gebhart/patrepeval huggingface dataset:
Long-Termin VivoClearance of Gadolinium-Based AGuIX Nanoparticles and Their Biocompatibility after Systemic Injection (2015)

We previously reported the synthesis of gadolinium-based nanoparticles (NPs) denoted AGuIX (activation and guiding of irradiation by X-ray) NPs and demonstrated their potential as an MRI contrast agent and their efficacy as radiosensitizing particles during X-ray cancer treatment. Here we focus on the elimination kinetics of AGuIX NPs from the subcellular to whole-organ scale using original and complementary methods such as laser-induced breakdown spectroscopy (LIBS), intravital two-photon microscopy, inductively coupled plasma optical emission spectrometry (ICP-OES), transmission electron microscopy (TEM), and electrospray ionization mass spectrometry (ESI-MS). This combination of techniques allows the exact mechanism of AGuIX NPs elimination to be elucidated, including their retention in proximal tubules and their excretion as degraded or native NPs. Finally, we demonstrated that systemic AGuIX NP administration induced moderate and transient effects on renal function. These results provide useful and promising preclinical information concerning the safety of theranostic AGuIX NPs.
Resilient distributed datasets: a fault-tolerant abstraction for in-memory cluster computing (2012)

We present Resilient Distributed Datasets (RDDs), a distributed memory abstraction that lets programmers perform in-memory computations on large clusters in a fault-tolerant manner. RDDs are motivated by two types of applications that current computing frameworks handle inefficiently: iterative algorithms and interactive data mining tools. In both cases, keeping data in memory can improve performance by an order of magnitude. To achieve fault tolerance efficiently, RDDs provide a restricted form of shared memory, based on coarsegrained transformations rather than fine-grained updates to shared state. However, we show that RDDs are expressive enough to capture a wide class of computations, including recent specialized programming models for iterative jobs, such as Pregel, and new applications that these models do not capture. We have implemented RDDs in a system called Spark, which we evaluate through a variety of user applications and benchmarks. 1
AutoBI - a tool for automatic toBI annotation (2010)

This paper describes the AuToBI tool for automatic generation of hypothesized ToBI labels. While research on automatic prosodic annotation has been conducted for many years, AuToBI represents the first publicly available tool to automatically detect and classify the breaks and tones that make up the ToBI annotation standard. This paper describes the feature extraction routines as well as the classifiers used to detect and classify the prosodic events of the ToBI standard. Additionally, we report performance evaluating AuToBI models trained on the Boston Directions Corpus on the Columbia Games Corpus. By evaluating on distinct speakers domains and recording conditions, this evaluation represents an accurate representation of the performance of the system when applied to novel spoken material.
Overexpression of PSF1 is correlated with poor prognosis in hepatocellular carcinoma patients (2014)

These results suggest that the inhibition of PSF1 might provide new therapeutic approaches for HCC.
Cells and cytokines in immunotherapy and gene therapy of cancer. (1999)

An enormous effort using a great variety of approaches has been undertaken in the last decade to translate basic and clinical research into successful cancer therapies. This review summarizes recent results of experiments and trials using cellular and cytokine therapy, as well as gene therapy, to exploit immune responses to tumors.
THE GLOBAL POSITIONING SYSTEM-NAVIGATION TOOL OF THE FUTURE (2012)

Navigation is an important issue in maritime transport In todays world, marine accidents and their effects to environment are key factors for maritime safety. GPS / DGPS are introduced as navigational tool of the future. Structure and positioning principles of GPS / DGPS are explained. Operational issues of the systems are discussed. Benefits of GPS / DGPS on safety improvements and cost efficiencies are examined.
[Small interfering RNA suppression of transducer and activator of transcription 3 (STAT3) signaling pathway: inhibitory effect on proliferation of human esophageal squamous carcinoma cells]. (2007)

STAT3 siRNA specifically and efficiently blocks the constitutively activated STAT3 signaling pathway in human esophageal squamous carcinoma cells, resulting in cell cycle arrest and proliferation inhibition.
Oligomerization of the human cytomegalovirus major envelope glycoprotein complex gB (gp55-116) (1992)

The disulfide-linked glycoprotein B (gB; gp55-116) complex of human cytomegalovirus represents the most abundant and immunogenic component of the virion envelope. We have studied the oligomerization and transport of this molecule, using a series of murine monoclonal antibodies. Our results indicated that oligomerization of this molecule occurred shortly after its synthesis, with a half-time of maximal formation of approximately 25 min. The oligomeric form had an estimated mass of 340,000 Da and likely consisted of a homodimer of the gp55-116 complex. By using a conformation-specific monoclonal antibody, postoligomerization folding of this molecule was demonstrated. This event exhibited an unusually prolonged half-maximal time of approximately 160 min. Both oligomerization and folding occurred in the endoplasmic reticulum. Oligomerization and folding occurred in the absence of carbohydrate modifications, although likely at lower efficiency. Finally, the oligomeric and folded forms were shown to be transported to the surface of infected cells and infectious virions.
Multichannel Sampling of Signals With Finite Rate of Innovation (2010)

In this letter, we present a possible extension of the theory of sampling signals with finite rate of innovation (FRI) to the case of multichannel acquisition systems. The essential issue of a multichannel system is that each channel introduces different unknown delays and gains that need to be estimated for the calibration of the channels. We pose both the synchronization stage and the signal reconstruction stage as a parametric estimation problem and demonstrate that a simultaneous exact synchronization of the channels and reconstruction of the FRI signal is possible. We also consider the case of noisy measurements and evaluate the Cramér–Rao bounds (CRB) of the proposed system. Numerical results as well as the CRB show clearly that multichannel systems are more resilient to noise than the single-channel ones.
HIV-1 infection of human CD4+ T cells in vitro. Differential induction of apoptosis in these cells. (1994)

The H9 and CEM CD4+ T cell lines were infected with HIV-1 (NY5/LAV-1 isolate) and monitored for losses in cell viability, syncytium formation, and internucleosomal DNA cleavage (a marker for apoptosis). H9 cells were found to undergo cell death via apoptosis as a result of HIVNY5 infection, but this effect was not apparent in CEM cell cultures. The differential effects of HIV-1NY5 in terms of its apoptosis-inducing properties correlated with the relative abilities of H9 and CEM cells in supporting replication of this HIV-1 isolate, since infected CEM cell cultures produced 10-fold lower levels of HIV-1 p24 protein, and very few of these cells stained positive for cell-associated p24 by comparison with H9 cell cultures infected at the same multiplicity of infection. Furthermore, a different HIV-1 isolate (RF), which replicated equally efficiently in both H9 and CEM cells, produced similar levels of apoptosis in these cultures. HIV-1NY5 was also found to be capable of inducing apoptosis in purified peripheral blood CD4+ T cells as well as inhibiting anti-CD3-driven proliferation of these cells. In contrast, incubation of purified CD8+ T cells with HIV-1NY5 under similar conditions produced no cytopathic effects. Substantial levels of apoptosis were also recorded in HIV-1NY5-infected PHA blasts cell cultures. Soluble rHIV-1IIIB type CHO-derived gp120 was found to mimic the effects of HIV in terms of inhibition of anti-CD3/TCR mAb-induced proliferation of T cells, but apoptosis was not detected in gp120-treated T cell cultures whether cross-linked or used in conjunction with anti-CD3 mAb or not. We conclude therefore that both HIV-1NY5 and HIV-1RF isolates have the capacity to directly trigger apoptotic cell death in CD4+ T cells and that this appears to be at least partly associated with the efficiency of virus replication in these cells.
Speech processing strategies for a multichannel cochlear prosthesis (1985)

status: Published
Shortened Hydroxyacyl Chains on Lipid A of Escherichia coli Cells Expressing a Foreign UDP-N-Acetylglucosamine O-Acyltransferase (1997)

The first reaction of lipid A biosynthesis in Gram-negative bacteria is catalyzed by UDP-N-acetylglucosamine (UDP-GlcNAc) O-acyltransferase, the product of the lpxA gene. The reaction involves the transfer of an acyl chain from hydroxyacyl-acyl carrier protein (ACP) to the glucosamine 3-OH position of UDP-GlcNAc. The lipid A isolated from Escherichia coli contains (R)-3-hydroxymyristate at the 3 and 3' positions. Accordingly, LpxA of E. coli is highly selective for (R)-3-hydroxymyristoyl-ACP over ACP thioesters of longer or shorter acyl chains. We now demonstrate that the lpxA gene from Neisseria meningitidis encodes a similar acyltransferase that selectively utilizes 3-hydroxylauroyl-ACP. Strains of E. coli harboring the temperature-sensitive lpxA2 mutation make very little lipid A and lose viability rapidly at 42 degrees C. We have created an E. coli strain in which the chromosomal lpxA2 mutation is complemented by the N. meningitidis lpxA gene introduced on a plasmid. This strain, RO138/pTO6, grows similarly to wild type cells at 42 degrees C and produces wild type levels of lipid A. However, the lipid A isolated from RO138/pTO6 contains mostly hydroxylaurate and hydroxydecanoate in the 3 and 3' positions. The strain RO138/pTO6 is more susceptible than wild type to certain antibiotics at 42 degrees C. This is the first report of an E. coli strain growing with shortened hydroxyacyl chains on its lipid A. The lpxA gene product appears to be a critical determinant of the length of the ester-linked hydroxyacyl chains found on lipid A in living cells.
Reactions at supercritical conditions: Applications and fundamentals (1995)

Abstract Supercritical fluids posses properties that make them attractive as media for chemical reactions. Conducting chemical reactions at supercritical conditions affords opportunities to manipulate the reaction environment (solvent properties) by manipulating pressure, to enhance the solubilities of reactants and products, to eliminate interphase transport limitations on reaction rates, and to integrate reaction and separation unit operations. Supercritical conditions may be advantageous for reactions involved in fuels processing, biomass conversion, biocatalysis, homogeneous and heterogeneous catalysis, environmental control, polymerization, materials synthesis, and chemical synthesis. Moreover, supercritical fluids can be used profitably in fundamental chemical investigations of intermolecular interactions and their influence on chemical processes. Work on chemical reactions in and with supercritical fluids is reviewed. We discuss both fundamental studies and applications of reactions at supercritical conditions, with focus on work published after 1985.
Bone Morphogenetic Protein-1 (BMP-1) Cleaves Human Proapolipoprotein A1 and Regulates Its Activation for Lipid Binding (2007)

Apolipoprotein A1 (apo A1), the major protein of high-density lipoprotein, is secreted as a proprotein and then cleaved by an uncharacterized metalloproteinase. Here this enzyme is identified as C-terminal procollagen endoproteinase/bone morphogenetic protein-1 (BMP-1). Studies with recombinant BMP-1, BMP-1 antibody, and BMP-1 siRNA establish this proteinase as the major or only apo A1-converting activity secreted by human liver-derived (HepG2) cells and CHO cells stably expressing human apo A1. BMP-1 stimulates the conversion of newly secreted proapo A1 to its phospholipid- (PL-) binding form. In this way it promotes formation of functional HDL and reverse cholesterol transport, while inhibiting filtration and clearance of uncleaved proprotein. Alpha2-macroglobulin, a protease inhibitor secreted as part of the innate immune response, inhibits BMP-1 activity and blocks the maturation of proapo A1. The decrease in circulating apo A1 levels that is characteristic of the response to inflammation and infection may be mediated, at least in part, via BMP-1 by this novel mechanism.
Solution Structure of a Naturally-Occurring Zinc−Peptide Complex Demonstrates that the N-Terminal Zinc-Binding Module of the Lasp-1 LIM Domain Is an Independent Folding Unit, (1996)

The three-dimensional solution structure of the 1:1 complex between the synthetic peptide ZF-1 and zinc was determined by 1H NMR spectroscopy. The peptide, initially isolated from pig intestines, is identical in sequence to the 30 N-terminal amino acid residues of the human protein Lasp-1 belonging to the LIM domain protein family. The final set of 20 energy-refined NMR conformers has an average rmsd relative to the mean structure of 0.55 A for the backbone atoms of residues 3-30. Calculations without zinc atom constraints unambiguously identified Cys 5, Cys 8, His 26, and Cys 29 as the zinc-coordinating residues. LIM domains consist of two sequential zinc-binding modules and the NMR structure of the ZF-1-zinc complex is the first example of a structure of an isolated module. Comparison with the known structures of the N-terminal zinc-binding modules of both the second LIM domain of chicken CRP and rat CRIP with which ZF-1 shares 50% and 43% sequence identity, respectively, supports the notion that the zinc-binding modules of the LIM domain have a conserved structural motif and identifies local regions of structural diversity. The similarities include conserved zinc-coordinating residues, a rubredoxin knuckle involving Cys 5 and Cys 8, and the coordination of the zinc ion by histidine N delta in contrast to the more usual coordination by N epsilon observed for other zinc-finger domains. The present structure determination of the ZF-1-zinc complex establishes the N-terminal half of a LIM domain as an independent folding unit. The structural similarities of N- and C-terminal zinc-binding modules of the LIM domains, despite limited sequence identity, lead to the proposal of a single zinc-binding motif in LIM domains. The coordinates are available from the Brookhaven protein data bank, entry 1ZFO.
Adipokines Mediate Inflammation and Insulin Resistance (2013)

For many years, adipose tissue was considered as an inert energy storage organ that accumulates and stores triacylglycerols during energy excess and releases fatty acids in times of systemic energy need. However, over the last two decades adipose tissue depots have been established as highly active endocrine and metabolically important organs that modulate energy expenditure and glucose homeostasis. In rodents, brown adipose tissue plays an essential role in non-shivering thermogenesis and in energy dissipation that can serve to protect against diet-induced obesity. White adipose tissue collectively referred too as either subcutaneous or visceral adipose tissue is responsible for the secretion of an array of signaling molecules, termed adipokines. These adipokines function as classic circulating hormones to communicate with other organs including brain, liver, muscle, the immune system, and adipose tissue itself. The dysregulation of adipokines has been implicated in obesity, type 2 diabetes, and cardiovascular disease. Recently, inflammatory responses in adipose tissue have been shown as a major mechanism to induce peripheral tissue insulin resistance. Although leptin and adiponectin regulate feeding behavior and energy expenditure, these adipokines are also involved in the regulation of inflammatory responses. Adipose tissue secretes various pro- and anti-inflammatory adipokines to modulate inflammation and insulin resistance. In obese humans and rodent models, the expression of pro-inflammatory adipokines is enhanced to induce insulin resistance. Collectively, these findings have suggested that obesity-induced insulin resistance may result, at least in part, from an imbalance in the expression of pro- and anti-inflammatory adipokines. Thus we will review the recent progress regarding the physiological and molecular functions of adipokines in the obesity-induced inflammation and insulin resistance with perspectives on future directions.
Phosphorylated ERM Is Responsible for Increased T Cell Polarization, Adhesion, and Migration in Patients with Systemic Lupus Erythematosus (2007)

Systemic lupus erythematosus (SLE) is an autoimmune/inflammatory disease characterized by autoantibody production and abnormal T cells that infiltrate tissues through not well-known mechanisms. We report that SLE T lymphocytes display increased levels of CD44, ezrin, radixin, and moesin (ERM) phosphorylation, stronger actin polymerization, higher polar cap formation, and enhanced adhesion and chemotactic migration compared with T cells from patients with rheumatoid arthritis and normal individuals. Silencing of CD44 by CD44 small interfering RNA in SLE T cells inhibited significantly their ability to adhere and migrate as did treatment with Rho kinase and actin polymerization inhibitors. Forced expression of T567D-ezrin, a phosphorylation-mimic form, enhanced remarkably the adhesion and migration rate of normal T cells. Anti-CD3/TCR autoantibodies present in SLE sera caused increased ERM phosphorylation, adhesion, and migration in normal T cells. pERM and CD44 are highly expressed in T cells infiltrating in the kidneys of patients with lupus nephritis. These data prove that increased ERM phosphorylation represents a key molecular abnormality that guides T cell adhesion and migration in SLE patients.
Advances in coronary angioplasty (1990)

From the Division of Cardiology, Department of Internal Medicine, University of Michigan Medical Center Ann Arbor Michigan, USA. USA
Efficacy and Pharmacology of the NLRP3 Inflammasome Inhibitor CP-456,773 (CRID3) in Murine Models of Dermal and Pulmonary Inflammation (2016)

A critical component of innate immune response to infection and tissue damage is the NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome, and this pathway and its activation products have been implicated in the pathophysiology of a variety of diseases. NLRP3 inflammasome activation leads to the cleavage of pro-IL-1β and pro-IL-18, as well as the subsequent release of biologically active IL-1β, IL-18, and other soluble mediators of inflammation. In this study, we further define the pharmacology of the previously reported NLRP3 inflammasome-selective, IL-1β processing inhibitor CP-456,773 (also known as MCC950), and we demonstrate its efficacy in two in vivo models of inflammation. Specifically, we show that in human and mouse innate immune cells CP-456,773 is an inhibitor of the cellular release of IL-1β, IL-1α, and IL-18, that CP-456,773 prevents inflammasome activation induced by disease-relevant soluble and crystalline NLRP3 stimuli, and that CP-456,773 inhibits R848- and imiquimod-induced IL-1β release. In mice, CP-456,773 demonstrates potent inhibition of the release of proinflammatory cytokines following acute i.p. challenge with LPS plus ATP in a manner that is proportional to the free/unbound concentrations of the drug, thereby establishing an in vivo pharmacokinetic/pharmacodynamic model for CP-456,773. Furthermore, CP-456,773 reduces ear swelling in an imiquimod cream-induced mouse model of skin inflammation, and it reduces airway inflammation in mice following acute challenge with house dust mite extract. These data implicate the NLRP3 inflammasome in the pathogenesis of dermal and airway inflammation, and they highlight the utility of CP-456,773 for interrogating the contribution of the NLRP3 inflammasome and its outputs in preclinical models of inflammation and disease.
Future Research Directions in Acute Lung Injury: Summary of a National Heart, Lung, and Blood Institute Working Group (2003)

Acute lung injury (ALI) and its more severe form, the acute respiratory distress syndrome (ARDS), are syndromes of acute respiratory failure that result from acute pulmonary edema and inflammation. The development of ALI/ARDS is associated with several clinical disorders including direct pulmonary injury from pneumonia and aspiration as well as indirect pulmonary injury from trauma, sepsis, and other disorders such as acute pancreatitis and drug overdose. Although mortality from ALI/ARDS has decreased in the last decade, it remains high. Despite two major advances in treatment, low VT ventilation for ALI/ARDS and activated protein C for severe sepsis (the leading cause of ALI/ARDS), additional research is needed to develop specific treatments and improve understanding of the pathogenesis of these syndromes. The NHLBI convened a working group to develop specific recommendations for future ALI/ARDS research. Improved understanding of disease heterogeneity through use of evolving biologic, genomic, and genetic approaches should provide major new insights into pathogenesis of ALI. Cellular and molecular methods combined with animal and clinical studies should lead to further progress in the detection and treatment of this complex disease.
Modulating laser intensity profile ellipticity for microstructural control during metal additive manufacturing (2017)

Additively manufactured (AM) metals are often highly textured, containing large columnar grains that initiate epitaxially under steep temperature gradients and rapid solidification conditions. These unique microstructures partially account for the massive property disparity existing between AM and conventionally processed alloys. Although equiaxed grains are desirable for isotropic mechanical behavior, the columnar-to-equiaxed transition remains difficult to predict for conventional solidification processes, and much more so for AM. In this study, the effects of laser intensity profile ellipticity on melt track macrostructures and microstructures were studied in 316L stainless steel. Experimental results were supported by temperature gradients and melt velocities simulated using the ALE3D multi-physics code. As a general trend, columnar grains preferentially formed with increasing laser power and scan speed for all beam profiles. However, when conduction mode laser heating occurs, scan parameters that result in coarse columnar microstructures using Gaussian profiles produce equiaxed or mixed equiaxed-columnar microstructures using elliptical profiles. By modulating spatial laser intensity profiles on the fly, site-specific microstructures and properties can be directly engineered into additively manufactured parts.
Synthesis and Characterization of Electron-Deficient Pentacenes (2005)

[structure: see text]. Halogen functional groups on pentacene can be used both as synthetic handles for further functionalization as well as to tune the pi-stacking in these systems. The halogenated pentacene derivatives described here (X = Br, X' = H, and X = X' = F) are all stable and soluble, with reduction potentials significantly lower than that of the parent functionalized pentacene (X = X' = H). The bromopentacenes could be further elucidated to pentacene nitriles, further decreasing the acene's reduction potential, while the charge-carrier mobility in the fluorinated systems was shown to scale with the degree of fluorine substitution.
Thymidine kinase 1 in serum predicts increased risk of distant or loco-regional recurrence following surgery in patients with early breast cancer. (2007)

Our results indicate that the S-TK1 concentration is higher in patients developing distant and/or loco-regional recurrence 3 months post-surgery.