gebhart/patrepeval huggingface dataset:
Biochemical Study and Technical Applications of Fungal Pectinase (2006)

Pectinases are a group of enzymes produced by bacteria, fungi, higher plants and animals. Pectinases can modify and degrade pectins, a class of heterogeneous and multifunctional polysaccharides present in middle lamellae and primary cell walls of plants. Pectins have been showed to play diverse roles in cell physiology, growth, adhesion and separation. Pectinases are used technically in the processing of fiber production and fruit juice or wine making. We have studied the mechanisms and applications of pectinases, especially in retting, a microbiological process where bast fibers in flax and other bast fiber cultivars are released from each other and from the woody core. A strong correlation was found between the ability to perform retting and the degradation of sparsely esterified pectin, a substrate of polygalacturonase. This led to the conclusion that polygalacturonase plays a key role in the enzymatic retting of flax. We purified and characterized an extracellular polygalacturonase produced by Rhizopus oryzae, a very potent retting organism. The purified enzyme which appeared to be the single active component in retting, has non-methylated polygalacturonan as its preferred substrate. Peptide sequences indicate that the enzyme, like another polygalacturonase (EC. 3.2.1.15), belongs to glycosyl hydrolase family 28. It contains, however, an N-terminal sequence absent from other fungal pectinases, but present in an enzyme from the phytopathogenic bacterium, Ralstonia solanacearum. Our finding that removal of calcium ions from the plant material by pre-incubation in dilute acid in enzymatic retting could reduce enzyme consumption by several orders of magnitude, improves the economical feasibility of the enzymatic retting process. Comparisons with different acids showed that the action was mainly pH dependent. Pectinases were employed as analytical tools in a study of stored wood discoloration and, together with cellulases, in a mechanical process for making pulp from flax and hemp in paper production.
3D-QSAR Study on a Series of Bcl-2 Protein Inhibitors Using Comparative Molecular Field Analysis (2011)

In this manuscript, three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using comparative molecule field analysis (CoMFA) techniques were applied to provide the structural information of Bcl-2 inhibitors. The CoMFA model obtained from the training set were all statistically significant with the cross-validated coefficients (q(2)) of 0.568 and conventional coefficients (r(2)) of 0.991. The contribution of steric field and the electrostatic field is 0.635 and 0.365, respectively. The 3D-QSAR model was furthermore validated by a test set of 6 molecules. The predicted correlation coefficient (r(2)(pred)) on the test set is 0.582. Therefore, the 3D-QSAR models built may be used to exhibit the necessary ligand-based structural environment as well as to design novel Bcl-2 inhibitors with increasing activities.
Rate-distortion optimization using structural information in H.264 strictly Intra-frame encoder (2010)

In this paper we employ Structural Similarity Index (SSIM) metric in the rate-distortion optimizations of H.264 strictly I-frame encoder to choose the best prediction mode(s). The SSIM is designed to improve on traditional metrics like PSNR and MSE, which have been proved to be inconsistent with human eye perception. The required modifications are done on the JVT reference software JM92 program. The simulation results show that there is reduction in bit rate by 3% while maintaining almost the same video quality and better encoding time.
Computed tomography of the gastroesophageal junction. (1984)

Computed tomography (CT) of the chest and abdomen has proved to be helpful in the preoperative staging of both esophageal and gastric carcinoma. The gastroesophageal junction however, is a difficult area to evaluate as variations in normal anatomy may mimic pathological processes. Pseudomasses at the gastroesophageal junction can be confused with neoplasm. The CT appearance of the GE junction was evaluated in 150 normal patients. CT scans were also performed on 15 patients with carcinoma involving the GE junction. Twenty cases of benign diseases of the GE junction were also studied by CT. Anatomy--The normal anatomy of the gastroesophageal junction will be illustrated with both line diagrams and CT images. The hepatogastric ligament and the caudate lobe of the liver will be demonstrated and their use in locating the GE junction will be shown. Technique--A short segment describing the appropriate technique for CT of the gastroesophageal junction will follow. The use of oral and intravenous contrast will be discussed. The need for distension of the stomach with effervescent agents and oral contrast as well as the use of decubitus and prone positioning will be emphasized when a mass-like density is seen at the GE junction. Examples will be provided. A pseudomass at the GE junction on a supine CT will be shown that disappears with distension and decubitus scanning. This will be used to lead into the next section on neoplasm in which the first example will have an identical appearance on supine CT images. Neoplasm--The relative incidence of gastric adenocarcinoma and esophageal squamous cell carcinoma at the GE junction will be briefly reviewed. The similar CT appearance of the neoplasms will be described and liberally illustrated. Metastatic involvement of lymph nodes adjacent to the GE junction will also be shown. The staging classification for CT evaluation of GE neoplasms will be reviewed. The utility of preoperative staging of esophageal and gastric neoplasms will be briefly reviewed and applied to the GE junction. Our series of patients with cancer of the GE junction will be discussed. The importance of the CT detection of criteria of inoperability will be demonstrated with examples of metastatic involvement of the liver and lymph nodes as well as direct invasion of adjacent organs. Benign Disease--Examples of benign stricture, hiatal hernia, and achalasia will be illustrated. Our cases where CT scans helped rule out a malignant process that had been suggested on barium studies will be reviewed. Summary and Conclusions--Important points of technique, normal anatomy, benign and malignant disease will be briefly reviewed.
The Addition of Chloro- and Ethoxysilanes to Vinyl and Allyl Monomers<sup>1,2</sup> (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Addition of Chloro- and Ethoxysilanes to Vinyl and Allyl Monomers1,2Leon Goodman, Robert M. Silverstein, and Allen BenitezCite this: J. Am. Chem. Soc. 1957, 79, 12, 3073–3077Publication Date (Print):June 1, 1957Publication History Published online1 May 2002Published inissue 1 June 1957https://pubs.acs.org/doi/10.1021/ja01569a023https://doi.org/10.1021/ja01569a023research-articleACS PublicationsRequest reuse permissionsArticle Views170Altmetric-Citations34LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Electron-beam lithography for small MOSFET's (1981)

Electron-beam lithography with a novel multilevel resist structure together with two-dimensional process and device modeling and dry processing with reactive sputter etching have been employed to produce silicon-gate NMOS devices with micrometer and submicrometer channel lengths. Results for transistors and ring oscillators are reported.
A supramolecular nematic phase in sulfonated polyaramides (2004)

A water-soluble polyaramide "sulfo-invert-PPTA" surprisingly, already at a molecular weight of 10,000 g mol(-1), exhibits a nematic liquid crystalline phase in water at very low polymer concentrations, around 1-2wt%, indicating that supramolecular assemblies of molecules are the building blocks of the nematic phase.
Human recombinant granulocyte-macrophage colony-stimulating factor increases cell-to-cell adhesion and surface expression of adhesion-promoting surface glycoproteins on mature granulocytes. (1986)

Human granulocyte-macrophage colony-stimulating factor (GM-CSF) has been shown to inhibit migration of mature granulocytes and to enhance their antibody-dependent cellular cytotoxicity. We found that human recombinant GM-CSF also enhanced granulocyte-granulocyte adhesion and increased by two- to threefold the surface expression of Mo1 and LeuM5 (P150, 95), two members of a family of leukocyte adhesion molecules (Leu-CAM). Increased Mo1 surface expression occurred within 15 min at 37 degrees C and was maximal at the migration inhibitory concentration of 500 pM. One-half maximal rise in the expression of Mo1 on the cell surface occurred at 5 pM. The chemotactic peptide f-Met-Leu-Phe produced a comparable rise in surface Mo1 with one-half maximal expression occurring at 7 nM. Both GM-CSF and f-Met-Leu-Phe produced optimal granulocyte-granulocyte adhesion at 500 pM and 100 nM, respectively. This adhesion-promoting effect induced by either stimulus was inhibited by a mouse monoclonal antibody directed against Mo1 antigen. These data indicate that GM-CSF promotes cell-to-cell adhesion, presumably through enhanced expression of leukocyte adhesion molecules. This mechanism may explain, in part, the known effects of GM-CSF on the function of mature granulocytes.
Novel assays for the detection of botulinum toxins in foods. (1999)

Currently the only accepted method for the detection of botulinum neurotoxin in contaminated samples is the mouse bio-assay. Although highly sensitive this test has a number of drawbacks: it is expensive to perform, lacks specificity and involves the use of animals. With increasing resistance to such animal tests there is a need to replace the bio-assay with a reliable in vitro test. Over the past six years it has been demonstrated that all the botulinum neurotoxins act intracellularly as highly specific zinc endoproteases, cleaving proteins involved in the control of secretion of neurotransmitters. In the work described, this enzymatic activity has been utilised in assay formats for the detection in foods of neurotoxin from the serotypes involved in food-borne outbreaks in man. These assays have been shown to have a greater sensitivity, speed and specificity than the mouse bio-assay. It is envisaged that such assays will prove realistic alternatives to animal based tests.
Nucleotide sequence of the gene for aqualysin I (a thermophilic alkaline serine protease) of <i>Thermus aquaticus</i> YT‐1 and characteristics of the deduced primary structure of the enzyme (1988)

Aqualysin I is an alkaline serine protease which is secreted into the culture medium by Thermus aquaticus YT-1, an extreme thermophile [Matsuzawa, H., Hamaoki, M. & Ohta, T. (1983) Agric. Biol. Chem. 47, 25-28]. The gene encoding aqualysin I was cloned into Escherichia coli using synthetic oligodeoxyribonucleotides as hybridization probes. The nucleotide sequence of the cloned DNA was determined. The primary structure of aqualysin I, deduced from the nucleotide sequence, agreed with the NH2-terminal sequence previously reported and the determined amino acid sequences, including the COOH-terminal sequence, of the tryptic peptides derived from aqualysin I. Aqualysin I comprised 281 amino acid residues and its molecular mass was determined to be 28,350. On alignment of the whole amino acid sequence, aqualysin I showed high sequence homology with the subtilisin-type serine proteases, and 43% identity with proteinase K, 37-39% with subtilisins and 34% with thermitase. Extremely high sequence identity was observed in the regions containing the active-site residues, corresponding to Asp32, His64 and Ser221 of subtilisin BPN'. The nucleotide sequence of the cloned DNA (1105 nucleotides) revealed that it contains the entire gene encoding aqualysin I and one open reading frame without a translational stop codon. Therefore, aqualysin I was considered to be produced as a large precursor, which contains a NH2-terminal portion, the protease and a COOH-terminal portion. The G + C content of the coding region for aqualysin I was 64.6%, which is lower than those of other Thermus genes (68-74%). The codon usage in the aqualysin I gene was rather random in comparison with that in other Thermus genes.
Feature Engineering and Selection: A Practical Approach for Predictive Models (2019)

The process of developing predictive models includes many stages. Most resources focus on the modeling algorithms but neglect other critical aspects of the modeling process. This book describes techniques for finding the best representations of predictors for modeling and for nding the best subset of predictors for improving model performance. A variety of example data sets are used to illustrate the techniques along with R programs for reproducing the results.
A Molecular-based Magnet Test for Malaria (1995)

The molecular-based magnet test for malaria is shown to be more sensitive than the thin blood film test. The globally used thin blood film test is less sensitive because it uses preparation steps that result in the reduction of the absolute number of diagnostically pertinent erythrocytes. Several reports of diagnostic error with the thin film test and the thick film test have appeared in the literature. In marked contrast to the commonly accepted tests, the magnet test concurrently partitions and concentrates the infected erythrocytes present in the initial sample. The magnetic test permits a brief and sensitive microscopic-based enumeration of the malaria-infected erythrocytes in the enriched sample. Diagnostically pertinent hemozoin is simply identified through two of its specific molecular properties: paramagnetism and birefringence. The former property mediates the capture and enrichment of malaria-infected erythrocytes within the magnetic flux and the latter property manifests the characteristic birefringence demonstrated by polarized light.
A practical approach to minimally invasive breast biopsy. (1996)

With the development of stereotactic or ultrasound-guided, large-core percutaneous breast biopsy and the evolution of mammotomy, radiologists are now able to render definitive diagnoses of breast lesions. To ensure success, however, there must be a commitment at the outset to put into place the required personnel and equipment. The radiologists involved must conscientiously adhere to standardized technique and be willing to assume clinical responsibility, including comprehensive follow-up methods. With these commitments, radiologists can substantially increase their contribution to the care of patients with a breast abnormality.
Pade approximation of large-scale dynamic systems with Lanczos methods (2002)

The utility of Lanczos methods (1950) for the approximation of large-scale dynamical systems is considered. In particular, it is shown that the Lanczos method is a technique for yielding Pade approximants which has several advantages over more traditional explicit moment matching approaches. An extension of the Lanczos algorithm is developed for computing multipoint Pade approximations of descriptor systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Mitochondrial Fission Induces Glycolytic Reprogramming in Cancer-Associated Myofibroblasts, Driving Stromal Lactate Production, and Early Tumor Growth (2012)

Recent studies have suggested that cancer cells behave as metabolic parasites, by inducing oxidative stress in adjacent normal fibroblasts. More specifically, oncogenic mutations in cancer cells lead to ROS production and the "secretion" of hydrogen peroxide species. Oxidative stress in stromal fibroblasts then induces their metabolic conversion into cancer-associated fibroblasts. Such oxidative stress drives the onset of autophagy, mitophagy, and aerobic glycolysis in fibroblasts, resulting in the local production of high-energy mitochondrial fuels (such as L-lactate, ketone bodies, and glutamine). These recycled nutrients are then transferred to cancer cells, where they are efficiently burned via oxidative mitochondrial metabolism (OXPHOS). We have termed this new energy-transfer mechanism "Two-Compartment Tumor Metabolism", to reflect that the production and consumption of nutrients (L-lactate and other catabolites) is highly compartmentalized. Thus, high-energy onco-catabolites are produced by the tumor stroma. Here, we used a genetic approach to stringently test this energy-transfer hypothesis. First, we generated hTERT-immortalized fibroblasts which were genetically re-programmed towards catabolic metabolism. Metabolic re-programming towards glycolytic metabolism was achieved by the recombinant over-expression of MFF (mitochondrial fission factor). MFF over-expression results in extensive mitochondrial fragmentation, driving mitochondrial dysfunction. Our results directly show that MFFfibroblasts undergo oxidative stress, with increased ROS production, and the onset of autophagy and mitophagy, both catabolic processes. Mechanistically, oxidative stress induces autophagy via NF-kB activation, also providing a link with inflammation. As a consequence MFF-fibroblasts showed intracellular ATP depletion and the extracellular secretion of L-lactate, a critical onco-catabolite. MFF-fibroblasts also showed signs of myofibroblast differentiation, with the expression of SMA and calponin. Importantly, MFF-fibroblasts signficantly promoted early tumor growth (up to 6.5-fold), despite a 20% overall reduction in angiogenesis. Thus, catabolic metabolism in cancer-associated fibroblasts may be a critical event during tumor intiation, allowing accelerated tumor growth, especially prior to the onset of neoangiogenesis.
Deregulation of gluconeogenic structural genes by variants of the transcriptional activator Cat8p of the yeast <i>Saccharomyces cerevisiae</i> (1999)

In the yeast Saccharomyces cerevisiae, growth with a non-fermentable carbon source requires co-ordinate transcriptional activation of gluconeogenic structural genes by an upstream activation site (UAS) element, designated CSRE (carbon source-responsive element). The zinc cluster protein encoded by CAT8 is necessary for transcriptional derepression mediated by a CSRE. Expression of CAT8 as well as transcriptional activation by Cat8p is regulated by the carbon source, requiring a functional Cat1p (= Snf1p) protein kinase. The importance of both regulatory levels was investigated by construction of CAT8 variants with a constitutive transcriptional activation domain (INO2TAD) and/or a carbon source-independent promoter (MET25 ). Whereas a reporter gene driven by a CSRE-dependent synthetic minimal promoter showed a 40-fold derepression with wild-type CAT8, an almost constitutive expression was found with a MET25-CAT8-INO2TAD fusion construct due to a dramatically increased gene activation under conditions of glucose repression. Similar results were obtained with the mRNA of the isocitrate lyase gene ICL1 and at the level of ICL enzyme activity. Taking advantage of a Cat8p size variant, we demonstrate its binding to the CSRE. Our data show that carbon source-dependent transcriptional activation by Cat8p is the most important mechanism affecting the regulated expression of gluconeogenic structural genes.
일반학술논문 : 단일채널 공간 모형은 대칭성 지각을 잘 설명하지 못한다 (1992)

인간의 대칭성 지각에 대한 현존 모형은 점비교 모형과 밀도비교 모형으로 요약할 수 있는데, 이 두 모형은 모두 공간적 영역의 정보인 흑백도를 바탕으로 하는 단일채널 모형이다. 현존 단일채널 공간 모형은 대칭축으로부터 다른 거리에 위치한 정보가 인간의 대칭성 지각에 다른 영향을 미친다는 것(예, Barlow와 Reeves, 1979)을 설명하지 못한다. 따라서 대칭축으로부터의 거리에 따른 정보의 상대적인 효과를 현존 단일채널 공간 모형에 가중치의 형태로 포함시켜 인간의 대칭성 지각을 설명하려고 하였다. 실험 1에서 Barlow와 Reeves의 연구가 재현되고 그 결과를 다중회귀분석하여 가중치를 구하였다. 그러나 실험 2에서 다른 상황에서의 인간의 대칭성 지각을 수정된 가중치 밀도비교 모형이 설명하지 못하므로서, 인간 시각체계의 대칭성 지각 모형은 단일채널 공간 모형이 아니라는 가능성을 시사하였다. 단일채널 공간 모형과는 달리 공간빈도 영역에서의 정보를 이용하여 다중채널을 통해 정보를 처리하는 다중채널 모형이 대칭성 지각에서도 사용될 수 있는 가능성에 대해서 논의되었다.
Automated measurements in obstetric ultrasound images (2002)

Measurement of the fetal head circumference and diameters in addition to the femur length is crucial for the estimation of fetal age and growth pattern. Due to the noisy nature of ultrasound images and variation in image acquisition and measurement techniques, manual measurements of these parameters are subject to inter and intra-observer variability. The main objective of this work is to apply morphologically-based algorithms in order to recognize the fetal head contour in the ultrasound image, refine its shape and compensate for different irregularities, then correctly measure its dimensions, thus attaining accuracy and reproducibility of measurements. The automation algorithms utilize morphological operations, Hough transforms, and tracing methods. Measurements performed using the automation algorithms were closely correlated to those obtained manually and have been verified using many cases. Automation algorithms can be further improved to be performed online and can be implemented in the ultrasound machine, thus achieving consistency of fetal measurements.
Characterization of a ceramide-activated protein kinase: stimulation by tumor necrosis factor alpha. (1991)

Recent investigations have identified a signal-transduction system involving sphingomyelin and derivatives. In this paradigm, sphingomyelin hydrolysis by a sphingomyelinase generates ceramide, which may be converted to the protein kinase C inhibitor sphingosine or to ceramide 1-phosphate. Ceramide may have second-messenger function because it induces epidermal growth factor receptor phosphorylation, presumably on Thr-669 in A-431 cells. The present studies describe a kinase that may mediate ceramide action. With a 19-amino acid epidermal growth factor receptor peptide containing Thr-669, a membrane-bound activity that phosphorylated the peptide was detected in A-431 cells. Activity was linearly related to ATP (0.3-300 microM) and peptide concentration (0.02-1 mg/ml), possessed a physiologic pH optimum (pH 7.0-7.4), and was Mg(2+)-dependent. Other cations--Ca2+, Mn2+, and Zn(2+)--were ineffective. Natural and synthetic ceramide induced time- and concentration-dependent enhancement of kinase activity. Ceramide (0.5 microM) increased kinase activity 2-fold by 30 s, and activity remained elevated for at least 15 min. As little as 0.001 microM ceramide was effective, and 1 microM ceramide induced maximal phosphorylation. Sphingosine was similarly effective. Because tumor necrosis factor (TNF) alpha rapidly induces sphingomyelin hydrolysis to ceramide during monocytic differentiation of HL-60 cells, its effects on kinase activity were assessed. Kinase activity was increased 1.5-fold at 5 min and 2-fold at 2 hr in membranes derived from TNF-stimulated cells. The effective concentration range was 3 pM-30 nM TNF. Exogenous ceramide induced a similar effect. In sum, these studies demonstrate the existence of an unusual Mg(2+)-dependent ceramide-activated protein kinase that may mediate some aspects of TNF-alpha function.