gebhart/patrepeval huggingface dataset:
Human papillomavirus type‐16‐related DNA in genital Bowen's disease and in bowenoid papulosis (1983)

32P-labelled DNA of HPV 16 which has been isolated and molecularly cloned from a cervical carcinoma (Dürst et al., 1983) was used to screen the cellular DNAs obtained from 20 different biopsies of Morbus Bowen or Bowenoid papulosis, respectively, by Southern blot analysis. Under conditions of differing stringency for the hybridization, HPV 16 DNA or related sequences were identified in 6 out of 10 cases of Morbus Bowen (4 out of 5 from a genital localization) and in 8 out of 10 biopsies from Bowenoid papulosis. One additional case of the latter disease contained DNA sequences of an HPV type not yet classified. There is evidence for the presence of another HPV DNA in two of the HPV-16-positive tumors. A large number of normal genital tissue samples were negative for HPV DNA.
A bacterial clone synthesizing proinsulin. (1978)

We have cloned double-stranded cDNA copies of a rat preproinsulin messenger RNA in Escherichia coli chi1776, using the unique Pst endonuclease site of plasmid pBR322 that lies in the region encoding amino acids 181-182 of penicillinase. This site was reconstructed by inserting the cDNA with an oligo(dG)-oligo(dC) joining procedure. One of the clones expresses a fused protein bearing both insulin and penicillinase antigenic determinants. The DNA sequence of this plasmid shows that the insulin region is read in phase; a stretch of six glycine residues connects the alanine at position 182 of penicillinase to the fourth amino acid, glutamine, of rat proinsulin.
Characteristics and Clinical Impacts of the Immune Environments in Colorectal and Renal Cell Carcinoma Lung Metastases: Influence of Tumor Origin (2013)

Our results show a major prognostic value of the immune pattern (CD8(+)/DC-LAMP(+) cell densities) in colorectal carcinoma and RCC, reproducible from primary to metastatic tumors, although with opposite clinical impacts, and highlight the role of the tumor cell in shaping its immune environment.
How Many Clusters? Which Clustering Method? Answers Via Model-Based Cluster Analysis (1998)

Journal Article How Many Clusters? Which Clustering Method? Answers Via Model-Based Cluster Analysis Get access C. Fraley, C. Fraley Department of Statistics, University of Washington, USA Email: fraley@stat.washington.edu Search for other works by this author on: Oxford Academic Google Scholar A. E. Raftery A. E. Raftery Department of Statistics, University of Washington, USA Email: fraley@stat.washington.edu Search for other works by this author on: Oxford Academic Google Scholar The Computer Journal, Volume 41, Issue 8, 1998, Pages 578–588, https://doi.org/10.1093/comjnl/41.8.578 Published: 01 January 1998
PUTATIVE VIRULENCE FACTORS OF CANDIDA ALBICANS (1991)

INTRODUCTION 187 Hypothetical Set of Virulence Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . 188 Commensal or Opportunistic Pathogen? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188 Purpose of Review . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189 HYPHAL PRODUCTION 190 Early Observation . . . . . . . . . .. . . , .... .. .. . . . . .. . . .. .. ...... . . . . . . . . .. . . . . . . .. .. . . . . . ,. 190 Inherent Experimental Diff iculties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . 191 Recent Observations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . 193 Other Approaches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197 PROTEINASE ACTIVITy 197 Is There Only One Proteinase? 198 Evidence For and Against Proteinase . .... . . . . . . . . . . . . . . ....... ... . . . . . . ....... . . . . . .... . . ... 1 99 ADHERENCE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ... . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . 203 Classification of Receptor-Ligand Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204 How Many Receptor-Ligand Molecules on C. albicans Are There? . . . . . . . . . . . . . . .... . 205 Virulence Role . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206 VARIABILITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . .. . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207 Chromosomal Instabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208 Antigenic Variabilit y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . 208 OTHER ATTRIBUTES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ,.. . . ...... . . . . . 209 Suppression-Activation of Host-Acquired Specific Immunity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209 CONCLUDING REMARKS 209
Systemic Induction of the Angiogenesis Switch by the Tetraspanin D6.1A/CO-029 (2006)

Expression of the tetraspanin CO-029 is associated with poor prognosis in patients with gastrointestinal cancer. In a pancreatic tumor line, overexpression of the rat homologue, D6.1A, induces lethally disseminated intravascular coagulation, suggesting D6.1A engagement in angiogenesis. D6.1A-overexpressing tumor cells induce the greatest amount of angiogenesis in vivo, and tumor cells as well as exosomes derived thereof strikingly increase endothelial cell branching in vitro. Tumor cell-derived D6.1A stimulates angiogenic factor transcription, which includes increased matrix metalloproteinase and urokinase-type plasminogen activator secretion, pronounced vascular endothelial growth factor expression in fibroblasts, vascular endothelial growth factor receptor expression, and strong D6.1A up-regulation in sprouting endothelium. Thus, D6.1A initiates an angiogenic loop that, probably due to the abundance of D6.1A in tumor-derived exosomes, reaches organs distant from the tumor. Most importantly, because of the strong D6.1A up-regulation on sprouting capillaries, angiogenesis could be completely inhibited by a D6.1A-specific antibody, irrespective of whether or not the tumor expresses D6.1A. Tetraspanins have been suggested to be involved in morphogenesis. This is the first report that a tetraspanin, CO-029/D6.1A, promotes tumor growth by its capacity to induce systemic angiogenesis that can effectively, and with high selectivity for sprouting endothelium, be blocked by a D6.1A-specific antibody.
Sleep apnoea and sympathetic nervous system activity: a review (1996)

A review was made of the literature relating sleep apnoea to sympathetic nervous system (SNS) activity, as inferred from catecholamine levels or muscle sympathetic nerve activity (MSNA). Twenty‐four studies were located. Most studies reported an elevation of norepinephrine and MSNA, both during sleep and wakefulness among individuals with sleep apnoea. However, studies rarely controlled for known confounders of sympathetic activity, making the validity of the findings questionable.
SUSurE: Speeded Up Surround Extrema feature detector and descriptor for realtime applications (2009)

There has been significant research into the development of visual feature detectors and descriptors that are robust to a number of image deformations. Some of these methods have emphasized the need to improve on computational speed and compact representations so that they can enable a range of real-time applications with reduced computational requirements. In this paper we present modified detectors and descriptors based on the recently introduced CenSurE [1], and show experimental results that aim to highlight the computational savings that can be made with limited reduction in performance. The developed methods are based on exploiting the concept of sparse sampling which may be of interest to a range of other existing approaches.
Discovery and Validation of a Prostate Cancer Genomic Classifier that Predicts Early Metastasis Following Radical Prostatectomy (2013)

A genomic classifier was developed and validated in a large patient cohort enriched with prostate cancer metastasis patients and a rising PSA that went on to experience metastatic disease. This early metastasis prediction model based on genomic expression in the primary tumor may be useful for identification of aggressive prostate cancer.
Oxcarbazepine versus phenytoin monotherapy for epilepsy (2006)

For patients with partial onset seizures oxcarbazepine is significantly less likely to be withdrawn, but current data do not allow a statement as to whether oxcarbazepine is equivalent, superior or inferior to phenytoin in terms of seizure control. Guidelines recommend carbamazepine as a first line treatment for patients with partial onset seizures and more evidence is needed regarding the comparative effects of oxcarbazepine and carbamazepine to further inform policy. For patients with generalized onset tonic-clonic seizures, valproate is considered the first line standard treatment and the results of this review do not inform current treatment policy. Misclassification of patients' epilepsy type may have confounded the results of this review.
X-Ray Crystallography of Biomacromolecules: A Practical Guide (2007)

Preface. Part I Principles and Methods. 1 Introduction. 1.1 Crystals and Symmetry. 1.2 Protein Solubility. 1.3 Experimental Techniques. 1.4 Crystallization Screenings. 1.5 High-Throughput Crystallization, Imaging, and Analysis. References. 2 Experimental Techniques. 2.1 X-Ray Sources. 2.2 Detectors. 2.3 Crystal Mounting and Cooling. 2.4 Data Collection Techniques. References. 3 Principles of X-Ray Diffraction by a Crystal. 3.1 Rational Mathematical Representation of Waves. 3.2 Principles of X-Ray Diffraction by a Crystal. References. 4 Diffraction Data Evaluation. 4.1 Introductory Remarks. 4.2 Geometric Principles in the Rotation Technique with Normal Flat Detector. 4.3 Autoindexing of Oscillation Images. 4.4 Beam Divergence, Mosaicity, and Partiality. 4.5 Integration of Diffraction Spots. 4.6 Post-Refinement, Scaling, and Averaging of Diffraction Data. References. 5 Methods for Solving the Phase Problem. 5.1 Isomorphous Replacement. 5.2 Anomalous Scattering. 5.3 Determination of Heavy-Atom Positions. 5.4 Phase Calculation. 5.5 Patterson Search Methods (Molecular Replacement). References. 6 Phase Improvement by Density Modification and Phase Combination. 6.1 Introduction. 6.2 Solvent Flattening. 6.3 Histogram Matching. 6.4 Molecular Averaging. 6.5 Sayre's Equation. 6.6 Atomization. 6.7 Phase Combination. 6.8 Difference Fourier Technique. References. 7 Model Building and Refinement. 7.1 Model Building. 7.2 Crystallographic Refinement. 7.3 Verification and Accuracy of Structure Determination. References. 8 Crystal Structure Determination of the Time-Course of Reactions and of Unstable Species. 8.1 Introduction. 8.2 Triggering Methods. 8.3 Trapping Methods. 8.4 Laue Diffraction. References. 9 Structural Genomics. 9.1 Introduction. 9.2 Target Selection. 9.3 Production of Recombinant Proteins. 9.4 Aspects of Automation. References. Part II Practical Examples. Introductory Remarks. 10 Data Evaluation. 10.1 Autoindexing, Refinement of Cell Parameters, and Reflection Integration. 10.2 Scaling of Intensity Diffraction Data. 10.3 A Complex Example of Space Group Determination. References. 11 Determination of Anomalous Scatterer or Heavy Atom Positions. 11.1 Application of Direct Methods. 11.2 Vector Verification Methods. 11.3 Comparison of the Results from SnB and RSPS. References. 12 MIRAS and MAD Phasing with the Program SHARP. 12.1 MAD Phasing with the Program SHARP for 4-BUDH. References. 13 Molecular Replacement. 13.1 Phase Determination of PKC-iota with Program Molrep. References. 14 Averaging about Non-Crystallographic Symmetry (NCS) for 4-BUDH. 14.1 Determination of NCS Operators for 4-BUDH. 14.2 Electron Density Map Averaging for 4-BUDH. References. 15 Model Building and More. 15.1 A Very Personal Short Introduction to the Computer Graphics Modeling Program O. 15.2 Introduction of the Four Fe-Sites per Fe-S-Cluster and New SHARP-Phasing for 4-BUDH. 15.3 Crystallographic Refinement and Final Steps. References. Subject Index.
Transient tyrosine phosphorylation of p34cdc2 is an early event in radiation‐induced apoptosis of prostate cancer cells (1997)

BACKGROUND Previous studies have demonstrated that androgen-independent human prostate cancer cells undergo radiation-induced apoptosis. The present study investigated the early events that trigger the apoptotic response of prostate cancer cells after exposure to ionizing irradiation. METHODS Human prostate cancer cells (PC-3) were exposed to single doses of ionizing irradiation, and the immediate protein phosphorylation events were temporally correlated with induction of apoptosis. Apoptosis among the irradiated cell populations was evaluated using the fluorescein-terminal transferase assay. RESULTS The kinetics of phosphorylation of a Mr 34,000 substrate followed a transient course: an initial increase was observed after 10 min postirradiation, reaching maximum levels by 60 min, and the protein subsequently underwent rapid dephosphorylation. Subsequent analysis revealed that the substrate for this tyrosine phosphorylation is the serine/threonine p34cdc2 protein kinase, a cell cycle regulatory protein that controls cell entry into mitosis. This enhanced phosphorylation temporally preceded the radiation-induced apoptotic DNA fragmentation as detected by the terminal transferase technique. Arresting the cells in G0/G1 phase by pretreatment with suramin totally abrogated radiation-induced phosphorylation of p34cdc2 protein at the tyrosine residue, indicating that this posttranslational modification occurs in cell populations that escape G2 arrest and undergo apoptosis in response to radiation. CONCLUSIONS These results suggest that a rapid and transient phosphorylation of a protein that controls mitotic progression precedes and potentially triggers radiation-induced apoptosis in prostate cancer cells. Prostrate 32:266–271, 1997. © 1997 Wiley-Liss, Inc.
HPSm2: A refined single-chip microengine (1988)

The authors describe the high-performance single-chip microarchitecture of HPSm, which is being refined to provide a second chip, the HPSm2, with a 33% performance improvement. They relate how they are achieving this by making the HPS data path more regular and migrating many of the hardware functions to the compiler.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The signature of an air gun array; computation from near-field measurements including interactions (1982)

Abstract We designed a system to enable the signature of an air gun array to be calculated at any point in the water from a number of simultaneous independent measurements of the near-field pressure field [subject of a patent application]. The number of these measurements must not be less than the number of guns in the array.The underlying assumption in our method is that the oscillating bubble produced by an air gun is small compared with the wavelengths of seismic interest. Each bubble thus behaves as a point source, both in the generation of seismic waves and in its response to incident seismic radiation produced by other nearby bubbles. It follows that the interaction effects between the bubbles may be described in terms of spherical waves.The array of interacting guns is equivalent to a notional array of noninteracting guns whose combined seismic radiation is identical. The seismic signatures of the equivalent independent elements of this notional array can be determined from the near-field measurements. The seismic radiation pattern emitted by the whole array can be computed from these signatures by linear superposition, with a spherical correction applied.The method is tested by comparing far-field signatures computed in this way with field measurements made in deep water. The computed and measured signatures match each other very closely. By comparison, signatures computed neglecting this interaction are a poor match to the measurements.
Effects of a Modified Dye-Labeled Nucleotide Spacer Arm on Incorporation by Thermophilic DNA Polymerases (2006)

The ability of eight commercially available thermophilic DNA polymerases to sequentially incorporate fluorescently labeled nucleotides sequentially was analyzed by a gel based primer extension assay. Cy5-dUTP or a variant nucleotide in which the linker had been lengthened by 14 atoms between the dye and the nucleobase were compared. We found that the Cy5-dUTP with a longer linker resulted in longer primer extension lengths. Furthermore, some of the assayed polymerases are capable of extending the primer to the full or near full length of 30 nucleotides using dye-labeled nucleotides exclusively.
Panel of twenty-five independent man-rodent hybrids for human genetic marker mapping. (1986)

To increase the efficiency of the human gene mapping, a panel of 25 man-rodent hybrids was selected out of 200 independent man-rodent hybrids produced in our laboratory since 1969. The hybrid panel was selected in such a fashion as to allow the asignment of a human marker M by respecting the two following complementary criteria: correlation between M and a chromosome and exclusion of the other chromosomes. The panel characteristics allowing the use of these two criteria were presented and discussed. A first series of enzyme markers were analysed to test the validity of the hybrid panel for the human gene mapping. The different possibilities and limits of the hybrid panel were also discussed, especially for the assignment of markers with DNA probes.
Evidence of protein kinase C involvement in phorbol diester-stimulated arachidonic acid release and prostaglandin synthesis. (1987)

Many stimulators of prostaglandin production are thought to activate the Ca2+- and phospholipid-dependent protein kinase first described by Nishizuka and his colleagues (Takai, Y., Kishimoto, A., Iwasa, Y., Kawahara, Y., Mori, T., and Nishizuka, Y. (1979) J. Biol. Chem. 254, 3692-3695. In this paper we report evidence that the activation of protein kinase C caused by 12-O-tetradecanoylphorbol-13-acetate (TPA) is involved in the increased prostaglandin production induced by 12-O-tetradecanoylphorbol-13-acetate in Madin-Darby canine kidney (MDCK) cells. We have shown that TPA activates protein kinase C in MDCK cells with similar dose response curve as observed for TPA induction of arachidonic acid release in MDCK cells. Activation of protein kinase C was associated with increased phosphorylation of proteins of 40,000 and 48,000 daltons. We used two compounds (1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine (ET-18-OMe) and 1-(5-isoquinolinesulfonyl)piperazine) known to inhibit protein kinase C by different mechanisms to further examine if activation of protein kinase C was involved in the increased synthesis of prostaglandins in TPA-treated MDCK cells. We found that both compounds inhibited protein kinase C partially purified from MDCK cells and that ET-18-OMe inhibited the phosphorylation of proteins by protein kinase C in the intact cells. Addition of either compound during or after TPA treatment decreased both release of arachidonic acid from phospholipids and prostaglandin synthesis. Release of [3H]arachidonic acid from phosphatidylethanolamine in TPA-treated cells was blocked by ET-18-OMe or 1-(5-isoquinolinesulfonyl)piperazine addition. However, arachidonic acid release stimulated by A23187 is not blocked by Et-18-OMe. When assayed in vitro, treatment of cells with Et-18-OMe did not prevent the enhanced conversion of arachidonic acid into prostaglandins induced by pretreatment of cells with TPA. Our results suggest that the stimulation of phospholipase A2 activity by TPA occurs via activation of protein kinase C by TPA.
Strategies for culture of ‘unculturable’ bacteria (2010)

Molecular ecology methods are now well established for the culture-independent characterization of complex bacterial communities associated with various environmental and animal habitats and are revealing the extent of their diversity. By comparison, it has become clear that only a small minority of microorganisms are readily cultivated in vitro, with the majority of all bacteria remaining 'unculturable' using standard methods. Yet, it is only through the isolation of bacterial species in pure culture that they may be fully characterized, both for their physiological and pathological properties. Hence, the endeavour to devise novel cultivation methods for microorganisms that appear to be inherently resistant to artificial culture is a most important one. This minireview discusses the possible reasons for 'unculturability' and evaluates advances in the cultivation of previously unculturable bacteria from complex bacterial communities. Methods include the use of dilute nutrient media particularly suited for the growth of bacteria adapted to oligotrophic conditions, and the provision of simulated natural environmental conditions for bacterial culture. This has led to the recovery of 'unculturables' from soil and aquatic environments, likely to be due to the inclusion of essential nutrients and/or signalling molecules from the native environment.
Small gauge gelfoam plug liver biopsy in high risk patients: Safety and diagnostic value (1996)

The performance of a percutaneous core biopsy of the liver may be contraindicated in patients at higher risk of haemorrhage. In this clinical setting, gelfoam plug embolization of the needle track has been proposed to minimize haemorrhagic complications of biopsy. In the present study, gelfoam plug liver biopsy was performed in 51 consecutive patients at increased risk of haemorrhage. An 18 gauge spring-loaded disposable cutting needle was used through a 4 French sheath. The biopsy track was embolized by three to four gelfoam pledgets. In every patients, the cores of hepatic tissue were adequate for histopathological diagnosis. There were no fatalities and no serious complications. Gelfoam plug liver biopsy using this needle and sheath in combination appears to be a safe procedure and produces diagnostic cores for histological analysis. This method represents an alternative to transjugular liver biopsy and is technically more straight-forward to perform.
Telomerase reverse transcriptase promotes cardiac muscle cell proliferation, hypertrophy, and survival (2001)

Cardiac muscle regeneration after injury is limited by "irreversible" cell cycle exit. Telomere shortening is one postulated basis for replicative senescence, via down-regulation of telomerase reverse transcriptase (TERT); telomere dysfunction also is associated with greater sensitivity to apoptosis. Forced expression of TERT in cardiac muscle in mice was sufficient to rescue telomerase activity and telomere length. Initially, the ventricle was hypercellular, with increased myocyte density and DNA synthesis. By 12 wk, cell cycling subsided; instead, cell enlargement (hypertrophy) was seen, without fibrosis or impaired function. Likewise, viral delivery of TERT was sufficient for hypertrophy in cultured cardiac myocytes. The TERT virus and transgene also conferred protection from apoptosis, in vitro and in vivo. Hyperplasia, hypertrophy, and survival all required active TERT and were not seen with a catalytically inactive mutation. Thus, TERT can delay cell cycle exit in cardiac muscle, induce hypertrophy in postmitotic cells, and promote cardiac myocyte survival.