gebhart/patrepeval huggingface dataset:
Rapid and sensitive colorimetric method for visualizing biotin-labeled DNA probes hybridized to DNA or RNA immobilized on nitrocellulose: Bio-blots. (1983)

Biotin-labelled DNA probes, prepared by nick-translation in the presence of biotinylated analogs of TTP, are hybridized to DNA or RNA immobilized on nitrocellulose filters. After removal of residual probe, the filters are incubated for 2--5 min with a preformed complex made with avidin-DH (or streptavidin) and biotinylated polymers of intestinal alkaline phosphatase. The filters are then incubated with a mixture of 5-bromo-4-chloro-3-indolyl phosphate and nitro blue tetrazolium, which results in the deposition of a purple precipitate at the sites of hybridization. This procedure will detect target sequences in the 1- to 10-pg range after enzyme incubation periods of 1 hr or less. The incubation period can be extended up to 24 hr, if required, to increase the color intensity of the hybridization signal. Furthermore, at high probe concentrations (250--7560 ng/ml), biotin-labeled DNA exhibits lower nonspecific binding to nitrocellulose than does radiolabeled DNA, so hybridization times required for the analysis of unique mammalian gene sequences can be decreased to 1--2 hr. This nonradiographic method of probe detection should be of general utility for genetic studies using Southern, RNA, or dot-blot hybridization protocols.
Plasma-Enhanced Atomic Layer Deposition of Ta-N Thin Films (2002)

The plasma-enhanced atomic layer deposition (PEALD) of tantalum nitrides (TaN) thin films has been performed using terbutylimidotris(diethylamido)tantalum and hydrogen radicals at a temperature of 260 degreesC. The film thickness per cycle is also self-limited at 0.8 Angstrom /cycle, which is thinner than that of the conventional atomic layer deposition (ALD), 1.1 Angstrom /cycle. X-ray diffraction analysis indicates that the as-deposited films are not amorphous but polycrystalline mixed with cubic TaN and TaC. The film crystallinity as well as the film density increases with the pulse time and the electrical power of the hydrogen plasma used. By using the hydrogen radical as a reducing agent instead of NH3, which is a typical reactant gas used in ALDs and metallorganic chemical vapor depositions of TaN, the films show a much lower electrical resistivity and show no aging effects under exposure to air, owing to the increased film density and crystallinity, and the presence of TaC bonding. In addition, it has been shown that films, which are formed by the PEALD, retain perfect step coverage on the submicrometer holes with an aspect ratio of 10:1. (C) 2001 The Electrochemical Society.
Biologically active taxol analogs with deleted A-ring side chain substituents and variable C-2' configurations (1991)

Taxol, a potent inhibitor of cell replication, enhances the assembly of tubulin into stable microtubules and promotes the formation of microtubule bundles in cells. In addition to its unique mechanism of action, taxol exhibits unusual promise as an antitumor agent, but its application in cancer chemotherapy is hampered by its limited availability. In order to better define the structure-activity profile of taxol for the design of more accessible drugs and to provide insight into the chemical features of the taxol-microtubule interaction, taxol analogues 3-8, with deleted A-ring side chain substituents and both R and S C-2' configurations, were synthesized from baccatin III through esterification at the hindered 13-hydroxyl. Employing an improved hydroxyl protection strategy, lactate analogues 3 and 4 were prepared with reasonable efficiency owing to their simple side-chain structures, while N-benzoylisoserine analogues 7 and 8 were synthesized through esterification reactions whose rates were enhanced greatly by the participation of the amide functionality. Although less biologically active than taxol, analogues 5-7 were found to promote the polymerization of tubulin and to be cytotoxic; 5 and 6 were considerably more effective than 7, whereas 3, 4, and 8 were least active. Interestingly, tubulin polymerization was sensitive to the C-2' configuration only when the amide substituent was present in the side chain. This observation suggests that the 3'-amide substituent plays an important role in preorganizing the taxol side chain to bind to microtubules.
Macrophage-Mediated Proteolytic Remodeling of the Extracellular Matrix in Atherosclerosis Results in Neoepitopes: A Potential New Class of Biochemical Markers (2010)

Worldwide, cardiovascular disease (CVD) is the leading cause of death. Most CVD-related deaths are caused by years of preceding atherogenesis and the extensive development of atherosclerotic plaques, some of which may rupture to cause myocardial infarction. Macrophages are known to have a role in almost all stages of atherosclerosis, by both initiating atherosclerotic plaques and degrading them through the secretion of proteolytic enzymes leading to rupture. This review summarizes the literature on the role of macrophages and their proteolytic activity on proteins in the extracellular matrix (ECM) of the atherosclerotic plaque with a view to suggest a novel approach for identification of vulnerable plaques and turnover by the use of a new type of biomarker. The PubMed database was searched using the terms macrophages, foam cells, atherosclerosis, CVD, ECM remodeling, biomarker, neoepitope, matrix metalloproteinase (MMP), and protease. Atherosclerotic plaques are primarily composed of the protein type I and III collagen, and smaller quantities of elastin and proteoglycans. Macrophages secrete an array of proteases, including MMPs, cathepsins, and aggrecanases, with the ability to degrade most of the constituents of the ECM of the atherosclerotic plaque. At present it is not clear which proteases play pivotal roles at distinct stages of pathogenesis, rather that the combined proteolytic potential with some proteases at early stages and other at later stages may result in plaque rupture. This macrophage-mediated proteolysis and remodeling of the ECM play important roles in many stages of atherosclerosis. The degradation fragments of these ECM events are specific neoepitopes, which are released into the circulation. The identification of these pathologically relevant neoepitopes leads to novel biomarkers able to identify the formation and degradation of plaques providing different biological information than traditionally used biomarkers.
A Reliable and Secure UNIX Connection Service. (1987)

Distributed programs require a method for processes residing on different machines to identify each other and establish communication. One method is to provide a special connection service to perform this task. A good connection service should be easy to use. It should allow arbitrary processes to connect to each other as well as helping client processes to connect to server processes. It should provide location transparency; that is, the programmer should not have to know the network address of a process to connect to it. The connection service should be reliable. It should provide a way for a process to establish the identity of the user associated with the process to which it has connected, and to communicate securely with that process.
Cloning and characterization of Unp: A novel nuclear proto-oncogene. (1994)

The cloning and characterization of a novel gene, Unp (for Ubiquitin-specific Nuclear Protease), is described in this thesis. This gene was identified during a survey for candidate genes for the retroviral insertional mutation Mpv 20. Unp is transcribed into two ubiquitously expressed mRNAs of approximately 3.5 and 3.7 kb. The two mRNAs vary at their $3\prime$ ends due to alternative usage of two degenerate polyadenylation signals. The $5\prime$ UTR of Unp contains several minicistrons, which suggest a growth related function for this gene. The Unp gene has been mapped to mouse chromosome 9 and human chromosome 3 in a region which is implicated in several types of human cancers based on loss of heterozygocity. This suggests a possible tumor suppressor function for this gene. The predicted amino acid sequence of the Unp protein contains several conserved motifs, including p53 type nuclear localization signal, consensus for binding to the retinoblastoma protein, and the Cys and His domains conserved in yeast ubiquitin proteases. The pRb binding consensus is present in the region of Unp which shares homology to the recombinant human oncogene tre-2. Unp protein is localized in the nucleus and migrates at a higher molecular mass than expected, suggesting that this protein is post-translationally modified. Unp is tumorigenic in athymic mice showing that it is a proto-oncogene. The protein product of Unp is a ubiquitin-specific protease. The Unp gene is highly polymorphic in humans, and loss of Unp sequences is detected in 1 out of the 7 informative human lung tumors analyzed.
A FACILE SYNTHESIS OF NEW 4-(PHENYLAMINO)THIENO[3,2-d]PYRIMIDINES USING 3-AMINOTHIOPHENE-2-CARBOXAMIDE (2007)

Article A FACILE SYNTHESIS OF NEW 4-(PHENYLAMINO)THIENO[3,2-d]PYRIMIDINES USING 3-AMINOTHIOPHENE-2-CARBOXAMIDE was published on February 1, 2007 in the journal Heterocyclic Communications (volume 13, issue 1).
Role of Fcγ receptor IIb polymorphism in the genetic background of systemic lupus erythematosus: Insights from Asia (2005)

FCGR2B codes for an inhibitory receptor expressed in B cells and monocytes. Polymorphisms of Fcgr2b in mice have been shown to be associated with autoimmune diseases including systemic lupus erythematosus (SLE) and targeted disruption of Fcgr2b renders mice susceptible to induced or spontaneous autoimmunity, depending on the genetic background. Polymorphism screening of FCGR2B has been hampered by the complexity and extreme homology among FCGR family members. We established a specific genotyping system, detected a SNP that changes position 232 amino acid in the transmembrane region from Ile to Thr and found a significant association of 232Thr with SLE in the Japanese, Thai and Chinese populations. In contrast, promoter polymorphism of FCGR2B, but not Ile232Thr, was shown to be associated with SLE in Caucasians. Linkage disequilibrium was observed among FCGR2A, 2B, 3A and 3B genes with varying degrees, but in the Asian populations, each of FCGR2B, 3A and 3B genes was suggested to contribute to the susceptibility to SLE. These results indicate that FCGR2B is a susceptibility gene to SLE in the context of a genetic background, both in humans and mice.
Augmenting Mobile 3G with WiFi (2010)

Holographic laser beam scanners utilizing a main substrate of simple geometry and an auxiliary reflector are described. The design parameters have been defined and the resolution capabilities analyzed. An experimental scanner using a flat main substrate and a convex auxiliary reflector has been constructed. Diffraction limited reconstructions have been obtained throughout the entire scanning range. A method for dynamically stabilizing the scanning beam is described. Since the main substrate on which the holograms are recorded is either flat or slightly concave, they lend themselves to low cost replication.
Use of electrospray ionization mass spectrometry to probe antisense peptide interactions (1994)

Electrospray ionization mass spectrometry with a magnetic sector instrument has been used to test for non-covalent interactions between human angiotensin II (M(r) 1046) and eight synthetic octapeptides that are considered complementary peptides (encoded by DNA sequences complementary to the DNA sequence that codes for human angiotensin II) or analogues of these antisense peptides. The relative abundance of the doubly charged heterodimer complex broadly correlates to the trend observed with solution-phase studies such as 1H nuclear magnetic resonance. Dissociation constants for the reaction in solution are in the high micromolar range. Electrospray ionization can potentially be a sensitive method for rapidly screening weak molecular interactions. Further work is necessary to study the possible gas-phase contributions to the observed binding interactions indicated in the mass spectrometry data.
Interpolating nets of curves by smooth subdivision surfaces (1999)

A subdivision algorithm is presented for the computation and representation of a smooth surface of arbitrary topological type interpolating a given net of smooth curves. The algorithm belongs to a new class of subdivision schemes called combined subdivision schemes. These schemes can exactly interpolate a net of curves given in any parametric representation. The surfaces generated by our algorithm are G 2 except at a finite number of points, where the surface is G 1 and has bounded curvature. The algorithm is simple and easy to implement, and is based on a variant of the famous Catmull-Clark subdivision scheme.
Erythropoietin and the differentiation of red blood cells. (1975)

Erythropoietin is the primary factor regulating red blood cell formation in mammals and some other animals. It has been purified from plasma derived from anemic sheep and from the urine of anemic patients and is a glycoprotein. The sheep hormone has a molecular weight of 46,000 and appears to consist of a single chain. The carbohydrate and amino acid compositions where known, are summarized, as are the known structural requirements for biological activity. Its mode of action as the inducer of red cell differentiation has been studied in marrow cell and fetal liver cell cultures. Erythropoietin interacts first with a protein receptor on its target cell causing the appearance of a cytoplasmic protein thought to be a mediator that, in turn, causes an increased rate of transcription in the target cell nuclei. There are several different species of RNA synthesized before the cells initiate hemoglobin synthesis. The effect on transcription is only indirectly dependent on DNA synthesis. Some properties of the primitive erythropoietin-responsive cell are discussed and a cellular model for blood cell differentiation is presented.
Speech enhancement based on perceptually motivated bayesian estimators of the magnitude spectrum (2005)

The traditional minimum mean-square error (MMSE) estimator of the short-time spectral amplitude is based on the minimization of the Bayesian squared-error cost function. The squared-error cost function, however, is not subjectively meaningful in that it does not necessarily produce estimators that emphasize spectral peak (formants) information or estimators which take into account auditory masking effects. To overcome the shortcomings of the MMSE estimator, we propose in this paper Bayesian estimators of the short-time spectral magnitude of speech based on perceptually motivated cost functions. In particular, we use variants of speech distortion measures, such as the Itakura-Saito and weighted likelihood-ratio distortion measures, which have been used successfully in speech recognition. Three classes of Bayesian estimators of the speech magnitude spectrum are derived. The first class of estimators emphasizes spectral peak information, the second class uses a weighted-Euclidean cost function that implicitly takes into account auditory masking effects, and the third class of estimators is designed to penalize spectral attenuation. Of the three classes of Bayesian estimators, the estimators that implicitly take into account auditory masking effect performed the best in terms of having less residual noise and better speech quality.
In vitro interaction of a polypeptide homologous to human Ro/SS-A antigen (calreticulin) with a highly conserved amino acid sequence in the cytoplasmic domain of integrin .alpha. subunits (1991)

We endeavored to identify proteins interacting with KLGFFKR, a highly conserved motif in the cytoplasmic domain adjacent to the transmembrane domain of the alpha subunit of integrins. We found that affinity chromatography of cell extracts with this peptide followed by elution with EDTA resulted in the isolation of a 60-kDa protein (p60). The N-terminal amino acid sequence of this 60-kDa polypeptide was found to be highly homologous to the Ro/SS-A antigen, a 60-kDa protein homologous to calreticulin and Aplysia "memory molecule". The binding of p60 was found to be specific for the KLGFFKR sequence since this polypeptide did not bind to a peptide with a scrambled amino acid sequence (KLRFGFK), and it was also specifically eluted from the KLGFFKR affinity matrix ith soluble KLGFFKR peptide but not with the scrambled peptide. Solid phase in vitro binding assays demonstrated specific interaction of p60 with integrin alpha 3 and alpha 5 subunits but not with the beta 1 subunit. Furthermore, p60 could be copurified with alpha 3 beta 1 following coincubation in vitro. These interactions could be inhibited by KLGFFKR peptide and also by EDTA, indicating sequence-specific and divalent cation dependent binding. Despite the fact that calreticulin is thought to be localized in the endoplasmic reticulum, a pool of Ro/SS A antigen homologous 60-kDa polypeptide was found to be present in the soluble cytoplasm, indicating the feasibility of an interaction of p60 with the integrin alpha subunits. Our data suggest that p60 (Ro/SS-A Ag) can specifically bind to integrin alpha subunits via the highly conserved KLGFFKR amino acid sequence.
Why Alphabetic Keyboards Are Not Easy to Use: Keyboard Layout Doesn't Much Matter (1982)

These studies demonstrate the inferiority of alphabetically organized keyboards as compared with a randomly organized keyboard and the standard Sholes (qwerty) keyboard. Use of the alphabetic keyboard requires considerable mental processing; the novice is faced with a trade-off between mental processing and visual search, and this makes different keyboard layouts equivalent. Comparison of different keyboard layouts by computer simulation of expert typing shows surprisingly little effect of keyboard arrangement for a wide class of keyboards. Performance with some alphabetical layouts is quite slow, but with others, it is within 2% of the speed achieved when using the Sholes keyboard. Performance with the Dvorak keyboard is only improved by about 5% over performance on the Sholes keyboard. The conclusion is that it is not worthwhile to use alphabetic keyboards for novice typists, nor to change to the Dvorak layout for experts. Keyboards can probably be improved, but only through radical redesign of the present physical key configuration.
Coniferyl aldehyde 5-hydroxylation and methylation direct syringyl lignin biosynthesis in angiosperms (1999)

A central question in lignin biosynthesis is how guaiacyl intermediates are hydroxylated and methylated to the syringyl monolignol in angiosperms. To address this question, we cloned cDNAs encoding a cytochrome P450 monooxygenase (LsM88) and a caffeate O-methyltransferase (COMT) from sweetgum (Liquidambar styraciflua) xylem. Mass spectrometry-based functional analysis of LsM88 in yeast identified it as coniferyl aldehyde 5-hydroxylase (CAld5H). COMT expressed in Escherichia coli methylated 5-hydroxyconiferyl aldehyde to sinapyl aldehyde. Together, CAld5H and COMT converted coniferyl aldehyde to sinapyl aldehyde, suggesting a CAld5H/COMT-mediated pathway from guaiacyl to syringyl monolignol biosynthesis via coniferyl aldehyde that contrasts with the generally accepted route to sinapate via ferulate. Although the CAld5H/COMT enzyme system can mediate the biosynthesis of syringyl monolignol intermediates through either route, k(cat)/K(m) of CAld5H for coniferyl aldehyde was approximately 140 times greater than that for ferulate. More significantly, when coniferyl aldehyde and ferulate were present together, coniferyl aldehyde was a noncompetitive inhibitor (K(i) = 0.59 microM) of ferulate 5-hydroxylation, thereby eliminating the entire reaction sequence from ferulate to sinapate. In contrast, ferulate had no effect on coniferyl aldehyde 5-hydroxylation. 5-Hydroxylation also could not be detected for feruloyl-CoA or coniferyl alcohol. Therefore, in the presence of coniferyl aldehyde, ferulate 5-hydroxylation does not occur, and the syringyl monolignol can be synthesized only from coniferyl aldehyde. Endogenous coniferyl, 5-hydroxyconiferyl, and sinapyl aldehydes were detected, consistent with in vivo operation of the CAld5H/COMT pathway from coniferyl to sinapyl aldehydes via 5-hydroxyconiferyl aldehyde for syringyl monolignol biosynthesis.
Intragenic homozygous deletion of the WT1 gene in Wilms' tumor. (1992)

One example of intragenic homozygous deletion of the WT1 gene on chromosome 11p13 was found after screening 42 samples of Wilms' tumor DNA from Japanese patients. After construction of a restriction map for the genomic sequence covering the 3' half of the gene, the deletion was analysed at the nucleotide sequence level. The deletion occurred in the patient's germline on his paternal chromosome, and most of the short arm of his maternal chromosome 11 was subsequently lost in the tumor. The size of the deletion was about 8 kb, removing exons 6 and 7 and resulting in premature termination. The deletion seemed to be created by recombination between short homologous sequences found in an Alu repeat, with a 16-bp duplication left at the junction. This case conforms to a two-hit model for the genesis of a certain group of tumors, and supports the hypothesis that WT1 is one of the recessive oncogenes responsible for Wilms' tumor.
Recent Advances in Mechanisms and Treatments of Airway Remodeling in Asthma: A Message from the Bench Side to the Clinic (2011)

Airway remodeling in asthma is a result of persistent inflammation and epithelial damage in response to repetitive injury. Recent studies have identified several important mediators associated with airway remodeling in asthma, including transforming growth factor-, interleukin (IL)-5, basic fibroblast growth factor, vascular endothelial growth factor, LIGHT, tumor necrosis factor (TNF)-, thymic stromal lymphopoietin, IL-33, and IL-25. In addition, the epithelium mesenchymal transformation (EMT) induced by environmental factors may play an important role in initiating this process. Diagnostic methods using sputum and blood biomarkers as well as radiological interventions have been developed to distinguish between asthma sub-phenotypes. Human clinical trials have been conducted to evaluate biological therapies that target individual inflammatory cells or mediators including anti IgE, anti IL-5, and anti TNF-. Furthermore, new drugs such as c-kit/platelet-derived growth factor receptor kinase inhibitors, endothelin-1 receptor antagonists, calcium channel inhibitors, and HMG-CoA reductase inhibitors have been developed to treat asthma-related symptoms. In addition to targeting specific inflammatory cells or mediators, preventing the initiation of EMT may be important for targeted treatment. Interestingly, bronchial thermoplasty reduces smooth muscle mass in patients with severe asthma and improves asthma-specific quality of life, particularly by reducing severe exacerbation and healthcare use. A wide range of different therapeutic approaches has been developed to address the immunological processes of asthma and to treat this complex chronic illness. An important future direction may be to investigate the role of mediators involved in the development of airway remodeling to enhance asthma therapy.
Semiconductor-Metal Nanoparticle Molecules: Hybrid Excitons and the Nonlinear Fano Effect (2006)

Modern nanotechnology opens the possibility of combining nanocrystals of various materials with very different characteristics in one superstructure. Here we study theoretically the optical properties of hybrid molecules composed of semiconductor and metal nanoparticles. Excitons and plasmons in such a hybrid molecule become strongly coupled and demonstrate novel properties. At low incident light intensity, the exciton peak in the absorption spectrum is broadened and shifted due to incoherent and coherent interactions between metal and semiconductor nanoparticles. At high light intensity, the absorption spectrum demonstrates a surprising, strongly asymmetric shape. This shape originates from the coherent internanoparticle Coulomb interaction and can be viewed as a nonlinear Fano effect which is quite different from the usual linear Fano resonance.