gebhart/patrepeval huggingface dataset:
Frequent alteration of p63 expression in human primary bladder carcinomas. (2000)

p63, a recently identified member of the p53 gene family, encodes multiple products with transactivating, death-inducing, and dominant-negative activities. To explore the penetrance of p63 in bladder carcinogenesis, we performed expression and mutation analyses of two major isotypes, TAp63 and deltaNp63, in 63 bladder specimens. In 12 normal tissues, TAp63 was expressed at an easily detectable level whereas deltaNp63 was absent or extremely low. While none of 47 carcinomas showed allelic deletion of the gene, marked reduction of TAp63 and abnormal overexpression of deltaNp63 were found in 25 (53.2%) and 30 (63.8%) carcinomas, respectively. Tumor-specific alteration of TAp63 and deltaNp63 expression was identified in two and three of six matched sets, respectively. In addition, reduced expression of TAp63 showed a correlation with tumor stage and grade. Abnormal expression of TAp63 or deltaNp63 isoform was also observed in three of four cell lines, and treatment with 5-Aza-2'-deoxycytidine led to up- or down-regulation of TAp63 and/or deltaNp63 expression, suggesting that the promoters of both isoforms might be affected by DNA methylation, but not in a reciprocal fashion. No sequence alteration of p63 was identified in 47 carcinomas whereas 17 (34.8%) of these showed p53 mutations, and no association between p63 expression and the mutational status of p53 or expression of p21Waf1, MDM2, and 14-3-3sigma was recognized. Our data suggest that altered expression of p63 is a frequent event in bladder carcinogenesis and might contribute to the progression of bladder tumors, possibly via the mechanism(s) distinct from the p53 pathway.
Update and perspectives on congenital disorders of glycosylation (2001)

Defects in nine genes of the N-linked glycosylation pathway cause congenital disorders of glycosylation (CDGs) and serious medical consequences. Although glycobiology is seldom featured in a general medical education, an increasing number of physicians are becoming acquainted with the field because it directly impacts patient diagnosis and care. Medical practice and attitudes will change in the postgenomic era, and glycobiology has an opportunity to be a cornerstone of part of that new perspective. This review of recent developments in the CDG field describes the biochemical and molecular basis of these disorders, describes successful experimental approaches, and points out a few perspectives on current problems. The broad, multisystemic presentations of these patients emphasize that glycobiology is very much a general medical science, cutting across many traditional medical specialties. The glycobiology community is well poised to provide novel perspectives for the dedicated clinicians treating both well-known and emerging human diseases.
Cloning PCR Products (1994)

It is often necessary to clone PCR products. In this chapter, the advantages and disadvantages of various strategies are discussed. It should be kept in mind, however, that PCR can be used to achieve many objectives—such as obtaining sequence information, preparing probes for hybridization analysis, and constructing new hybrid genes—without ever cloning the PCR products. In some instances, it is even advantageous not to clone the products, as described in other chapters.
Membrane topology of aquaporin CHIP. Analysis of functional epitope-scanning mutants by vectorial proteolysis. (1994)

CHIP is the archetypal member of the aquaporins, a widely expressed family of membrane water channels. The NH2- and COOH-terminal halves of CHIP are sequence-related, and hydropathy analysis predicted six membrane-spanning domains with five connecting loops (A-E). Here, we determined the membrane topology of CHIP expressed in Xenopus oocytes using biologically active recombinant channels. CHIP is glycosylated at Asn-42, indicating loop A is exofacial. An epitope from the coronavirus E1 glycoprotein was inserted into CHIP and localized to the outer or inner leaflet of the membrane by alpha-chymotrypsin digestion of intact oocytes or inside-out membrane vesicles. The E1 epitope at Thr-120 was protease-sensitive in intact oocytes, indicating that loop C is exofacial. The E1 epitope at Lys-6, Arg-162, or Lys-267 was protease-sensitive in inside-out membrane vesicles, confirming the cytoplasmic location of the NH2 and COOH termini and loop D. Insertions into loops B and E did not produce active water channels, but their cleavage patterns were consistent with inner (loop B) and outer (loop E) leaflet locations. This study indicates that the functional CHIP molecule is a unique structure with two internal repeats oriented 180 degrees to each other within the membrane.
Standardized and simplified nomenclature for proteins common to all retroviruses (1988)

We propose a revised standardized nomenclature for the proteins common to all retroviruses on the basis of biological function, enzymatic activity, and/or virion location data. (We do not discuss proteins specific for subfamilies or only some retroviruses.)
Anti-inflammatory effects of a new tumour necrosis factor-alpha (TNF-α) inhibitor (CNI-1493) in collagen-induced arthritis (CIA) in rats (1999)

A recently developed compound, a multivalent guanylhydrazone (CNI-1493) that inhibits TNF-alpha production by suppressing TNF-alpha translational efficiency, was administered in an experimental model of collagen type II-induced arthritis in DA rats. CNI-1493 was injected daily intraperitoneally either before the onset of arthritis or after the establishment of clinical disease. Prophylactic treatment with CNI-1493 significantly prevented or delayed the onset and suppressed the severity of arthritis in a dose-dependent manner. Therapeutic intervention with CNI-1493 in established joint disease also resulted in a significant reduction of clinical signs of arthritis in treated animals. No severe side-effects were noted when animals were treated with daily CNI-1493 doses up to 5 mg/kg. An immunohistochemical study was performed which demonstrated that CNI-1493 led to a reduced expression of TNF-alpha at the site of disease activity. Thus, CNI-1493 with documented inhibitory effects on TNF-alpha synthesis, has proven successful in ameliorating the course of arthritis in CIA. We believe that the use of a compound such as CNI-1493 with a defined mode of action provides a useful tool for dissecting and understanding important pathogenic mechanisms operating in the development of chronic arthritis.
Catalytic Decarboxylation of Petroleum Acids from High Acid Crude Oils over Solid Acid Catalysts (2008)

The presence of petroleum acids in crude oils is a key problem in refineries due to corrosion to industrial units. To economically and effectively remove the petroleum acids from high acid crude oils is an urgent project. A theoretical and experimental study to develop a catalytic decarboxylation process to remove petroleum acids from high acid crude oils was conducted. By using the molecular simulation technology, a solid acid catalyst was constructed for removing petroleum acids. The experimental results indicated that the acid removal rate of a high acid crude oil with a total acid number (TAN) of 12.52 over the solid acid catalyst of MLC500 was up to 97% at a volume space velocity of 8 h−1, ratio of catalyst to oil of 7.5, and temperature of 460 °C in the fixed fluid bed reactor.
Integrated Approach to 3D Near-surface Characterization (2008)

An integrated approach to 3D geologic and elastic characterization of the near surface is presented. The integration of high spatial resolution, relatively low-confidence remote sensing, and geologic data with sparse spatial resolution, high-confidence geophysical data in a GIS database allows for cross-calibration of both types of datasets, thus providing calibrated near-surface models. The method comprises the generation of a 3D near-surface geologic model, from which the input for a 3D elastic model is obtained. The elastic model is then calibrated with seismic data to provide the final 3D near-surface model. The method has been demonstrated at two case histories covering geomorphological features typical for desert areas in North Africa and the Middle East.
2-Thioalkyl penems: an efficient synthesis of sulopenem, a (5R,6S)-6-(1(R)-hydroxyethyl)-2-[(cis-1-oxo-3-thiolanyl)thio]-2-penem antibacterial (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2-Thioalkyl penems: an efficient synthesis of sulopenem, a (5R,6S)-6-(1(R)-hydroxyethyl)-2-[(cis-1-oxo-3-thiolanyl)thio]-2-penem antibacterialRobert A. Volkmann, Paul R. Kelbaugh, Deane M. Nason, and V. John JasysCite this: J. Org. Chem. 1992, 57, 16, 4352–4361Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/jo00042a010https://doi.org/10.1021/jo00042a010research-articleACS PublicationsRequest reuse permissionsArticle Views1810Altmetric-Citations81LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Expression of basic fibroblast growth factor in synovial tissue from patients with rheumatoid arthritis and degenerative joint disease. (1995)

Synovial tissue from patients with RA, DJD, and trauma express bFGF. Increased bFGF staining in the hyperplastic lining synoviocytes and at the pannus-cartilage interface suggests that bFGF may play a role in synovial hyperplasia and joint destruction. Strong cytoplasmic bFGF staining found in mast cells and vascular cells indicates that these cells are the major sources of tissue bFGF.
Automatic computer detection of clustered calcifications in digital mammograms (1990)

The automatic detection of clusters of calcifications in digital mammograms has been investigated using image analysis techniques. The calcifications were segmented from the background of normal breast structure in the mammogram using a local area thresholding process. This procedure also identified other breast structures and the digital image properties of all segmented objects were analysed to extract clusters of calcifications. Seventy five clinical mammograms were digitised. These were divided into training and test sets of 25 and 50 films respectively. The results for the test set of 50 complete clinical mammograms show that the computer system achieves a 25/25 true positive film classification (i.e. those containing clusters of calcifications) with false positive clusters detected in 4/50 films. There were no false negative film classifications.
Optimization Of A Wavelength Demultiplexer In Fiber Optics Using Gold Echelette Gratings (1984)

A theoretical optimization of the efficiency of gold echelette gratings on silicon substrate is achieved, in order to obtain wavelength demultiplexers with a high efficiency in the ranges 0.78 &mu;m- 0.9 &mu;m or 1.2 &mu;m - 1.35 &mu;m. The experimental results confirm the theoretical predictions.
Microfluidic lab-on-a-chip platforms: requirements, characteristics and applications (2010)

This critical review summarizes developments in microfluidic platforms that enable the miniaturization, integration, automation and parallelization of (bio-)chemical assays (see S. Haeberle and R. Zengerle, Lab Chip, 2007, 7, 1094-1110, for an earlier review). In contrast to isolated application-specific solutions, a microfluidic platform provides a set of fluidic unit operations, which are designed for easy combination within a well-defined fabrication technology. This allows the easy, fast, and cost-efficient implementation of different application-specific (bio-)chemical processes. In our review we focus on recent developments from the last decade (2000s). We start with a brief introduction into technical advances, major market segments and promising applications. We continue with a detailed characterization of different microfluidic platforms, comprising a short definition, the functional principle, microfluidic unit operations, application examples as well as strengths and limitations of every platform. The microfluidic platforms in focus are lateral flow tests, linear actuated devices, pressure driven laminar flow, microfluidic large scale integration, segmented flow microfluidics, centrifugal microfluidics, electrokinetics, electrowetting, surface acoustic waves, and dedicated systems for massively parallel analysis. This review concludes with the attempt to provide a selection scheme for microfluidic platforms which is based on their characteristics according to key requirements of different applications and market segments. Applied selection criteria comprise portability, costs of instrument and disposability, sample throughput, number of parameters per sample, reagent consumption, precision, diversity of microfluidic unit operations and the flexibility in programming different liquid handling protocols (295 references).
歌者中的高级传教士——菲舍一迪斯考：“知识型歌手”？ (2000)

究竟何所谓“知识型歌手(Intelleetual Singer)?在音乐圈里似乎有许多人同意：成为一个“知识型歌手”不是什么好事。一部分人对“知识型歌手”的定义是：一名在表演中任由理智凌驾情感之上的歌手，另一部分人会在一名歌手以牺牲音乐感为代价过分注重词句时而把他称之为“知识型的”。如果一名歌手被看出试图以重视字面诠释来弥补自己的嗓音缺陷，
Therapeutic Effects of Substances Occurring in Higher Basidiomycetes Mushrooms: A Modern Perspective (1999)

This review highlights some of the recently isolated and identified substances of higher Basidiomycetes mushrooms origin that express promising antitumor, immune modulating, cardiovascular and hypercholesterolemia, antiviral, antibacterial, and antiparasitic effects. Medicinal mushrooms have a long history of use in folk medicine. In particular, mushrooms useful against cancers of the stomach, esophagus, lungs, etc. are known in China, Russia, Japan, Korea, as well as the U.S.A. and Canada. There are about 200 species of mushrooms that have been found to markedly inhibit the growth of different kinds of tumors. Searching for new antitumor and other medicinal substances from mushrooms and to study the medicinal value of these mushrooms have become a matter of great significance. However, most of the mushroom origin antitumor substances have not been clearly defined. Several antitumor polysaccharides such as hetero-beta-glucans and their protein complexes (e.g., xyloglucans and acidic beta-glucan-containing uronic acid), as well as dietary fibers, lectins, and terpenoids have been isolated from medicinal mushrooms. In Japan, Russia, China, and the U.S.A. several different polysaccharide antitumor agents have been developed from the fruiting body, mycelia, and culture medium of various medicinal mushrooms (Lentinus edodes, Ganoderma lucidum, Schizophyllum commune, Trametes versicolor, Inonotus obliquus, and Flammulina velutipes). Both cellular components and secondary metabolites of a large number of mushrooms have been shown to effect the immune system of the host and therefore could be used to treat a variety of disease states.
Hierarchical text classification and evaluation (2002)

Hierarchical classification refers to the assignment of one or more suitable categories from a hierarchical category space to a document. While previous work in hierarchical classification focused on virtual category trees where documents are assigned only to the leaf categories, we propose a top-down level-based classification method that can classify documents to both leaf and internal categories. As the standard performance measures assume independence between categories, they have not considered the documents incorrectly classified into categories that are similar to or not far from correct ones in the category tree. We therefore propose category-similarity measures and distance-based measures to consider the degree of misclassification in measuring the classification performance. An experiment has been carried out to measure the performance of our proposed hierarchical classification method. The results showed that our method performs well for a Reuters text collection when enough training documents are given and the new measures have indeed considered the contributions of misclassified documents.
Antimicrobial Activity of Sodium Bicarbonate (1988)

ABSTRACT Sodium bicarbonate (SB) inhibited the growth of bacteria and yeasts in agar media model systems under certain conditions. Escherichia coli, Lactobacillus plantarum, Staphylococcus aureus , and Pseudomonas aeruginosa aerobic plate counts were reduced 10,000‐fold by 0.12M (1% w/v) SB. Saccharomyces cerevisiae and Hansenula wingei were more sensitive; counts were reduced 100,000‐fold by 0.06M SB. Potassium bicarbonate was equally inhibitory, but equimolar sodium chloride had no effect, ruling out osmotic‐ and sodium‐mediated mechanisms of inhibition. The bicarbonate ion was identified as the probable cause of SB‐mediated inhibition although, in some cases, pH elevation played a significant role.
Overview of the MPEG Activity on Point Cloud Compression (2016)

Summary form only given. We present an overview of the MPEG activity on Point Cloud Compression (PCC). This activity aims to satisfy the growing need for lossless and lossy PCC in industry. It follows recent advances in consumer electronics in 3D reconstruction and capturing. We present the preliminary architecture, test datasets and the test model reference software implementation. Contributions beyond the state of the art in PCC include lossy coding of color attributes and lossy inter-predictive coding.
Salmonella effectors within a single pathogenicity island are differentially expressed and translocated by separate type III secretion systems (2002)

Pathogenicity islands (PAIs) are large DNA segments in the genomes of bacterial pathogens that encode virulence factors. Five PAIs have been identified in the Gram-negative bacterium Salmonella enterica. Two of these PAIs, Salmonella pathogenicity island (SPI)-1 and SPI-2, encode type III secretion systems (TTSS), which are essential virulence determinants. These 'molecular syringes' inject effectors directly into the host cell, whereupon they manipulate host cell functions. These effectors are either encoded with their respective TTSS or scattered elsewhere on the Salmonella chromosome. Importantly, SPI-1 and SPI-2 are expressed under distinct environmental conditions: SPI-1 is induced upon initial contact with the host cell, whereas SPI-2 is induced intracellularly. Here, we demonstrate that a single PAI, in this case SPI-5, can encode effectors that are induced by distinct regulatory cues and targeted to different TTSS. SPI-5 encodes the SPI-1 TTSS translocated effector, SigD/SopB. In contrast, we report that the adjacently encoded effector PipB is part of the SPI-2 regulon. PipB is translocated by the SPI-2 TTSS to the Salmonella-containing vacuole and Salmonella-induced filaments. We also show that regions of SPI-5 are not conserved in all Salmonella spp. Although sigD/sopB is present in all Salmonella spp., pipB is not found in Salmonella bongori, which also lacks a functional SPI-2 TTSS. Thus, we demonstrate a functional and regulatory cross-talk between three chromosomal PAIs, SPI-1, SPI-2 and SPI-5, which has significant implications for the evolution and role of PAIs in bacterial pathogenesis.
OPT: a package of computer programs for parameter optimisation in clinical pharmacokinetics. (1982)

1 OPT is a series of computer programs designed to assist dose optimisation for individual patients. It is based on Bayesian Statistical Theory and Maximum Likelihood Estimation. 2 OPT uses prior information on the distribution of population pharmacokinetic parameters and plasma drug concentration measurements to obtain the "most likely' set of parameters for the individual. 3 Complex dosage regimes and non-steady state conditions can be handled. 4 OPT is designed for use in a Clinical Pharmacokinetics Laboratory where informed interpretation of results is essential. 5 The drugs for which the system is currently available include theophylline, digoxin, lignocaine, disopyramide, gentamicin and phenytoin (steady state data only).
Teaching computers to fold proteins (2004)

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. In a test with 24 peptides of known structure, none folded correctly with the initial potential functions, but two-thirds came within 3 A to their native fold after optimizing the potential functions.
International Prevalence, Recognition, and Treatment of Cardiovascular Risk Factors in Outpatients With Atherothrombosis (2006)

This large, international, contemporary database shows that classic cardiovascular risk factors are consistent and common but are largely undertreated and undercontrolled in many regions of the world.
Molecular Characterization of Inflammatory Myofibroblastic Tumors With Frequent ALK and ROS1 Gene Fusions and Rare Novel RET Rearrangement (2015)

Approximately 50% of conventional inflammatory myofibroblastic tumors (IMTs) harbor ALK gene rearrangement and overexpress ALK. Recently, gene fusions involving other kinases have been implicated in the pathogenesis of IMT, including ROS1 and in 1 patient PDGFRB. However, it remains uncertain whether the emerging genotypes correlate with clinicopathologic characteristics of IMT. In this study, we expand the molecular investigation of IMT in a large cohort of different clinical presentations and analyze for potential genotype-phenotype associations. Criteria for inclusion in the study were typical morphology and tissue availability for molecular studies. The lack of ALK immunoreactivity was not an excluding factor. As overlapping gene fusions involving actionable kinases are emerging in both IMT and lung cancer, we set out to evaluate abnormalities in ALK, ROS1, PDGFRB, NTRK1, and RET by fluorescence in situ hybridization. In addition, next-generation paired-end RNA sequencing and FusionSeq algorithm was applied in 4 cases, which identified EML4-ALK fusions in 2 cases. Of the 62 IMTs (25 children and 37 adults), 35 (56%) showed ALK gene rearrangement. Of note, EML4-ALK inversion was noted in 7 (20%) cases, seen mainly in the lung and soft tissue of young children including 2 lesions from newborns. There were 6 (10%) ROS1-rearranged IMTs, all except 1 presenting in children, mainly in the lung and intra-abdominally and showed a distinctive fascicular growth of spindle cells with long cell processes, often positive for ROS1 immunohistochemistry. Two of the cases showed TFG-ROS1 fusions. Interestingly, 1 adult IMT revealed a RET gene rearrangement, a previously unreported finding. Our results show that 42/62 (68%) IMTs are characterized by kinase fusions, offering a rationale for targeted therapeutic strategies. Interestingly, 90% of fusion-negative IMTs were seen in adults, whereas >90% of pediatric IMT showed gene rearrangements. EML4-ALK inversion and ROS1 fusions emerge as common fusion abnormalities in IMT, closely recapitulating the pattern seen in lung cancer.