gebhart/patrepeval huggingface dataset:
Nonalcoholic Fatty Liver, Steatohepatitis, and the Metabolic Syndrome (2003)

Nonalcoholic fatty liver disease (NAFLD) has been associated with the insulin-resistance syndrome, at present defined as the metabolic syndrome, whose limits were recently set. We assessed the prevalence of the metabolic syndrome in 304 consecutive NAFLD patients without overt diabetes, on the basis of 3 or more criteria out of 5 defined by the U.S. National Institutes of Health (waist circumference, glucose, high-density lipoprotein [HDL]-cholesterol, triglycerides, and arterial pressure). The prevalence of the metabolic syndrome increased with increasing body mass index, from 18% in normal-weight subjects to 67% in obesity. Insulin resistance (Homeostasis Model Assessment method) was significantly associated with the metabolic syndrome (odds ratio [OR], 2.5; 95% CI, 1.5-4.2; P <.001). Liver biopsy was available in 163 cases (54%). A total of 120 patients (73.6%) were classified as having nonalcoholic steatohepatitis (NASH); 88% of them had a metabolic syndrome (vs. 53% of patients with pure fatty liver; P <.0001). Logistic regression analysis confirmed that the presence of metabolic syndrome carried a high risk of NASH among NAFLD subjects (OR, 3.2; 95% CI, 1.2-8.9; P =.026) after correction for sex, age, and body mass. In particular, the syndrome was associated with a high risk of severe fibrosis (OR, 3.5; 95% CI, 1.1-11.2; P =.032). In conclusion, the presence of multiple metabolic disorders is associated with a potentially progressive, severe liver disease. The increasing prevalence of obesity, coupled with diabetes, dyslipidemia, hypertension, and ultimately the metabolic syndrome puts a very large population at risk of forthcoming liver failure in the next decades.
Photoreactivity of 5-iodouracil-containing DNA-Z complex (2001)

It is revealed that double-strand RN A adenosine deaminase 1 binds to Z-DNA and NH 2 -terminus Za domain is responsible for the high affinity binding. In order to investigate the structure of Z-DNA induced by Za, the photoreactions of 5-halouracil-containing Z-DNA in the presence and the absence of Za were investigated. It was demonstrated that the C2'a-hydroxylated product was efficiently produced in Z-DNA induced by Za compared to that under high salt concentration.
An enhanced DSP architecture for the seven multimedia functions: the Mpact 2 media processor (2002)

This paper reviews the architectural enhancements to the second generation of a VLIW media processor. The concept of a media processor is introduced and its application in an x86 family personal computer platform is described. The architectural choices made in the original Mpact media processor are explained as are how they were extended in the latest version based on design experience and changing requirements.
Using model membranes for the study of amyloid beta:lipid interactions and neurotoxicity (2007)

One of the major tasks in understanding the etiopathogenesis of amyloid beta-induced neurotoxicity of Alzheimer's disease (AD), is in fully capturing the large number of the biochemical processes that influence each other during the course of the disease, in vivo. Model membranes possess, as their main strength, the ability to enable the researcher to manipulate a 'biological' micro-vesicle under a controlled environment. This review narrowly focuses on discussing the exploitation of model membranes for improved understanding of some of the mechanisms governing AD's amyloid beta-induced neurotoxicity. Amyloid beta (Abeta) is cleaved from a membrane-located amyloid precursor protein by membrane-located enzymes. The relative spatial localization of the involved biomolecules within the membrane bilayer is crucial in influencing Abeta production, its aggregation on the membrane surface or insertion into the membrane, and fibril formation: all important processes in causing neurotoxicity. The lipid composition of the bilayer is similarly important. The review also attempts to highlight current and future challenges in using model membranes for studying biochemical processes.
Underwater Image Restoration Based on Image Blurriness and Light Absorption (2017)

Underwater images often suffer from color distortion and low contrast, because light is scattered and absorbed when traveling through water. Such images with different color tones can be shot in various lighting conditions, making restoration and enhancement difficult. We propose a depth estimation method for underwater scenes based on image blurriness and light absorption, which can be used in the image formation model (IFM) to restore and enhance underwater images. Previous IFM-based image restoration methods estimate scene depth based on the dark channel prior or the maximum intensity prior. These are frequently invalidated by the lighting conditions in underwater images, leading to poor restoration results. The proposed method estimates underwater scene depth more accurately. Experimental results on restoring real and synthesized underwater images demonstrate that the proposed method outperforms other IFM-based underwater image restoration methods.
Gene expression in recombinant microorganisms. (1994)

Gene Expression in Recombinant Escherichia coli, Joan Stader Gene Expression in Recombinant Bacillus, Matti Sarvas Gene Expression in Recombinant Yeast, Albert Hinnen, Frank Buxton, Bhabotosh Chaudhuri, Jutta Heim, Thomas Hottiger, Bernd Meyhack, and Gabriele Pohlig Gene Expression in Methylotrophic Yeasts, Gerd Gellissen, Cornelis P. Hollenberg, and Zbigniew A. Janowicz Gene Expression in Filamentous Fungi: Expression of Pectinases and Glucose Oxidase in Aspergillus niger, Jaap Visser, Henk-Jan Bussink, and Cor Witteveen Gene Expression in Recombinant Streptomyces, Richard H. Baltz Recombinant Microorganisms: Safety and Regulatory Aspects, Anthony J. Taylor
Long-wavelength first hyperpolarizability measurements by hyper-Rayleigh scattering (1996)

A hyper-Rayleigh scattering (HRS) system based on an optical parametric power oscillator is described. The first hyperpolarizability, beta, of Crystal Violet dye was measured at 1450 and 1500 nm. The resonance-free beta value, beta(0), for this octupole was found to be comparable with that of the dipolar dye Disperse Red 1 but with the nonlinearity-transparency trade-off worse for the octupole. The discrepancy in beta(0) with that reported previously is explained in terms of resonance and the adequacy of the octupolar three-state model. The possibility of dye aggregation by solvent-dependent HRS is investigated.
Xenobiotic-inducible Transcription of Cytochrome P450 Genes (1995)

Numerous foreign chemicals (xenobiotics) confront us daily; such compounds often are lipophilic and may accumulate to toxic levels unless they are metabolized to water-soluble products that can be readily excreted. A cytochrome P450 enzyme(s) often catalyzes the initial step in such detoxification pathways. Multiple forms of cytochrome P450 exist; these enzymes are notable for their broad and overlapping substrate specificities. Although P450s usually mediate detoxification reactions, under some circumstances they activate their substrates to carcinogenic, mutagenic, and/or cytotoxic products.
Novel oligonucleotide analogues based on morpholino nucleoside subunits – Antisense technologies: New chemical possibilities (2009)

Even several decades after pioneer publications there is continued interest in the construction and synthesis of a variety of novel oligonucleotide analogues. The first oligonucleotide analogues which had a regular, predetennined structure containing nucleoside units joined with carbonate, carbamate, hydroxyacetate and hydroxyacetamide tethers have been developed in the 1970s. Further progress in oligonucleotide synthetic methods during the 1980s stimulated the development of a variety of oligonucleotide analogues containing modified carbohydrate and phosphate backbones. Particular attention has been given to the PNA (peptide nucleic acids), inorpholino, and negatively charged PNA oligonucleotide analogues, which showed the most promise in a number of biological applications, such as diagnostics, nucleic acid analyses, and gene expression. The cost of parent compounds and oligonucleotide analogue synthesis is one of the most limiting factors to broad application. Studies that succeed in resolving this cost problem in the most effective way would be beneficial. Herein is presented a short review on oligonucleotide analogues that can be synthesized from inexpensive parent compounds - ribonucleosides - with or without the protection of heterocyclic bases, and with minimal protection of other reactive functions.
Evaluation of Methane Generation Rate Constant(k) by Estimating Greenhouse Gas Emission in Small Scale Landfill (2014)

본 연구에서는 현재 사용 중인 2곳(H, Y 매립지)의 소규모 매립장에 대한 매립지 특성 자료수집과 현장측정을 통한 LFG 배출량 산정을 수행하였으며, 이를 이용하여 이들 매립지에 적합한 2006 IPCC FOD 방법 적용 시 입력변수로 사용되는 메탄발생속도상수(k)를 산출하여 보았다. 또한 이 결과를 default 값을 적용한 2006 IPCC GL의 FOD 방법에 의한 메탄 배출량 산정결과와 비교함으로써 특정매립지에 대한 동일한 k값 적용의 타당성을 평가해 보았다. 매립지의 폐기물 조성 data를 이용한 DOC 산정 결과, 매립되어지는 폐기물의 물리적 조성 차이로 인하여 H 매립지(1997~2011)는 13.16 %~23.79 % (<TEX>$16.52{\pm}3.84%$</TEX>)로 나타났으며, Y 매립지(1994~2011)는 7.24 %~34.67 % (<TEX>$14.56{\pm}7.30%$</TEX>)의 값을 보여 IPCC 가이드라인에서 제시한 Bulk waste 타입의 기본값인 18.0 %와 비교할 때 H 매립지보다 Y 매립지가 큰 차이를 보였다. 2006 IPCC GL에 제시된 FOD방법의 메탄 배출량 산정식을 이용한 k값 산정 결과, H 매립지의 산정된 평균 k값은 <TEX>$0.0413yr^{-1}$</TEX>, Y 매립지의 산정된 평균 k값은 <TEX>$0.0117yr^{-1}$</TEX>로 나타나 IPCC 가이드라인에 제시된 기본값인 <TEX>$0.09yr^{-1}$</TEX>에 비하여 상대적으로 낮은 값을 보였다. 따라서 2006 IPCC 가이드라인의 defaults value(k=0.09) 값에 의한 온실가스 배출량 산정결과는 현장측정을 통해 산정된 k값에 의한 추정값에 비하여 과대평가될 수 있어 매립지에서 발생하는 정확한 온실가스 배출량 예측을 위해서는 각각의 매립지별 현장측정을 통한 고유의 k값 결정을 통한 산정이 진행되어야 할 것으로 판단된다. In this study, greenhouse gas emission for small scale landfill (H and Y landfill) was investigated to deduce special the methane generation rate constant(k). To achieve the purpose, the data of physical composition was collected and amount of LFG emission was calculated by using FOD method suggested in 2006 IPCC GL. Also, amount of LFG emission was directly measured in the active landfill sites. By comparing the results, the methane generation rate constant(k), which was used as input variable in FOD method suggested in 2006 IPCC GL, was deduced. From the results on the physical composition, it was shown that the ranges of DOC per year in H (1997~2011) and Y (1994~2011) landfill sites were 13.16 %~23.79 % (<TEX>$16.52{\pm}3.84%$</TEX>) and 7.24 %~34.67 % (<TEX>$14.56{\pm}7.30%$</TEX>), respectively. The DOC results showed the differences with the suggested values (= 18 %) in 2006 IPCC GL. The average values of methane generation rate constant(k) from each landfill site were <TEX>$0.0413yr^{-1}$</TEX> and <TEX>$0.0117yr^{-1}$</TEX>. The results of methane generation rate constant(k) was shown big difference with 2006 IPCC GL defualt value (k = 0.09). It was confirmed that calculation results of greenhouse gas emission using default value in 2006 IPCC GL show excessive output.
Porphyromonas gingivalis Outer Membrane Vesicles Exclusively Contain Outer Membrane and Periplasmic Proteins and Carry a Cargo Enriched with Virulence Factors (2014)

Porphyromonas gingivalis, a keystone pathogen associated with chronic periodontitis, produces outer membrane vesicles (OMVs) that carry a cargo of virulence factors. In this study, the proteome of OMVs was determined by LC-MS/MS analyses of SDS-PAGE fractions, and a total of 151 OMV proteins were identified, with all but one likely to have originated from either the outer membrane or periplasm. Of these, 30 exhibited a C-terminal secretion signal known as the CTD that localizes them to the cell/vesicle surface, 79 and 27 were localized to the vesicle membrane and lumen respectively while 15 were of uncertain location. All of the CTD proteins along with other virulence factors were found to be considerably enriched in the OMVs, while proteins exhibiting the OmpA peptidoglycan-binding motif and TonB-dependent receptors were preferentially retained on the outer membrane of the cell. Cryo-transmission electron microscopy analysis revealed that an electron dense surface layer known to comprise CTD proteins accounted for a large proportion of the OMVs' volume providing an explanation for the enrichment of CTD proteins. Together the results show that P. gingivalis is able to specifically concentrate and release a large number of its virulence factors into the environment in the form of OMVs.
Methylation as a Crucial Step in Plant microRNA Biogenesis (2005)

Methylation on the base or the ribose is prevalent in eukaryotic ribosomal RNAs (rRNAs) and is thought to be crucial for ribosome biogenesis and function. Artificially introduced 2'-O-methyl groups in small interfering RNAs (siRNAs) can stabilize siRNAs in serum without affecting their activities in RNA interference in mammalian cells. Here, we show that plant microRNAs (miRNAs) have a naturally occurring methyl group on the ribose of the last nucleotide. Whereas methylation of rRNAs depends on guide RNAs, the methyltransferase protein HEN1 is sufficient to methylate miRNA/miRNA* duplexes. Our studies uncover a new and crucial step in plant miRNA biogenesis and have profound implications in the function of miRNAs.
General test result checking with log file analysis (2003)

We describe and apply a lightweight formal method for checking test results. The method assumes that the software under test writes a text log file; this log file is then analyzed by a program to see if it reveals failures. We suggest a state-machine-based formalism for specifying the log file analyzer programs and describe a language and implementation based on that formalism. We report on empirical studies of the application of log file analysis to random testing of units. We describe the results of experiments done to compare the performance and effectiveness of random unit testing with coverage checking and log file analysis to other unit testing procedures. The experiments suggest that writing a formal log file analyzer and using random testing is competitive with other formal and informal methods for unit testing.
Tandem connectionist feature extraction for conventional HMM systems (2002)

Hidden Markov model speech recognition systems typically use Gaussian mixture models to estimate the distributions of decorrelated acoustic feature vectors that correspond to individual subword units. By contrast, hybrid connectionist-HMM systems use discriminatively-trained neural networks to estimate the probability distribution among subword units given the acoustic observations. In this work we show a large improvement in word recognition performance by combining neural-net discriminative feature processing with Gaussian-mixture distribution modeling. By training the network to generate the subword probability posteriors, then using transformations of these estimates as the base features for a conventionally-trained Gaussian-mixture based system, we achieve relative error rate reductions of 35% or more on the multicondition Aurora noisy continuous digits task.
Human Interface Hardware for Virtual Laparoscopic Surgery (1995)

Among the most technically viable and economically feasible applications of virtual reality technology is the simulation of minimally invasive medical procedures such as Laparoscopic and Endoscopic surgery. From procedure planning to medical training, such virtual reality simulations have generated much interest from both the research and industrial communities. Although there is significant development activity in the area of virtual simulation of Laparoscopic and Endoscopic procedures, this work is often hindered when researchers find that no off-the-shelf tools satisfy the human interface requirements of virtual reality surgical simulations. The Virtual Laparoscopic lnterface&amp;trade; is a new product from Immersion Corporation which provides an easy to integrate, off-the-shelf solution to the human interface requirements associated with simulating Laparoscopic and Endoscopic surgical procedures. Although only a single component of a full virtual simulation environment, this piece of hardware provides an affordable and easy to integrate solution to simulating and tracking the manual activities associated with minimally invasive medical procedures. Two commercial versions of the hardware are available. One is solely a human input device, tracking manipulations of real surgical tools mounted in a virtual patient. The hardware feeds tool position and tool orientation information to the host computer. The second is both an input and output device, tracking manipulations of the surgical tools while also providing realistic force feedback to the user through the tool handle.
Genetic variants in fibroblast growth factor receptor 2 (FGFR2) contribute to susceptibility of breast cancer in Chinese women (2008)

Fibroblast growth factor receptor 2 (FGFR2) belongs to the FGFR family, which plays an important role in cell growth, invasiveness, motility and angiogenesis. In human breast cancer, expression of FGFR2 is estrogen receptor (ER)-dependent and correlates with a lower rate of apoptosis. Recently, whole-genome association studies have identified several single-nucleotide polymorphisms (SNPs) of FGFR2 as novel breast cancer susceptibility loci. In the present study of 1049 breast cancer patients and 1073 cancer-free controls, we assessed whether polymorphisms of FGFR2 are associated with breast cancer risk in Chinese women and whether these associations are stronger in women with a reproductive history suggestive of greater exposure to endogenous estrogens. We genotyped three FGFR2 polymorphisms (rs2981582C/T, rs1219648A/G and rs2420946C/T) using the SNPstream 12-plex platform. Each of the three SNPs was significantly associated with increased breast cancer risk in a dose-dependent manner. Compared with women with 0-2 risk loci, those with 3 risk loci had a 1.36-fold increased odds of breast cancer (95% confidence interval = 1.13-1.62, P = 0.001). In stratified analyses, associations between the presence of 3 risk loci and breast cancer were stronger among women with ER- and/or progesterone receptor-positive cancers, premenopausal women and women with an older age at first live birth. Furthermore, there was a significant additive interaction between risk genotypes and menopausal status (P for multiplication interaction/additive interaction: 0.083/0.037). These findings indicate that genetic variants in FGFR2 may contribute to breast cancer occurrence in Chinese women, possibly through pathways related to estrogen and/or progesterone.
Aberrant CD40-Induced NF-κB Activation in Human Lupus B Lymphocytes (2012)

Auto-reactive B lymphocytes and its abnormal CD40 signaling play important roles in the pathogenesis of systemic lupus erythematosus (SLE). In this study, we analyzed CD40 expression and CD40/CD154 induced activation of NF-κB signaling pathway in B cells from SLE patients. B cells from healthy volunteers and tonsilar B cells from chronic tonsillitis were used as negative and positive controls. Results showed CD40-induced NF-κB signaling was constitutively activated in B cells from active lupus patients, including decreased CD40 in raft portion, increased phosphorylation and degradation of IκBα, phosphorylation of P65, as well as increased nuclear translocation of P65, P50, c-Rel, which could be blocked by anti-CD154. CD154 stimulation could induce further phosphorylation and degradation of IκBα, as well as phosphorylation of P65 and nuclear translocation of P65. In addition, CD40-induced kinase activities in B cells from lupus patients mimicked that of tonsil B cells, in that IKKα/β were more activated compared to normal B cells. CD40-induced NF-κB activity was blocked by both IκB phosphorylation and proteosome degradation inhibitors in both lupus and normal B cells. All together, our findings revealed that canonical NF-κB signaling is constitutively activated in active lupus and is mediated by CD154/CD40. CD40 induced NF-κB activation is different in human lupus B lymphocytes compared with normal B cells.
Metal–Organic Frameworks of Vanadium as Catalysts for Conversion of Methane to Acetic Acid (2011)

A catalytic system combining the high activity of homogeneous catalysts and the ease of use of heterogeneous catalysts for methane activation is reported. The vanadium-containing metal-organic frameworks (MOFs) MIL-47 and MOF-48 are found to have high catalytic activity and chemical stability. They convert methane selectively to acetic acid with 70% yield (490 TON) based on K(2)S(2)O(8) as an oxidant. Isotopic labeling experiments showed that two methane molecules are converted to the produced acetic acid. The MOF catalysts are reusable and remain catalytically active for several recycling steps without losing their crystalline structures.
Bexarotene Is Effective and Safe for Treatment of Refractory Advanced-Stage Cutaneous T-Cell Lymphoma: Multinational Phase II-III Trial Results (2001)

Bexarotene is the first in a novel class of pharmacologic agents, the RXR-selective retinoids, or rexinoids. Bexarotene is orally administered, safe, and generally well tolerated with reversible side effects, and is effective for the treatment of advanced, refractory CTCL.
Polynomial filters for image and video processing (2002)

We review the class of polynomial filters and their extensions, first introducing the Volterra (1887, 1913, 1959) series expansion that is at the basis of such filters. The main concepts and properties are given with reference to 1-D signals, while extensions to multidimensional (M-D) signals are then considered. Applications of such filters to image and video processing are also shown.
High Intercommunity Variation in Adolescent Cigarette Smoking in a 10-Community Field Experiment (1992)

The authors report levels of intercommunity variation in rates of cigarette smoking observed during the course of an evaluation of the influence of three mass media campaigns on the initi ation of adolescent cigarette smoking. Despite careful design and statistical adjustment for a set of 10 known sociodemographic and personality correlates of adolescent cigarette smoking, high intercommunity variation precluded the detection of media campaign effects in this study. The authors discuss the general implications of high intercommunity variation for studies using the individual as the unit of analysis when the unit of randomization is the community.