gebhart/patrepeval huggingface dataset:
Role of Oral Bacteria in Respiratory Infection (1999)

An association between oral conditions such as periodontal disease and several respiratory conditions has been noted. For example, recent evidence has suggested a central role for the oral cavity in the process of respiratory infection. Oral periodontopathic bacteria can be aspirated into the lung to cause aspiration pneumonia. The teeth may also serve as a reservoir for respiratory pathogen colonization and subsequent nosocomial pneumonia. Typical respiratory pathogens have been shown to colonize the dental plaque of hospitalized intensive care and nursing home patients. Once established in the mouth, these pathogens may be aspirated into the lung to cause infection. Other epidemiologic studies have noted a relationship between poor oral hygiene or periodontal bone loss and chronic obstructive pulmonary disease. Several mechanisms are proposed to explain the potential role of oral bacteria in the pathogenesis of respiratory infection: 1. aspiration of oral pathogens (such as Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, etc.) into the lung to cause infection; 2. periodontal disease-associated enzymes in saliva may modify mucosal surfaces to promote adhesion and colonization by respiratory pathogens, which are then aspirated into the lung; 3. periodontal disease-associated enzymes may destroy salivary pellicles on pathogenic bacteria to hinder their clearance from the mucosal surface; and 4. cytokines originating from periodontal tissues may alter respiratory epithelium to promote infection by respiratory pathogens.
5′-Terminal Sequences of Spring Viremia of Carp Virus RNA Synthesized In Vitro (1979)

Sequence analyses have been undertaken on the 5' termini of the RNA species synthesized in vitro at 22 degrees C by Spring viremia of carp virion (SVCV)-associated transcriptase by using virus grown in mammalian BHK-21 cells. SVCV product RNA was synthesized in the absence or presence of low (0.56 muM) or high (0.8 mM) concentrations of added S-adenosyl-l-methionine (SAM). Two major sequences obtained in the absence (or in low concentrations) of SAM have been shown to be GpppAp and GpppAmpAp(C). A minor sequence detected when a low concentration of [(3)H]SAM was added to reaction mixtures was 7mGpppAmpAp. Larger quantities of the 7mGpppAmpAp(C) sequence, in addition to the GpppAmpAp(C) sequence, were obtained when high concentrations of SAM were used, and under these conditions no GpppAp sequences were detected. It has further been shown that with low concentrations of [(3)H]SAM the principle in vitro methylation of adenosine in SVCV product RNA occurred at the 2'-O-ribose position; no methylation at the N(6)-adenosine position and no internal product RNA methylation were detected. Comparison of the SVCV results to the published data on the 5'-terminal structures of the in vitro or in vivo mRNA species of vesicular stomatitis virus Indiana and vesicular stomatitis virus New Jersey suggests that the 5' sequences of transcript RNA of different rhabdoviruses may have been conserved.
Pharmacokinetics, Pharmacodynamics, Safety, and Tolerability of a Single-Dose of NN2211, a Long-Acting Glucagon-Like Peptide 1 Derivative, in Healthy Male Subjects (2002)

This study provides evidence that NN2211 has a pharmacokinetic profile consistent with once-daily dosing in humans.
Adenovirus serotype 5 E1A sensitizes tumor cells to NKG2D-dependent NK cell lysis and tumor rejection (2005)

The expression of the Adenovirus serotype 5 (Ad5) E1A oncogene sensitizes tumor cells to natural killer (NK) cell-mediated killing and tumor rejection in vivo. These effects are dependent on the ability of E1A to bind the transcriptional coadaptor protein p300. To test the hypothesis that E1A up-regulates ligands recognized by the NKG2D-activating receptor, we stably transfected the highly tumorigenic mouse fibrosarcoma cell line MCA-205 with Ad5-E1A or a mutant form of E1A that does not interact with p300 (E1A-Deltap300). Ad5-E1A, but not E1A-Deltap300, up-regulated the expression of the NKG2D ligand retinoic acid early inducible (RAE)-1, but not murine ULBP-like transcript 1, another NKG2D ligand, in four independently derived MCA-205 transfectants. The up-regulation of RAE-1 by E1A targeted MCA-205 tumor cells to lysis by NK cells, resulting in NKG2D-dependent tumor rejection in vivo. Moreover, the up-regulation of NKG2D ligands by E1A was not limited to mouse tumor cells, as E1A also increased the expression of NKG2D ligands on primary baby mouse kidney cells, human MB435S breast cancer cells, and human H4 fibrosarcoma cells.
Prospective comparison of blood and peritoneal lymphocytes from continuous ambulatory peritoneal dialysis patients. (1992)

Although a few studies have analyzed the characteristics of peritoneal lymphocytes from continuous ambulatory peritoneal dialysis (CAPD) patients, there have been no definitive longitudinal investigations comparing peripheral blood lymphocytes (PBL) with peritoneal lymphocytes (PL) from these patients. Therefore, the purpose of this study was to prospectively compare the phenotypes of PBL and PL of CAPD patients and to determine if phenotypic changes occurred from the initiation of CAPD therapy over the subsequent 12 months. Patients were categorized into younger (< 60 years) or older (> 60 years) to determine if age-related factors contributed to differences in lymphocyte phenotypes. Blood and overnight peritoneal dialysate effluents (PDE) were obtained from 18 patients at the initiation of CAPD therapy and for 11 successive months. Fourteen lymphocyte subsets were quantitated using monoclonal antibodies and flow cytometry analysis. CAPD patients had significantly higher percentages of peripheral activated T (CD3+/HLA-DR+) cells and natural killer (CD57+) cells at the beginning of CAPD than normal controls. There were significantly greater percentages of B cells, activated T cells, and suppressor T (CD8+/CD11b+) cells and significantly fewer helper T (CD4+) cells in the PDE as compared with the patients' peripheral lymphocytes. No significant changes were observed over time in the phenotypes of PBL and only one PL phenotype showed significant changes with fluctuating levels of CD4+/CD45RA+ cells with continued peritoneal dialysis. In general, these findings suggest that although both PBL and PL activation is occurring in clinically uninfected patients, the characteristics of lymphocytes are stable over time.
Investigating the stationarity of paediatric aspiration signals (2005)

An aspiration signal is the time-varying anterior-posterior acceleration measured infero-anterior to the thyroid notch when foreign material enters the airway during inspiration. The hypothesis of weak stationarity is tested on aspiration signals by the reverse arrangements test. Results indicate that aspiration signals cannot be uniformly regarded as weakly stationary. Forty-five percent of the examined signals violated the stationarity hypothesis. For these signals, time-varying variance and spectral density structure are identified as major sources of nonstationarity. Stationarity test results generally corroborate qualitative clinical descriptions of aspiration. However, stationarity analysis indicates that aspiration signals are highly heterogenous, a finding which poses significant challenges to the automatic detection of aspirations by accelerometry.
Hepatitis B virus X protein promotes the growth of hepatocellular carcinoma by modulation of the Notch signaling pathway (2012)

Hepatitis B virus X protein (HBx) plays a crucial role in the development of hepatocellular carcinoma (HCC), however, little is known about the mechanism. Here, we investigated the relationship between HBx and Notch signaling in HepG2 cells after they were transfected with the HBx gene. It was found that HBx upregulated the expression of Notch-1, Jagged-1 and Hes-1 at the transcriptional level by binding to the Notch-1 intracellular domain, which is congruent with the observations of enhanced malignant biological activities of HBx-transfected HepG2 cells compared with normal HepG2 cells. However, while Notch signaling was blocked, the HBx-induced abnormalities were partially reversed. These findings suggest that HBx may promote the progression of HCC via the activated Notch pathway.
The use of stabilized CMOS delay lines for the digitization of short time intervals (1993)

The basic advantages and limitations of using integrated digital CMOS delay lines for the digitization of short time intervals are discussed. Accuracies of 6-7 b and single-shot resolutions from 0.1 to 10 ns are demonstrated to be realizable using fully integrated, tapped, and voltage-controlled CMOS delay lines as a time base for the measurement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Human Pluripotent Stem Cells Differentiated in Fully Defined Medium Generate Hematopoietic CD34+ and CD34− Progenitors with Distinct Characteristics (2011)

Short-term, animal protein-free culture conditions are sufficient to sustain the differentiation of human ESC and iPSC into primitive hematopoietic progenitors, which, in turn, produce more mature blood cell types. However, additional factors have yet to be identified to allow their differentiation into definitive erythroid cultures.
Parallel index and query for large scale data analysis (2011)

Modern scientific datasets present numerous data management and analysis challenges. State-of-the-art index and query technologies are critical for facilitating interactive exploration of large datasets, but numerous challenges remain in terms of designing a system for processing general scientific datasets. The system needs to be able to run on distributed multi-core platforms, efficiently utilize underlying I/O infrastructure, and scale to massive datasets.
New Methods for Proteomic Research: Preparation of Proteins with N-Terminal Cysteines for Labeling and Conjugation This research was supported by the NIH (R37 GM44154). (2002)

The highly selective tobacco etch virus Nla protease (TEV protease) can be used to remove affinity tags with mutated cleavage sites to produce proteins for site-specific labeling and chemoselective ligations (see scheme). This provides a simple, efficient method for producing proteins with N-terminal cysteines for proteomic applications.
MOLECULAR AND CELLULAR ASPECTS OF THE ARBUSCULAR MYCORRHIZAL SYMBIOSIS (1999)

Arbuscular mycorrhizae are symbiotic associations formed between a wide range of plant species including angiosperms, gymnosperms, pteridophytes, and some bryophytes, and a limited range of fungi belonging to a single order, the Glomales. The symbiosis develops in the plant roots where the fungus colonizes the apoplast and cells of the cortex to access carbon supplied by the plant. The fungal contribution to the symbiosis is complex, but a major aspect includes the transfer of mineral nutrients, particularly phosphate from the soil to the plant. Development of this highly compatible association requires the coordinate molecular and cellular differentiation of both symbionts to form specialized interfaces over which bi-directional nutrient transfer occurs. Recent insights into the molecular events underlying these aspects of the symbiosis are discussed.
Rapamycin reduced pulmonary vascular remodelling by inhibiting cell proliferation via Akt/mTOR signalling pathway down-regulation in the carotid artery–jugular vein shunt pulmonary hypertension rat model (2017)

Rapamycin reduced pulmonary vascular remodelling by inhibiting cell proliferation via Akt/mTOR signalling pathway down-regulation in the CA-JV shunt-induced PAH model in rats. Thus, rapamycin may be a novel candidate drug for the treatment of PAH.
Pathogenesis of cutaneous lupus erythematosus: common and different features in distinct subsets (2010)

The term 'cutaneous lupus erythematosus' (CLE) comprises several related autoimmune skin disorders, defined as 'specific' skin manifestations of lupus erythematosus (LE). The spectrum of clinical presentation of CLE is wide, reaching from mild erythema to disseminated scarring skin lesions. There is increasing knowledge concerning the pathogenesis of LE skin lesions and it has been shown that a complex network of cutaneous cytokines, chemokines and adhesion molecules orchestrate and promote tissue injury observed in LE skin lesions. However, a complete understanding of the diverse pathophysiological mechanisms in the different CLE subsets does not exist. Here we review the main pathological features described in CLE patients against the background of the clinical diversity of different CLE subtypes.
DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes (2002)

The light-harvesting properties of cationic conjugated polymers are used to sensitize the emission of a dye on a specific peptide nucleic acid (PNA) sequence for the purpose of homogeneous, "real-time" DNA detection. Signal transduction is controlled by hybridization of the neutral PNA probe and the negative DNA target. Electrostatic interactions bring the hybrid complex and cationic polymer within distances required for Förster energy transfer. Conjugated polymer excitation provides fluorescein emission >25 times higher than that obtained by exciting the dye, allowing detection of target DNA at concentrations of 10 pM with a standard fluorometer. A simple and highly sensitive assay with optical amplification that uses the improved hybridization behavior of PNA/DNA complexes is thus demonstrated.
Murine alanine aminotransferase: cDNA cloning, functional expression, and differential gene regulation in mouse fatty liver (2004)

Alanine aminotransferase (ALT) is a widely used index of liver integrity or hepatocellular damage in clinics as well as a key enzyme in intermediatary metabolism. In this study, we have cloned the complementary DNAs of murine homologues of human alanine aminotransferase 1 and 2 (ALT1 and ALT2). The deduced peptides of murine ALT1 (mALT1) and ALT2 (mALT2) share 87% and 93% identity, respectively, with their human counterparts at the amino acid level. Murine ALT genes localize to separate chromosomes, with mALT1 gene (gpt1) on chromosome 15 and mALT2 gene (gpt2) on chromosome 8. The murine gpt1 and gpt2 differ in messenger RNA expression: gpt1 is mainly expressed in liver, bowel, and white adipose tissue and gpt2 is highly expressed in muscle, liver, and white adipose tissue. Expression of recombinant mALT1 and mALT2 proteins in Escherichia coli (E. coli) produced functional enzymes that catalyze alanine transamination. The potential diagnostic value of ALT isoenzymes in liver disease was evaluated in an obese animal model. In fatty livers of obese mice, ALT2 gene expression is induced 2-fold, but ALT1 remains the same. Furthermore, in fatty liver, total hepatic ALT activity is elevated significantly by 30% whereas aspartate aminotransferase (AST) activity remains unchanged. In conclusion, these results indicate that ALT2 may be responsible for the increased ALT activity in hepatic steatosis and provide evidence that an ALT isoenzyme-specific assay may have more diagnostic value than the total ALT activity assay currently in clinical use.
Measurement of Hole Volume in Amorphous Polymers Using Positron Spectroscopy (1996)

Positron annihilation lifetime spectroscopy (PALS) measurements, in the temperature range 110−480 K, are given for three linear, amorphous polymers. Based on these measurements, a method is proposed for evaluating the hole volume in amorphous thermoplastics. Our studies show that hole volume is composed of static and dynamic components. We demonstrate that the dynamic component, which is a result of the thermal vibrations of the molecular chains, is strongly correlated to thermodynamic volume/density fluctuations. The static hole volume is interpreted as “frozen-in” fluctuations, which are manifested as nanometer-sized flaws in the packing of molecular chains. The results from PALS measurements reported in our work are in very good agreement with results from small-angle X-ray scattering measurements.
Evidence for targeted gene delivery to Hep G2 hepatoma cells in vitro (1988)

We have developed a system for targeting foreign DNA to hepatocytes in vitro using a soluble DNA carrier that takes advantage of receptor-mediated endocytosis to achieve internalization. The idea is based on the fact that hepatocytes possess a unique receptor that binds and internalizes galactose-terminal (asialo)glycoproteins. To create a targetable carrier system that could bind DNA in a nondeforming manner, we used poly(L-lysine) to bind DNA in a strong but noncovalent interaction. An asialoglycoprotein, asialoorosomucoid (AsOR), was chemically coupled to poly(L-lysine) to form an asialoorosomucoid-poly(L-lysine) conjugate. Various proportions of conjugate to DNA were tested to determine conditions that maximized DNA content in a soluble complex and that limited solubility of complexes. To test the targetable gene delivery system, AsOR-poly(L-lysine) conjugate was complexed to the plasmid pSV2 CAT containing the gene for chloramphenicol acetyltransferase (CAT) driven by an SV-40 promoter. We tested this complex using a model system consisting of human hepatoma cell line Hep G2 [asialoglycoprotein receptor (+)], hepatoma SK-Hep 1, IMR-90 fibroblasts, and uterine smooth muscle [receptor (-)] cells. Each cell line was incubated with 0.2 micron filtered AsOR-poly(L-lysine)-DNA complex or controls consisting of DNA plus AsOR, DNA plus poly(L-lysine), or DNA alone. Cells were assayed for the presence of CAT activity as a measure of gene transformation. SK-Hep 1, IMR-90, and smooth muscle [receptor (-)] cells produced no detectable acetylated chloramphenicol derivatives under any of these conditions.(ABSTRACT TRUNCATED AT 250 WORDS)
Electrochemical Nanoimprinting with Solid-State Superionic Stamps (2007)

This letter presents a solid-state electrochemical nanoimprint process for direct patterning of metallic nanostructures. It uses a patterned solid electrolyte or superionic conductor (such as silver sulfide) as a stamp and etches a metallic film by an electrochemical reaction. Our preliminary experiments demonstrate repeatable and high-fidelity pattern transfer with features down to 50 nm on silver films of thicknesses ranging from 50 to 500 nm. As the process is conducted in an ambient environment and does not involve the use of liquids, it displays potential for single-step, high-throughput, large-area manufacturing of metallic nanostructures. The use of superionic conductors in manufacturing opens up a new and potentially energy-efficient approach to nanopatterning and fabrication. It offers a highly competitive approach, both as a stand-alone process and as a complement of other nanofabrication techniques, to fabricating chemical sensors, photonic and plasmonic structures, and electronic interconnects.
Metabolomic and Proteomic Analysis of a Clonal Insulin-Producing β-Cell Line (INS-1 832/13) (2007)

Metabolites generated from fuel metabolism in pancreatic beta-cells control exocytosis of insulin, a process which fails in type 2 diabetes. To identify and quantify these metabolites, global and unbiased analysis of cellular metabolism is required. To this end, polar metabolites, extracted from the clonal 832/13 beta-cell line cultured at 2.8 and 16.7 mM glucose for 48 h, were derivatized followed by identification and quantification, using gas chromatography (GC) and mass spectrometry (MS). After culture at 16.7 mM glucose for 48 h, 832/13 beta-cells exhibited a phenotype reminiscent of glucotoxicity with decreased content and secretion of insulin. The metabolomic analysis revealed alterations in the levels of 7 metabolites derived from glycolysis, the TCA cycle and pentose phosphate shunt, and 4 amino acids. Principal component analysis of the metabolite data showed two clusters, corresponding to the cells cultured at 2.8 and 16.7 mM glucose, respectively. Concurrent changes in protein expression were analyzed by 2-D gel electrophoresis followed by LC-MS/MS. The identities of 86 spots corresponding to 75 unique proteins that were significantly different in 832/13 beta-cells cultured at 16.7 mM glucose were established. Only 5 of these were found to be metabolic enzymes that could be involved in the metabolomic alterations observed. Anticipated changes in metabolite levels in cells exposed to increased glucose were observed, while changes in enzyme levels were much less profound. This suggests that substrate availability, allosteric regulation, and/or post-translational modifications are more important determinants of metabolite levels than enzyme expression at the protein level.
Explaining effects of eye gaze on mediated group conversations: (2002)

We present an experiment examining effects of gaze on speech during three-person conversations. Understanding such effects is crucial for the design of teleconferencing systems and Collaborative Virtual Environments (CVEs). Previous findings suggest subjects take more turns when they experience more gaze. We evaluated whether this is because more gaze allowed them to better observe whether they were being addressed. We compared speaking behavior between two conditions: (1) in which subjects experienced gaze synchronized with conversational attention, and (2) in which subjects experienced random gaze. The amount of gaze experienced by subjects was a covariate. Results show subjects were 22% more likely to speak when gaze behavior was synchronized with conversational attention. However, covariance analysis showed these results were due to differences in amount of gaze rather than synchronization of gaze, with correlations of .62 between amount of gaze and amount of subject speech. Task performance was 46% higher when gaze was synchronized. We conclude it is commendable to use synchronized gaze models when designing CVEs, but depending on task situation, random models generating sufficient amounts of gaze may suffice.
Cargo-dependent cytotoxicity and delivery efficacy of cell-penetrating peptides: a comparative study (2007)

The use of CPPs (cell-penetrating peptides) as delivery vectors for bioactive molecules has been an emerging field since 1994 when the first CPP, penetratin, was discovered. Since then, several CPPs, including the widely used Tat (transactivator of transcription) peptide, have been developed and utilized to translocate a wide range of compounds across the plasma membrane of cells both in vivo and in vitro. Although the field has emerged as a possible future candidate for drug delivery, little attention has been given to the potential toxic side effects that these peptides might exhibit in cargo delivery. Also, no comprehensive study has been performed to evaluate the relative efficacy of single CPPs to convey different cargos. Therefore we selected three of the major CPPs, penetratin, Tat and transportan 10, and evaluated their ability to deliver commonly used cargos, including fluoresceinyl moiety, double-stranded DNA and proteins (i.e. avidin and streptavidin), and studied their effect on membrane integrity and cell viability. Our results demonstrate the unfeasibility to use the translocation efficacy of fluorescein moiety as a gauge for CPP efficiency, since the delivery properties are dependent on the cargo used. Furthermore, and no less importantly, the toxicity of CPPs depends heavily on peptide concentration, cargo molecule and coupling strategy.
Aegis: A Single-Chip Secure Processor (2007)

In this article, we introduce a single-chip secure processor called Aegis. In addition to supporting mechanisms to authenticate the platform and software, our processor incorporates mechanisms to protect the integrity and privacy of applications from physical attacks as well as software attacks. Therefore, physically secure systems can be built using this processor. Two key primitives, physical unclonable functions (PUFs) and off-chip memory protection, enable the physical security of our system. These primitives can also be easily applied to other secure computing systems to enhance their security.