gebhart/patrepeval huggingface dataset:
The Effect of Phosphatidylserine on T Cell and Dendritic Cell Function (90.2) (2009)

Abstract Phosphatidylserine (PS) is a phospholipid of plasma membrane. PS is located in the inner leaflet of plasma membrane but turns to outer leaflet when cell death program is initiated. It has been demonstrated that PS on apoptotic cells plays an important role in modulating immune responses. However, whether apoptotic cells release soluble PS which may subsequently affect immunocytes is not known. Recently, we found that apoptotic cells released soluble PS to the culture media which could block the binding of anti-PS antibody to apoptotic cells. To address how soluble PS influences T cell and dendritic cell function, we examined the effect of water-soluble PS (Avanti Polar Lipids, &amp;gt;95% purity with no endotoxin) on T cell proliferation, and monocyte-derived dendritic cell (DC) cytokine and chemokine production. Our results demonstrated that PS suppressed T cell proliferation in a significant dose-dependent manner. However, PS appeared not affecting T cell early activation based on the normal up-regulation of CD69. On DCs, PS did not induce any cytokine or chemokine production. However, PS significantly altered LPS-stimulated DC cytokine and chemokine producing profiles. We found that PS enhanced LPS-induced IL-1beta, IL-alpha, GM-CSF and IL-6, but suppressed IL-10, IL-12p40 as well as most chemokines tested. There was no significant influence on DC maturation. Our findings indicate that the apoptotic cells may modulate immune responses through releasing soluble PS. The mechanisms of PS effect on T cells and DCs are being investigated.
Small Cell Lung Cancer Guidelines (2006)

In 2005, approximately 26,000 new cases of small cell lung cancer were diagnosed in the United States. When compared with non-small cell lung cancer, SCLC generally has a more rapid doubling time, a higher growth fraction, and earlier development of widespread metastases. SCLC is highly sensitive to initial chemotherapy and radiotherapy. Treatment with chemotherapy plus chest radiotherapy can be curative for some patients with limited-stage SCLC, whereas most patients with extensive-stage disease who undergo chemotherapy alone experience palliated symptoms and prolonged survival. The updated 2006 NCCN guidelines include new principles of surgical resection as well as chemotherapy and radiation dosage changes. For the most recent version of the guidelines, please visit NCCN.org
Use of tacrolimus, a potent antifibrotic agent, in bleomycin-induced lung fibrosis (2006)

Idiopathic pulmonary fibrosis has a poor prognosis and few efficacious treatments. The immunosuppressant cyclosporin A has been shown to inhibit tumour growth factor (TGF)-beta-induced collagen deposition in vitro, and is widely used in Japan as a potent antifibrotic agent. Tacrolimus (FK506) is another attractive immunosuppressant, which may be useful in the treatment of pulmonary fibrosis. The aim of the present study was to elucidate the antifibrotic effect of FK506. The inhibitory effect of FK506 on collagen synthesis in cultured lung fibroblastic cells, TIG-3-20, and its antifibrotic effect on bleomycin (BLM)-induced pulmonary fibrosis in mice was investigated. FK506 inhibited TGF-beta-induced collagen synthesis, and suppressed the expression of TGF-beta type I receptor (TbetaR-I) in TIG-3-20 cells. Consistent with the in vitro findings, FK506 treatment starting on day 6 attenuated BLM-induced pulmonary fibrosis, in part, via reduced TbetaR-I expression. FK506 treatment in the acute BLM injury phase unexpectedly increased pro-inflammatory cytokine levels in bronchoalveolar lavage fluid and enhanced lung injury, resulting in poor survival. In conclusion, the present results suggest that FK506 has a potent antifibrotic effect and may be useful for the treatment of pulmonary fibrosis, although its use in the acute inflammatory phase may exacerbate lung injury.
Management of cardiac arrest patients in the ICU: is keeping a cool head the standard of care? (2009)

The author considers the application and potential effects of therapeutic hypothermia in patients admitted to the intensive care unit with out-of-hospital cardiac arrest. (non-author abstract)
A review of co-processed directly compressible excipients. (2005)

Direct compression is the preferred method for the preparation of tablets. The present review outlines the importance of the functionality of the directly compressible adjuvants in the formulation of tablets. The co-processing is the most widely explored method for the preparation of directly compressible adjuvants because it is cost effective and can be prepared in-house based on the functionality required. Hence, the present review focuses on the properties of the co-processed directly compressible adjuvants available in the market.
CEACAM5-Targeted Therapy of Human Colonic and Pancreatic Cancer Xenografts with Potent Labetuzumab-SN-38 Immunoconjugates (2009)

The promising labetuzumab-SN-38 conjugates developed showed selective therapeutic efficacy in human tumor models at nontoxic doses that were a fraction of the CPT-11 doses used.
Biomimetic sensory abstraction using hierarchical quilted self-organizing maps (2006)

We present an approach for abstracting invariant classifications of spatiotemporal patterns presented in a high-dimensionality input stream, and apply an early proof-of-concept to shift and scale invariant shape recognition. A model called Hierarchical Quilted Self-Organizing Map (HQSOM) is developed, using recurrent self-organizing maps (RSOM) arranged in a pyramidal hierarchy, attempting to mimic the parallel/hierarchical pattern of isocortical processing in the brain. The results of experiments are presented in which the algorithm learns to classify multiple shapes, invariant to shift and scale transformations, in a very small (7×7 pixel) field of view.
Three-dimensional modeling of human organs and its application to diagnosis and surgical planning (1993)

We describe a method to obtain a 3D representation of objects given by a series of parallel cross-sections. We define a contour-to-contour connection based on geometric closeness and show a practical way to calculate an approximation using the Delaunay triangulation. The performance of our method is shown on several medical examples. We further evaluate the precision of 3D models reconstructed from synthetic data and compare it to the marching cube reconstruction. In the third part, we use the 3D model of a pelvis and a fetal head for simulating a delivery. We calculate the forces applying on the head and define a measure of adequateness. This measure may be interesting for the decision of making a cesarean section. Keywords: 3D reconstruction, Delaunay triangulation, Voronoi diagram, Hausdorff distance, robotics, obstetrics. Acknowledgement I am deeply indebted to my supervisor Jean-Daniel Boissonnat. He gave me the opportunity to work at INRIA in a stimulating environment and on ...
ReVirt (2002)

Current system loggers have two problems: they depend on the integrity of the operating system being logged, and they do not save sufficient information to replay and analyze attacks that include any non-deterministic events. ReVirt removes the dependency on the target operating system by moving it into a virtual machine and logging below the virtual machine. This allows ReVirt to replay the system's execution before, during, and after an intruder compromises the system, even if the intruder replaces the target operating system. ReVirt logs enough information to replay a long-term execution of the virtual machine instruction-by-instruction. This enables it to provide arbitrarily detailed observations about what transpired on the system, even in the presence of non-deterministic attacks and executions. ReVirt adds reasonable time and space overhead. Overheads due to virtualization are imperceptible for interactive use and CPU-bound workloads, and 13--58% for kernel-intensive workloads. Logging adds 0--8% overhead, and logging traffic for our workloads can be stored on a single disk for several months.
The Crocacins: Novel Natural Products as Leads for Agricultural Fungicides (2003)

A short route to the synthesis of analogues of the antifungal but unstable natural product crocacin D was developed. A wide range of compounds were made in which the complex side chain was replaced by simple aromatic units, and many of them showed high activity in a mitochondrial beef heart respiration assay. Some of these compounds were active against plant pathogenic fungi of agricultural importance in glasshouse tests. In order to find compounds with greater stability than the natural crocacins, the photolabile (Z)-enamide was replaced with many different moieties, but none gave rise to useful fungicidal activity.
Novel Hydrazino-Carbonyl-Amino- Methylated Polystyrene (HCAM) Resin Methodology for the Synthesis of P1-Aldehyde Protease Inhibitor Candidates (1999)

[structure: see text] A new strategy for the synthesis of peptidyl and peptidomimetic P1-aldehydes 3 on HCAM solid support is described. The appropriate C-terminal aldehyde precursors were prepared and anchored to a resin support via a semicarbazone linkage (HCAM resin). After synthetic elaboration, acidic hydrolysis efficiently delivered C-terminal target aldehydes 3a-h in good overall yields and in excellent purity.
Effect of epidermal growth factor on growth and postnatal development of the rabbit liver (1987)

The effect of epidermal growth factor (EGF) on the postnatal development of the liver was examined. New Zealand White rabbits received 40 micrograms.kg-1.day-1 EGF from days 3 to 17 of age either intraperitoneally or orogastrically, whereas controls received saline. At days 18-20, animals underwent cannulation of the common duct using halothane anesthetic. Biliary output was measured directly for three 1-h periods: under basal conditions and in response to intravenous infusion of exogenous glycodeoxycholic acid at 0.75 and 1.5 mumol.min-1.kg-1, respectively. The bile salt pool size was measured by isotope dilution. Final mean body weight of intraperitoneal and orogastric groups did not differ from controls. Liver we weight, DNA, and protein content were significantly increased in intraperitoneally treated animals without morphological or biochemical evidence of fat deposition. Both intraperitoneal and orogastric EGF significantly increased bile salt secretion in the basal period and as a response to exogenous bile acid infusion. Bile flow was significantly increased in response to 1.5 mumol.min-1.kg-1 infusion of glycodeoxycholic acid. The bile salt pool was increased by both intraperitoneal and orogastric EGF. Administration of EGF resulted in a precocious development of glucokinase (EC 2.7.1.2) activity in the liver. EGF had no effect on serum cortisol, corticosterone, triiodothyronine, thyroxine, or free thyroxine levels. These findings suggest that in the neonatal period EGF can promote hepatic growth and maturation.
Role of glycoprotein B of herpes simplex virus type 1 in viral entry and cell fusion (1988)

Glycoprotein B (gB) of herpes simplex virus type 1 is an envelope protein that is essential for viral growth. We previously reported the isolation of two gB-null viruses, which form gB-free virions in nonpermissive cells. In the present study, these gB-free virions were shown to bind to the cell surface at the same rate as the wild-type virus. They failed, however, to form plaques and to synthesize virus-specific proteins upon infection. Their plating efficiency was significantly enhanced by treatment with polyethylene glycol, a membrane fusion agent. Therefore, gB is required in a stage after viral attachment but before the expression of the virus-specific proteins. A gB-null syncytial virus was isolated, which contained a gB defect and a syncytial mutation in another genetic locus. It caused complete fusion of gB-transformed cells but no fusion on untransformed cells, indicating the essential role of gB in virus-induced cell fusion. Mutations located at two independent sites in the cytoplasmic domain of gB were transferred to viral DNA and shown to confer a syncytial phenotype to the virus. A transient-expression assay was developed to determine the ability of a set of plasmids containing addition and nonsense mutations in the gB gene to complement the cell-fusion defect in the gB-null syncytial virus. Mutations in plasmids, including those located in the extracytoplasmic domain of gB, were identified that reduced the fusion activity of gB. Therefore, gB contains different functional regions responsible for fusion induction and its inhibition.
Disruption of genes encoding pyruvate dehydrogenase kinases leads to retarded growth on acetate and ethanol in Saccharomyces cerevisiae (2007)

Two open reading frames, YIL042c (PKP1) and YGL059w, with 25% sequence similarity to human pyruvate dehydrogenase kinases, were shown to have protein kinase activity. Using GFP fusions, it was demonstrated that the proteins localize in discrete submitochondrial regions. Strains with a null mutation in these loci grew poorly on acetate and ethanol as carbon sources. Doubling times increased from ca. 4 h in the wild-type to > 6 h for the mutants. Growth rates of the mutants could be restored to wild-type levels by simultaneous disruption of the PDA1 gene, encoding the E1alpha subunit of the pyruvate dehydrogenase complex. This observation and the pyruvate dehydrogenase activities measured in the mutant strains and the wild-type grown on glucose or acetate suggest that the slow growth phenotype on C2 carbon sources is caused by a futile cycle in which phosphoenolpyruvate is converted back to acetyl coenzyme A.
A new reporter cell line to monitor HIV infection and drug susceptibilityin vitro (1997)

Determination of HIV infectivity in vitro and its inhibition by antiretroviral drugs by monitoring reduction of production of p24 antigen is expensive and time consuming. Such assays also do not allow accurate quantitation of the number of infected cells over time. To develop a simple, rapid, and direct method for monitoring HIV infection, we generated a stable T-cell line (CEM) containing a plasmid encoding the green fluorescent protein (humanized S65T GFP) driven by the HIV-1 long terminal repeat. Clones were selected that displayed low constitutive background fluorescence, but a high level of GFP expression upon infection with HIV. HIV-1 infection induced a 100- to 1,000-fold increase in relative fluorescence of cells over 2 to 4 days as monitored by fluorescence microscopy, cytofluorimetry, and flow cytometry. Addition of inhibitors of reverse transcriptase, protease, and other targets at different multiplicities of infection permitted the accurate determination of drug susceptibility. This technique also permitted quantitation of infectivity of viral preparations by assessment of number of cells infected in the first round of infection. In conclusion, the CEM-GFP reporter cell line provides a simple, rapid, and direct method for monitoring HIV infectivity titers and antiretroviral drug susceptibility of syncytium-inducing strains.
Remote laboratory experimentation (1998)

The aim of this work is to provide the students of both Case Western Reserve and Cooper Union Universities with remote access to the Bytronic Process Control unit, referred to as the process rig, in the Process Control and Automation Laboratory at Case Western Reserve University over the Internet. Using a web browser, the user can log-in parameters from a remote client to a LabVIEW G web server which is connected to the process rig via a PLC control module. When the server receives a request specifying a Common Gateway Interface Virtual Instrument (CGI VI), the server loads the VI and starts its execution. The CGI then reads the information that came with the request, controls the operation of the process rig in accordance with the parameters posted by the user and writes the data that is to be returned to the client. The output data files are also uploaded to an anonymous ftp-site from which the user can download them for further processing.
Trypanosoma cruzi Trans-sialidase Operates through a Covalent Sialyl−Enzyme Intermediate:  Tyrosine Is the Catalytic Nucleophile (2003)

Modified sialic acid substrates have been used to label Trypanosoma cruzi trans-sialidase, demonstrating that the enzyme catalyses the transfer of sialic acid through a covalent glycosyl-enzyme intermediate, a mechanism common to most retaining glycosidases. Peptic digestion of labeled protein, followed by LC-MS/MS analysis of the digest, identified Tyr342 as the catalytic nucleophile. This is the first such example of a retaining glycosidase utilizing an aryl glycoside intermediate. It is suggested that this alternative choice of nucleophile is a consequence of the chemical nature of sialic acid. A Tyr/Glu couple is invoked to relay charge from a remote glutamic acid, thereby avoiding electrostatic repulsion with the sialic acid carboxylate group.
Biologically active monomeric and heterodimeric recombinant human calpain I produced using the baculovirus expression system (1996)

Calpain I is a heterodimeric protein that is part of a family of calcium-activated intracellular cysteine proteases presumed to play a role in mediating signals transduced by calcium. Expression of bioactive recombinant human calpain I has been achieved using the baculovirus expression system, by either co-infection with two viruses, each expressing one of the subunits, or infection with a single virus containing both subunits. The approximately 80 kDa catalytic subunit exhibited calcium-dependent proteolytic activity when expressed alone or with the approximately 30 kDa regulatory subunit. Baculoviral recombinant calpain I appeared fully active in that the catalytic subunit in unpurified cell extracts exhibited calcium-dependent autocatalytic cleavage at the correct locus. The amount of approximately 80 kDa subunit accumulated at steady state was greatly increased by co-expression of the approximately 30 kDa subunit, suggesting a possible role for enzyme stabilization by the latter subunit. The recombinant human calpain I was purified to near homogeneity and compared with purified native human erythrocyte calpain I. The recombinant and native enzymes had equivalent inhibition constants for structurally diverse calpain inhibitors, identical calcium activation profiles, and similar specific activities, demonstrating the suitability of using the recombinant protein for studies of the native enzyme.
Cyclooxygenase-2 Activation Mediates the Proangiogenic Effect of Nitric Oxide in Colorectal Cancer (2004)

Our data showed a prominent role of nitric oxide in stimulating COX-2 activity in colorectal cancer. This interaction is likely to produce a cooperative effect in promoting angiogenesis through PGE(2)-mediated increase in VEGF production.
Neural Network Approach to Background Modeling for Video Object Segmentation (2007)

This paper presents a novel background modeling and subtraction approach for video object segmentation. A neural network (NN) architecture is proposed to form an unsupervised Bayesian classifier for this application domain. The constructed classifier efficiently handles the segmentation in natural-scene sequences with complex background motion and changes in illumination. The weights of the proposed NN serve as a model of the background and are temporally updated to reflect the observed statistics of background. The segmentation performance of the proposed NN is qualitatively and quantitatively examined and compared to two extant probabilistic object segmentation algorithms, based on a previously published test pool containing diverse surveillance-related sequences. The proposed algorithm is parallelized on a subpixel level and designed to enable efficient hardware implementation.
Defective Mre11-dependent Activation of Chk2 by Ataxia Telangiectasia Mutated in Colorectal Carcinoma Cells in Response to Replication-dependent DNA Double Strand Breaks (2006)

The Mre11.Rad50.Nbs1 (MRN) complex binds DNA double strand breaks to repair DNA and activate checkpoints. We report MRN deficiency in three of seven colon carcinoma cell lines of the NCI Anticancer Drug Screen. To study the involvement of MRN in replication-mediated DNA double strand breaks, we examined checkpoint responses to camptothecin, which induces replication-mediated DNA double strand breaks after replication forks collide with topoisomerase I cleavage complexes. MRN-deficient cells were deficient for Chk2 activation, whereas Chk1 activation was independent of MRN. Chk2 activation was ataxia telangiectasia mutated (ATM)-dependent and associated with phosphorylation of Mre11 and Nbs1. Mre11 complementation in MRN-deficient HCT116 cells restored Chk2 activation as well as Rad50 and Nbs1 levels. Conversely, Mre11 down-regulation by small interference RNA (siRNA) in HT29 cells inhibited Chk2 activation and down-regulated Nbs1 and Rad50. Proteasome inhibition also restored Rad50 and Nbs1 levels in HCT116 cells suggesting that Mre11 stabilizes Rad50 and Nbs1. Chk2 activation was also defective in three of four MRN-proficient colorectal cell lines because of low Chk2 levels. Thus, six of seven colon carcinoma cell lines from the NCI Anticancer Drug Screen are functionally Chk2-deficient in response to replication-mediated DNA double strand breaks. We propose that Mre11 stabilizes Nbs1 and Rad50 and that MRN activates Chk2 downstream from ATM in response to replication-mediated DNA double strand breaks. Chk2 deficiency in HCT116 is associated with defective S-phase checkpoint, prolonged G2 arrest, and hypersensitivity to camptothecin. The high frequency of MRN and Chk2 deficiencies may contribute to genomic instability and therapeutic response to camptothecins in colorectal cancers.
Reducing Transmission Losses in Hollow THz Waveguides (2011)

Research on reducing material absorption in Terahertz (THz) waveguides has lead to development of guiding structures with transmission losses as low as 1 dB/m. Among waveguides that exhibit low loss at THz frequencies are the dielectric-lined hollow cylindrical metallic waveguides. Loss reduction in this waveguide is attributed to an ideal profile of the dominant hybrid HE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> mode. This mode profile also results in relatively low dispersion and very high coupling efficiency. In this contribution we overview properties of dielectric-lined hollow cylindrical metallic waveguides for THz waves, their design principles and the fabrication process. The impact of the mode profile on losses and dispersion at THz frequencies is confirmed experimentally by THz near-field imaging and THz time-domain spectroscopy and numerically by the finite element method.