gebhart/patrepeval huggingface dataset:
Molecular Pathways in Head and Neck Cancer: EGFR, PI3K, and More (2013)

The treatment of head and neck squamous cell carcinoma (HNSCC) is set to undergo rapid changes, as novel treatment targets informed by genomic profiling and novel molecularly targeted therapies continue to make strides. In this review we provide an overview of the latest developments regarding (1) EGFR targeting for HNSCC, (2) PI3K as a novel treatment target, and (3) newly described key genetic events in HNSCC such as NOTCH1 mutations and emerging candidate targets including ALK1 and hedgehog. The first molecular targeting strategy to demonstrate a survival advantage for patients with HNSCC has emerged in the context of EGFR biology. Cetuximab remains the only U.S. Food and Drug Administration (FDA)-approved targeted therapy available for HNSCC, but EGFR as a target has not been individualized in this disease. The PI3K-AKT pathway is downstream of EGFR and is emerging as potentially one of the most important pathways in HNSCC. PIK3CA is the most frequently mutated oncogene for HNSCC (approximately 20%) and may play a role for both HPV-negative and HPV-positive tumors. Multiple therapeutic strategies targeting PI3K are being explored, and multiple agents either alone or in combination are in development. NOTCH1 is a key tumor suppressor gene and its genetic alterations lead to abnormal pathway activation. ALK1 is a novel target involved in angiogenesis, and efficacy in patients with HNSCC was documented in an early inhibitor trial. The hedgehog pathway modulates EGFR dependence and epithelial to mesenchymal transition (EMT), a key invasion and drug-resistance mechanism in HNSCC.
Recall of long-lived immunity to Mycobacterium tuberculosis infection in mice. (1995)

Our study investigates the recall of immunity in the mouse model of memory immunity to tuberculosis infection. The results provide evidence that recall of immunity is expressed as an accelerated accumulation of potent effector cells in the infected target organs. These effector cells were recruited from the resting pool of memory cells and were immediately triggered to exert their effector functions, leading to a massive release of Th1 cytokines detectable both in splenic extracts and in the serum within the first 24 h of infection. During a primary infection, in contrast, a 14-day delay was observed before significant cytokine levels were reached. After the initial effector phase, the cells blasted and entered into clonal expansion, resulting in a rapid increase in the total number of CD4 CD45RBlow cells in the spleen. The recall of memory immunity was highly efficient and controlled an infectious challenge within the first week. The molecules recognized by the memory effector subset were the proteins secreted from Mycobacterium tuberculosis during growth. By separating the CD4 population into CD45RBhigh and CD45RBlow subsets, the memory effector cells were demonstrated to reside predominantly in the activated population of CD45RBlow CD44high LFA-1high L-selectinlow cells. The key antigenic targets recognized by these cells were identified as Ag85B and a secreted 6-kDa protein (ESAT-6) that elicited the release of exceedingly high levels of IFN-gamma. ESAT-6 was biochemically purified, characterized, and the gene encoding the protein was cloned.
Effects of D-cycloserine on extinction of conditioned freezing. (2003)

The present study tested the prediction that D-cycloserine (DCS), a partial N-methyl-D-aspartate agonist, would facilitate extinction of conditioned freezing in male Sprague-Dawley rats. Rats received 5 light-shock pairings (conditioning). The following day, rats received 6 light-alone presentations (extinction training). Twenty-four hours later, rats received 1 light-alone presentation (test). Subcutaneous DCS injection before or after extinction training significantly enhanced extinction, and the dose-response curve for this effect was linear. Increasing the delay of DCS administration after extinction training led to a linear decrease in the facilitatory effect. The effect of systemic administration was replicated by intra-basolateral amygdala infusion. These results suggest that DCS facilitates extinction of conditioned freezing by acting on consolidation processes partly mediated by the basolateral amygdala.
A high-performance system for automation of the polymerase chain reaction. (1991)

A high-performance PCR system has been developed which reduces the time required for PCR, increases the throughput, reduces reagent consumption and ensures reproducibility of amplification. Integration of sophisticated temperature control with optimally designed vessels has resulted in an amplification system which produces unique benefits. These include rapid amplification, the elimination of the need for oil, even for small volumes, and a microplate format which provides liquid handling automation benefits.
Randomized controlled trial of deutetrabenazine for tardive dyskinesia (2017)

This study provides Class I evidence that in patients with TD, deutetrabenazine reduces AIMS scores.
Nature of light scattering in dental enamel and dentin at visible and near-infrared wavelengths (1995)

The light-scattering properties of dental enamel and dentin were measured at 543, 632, and 1053 nm. Angularly resolved scattering distributions for these materials were measured from 0° to 180° using a rotating goniometer. Surface scattering was minimized by immersing the samples in an index-matching bath. The scattering and absorption coefficients and the scattering phase function were deduced by comparing the measured scattering data with angularly resolved Monte Carlo light-scattering simulations. Enamel and dentin were best represented by a linear combination of a highly forward-peaked Henyey-Greenstein (HG) phase function and an isotropic phase function. Enamel weakly scatters light between 543 nm and 1.06 µm, with the scattering coefficient (µ(s)) ranging from µ(s) = 15 to 105 cm(-1). The phase function is a combination of a HG function with g = 0.96 and a 30-60% isotropic phase function. For enamel, absorption is negligible. Dentin scatters strongly in the visible and near IR (µ(s)≅260 cm(-1)) and absorbs weakly (µ(a) ≅ 4 cm(-1)). The scattering phase function for dentin is described by a HG function with g = 0.93 and a very weak isotropic scattering component (˜ 2%).
Role of the viaB locus in synthesis, transport and expression of Salmonella typhi Vi antigen (1995)

The Vi antigen is a capsular polysaccharide expressed by Salmonella typhi, the agent of human typhoid fever. Expression of this antigen is controlled by the viaA and viaB chromosomal loci. The viaB locus is composed of 11 genes designated tviA-tviE (typhi Vi), vexA-vexE (Vi antigen export) and ORF11. We constructed S. typhi Ty2 strains carrying non-polar mutations in ten genes located at the viaB locus and examined the individual contribution of each gene to Vi phenotype. Phenotypes of the mutants and complementation experiments suggested that synthesis of Vi antigen monomer was catalysed by the TviB and TviC polypeptides. Subsequent polymerization of the polysaccharide might be catalysed by the TviE protein, but required functional TviD product. Proteins encoded by vexA, vexB and vexC directed transport of the polymer to the bacterial cell surface. Anchoring of the Vi antigen at the bacterial cell surface was dependent of the VexE protein. The TviA protein was not essential for Vi polymer synthesis. However, disruption of the tviA gene on S. typhi Ty2 chromosome strongly decreased expression of Vi antigen. This defect was fully complemented by providing tviA in trans on a recombinant plasmid. By using lacZ transcriptional fusions, it was shown that the TviA product positively regulated co-transcription of the tviA and tviB genes from a promoter located upstream of tviA. Moreover, we showed that a tviAB-lacZ fusion was not expressed in a viaA (rcsB) mutant of S. typhi.(ABSTRACT TRUNCATED AT 250 WORDS)
Apolipoprotein E Binding to Low Density Lipoprotein Receptor-related Protein-1 Inhibits Cell Migration via Activation of cAMP-dependent Protein Kinase A (2003)

Smooth muscle cell migration and proliferation contribute to neointimal hyperplasia and vascular stenosis after endothelial denudation. Previous studies revealed that apolipoprotein E (apoE) is an effective inhibitor of platelet-derived growth factor-directed smooth muscle cell migration and proliferation and that the anti-migratory function is mediated via apoE binding to low density lipoprotein receptor-related protein-1 (LRP-1). This study was undertaken to identify the intracellular pathway by which apoE binding to LRP-1 results in inhibition of smooth muscle cell migration. The results showed that apoE increased intracellular cAMP levels 3-fold after 5 min, and the increase was sustained for more than 1 h. As a consequence, apoE also increased protein kinase A (PKA) activity in smooth muscle cells. Importantly, suppression of PKA activity with a cell-permeable peptide inhibitor of PKA abolished the inhibitory effect of apoE on smooth muscle cell migration. These results indicated that apoE inhibition of smooth muscle cell migration is mediated via the activation of cAMP-dependent PKA. Additional experiments revealed that apoE also inhibited fibroblasts migration toward platelet-derived growth factor by a similar mechanism of cAMP-dependent PKA activation. It is noteworthy that apoE failed to increase cAMP levels or inhibit migration of LRP-1-negative mouse embryonic fibroblasts and LRP-1-deficient smooth muscle cells. Taken together, these findings established the mechanism by which apoE inhibits cell migration, i.e. via cAMP-dependent protein kinase A activation as a consequence of its binding to LRP-1.
Iterative Identification and Restoration of Images (1991)

The blur identification problem is formulated as a constrained maximum-likelihood problem. The constraints directly incorporate a priori known relations between the blur (and image model) coefficients, such as symmetry properties, into the identification procedure. The resulting nonlinear minimization problem is solved iteratively, yielding a very general identification algorithm. An example of blur identification using synthetic data is given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Perturbation of Fluorescence by Nonspecific Interactions between Anionic Poly(phenylenevinylene)s and Proteins:  Implications for Biosensors (2004)

The use of anionic water-soluble conjugated polymers (CPs) for sensing the presence of avidin by use of a biotin-modified fluorescence quencher was studied. The molecules involved in the study included poly[2-methoxy-5-(3'-propyloxysulfonate)-1,4-phenylenevinylene] with either lithium (Li+-MPS-PPV) or sodium (Na(+)-MPS-PPV) countercations, the well-defined oligomer pentasodium 1,4-bis(4'(2",4"-bis(butoxysulfonate)-styryl)-styryl)2-butoxysulfonate-5-methoxybenzene (5R5-), the quenchers N-methyl-4,4'-pyridylpyridinium iodide (mMV+) and [N-(biotinoyl)-N'-(acetyl 4,4'-pyridylpyridinium iodide)] ethylenediamine (BPP+), which contains a molecular recognition fragment (biotin) attached to a unit that accepts an electron from a CP excited state, and the proteins avidin, tau, BSA, and pepsin A. Fluorescence quenching experiments were examined in a variety of conditions. Experiments carried out in water and in ammonium carbonate buffer (which ensures avidin/biotin complexation) reveal that nonspecific interactions between the CP and the proteins cause substantial perturbations on the CP fluorescence. The overall findings are not consistent with a simple mechanism whereby avidin complexation of BPP+ leads to encapsulation of the quencher molecule and recovery of Li+-MPS-PPV fluorescence. Instead, we propose that binding of BPP+ to avidin results in the quenching unit attaching to a positively charged macromolecule. Electrostatic attraction to the negatively charged conjugated polymer results in closer proximity to the quencher. Therefore, more enhanced fluorescence quenching is observed.
The aetiology of sperm protamine abnormalities and their potential impact on the sperm epigenome (2008)

During the elongating spermatid stage of spermatogenesis, there is a step-wise replacement of nuclear histones with protamines 1 and 2. In fertile men, the ratio of protamine 1/protamine 2 (P1/P2) is within the narrow range of 0.8-1.2. Ratios above or below that range are associated with infertility, exhibiting a wide range of defects including decreased sperm counts, morphology, fertilization ability, and embryo implantation capacity. In this review, we highlight studies evaluating potential causes of abnormal protamine expression, including the sequencing of genes relevant to protamine expression in both affected patients and controls. While the variants of the protamine genes themselves do not appear to be responsible for most observed defects, variants of the Contrin gene, a transcription factor and translation repressor, appear to be contributory to some cases of abnormal expression. Additionally, we explore the potential effects of abnormal protamine replacement on the epigenome of human sperm. Ongoing studies are evaluating the role of retained histones and DNA methylation in sperm, which may be affected in sperm with aberrant protamine replacement. This important area of epigenetic research has profound clinical implications.
A synthesis of αβ-unsaturated aldehydes (1974)

T. M. Cresp, M. V. Sargent and P. Vogel, J. Chem. Soc., Perkin Trans. 1, 1974, 37 DOI: 10.1039/P19740000037
Interactions between SH2 domains and tyrosine-phosphorylated platelet-derived growth factor beta-receptor sequences: analysis of kinetic parameters by a novel biosensor-based approach. (1993)

The interaction between SH2 domains and phosphotyrosine-containing sequences was examined by real-time measurements of kinetic parameters. The SH2 domains of the p85 subunit of the phosphatidylinositol 3-kinase as well as of other signaling molecules were expressed in bacteria as glutathione S-transferase fusion proteins. Phosphotyrosine-containing peptides, corresponding to two autophosphorylation sites on the human platelet-derived growth factor beta-receptor that are responsible for phosphatidylinositol 3-kinase binding, were synthesized and used as capturing molecules, immobilized on a biosensor surface. The association and dissociation rate constants for binding to both sites were determined for intact p85 and the recombinant SH2 domains. High association rates were found to be coupled to very fast dissociation rates for all interactions studied. A binding specificity was observed for the two SH2 domains of p85, with the N-terminal SH2 binding with high affinity to the Tyr-751 site but not to the Tyr-740 site, and the C-terminal SH2 interacting strongly with both sites. This approach should be generally applicable to the study of the specificity inherent in the assembly of signaling complexes by activated protein-tyrosine kinase receptors.
Tumor necrosis factor alpha polymorphism correlates with deleterious effects of ultraviolet B light on cutaneous immunity. (1993)

Intradermally injected tumor necrosis factor alpha (TNF-alpha) mimics the effects of UV B light (UVB) radiation and neutralizing anti-TNF-alpha antibodies abolish the deleterious effects of UVB on induction of contact hypersensitivity suggesting that TNF-alpha is the major mediator of UVB effects on cutaneous immunity. In the present study we have shown that in lipopolysaccharide-sensitive inbred strains of mice, the ability of acute, low-dose UVB radiation to impair the induction of contact hypersensitivity to dinitrofluorobenzene is genetically determined by polymorphic alleles at the Tnf alpha locus. We have analyzed by the sequence analysis and restriction fragment length polymorphism the Tnf alpha alleles of numerous inbred strains expressing UVB susceptibility (UVB-S) and UVB-resistance (UVB-R). The Tnf alpha alleles of all UVB-R, but not UVB-S, strains contain a BamHI site in the first intron. Moreover, the 5' regulatory region of the Tnf alpha allele of UVB-R mice possesses a (CA)14 minirepeat that is located immediately 5' of the cytokine response element nearest the tumor-associated transplantation antigen box. By contrast, the Tnf alpha alleles of UVB-S mice display repeats of < > 14 at this site. It is proposed that the unique microsatellite of UVB-R mice impairs transcriptional efficiency at Tnf alpha compared to UVB-S mice and that the quantitative difference in Tnf alpha produced intracutaneously in response to UVB radiation accounts for the phenotypic traits of UVB-R and UVB-S.
Synthesis and Biological Evaluation of Acyclic 3-[(2-Hydroxyethoxy)methyl] Analogues of Antiviral Furo- and Pyrrolo[2,3-d]pyrimidine Nucleosides (2005)

The remarkably potent and specific activity against varicella-zoster virus (VZV) shown by 2'-deoxynucleosides of furo[2,3-d]pyrimidin-2(3H)-one and related ring systems is dependent on key structural features including the length and nature of the side-chain at C6 and the structure and stereochemistry of the sugar moiety at N3. Removal of the 3'-hydroxyl group from potent anti-VZV 2'-deoxynucleosides results in loss of the VZV activity, but such 2',3'-dideoxynucleoside analogues have shown anti-HCMV activity. We now report acyclic analogues with comparable side-chains at C6, but with the sugar moiety at N3 replaced with the (2-hydroxyethoxy)methyl group (present in the antiherpes drug acyclovir). Examples of both furo[2,3-d]- and pyrrolo[2,3-d]pyrimidin-2(3H)-one acyclic analogues were prepared and evaluated in a number of virus-infected cells and in tumor cell cultures. Certain of the long-chain analogues showed activity against VZV and HCMV. No significant activity against other DNA and RNA virus replication or against tumor cell proliferation was observed.
Migration of dendritic cells in response to formyl peptides, C5a, and a distinct set of chemokines (1995)

Trafficking to tissues and then to lymph nodes is a crucial aspect of the immunobiology of dendritic cells. The present study was designed to identify molecules able to direct the migration of human blood-derived dendritic cells. fMLP (representative of formyl peptides of bacterial origin), C5a, and the C-C chemokines monocyte chemotactic protein (MCP)-3, MIP-1 alpha/LD78, and RANTES elicited chemotactic migration and a rise of intracellular free calcium in dendritic cells. In contrast, the C-X-C chemokines IL-8 and IP-10 and the C-C chemokines MCP-1 and MCP-2 were inactive as chemoattractants. Thus, dendritic cells respond to classical chemotactic signals and to a set of chemokines distinct from that active on monocytes and neutrophils. Chemoattractants are likely to contribute to localization and trafficking of dendritic cells and provide tools to recruit these cells in the design of immunization strategies.
Microbiological Synthesis of Adenine Arabinoside (1985)

The microbiological synthesis of 9-βd-arabinofuranosyl adenine (ara-A, an antiviral drug) from adenine and arabinofuranosyluracil (ara-U) is described. Various bacteria, especially Enterobacter aerogenes, Escherichia coli, Erwinia herbicola and Aeromonas salmonicida, were found to be able to transfer the arabinofuranosyl moiety of ara-U to adenine (transarabinosylation) in the presence of inorganic phosphate. The optimum conditions for the transarabinosylation were pH 7.0 and 60°C. No reaction was observed in the absence of inorganic phosphate and its optimum concentration was around 30 mM. Six grams of ara-A was produced in liter of reaction mixture in the presence of wet cell paste of Enterobacter aerogenes AJ 11125. Ara-A formed was precipitated in the reaction mixture and isolated with an 87% yield. Physicochemical data for the compound agreed with those of authentic ara-A.
X-ray Powder Diffraction Data for 12 Drugs in Current Use (2000)

Characterization of bulk drugs has become increasingly important in the pharmaceutical industry. A multitude of analytical techniques are commonly employed for this purpose. In this work X-ray diffraction data have been obtained for 12 well-known drugs in current use by the powder diffractometer technique. They include atenolol, benactyzine hydrochloride, dicyclomine (dicycloverine) hydrochloride, dyclonine hydrochloride, dimenhydrinate, guanethidine sulfate (ismelin), halozone, metoclopramide, oxprenolol hydrochloride, oxybuprocaine (benoxinate) hydrochloride, primidone, and thiomersal (thimerosal) sodium. The results, obtained by using the McCreery and Byström−Asklund methods of sample loading, were averaged and tabulated in terms of the lattice spacings and the relative line intensities. One of the advantages of the method is that it provides additional information about the crystalline state of the active ingredients. Furthermore, the crystalline state is related to the suspendibility, rheology, bioavailability, and possible stability of pharmaceutical formulations during manufacturing process and storage time.
Generating code from hierarchical state-based requirements (2002)

Computer software is playing an increasingly important role in safety-critical embedded computer systems, where incorrect operation of the software could lead to loss of life, substantial material or environmental damage, or large monetary losses. Although software is a powerful and flexible tool for industry, these very advantages have contributed to a corresponding increase in system complexity. In a previous investigation, the Irvine Safety Research Group developed a requirements specification language called the Requirements State Machine Language (RSML) suitable for the specification of safety critical control embedded systems. To simplify and automate the design and implementation process, we have investigated the possibility of automatically generating code from RSML specifications.
Growth factor‐induced signal transduction in adherent mammalian cells is sensitive to gravity (1999)

Epidermal growth factor (EGF) activates a well-characterized signal transduction cascade in a wide variety of cells. This activation leads to increased cell proliferation in most cell types. Among the early effects evoked by EGF are receptor clustering, cell rounding, and early gene expression. The influence of gravity on EGF-induced EGF receptor clustering and gene expression as well as on actin polymerization and cell rounding have been investigated in adherent A431 epithelial cells with the use of sounding rockets to create microgravity conditions. EGF-induced c-fos and c-jun expression decreased in microgravity. This was caused by alteration of the EGF receptor and protein kinase C-mediated signal transduction pathways. In contrast, neither the binding of EGF to the receptor nor the receptor clustering were changed under microgravity conditions. Because cell morphology was also modulated under microgravity conditions, and the growth factor-induced signal transduction cascades have been demonstrated to be linked to the actin microfilament system, it is tempting to suggest that the actin microfilament system constitutes the gravity-sensitive cell component.