition, revealing a unique mechanism of DNA hypervariation for microbial adaptation.
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs (2008)

We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25-50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of approximately 8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.
CD47 and the 19 kDa Interacting Protein-3 (BNIP3) in T Cell Apoptosis (2003)

CD47 is a surface receptor that induces either coactivation or apoptosis in lymphocytes, depending on the ligand(s) bound. Interestingly, the apoptotic pathway is independent of caspase activation and cytochrome c release and is accompanied by early mitochondrial dysfunction with suppression of mitochondrial membrane potential (Deltapsim). Using CD47 as bait in a yeast two-hybrid system, we identified the Bcl-2 homology 3 (BH3)-only protein 19 kDa interacting protein-3 (BNIP3), a pro-apoptotic member of the Bcl-2 family, as a novel partner. Interaction between CD47 and the BH3-only protein was confirmed by immunoprecipitation analysis, and CD47-induced apoptosis was inhibited by attenuating BNIP3 expression with antisense oligonucleotides. Finally, we showed that the C-terminal domain of thrombospondin-1 (TSP-1), but not signal-regulatory protein (SIRPalpha1), is the ligand for CD47 involved in inducing cell death. Immunofluorescence analysis of CD47 and BNIP3 revealed a partial colocalization of both molecules under basal conditions. After T cell stimulation via CD47, BNIP3 translocates to the mitochondria to induce apoptosis. These results show that the BH3-dependent apoptotic pathways, previously shown to be activated by intracellular pro-apoptotic events, can also be turned on by surface receptors. This new pathway results in a fast induction of cell death resembling necrosis, which is likely to play an important role in lymphocyte regulation at inflammatory sites and/or in the vicinity of thrombosis.
Optimization by Direct Search: New Perspectives on Some Classical and Modern Methods (2003)

Direct search methods are best known as unconstrained optimization techniques that do not explicitly use derivatives. Direct search methods were formally proposed and widely applied in the 1960s but fell out of favor with the mathematical optimization community by the early 1970s because they lacked coherent mathematical analysis. Nonetheless, users remained loyal to these methods, most of which were easy to program, some of which were reliable. In the past fifteen years, these methods have seen a revival due, in part, to the appearance of mathematical analysis, as well as to interest in parallel and distributed computing. This review begins by briefly summarizing the history of direct search methods and considering the special properties of problems for which they are well suited. Our focus then turns to a broad class of methods for which we provide a unifying framework that lends itself to a variety of convergence results. The underlying principles allow generalization to handle bound constraints and linear constraints. We also discuss extensions to problems with nonlinear constraints.
Region adaptive spectral transformation For wavelet based color image compression (2009)

In general, each region of a color image exhibits different spectral characteristics. Therefore, the energy compaction characteristic of a single global spectral transformation is rather weak for compression purposes. In this paper, we propose that different groups of wavelet coefficients of a color image be subjected to different spectral transformations prior to the spectral planes being coded by a wavelet-based image coder such as CSPIHT (Color Set Partitioning in Hierarchical Trees, [Kassim, Lee; 2003]). The decomposition of the color image into such groups is succintly represented with a quadtree structure which is optimized for rate-distortion performance by means of a known analytical rate-distortion model for wavelet-based image codecs. The experiments show that, when integrated with the CSPIHT coder, the proposed region adaptive transformation method yields compression gains of 0.4-0.5 dB, on the average, for rates between 0.5bpp and 2.5bpp over the single global transformation method.