gebhart/patrepeval huggingface dataset:
Massively Parallel (“Next-Generation”) DNA Sequencing (2015)

Featured Article : Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376–80.4

Since Watson and Crick's 1953 landmark discovery that biological information was encoded as a sequence of chemical building blocks (DNA), a significant component of genetic research has been devoted to not only establishing disease–gene associations but also identifying genetic determinants for human quantitative traits such as blood pressure, body mass index, and pigmentation. Essential to this research is the technology to accurately characterize component nucleotides in exactly the order in which they naturally appear: “sequencing” of DNA. The first developed technologies, Maxam-Gilbert's strand cleavage-based techniques (1976) and the Sanger dideoxy chain-termination (1978), sequenced disease-gene candidate regions that were identified through linkage mapping, with subsequent isolation of both the responsible gene and the spectrum of causative mutations.

Based on these successes, the Human Genome Project was launched in 1990 and, in 2001, buoyed by Sanger sequencing, the first human reference genome was published (1). Although that article formally marked the transition to the “genomics era,” its cost of $2.7 billion and 10 years of extensive human capital across 20 collaborative centers worldwide highlighted to us that the process of sequencing would need to …
A case of HER-2-positive recurrent breast cancer showing a clinically complete response to trastuzumab-containing chemotherapy after primary treatment of triple-negative breast cancer (2011)

We report a case of HER-2-positive recurrent breast cancer showing a clinically complete response to trastuzumab-containing chemotherapy 6 years after primary treatment of triple-negative breast cancer. The primary tumor was negative for HER-2 as determined by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) (1+, and ratio, 1.1), but examination of the recurrent lymph node metastasis showed positivity for HER-2 by FISH (ratio, 5.2). No lesions were detected in either her left breast or in other organs, and the patient was diagnosed as having HER-2-positive recurrent disease. Combination chemotherapy using weekly paclitaxel and trastuzumab was initiated, and a clinically complete response was achieved. This report suggests the benefit of routine evaluation of HER-2 status in recurrent breast cancer with the introduction of HER-2-targeting agents.
A comparison of user interfaces for panning on a touch-controlled display (1995)

Article A comparison of user interfaces for panning on a touch-controlled display Share on Author: Jeff A. Johnson Sun Microsystems, 2550 Garcia Ave., MS UMTV12-33, Mountain View, CA Sun Microsystems, 2550 Garcia Ave., MS UMTV12-33, Mountain View, CAView Profile Authors Info & Claims CHI '95: Proceedings of the SIGCHI Conference on Human Factors in Computing SystemsMay 1995 Pages 218–225https://doi.org/10.1145/223904.223932Online:01 May 1995Publication History 21citation995DownloadsMetricsTotal Citations21Total Downloads995Last 12 Months28Last 6 weeks6 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Feature-Ranking Methodology to Diagnose Design-Silicon Timing Mismatch (2009)

For sub-65-nm design, many timing effects, if not explicitly and accurately modeled and simulated, can result in an unexpected timing mismatch between simulated and observed timing behavior on silicon chips. We describe a feature-ranking methodology to analyze and rank potential design-related issues, explaining how diverse features can be used to encode the potential design issues and how features can be interpreted properly.
Instant messaging with mobile phones to support awareness (2002)

To provide an instant message service for mobile phone users, we developed a system that enables members of a community to share their awareness information with mobile phones. Our system provides users with functions to send chat messages and set awareness information such as icons and memos in a community. We describe our observations about users' activities in a trial of our system. Based on our observations, the interaction between awareness channels and chat channels is also discussed.
Identification of Circulating Fibrocytes as Precursors of Bronchial Myofibroblasts in Asthma (2003)

The mechanisms contributing to airway wall remodeling in asthma are under investigation to identify appropriate therapeutic targets. Bronchial myofibroblasts would represent an important target because they play a crucial role in the genesis of subepithelial fibrosis, a characteristic feature of the remodeling process, but their origin is poorly understood. We hypothesized that they originate from fibrocytes, circulating cells with the unique characteristic of expressing the hemopoietic stem cell Ag CD34 and collagen I. In this study we show that allergen exposure induces the accumulation of fibrocyte-like cells in the bronchial mucosa of patients with allergic asthma. These cells are CD34-positive; express collagen I and alpha-smooth muscle actin, a marker of myofibroblasts; and localize to areas of collagen deposition below the epithelium. By tracking labeled circulating fibrocytes in a mouse model of allergic asthma, we provide evidence that fibrocytes are indeed recruited into the bronchial tissue following allergen exposure and differentiate into myofibroblasts. We also show that human circulating fibrocytes acquire the myofibroblast phenotype under in vitro stimulation with fibrogenic cytokines that are produced in exaggerated quantities in asthmatic airways. These results indicate that circulating fibrocytes may function as myofibroblast precursors and may contribute to the genesis of subepithelial fibrosis in asthma.
Space-time coding for UMTS. Performance evaluation in combination with convolutional and turbo coding (2002)

Space-time codes provide both diversity and coding gain when using multiple transmit antennas to increase spectral efficiency over wireless communications systems. Space-time block codes have already been included in the standardization process of UMTS in conjunction with conventional channel codes (convolutional and turbo codes). We discuss different encoding and decoding strategies when transmit diversity is combined with conventional channel codes, and present simulations results for the TDD and FDD modes of UTRA.
Int-B13, an Unusual Site-Specific Recombinase of the Bacteriophage P4 Integrase Family, Is Responsible for Chromosomal Insertion of the 105-Kilobase clc Element of Pseudomonas sp. Strain B13 (1998)

Pseudomonas sp. strain B13 carries the clcRABDE genes encoding chlorocatechol-degradative enzymes on the self-transmissible 105-kb clc element. The element integrates site and orientation specifically into the chromosomes of various bacterial recipients, with a glycine tRNA structural gene (glyV) as the integration site. We report here the localization and nucleotide sequence of the integrase gene and the activity of the integrase gene product in mediating site-specific integration. The integrase gene (int-B13) was located near the right end of the clc element. It consisted of an open reading frame (ORF) of maximally 1,971 bp with a coding capacity for 657 amino acids (aa). The full-length protein (74 kDa) was observed upon overexpression and sodium dodecyl sulfate-polyacrylamide gel electrophoresis separation. The N-terminal 430 aa of the predicted Int-B13 protein had substantial similarity to integrases from bacteriophages of the P4 family, but Int-B13 was much larger than P4-type integrases. The C-terminal 220 aa of Int-B13 were homologous to an ORF flanking a gene cluster for naphthalene degradation in Pseudomonas aeruginosa PaK1. Similar to the bacteriophages phiR73 and P4, the clc element integrates into the 3' end of the target tRNA gene. This target site was characterized from four different recipient strains into which the clc element integrated, showing sequence specificity of the integration. In Pseudomonas sp. strain B13, a circular form of the clc element, which carries an 18-bp DNA sequence identical to the 3'-end portion of glyV as part of its attachment site (attP), could be detected. Upon chromosomal integration of the clc element into a bacterial attachment site (attB), a functional glyV was reconstructed at the right end of the element. The integration process could be demonstrated in RecA-deficient Escherichia coli with two recombinant plasmids, one carrying the int-B13 gene and the attP site and the other carrying the attB site of Pseudomonas putida F1.
Structural basis for NKG2A/CD94 recognition of HLA-E (2008)

The NKG2x/CD94 (x = A, C, E) natural killer-cell receptors perform an important role in immunosurveillance by binding to HLA-E complexes that exclusively present peptides derived from MHC class I leader sequences, thereby monitoring MHC class I expression. We have determined the crystal structure of the NKG2A/CD94/HLA-E complex at 4.4-A resolution, revealing two critical aspects of this interaction. First, the C-terminal region of the peptide, which displays the most variability among class I leader sequences, interacts entirely with CD94, the invariant component of these receptors. Second, residues 167-170 of NKG2A/C account for the approximately 6-fold-higher affinity of the inhibitory NKG2A/CD94 receptor compared to its activating NKG2C/CD94 counterpart. These residues do not contact HLA-E or peptide directly but instead form part of the heterodimer interface with CD94. An evolutionary analysis across primates reveals that whereas CD94 is evolving under purifying selection, both NKG2A and NKG2C are evolving under positive selection. Specifically, residues at the CD94 interface have evolved under positive selection, suggesting that the evolution of these genes is driven by an interaction with pathogen-derived ligands. Consistent with this possibility, we show that NKG2C/CD94, but not NKG2A/CD94, weakly but specifically binds to the CMV MHC-homologue UL18. Thus, the evolution of the NKG2x/CD94 family of receptors has likely been shaped both by the need to bind the invariant HLA-E ligand and the need to avoid subversion by pathogen-derived decoys.
Radiative Energy Transfer in GaN:Mg/Al2O3:Cr3+ Epitaxial Systems (1993)

A photoluminescence study of undoped and Mg-doped GaN epitaxial layers grown by means of metalorganic vapor phase epitaxy (MOVPE) on sapphire (Al 2 O 3 ) substrates is reported. In undoped n-type GaN the characteristic exciton emissions are observed near the band gap ( E g =3.47 eV). Mg-doped GaN shows a very strong blue donor-acceptor recombination band at about 3.2 eV. Only in these samples is a sharp line detected at 1.79 eV which is due to the characteristic R 1,2 lines of Cr 3+ (3d 3 ) trace impurities in the Al 2 O 3 substrate. An obvious explanation for this effect is the very efficient radiative energy transfer from the GaN:Mg layer emitting blue photons into the absorption band 4 A 2 → 4 T 1 of Cr 3+ (3d 3 ) trace impurities in the Al 2 O 3 substrate.
Lensless wide-field fluorescent imaging on a chip using compressive decoding of sparse objects (2010)

We demonstrate the use of a compressive sampling algorithm for on-chip fluorescent imaging of sparse objects over an ultra-large field-of-view (>8 cm(2)) without the need for any lenses or mechanical scanning. In this lensfree imaging technique, fluorescent samples placed on a chip are excited through a prism interface, where the pump light is filtered out by total internal reflection after exciting the entire sample volume. The emitted fluorescent light from the specimen is collected through an on-chip fiber-optic faceplate and is delivered to a wide field-of-view opto-electronic sensor array for lensless recording of fluorescent spots corresponding to the samples. A compressive sampling based optimization algorithm is then used to rapidly reconstruct the sparse distribution of fluorescent sources to achieve approximately 10 microm spatial resolution over the entire active region of the sensor-array, i.e., over an imaging field-of-view of >8 cm(2). Such a wide-field lensless fluorescent imaging platform could especially be significant for high-throughput imaging cytometry, rare cell analysis, as well as for micro-array research.
Antiatherogenic Effects of <i>Phyllanthus Emblica</i> Associated with Corilagin and its Analogue (2005)

Oxidized low-density lipoprotein (ox-LDL) is the main etiologic factor in atherogenesis, and antioxidants are accepted as effective treatment of atherosclerosis. The aim of this study was to clarify whether the mechanism of the antiatherogenic effects of the herb Phyllanthus Emblica, which is widely used to treat atherosclerosis-related diseases, is associated with ox-LDL via its compounds of soluble tannin, corilagin (beta-1-O-galloyl-3,6-(R)-hexahydroxydiphenoyl-d-glucose), and its analogue Dgg16 (1,6-di-O-galloyl-beta-d-glucose). Human umbilical vein endothelial cells, ECV-304, were incubated with ox-LDL (50 mg/l), treated with corilagin or Dgg16 at different doses (0.0001—0.1 mmol/l), and then incubated with monocytes. Malondialdehyde (MDA) in the culture media was determined and the number of monocytes adhering to ECV-304 cells was counted with cytometry. In another experiment, the rat vascular smooth muscular cells (VSMC) were incubated in media with or without ox-LDL (50 mg/l), and with corilagin or Dgg16 also at different doses (0.0001—0.1 mol/l), the proliferation of which was assayed with MTT. The results showed that both corilagin and Dgg16 were able to decrease MDA, prevented ECV-304 cells from being adhering to by monocytes, and inhibited VSMC proliferation activated by ox-LDL. The results suggest that the two compounds are effective in inhibiting the progress of atherosclerosis by alleviating oxidation injury or by inhibiting ox-LDL-induced VSMC proliferation, which may be promising mechanisms for treating atherosclerosis.
Dyes and Dye Intermediates (2009)

Abstract The first synthetic dye, Mauveine, was discovered by Perkins in 1856, hence the dye industry is mature.The scale and growth of the dye industry depends on textiles. The most important textiles are cotton and polyester. Dyes may be classified according to their chemical structure or application method. Chemical classification is the most appropriate since it identifies dyes belonging to a group that has characteristic properties. Secondly, there are a manageable number of chemical groups (about a dozen). Also it is most used by dye chemists and technologists. Classification by use falls into the following: reactive, direct, vat, sulfur, mordant, disperse, basic, solvent, and acid dyes. Dyes are named either by their commercial trade name or by their CI (Colour Index) name. Classification by chemical name is detailed starting with the most important, azo dyes. Chemistry of the primary dye intermediates is discussed. Equipment and basics of dye manufacture are given. The toxic nature of some dyes and their intermediates is known. Dyes, because of their intense color, present special problems in effluent discharge. Removal and treatment of these wastes are detailed.
Highly stretchable, conductive, and transparent nanotube thin films (2009)

We have studied the electrical and optical properties of transparent and conductive nanotube thin films subjected to extremely large strains, both isotropic and anisotropic. The films maintain electrical conductivity for strains up to 700% and the eventual loss of conductivity is due primarily to the buildup of cracks in the nanotube films. We also measured the change in optical transmittance and explain the observed haziness of the films by considering the micrometer sized cluster. This study of transparent nanotube films as stretchable electrodes is crucial for many applications, in particular, for medical implantation of electronic devices.
Misconceptions about the new combination vaccine (2004)

Misconceptions about the new combination vaccinePentavalent vaccine is better in many ways
Long Term Behavior of Lithographically PreparedIn VitroNeuronal Networks (2002)

We measured the long term spontaneous electrical activity of neuronal networks with different sizes, grown on lithographically prepared substrates and recorded with multi-electrode-array technology. The time sequences of synchronized bursting events were used to characterize network dynamics. All networks exhibit scale-invariant Lévy distributions and long-range correlations. These observations suggest that different-size networks self-organize to adjust their activities over many time scales. As predictions of current models differ from our observations, this calls for revised models.
Differential Usage of Signal Transduction Pathways Defines Two Types of Serum Response Factor Target Gene (2001)

Activation of the transcription factor serum response factor (SRF) is dependent on Rho-controlled changes in actin dynamics. We used pathway-specific inhibitors to compare the roles of actin dynamics, extracellular signal-regulated kinase (ERK) signaling, and phosphatidylinositol 3-kinase in signaling either to SRF itself or to four cellular SRF target genes. Serum, lysophosphatidic acid, platelet-derived growth factor, and phorbol 12-myristate 13-acetate (PMA) each activated transcription of a stably integrated SRF reporter gene dependent on functional RhoA GTPase. Inhibition of mitogen-activated protein kinase-ERK kinase (MEK) signalling reduced activation of the SRF reporter by all stimuli by about 50%, except for PMA, which was effectively blocked. Inhibition of phosphatidylinositol 3-kinase slightly reduced reporter activation by serum and lysophosphatidic acid but substantially inhibited activation by platelet-derived growth factor and PMA. Reporter induction by all stimuli was absolutely dependent on actin dynamics. Regulation of the SRF (srf) and vinculin (vcl) genes was similar to that of the SRF reporter gene; activation by all stimuli was Rho-dependent and required actin dynamics but was largely independent of MEK activity. In contrast, activation of fos and egr1 occurred independently of RhoA and actin polymerization but was almost completely dependent on MEK activation. These results show that at least two classes of SRF target genes can be distinguished on the basis of their relative sensitivity to RhoA-actin and MEK-ERK signaling pathways.
Structural characterization of the Mr = 55,000 antigen (ZP3) of porcine oocyte zona pellucida. Purification and characterization of alpha- and beta-glycoproteins following digestion of lactosaminoglycan with endo-beta-galactosidase. (1987)

The major macromolecular component of the porcine oocyte zona pellucida is a Mr = 55,000 antigen, termed ZP3, comprised of greater than 25 charge isomers. ZP3 was purified to apparent electrophoretic homogeneity from nonreduced, sodium dodecyl sulfate-treated porcine zonae pellucidae by chromatography on Sephacryl S-400 and hydroxylapatite resins. The carbohydrate moiety of purified ZP3 was comprised of a heterogeneous population of acidic lactosaminoglycans as evidenced by the saccharide composition and size distribution of glycopeptides produced by Pronase digestion of ZP3, as well as by the sensitivity of ZP3 to digestion with Escherichia freundii endo-beta-galactosidase. Endo-beta-galactosidase-digested ZP3 was resolved by gel electrophoresis into two components, termed alpha-glycoprotein and beta-glycoprotein, with Mr values (nonreduced) of 46,000 and 42,000, respectively. Each was comprised of fewer and more neutral charge isomers than ZP3. Following purification by reverse phase high performance liquid chromatography, the alpha- and beta-glycoproteins of endo-beta-galactosidase-digested ZP3 were distinguished on the basis of amino acid and carbohydrate compositions, amino-terminal sequence analyses and peptide mapping experiments, thus suggesting differences in the primary structures of their respective polypeptide moieties. Corresponding dissimilarities in the immunoreactivities of the alpha- and beta-glycoproteins toward polyclonal antisera raised against ZP3, alpha-glycoprotein, and beta-glycoprotein were revealed by competitive binding radioimmunoassays as well as by immunoblotting experiments. Collectively, the data were interpreted to indicate that the Mr = 55,000 antigen of porcine oocyte zona pellucida is in fact comprised of overlapping families of charge isomers corresponding to two structurally and immunologically distinct lactosaminoglycan-containing glycoproteins.
Nootropics: pharmacological properties and therapeutic use. (1995)

This review summarizes the results of studies investigating the pharmacological properties, mechanisms of action, preclinical and clinical effects of nootropic drugs, and tries to integrate this knowledge in order to identify neuronal mechanisms underlying their therapeutic benefits and side effects.
Cell-by-cell construction of living tissue (2002)

This paper outlines investigations into a potentially revolutionary approach to tissue engineering. Tissue is a complex 3D structure that contains many different biomaterials such as cells, proteins, and extracellular matrix molecules that are ordered in a very precise way to serve specific functions. In order to replicate such complex structure, it is necessary to have a tool that could deposit all these materials in an accurate and controlled fashion. Most methods to fabricate living 3D structures involve techniques to engineer biocompatible scaffolding, which is then seeded with living cells to form tissue. This scaffolding gives the tissue needed support, but the resulting tissue inherently has no microscopic cellular structure because cells are injected into the scaffolding where they adhere ta random. Wee have developed a novel technique that actually engineers tissue, not scaffolding, that includes the mesoscopic cellular structure inherent in natural tissues. This approach uses a laser-based rapid prototyping system known as matrix assisted pulsed laser evaporation direct write to construct living tissue cell-by- cell. This manuscript details our efforts to rapidly and reproducibly fabricate comlpex 2D and 3D tissue structures with MAPLE-DW by placing different cells and biomaterials accurately and adherently on the mesoscopic scale.
Toward a General Strategy for the Synthesis of Heterobimetallic Coordination Complexes for Use as Precursors to Metal Oxide Materials:  Synthesis, Characterization, and Thermal Decomposition of Bi2(Hsal)6·M(Acac)3 (M = Al, Co, V, Fe, Cr) (2004)

Bismuth(III) salicylate, [Bi(Hsal)(3)](n), reacts readily with the trivalent metal beta-diketonate compounds M(acac)(3) (acac = acetylacetonate; M = Al, V, Cr, Fe, Co) to produce trinuclear coordination complexes of the general formula Bi(2)(Hsal)(6).M(acac)(3) (M = Al, V, Cr, Fe, Co) in 60-90% yields. Spectroscopic and single crystal X-ray diffraction experiments indicate that these complexes possess an unusual asymmetric nested structure in both solution and solid state. Upon standing in dichloromethane solution, Bi(2)(Hsal)(6).Co(acac)(3) eliminates Bi(Hsal)(3) to give the 1:1 adduct Bi(Hsal)(3).Co(acac)(3). The 2:1 heterobimetallic molecular compounds undergo facile thermal decomposition on heating in air to 475 degrees C to produce heterometallic oxide materials, which upon annealing for 2 h at 700 degrees C form crystalline oxide materials. The synthetic approach detailed here represents a unique, general approach to the formation of heterobimetallic bismuth-based coordination complexes via the coordination of M(acac)(3) complexes to bismuth(III) salicylate.