gebhart/patrepeval huggingface dataset:
A guide to the Proteomics Identifications Database proteomics data repository (2009)

The Proteomics Identifications Database (PRIDE, www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data. Here, we point out the main functionalities of PRIDE both as a submission repository and as a source for proteomics data. We describe the main features for data retrieval and visualization available through the PRIDE web and BioMart interfaces. We also highlight the mechanism by which tailored queries in the BioMart can join PRIDE to other resources such as Reactome, Ensembl or UniProt to execute extremely powerful across-domain queries. We then present the latest improvements in the PRIDE submission process, using the new easy-to-use, platform-independent graphical user interface submission tool PRIDE Converter. Finally, we speak about future plans and the role of PRIDE in the ProteomExchange consortium.
Thermally Induced Pulses in Magnetoresistive Heads (1974)

The thermal response of a magnetoresistive head is analyzed for frictional heating between the head surface and dust particles or other asperities on the recording medium surface during relative motion of head and medium. A theoretical model is presented showing that pulses are induced in the output of a magnetoresistive head as a result of this frictional heating. The model predicts the dependence of these noise spikes on the thermal properties of the substrate and cover chip for the magnetoresistive head, the dimensions of the magnetoresistive stripe, the head-medium relative velocity, and the rate of frictional heat generation. Experimental verification of the theoretical model is obtained by scanning a focused laser beam across a head.
Morphogenetic and toxin composition variability of Alexandrium tamarense (Dinophyceae) from the east coast of Russia (2007)

Abstract Twenty-seven clones were established from elongate Alexandrium sp. cysts collected in six regions along the Russian Pacific coast. All isolates were identified as Alexandrium tamarense via detailed epifluoresence microscopy of thecal plates. Morphological differences of both cultured and wild cells from the study regions mainly occurred in the shape of the cell (length/width ratio), degree of development of the sulcal list, and the shape of the posterior sulcal (S.p.) and second antapical (2″″) plates. Cells were divided into two cell types: ‘short’ (isodiametrical or wide) and ‘tall’. Each cell type exhibits specific features of tabulation, mainly the shape of the S.p. and 2″″ plates and was dominant in each particular region of the study. The short type, with a wide S.p. and reduced length in the dorsoventral 2″″ plates, was characteristic of A. tamarense from Primorye and southern Sakhalin Island. The tall cells, i.e., with cell length exceeding width, and having and elongate S.p. and dorsoven...
The Functions of Signal Transducers and Activators of Transcriptions 1 and 3 as Cytokine-Inducible Proteins (2010)

The signal transducers and activators of transcription (STAT)1 and STAT3 genes are specifically activated by phosphorylated STATs 1 and 3, respectively, resulting in large and prolonged increases in the levels of unphosphorylated STATs (U-STATs) in response to interferons (for STAT1) or ligands that activate gp130, such as IL-6 (for STAT3). U-STATs 1 and 3 are transcription factors that drive gene expression by mechanisms distinct from those used by phosphorylated STATs. U-STAT3 drives expression of many proteins not induced by phospho-STAT3, including several that are important in tumorigenesis. U-STAT1 prolongs and increases expression of a subset of proteins induced initially in response to phospho-STAT1, leading to antiviral and immune responses that are long-lived. U-STAT1 levels are also high in some cancers, and the protein products of genes induced by U-STAT1 enhance resistance to DNA damage. Therefore, interferons not only drive short-term expression of proteins that inhibit growth and promote apoptosis and immune surveillance, but also promote long-term expression of proteins that facilitate tumor survival.
Varicella-Zoster Virus Transfer to Skin by T Cells and Modulation of Viral Replication by Epidermal Cell Interferon-α (2004)

Primary infection with varicella-zoster virus (VZV) causes the characteristic syndrome of varicella, or chickenpox. Experiments in severe combined immunodeficiency mice with human skin grafts (SCIDhu mice) indicate that VZV infection of T cells can mediate transfer of infectious virus to skin. VZV-infected T cells reached epithelial sites of replication within 24 h after entering the circulation. Memory CD4+ T cells were the predominant population recovered from skin in SCIDhu mice given uninfected or infected mononuclear cells, suggesting that immune surveillance by memory T cells may facilitate VZV transfer. The increased susceptibility of memory T cells to VZV infection may further enhance their role in VZV pathogenesis. During VZV skin infection, viral gene products down-regulated interferon-alpha to permit focal replication, whereas adjacent epidermal cells mounted a potent interferon-alpha response against cell-cell spread. Interleukin-1alpha, although activated in VZV-infected cells, did not trigger expression of endothelial adhesion molecules, thereby avoiding early recruitment of inflammatory cells. The prolonged varicella incubation period appears to represent the time required for VZV to overcome antiviral responses of epidermal cells and generate vesicles at the skin surface. Modulation of VZV replication by cutaneous innate immunity may avoid an incapacitating infection of the host that would limit opportunities for VZV transmission.
Uncovering the missing data in the gas cloud with P-P wave imaging: The first deepwater OBN survey from Southeast Asia (2018)

The presence of gas in the overburden challenges significantly the seismic imaging process, also affecting deeper targets at the reservoir level. The challenges include complex wave kinematics, variable illumination, and the loss of signal strength and frequency bandwidth. A comprehensive strategy is required to overcome these challenges and achieve step-change improvements in the final seismic images. We present a case study from a challenging deep-water oil field in Southeast Asia. The project consisted of acquisition, processing, interpretation, and QI groups working as an integrated team to meet the project objectives. The project utilized a multifaceted approach of combining ocean-bottom node seismic data, optimizing preprocessing, building a high-resolution earth model, and using high-end imaging techniques to significantly improve the overall quality of the seismic image beneath the large bodies of gas hydrates, clouds, and free gas. The new data allow improved structural and stratigraphic interpretation, providing a better understanding of the reservoir model, and reducing the uncertainty related to the reservoir volume, connectivity, and compartmentalization, thereby contributing significantly to the geological understanding of the field and influencing future development decisions. Presentation Date: Thursday, October 18, 2018 Start Time: 8:30:00 AM Location: 204C (Anaheim Convention Center) Presentation Type: Oral
Factors Affecting the Performance of 5 Cerebral Oximeters During Hypoxia in Healthy Volunteers (2013)

While responsive to desaturation, cerebral oximeters exhibited large variation in reading errors between subjects, with mean bias possibly related to variations in the ratio of arterial and venous blood in the sampling area of the brain. This ratio is probably not fixed, as assumed by the manufacturers, but dynamically changes with hypoxia. Better understanding these factors could improve the performance of cerebral oximeters and help establish saturation or blood flow thresholds for brain well-being.
Structure of the peptide network of pneumococcal peptidoglycan. (1987)

The peptide network of Streptococcus pneumoniae cell walls was solubilized using the pneumococcal autolytic amidase (N-acetylmuramoyl-L-alanine amidase, EC 3.5.1.28). The peptide material was fractionated into size classes by gel filtration followed by reverse-phase high-performance liquid chromatography which resolved the peptide population into over 40 fractions. About 40% of the lysines present participate in cross-links between stem peptides. The main components (3 monomers, 5 dimers, and 2 trimers), accounting for 77% of all the wall peptides, were purified. Their structures were determined using a combination of amino acid and end-group analysis, mass spectrometry, and gas-phase sequencing. Two different types of cross-links between stem peptides were found. In the most abundant type there is an alanylserine cross-bridge between the alanine in position 4 of the donor stem peptide and the lysine at position 3 of the acceptor peptide, as in type A3 peptidoglycan. In the second type of cross-link there is no intervening cross-bridge, as in the type A1 peptidoglycan of Gram-negative bacteria. The data indicate that pneumococcal peptidoglycan has a structural complexity comparable to that recently shown in some Gram-negative species.
Targeting of murine radiolabeled monoclonal antibodies in the lymphatics. (1987)

The tissue localization of a radiolabeled monoclonal antibody directed against a mouse Class I major histocompatibility antigen has been determined in mice following i.v. and s.c. administration. When labeled antibody was given s.c., radioactivity rapidly accumulated in regional lymph nodes draining the injection site, allowing visualization of the nodes by gamma camera imaging within minutes of injection. At 2 h after s.c. injection, radioactivity in regional nodes was present largely as intact antibody, but considerable degradation of antibody present in nodes was noted by 12 h after injection. Since little of the radioactivity reached the blood stream, visualization of regional nodes was possible for long periods after dosing. In contrast, antibody given i.v. showed no significant accumulation in lymph nodes at any time after dosing.
How to Measure Diffusion Coefficient of Biomolecules in Living Cells (2009)

It is quite important to understand behavior of biomolecules in terms of the diffusion coefficient inside live cells since the diffusion speed of biomolecules sometimes affects the result of chemical reactions with downstream target molecules. Here, we introduce several technologies to measure diffusion coefficient of biomolecules in living cells, and discuss about biological meaning of diffusion measurement analysis.
An analysis of error inducing parameters in multihop sensor node localization (2005)

Ad hoc localization of wireless sensor nodes is a fundamental problem in wireless sensor networks. Despite the recent proposals for the development of ad hoc localization algorithms, the fundamental behavior in systems using measurements has not been characterized. In this paper, we take a first step toward such a characterization by examining the behavior of error inducing parameters in multihop localization systems in an algorithm independent manner. We first derive the Crame Rao Bound for Gaussian measurement error for multihop localization systems using distance and angular measurements. Later on, we use these bounds on a carefully controlled set of scenarios to study the trends in the error induced by the measurement technology accuracy, network density, beacon node concentration, and beacon uncertainty. By exposing these trends, the goal of this paper is to develop a fundamental understanding of the error behavior that can provide a set of guidelines to be considered during the design and deployment of multihop localization systems.
Spontaneous parametric down-conversion in waveguides: A backward Heisenberg picture approach (2008)

We develop a fully quantum-mechanical approach for the description of spontaneous parametric down-conversion in waveguides. Our method allows us to write an expression for the quantum state easily and directly, even when multiple photon pairs are generated in the process. The role of material dispersion in the normalization of the modes of the system, usually neglected, is properly treated here. The example of an ${\text{Al}}_{y}{\text{O}}_{x}/{\text{Al}}_{0.5}{\text{Ga}}_{0.5}\text{As}$ ridge waveguide is discussed to illustrate the application of the formalism.
Evaluation of substrates for use on a piezoelectric detector for sulfur dioxide (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEvaluation of substrates for use on a piezoelectric detector for sulfur dioxideMichael W. Frechette, James L. Fasching, and Douglas M. RosieCite this: Anal. Chem. 1973, 45, 9, 1765–1766Publication Date (Print):August 1, 1973Publication History Published online1 May 2002Published inissue 1 August 1973https://pubs.acs.org/doi/10.1021/ac60331a037https://doi.org/10.1021/ac60331a037research-articleACS PublicationsRequest reuse permissionsArticle Views30Altmetric-Citations17LEARN 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
Fluidized‐bed heat transfer: A generalized dense‐phase correlation (1956)

Abstract A fluidized‐bed heat transfer mechanism is proposed that assumes that the chief resistance to heat exchange between a confining wall and a fluidized bed is in the laminar film at the vessel boundary. Heat flow through the film is by conduction. As the solids‐particle velocity along the wall will modify film thickness, correlation of film coefficients in terms of particle velocities or the equivalent suggests itself. That heat transport from the boundary of the heating element to the fluidized core proceeds by way of turbulent solids mixing seems indicated by the considerable effect that the solids heat capacity appears to exert on over‐all coefficients. The resulting correlation is examined critically in relation to pertinent literature data. The effect of fluidized‐bed parameters on heat transfer coefficients is considered, and applicability and limits of the correlation are ascertained.
Strongly Phosphorescent Iridium(III)–Porphyrins – New Oxygen Indicators with Tuneable Photophysical Properties and Functionalities (2011)

Synthesis and characterization of four iridium(III)-octaethylporphyrins and a π-extended iridium(III)-benzoporphyrin are presented. Strong room-temperature phosphorescence was observed for all of the complexes with quantum yields of up to 30 %. Axial ligands were introduced to tune the photophysical properties and the solubility. Complexes bearing lipophilic ligands such as pyridine or N-(n-butyl)imidazole were incorporated into polystyrene to obtain optical oxygen sensors. Covalent coupling of the dye is possible by introduction of ligands with binding domains (1-imidazoleacetic acid). This enabled preparation of a water-soluble oxygen probe (by staining bovine serum albumin) and a trace oxygen sensor (by coupling to amino-modified silica gel).
Purification and characterization of VanR and the cytosolic domain of VanS: A two-component regulatory system required for vancomycin resistance in Enterococcus faecium BM4147 (1993)

Resistance to the glycopeptide antibiotic vancomycin requires five genes. Two of these, vanR and vanS, have sequence homology to cytoplasmic response regulatory (VanR) and transmembrane sensory (VanS) proteins of two-component regulatory systems used to sense and transduce environmental signals. We report the overproduction and purification to homogeneity of VanR (27 kDa) and of a fusion protein of VanS (residues 95-374, the cytosolic domain) to the maltose binding protein (MBP), yielding a MBP-VanS protein of 76 kDa. The MBP-VanS fusion protein displayed an ATP-dependent autophosphorylation on a histidine residue with a rate of 0.17 min-1 and a phosphorylation stoichiometry of 10-15%. 32P-PhosphoMBP-VanS transferred the phosphoryl group to VanR. 32P-Phospho VanR showed chemical stability anticipated for an aspartyl phosphate and was relatively stable to hydrolysis (t1/2 = 10-12 h). Thus, the vancomycin resistance operon appears to have collected and specifically tailored the His kinase and Asp phosphoryl receptor of two-component signal transduction logic for sensing extracellular vancomycin and turning on structural genes, vanA and vanH, to make altered peptidoglycan structures such that vancomycin does not bind.
Experimental analysis and parameter optimization of pdc bit for rock drilling trolley (2019)

Abstract The design parameters of PDC bits for rock drilling trolley have not been studied in depth and it is lack of theoretical research basis. So the service life of the bits for tunnel tunneling construction cannot meet the design and application requirements. Taking three-arm rock drilling trolley as the experimental platform, the key parameters of PDC bit crown profile shape, caster angle, cutting tooth size, tooth arrangement density, inner cone angle, outer swing angle and crown top shape for rock drilling trolley are designed by combining the optimum design method, empirical numerical value and experimental correction. The key parameters were optimized and improved through a set of manufactured bits, and a set of drills were manufactured again for the following experiment. The experimental data in second stage shows that the broken and drop defects of the improved bits are greatly reduced. The drilling depth is significantly increased, and the service life is also improved, which meets the requirements of design and operation.
Computer operation via face orientation (2003)

Computer operation via face orientation provides a means of communication for people with severe physical disability. The authors present a near-real-time computer system to track the eyes and the nose of a subject and compute the direction of the face. As presented by K. Ohmura et al. (1988), the direction can be computed from three natural feature points extracted from the face. The computational approach taken in this system is motivated by the practical requirements of near-real-time performance and accuracy. The approach is based on the reflection characteristic of the cornea. Any bright light source forms a twinkle in the eye that is fixed as long as the light source is fixed. Face direction detection is treated as a 2D tracking problem. The eye twinkles are extracted from the image and used to locate the nose. A final experiment shows that the face direction obtained from the three feature points is precise enough to control the mouse cursor to make selection from a menu with large light buttons.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A &#x003E; 89% efficient LED driver with 0.5V supply voltage for applications requiring low average current (2013)

A modified boost converter topology is proposed to achieve better than 89% efficiency as an LED driver for applications in which low supply voltage and low average current are desired such as in a photoplethysmographic (PPG) heart rate (HR) monitor device. The approach embraces pulsing of the LED current, and allows a highly digital implementation for varying LED brightness based on Pulse Density Modulation (PDM). Measured results indicate that the LED driver, which is implemented in 180nm CMOS along with an external inductor, achieves an output current range of 28uA to 1.3mA with 6 current settings while maintaining >89% efficiency over a supply voltage range of 0.5 to 0.6V.
Dynamic Behavior of Labyrinth Seals in Oilfree Labyrinth-Piston Compressors (1984)

After a brief introduction to the basic principles of the labyrinth com~ressor, 3 sections are devoted to discuss~ng various cylinder results from research into labyrinth flow and its effects on the oscillatable piston/piston rod system.The lst section describes theoretical studies on labyrinth flow.Computed results derived from dynamic flow processes in a cylindrical labyrinth display good coincidence with the measured results.The theoretical gas pressure and temperature histories in the labyrinth and the gas loss quantities entailed are illustrated.
Polymers with pendant isocyanate groups. II. Dual synthesis and properties of poly(acrylonitrile-co-styryl isocyanate) (1976)

The copolymer poly(acrylonitrile-co-styryl isocyanate) was prepared directly in bulk by radical initiation either from the monomer pair acrylonitrile–cinnamoyl azide or from the pair acrylonitrile–styryl isocyanate. The copolymerization parameters, calculated by the conventional scheme, are r1, = 3.5 ± 0.5; r2 = 0 ± 0.5, for the first pair and r1 = 9 ± 0.5; r2 = 0 ± 0.5 for the second pair. The basic physical properties (solubility, intrinsic viscosity, and thermal behavior) of the new copolymer were determined and the chemical reactions of the isocyanate group with alcohol and with dimethylformamide were investigated.
Effects of <scp>M</scp>1 and <scp>M</scp>4 activation on excitatory synaptic transmission in <scp>CA</scp>1 (2017)

Abstract Hippocampal networks are particularly susceptible to dysfunction in many neurodegenerative diseases and neuropsychiatric disorders including Alzheimer's disease, Lewy body dementia, and schizophrenia. CA1, a major output region of the hippocampus, receives glutamatergic input from both hippocampal CA3 and entorhinal cortex, via the Schaffer collateral (SC) and temporoammonic (TA) pathways, respectively. SC and TA inputs to CA1 are thought to be differentially involved in the retrieval of previously stored memories versus the encoding of novel information, and switching between these two crucial hippocampal functions is thought to critically depend on acetylcholine (ACh) acting at muscarinic receptors. In this study, we aimed to determine the roles of specific subtypes of muscarinic receptors in mediating the neuromodulatory effects of ACh on glutamatergic synaptic transmission in the SC and TA pathways of CA1. Using selective pharmacological activation of M1 or M4 receptors along with extracellular and intracellular electrophysiology recordings from adult rat hippocampal slices, we demonstrate that activation of M1 receptors increases spontaneous spike rates of neuronal ensembles in CA1 and increases the intrinsic excitability of pyramidal neurons and interneurons. Selective activation of M4 receptors inhibits glutamate release in the SC pathway, while leaving synaptic transmission in the TA pathway comparatively intact. These results suggest specific mechanisms by which M1 and M4 activation may normalize CA1 circuit activity following disruptions of signaling that accompany neurodegenerative dementias or neuropsychiatric disorders. These findings are of particular interest in light of clinical findings that xanomeline, an M1/M4 preferring agonist, was able to improve cognitive and behavioral symptoms in patients with Alzheimer's disease or schizophrenia.