gebhart/patrepeval huggingface dataset:
p21WAF1/CIP1 Is Upregulated by the Geranylgeranyltransferase I Inhibitor GGTI-298 through a Transforming Growth Factor β- and Sp1-Responsive Element: Involvement of the Small GTPase RhoA (1998)

We have recently reported that the geranylgeranyltransferase I inhibitor GGTI-298 arrests human tumor cells at the G1 phase of the cell cycle and increases the protein and RNA levels of the cyclin-dependent kinase inhibitor p21(WAF1/CIP1). Here, we show that GGTI-298 acts at the transcriptional level to induce p21(WAF1/CIP1) in a human pancreatic carcinoma cell line, Panc-1. This upregulation of p21(WAF1/CIP1) promoter was selective, since GGTI-298 inhibited serum responsive element- and E2F-mediated transcription. A functional analysis of the p21(WAF1/CIP1) promoter showed that a GC-rich region located between positions -83 and -74, which contains a transforming growth factor beta-responsive element and one Sp1-binding site, is sufficient for the upregulation of p21(WAF1/CIP1) promoter by GGTI-298. Electrophoretic mobility shift assays showed a small increase in the amount of DNA-bound Sp1-Sp3 complexes. Furthermore, the analysis of Sp1 transcriptional activity in GGTI-298-treated cells by using GAL4-Sp1 chimera or Sp1-chloramphenicol acetyltransferase reporter revealed a significant increase in Sp1-mediated transcription. Moreover, GGTI-298 treatment also resulted in increased Sp1 and Sp3 phosphorylation. These results suggest that GGTI-298-mediated upregulation of p21(WAF1/CIP1) involves both an increase in the amount of DNA-bound Sp1-Sp3 and enhancement of Sp1 transcriptional activity. To identify the geranylgeranylated protein(s) involved in p21(WAF1/CIP1) transcriptional activation, we analyzed the effects of the small GTPases Rac1 and RhoA on p21(WAF1/CIP1) promoter activity. The dominant negative mutant of RhoA, but not Rac1, was able to activate p21(WAF1/CIP1). In contrast, constitutively active RhoA repressed p21(WAF1/CIP1). Accordingly, the ADP-ribosyl transferase C3, which specifically inhibits Rho proteins, enhanced the activity of p21(WAF1/CIP1). Taken together, these results suggest that one mechanism by which GGTI-298 upregulates p21(WAF1/CIP1) transcription is by preventing the small GTPase RhoA from repressing p21(WAF1/CIP1) induction.
Plant Regeneration in Indian Mustard [Brassica juncea (Linn.) Czern & Coss]: Experimental Investigation (2021)

Brassica juncea is an important mustard species grown for edible oil in India. The current study establishes an efficient and reproducible plant regeneration protocol from callus employing mature cotyledons and seeds as explants and embryogenic cell suspension cultures derived from embryogenic friable calli. MS basal media enriched with 3.0 mgl-1 2, 4-D produced the best callus induction. Supplementation of 0.5 mgl-1 BAP in combination with 0.5-1.0 mgl-1 2,4-D resulted in further regeneration via embryogenesis/ organogenesis. The superiority of mature seeds as explants has been demonstrated, implying that this explant has greater morphogenic potential. Furthermore, the genotype, type (s), and relative concentrations and combinations of plant growth regulators all had a substantial impact on the success of plantlet regeneration. In the future, these techniques could be used for genetic transformation and in vitro selection of Indian mustard elite genotypes.
130 Acoustic Improvement of High Pressure Fuel Pump (2012)

Recently, the need for noise reduction of high pressure fuel pump has been increasing due to rising environmental consciousness and improving comfort. Based on our acoustic investigation under idling condition, we identified that the solenoid noise and the compression noise are dominant on high pressure fuel pump. We have investigated the acoustic improvement technique of the solenoid noise for high pressure fuel pump and came to a conclusion that the solenoid noise can be reduced can be redused ca. 3dB by using optimization of control parameters and a reduced spring force. In this paper, we explain the concept of noise reduction, the control method and the extent of acoustic improvement.
Myoglobin and Hemoglobin: Discoloration, Lipid Oxidation, and Solvent Access to the Heme Pocket (2022)

Conversion of the heme iron in myoglobin (Mb) and hemoglobin (Hb) from Fe2+ to Fe3+ is a critical step that causes quality deterioration—such as discoloration and generation of oxidative species, including dissociated heme, that oxidize lipids and proteins—in muscle foods. Increased solvent access to the heme pocket has been proposed to cause oxidation of the heme iron and decrease heme affinity for the globin, although empirical results are lacking. This review introduces plasma-induced modification of biomolecules (PLIMB) as an approach to modify amino acids of Mb and Hb and thereby assess solvent access to the heme pocket. After PLIMB, liquid chromatography tandem mass spectrometry peptide analysis and a user-friendly, software platform are used to quantify modified amino acid side chains of the heme proteins. Our findings indicate that PLIMB➔liquid chromatography-tandem mass spectrometry provides a platform to measure solvent access to portions of the heme pocket environment. Evaluation of PLIMB under additional conditions(e.g., different pH values) can differentiate the role of solvent access to the heme pocket relative to the“outer-sphere”mechanism of heme protein oxidation and the ability of hydrogen bonding to stabilize heme within metHb. Some aspects of heme protein-mediated lipid oxidation that occur at low O2partial pressures are discussed in relationship to solvent access to the heme pocket. Other approaches to study mechanisms of discoloration and lipid oxidation related to Mb/Hb oxidation and heme loss from metHb are also discussed.
Observation of New Ξc0 Baryons Decaying to Λc+K− (2020)

The Λ_{c}^{+}K^{-} mass spectrum is studied with a data sample of pp collisions at a center-of-mass energy of 13 TeV corresponding to an integrated luminosity of 5.6 fb^{-1} collected by the LHCb experiment. Three Ξ_{c}^{0} states are observed with a large significance and their masses and natural widths are measured to be m[Ξ_{c}(2923)^{0}]=2923.04±0.25±0.20±0.14 MeV, Γ[Ξ_{c}(2923)^{0}]=7.1±0.8±1.8 MeV, m[Ξ_{c}(2939)^{0}]=2938.55±0.21±0.17±0.14 MeV, Γ[Ξ_{c}(2939)^{0}]=10.2±0.8±1.1 MeV, m[Ξ_{c}(2965)^{0}]=2964.88±0.26±0.14±0.14 MeV, Γ[Ξ_{c}(2965)^{0}]=14.1±0.9±1.3 MeV, where the uncertainties are statistical, systematic, and due to the limited knowledge of the Λ_{c}^{+} mass. The Ξ_{c}(2923)^{0} and Ξ_{c}(2939)^{0} baryons are new states. The Ξ_{c}(2965)^{0} state is in the vicinity of the known Ξ_{c}(2970)^{0} baryon; however, their masses and natural widths differ significantly.
Fourth workshop on exploiting semantic annotations in information retrieval (ESAIR) (2011)

There is an increasing amount of structure on the Web as a result of modern Web languages, user tagging and annotation, and emerg- ing robust NLP tools. These meaningful, semantic, annotations hold the promise to significantly enhance information access, by enhancing the depth of analysis of today's systems. Currently, we have only started exploring the possibilities and only begin to un- derstand how these valuable semantic cues can be put to fruitful use. Unleashing the potential of semantic annotations requires us to think outside the box, by combining the insights of natural lan- guage processing (NLP) to go beyond bags of words, the insights of databases (DB) to use structure efficiently even when aggregating over millions of records, the insights of information retrieval (IR) in effective goal-directed search and evaluation, and the insights of knowledge management (KM) to get grips on the greater whole. This workshop aims to bring together researchers from these dif- ferent disciplines and work together on one of the greatest chal- lenges in the years to come. The desired result of the workshop will be to gain concrete insight into the potential of semantic an- notations, and in concrete steps to take this research forward; to synchronize related research happening in NLP, DB, IR, and KM, in ways that combine the strengths of each discipline; and to have a lively, interactive workshop where every participant contributes actively and which inspires attendees to think freely and creatively, working towards a common goal.
Rational Design of Vitamin D3 Analogues Which Selectively Restore Activity to a Vitamin D Receptor Mutant Associated with Rickets (2002)

[formula: see text] Vitamin D3-resistant rickets (VDRR) is associated with mutations to the Vitamin D receptor (VDR) which effect ligand-dependent transactivation. Some VDRR associated mutants directly disrupt ligand binding. Using the reported VDR-1,25-dihydroxy vitamin D3 (1,25(OH)2D3) cocrystal structure, three 1,25(OH)2D3 analogues were designed to uniquely complement the rickets associated mutant VDR(Arg274-->Leu). The three analogues were 17 to 286 times more potent than 1,25(OH)2D3 with the mutant in cell-based assays and did not substantially activate cellular calcium influx.
Figure S12 from Pharmacologic Properties and Preclinical Activity of Sasanlimab, A High-affinity Engineered Anti-Human PD-1 Antibody (2023)

&lt;p&gt;Supplementary Figure 12 shows the ELISA assay with the dose-dependent C1q binding to plate-adsorbed sasanlimab and the ADCC assay of sasanlimab performed with activated T cells (target cells) and stimulated PBMCs (effector cells).&lt;/p&gt;
Sex-specific responses to slow progressive pressure overload in a large animal model of HFpEF (2022)

Approximately 50% of all heart failure (HF) diagnoses can be classified as HF with preserved ejection fraction (HFpEF). HFpEF is more prevalent in females compared with males, but the underlying mechanisms are unknown. We previously showed that pressure overload (PO) in male felines induces a cardiopulmonary phenotype with essential features of human HFpEF. The goal of this study was to determine if slow progressive PO induces distinct cardiopulmonary phenotypes in females and males in the absence of other pathological stressors. Female and male felines underwent aortic constriction (banding) or sham surgery after baseline echocardiography, pulmonary function testing, and blood sampling. These assessments were repeated at 2 and 4 mo postsurgery to document the effects of slow progressive pressure overload. At 4 mo, invasive hemodynamic studies were also performed. Left ventricle (LV) tissue was collected for histology, myofibril mechanics, extracellular matrix (ECM) mass spectrometry, and single-nucleus RNA sequencing (snRNAseq). The induced pressure overload (PO) was not different between sexes. PO also induced comparable changes in LV wall thickness and myocyte cross-sectional area in both sexes. Both sexes had preserved ejection fraction, but males had a slightly more robust phenotype in hemodynamic and pulmonary parameters. There was no difference in LV fibrosis and ECM composition between banded male and female animals. LV snRNAseq revealed changes in gene programs of individual cell types unique to males and females after PO. Based on these results, both sexes develop cardiopulmonary dysfunction but the phenotype is somewhat less advanced in females.<b>NEW & NOTEWORTHY</b> We performed a comprehensive assessment to evaluate the effects of slow progressive pressure overload on cardiopulmonary function in a large animal model of heart failure with preserved ejection fraction (HFpEF) in males and females. Functional and structural assessments were performed at the organ, tissue, cellular, protein, and transcriptional levels. This is the first study to compare snRNAseq and ECM mass spectrometry of HFpEF myocardium from males and females. The results broaden our understanding of the pathophysiological response of both sexes to pressure overload. Both sexes developed a robust cardiopulmonary phenotype, but the phenotype was equal or a bit less robust in females.
Carrier relaxation dynamics of ZnxCd1−xSe/C core/shell nanocrystals with phase separation as studied by time-resolved cathodoluminescence (2009)

The optical properties and carrier relaxation kinetics of ZnxCd1−xSe/C core/shell nanocrystals with compositional phase separation occurring on a ∼1–5 nm size scale were examined with time-resolved cathodoluminescence (CL) spectroscopy and imaging. The CL spectral lineshape was found to depend on the level of excitation, temperature, and the time-window during time-delayed spectroscopy. The kinetics of carrier thermalization and transfer between Cd-rich phase-separated regions and the homogenous ZnCdSe alloy were examined. We show that the rare phenomenon of compositional phase separation in II-VI nanocrystals leads to interesting and potentially useful optical properties.
Materials Design and Synthetic Strategies to Enhance Electron Transport in Composite Materials (2017)

Electroactive materials are typically incorporated into batteries through the fabrication of composite electrodes including additives to enhance conductivity and to mechanically bind the components. These structures provide an opportunity to decrease inert material content if multifunctional materials can be designed and employed. For example, redox active materials that incorporate silver cation (Ag + ) demonstrate the possibility for in-situ generation of an electrically conductive percolation network of Ag 0 metallic nanoparticles through a reduction displacement reaction. This paradigm has been demonstrated with silver vanadium phosphorous oxide (Ag 2 VO 2 PO 4 ) where the electrical conductivity increased 15,000-fold upon lithiation. This presentation provides new strategies for the deliberate design of composite materials taking advantage of the opportunity for in-situ reduction displacement to form conductive networks. Several new approaches will be described. These include a one pot synthetic approach for the direct formation of a composite where one component is silver ion containing and the second is not. Additionally, surface modification approaches to generate conductive surface coatings will be introduced. These methods can significantly benefit the electrochemistry compared to composites formed by mechanical mixing alone, as will be illustrated in this presentation.
Dupilumab Efficacy and Safety in Moderate-to-Severe Uncontrolled Asthma (2018)

In this trial, patients who received dupilumab had significantly lower rates of severe asthma exacerbation than those who received placebo, as well as better lung function and asthma control. Greater benefits were seen in patients with higher baseline levels of eosinophils. Hypereosinophilia was observed in some patients. (Funded by Sanofi and Regeneron Pharmaceuticals; LIBERTY ASTHMA QUEST ClinicalTrials.gov number, NCT02414854 .).
Supplementary Figure 1 from Molecular Imaging of TGFβ-Induced Smad2/3 Phosphorylation Reveals a Role for Receptor Tyrosine Kinases in Modulating TGFβ Signaling (2023)

&lt;p&gt;PDF file - 79K&lt;/p&gt;
Monitoring Rehabilitation Parameters In Stroke Patients (2017)

This research presents the development and testing of a system for monitoring functional parameters in stroke patients undergoing rehabilitation. Benefits of real-time automated monitoring will improve measurement consistency and accuracy, reduce consultant time, earlier discharge, less hospital beds required and delivery of controlled, repetitive training. The system uses three devices: (1) the Myo gesture control armband (Thalmic Labs) to detect EMG signals, angles and acceleration; (2) the Arm Motion Monitoring and Recovery Improvement Toolkit (AMMRIT) (custom built) arm exoskeleton to monitor the whole arm angles and (3) the Kinect Sensor (Microsoft) to detect facial expressions. Stroke is the second most common cause of death and the leading cause of disability in Europe. The incidence rate is approximately 16 per 10,000 per year in the UK. One of the most effective treatments following stroke is physiotherapy which can help the patient relearn how to move the limbs. Quantifying the progress of functional recovery is technically complex because of the multi-joined structure of the arm. Currently there is no single portable system available that can provide objective measurement and analysis to monitor functional recovery for Early Supported Discharge (ESD). We developed the AMMRIT which can guide as well as assess the arm’s functional recovery of patients. In this research we combine the device with Myo armband and Kinect sensor to monitor a wide range of functional parameters to accurately assess the rehabilitation progression.
Coincident ruddy turnstone migration and horseshoe crab spawning creates an ecological ‘hot spot’ for influenza viruses (2010)

Since 1985, avian influenza virus surveillance has been conducted annually from mid-May to early June in charadriiform species from the families Scolopacidae and Laridae (shorebirds and gulls) at Delaware Bay in the northeast United States. The mass migrations of shorebirds, gulls and horseshoe crabs (Limulus polyphemus) coincide at that time, and large numbers of migrating birds pause at Delaware Bay to feed on horseshoe crab eggs deposited at the high-tide line. Influenza viruses are consistently isolated from charadriiform birds at Delaware Bay, at an overall rate approximately 17 times the combined rate of isolation at all other surveillance sites worldwide (490 isolates/9474 samples, 5.2% versus 49 isolates per 15,848 samples, 0.3%, respectively; Proportion test, p < 0.0001). The likelihood of isolating influenza viruses at Delaware Bay is dependent on the presence of ruddy turnstone (Arenaria interpres) at the sampling site (G-test of independence, p < 0.001). The convergence of host factors and environmental factors results in a unique ecological 'hot spot' for influenza viruses in Charadriiformes.
Implicitly Parallel Programming Models for Thousand-Core Microprocessors (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
expa: a program for calculating extreme pathways in biochemical reaction networks (2004)

palsson@ucsd.edu.
The Power of Silk Technology for Energy Applications (2021)

Abstract Silk fibers are a remarkable material made of proteins possessing excellent mechanical properties that match or even outperform, in some aspects, high performance fibers such as Kevlar and steel. Silk proteins can be further produced recombinantly, allowing the possibility for genetic modification, enhancing silks’ already impressive range of benefits. Thus far, little research has explored the possibility of incorporating silk‐based materials in electronic or energy systems. With an increasing global concern for climate change and the dwindling reserves of fossil fuels, silk (or silk‐derived) hybrid materials are a promising avenue of scientific exploration in energy storage and conversion devices, flexible and wearable electronics and even as photovoltaic devices, which will be reviewed here within. Despite this, silk has seen only little interest for applications in hybrid energy devices in the recent years. Here within, some of the applications and benefits of silk‐based materials in several systems including: flexible electronics, thermal and thermoelectric devices, mechanical energy devices, sensors, and photovoltaic solar cells are examined. In addition to biocompatibility, high tensile strength, and renewability, silk also adds many benefits to hybrid energy systems such as tunability, multifunctionality, and versatility, making silk one of the most all‐encompassing materials for use in hybrid devices.
Platelet Adhesion to Collagen Under Flow Causes Dissociation of a Phosphoprotein Complex of Heat-Shock Proteins and Protein Phosphatase 1 (1997)

Phosphorylation/dephosphorylation events in human blood platelets were investigated during their adhesion to collagen under flow conditions. Using 32P-labeled platelets and one-dimensional gel electrophoresis, we found that adhesion to collagen mediated primarily by the alpha2beta1 integrin resulted in a strong dephosphorylation of several protein bands. Neither adhesion to polylysine nor thrombin-induced aggregation caused similar protein dephosphorylation. In addition, treatment with okadaic acid (OA), an inhibitor of serine/threonine protein phosphatases type 1 (PP1) and 2A (PP2A), caused significant inhibition of adhesion, suggesting that adhesion is regulated by OA-sensitive phosphatases. Recent studies indicate that phosphatases may be associated with the heat-shock proteins. Immunoprecipitations with antibodies against either the heat-shock cognate protein 70 (hsc70) or heat-shock protein 90 (hsp90) showed the presence of a phosphoprotein complex in 32P-labeled, resting human platelets. Antibody probing of this complex detected hsc70, hsp90, two isoforms of the catalytic subunit of PP1, PP1C alpha and PP1C delta, as well as the M regulatory subunit of PP1 (PP1M). OA, at concentrations that markedly blocked platelet adhesion to collagen, caused hyperphosphorylation of the hsc70 complex. In platelets adhering to collagen, hsc70 was completely dephosphorylated and hsp90, PP1 alpha, and PP1M were dissociated from the complex, suggesting involvement of heat-shock proteins and protein phosphatases in platelet adhesion.
Modeling of Cell-to-Cell Communication Processes with Petri Nets Using the Example of Quorum Sensing (2010)

The understanding of the molecular mechanism of cell-to-cell communication is fundamental for system biology. Up to now, the main objectives of bioinformatics have been reconstruction, modeling and analysis of metabolic, regulatory and signaling processes, based on data generated from high-throughput technologies. Cell-to-cell communication or quorum sensing (QS), the use of small molecule signals to coordinate complex patterns of behavior in bacteria, has been the focus of many reports over the past decade. Based on the quorum sensing process of the organism Aliivibrio salmonicida, we aim at developing a functional Petri net, which will allow modeling and simulating cell-to-cell communication processes. Using a new editor-controlled information system called VANESA (http://vanesa.sf.net), we present how to combine different fields of studies such as life-science, database consulting, modeling, visualization and simulation for a semi-automatic reconstruction of the complex signaling quorum sensing network. We show how cell-to-cell communication processes and information-flow within a cell and across cell colonies can be modeled using VANESA and how those models can be simulated with Petri net network structures in a sophisticated way.