gebhart/patrepeval huggingface dataset:
Detection of DNA amplification in 17 primary breast carcinomas with homogeneously staining regions by a modified comparative genomic hybridization technique (1994)

A modified comparative genomic hybridization (mCGH) technique was applied to a series of 17 primary breast carcinomas in which cytogenetic study (CG) demonstrated the presence of homogeneously staining region(s), suggesting the occurrence of DNA amplification. mCGH demonstrated recurrent amplifications of the whole chromosome arms 8q (9 times) and 1q (7 times) and of DNA loci in the following bands: 11q13 (6 times), 9p13 and 17q21.1 (4 times), 1q21.1 and 16p11.2 (3 times), and 8q22, 8q24.1, 10q22, 15q26, 17q23, and 20q13.3 (twice). Amplification of whole chromosome arms is likely to have resulted from unbalanced translocations or isochromosomes, whereas amplifications of smaller chromosomal segments probably arose through real DNA amplification processes. In all tumors but one, more than one amplified locus was detected. The fact that many chromosomal sites were involved suggests that the process of amplification is complex and that many genes are potential targets.
miRGen 2.0: a database of microRNA genomic information and regulation (2009)

MicroRNAs are small, non-protein coding RNA molecules known to regulate the expression of genes by binding to the 3'UTR region of mRNAs. MicroRNAs are produced from longer transcripts which can code for more than one mature miRNAs. miRGen 2.0 is a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data. Expression profiles of microRNAs in several tissues and cell lines, single nucleotide polymorphism locations, microRNA target prediction on protein coding genes and mapping of miRNA targets of co-regulated miRNAs on biological pathways are also integrated into the database and user interface. The miRGen database will be continuously maintained and freely available at http://www.microrna.gr/mirgen/.
Vpx of simian immunodeficiency virus is localized primarily outside the virus core in mature virions (1993)

Human immunodeficiency virus type 2 and the related simian immunodeficiency virus (SIV) contain a unique regulatory gene, vpx. The Vpx protein is packaged in mature virions and is required for efficient viral replication in peripheral blood lymphocytes and macrophages. To study the localization of Vpx in mature virions, conical and bar-shaped core structures of SIV from macaques (SIVmac) were purified. The SIVmac core has a density of approximately 1.25 g/cm3, compared with 1.16 g/cm3 for an intact virion. The relative proportions of major capsid protein (p27) and reverse transcriptase activity were similar for intact virions and core structures. The majority of matrix protein (p14) was removed from the purified core structure, suggesting its association with the viral membrane. Similarly, most of the Vpx protein was absent from the purified core structure. This result suggests that as with the matrix protein, the majority of Vpx proteins are localized outside the virus core. The localization of Vpx suggests that it may be involved in virus entry such as penetration or uncoating.
Human Metapneumovirus (HMPV) Binding and Infection Are Mediated by Interactions between the HMPV Fusion Protein and Heparan Sulfate (2012)

Human metapneumovirus (HMPV) is a major worldwide respiratory pathogen that causes acute upper and lower respiratory tract disease. The mechanism by which this virus recognizes and gains access to its target cell is still largely unknown. In this study, we addressed the initial steps in virus binding and infection and found that the first binding partner for HMPV is heparan sulfate (HS). While wild-type CHO-K1 cells are permissive to HMPV infection, mutant cell lines lacking the ability to synthesize glycosaminoglycans (GAGs), specifically, heparan sulfate proteoglycans (HSPGs), were resistant to binding and infection by HMPV. The permissiveness to HMPV infection was also abolished when CHO-K1 cells were treated with heparinases. Importantly, using recombinant HMPV lacking both the G and small hydrophobic (SH) proteins, we report that this first virus-cell binding interaction is driven primarily by the fusion protein (HMPV F) and that this interaction is needed to establish a productive infection. Finally, HMPV binding to cells did not require β1 integrin expression, and RGD-mediated interactions were not essential in promoting HMPV F-mediated cell-to-cell membrane fusion. Cells lacking β1 integrin, however, were less permissive to HMPV infection, indicating that while β1 integrins play an important role in promoting HMPV infection, the interaction between integrins and HMPV occurs after the initial binding of HMPV F to heparan sulfate proteoglycans.
The human follicular dendritic cell line FDC-1 binds immune complexes and promotes somatic hypermutation. (2001)

The human follicular dendritic cell line FDC-1 binds immune complexes and promotes somatic hypermutation.
Reconstitution of Yeast Farnesyltransferase from Individually Purified Subunits (2003)

Farnesyltransferase (FTase) is a heterodimeric enzyme consisting of an α- and a β-subunit involved in a crucial C-terminal modification of various proteins, including Ras (1–3). This modification by a 15-carbon isoprenyl (farnesyl) group is essential for proper localization and function of these proteins (4–6). Because the membrane localization is necessary for Ras function, inhibiting FTase will prevent this localization, which in turn will block the ability of Ras to transform cells. Therefore, the structure and function of FTase has recently been intensively studied. Many studies have characterized substrate recognition by FTase in hope of being able to design small molecules that can act as anticancer drugs by specifically inhibiting this enzyme (1–7). Recently, the structure of the rat FTase has been solved (8).
Studies on antigens of C-type primate viruses and antibodies to them at patients with myeloid leukemia and potentially preleukemic hematological disorders. (1980)

Peripheral leucocytes from patients with chronic myeloid leukemia were examined for the presence of oncornavirus p30 antigens by indirect cytoplasmic immunofluorescence. The leucocytes of patients who could be kept in balance by chemotherapy proved to be negative or contained the p30 antigen of baboon endogenous oncornavirus. In the leucocytes of patients being in blastoid crisis, an antigen related to the p30 antigen of simian sarcoma virus was detected. In five of six patients decrease in sensitivity to chemotherapy, or blastoid crisis, was preceded by expression of leukaemia-sarcoma virus p30 antigen(s). Plasma samples of patients with acute myeloid leukemia (AML) and potentially preleukemic hematological disorders were studied for the presence of anti-HL 23 virus antibodies by indirect membrane immunofluorescence. In patients with untreated AML, antibodies could be detected when the peripheral leucocyte count was low. After treatment of AML with cytostatic drugs the presence of high titer antibodies was connected with long lasting remission. Of twelve patients with potentially preleukemic disorders, five proved to be positive for the presence of HL 23-specific antibodies. In half a year period development of overt leukemic disease could be observed in four patients, who proved to be antibody negative in the preleukemic phase.
Human fibroblast collagenase. Complete primary structure and homology to an oncogene transformation-induced rat protein. (1986)

We have determined the complete sequence of the cDNA clone representing the full size human skin collagenase mRNA. Collagenase is synthesized in preproenzyme form, Mr 54,092, with a 19 amino acid long signal peptide. The primary secretion products of the enzyme consist of a minor glycosylated form, Mr 57,000, and a major unmodified polypeptide of predicted Mr 51,929. Proteolytic activation of human skin procollagenase results in removal of 81 amino acid residues from the amino-terminal portion of the proenzyme. Both potential N-glycosylation sites are contained within the proteolytically activated form of the enzyme. The primary structure of the coding region of the presented clone is homologous to an oncogene-induced rat protein whose function is still unknown, although preliminary observations suggest that it is not rat skin collagenase.
Problems of the nanoimprinting technique for nanometer scale pattern definition (1998)

We have tested nanoimprint lithography, a new and promising technique for nanometer-scale pattern definition. Preliminary experiments reveal that, besides severe sticking and adhesion problems, the problem of material transport is one inherent to this technique. There are clear indications that most of the effects found may be understood in terms of material transport. We performed experiments within a well defined pressure and temperature window which ranged from 60 to 100 bar and from 50 to 90 °C above the glass transition temperature of the poly(methylmethacrylate)-like polymer used. As a result, the quality of imprint is evaluated with respect to full area pattern transfer, based on a qualitative scanning electron microscope investigation of the fully imprinted area of 2 cm × 2 cm patterned with features of different size and shape. Optimum conditions for imprint quality are found around 100 bar and 90 °C above Tg for the specific polymer used. Although material transport will limit nanoimprint performance in general, it is found that periodic patterns and isolated or small area negative stamp relief patterns are most suitable for high quality nanoimprinting.
I–V characteristics of resonant tunneling devices: Difference equation method (1998)

We have developed a full-band-structure-based theory to calculate the transmission coefficients through nanostructures of semiconductor quantum wells and barriers. This method, based on the solution to a difference equation, is efficient, numerically stable, and accurate. The I–V characteristics of realistic resonant tunneling diodes are calculated, and this method enables us to follow the contribution to the spatially resolved current from channels mediated by different valleys. We have carried out a systematic study of I–V characteristics in GaAs/AlAs double-barrier resonant structures using a second-neighbor tight-binding Hamiltonian. Our calculations clearly show that the energy separation between the quantized Γ state in GaAs and X state in AlAs plays a crucial role in determining the peak-to-valley current ratio. We further show that the quantized states and peak-to-valley current ratio are sensitively dependent on the tight-binding parameters.
Augmented Reality Based Museum Guidance System for Selective Viewings (2007)

There have been several museum and exhibition guidance systems that are based on RFID and visual tags. Using these systems, additional information on the paintings and exhibits may be provided in the forms of text, image, speech, and video. However, at museums and exhibitions, many tourists are often interested in exhibits of some particular style, authors, or coteries. Previously developed guide systems do not provide such functionality to the best of our knowledge. The proposed Augmented Reality based guidance system may guide the users to exhibits of their interest for selective viewings. Location of the next exhibit of interest may be informed to the users as well as additional multimedia information on the exhibits of interest. Such information is shown on the Augmented Reality views of the user's display device. The proposed system is composed an Ultra-Mobile PC (UMPC), an inertia tracker, and a camera. In the beginning, the user may select his/her preference on the exhibits from the menu, and then the system starts guiding by showing the relative orientation, distance, and visual cue to find match. When the user finds and locates the matching visual cue within a matching box of the display screen, the system provides multimedia information on the exhibit. According to the preliminary user test, the proposed system is convenient and useful for navigating through large-scale exhibitions.
Analysis of multiphase space vector pulse-width modulation based on multiple d-q spaces concept (2005)

Multiphase motors are usually designed to have the concentrated winding and nonsinusoidal airgap flux density distribution in order to maximize the torque per ampere. This means that the phase voltage of a multiphase motor has the nonsinusoidal waveform. Accordingly, the conventional analysis on a multiphase space vector pulse-width modulation (SVPWM), which is confined to a sinusoidal phase voltage, should be extended to a nonsinusoidal phase voltage. In this paper, based on a multiple d-q spaces concept a novel analysis on a multiphase SVPWM to synthesize an arbitrary nonsinusoidal phase voltage is proposed. Throughout this paper, a five-phase inverter is used as a practical example. The basic concepts can be easily extended to an n-phase inverter.
Characteristics of chylomicron binding and lipid uptake by endothelial cells in culture. (1979)

Bovine vascular endothelial cells bind chylomicrons via a high affinity membrane receptor site. Subsequent to binding, the chylomicron apoprotein was neither internalized nor degraded by either sparse or confluent (contact-inhibited) cells. However, the adsorption of chylomicrons was associated with interiorization of chylomicron cholesteryl ester and triglyceride and the hydrolysis of these lipids to free cholesterol and unesterified fatty acids by a lysosome-dependent pathway. This pathway was active in both subconfluent and contact-inhibited cells. The chylomicron free cholesterol so produced inhibited endogeneous cholesterol synthesis measured in terms of the incorporation of [1-14C]-acetate into sterol. An excess of high density lipoprotein was 2- to 3-fold more effective in reducing both binding of chylomicrons and interiorization of chylomicron lipid than was low density lipoprotein. Chylomicron binding was not "down-regulated" by preincubation of the cells with low density lipoprotein or chylomicrons. The results are discussed in the context of cholesterol sources for contact-inhibited endothelial cells which do not interiorize low density lipoprotein cholesterol.
Sterically blocking adhesion of cells to biological surfaces with a surface‐active copolymer containing poly(ethylene glycol) and phenylboronic acid (2001)

Graft copolymers were designed that could spontaneously bind to biological surfaces and block subsequent recognition and adhesion at those surfaces. Phenylboronic acid (PBA) moieties in the polymer backbone provided binding to surfaces, forming reversible covalent complexes with cis-diols found in many biological molecules. Pendant poly(ethylene glycol) (PEG) side chains sterically protected those surfaces from subsequent interactions with other proteins and cells. The PEG and PBA grafting ratios on these poly-L-lysine-graft-(PEG;PBA) copolymers [PLL-g-(PEG;PBA)] were varied, and the polymers were tested in models relevant to undesirable wound-healing responses such as peritoneal adhesion formation and posterior capsule opacification. PLL-g-(PEG;PBA) polymers spontaneously coated tissue culture polystyrene and completely blocked rabbit lens epithelial cell adhesion to the surface over a wide range of PEG grafting ratios. PLL-g-(PEG;PBA)s with optimal grafting ratios were able to coat adsorbed serum proteins or extracellular matrices and block cell spreading on the surfaces at 4 h, although the effect was lost within 24 h. The polymer also enhanced the efficacy of surgical lysis of peritoneal adhesions in rats. The reversible covalent complexes formed by the PBA moieties on the copolymer backbone were more effective at binding biological surfaces than electrostatic interactions formed via a copolymer lacking the PBA moieties, that is, PLL-g-PEG.
Field trial results of a band hopping OFDM system (1999)

Performance results from field trial of band hopping OFDM are presented in this paper. Band hopping OFDM utilizes OFDM and slow frequency hopping techniques to provide essential needs for future wireless communications systems. OFDM is currently utilized in digital audio and video broadcasting and DSL. It has been also standardized for wireless LAN applications. A testbed was developed and used in field trials in a suburban area to prove the performance of the band hopping OEDM system. The results indicate that the system is robust against impaired mobile channel conditions. They also show that the system provides superior performance in a multi-path fading environment. Finally, these results support the feasibility of band hopping OFDM techniques for high-speed wireless packet data applications.
Methods in high resolution gas chromatography. Two‐dimensional techniques (1978)

Abstract Basic methodology to effect the separation of complex samples by gas chromatography is discussed from an experimental point of view. Several possibilities are presented which are commonly used to enhance the information content of a gas chromatographic run. These include incorporation of more than one set of retention data, multiple detectors, and special column switching techniques. These and other techniques have sometimes been labeled “multidimensional” in the literature. An attempt is made to define the term “two‐dimensional chromatography”. The review is divided into sections which point out the different directions which have been taken to deconvolute chromatographically unresolved components. Particular emphasis is placed on technology which is capable of dealing with samples of extreme complexity, and instrumentation for trace‐ and ultratrace analysis is dicussed with specific examples. The future of two‐dimensional techniques in gas chromatography is looked into.
New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice (2015)

We identified and validated novel DNA methylation markers strongly associated with pancreatic cancer. On pilot testing in pancreatic juice, best markers (especially CD1D) highly discriminated pancreatic cases from controls.
Study of Mesa Undercuts Produced in GaAs with  H 3 PO 4 ‐ Based Etchants (1989)

In the fabrication of devices with small active device dimensions, the undercuts caused by chemical etchants become very important. The nature of undercuts and the change in geometry of patterns with different compositions of etchants have been critically analyzed. The etch profiles along [110] and [110] directions of a (100)‐oriented slice were also analyzed by the study of cross‐sections of rectangular mesas and small geometry square patterns. The variation of the aspect ratios with the composition was analyzed, and the range of the etchant composition yielding minimum undercuts was determined. Photographs of overhanging resist provide a good estimate of the nature of both profiles and undercut.
Concise Total Synthesis and Stereochemical Revision of (+)-Naseseazines A and B: Regioselective Arylative Dimerization of Diketopiperazine Alkaloids (2011)

Concise and enantioselective total syntheses of (+)-naseseazines A and B are described. Our regioselective and directed dimerization of diketopiperazines provides their critical C3-C(sp(2)) linkages, an assembly with plausible biogenetic relevance. We revise the absolute stereochemistry of (+)-naseseazines A and B.
Sonic hedgehog and CDX2 expression in the stomach (2008)

Sonic hedgehog (Shh) is an essential regulator of patterning processes throughout development, and CDX proteins act as the master regulators for intestinal development and differentiation. Shh and CDX2 seem to be interdependently linked with cellular differentiation through different signal cascades. We have recently shown that the loss of Shh and aberrant expression of CDX2 in Helicobacter pylori (H. pylori)-associated atrophic gastritis can be modified by H. pylori eradication prior to incomplete intestinal metaplasia. On the other hand, abnormal signaling of the hedgehog pathway has been reported in gastric cancer, especially diffuse-type cancer and advanced gastric cancer, and Shh acts as a proliferation factor in both the normal mucosa and malignant lesions. CDX2 expressed in the early stage of gastric carcinogenesis is associated with the intestinal phenotypic region and thus with a better outcome. However, it remains unclear how Shh and CDX2 are involved with intestinal transformation and further carcinogenesis.
The preparation of mitomycin C, adriamycin and daunomycin covalently bound to antibodies as improved cancer chemotherapeutic agents. (1981)

Mitomycin C, daunomycin and adriamycin, three potent cancer chemotherapeutic agents, were linked to immunoglobulins by the cyanogen bromide method and the conjugates were separated on Sepharose 6B. The most suitable conditions for binding of the drug to the antibody, while retaining both antibody and drug activity, included the use of 25-50 mol of cyanogen bromide per mol of IgG at pH 11 for the activation of immunoglobulin. The extent of substitution in this preparation was about 1 mol of drug per mol of IgG. This conjugate might be considered as a sustained release form of the antitumor agent.
Antibacterial Properties of Silver‐Doped Titania (2007)

Silver-doped titania nanoparticles (see image) in specific concentrations show a higher efficacy than pure silver nanoparticles towards the inhibition and annihilation of E. coli bacteria. The doped titania particles are synthesized via a sol–gel method. Antibacterial studies of the silver-doped titania particles in both a liquid-nutrient growth medium and on agar plates are shown; this approach may offer a simple low-cost method for fabricating antibacterial surfaces.
THE CONCENTRATIONS OF CYSTEINE AND CYSTINE IN HUMAN BLOOD PLASMA (1960)

Studies on the amino acid content of physiological fluids have usually been carried out under conditions that would permit any cysteine present to be oxidized to cystine prior to analysis. Consequently, little quantitative information has been obtained concerning the relative amounts of the -SH and the -S-S- forms of the amino acid in plasma. To know whether both forms are present is of particular importance in the study of excretion of amino acids by the kidney. Cystine is an amino acid which appears in abnormal quantities in the urine in several pathological conditions (1). Failure of tubular reabsorption has usually been invoked to explain this fact (2), an explanation which tacitly assumes that it is cystine (the -S-S- form) not cysteine (the -SH form) that is circulating in the blood and is cleared by the kidney. If cysteine were to be the predominant form normally circulating, oxidation to cystine in the kidney would be required in order to account for the excretion of the disulfide in the urine. Fujita and Numata (3) and Smith and Tuller (4) have reported the presence of cysteine in blood. Another observation which could bear on the subject is that of Brand, Cahill and Harris (5) who showed that the amount of cystine in the urine of a cystinuric subject rose after feeding cysteine and methionine, but not after the ingestion of cystine, the sulfur of which appeared almost exclusively as urinary sulfate. With these thoughts in view, a method has been