gebhart/patrepeval huggingface dataset:
Association of Polymorphisms of Interleukin-8, CXCR1, CXCR2, and Selectin With Allograft Outcomes in Kidney Transplantation (2010)

The donor CXCR1 -2668 GA/AA genotypes were an independent risk factor for acute rejection in kidney transplantation.
Rapid mass spectrometric peptide sequencing and mass matching for characterization of human melanoma proteins isolated by two-dimensional PAGE. (1995)

We report a general mass spectrometric approach for the rapid identification and characterization of proteins isolated by preparative two-dimensional polyacrylamide gel electrophoresis. This method possesses the inherent power to detect and structurally characterize covalent modifications. Absolute sensitivities of matrix-assisted laser desorption ionization and high-energy collision-induced dissociation tandem mass spectrometry are exploited to determine the mass and sequence of subpicomole sample quantities of tryptic peptides. These data permit mass matching and sequence homology searching of computerized peptide mass and protein sequence data bases for known proteins and design of oligonucleotide probes for cloning unknown proteins. We have identified 11 proteins in lysates of human A375 melanoma cells, including: alpha-enolase, cytokeratin, stathmin, protein disulfide isomerase, tropomyosin, Cu/Zn superoxide dismutase, nucleoside diphosphate kinase A, galaptin, and triosephosphate isomerase. We have characterized several posttranslational modifications and chemical modifications that may result from electrophoresis or subsequent sample processing steps. Detection of comigrating and covalently modified proteins illustrates the necessity of peptide sequencing and the advantages of tandem mass spectrometry to reliably and unambiguously establish the identity of each protein. This technology paves the way for studies of cell-type dependent gene expression and studies of large suites of cellular proteins with unprecedented speed and rigor to provide information complementary to the ongoing Human Genome Project.
HER2 Overexpression Elicits a Proinflammatory IL-6 Autocrine Signaling Loop That Is Critical for Tumorigenesis (2011)

HER2 overexpression occurs in approximately 25% of breast cancers, where it correlates with poor prognosis. Likewise, systemic inflammation in breast cancer correlates with poor prognosis, although the process is not understood. In this study, we explored the relationship between HER2 and inflammation, comparing the effects of overexpressing wild-type or mutated inactive forms of HER2 in primary human breast cells. Wild-type HER2 elicited a profound transcriptional inflammatory profile, including marked elevation of interleukin-6 (IL-6) expression, which we established to be a critical determinant of HER2 oncogenesis. Mechanistic investigations revealed that IL-6 secretion induced by HER2 overexpression activated Stat3 and altered gene expression, enforcing an autocrine loop of IL-6/Stat3 expression. Both mouse and human in vivo models of HER2-amplified breast carcinoma relied critically on this HER2-IL-6-Stat3 signaling pathway. Our studies offer the first direct evidence linking HER2 to a systemic inflammatory mechanism that orchestrates HER2-mediated tumor growth. We suggest that the HER2-IL-6-STAT3 signaling axis we have defined in breast cancer could prompt new therapeutic or prevention strategies for treatment of HER2-amplified cancers.
Nonuniform expression of a mouse mammary tumor virus-driven int-2/Fgf-3 transgene in pregnancy-responsive breast tumors. (1992)

We have developed transgenic mice in which expression of the mouse int-2/Fgf-3 gene is regulated by a single long terminal repeat from mouse mammary tumor virus. Such mice contain and transmit a replica of the activated int-2/Fgf-3 allele present in a spontaneous mammary tumor from a BR6 mouse. Although free of infectious mouse mammary tumor virus and with a different genetic background, the transgenic mice develop pregnancy-responsive mammary epithelial proliferations that are similar to the early stages of tumorigenesis in the BR6 strain. Histological examination revealed that most of these tumors showed pronounced tubular and acinar structures, features usually associated with morphological differentiation. In some cases, the tumors were locally invasive, causing disruption of the dermis which manifested itself as local hair loss. In situ hybridization showed that patterns of transgene expression in the abnormal glands were markedly nonuniform. In contrast, mouse mammary tumor virus-induced neoplasms showed more uniform expression of int-2/Fgf-3, as did the urogenital epithelial proliferations that occur among males of this transgenic line. These data suggest that mammary tumors in virally infected animals may depend primarily on autocrine stimulation by the int-2/Fgf-3 gene product, whereas both autocrine and paracrine mechanisms may contribute to tumors and hyperplasias found in transgenic animals.
Single half-wavelength ultrasonic particle filter: Predictions of the transfer matrix multilayer resonator model and experimental filtration results (2002)

The quantitative performance of a "single half-wavelength" acoustic resonator operated at frequencies around 3 MHz as a continuous flow microparticle filter has been investigated. Standing wave acoustic radiation pressure on suspended particles (5-microm latex) drives them towards the center of the half-wavelength separation channel. Clarified suspending phase from the region closest to the filter wall is drawn away through a downstream outlet. The filtration efficiency of the device was established from continuous turbidity measurements at the filter outlet. The frequency dependence of the acoustic energy density in the aqueous particle suspension layer of the filter system was obtained by application of the transfer matrix model [H. Nowotny and E. Benes, J. Acoust. Soc. Am. 82, 513-521 (1987)]. Both the measured clearances and the calculated energy density distributions showed a maximum at the fundamental of the piezoceramic transducer and a second, significantly larger, maximum at another system's resonance not coinciding with any of the transducer or empty chamber resonances. The calculated frequency of this principal energy density maximum was in excellent agreement with the optimal clearance frequency for the four tested channel widths. The high-resolution measurements of filter performance provide, for the first time, direct verification of the matrix model predictions of the frequency dependence of acoustic energy density in the water layer.
Starburst Dendrimers: Molecular‐Level Control of Size, Shape, Surface Chemistry, Topology, and Flexibility from Atoms to Macroscopic Matter (1990)

Abstract Starburst dendrimers are three‐dimensional, highly ordered oligomeric and polymeric compounds formed by reiterative reaction sequences starting from smaller molecules—“initiator cores” such as ammonia or pentaerythritol. Protecting group strategies are crucial in these syntheses, which proceed via discrete “Aufbau” stages referred to as generations. Critical molecular design parameters (CMDPs) such as size, shape, and surface chemistry may be controlled by the reactions and synthetic building blocks used. Starburst dendrimers can mimic certain properties of micelles and liposomes and even those of biomolecules and the still more complicated, but highly organized, building blocks of biological systems. Numerous applications of these compounds are conceivable, particularly in mimicking the functions of large biomolecules as drug carriers and immunogens. This new branch of “supramolecular chemistry” should spark new developments in both organic and macromolecular chemistry.
Current role of thalidomide in cancer treatment (2000)

Thalidomide (Thalidomid, Celgene, Warren, NJ) is a putative anti-angiogenesis and immunomodulatory agent that has demonstrated activity in various dermatologic and rheumatologic conditions in addition to Crohn's disease. The biologic effects of thalidomide and the clinical trials conducted in solid tumors, hematologic malignancies, chronic graft-versus-host disease (GVHD), and cancer-related cachexia are reviewed. A summary of the preliminary results of ongoing clinical trials is presented, and the future directions of thalidomide research in the oncology are discussed.
A Short Physical Performance Battery Assessing Lower Extremity Function: Association With Self-Reported Disability and Prediction of Mortality and Nursing Home Admission (1994)

This study provides evidence that performance measures can validly characterize older persons across a broad spectrum of lower extremity function. Performance and self-report measures may complement each other in providing useful information about functional status.
PIXOR: Real-time 3D Object Detection from Point Clouds (2018)

We address the problem of real-time 3D object detection from point clouds in the context of autonomous driving. Speed is critical as detection is a necessary component for safety. Existing approaches are, however, expensive in computation due to high dimensionality of point clouds. We utilize the 3D data more efficiently by representing the scene from the Bird's Eye View (BEV), and propose PIXOR, a proposal-free, single-stage detector that outputs oriented 3D object estimates decoded from pixel-wise neural network predictions. The input representation, network architecture, and model optimization are specially designed to balance high accuracy and real-time efficiency. We validate PIXOR on two datasets: the KITTI BEV object detection benchmark, and a large-scale 3D vehicle detection benchmark. In both datasets we show that the proposed detector surpasses other state-of-the-art methods notably in terms of Average Precision (AP), while still runs at 10 FPS.
Design of Three-Pole Bulk Acoustic Wave Coupled Resonator Filters (2008)

The control of longitudinal coupling in bulk acoustic wave (BAW) resonators makes it possible to design multilayer coupled resonator filters (CRF) with a desired response. This paper presents the methodology to face this kind of designs with a set of closed-form expressions that allow to control the coupling between resonators, and to determine the structure geometry of a three-pole CRF. A network transformation from the Mason model to an equivalent electric circuit makes it possible to apply the insertion loss filter design method. An UMTS RF filter has been designed using the proposed methodology.
Phosphatidylazidothymidine and phosphatidyl-ddC: assessment of uptake in mouse lymphoid tissues and antiviral activities in human immunodeficiency virus-infected cells and in Rauscher leukemia virus-infected mice (1994)

During the early stages of human immunodeficiency virus (HIV) infection, although symptoms are absent and viral replication in peripheral blood mononuclear cells is low, substantial levels of HIV replication can be documented in lymphoid tissue [G. Pantaleo, C. Graziosi, J.F. Demarest, L. Butini, M. Montroni, C.H. Fox, J.M. Orenstein, D.P. Kotler, and A.S. Fauci, Nature (London) 362:355-358, 1993, and J. Embretsen, M. Zupancic, J.L. Ribas, A. Burke, P. Racz, K. Tenner-Tacz, and A.T. Haase, Nature (London) 362:359-362, 1993]. This observation suggests that earlier treatment of HIV infection may be indicated and that strategies for enhancing drug targeting to the lymphoid tissue reservoris of HIV infection may be beneficial. To address this issue, we synthesized dioleoylphosphatidyl-ddC (DOP-ddC) and dipalmitoylphosphatidyl-3'-azido-3'-deoxythymidine (DPP-AZT), phospholipid prodrugs which form lipid bilayers and which are readily incorporated into liposomes. The anti-HIV activity of DOP-ddC was similar to that of ddC in HIV type 1-infected HT4-6C cells, but DPP-AZT was considerably less active than AZT in HT4-6C cells. Liposomes containing DOP-[3H]ddC or DPP-[3H]AZT administered intraperitoneally to mice produced greater levels of total radioactivity over time in plasma, spleen, and lymphoid tissue relative to the results with [3H]ddC and [3H]AZT, respectively. DPP-AZT administered intraperitoneally in liposomes as a single daily dose to mice infected with Rauscher leukemia virus prevented increased spleen weight and reverse transcriptase levels in serum with a dose-response roughly comparable to that of AZT given continuously in the drinking water. DOP-ddC, DPP-AZT, and lipid conjugates of other antiretroviral nucleosides may provide higher levels of drug over time in plasma and in lymph nodes and spleen, important reservoirs of HIV infection, and may represent an interesting alternative approach to antiviral nucleoside treatment of AIDS.
In the Thick of It (2011)

In the 20 years since the discovery of the first mutation linked to familial hypertrophic cardiomyopathy (HCM), an astonishing number of mutations affecting numerous sarcomeric proteins have been described. Among the most prevalent of these are mutations that affect thick filament binding proteins, including the myosin essential and regulatory light chains and cardiac myosin binding protein (cMyBP)-C. However, despite the frequency with which myosin binding proteins, especially cMyBP-C, have been linked to inherited cardiomyopathies, the functional consequences of mutations in these proteins and the mechanisms by which they cause disease are still only partly understood. The purpose of this review is to summarize the known disease-causing mutations that affect the major thick filament binding proteins and to relate these mutations to protein function. Conclusions emphasize the impact that discovery of HCM-causing mutations has had on fueling insights into the basic biology of thick filament proteins and reinforce the idea that myosin binding proteins are dynamic regulators of the activation state of the thick filament that contribute to the speed and force of myosin-driven muscle contraction. Additional work is still needed to determine the mechanisms by which individual mutations induce hypertrophic phenotypes.
Multiphoton Excitation of Fluorescence near Metallic Particles:  Enhanced and Localized Excitation (2002)

We examined the effects of silver island films on multiphoton excitation of rhodamine derivatives and biochemical fluorophores. The fluorophores were studied in approximately 1 <i>μ</i>m thick samples between two quartz slides coated with silver islands. Intensity and lifetime measurements of rhodamine B demonstrated enhanced two-photon excitation near the metal particles. Time-resolved measurements showed a decreased lifetime of RhB with two-photon excitation as compared to unsilvered quartz slides, which indicates the two-photon excitation was localized near the metal particles. Additionally, rhodamine B showed increased photostability with two-photon excitation near metal particles, which is consistent with the shorter lifetime. For lower quantum yield fluorophores such as rose bengal, eosin, 1-anilinonaphthalene-8-sulfonic acid, and coumarin 152, we found the emission from the micron thick sample was almost completely due to the fluorophores near the silver particles, perhaps to within 300 Å of the metal surfaces. These results suggest the use of metal particles for localized multiphoton excitation of biological macromolecules or cells. Additionally, one can imagine metal colloids with bound fluorophores being selectively excited when placed in highly fluorescent samples such as tissue samples.
A new synthetic route to tert-butyloxycarbonylaminoacyl-4-(oxymethyl)phenylacetamidomethyl-resin, an improved support for solid-phase peptide synthesis (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new synthetic route to tert-butyloxycarbonylaminoacyl-4-(oxymethyl)phenylacetamidomethyl-resin, an improved support for solid-phase peptide synthesisAlexander R. Mitchell, Stephen B. H. Kent, Martin Engelhard, and R. B. MerrifieldCite this: J. Org. Chem. 1978, 43, 14, 2845–2852Publication Date (Print):July 1, 1978Publication History Published online1 May 2002Published inissue 1 July 1978https://pubs.acs.org/doi/10.1021/jo00408a022https://doi.org/10.1021/jo00408a022research-articleACS PublicationsRequest reuse permissionsArticle Views1228Altmetric-Citations301LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cell-free Protein Synthesis from a Release Factor 1 Deficient Escherichia coli Activates Efficient and Multiple Site-specific Nonstandard Amino Acid Incorporation (2013)

Site-specific incorporation of nonstandard amino acids (NSAAs) into proteins enables the creation of biopolymers, proteins, and enzymes with new chemical properties, new structures, and new functions. To achieve this, amber (TAG codon) suppression has been widely applied. However, the suppression efficiency is limited due to the competition with translation termination by release factor 1 (RF1), which leads to truncated products. Recently, we constructed a genomically recoded Escherichia coli strain lacking RF1 where 13 occurrences of the amber stop codon have been reassigned to the synonymous TAA codon (rEc.E13.ΔprfA). Here, we assessed and characterized cell-free protein synthesis (CFPS) in crude S30 cell lysates derived from this strain. We observed the synthesis of 190±20 μg/mL of modified soluble superfolder green fluorescent protein (sfGFP) containing a single p-propargyloxy-L-phenylalanine (pPaF) or p-acetyl-L-phenylalanine. As compared to the parent rEc.E13 strain with RF1, this results in a modified sfGFP synthesis improvement of more than 250%. Beyond introducing a single NSAA, we further demonstrated benefits of CFPS from the RF1-deficient strains for incorporating pPaF at two- and five-sites per sfGFP protein. Finally, we compared our crude S30 extract system to the PURE translation system lacking RF1. We observed that our S30 extract based approach is more cost-effective and high yielding than the PURE translation system lacking RF1, ∼1000 times on a milligram protein produced/$ basis. Looking forward, using RF1-deficient strains for extract-based CFPS will aid in the synthesis of proteins and biopolymers with site-specifically incorporated NSAAs.
Specific antiviral activity of a poly(L-lysine)-conjugated oligodeoxyribonucleotide sequence complementary to vesicular stomatitis virus N protein mRNA initiation site. (1987)

Antisense oligonucleotides represent an interesting tool for selective inhibition of gene expression, but their efficient introduction within intact cells proved to be difficult to realize. As a step toward this goal, small (13- or 15-mer) synthetic oligodeoxyribonucleotides have been coupled at their 3' ends to epsilon-amino groups of lysine residues of poly(L-lysine) (Mr, 14,000). A 15-mer oligonucleotide-poly(L-lysine) conjugate complementary to the initiation region of vesicular stomatitis virus (VSV) N-protein mRNA specifically inhibits the synthesis of VSV proteins and exerts an antiviral activity against VSV when added in the cell culture medium at doses as low as 100 nM. Neither synthesis of cellular proteins nor multiplication of encephalomyocarditis virus was affected significantly by this oligonucleotide conjugate. The data suggest that oligonucleotide-poly(L-lysine) conjugates might become effective for studies on gene expression regulation and for antiviral chemotherapy.
Future Combined Vaccines (1996)

The increasing number of useful vaccines for infants and children justifies the development of new combined vaccines. New methodologies are needed for evaluation of efficacy, especially for acellular pertussis vaccines. Such evaluation requires the use of previous immunogenicity studies as a means to seek immune interference that might lead to decreased efficacy. Finally, definitive efficacy could be assessed by long-term postmarketing epidemiologic surveillance. Different combinations are discussed in relation to age of recipients (infants, children, adolescents, and adults) and national or regional epidemiologies.
Kallistatin: a novel human serine proteinase inhibitor. Molecular cloning, tissue distribution, and expression in Escherichia coli. (1993)

We have recently purified a novel human serine proteinase inhibitor (serpin), designated as kallistatin, which binds to tissue kallikrein and inhibits kallikrein's kininogenase and amidolytic activities. In the present studies, we have cloned a full-length cDNA encoding kallistatin from human liver RNA by the polymerase chain reaction. The cDNA is 1284 base pairs in length and encodes 427 amino acid residues, including a 26-residue signal peptide and a 401-residue mature peptide. The translated amino acid sequence of kallistatin matches with the protein sequence and shares 44-46% sequence identity with human alpha 1-antichymotrypsin, protein C inhibitor, corticosteroid-binding globulin, alpha 1-antitrypsin, thyroxin-binding globulin, and rat kallikrein-binding protein. Kallistatin is a new member of the serpin superfamily with a unique reactive site P1-P1' of Phe-Ser. Four potential glycosylation sites are found in the translated amino acid sequence of kallistatin. In a Southern blot analysis following reverse transcription and polymerase chain reaction, kallistatin was found to be expressed in human liver, stomach, pancreas, kidney, aorta, testes, prostate, artery, atrium, ventricle, lung, renal proximal tubular cell, and a colonic carcinoma cell line T84. A genomic Southern blot using the full-length kallistatin cDNA probe revealed simple banding patterns suggesting the gene encoding kallistatin is single-copied. The kallistatin cDNA encoding the mature peptide was expressed in Escherichia coli. The recombinant kallistatin forms an SDS-stable complex with 125I-human tissue kallikrein and has a molecular mass of 40 kDa. The cloning of human kallistatin cDNA established the identity of the novel kallikrein inhibitor and its expression in a functional form in E. coli provides means for studying its structure-function relationship through protein engineering.
Experimental investigation of subharmonic generation in an acoustic interferometer (1975)

The author has shown previously [J. Acoust. Soc. Am. 49, 119(A) (1971)] that the nonlinear properties of the medium can induce coupling among the modes in a multiresonant system and that the threshold and steady-state response of subharmonic components can be predicted. In the present work, coupling induced by nonlinear properties is further illustrated by observing the subharmonic generation phenomenon in an acoustic interferometer. The experimental investigation was conducted with a 1.5-MHz driving signal and used filtered and degassed water as the medium. Data concerned with the actual modes of the interferometer, the loss factor associated with the subharmonic modes, and the threshold of subharmonic generation, with length of the interferometer and the driving frequency varying, are consistent with the analytic results, provided that cavitation is carefully avoided. Subject Classification: 25.15, 25.20; 30.75.