gebhart/patrepeval huggingface dataset:
Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing (2016)

Escherichia coli strains are classified based on O-antigens that are components of the lipopolysaccharide (LPS) in the cell envelope. O-antigens are important virulence factors, targets of both the innate and adaptive immune system, and play a role in host-pathogen interactions. Because they are highly immunogenic and display antigenic specificity unique for each strain, O-antigens are the biomarkers for designating O-types. Immunologically, 185 O-serogroups and 11 OX-groups exist for classification. Conventional serotyping for O-typing entails agglutination reactions between the O-antigen and antisera generated against each O-group. The procedure is labor intensive, not always accurate, and exhibits equivocal results. In this report, we present the sequences of 71 O-antigen gene clusters (O-AGC) and a comparison of all 196 O- and OX-groups. Many of the designated O-types, applied for classification over several decades, exhibited similar nucleotide sequences of the O-AGCs and cross-reacted serologically. Some O-AGCs carried insertion sequences and others had only a few nucleotide differences between them. Thus, based on these findings, it is proposed that several of the E. coli O-groups may be merged. Knowledge of the O-AGC sequences facilitates the development of molecular diagnostic platforms that are rapid, accurate, and reliable that can replace conventional serotyping. Additionally, with the scientific knowledge presented, new frontiers in the discovery of biomarkers, understanding the roles of O-antigens in the innate and adaptive immune system and pathogenesis, the development of glycoconjugate vaccines, and other investigations, can be explored.
The Id gene is activated by serum but is not required for de-differentiation in rat vascular smooth muscle cells (1991)

Primary rat vascular smooth muscle cells cultured on fibronectin in the absence of serum lost smooth-muscle-specific myosin heavy chain but did not enter the cell cycle and proliferate until they were stimulated by serum. Under these conditions accumulation of Id mRNA occurred only in response to serum and was maximal during the G1 phase of the cycle.
Immune Response in Patients With Newly Diagnosed Glioblastoma Multiforme Treated With Intranodal Autologous Tumor Lysate-dendritic Cell Vaccination After Radiation Chemotherapy (2011)

Patients with glioblastoma multiforme (GBM) are profoundly immunosuppressed and may benefit from restoration of an antitumor immune response in combination with conventional radiation therapy and temozolomide (TMZ). The optimal strategies to evaluate clinically relevant immune responses to treatment have yet to be determined. The primary objective of our study was to determine immunologic response to cervical intranodal vaccination with autologous tumor lysate-loaded dendritic cells (DCs) in patients with GBM after radiation therapy and TMZ. We used a novel hierarchical clustering analysis of immune parameters measured before and after vaccination. Secondary objectives were to assess treatment feasibility and to correlate immune response with progression-free survival (PFS) and overall survival. Ten eligible patients received vaccination. Tumor-specific cytotoxic T-cell response measured after vaccination was enhanced for the precursor frequency of CD4+ T and CD4+ interferon γ-producing cells. Hierarchical clustering analysis of multiple functional outcomes discerned 2 groups of patients according to their immune response, and additionally showed that patients in the top quintile for at least one immune function parameter had improved survival. There were no serious adverse events related to DC vaccination. All patients were alive at 6 months after diagnosis and the 6-month PFS was 90%. The median PFS was 9.5 months and overall survival was 28 months. In patients with GBM, immune therapy with DC vaccination after radiation and TMZ resulted in tumor-specific immune responses that were associated with prolonged survival. Our data suggest that DC vaccination in combination with radiation and chemotherapy in patients with GBM is feasible, safe, and may induce tumor-specific immune responses.
Evolving therapeutic targets in renal cell carcinoma (2013)

The number of approved treatments for advanced RCC continues to grow, but additional work is needed to further delineate the optimal drug, combination of agents, or sequence best suited to each subtype of RCC.
Nanopore Fabrication by Controlled Dielectric Breakdown (2014)

Nanofabrication techniques for achieving dimensional control at the nanometer scale are generally equipment-intensive and time-consuming. The use of energetic beams of electrons or ions has placed the fabrication of nanopores in thin solid-state membranes within reach of some academic laboratories, yet these tools are not accessible to many researchers and are poorly suited for mass-production. Here we describe a fast and simple approach for fabricating a single nanopore down to 2-nm in size with sub-nm precision, directly in solution, by controlling dielectric breakdown at the nanoscale. The method relies on applying a voltage across an insulating membrane to generate a high electric field, while monitoring the induced leakage current. We show that nanopores fabricated by this method produce clear electrical signals from translocating DNA molecules. Considering the tremendous reduction in complexity and cost, we envision this fabrication strategy would not only benefit researchers from the physical and life sciences interested in gaining reliable access to solid-state nanopores, but may provide a path towards manufacturing of nanopore-based biotechnologies.
Focal reversible deactivation of cerebral metabolism affects water diffusion (2008)

The underlying biophysical mechanisms which affect cerebral diffusion contrast remain poorly understood. We hypothesized that cerebral metabolism may affect cerebral diffusion contrast. The purpose of this study was to develop the methodology to reversibly deactivate cerebral metabolism and measure the effect on the diffusion MRI signal. We developed an MRI-compatible cortical cooling system to reversibly deactivate cortical metabolism in rhesus monkey area V1 and used MR thermometry to calculate three-dimensional temperature maps of the brain to define the extent of deactivated brain in vivo. Significant changes in the apparent diffusion coefficient (ADC) were only observed during those experiments in which the cortex was cooled below the metabolic cutoff temperature of 20 degrees C. ADC decreases (12-20%) were observed during cortical cooling in regions where the temperature did not change. The normalized in vivo ADC as function of temperature was measured and found to be equivalent to the normalized ADC of free water at temperatures above 20 degrees C, but was significantly decreased below 20 degrees C (20-25% decrease). No changes in fractional anisotropy were observed. In future experiments, we will apply this methodology to quantify the effect of reversible deactivation on neural activity as measured by the hemodynamic response and compare water diffusion changes with hemodynamic changes.
Fast texture synthesis using tree-structured vector quantization (2000)

Texture synthesis is important for many applications in computer graphics, vision, and image processing. However, it remains difficult to design an algorithm that is both efficient and capable of generating high quality results. In this paper, we present an efficient algorithm for realistic texture synthesis. The algorithm is easy to use and requires only a sample texture as input. It generates textures with perceived quality equal to or better than those produced by previous techniques, but runs two orders of magnitude faster. This permits us to apply texture synthesis to problems where it has traditionally been considered impractical. In particular, we have applied it to constrained synthesis for image editing and temporal texture generation. Our algorithm is derived from Markov Random Field texture models and generates textures through a deterministic searching process. We accelerate this synthesis process using tree-structured vector quantization.
Spatiotemporal Periodicity During Atrial Fibrillation in the Isolated Sheep Heart (1998)

Reentry in anatomically or functionally determined circuits forms the basis of spatiotemporal periodic activity during AF. The cycle length of sources in the LA determines the dominant peak in the frequency spectra in this experimental model of AF.
A simple procedure for maximum yield of high-quality plasmid DNA. (1990)

We have established a simple procedure for the rapid isolation of high-quality plasmid DNA suitable for various molecular techniques and provided a step-by-step protocol. The DNA samples isolated by this procedure have been used successfully for double-stranded DNA sequencing, restriction enzyme mapping, subcloning, in vitro mutagenesis, generation of deletion clones and so on. The procedure is highly reproducible, and superior quality DNA can be obtained without the use of phenol, chloroform or other organic solvents.
Mapping the Optical Properties of CdSe/CdS Heterostructure Nanocrystals: The Effects of Core Size and Shell Thickness (2009)

Here we present the first comprehensive report on CdSe/CdS heterostructure nanocrystals. The effects of core size and shell thickness on the optical properties of CdSe/CdS heterostructure nanocrystals are investigated. We report a reliable synthetic method to grow thick CdS shells on CdSe cores with sizes ranging from 2.5-4.7 nm. We provide a calibration curve, which enables determination of CdS shell thickness (+/-0.1 nm) over a wide range of core sizes, circumventing the need for time-consuming HRTEM analyses. Epitaxial growth of the shells was verified by HRTEM, XRD, and SAED. In-situ reaction measurements revealed the average per particle (p) deposition rates for cadmium and sulfur to be k(Cd) = 5.38 x 10(-25) mol s(-1) p(-1) and k(S) = 4.83 x 10(-24) mol s(-1) p(-1). Faster sulfur deposition rates are attributed to the absence of strong sulfur binding ligands in the growth medium. Through the rigorous use of high resolution transmission electron microscopy, a direct link between the dimensions of the heterostructures and their band-edge transition energies, quantum yields, and excited state lifetimes is established. The experiments show that the band-edge transition energies of the core samples, which initially span approximately 431 meV, condense to span only 163 meV after the growth of a 6 monolayer-thick CdS shell. Furthermore, shifts in the band-edge transition energies were found to be extremely sensitive to core size. The QY of the as-prepared core/shells ranged from 25 to 60%. The QYs and band-edge lifetimes of the core/shells were found to depend upon the ligands adsorbed to the particle surface. These data prove that one or both of the charge carriers still has access to the particle surface despite the presence of a 2.2 nm thick CdS shell.
Single-Crystal-like Materials by the Self-Assembly of Cube-Shaped Lead Zirconate Titanate (PZT) Microcrystals (2005)

We demonstrated the formation of single-crystal-like materials that contain preferentially oriented arrays of lead zirconate titanate (PZT) cube-shaped particles by self-assembly. Hydrothermally synthesized PZT particles with a bulk composition of Zr/Ti = 70/30 were used in making microcrystal arrays. Spreading a suspension containing PZT cube-shaped particles, 2-propanol, and mineral oil at the air-water interface produced a one-dimensional planar array of PZT particles on the water surface. The array so formed was subsequently transferred onto a flat or curved substrate. X-ray diffraction and electron backscattered diffraction analyses revealed that most of the cube-shaped particles in the array were oriented with their pseudocubic (001) direction aligned parallel to the normal direction of the substrate surface. Filling the arrays with matrixes produced monolayer or multilayer textured composites. The piezoelectric properties of oriented cube-shaped micron-sized particles in the self-assembled arrays were measured using a modified atomic force microscope to reveal the ferroelectric nature of the PZT arrays.
Twenty years of investigating angiotensin activity: an overview. (1991)

A short account of the renin-angiotensin-aldosterone system is given with emphasis on the relationship between the octapeptide angiotensin II and its decapeptide precursor angiotensin I. Although the decapeptide is generally assumed to have no biological activity, extensive investigations have indicated that such an assumption is almost certainly unjustified. The implications of the findings are briefly outlined and discussed.
Determination of the depth of bromine atoms in bilayers formed from bromolipid probes (1987)

X-ray diffraction analysis has been performed on a series of 1-palmitoyl-2-dibromostearoyl-phosphatidylcholines (BRPCs) with bromine atoms at the 6, 7-, the 11, 12-, or the 15, 16-positions on the sn-2 acyl chains. The diffraction patterns indicate that, when hydrated, each of these lipids forms liquid-crystalline bilayers at 20 degrees C. For each lipid, electron density profiles and continuous Fourier transforms were calculated by the use of swelling experiments. In the electron profiles, high-density peaks, due to the bromine atoms, are observed. The separation between these bromine peaks in the profile decreases as the bromine atoms are moved toward the terminal methyl of the acyl chain. For the 6, 7- and 11, 12-bromolipids, experimental Fourier transforms can be approximated by the sum of the transform of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and the transform of two symmetrically placed peaks of electron density (the bromines). For the case of the 15, 16-bromolipids, a better fit is obtained for the transforms of a model bilayer where the thickness of the methylene chain region of the bilayer is 3 A greater than that of POPC. Our analysis indicates the following: for each of these bromolipids, the bromines are well localized in the bilayer; the distance of the bromines from the head-group-hydrocarbon boundary are 3.5, 8.0, and 14 A, for 6, 7-, 11, 12-, and 15, 16-BRPC, respectively; the bilayer thickness and perturbation to bilayer hydrocarbon chain packing caused by the bromine atoms depend on the position of the bromines on the hydrocarbon chain.
A Strategy for the Chemoselective Synthesis of O-Linked Glycopeptides with Native Sugar−Peptide Linkages (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Strategy for the Chemoselective Synthesis of O-Linked Glycopeptides with Native Sugar−Peptide LinkagesElena C. Rodriguez, Katharine A. Winans, David S. King, and Carolyn R. BertozziView Author Information Department of Chemistry and Howard Hughes Medical Institute University of California, Berkeley, California 94720 Cite this: J. Am. Chem. Soc. 1997, 119, 41, 9905–9906Publication Date (Web):October 15, 1997Publication History Received20 May 1997Published online15 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/ja971633phttps://doi.org/10.1021/ja971633prapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1285Altmetric-Citations92LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aldehydes,Ligation,Monomers,Oligosaccharides,Peptides and proteins Get e-Alerts
Simultaneous glycoproteomics on the basis of structure using ion mobility-mass spectrometry (2009)

Simultaneous glycoproteomic characterization using rapid (mus to ms) structural separations provided by ion mobility-mass spectrometry (IM-MS) is described. Advantages from using both ESI and MALDI ion sources are presented with future implications toward high throughput glycan and glycoconjugate characterization.
Characteristics of Articular Chondrocytes Seeded in Collagen Matrices in Vitro (1998)

This study directly compared the behavior of adult human and canine and young bovine (calf) chondrocytes in porous type I and II collagen matrices. Certain characteristics of the cells varied among these groups, with the calf cells being relatively heterogeneous. There was a similar trend, however, in the behavior of the cells in the matrices with a majority of the cells in the type II sponge retaining their chondrocytic characteristics. Collagen production by chondrocytes in matrices, as assessed by SDS-PAGE, also varied with the chemistry of the matrix.
Planar Concave Grating Demultiplexer on a Nanophotonic Silicon-on-Insulator Platform (2006)

We present measurement results of a 4-channel silicon-on-insulator grating demultiplexer fabricated in a CMOS line. It has an ultra-small footprint of 280times150 mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , 20 nm channel spacing, on-chip loss of 7.5 dB and crosstalk of better than -30 dB
High mobility group A2 is a target for miRNA-98 in head and neck squamous cell carcinoma (2007)

These studies validate the observation that HMGA2 plays a prominent role in governing genotoxic responses. However, this may only represent cells growing under normal oxygen tensions. The demonstration that miRNA profiles are altered during hypoxia and repress a genotoxic response indicates that changes in microenvironment in eukaryotes mimic those of lower species and plants, where, for example, abiotic stresses regulate the expression of thousands of genes in plants at both transcriptional and posttranscriptional levels through a number of miRNAs and other small regulatory RNAs.
Activation of Lysosomal Function During Dendritic Cell Maturation (2003)

In response to a variety of stimuli, dendritic cells (DCs) transform from immature cells specialized for antigen capture into mature cells specialized for T cell stimulation. During maturation, the DCs acquire an enhanced capacity to form and accumulate peptide-MHC (major histocompatibility complex) class II complexes. Here we show that a key mechanism responsible for this alteration was the generalized activation of lysosomal function. In immature DCs, internalized antigens were slowly degraded and inefficiently used for peptide loading. Maturation induced activation of the vacuolar proton pump that enhanced lysosomal acidification and antigen proteolysis, facilitating efficient formation of peptide-MHC class II complexes. Lysosomal function in DCs thus appears to be specialized for the developmentally regulated processing of internalized antigens.
Involvement of p21Waf1 in mediating inhibition of paclitaxel-induced apoptosis by epidermal growth factor in MDA-MB-468 human breast cancer cells. (2000)

Paclitaxel (Taxol) is currently one of the most widely used anti-cancer drugs for human breast cancer. In this study, we investigated how epidermal growth factor (EGF) modulated paclitaxel-induced apoptosis in MDA-MB-468 human breast adenocarcinoma cells. Pulse-exposure of the cells to paclitaxel resulted in cell death through apoptosis. When EGF was present during the post-paclitaxel culture period, this paclitaxel-induced apoptosis was inhibited in an EGF dose-dependent manner. The induction of apoptosis by paclitaxel was accompanied by an elevated level of p34cdc2 kinase activity, which was inhibited in the presence of EGF during the post-paclitaxel culture period. Exposure of MDA-MB-468 cells to EGF induced expression of the cyclin-dependent kinase inhibitor p21Waf1. Incubation of paclitaxel-treated MDA-MB-468 cell extracts with EGF-treated MDA-MB-468 cell extract, which exhibited elevation of p34cdc2 activity, inhibited the kinase activity. This inhibition was not observed with p21Waf1-immunodepleted EGF-treated cell extract. Transfection of the cells with p21Waf1 antisense oligonucleotide abolished the induction of p21Waf1 and also significantly reduced inhibition by EGF of paclitaxel-induced apoptosis. These studies demonstrate that p21Waf1 plays a key role in the inhibition of paclitaxel-induced apoptosis by EGF in MDA-MB-468 cells.
Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity (2006)

In animals, most small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II (Pol II), but U6 snRNA is synthesized by RNA polymerase III (Pol III). In Drosophila melanogaster, the promoters for the Pol II-transcribed snRNA genes consist of approximately 21 bp PSEA and approximately 8 bp PSEB. U6 genes utilize a PSEA but have a TATA box instead of the PSEB. The PSEAs of the two classes of genes bind the same protein complex, DmSNAPc. However, the PSEAs that recruit Pol II and Pol III differ in sequence at a few nucleotide positions that play an important role in determining RNA polymerase specificity. We have now performed a bioinformatic analysis to examine the conservation and divergence of the snRNA gene promoter elements in other species of insects. The 5' half of the PSEA is well-conserved, but the 3' half is divergent. Moreover, within each species positions exist where the PSEAs of the Pol III-transcribed genes differ from those of the Pol II-transcribed genes. Interestingly, the specific positions vary among species. Nevertheless, we speculate that these nucleotide differences within the 3' half of the PSEA act similarly to induce conformational alterations in DNA-bound SNAPc that result in RNA polymerase specificity.
An effective photoplethysmography signal processing system based on EEMD method (2015)

This study proposed an effective signal processing system based on Ensemble Empirical Mode Decomposition (EEMD) method for the analysis of Photoplethysmography (PPG). The whole system was implemented on an ARM-based SoC development platform to attain the on-line non-stationary signal processing. A non-invasive near-infrared light sensing device was used to record the continuous PPG as the input signal. According to the non-stationary characteristics of PPG, EEMD is useful to achieve accurate analysis for PPG. The signal was decomposed into several Intrinsic Mode Functions (IMFs) by EEMD. The results showed that the proposed EEMD processor can effectively solve the mode mixing problem of Empirical Mode Decomposition (EMD). This study examined its possibility based on specific architecture with an on-board Xilinx FPGA. It was helpful for non-stationary biomedical signal processing and cardiovascular diseases research.
Cytokine profile in Behçet's disease patients (2002)

Our results suggest that the microenvironment of CD4+ T cells in active BD may induce the production of more cells committed to Th1 than in BD patients in remission and healthy controls.