gebhart/patrepeval huggingface dataset:
Mechanism of enhancement of microbial cell hydrophobicity by cationic polymers (1990)

Polycationic polymers have been noted for their effects in promoting cell adhesion to various surfaces, but previous studies have failed to describe a mechanism dealing with this type of adhesion. In the present study, three polycationic polymers (chitosan, poly-L-lysine, and lysozyme) were tested for their effects on microbial hydrophobicity, as determined by adhesion to hydrocarbon and polystyrene. Test strains (Escherichia coli, Candida albicans, and a nonhydrophobic mutant, MR-481, derived from Acinetobacter calcoaceticus RAG-1) were vortexed with hexadecane in the presence of the various polycations, and the extent of adhesion was measured turbidimetrically. Adhesion of all three test strains rose from near zero values to over 90% in the presence of low concentrations of chitosan (125 to 250 micrograms/ml). Adhesion occurred by adsorption of chitosan directly to the cell surface, since E. coli cells preincubated in the presence of the polymer were highly adherent, whereas hexadecane droplets pretreated with chitosan were subsequently unable to bind untreated cells. Inorganic cations (Na+, Mg2+) inhibited the chitosan-mediated adhesion of E. coli to hexadecane, presumably by interfering with the electrostatic interactions responsible for adsorption of the polymer to the bacterial surface. Chitosan similarly promoted E. coli adhesion to polystyrene at concentrations slightly higher than those which mediated adhesion to hexadecane. Poly-L-lysine also promoted microbial adhesion to hexadecane, although at concentrations somewhat higher than those observed for chitosan. In order to study the effect of the cationic protein lysozyme, adhesion was studied at 0 degree C (to prevent enzymatic activity), using n-octane as the test hydrocarbon. Adhesion of E. coli increased by 70% in the presence of 80 micrograms of lysozyme per ml. When the negatively charged carboxylate residues on the E. coli cell surface were substituted for positively charged ammonium groups, the resulting cells became highly hydrophobic, even in the absence of polycations. The observed "hydrophobicity" of the microbial cells in the presence of polycations is thus probably due to a loss of surface electronegativity. The data suggest that enhancement of hydrophobicity by polycationic polymers is a general phenomenon.
Phase I Trial of Anti-CD22 Recombinant Immunotoxin Moxetumomab Pasudotox (CAT-8015 or HA22) in Patients With Hairy Cell Leukemia (2012)

Moxetumomab pasudotox at doses up to 50 μg/kg QOD ×3 has activity in relapsed/refractory HCL and has a safety profile that supports further clinical development for treatment of this disease.
Sharing of receptor subunits and signal transduction pathway between the IL-4 and IL-13 receptor system. (1999)

In this review, we summarize the subunit structure of the interleukin (IL)-4 and IL-13 receptor system and the molecular mechanism of signals through the cytokine receptor systems. We have demonstrated that two different forms of IL-4R exist, classical and alternative. Classical IL-4R is predominantly expressed in hematopoietic cells and consists of IL-4R p140 (beta) and IL-2R gamma (gamma c) chains. The alternative form of IL-4R is predominantly expressed in nonhematopoietic cells and consists of IL-4R beta and IL-13R alpha' chains. Moreover, the alternative form of IL-4R is also used as a functional component in the IL-13R complex. For signal transduction through IL-4R and IL-13R, we have demonstrated that in nonhematopoietic cells, Janus protein tyrosine kinase (JAK) 2 is phosphorylated and activated instead of JAK3 tyrosine kinase. While JAK3 is required for signal transducer and activator of transcription-6 (STAT6) activation in hematopoietic cells, we recently demonstrated that in nonhematopoietic cells JAK2 is required for STAT6 activation for the alternative form of IL-4R. Thus, a major difference exists between hematopoietic and nonhematopoietic cells with regard to structure and signal transduction through the IL-4R and IL-13R systems.
NATsDB: Natural Antisense Transcripts DataBase (2006)

Natural antisense transcripts (NATs) are reverse complementary at least in part to the sequences of other endogenous sense transcripts. Most NATs are transcribed from opposite strands of their sense partners. They regulate sense genes at multiple levels and are implicated in various diseases. Using an improved whole-genome computational pipeline, we identified abundant cis-encoded exon-overlapping sense-antisense (SA) gene pairs in human (7356), mouse (6806), fly (1554), and eight other eukaryotic species (total 6534). We developed NATsDB (Natural Antisense Transcripts DataBase, http://natsdb.cbi.pku.edu.cn/) to enable efficient browsing, searching and downloading of this currently most comprehensive collection of SA genes, grouped into six classes based on their overlapping patterns. NATsDB also includes non-exon-overlapping bidirectional (NOB) genes and non-bidirectional (NBD) genes. To facilitate the study of functions, regulations and possible pathological implications, NATsDB includes extensive information about gene structures, poly(A) signals and tails, phastCons conservation, homologues in other species, repeat elements, expressed sequence tag (EST) expression profiles and OMIM disease association. NATsDB supports interactive graphical display of the alignment of all supporting EST and mRNA transcripts of the SA and NOB genes to the genomic loci. It supports advanced search by species, gene name, sequence accession number, chromosome location, coding potential, OMIM association and sequence similarity.
A Practical SNR-Guided Rate Adaptation (2008)

Rate adaptation is critical to the system performance of wireless networks. Typically, rate adaptation is considered as a MAC layer mechanism in IEEE 802.11. Most previous work relies only on frame losses to infer channel quality, but performs poorly if frame losses are mainly caused by interference. Recently SNR- based rate adaptation schemes have been proposed, but most of them have not been studied in a real environment. In this paper, we first conduct a systematic measurement-based study to confirm that in general SNR is a good prediction tool for channel quality, and identify two key challenges for this to be used in practice: (1) The SNR measures in hardware are often uncalibrated, and thus the SNR thresholds are hardware dependent. (2) The direct prediction from SNR to frame delivery ratio (FDR) is often over optimistic under interference conditions. Based on these observations, we present a novel practical SNR- Guided Rate Adaptation (SGRA) scheme. We implement and evaluate SGRA in a real test-bed and compare it with other three algorithms: ARF, RRAA and HRC. Our results show that SGRA outperforms the other three algorithms in all cases we have tested.
An Overview of the Salmonella Enteritidis Risk Assessment for Shell Eggs and Egg Products (2002)

This article summarizes a quantitative microbial risk assessment designed to characterize the public health impact of consumption of shell eggs and egg products contaminated with Salmonella Enteritidis (SE). This risk assessment's objectives were to: (1) establish the baseline risk of foodborne illness from SE, (2) identify and evaluate potential risk mitigation strategies, and (3) identify data gaps related to future research efforts. The risk assessment model has five modules. The Egg Production module estimates the number of eggs produced that are SE-contaminated. Shell Egg Processing, Egg Products Processing, and Preparation & Consumption modules estimate the increase or decrease in the numbers of SE organisms in eggs or egg products as they pass through storage, transportation, processing, and preparation. A Public Health Outcomes module then calculates the incidence of illnesses and four clinical outcomes, as well as the cases of reactive arthritis associated with SE infection following consumption. The baseline model estimates an average production of 2.3 million SE-contaminated shell eggs/year of the estimated 69 billion produced annually and predicts an average of 661,633, human illnesses per year from consumption of these eggs. The model estimates approximately 94% of these cases recover without medical care, 5% visit a physician, an additional 0.5% are hospitalized, and 0.05% result in death. The contribution of SE from commercially pasteurized egg products was estimated to be negligible. Five mitigation scenarios were selected for comparison of their individual and combined effects on the number of human illnesses. Results suggest that mitigation in only one segment of the farm-to-table continuum will be less effective than several applied in different segments. Key data gaps and areas for future research include the epidemiology of SE on farms, the bacteriology of SE in eggs, human behavior in food handling and preparation, and human responses to SE exposure.
Engineering of monoclonal antibodies and antibody-based fusion proteins: successes and challenges (2005)

Monoclonal antibodies (mAbs) and antibody-based fusion molecules have now come of age as therapeutics. Eighteen mAbs and two fusion molecules are on the market. mAbs directed against new targets are progressing at a rapid rate with the help of proteomics and genomics approaches. Many technical efforts have been made to generate a second-generation mAb with decreased immunogenicity and with optimised effector functions. The development of molecular engineering techniques applied to antibody molecules has also made it possible to design fusion molecules exhibiting different modules with bifunctional activities. Different approaches developed over the last two decades to generate and optimise therapeutic antibodies and antibody-based fusion molecules are described, with a particular focus on antibodies and fusion proteins used in oncology and inflammatory diseases. Some current technical challenges and trends are also discussed.
DIFFERENTIAL RADIOLABELLING OF LYMPHOCYTE MEMBRANE ALLOANTIGENS AND IMMUNOGLOBULINS: VARIATION OF H2O2 CONCENTRATION DURING LACTOPEROXIDASE CATALYZED CELL SURFACE RADIO‐IODINATION (1979)

The effect of H2O2 concentration on lactoperoxidase catalyzed cell surface radio-iodination and subsequent isolation of Murine splenic lymphocyte Ia, H-2K and Lyb-3 surface antigens and membrane immunoglobulins was studied. For most membrane polypeptides analyzed 0.3 mM H2O2 proved to be optimal for the recovery of radiolabelled antigens from detergent lysates of labelled cells by immunoprecipitation. Marked variations among surface antigens and membrane immunoglobulin polypeptide chains were observed for the iodination and recovery of these proteins above and below the optimal peroxide concentration. The results suggest that cell surface radio-iodination conditions should be standardized to the requirements of the particular membrane protein being studied. The differential iodination and recovery of discrete membrane components above and below optimal conditions may prove useful in the analysis of surface membrane protein structure and membrane association.
The α-Helical Domain Near the Amino Terminus Is Essential for Dimerization of Vascular Endothelial Growth Factor (1998)

Vascular endothelial growth factor (VEGF) is an endothelial cell-specific mitogen and a key mediator of aberrant endothelial cell proliferation and vascular permeability in a variety of human pathological situations such as tumor angiogenesis, diabetic retinopathy, or psoriasis. By amino-terminal deletion analysis and by site-directed mutagenesis we have identified a new domain within the amino-terminal alpha-helix that is essential for dimerization of VEGF. VEGF121 variants containing amino acids 8 to 121 or 14 to 121, respectively, either expressed in Escherichia coli and refolded in vitro, or expressed in Chinese hamster ovary cells, were in a dimeric conformation and showed full binding activity to VEGF receptors and stimulation of endothelial cell proliferation as compared with wild-type VEGF. In contrast, a VEGF121 variant covering amino acids 18 to 121, as well as a variant in which the hydrophobic amino acids Val14, Val15, Phe17, and Met18 within the amphipathic alpha-helix near the amino terminus were replaced by serine, failed to form biological active VEGF dimers. From these data we conclude that a domain between amino acids His12 and Asp19 within the amino-terminal alpha-helix is essential for formation of VEGF dimers, and we propose hydrophobic interactions between VEGF monomers to stabilize or favor dimerization.
M7: Next generation SPARC (2014)

This article consists of a collection of slides from the author's conference presentation on the special features, system design and architectures, processing capabilities, and targeted markets for Oracle's M7, the next generation SPARC family of products.
An iron catalyzed regioselective oxidation of terminal alkenes to aldehydes (2012)

Fe(BF(4))(2)·6H(2)O with pyridine-2,6-dicarboxylic acid and PhIO can efficiently catalyze the regioselective oxidation of terminal alkene derivatives to aldehydes under mild and benign reaction conditions.
Prevalence of Asymptomatic Nasopharyngeal Carriage of Chlamydia pneumoniae in Subjectively Healthy Adults: Assessment by Polymerase Chain Reaction-Enzyme Immunoassay and Culture (1995)

Although Chlamydia pneumoniae is a well-described and common respiratory tract pathogen, up to 90% of infections with this organism are thought to be asymptomatic. Because asymptomatic infection with C. pneumoniae has not been studied in a systematic manner, we conducted a prospective study of healthy adults to establish the prevalence of asymptomatic infection. Nasopharyngeal swab specimens were obtained from 104 subjectively healthy people and evaluated by culture and polymerase chain reaction-enzyme immunoassay (PCR-EIA) for the presence of the organism. Serum obtained from 103 of these individuals was tested by microimmunofluorescence for the titer of specific antibody to C. pneumoniae. For two individuals, C. pneumoniae was identified in nasopharyngeal specimens by culture and/or PCR-EIA; one of these individuals had an IgG titer of 1:256, whereas the other had no detectable antibody. Of the remaining 101 individuals with negative culture and PCR-EIA results, 19 fulfilled presently accepted serological criteria for acute infection; i.e., the IgM titer was > or = 1:16, the IgG titer was > or = 1:512, or both. On the basis of our findings, we conclude that asymptomatic upper airway infection and carriage with C. pneumoniae occur among subjectively healthy persons; we also propose that such individuals may represent a reservoir for this organism in the community. Further, this study demonstrates that currently available diagnostic tests for C. pneumoniae may be unable to accurately distinguish between infection responsible for respiratory tract disease and that representing carriage.
Feasibility of interstitial Doppler optical coherence tomography for in vivo detection of microvascular changes during photodynamic therapy (2006)

IS-DOCT is a potentially effective tool for real-time visualization and monitoring of the progress of PDT treatments. This capability may play an important role in elucidating the mechanisms of PDT in tumors, pre-treatment planning, feedback control for treatment optimization, determining treatment endpoints and post-treatment assessments.
Dexamethasone reduces tumor recurrence and metastasis after pancreatic tumor resection in SCID mice (2008)

DEX has a profound influence on the malignant phenotype of PDAC tumor cells in vitro in terms of inhibition of invasiveness and pro-inflammatory signaling. This was approved in vivo by reduced metastasizing capacity and reduced size of local tumor recurrence. Therefore, DEX-treatment appears to be an interesting therapeutical option in an adjuvant setting after pancreatic cancer resection.
Exploring API method parameter recommendations (2015)

A number of techniques have been developed that support method call completion. However, there has been little research on the problem of method parameter completion. In this paper, we first present a study that helps us to understand how developers complete method parameters. Based on our observations, we developed a recommendation technique, called Parc, that collects parameter usage context using a source code localness property that suggests that developers tend to collocate related code fragments. Parc uses previous code examples together with contextual and static type analysis to recommend method parameters. Evaluating our technique against the only available state-of-the-art tool using a number of subject systems and different Java libraries shows that our approach has potential. We also explore the parameter recommendation support provided by the Eclipse Java Development Tools (JDT). Finally, we discuss limitations of our proposed technique and outline future research directions.
Brain cholesterol turnover required for geranylgeraniol production and learning in mice (2006)

The mevalonate pathway produces cholesterol and nonsterol isoprenoids, such as geranylgeraniol. In the brain, a fraction of cholesterol is metabolized in neurons by the enzyme cholesterol 24-hydroxylase, and this depletion activates the mevalonate pathway. Brains from mice lacking 24-hydroxylase excrete cholesterol more slowly, and the tissue compensates by suppressing the mevalonate pathway. Here we report that this suppression causes a defect in learning. 24-Hydroxylase knockout mice exhibit severe deficiencies in spatial, associative, and motor learning, and in hippocampal long-term potentiation (LTP). Acute treatment of wild-type hippocampal slices with an inhibitor of the mevalonate pathway (a statin) also impairs LTP. The effects of statin treatment and genetic elimination of 24-hydroxylase on LTP are reversed by a 20-min treatment with geranylgeraniol but not by cholesterol. We conclude that cholesterol turnover in brain activates the mevalonate pathway and that a constant production of geranylgeraniol in a small subset of neurons is required for LTP and learning.
Hypercalcemia of cancer: an update. (1993)

Hypercalcemia of cancer is due to secretion of substances with parathyroid hormone (PTH)-like activity from tumours of the respiratory, gastrointestinal and urogenital tract as well as hematologic malignancies and breast cancer. PTH-related Protein (PTHrP) is secreted mainly from solid tumours and it has been recently recognized as being responsible for hypercalcemia mediated primarily via an increased renal reabsorption of calcium and secondly by an increased bone resorption. PTHrP-mRNA is expressed in a variety of normal tissues and has multiple physiologic and paracrine actions. Bone resorbing factors like the cytokines-lymphokines, interleukins, prostaglandins, TNF-alpha/TNF-beta, GM-CSF/G-CSF, TGF-alpha and TGF-beta are produced by certain solid and hematologic cancers and have also been implicated in tumour-induced hypercalcemia. The recently introduced PTHrP antagonists are hopeful therapeutic measures for the future.
Activin receptor‐like kinase5 inhibition suppresses mouse melanoma by ubiquitin degradation of Smad4, thereby derepressing eomesodermin in cytotoxic T lymphocytes (2013)

Varieties of transforming growth factor‐β (TGF‐β) antagonists have been developed to intervene with excessive TGF‐β signalling activity in cancer. Activin receptor‐like kinase5 (ALK5) inhibitors antagonize TGF‐β signalling by blocking TGF‐β receptor‐activated Smad (R‐Smad) phosphorylation. Here we report the novel mechanisms how ALK5 inhibitors exert a therapeutic effect on a mouse B16 melanoma model. Oral treatment with a novel ALK5 inhibitor, EW‐7197 (2.5 mg/kg daily) or a representative ALK5 inhibitor, LY‐2157299 (75 mg/kg bid) suppressed the progression of melanoma with enhanced cytotoxic T‐lymphocyte (CTL) responses. Notably, ALK5 inhibitors not only blocked R‐Smad phosphorylation, but also induced ubiquitin‐mediated degradation of the common Smad, Smad4 mainly in CD8 + T cells in melanoma‐bearing mice. Accordingly, T‐cell‐specific deletion of Smad4 was sufficient to suppress the progression of melanoma. We further identified eomesodermin (Eomes), the T‐box transcription factor regulating CTL functions, as a specific target repressed by TGF‐β via Smad4 and Smad3 in CD8 + T cells. Thus, ALK5 inhibition enhances anti‐melanoma CTL responses through ubiquitin‐mediated degradation of Smad4 in addition to the direct inhibitory effect on R‐Smad phosphorylation.
Nucleolin targeting AS1411 aptamer modified pH-sensitive micelles for enhanced delivery and antitumor efficacy of paclitaxel (2015)

Targeted drug delivery coupled with rapid drug release in cytoplasm is a powerful strategy to enhance efficacy and reduce off-target effects of anti-cancer drugs. Herein, we describe a dual-functional mixed micellar system consisting of a pH-responsive copolymer D-α-tocopheryl polyethylene glycol 1000-blockpoly-(β-amino ester) (TPGS-b-PBAE, TP) and AS1411 aptamer (Apt) decorated TPGS polymer (Apt-TPGS), which recognizes the over-expressed nucleolin on the plasma membrane of cancer cells. The anti-cancer drug paclitaxel (PTX) was encapsulated in the Apt-mixed micelles, and these drug-loaded micelles had a suitable particle size and zeta potential of 116.3 nm ± 12.4 nm and −26.2 mV ±4.2 mV, respectively. PTX/Apt-mixed micelles were stable at pH 7.4, but they dissociated and quickly released the encapsulated PTX in a weakly acidic environment (pH 5.5). Compared with non-Apt modified mixed micelles, more Apt-modified mixed micelles were internalized in SKOV3 ovarian cancer cells, whereas no significant difference in cellular uptake was observed in normal cells (LO2 cells). The enhanced transmembrane ability of Apt-modified mixed micelles was achieved through Apt-nucleolin interaction. With a synergistic effect of cancer cell recognition and pH-sensitive drug release, we observed significantly increased cytotoxicity and G2/M phase arrest against SKOV3 cells by PTX/Apt-mixed micelles. Intravenous administration of PTX/Apt-mixed micelles for 16 days significantly increased tumor accumulation of PTX, inhibited tumor growth, and reduced myelosuppression on tumor-bearing mice compared with free PTX injection. Therefore, this dual-functional Apt-mixed micellar system is a promising drug delivery system for targeted cancer therapy.
The continued development of the Spallation Neutron Source external antenna H− ion source (2010)

The U.S. Spallation Neutron Source (SNS) is an accelerator-based, pulsed neutron-scattering facility, currently in the process of ramping up neutron production. In order to ensure that the SNS will meet its operational commitments as well as provide for future facility upgrades with high reliability, we are developing a rf-driven, H(-) ion source based on a water-cooled, ceramic aluminum nitride (AlN) plasma chamber. To date, early versions of this source have delivered up to 42 mA to the SNS front end and unanalyzed beam currents up to approximately 100 mA (60 Hz, 1 ms) to the ion source test stand. This source was operated on the SNS accelerator from February to April 2009 and produced approximately 35 mA (beam current required by the ramp up plan) with availability of approximately 97%. During this run several ion source failures identified reliability issues, which must be addressed before the source re-enters production: plasma ignition, antenna lifetime, magnet cooling, and cooling jacket integrity. This report discusses these issues, details proposed engineering solutions, and notes progress to date.