gebhart/patrepeval huggingface dataset:
Systems Proteomics for Translational Network Medicine (2012)

Universal principles underlying network science, and their ever-increasing applications in biomedicine, underscore the unprecedented capacity of systems biology based strategies to synthesize and resolve massive high throughput generated datasets. Enabling previously unattainable comprehension of biological complexity, systems approaches have accelerated progress in elucidating disease prediction, progression, and outcome. Applied to the spectrum of states spanning health and disease, network proteomics establishes a collation, integration, and prioritization algorithm to guide mapping and decoding of proteome landscapes from large-scale raw data. Providing unparalleled deconvolution of protein lists into global interactomes, integrative systems proteomics enables objective, multi-modal interpretation at molecular, pathway, and network scales, merging individual molecular components, their plurality of interactions, and functional contributions for systems comprehension. As such, network systems approaches are increasingly exploited for objective interpretation of cardiovascular proteomics studies. Here, we highlight network systems proteomic analysis pipelines for integration and biological interpretation through protein cartography, ontological categorization, pathway and functional enrichment and complex network analysis.
Cell trafficking alterations caused by the H. pylori VacA toxin (2000)

Conference Abstract| October 01 2000 Cell trafficking alterations caused by the H. pylori VacA toxin M. de Bernard; M. de Bernard 1Centra CNR Biomembrane and Dipartimento di Scienze Biomediche, Università di Padova and CHIRON-Vaccines, Siena, Italy Search for other works by this author on: This Site PubMed Google Scholar W. Dundon; W. Dundon 1Centra CNR Biomembrane and Dipartimento di Scienze Biomediche, Università di Padova and CHIRON-Vaccines, Siena, Italy Search for other works by this author on: This Site PubMed Google Scholar C. MONTECUCCO; C. MONTECUCCO 1Centra CNR Biomembrane and Dipartimento di Scienze Biomediche, Università di Padova and CHIRON-Vaccines, Siena, Italy Search for other works by this author on: This Site PubMed Google Scholar M. Moschioni; M. Moschioni 1Centra CNR Biomembrane and Dipartimento di Scienze Biomediche, Università di Padova and CHIRON-Vaccines, Siena, Italy Search for other works by this author on: This Site PubMed Google Scholar E. Papini; E. Papini 1Centra CNR Biomembrane and Dipartimento di Scienze Biomediche, Università di Padova and CHIRON-Vaccines, Siena, Italy Search for other works by this author on: This Site PubMed Google Scholar R. Rappuoli; R. Rappuoli 1Centra CNR Biomembrane and Dipartimento di Scienze Biomediche, Università di Padova and CHIRON-Vaccines, Siena, Italy Search for other works by this author on: This Site PubMed Google Scholar M. Zoratti M. Zoratti 1Centra CNR Biomembrane and Dipartimento di Scienze Biomediche, Università di Padova and CHIRON-Vaccines, Siena, Italy Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (2000) 28 (5): A117. https://doi.org/10.1042/bst028a117a Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation M. de Bernard, W. Dundon, C. MONTECUCCO, M. Moschioni, E. Papini, R. Rappuoli, M. Zoratti; Cell trafficking alterations caused by the H. pylori VacA toxin. Biochem Soc Trans 1 October 2000; 28 (5): A117. doi: https://doi.org/10.1042/bst028a117a Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 2000 Biochemical Society2000 Article PDF first page preview Close Modal You do not currently have access to this content.
Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort (2020)

This study provides further evidence that baseline cellular and molecular characteristics of an individual's immune system influence vaccine responses, and highlights the utility of integrating information across many parallel molecular datasets.
Precipitation and Deposition of Aluminum-Containing Species in Tank Wastes (2002)

Aluminum-containing phases represent the most prevalent solids that can appear or disappear during the processing of radioactive tank wastes. Processes such as sludge washing and leaching are designed to dissolve Al-containing phases and thereby minimize the volume of high-level waste glass required to encapsulate radioactive sludges. Unfortunately, waste-processing steps that include evaporation can involve solutions that are supersaturated with respect to cementitious aluminosilicates that result in unwanted precipitation and scale formation. Of all the constituents of tank waste, limited solubility cementitious aluminosilicates have the greatest potential for clogging pipes and transfer lines, fouling highly radioactive components such as ion exchangers, and completely shutting down processing operations. For instance, deposit buildup and clogged drain lines experienced during the tank waste volume-reduction process at the Savannah River Site (SRS) required an evaporator to be shut down in October 1999. The Waste Processing Technology Section of Westinghouse Savannah River Company at SRS now is collaborating with team members from Pacific Northwest National Laboratory (PNNL) to verify the thermodynamic stability of aluminosilicate compounds under waste tank conditions in an attempt to solve the deposition and clogging problems. The primary objectives of this study are (1) to understand the major factors controlling precipitation, heterogeneous nucleation, and growth phenomena of relatively insoluble aluminosilicates; (2) to determine the role of organics for inhibiting aluminosilicate formation, and (3) to develop a predictive tool to control precipitation, scale formation, and cementation under tank waste processing conditions. The results of this work will provide crucial information for (1) avoiding problematical sludge processing steps and (2) identifying and developing effective technologies to process retrieved sludges and supernatants before ultimate vitrification of wastes.
A pyrimidine-5-carbonitrile acceptor combined with an ortho-linked donor for long lifetime through facilitated reverse intersystem crossing in thermally activated delayed fluorescence emitters (2020)

Molecular design combining a 4,6-diphenylpyrimidine-5-carbonitrile (PyCN) acceptor and an ortho-linked donor was developed to extend the lifetime of OLEDs with shortened the delayed fluorescence lifetime and promoted the reverse intersystem crossing.
From Single-Epitope Anti-Idiotypic Antibody Vaccines to Multiple-Epitope Recombinant Antigen Vaccines (2004)

s for the 19th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer, San Francisco, California, November 4-7, 2004: Dendritic Cells and Vaccines
A Flexible Model of HIV-1 Latency Permitting Evaluation of Many Primary CD4 T-Cell Reservoirs (2012)

Latently infected cells form the major obstacle to HIV eradication. Studies of HIV latency have been generally hindered by the lack of a robust and rapidly deployable cell model that involves primary human CD4 T lymphocytes. Latently infected cell lines have proven useful, but it is unclear how closely these proliferating cells recapitulate the conditions of viral latency in non-dividing CD4 T lymphocytes in vivo. Current primary lymphocyte models more closely reflect the in vivo state of HIV latency, but they are limited by protracted culture periods and often low cell yields. Additionally, these models are always established in a single latently infected cell type that may not reflect the heterogeneous nature of the latent reservoir. Here we describe a rapid, sensitive, and quantitative primary cell model of HIV-1 latency with replication competent proviruses and multiple reporters to enhance the flexibility of the system. In this model, post-integration HIV-1 latency can be established in all populations of CD4 T cells, and reactivation of latent provirus assessed within 7 days. The kinetics and magnitude of reactivation were evaluated after stimulation with various cytokines, small molecules, and T-cell receptor agonists. Reactivation of latent HIV proviruses was readily detected in the presence of strong activators of NF-kB. Latently infected transitional memory CD4 T cells proved more responsive to these T-cell activators than latently infected central memory cells. These findings reveal potentially important biological differences within the latently infected pool of memory CD4 T cells and describe a flexible primary CD4 T-cell system to evaluate novel antagonists of HIV latency.
Na+absorption by Claudius' cells is regulated by purinergic signaling in the cochlea (2012)

A negative baseline I(sc) was observed in the control solution (-12.50 ± 3.95 μA/cm(2), n = 8) and the addition of amiloride resulted in a decrease of I(sc) by 75.8%. The application of UTP, an agonist for P2Y purinergic receptors, led to a partial inhibition of I(sc) (by 38.2 ± 3.2%, n = 5), and subsequent addition of amiloride abolished the remaining I(sc).
Electron Pulse Radiolysis Determination of Hydroxyl Radical Rate Constants with Suwannee River Fulvic Acid and Other Dissolved Organic Matter Isolates (2007)

Pulse radiolysis experiments were conducted on dissolved organic matter (DOM) samples isolated as hydrophobic and hydrophilic acids and neutrals from different sources (i.e., stream, lake, wastewater treatment plant). Absolute bimolecular reaction rate constants for the reaction of hydroxyl radicals (*OH) with DOM (k*(OH), DOM) were determined. k*(OH, DOM) values are expressed as moles of carbon. Based on direct measurement of transient DOM radicals (DOM*) and competition kinetic techniques, both using pulse radiolysis, the k*(OH, DOM) value for a standard fulvic acid from the Suwannee River purchased from the International Humic Substances Society was (1.60 +/- 0.24) x 10(8) M(-1) s(-1). Both pulse radiolysis methods yielded comparable k*(OH, DOM) values. The k*(OH, DOM) values for the seven DOM isolates from different sources ranged from 1.39 x 10(8) M(-1) s(-1) to 4.53 x 10(8) M(-1) s(-1), and averaged 2.23 x 108 M(-1) s(-1) (equivalent to 1.9 x 10(4) (mgC/L)(-1) s(-1)). These values represent the first direct measurements of k*(OH, DOM,) and they compare well with literature values obtained via competition kinetic techniques during ozone or ultraviolet irradiation experiments. More polar, lower-molecular-weight DOM isolates from wastewater have higher k*(OH, DOM) values. In addition, the formation (microsecond time scale) and decay (millisecond time scale) of DOM* transients were observed for the first time. DOM* from hydrophobic acids exhibited broader absorbance spectra than transphilic acids, while wastewater DOM isolates had narrower DOM* spectra more skewed toward shorter wavelengths than did DOM* spectra for hydrophobic acids.
Orientation-dependent optical characterization of atomically thin transition metal ditellurides (2018)

Molybdenum ditellurides (MoTe2) have recently attracted attention owing to their excellent structurally tunable nature between 1T'(metallic)- and 2H(semiconducting)-phases; thus, the controllable fabrication and critical identification of MoTe2 are highly desired. Here, we semi-controllably synthesized 1T'- and 2H-MoTe2 crystals using the atmospheric pressure chemical vapor deposition (APCVD) technique and studied their grain-orientation dependency using polarization-sensitive optical microscopy, Raman scattering, and second-harmonic generation (SHG) microspectroscopy. The polycrystalline 1T'-MoTe2 phase with quasi-1D "Mo-Mo" zigzag chains showed anisotropic optical absorption, leading to a clear visualization of the lattice domains. On the other hand, 2H-MoTe2 lattice grains did not exhibit any discernible difference under polarized light illumination. The combined aforementioned microscopy techniques could be used as an easy-to-access and non-destructive tool for a quick and solid identification of intended lattice orientation development in industry-scale MoTe2 crystal manufacturing.
Bridging GPS outages using neural network estimates of INS position and velocity errors (2006)

INS and GPS are commonly integrated using a Kalman filter (KF) to provide a robust navigation solution, overcoming situations of GPS satellite signals blockage. This research presents an alternative method of bridging GPS outages requiring no prior knowledge of the INS and GPS sensor characteristics, called the artificial-intelligence-based segmented forward predictor. This method uses radial basis function neural networks to predict INS position and velocity errors during GPS outages, resulting in reliable performance. The performance of the proposed method is examined using real field test data of both navigational and tactical grade INS integrated with GPS. The results have shown that the proposed method outperforms KF, especially during long GPS outages.
MorphogenesbolAandmreBmediate the photoregulation of cellular morphology during complementary chromatic acclimation inFremyella diplosiphon (2014)

Photoregulation of pigmentation during complementary chromatic acclimation (CCA) is well studied in Fremyella diplosiphon; however, mechanistic insights into the CCA-associated morphological changes are still emerging. F. diplosiphon cells are rectangular under green light (GL), whereas cells are smaller and spherical under red light (RL). Here, we investigate the role of morphogenes bolA and mreB during CCA using gene expression and gene function analyses. The F. diplosiphon bolA gene is essential as its complete removal from the genome was unsuccessful. Depletion of bolA resulted in slow growth, morphological defects and the accumulation of high levels of reactive oxygen species in a partially segregated ΔbolA strain. Higher expression of bolA was observed under RL and was correlated with lower expression of mreB and mreC genes in wild type. In a ΔrcaE strain that lacks the red-/green-responsive RcaE photoreceptor, the expression of bolA and mre genes was altered under both RL and GL. Observed gene expression relationships suggest that mreB and mreC expression is controlled by RcaE-dependent photoregulation of bolA expression. Expression of F. diplosiphon bolA and mreB homologues in Escherichia coli demonstrated functional conservation of the encoded proteins. Together, these studies establish roles for bolA and mreB in RcaE-dependent regulation of cellular morphology.
Death after hematopoietic stem cell transplantation: changes over calendar year time, infections and associated factors (2019)

Information on incidence, and factors associated with mortality is a prerequisite to improve outcome after hematopoietic stem cell transplantation (HSCT). Therefore, 55'668 deaths in 114'491 patients with HSCT (83.7% allogeneic) for leukemia were investigated in a landmark analysis for causes of death at day 30 (very early), day 100 (early), at 1 year (intermediate) and at 5 years (late). Mortality from all causes decreased from cohort 1 (1980-2001) to cohort 2 (2002-2015) in all post-transplant phases after autologous HSCT. After allogeneic HSCT, mortality from infections, GVHD, and toxicity decreased up to 1 year, increased at 5 years; deaths from relapse increased in all post-transplant phases. Infections of unknown origin were the main cause of infectious deaths. Lethal bacterial and fungal infections decreased from cohort 1 to cohort 2, not unknown or mixed infections. Infectious deaths were associated with patient-, disease-, donor type, stem cell source, center, and country- related factors. Their impact varied over the post-transplant phases. Transplant centres have successfully managed to reduce death after HSCT in the early and intermediate post-transplant phases, and have identified risk factors. Late post-transplant care could be improved by focus on groups at risk and better identification of infections of "unknown origin".
Estimated Association Between Cytokines and the Progression to Diabetes: 10-year Follow-Up From a Community-Based Cohort (2019)

In this 10-year prospective study, NGT with higher serum RBP4 and PAI-1, and with lower adiponectin were associated with new-onset prediabetes and type 2 diabetes.
Laser warning receiver to identify the wavelength and angle of arrival of incident laser light (2023)

A laser warning receiver is disclosed which has up to hundreds of individual optical channels each optically oriented to receive laser light from a different angle of arrival. Each optical channel has an optical wedge to define the angle of arrival, and a lens to focus the laser light onto a multi-wavelength photodetector for that channel. Each multi-wavelength photodetector has a number of semiconductor layers which are located in a multi-dielectric stack that concentrates the laser light into one of the semiconductor layers according to wavelength. An electrical signal from the multi-wavelength photodetector can be processed to determine both the angle of arrival and the wavelength of the laser light.
A Robust, Efficiency Optimized Flux-Weakening Control Algorithm for PM Synchronous Machines (2007)

An enhanced flux-weakening control algorithm with optimized operating efficiency of permanent magnet synchronous machines (PMSM) is presented. It is robust to variation of dc bus voltage and load level; and insensitive to machine parameters. The developed speed/flux-weakening controller (SFWC) can automatically generate the required demagnetizing current and produce torque component at high speeds based on the d-q current cross-coupling effect. By selecting a voltage constant adaptive to load level and rotor speed, the demagnetizing current is optimized, resulting in less copper losses and higher efficiency especially under light load conditions in the flux-weakening region. Moreover, the proposed control scheme is able to achieve both flux weakening and speed regulation simultaneously using only one current regulator, in contrast to the conventional two- loop (d-q-axis) control approaches. Both computer simulation and experimental results are provided to verify its feasibility and effectiveness.
Ultraviolet (UV) Laser Implementation and Measurement Sensitivities in Filtered Rayleigh Scattering for Aerodynamic Flows (2023)

View Video Presentation: https://doi.org/10.2514/6.2023-4381.vid Filtered Rayleigh scattering (FRS) is a non-intrusive, seedless, optical measurement technique that provides time-averaged, planar measurements of three-component velocity, static temperature, and static density of aerodynamic flows. Previous work in FRS development has commonly employed 532 nm Nd:YAG lasers and iodine vapor cells due to the ready availability of optics, achievable laser power levels, and well-documented transmission spectrum of iodine in this wavelength range. However, significant improvements in the strength of the Rayleigh scattered signal can be attained by utilizing shorter laser wavelengths due to the dependence of the Rayleigh scattering signal on the inverse of the wavelength to the fourth power. This study assesses the implementation and theoretical feasibility of an FRS system nominally at 387 nm with the use of cesium vapor as the molecular filter. Cesium vapor exhibits two deep absorption lines corresponding to the 62S(1/2) → 82P(3/2) atomic transitions around 387 nm. These absorption lineshapes are considered along with camera specifications to simulate an ultraviolet filtered Rayleigh scattering (UV FRS) measurement of aerodynamic flows. A signal model is developed using numerical functions for the cesium vapor cell transmission, camera specifications, signal dependent shot noise, and signal independent electronic detector read noise. Using this noise-inclusive model, velocity, static temperature, and static density measurement sensitivities for this proposed configuration are analyzed by evaluating and deriving the Cramér-Rao lower bound (CRLB) for each quantity. The effects of different flow conditions, Mie and geometric scattering levels, cesium vapor cell temperatures, and spectral resolutions are demonstrated and compared to the evaluation of the CRLB for a 532 nm system, representing current and traditional measurement capabilities, with a 2 torr iodine cell as the filter over the same set of simulated conditions. It is shown that the best possible theoretical measurement results are obtained for high-speed wind tunnel condition flows and at high spectral resolution.
Modification and Characterization of the Polyvinyl Alcohol (PVA) Hydrogel with Surfactant-cellulose Nanocrystal (S-CNC) (2020)

Polyvinyl alcohol (PVA) hydrogel is attracting widespread attention for its biocompatibility, sterilization, and transparency, which are vital properties when it is used as material for articular cartilage or contact lenses. However, the inherent shortcomings of PVA hydrogel, such as poor thermal stability and mechanical properties limit its application. In this study, PVA hydrogel was reinforced with cellulose nanocrystal (CNC) coated by a surfactant (e.g., Span 60 and Tween 20). And then characterized their properties by DSL, TGA, FT-IR, and swelling ratio. We confirmed the surfactant-coating on CNC was successfully carried out from FT-IR, and PVA hydrogel was increased thermal degradation temperature from 330 oC to 351 oC with increasing S-CNC concentration. In addition, the swelling ratio of PVA hydrogel was decreased dramatically from 640% to 50% with increasing S-CNC concentration.
ChemInform Abstract: Chemical and Microbial Modifications of Spinosyn: Exploring Synergies Between Fermentation Microbiology and Organic Chemistry (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Synthesis and Structure−Activity-Relationships of 1H-Imidazo[4,5-c]quinolines That Induce Interferon Production (2005)

1H-Imidazo-[4,5-c]quinolines were prepared while investigating novel nucleoside analogues as potential antiviral agents. While these compounds showed no direct antiviral activity when tested in a number of cell culture systems, some demonstrated potent inhibition of virus lesion development in an intravaginal guinea pig herpes simplex virus-2 assay. We have determined that the in vivo antiviral activity can be attributed to the ability of these molecules to induce the production of cytokines, especially interferon (IFN), in this model. Subsequently, we found that the compounds also induce in vitro production of IFN in human peripheral blood mononuclear cells (hPBMCs). The in vitro results reported herein and the in vivo results reported previously led to the discovery of imiquimod, 26, which was developed as a topical agent and has been approved for the treatment of genital warts, actinic keratosis, and superficial basal cell carcinoma.