gebhart/patrepeval huggingface dataset:
The HER-2 Receptor and Breast Cancer: Ten Years of Targeted Anti–HER-2 Therapy and Personalized Medicine (2009)

The human epidermal growth factor receptor (HER-2) oncogene encodes a transmembrane tyrosine kinase receptor that has evolved as a major classifier of invasive breast cancer and target of therapy for the disease. The validation of the general prognostic significance of HER-2 gene amplification and protein overexpression in the absence of anti-HER-2 targeted therapy is discussed in a study of 107 published studies involving 39,730 patients, which produced an overall HER-2-positive rate of 22.2% and a mean relative risk for overall survival (OS) of 2.74. The issue of HER-2 status in primary versus metastatic breast cancer is considered along with a section on the features of metastatic HER-2-positive disease. The major marketed slide-based HER-2 testing approaches, immunohistochemistry, fluorescence in situ hybridization, and chromogenic in situ hybridization, are presented and contrasted in detail against the background of the published American Society of Clinical Oncology-College of American Pathologists guidelines for HER-2 testing. Testing issues, such as the impact of chromosome 17 polysomy and local versus central HER-2 testing, are also discussed. Emerging novel HER-2 testing techniques, including mRNA-based testing by real-time polymerase chain reaction and DNA microarray methods, HER-2 receptor dimerization, phosphorylated HER-2 receptors, and HER-2 status in circulating tumor cells, are also considered. A series of biomarkers potentially associated with resistance to trastuzumab is discussed with emphasis on the phosphatase and tensin homologue deleted on chromosome ten/Akt and insulin-like growth factor receptor pathways. The efficacy results for the more recently approved small molecule HER-1/HER-2 kinase inhibitor lapatinib are also presented along with a more limited review of markers of resistance for this agent. Additional topics in this section include combinations of both anti-HER-2 targeted therapies together as well as with novel agents including bevacizumab, everolimus, and tenespimycin. A series of novel HER-2-targeting agents is also presented, including pertuzumab, ertumaxomab, HER-2 vaccines, and recently discovered tyrosine kinase inhibitors. Biomarkers predictive of HER-2 targeted therapy toxicity are included, and the review concludes with a consideration of HER-2 status in the prediction of response to non-HER-2 targeted treatments including hormonal therapy, anthracyclines, and taxanes.
Heat shock proteins and immune system (2009)

Heat shock proteins (HSPs) such as HSP 60 (Hsp60), Hsp70, Hsp90, and gp96, have been reported to play important roles in antigen presentation and cross-presentation, activation of macrophages and lymphocytes, and activation and maturation of dendritic cells. HSPs contain peptide-binding domains that bind exposed hydrophobic residues of substrate proteins. As part of their molecular chaperone functions, HSPs bind and deliver chaperoned, antigenic peptides to MHC class I molecules at the cell surface for presentation to lymphocytes. HSPs also bind nonprotein molecules with exposed hydrophobic residues including lipid-based TLR ligands. Recombinant HSP products may be contaminated with pathogen-associated molecules that contain exposed hydrophobic residues such as LPS (a TLR4 ligand), lipoprotein (a TLR2 ligand), and flagellin (a TLR5 ligand). These contaminants appear to be responsible for most, if not all, reported in vitro cytokine effects of HSPs, as highly purified HSPs do not show any cytokine effects. We propose that HSPs are molecular chaperones that bind protein and nonprotein molecules with exposed hydrophobic residues. The reported antigen presentation and cross-presentation and in vitro HSP cytokine functions are a result of molecules bound to or chaperoned by HSPs but not a result of HSPs themselves.
919. Transition-metal complexes of seven-membered ring systems. Part I. The cycloheptatriene–metal complexes and related compounds (1958)

E. W. Abel, M. A. Bennett, R. Burton and G. Wilkinson, J. Chem. Soc., 1958, 4559 DOI: 10.1039/JR9580004559
NIGHTRIDER [TRADEMARK] THERMAL IMAGING CAMERA AND HUD DEVELOPMENT PROGRAM FOR COLLISION AVOIDANCE APPLICATIONS (2000)

This report describes a project which involved investigating new methods and technologies regarding the development of automotive head-up displays (HUD) and to develop an improved production-realistic prototype HUD capable of supporting night-riving applications and reliable operation. In the project, the NightDriver HUD was evaluated and an advanced HUD prototype was developed. NightDriver is a developmental automotive night-driving system consisting of a thermal imaging camera mounted on the front of the vehicle and a HUD mounted inside the vehicle within the driver's line or sight or on top of the instrument panel.
Contactless impedance measurement by magnetic induction - a possible method for investigation of brain impedance (1993)

Using a primary coil that induces eddy currents in a volume conductor, and a pair of secondary coils configured to form a differential transformer, it is possible to measure the conductivity of a volume conductor by the magnetic fields of the induced eddy currents. This method is especially favourable for measuring impedance of the brain, as the low conductance of the surrounding skull interferes only very slightly with the measuring process. In a simulation experiment a life-size skull model was filled with NaCl solutions of different concentrations in each half, so as to model the impedances of a normal and an oedematous hemisphere. The impedance differences could be clearly detected by a coil system of 25 mm diameter.
Infection of the middle nasal meatus of calves with Pasteurella haemolytica serotype 1 (1989)

Eight healthy nonstressed calves were inoculated with Pasteurella haemolytica serotype 1, by instilling a broth culture into the middle nasal meatus of the left nostril. The inoculated left nostrils shed P haemolytica from the ventral nasal meatus at a steady rate for a mean of 7 days, whereas the uninoculated right nostrils of the same calves shed P haemolytica sporadically and in lower concentrations. The duration, frequency, and concentration of P haemolytica shed from the inoculated nostrils was significantly (P less than 0.05) greater than from the nostrils of other healthy calves that had been exposed by instilling the culture into the ventral nasal meatus of both nostrils in a previous study. The concentration of antibodies (IgG, IgA, and IgM) to P haemolytica increased significantly (P less than 0.05) in serum and nasal secretions after exposure. Four weeks after initial P haemolytica exposure, calves were exposed to infectious bovine rhinotracheitis virus and became clinically ill. Four calves were induced to shed P haemolytica from both nostrils by the virus infection; thus, they were harboring the bacterium and were susceptible to active recolonization. Four calves were not induced to shed P haemolytica. The apparent reason was not that they were resistant to active colonization, but that they were no longer harboring the bacterium, because they became active shedders after they were reinfected with P haemolytica.
The fungicidal activity of substituted acetanilides and related compounds (1953)

Research Article| December 01 1953 The fungicidal activity of substituted acetanilides and related compounds N. G. Clark; N. G. Clark 1Research Department, Boots Pure Drug Co. Ltd., Nottingham Search for other works by this author on: This Site PubMed Google Scholar A. F. Hams A. F. Hams 1Research Department, Boots Pure Drug Co. Ltd., Nottingham Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1953) 55 (5): 839–851. https://doi.org/10.1042/bj0550839 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation N. G. Clark, A. F. Hams; The fungicidal activity of substituted acetanilides and related compounds. Biochem J 1 December 1953; 55 (5): 839–851. doi: https://doi.org/10.1042/bj0550839 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1953 CAMBRIDGE UNIVERSITY PRESS1953 Article PDF first page preview Close Modal You do not currently have access to this content.
A generalized hypothetical reference decoder for H.264/AVC (2003)

In video coding standards, a compliant bit stream must be decoded by a hypothetical decoder that is conceptually connected to the output of an encoder and consists of a decoder buffer, a decoder, and a display unit. This virtual decoder is known as the hypothetical reference decoder (HRD) in H.263 and the video buffering verifier in MPEG. The encoder must create a bit stream so that the hypothetical decoder buffer does not overflow or underflow. These previous decoder models assume that a given bit stream will be transmitted through a channel of a known bit rate and will be decoded (after a given buffering delay) by a device of some given buffer size. Therefore, these models are quite rigid and do not address the requirements of many of today's important video applications such as broadcasting video live or streaming pre-encoded video on demand over network paths with various peak bit rates to devices with various buffer sizes. In this paper, we present a new HRD for H.264/AVC that is more general and flexible than those defined in prior standards and provides significant additional benefits.
On the privacy preserving properties of random data perturbation techniques (2004)

Privacy is becoming an increasingly important issue in many data mining applications. This has triggered the development of many privacy-preserving data mining techniques. A large fraction of them use randomized data distortion techniques to mask the data for preserving the privacy of sensitive data. This methodology attempts to hide the sensitive data by randomly modifying the data values often using additive noise. We question the utility of the random value distortion technique in privacy preservation. We note that random objects (particularly random matrices) have "predictable" structures in the spectral domain and it develops a random matrix-based spectral filtering technique to retrieve original data from the dataset distorted by adding random values. We present the theoretical foundation of this filtering method and extensive experimental results to demonstrate that in many cases random data distortion preserve very little data privacy. We also point out possible avenues for the development of new privacy-preserving data mining techniques like exploiting multiplicative and colored noise for preserving privacy in data mining applications.
Site‐specific labeling of proteins for single‐molecule FRET by combining chemical and enzymatic modification (2006)

An often limiting factor for studying protein folding by single-molecule fluorescence resonance energy transfer (FRET) is the ability to site-specifically introduce a photostable organic FRET donor (D) and a complementary acceptor (A) into a polypeptide chain. Using alternating-laser excitation and chymotrypsin inhibitor 2 as a model, we show that chemical labeling of a unique cysteine, followed by enzymatic modification of a reactive glutamine in an N-terminally appended substrate sequence recognition tag for transglutaminase (TGase) affords stoichiometrically D-/A-labeled protein suitable for single-molecule FRET experiments. Thermodynamic data indicate that neither the presence of the TGase tag nor D/A labeling perturbs protein stability. As the N terminus in proteins is typically solvent accessible, a TGase tag can (in principle) be appended to any protein of interest by genetic engineering. Two-step chemical/enzymatic labeling may thus represent a simple, low-cost, and widely available strategy for D/A labeling of proteins for FRET-based single-molecule protein folding studies, even for non-protein-experts laboratories.
Virtual video editing in interactive multimedia applications (1989)

Drawing examples from four interrelated sets of multimedia tools and applications under development at MIT, the authors examine the role of digitized video in the areas of entertainment, learning, research, and communication.
Even Mild Hyperlactatemia Is Associated with Increased Mortality in Critically Ill Patients (2013)

Relative hyperlactatemia (lactate of 1.36 to 2.00 mM) within the first 24 hours of ICU admission is an independent predictor of hospital and ICU mortality in critically ill patients.
Hepatitis C virus variants from Nepal with novel genotypes and their classification into the third major group (1994)

Five isolates of hepatitis C virus (HCV) RNA from patients with chronic liver disease in Nepal were not classifiable into the known genotypes I/1a, II/1b, III/2a, IV/2b or V/3a using PCR with type-specific primers deduced from the HCV core gene. Their nucleotide sequences were determined for the 5'-terminal 1.5 kilobases and 3'-terminal 1.2 kilobases, covering 30% of the entire genome, and compared with each other and with reported sequences of HCV isolates of various genotypes. They were more similar to a reported HCV isolate (NZL1) of genotype V/3a (in 81.6 to 84.1% of their nucleotides and 85.7 to 88.7% of the deduced amino acid sequence) compared with the genotypes I/1a to IV/2b (in 69.3 to 74.7% and 72.3 to 77.4%, respectively). Hence they were considered to be variants of the third major group (group 3). The five HCV isolates shared 81.3 to 85.2% of nucleotide sequence and 85.4 to 89.3% of deduced amino acid sequence. Thus they were substantially different from each other. One of them was classified as genotype VI/3b due to an 88.2% similarity in nucleotide sequence to that of the reported HCV isolates of this genotype, whereas the remaining four were classified into provisional genotypes 3c, 3d, 3e and 3f. These HCV variants have evolved and remained in Nepal, and have not been observed in the other areas of the world.
Noninvasive methods to assess embryo quality (2005)

In performing embryo selection we need to develop processes that will be extremely critical, allowing us to limit the number of embryos replaced without detriment to pregnancy rates.
Dynamic scene view interpolation with multiple moving objects using layered representation (2005)

Given a pair of stream images of a dynamic scene with multiple moving object, how does the scene look like from a new viewing position in between two reference cameras? We tackle this interpolation problem using layered representation of the scene in this paper. The dynamic scene is separated into two different layers; a static background layer and a dynamically changing foreground layer. The foreground layer is further separated into sublayers according to the correspondences of each object in the scene. Different interpolation methods are used for the background and foreground layers. The joint view triangulation method is used for the background layer and interpolation using a local transformation of each object is used for the foreground layer. View interpolation of a dynamic scene is achieved by combining these separately interpolated background and foreground layers. Obtained photo-realistic interpolated images are presented.
Biosynthesis and Biological Activities of Lantibiotics with Unique Post‐Translational Modifications (1995)

Lantibiotics are biologically active peptides which contain the thioether amino acid lanthionine as well as several other modified amino acids. They can be broadly divided into two groups on the basis of their structures: type-A lantibiotics are elongated, amphiphilic peptides, while type-B lantibiotics are compact and globular. In the last decade there has been a marked increase in research interest in these peptides due both to the novel biosynthetic mechanisms by which they are produced, as well as to their potential applications. Lantibiotics are synthesised on the ribosome as a prepeptide which undergoes several post-translational modification events, including dehydration of specific hydroxyl amino acids to form dehydroamino acids, addition of neighbouring sulfhydryl groups to form thioethers and, in specific cases, other modifications such as introduction of D-alanine residues from L-serine, formation of lysinoalanine bridges, formation of novel N-terminal blocking groups and oxidative decarboxylation of a C-terminal cysteine. The genetic elements responsible for these specific modification reactions encode unique enzymes with hitherto unknown reaction mechanisms. Production of these peptides also requires accessory proteins including processing proteases, translocators of the ATP-binding cassette transporter family, regulatory proteins and dedicated producer self-protection mechanisms. While the principle biological activity of most type-B lantibiotics appears to be directed at the inhibition of enzyme functions, the type-A lantibiotics kill bacterial cells by forming pores in the cytoplasmic membrane.
Real-Time Reverse Transcriptase PCR Assay for Detection of Human Metapneumoviruses from All Known Genetic Lineages (2004)

The discovery of human metapneumovirus and its implications for respiratory tract disease have emphasized the need for a sensitive, specific, and rapid assay to detect this virus in a clinical setting. It recently became clear that human metapneumovirus can be grouped into at least four genetic lineages. Previously described assays for the detection of human metapneumovirus were developed by using limited sequence information and failed to detect viruses from all four genetic lineages with comparable sensitivities. Here we describe the development and evaluation of a real-time reverse transcriptase PCR assay that detects human metapneumovirus from the four known genetic lineages with equal specificities and sensitivities.
Sphingosine 1-Phosphate in Amniotic Fluid Modulates Cyclooxygenase-2 Expression in Human Amnion-derived WISH Cells (2003)

The metabolism of arachidonic acid, in particular the generation of prostaglandins (PGs), has been proposed to play a key role in the regulation of labor. Moreover, several extracellular proteins have been reported to modulate PG synthesis in amnion cells. In this study, we found that lipid components dissolved in the amniotic fluid modulate PG synthesis in WISH human amnion cells and identified one of these components as a sphingosine 1-phosphate (S1P). WISH cells express several S1P receptors including S1P1, S1P2, and S1P3. When WISH cells were stimulated with S1P, PGE2 synthesis increased in a concentration-dependent manner, showing maximal activity at around 100 nM. S1P treatment also caused the up-regulation of cyclooxygenase-2 (COX-2) mRNA and protein, which was apparent within 3-12 h of stimulation. In terms of the intracellular signaling pathway of S1P-induced WISH cell activation, we found that S1P stimulated two kinds of MAPK, ERK, and p38 kinase. We examined the roles of these two MAPKs in S1P-induced COX-2 expression. S1P-induced COX-2 expression was blocked completely by PD-98059 but not by SB-203580, suggesting that ERK has a critical role in the process. Transfection of S1P1 or S1P3 but not of S1P2 antisense oligonucleotide inhibited S1P-induced COX-2 expression and PGE2 production in WISH cells, indicating the involvements of S1P1 and S1P3 in the processes. This study demonstrates the physiological role of S1P in amniotic fluid and its effect on the modulation of COX-2 expression and PGs synthesis in WISH cells.
Monolithic Suspended Optical Waveguides for InP MEMS (2004)

We present a novel waveguide design for InP microelecromechanical systems. The substrate is removed from underneath the waveguide by sacrificial etching, and the suspended waveguide is supported by lateral tethers. This allows segments of the waveguide to be moved and prevents substrate leakage loss in the fixed segments of the waveguides. A single-mask fabrication process is developed that can be extended to more complex devices employing electrostatic actuation. Fabricated suspended waveguides exhibit a loss of 2.2 dB/cm and tether pairs exhibit 0.25-dB additional loss.
Optical Antenna Arrays on a Fiber Facet for in Situ Surface-Enhanced Raman Scattering Detection (2009)

This paper reports a bidirectional fiber optic probe for the detection of surface-enhanced Raman scattering (SERS). One facet of the probe features an array of gold optical antennas designed to enhance Raman signals, while the other facet of the fiber is used for the input and collection of light. Simultaneous detection of benzenethiol and 2-[(E)-2-pyridin-4-ylethenyl]pyridine is demonstrated through a 35 cm long fiber. The array of nanoscale optical antennas was first defined by electron-beam lithography on a silicon wafer. The array was subsequently stripped from the wafer and then transferred to the facet of a fiber. Lithographic definition of the antennas provides a method for producing two-dimensional arrays with well-defined geometry, which allows (i) the optical response of the probe to be tuned and (ii) the density of "hot spots" generating the enhanced Raman signal to be controlled. It is difficult to determine the Raman signal enhancement factor (EF) of most fiber optic Raman sensors featuring hot spots because the geometry of the Raman enhancing nanostructures is poorly defined. The ability to control the size and spacing of the antennas enables the EF of the transferred array to be estimated. EF values estimated after focusing a laser directly onto the transferred array ranged from 2.6 x 10(5) to 5.1 x 10(5).
A mouse model for hereditary hemorrhagic telangiectasia (HHT) type 2 (2003)

Hereditary hemorrhagic telangiectasia (HHT) is an autosomal-dominant disorder characterized by the age-dependent development of focal arteriovenous malformations and telangiectases. HHT type 2 is caused by loss of function mutations in activin receptor-like kinase 1 (ACVRL1 or ALK1). However, the factors that initiate lesion formation and those that influence disease progression remain unknown. Because heterozygous mice contain the appropriate genotype for an animal model of this disorder, mice heterozygous for a loss-of-function mutation in Acvrl1 were carefully examined for an HHT-like phenotype. These mice developed age-dependent vascular lesions in the skin, extremities, oral cavity and in the internal organs (lung, liver, intestine, spleen and brain), similar to those seen in HHT patients. Major histopathological features of the lesions included thin-walled dilated vessels in close proximity to each other, hemorrhage and fibrosis. Similar to HHT patients, the mice also exhibited gastrointestinal bleeding, as evidenced by positive fecal occult blood tests. An Acvrl1(+/-) mouse with profound liver involvement also displayed a secondary cardiac phenotype, similar to that observed in human patients. The similarity of affected organs, age-dependent penetrance, histological similarity of the lesions and recapitulation of a secondary phenotype suggest that the Acvrl1(+/-) mice are an appropriate animal model for the identification of additional genetic and environmental factors that cause pathology in HHT type 2 patients. In addition, studies utilizing this animal model can yield valuable information on the role of ALK1 in maintenance of adult vascular architecture including arteriovenous identity.