gebhart/patrepeval huggingface dataset:
Enabling Energy-Efficient and Quality Localization Services (2006)

Localization research has focused on improving the accuracy of pinpointing the physical location of a target. We think that the energy efficiency and the quality of the localization services (QoLS) are equally important properties of localization systems. We refer to the QoLS as the timely supply of the location information to the applications. Energy efficiency and quality are seemingly two contradictive goals in terms of determining the rate of triggering the localization systems to perform the necessary computation and communication. In that, a lower location sampling rate contributes to a lower level of energy consumption but in the meantime compromises the timeliness of acquiring the location information. Opting for energy efficient and quality localization services, we propose a mobility-aware mechanism that adapts the sampling rate to the target mobility. Results from our simulations confirm that the adaptive sampling approach is promising and effective.
Quantitating secretion rates of individual cells: Design of secretion assays (1998)

To observe events occurring in the microenvironment surrounding individual cells, a mathematical framework has been developed describing the behavior of a compound following its secretion by a single cell. This description is based on the diffusional and binding processes taking place in the vicinity of the cell surface. It allows prediction of the rate of capture and accumulation of a secreted compound around a single cell. This concept provides the basis for the design of two experimental assays for measuring single-cell secretion rates: (1) Cells are immobilized in hydrogel microbeads which contain capture sites for the secreted compound; and (2) artificial receptors are bound directly to the cell surface which are capable of binding molecules secreted by individual cells. This general methodology is developed in the specific case of the model organism Saccharomyces cerevisiae secreting a heterologous protein, but can be applied to any cell/secreted protein combination. Binding studies have shown that approximately 2 x 10(5) of these artificial receptors can be attached to the surface of a single yeast cell. At this surface density of a putative artificial receptor, it is predicted that single-cell secretion rates of 47 molecules/cell/sec of a 150 kDa protein can be detected. Simulations indicate that a microbead loaded with 5 x 10(6) capture antibodies will result in detection of secretion of this protein at rates as low as 4 molecules/cell/sec.
Expanding Dendritic Cells In Vivo Enhances the Induction of Oral Tolerance (1998)

The intestine is under perpetual challenge from both pathogens and essential nutrients, yet the mucosal immune system is able to discriminate effectively between harmful and innocuous Ags. It is likely that this selective immunoregulation is dependent on the nature of the APC at sites where gut Ags are processed and presented. Dendritic cells (DC) are considered the most potent of APC and are renowned for their immunostimulatory role in the initiation of immune responses. To investigate the role of DC in regulating the homeostatic balance between mucosal immunity and tolerance, we treated mice with Flt3 ligand (Flt3L), a growth factor that expands DC in vivo, and assessed subsequent systemic immune responsiveness using mouse models of oral tolerance. Surprisingly, mice treated with Flt3L to expand DC exhibited more profound systemic tolerance after they were fed soluble Ag. Most notably, tolerance could be induced in Flt3L-treated mice using very low doses of Ag that were ineffective in control animals. These findings contrast with the generally accepted view of DC as immunostimulatory APC and furthermore suggest a pivotal role for DC during the induction of tolerance following mucosal administration of Ag.
CD44 Interaction with Tiam1 Promotes Rac1 Signaling and Hyaluronic Acid-mediated Breast Tumor Cell Migration (2000)

In this study we have explored the interaction between CD44 (the hyaluronic acid (HA)-binding receptor) and Tiam1 (a guanine nucleotide exchange factor) in metastatic breast tumor cells (SP1 cell line). Immunoprecipitation and immunoblot analyses indicate that both the CD44v3 isoform and the Tiam1 protein are expressed in SP1 cells and that these two proteins are physically associated as a complex in vivo. Using an Escherichia coli-derived calmodulin-binding peptide-tagged Tiam1 fragment (i.e. the NH(2)-terminal pleckstrin homology (PHn) domain and an adjacent protein interaction domain designated as PHn-CC-Ex, amino acids 393-738 of Tiam1) and an in vitro binding assay, we have detected a specific binding interaction between the Tiam1 PHn-CC-Ex domain and CD44. Scatchard plot analysis indicates that there is a single high affinity CD44 binding site in the PHn-CC-Ex domain of Tiam1 with an apparent dissociation constant (K(d)) of 0.2 nM, which is comparable with CD44 binding (K(d) = approximately 0.13 nM) to intact Tiam1. These findings suggest that the PHn-CC-Ex domain is the primary Tiam1-binding region for CD44. Most importantly, the binding of HA to CD44v3 of SP1 cells stimulates Tiam1-catalyzed Rac1 signaling and cytoskeleton-mediated tumor cell migration. Transfection of SP1 cells with Tiam1cDNA promotes Tiam1 association with CD44v3 and up-regulates Rac1 signaling as well as HA/CD44v3-mediated breast tumor cell migration. Co-transfection of SP1 cells with PHn-CC-Ex cDNA and Tiam1 cDNA effectively inhibits Tiam1 association with CD44 and efficiently blocks tumor behaviors. Taken together, we believe that the linkage between CD44v3 isoform and the PHn-CC-EX domain of Tiam1 is required for HA stimulated Rac1 signaling and cytoskeleton-mediated tumor cell migration during breast cancer progression.
Influence of Music on Ratings of Perceived Exertion during 20 Minutes of Moderate Intensity Exercise (2000)

The effects of different types of music on ratings of perceived exertion (RPE) during 20 min. of moderate intensity exercise were examined. 27 physically active subjects (age 18-30 yr.) performed a graded exercise test on a cycle ergometer to establish peak aerobic power (VO2peak). Four 20-min. exercise sessions were performed at a power output equal to 70% of VO2peak in a soundproof visually sterile room. The sessions were randomly assigned from the conditions of fast upbeat music, classical music, self-selected music, and no music. Heart rate, peripheral RPE, central RPE, and overall RPE were measured every 5 min. during exercise. No significant differences were found in heart rate among the four conditions indicating similar exercise intensity during each condition. Each type of music resulted in a reduced peripheral, central, and overall RPE when compared with the no-music condition. The data indicate that different types of music can act as an effective passive distractor during exercise and are associated with lower ratings of perceived exertion.
Oxygen supply and oxygen-dependent gene expression in differentiating embryonic stem cells. (1996)

Blastocyst-derived pluripotent mouse embryonic stem cells can differentiate in vitro to form so-called embryoid bodies (EBs), which recapitulate several aspects of murine embryogenesis. We used this in vitro model to study oxygen supply and consumption as well as the response to reduced oxygenation during the earliest stages of development. EBs were found to grow equally well when cultured at 20% (normoxia) or 1% (hypoxia) oxygen during the first 5 days of differentiation. Microelectrode measurements of pericellular oxygen tension within 13- to 14-day-old EBs (diameter 510-890 micron) done at 20% oxygen revealed efficient oxygenation of the EBs' core region. Confocal laser scanning microscopy analysis of EBs incubated with fluorescent dyes that specifically stain living cells confirmed that the cells within an EB were viable. To determine the EBs' capability to sense low oxygen tension and to specifically respond to low ambient oxygen by modulating gene expression we quantified aldolase A and vascular endothelial growth factor (VEGF) mRNAs, since expression of these genes is upregulated by hypoxia in a variety of cells. Compared with the normoxic controls, we found increased aldolase A and VEGF mRNA levels after exposing 8- to 9-day-old EBs to 1% oxygen. We propose that EBs represent a powerful tool to study oxygen-regulated gene expression during the early steps of embryogenesis, where the preimplantation conceptus resides in a fluid environment with low oxygen tension until implantation and vascularization allow efficient oxygenation.
Development of Hot Gas Cleanup Technology for IGCC. Technical Development Trends of 3 Types Hot Gas Cleanup Process. (1996)

IGCC systeme are expected to be of practicable use in the near future, in view of its prominent environmental compatibility and higher thermal energy efficiency. The highest themal efficiency is achievable when the gas cleanup is conducted at a high temperature and pressure. To make the most of these characteristics of high thermal efficiency that is associated with this IGCC, development of hot gas cleanup technology is essential.IGC Association installed a 200t/d pilot plant in 1990 at Nakoso site, and a hot gas cleanup facility that is composed of the fluidized-bed desulfurization unit and the granular bed dust collector has been operating. Also, Fixed-bed type and Moving-bed type hot gas cleanup facilities were installed in 1993. The characteristics of desulfurization and dust removal were investigated using these facilities. Sulfur and dust concentration in the clean gas were under the target value. From its result, we confirmed that all the 3 types hot gas cleanup processes have high performance.
A thermodynamic approach to designing structure-free combinatorial DNA word sets (2005)

An algorithm is presented for the generation of sets of non-interacting DNA sequences, employing existing thermodynamic models for the prediction of duplex stabilities and secondary structures. A DNA 'word' structure is employed in which individual DNA 'words' of a given length (e.g. 12mer and 16mer) may be concatenated into longer sequences (e.g. four tandem words and six tandem words). This approach, where multiple word variants are used at each tandem word position, allows very large sets of non-interacting DNA strands to be assembled from combinations of the individual words. Word sets were generated and their figures of merit are compared to sets as described previously in the literature (e.g. 4, 8, 12, 15 and 16mer). The predicted hybridization behavior was experimentally verified on selected members of the sets using standard UV hyperchromism measurements of duplex melting temperatures (T(m)s). Additional experimental validation was obtained by using the sequences in formulating and solving a small example of a DNA computing problem.
Shape-time photography (2003)

We introduce a new method to describe shape relationships over time in a photograph. We acquire both range and image information in a sequence of frames using a stationary stereo camera. From the pictures taken, we compute a composite image consisting of the pixels from the surfaces closest to the camera over all the time frames. Through occlusion cues, this composite reveals 3-D relationships between the shapes at different times. We call the composite a shape-time photograph. Small errors in stereo depth measurements can create artifacts in the shape-time images. We correct most of these using a Markov network to estimate the most probable front-surface pixel, taking into account (a) the stereo depth measurements and their uncertainties, and (b) spatial continuity assumptions for the time-frame assignments of the front-surface pixels.
Distilling complexity to advance cardiac tissue engineering (2016)

The promise of cardiac tissue engineering is in the ability to recapitulate in vitro the functional aspects of a healthy heart and disease pathology as well as to design replacement muscle for clinical therapy. Parts of this promise have been realized; others have not. In a meeting of scientists in this field, five central challenges or "big questions" were articulated that, if addressed, could substantially advance the current state of the art in modeling heart disease and realizing heart repair.
Detection of bacteria in blood by centrifugation and filtration (1991)

Culture of blood is the most frequent means of diagnosing bacteremia. However, conventional blood culturing methods are slow in isolating bacteria. We developed a method for isolation of bacteria by centrifugation and filtration. Fresh human whole blood was inoculated with facultatively anaerobic and aerobic microorganisms (3 to 172 microorganisms per 5 ml). Seeded blood was then mixed with Ficoll-Hypaque (density, 1.149 +/- 0.002 g/ml) and centrifuged (386 x g) for 30 min at ambient temperature. The entire gradient (plasma, leukocytes, and Ficoll-Hypaque) was removed and filtered through a 0.22-micron membrane filter (Millipore). The filters were then placed on chocolate agar plates and incubated at 35 degrees C in a humidified atmosphere containing 5% CO2. For each bacterium tested, approximately 35 to 100% of the viable microorganisms were recovered when compared with control cultures (pour plates of seeded blood). All bacteria produced isolated colonies on filters after overnight incubation (18 h). This procedure may prove to be a more rapid method for isolating bacteria from clinical blood samples than the blood culture bottle technique.
Genetic and Physical Mapping (1990)

Begins a series that will present a volume two or three times a year with invited articles reviewing recent advances in gene mapping, arrangement, and function. The five articles in the initial volume discuss a fluorescence in situ hybridization approach, hybridization fingerprinting, yeast artifici
Tolfenamic Acid Induces Apoptosis and Growth Inhibition in Head and Neck Cancer: Involvement of NAG-1 Expression (2012)

Nonsteroidal anti-inflammatory drug-activated gene-1 (NAG-1) is induced by nonsteroidal anti-inflammatory drugs and possesses proapoptotic and antitumorigenic activities. Although tolfenamic acid (TA) induces apoptosis in head and neck cancer cells, the relationship between NAG-1 and TA has not been determined. This study investigated the induction of apoptosis in head and neck cancer cells treated by TA and the role of NAG-1 expression in this induction. TA reduced head and neck cancer cell viability in a dose-dependent manner and induced apoptosis. The induced apoptosis was coincident with the expression of NAG-1. Overexpression of NAG-1 enhanced the apoptotic effect of TA, whereas suppression of NAG-1 expression by small interfering RNA attenuated TA-induced apoptosis. TA significantly inhibited tumor formation as assessed by xenograft models, and this result accompanied the induction of apoptotic cells and NAG-1 expression in tumor tissue samples. Taken together, these results demonstrate that TA induces apoptosis via NAG-1 expression in head and neck squamous cell carcinoma, providing an additional mechanistic explanation for the apoptotic activity of TA.
Biomarkers for pancreatic cancer: Recent achievements in proteomics and genomics through classical and multivariate statistical methods (2014)

Pancreatic cancer (PC) is one of the most aggressive and lethal neoplastic diseases. A valid alternative to the usual invasive diagnostic tools would certainly be the determination of biomarkers in peripheral fluids to provide less invasive tools for early diagnosis. Nowadays, biomarkers are generally investigated mainly in peripheral blood and tissues through high-throughput omics techniques comparing control vs pathological samples. The results can be evaluated by two main strategies: (1) classical methods in which the identification of significant biomarkers is accomplished by monovariate statistical tests where each biomarker is considered as independent from the others; and (2) multivariate methods, taking into consideration the correlations existing among the biomarkers themselves. This last approach is very powerful since it allows the identification of pools of biomarkers with diagnostic and prognostic performances which are superior to single markers in terms of sensitivity, specificity and robustness. Multivariate techniques are usually applied with variable selection procedures to provide a restricted set of biomarkers with the best predictive ability; however, standard selection methods are usually aimed at the identification of the smallest set of variables with the best predictive ability and exhaustivity is usually neglected. The exhaustive search for biomarkers is instead an important alternative to standard variable selection since it can provide information about the etiology of the pathology by producing a comprehensive set of markers. In this review, the most recent applications of the omics techniques (proteomics, genomics and metabolomics) to the identification of exploratory biomarkers for PC will be presented with particular regard to the statistical methods adopted for their identification. The basic theory related to classical and multivariate methods for identification of biomarkers is presented and then, the most recent applications in this field are discussed.
In vitro and in vivo adenovirus-mediated p53 and p16 tumor suppressor therapy in ovarian cancer. (2001)

Overall, p16 demonstrated greater growth inhibition than p53 both in vivo and in vitro. The p16/p53 combination demonstrated a consistent trend toward increased growth suppression and apoptosis over p16 or p53 alone. Adenovirus-mediated p16 may be a viable future treatment for ovarian cancer.
High resolution magic angle spinning 1H nuclear magnetic resonance analysis of intact prostatic hyperplastic and tumour tissues (1998)

High resolution magic angle spinning (MAS) 1H nuclear magnetic resonance (NMR) spectra of whole pieces of human prostatic tissue (<40 mg per sample) from patients with benign prostatic hyperplasia (BPH) and malignant tumours have been obtained and compared with high resolution NMR solution state spectra obtained via a standard tissue extraction method. Well resolved MAS-NMR spectra of the tissue samples were obtained in which both cytosolic and membrane-related compounds could be identified. Two-dimensional 1H MAS-NMR measurements, including J-resolved and shift correlation spectra, were also obtained to allow metabolite signal assignment. In all cases high quality spectra were obtained that were rich in bioanalytical information on a wide range of intracellular metabolites and lipids. Marked differences were observed between MAS spectra from tumours versus BPH tissue, particularly in the lipid signals, which were much more intense in tumours. This was in contrast to the protein-free extracts of the same samples which showed much more similar NMR profiles for the two disease classes. These data indicate that MAS-NMR spectra of intact tissue biopsy samples give a wider range of bioanalytical information on small and large molecules than conventional, more labour intensive cell extraction procedures, and this strengthens the case for the use of MAS-NMR in clinical diagnostics.
Tenascin-C Expression in Equine Tendon-derived Cells During Proliferation and Migration (2013)

In vitro cell studies might be a useful tool for studying tendon pathology, but no suitable in vitro models exist for tendon disorders. The purpose of this study was to confirm whether cell scratch culture using tendon-derived fibroblasts can provide a suitable in vitro tendon disorder model. Extracellular matrix components were examined immunohistochemically in tendon tissue, and then their related gene expression levels were analyzed by conventional reverse transcription polymerase chain reaction (RT-PCR) and/or quantitative real-time RT-PCR in tissues and cells. Collagen type I (Col I), collagen type III (Col III), tenascin-C (TN-C) and cartilage oligomeric matrix protein (COMP) were detected in tendon tissue sections, and RT-PCR confirmed their expression in tendon tissue and cells. Cells that had been cultured from explanted tendon tissue maintained the characteristics of in vivo tendon cells. The combination of TN-C and COMP might be a useful marker of tendon cells because they display more tendon-specific expression than Col I and III. In particular, the significant increase of TN-C mRNA expression in the scratch wound assay, at 12 hr after scratching, concomitant with the regeneration of the cell sheet, indicates its crucial role in tendon cell proliferation and migration. Thus, TN-C appears to be a key factor in tendon wound healing. In vitro cell scratch assays using tendon cells appear to mimic the repair of tendon tissue after injury.
Lutetium Monophthalocyanine and Diphthalocyanine Complexes and Lithium Naphthalocyanine as Catalysts for Electrochemical CO[sub 2] Reduction (2003)

Phthalocyanine and naphthalocyanine complexes with redox-inactive metals adsorbed on activated carbon supports were shown to be effective catalysts for electroreduction in the form of gas diffusion electrodes, yielding carbon monoxide with current efficiencies up to ca. 75%. A mechanism for electroreduction catalyzed by these complexes has been proposed in which the key step is the coordination of a molecule to the external N-atom of the phthalocyanine or naphthalocyanine ring. © 2003 The Electrochemical Society. All rights reserved.
The usefulness of induced sputum in the diagnosis of Pneumocystis carinii pneumonia in patients with the acquired immunodeficiency syndrome. (1986)

Thirty-two patients with or suspected of having the acquired immunodeficiency syndrome were evaluated for opportunistic lung infection using examination of sputum induced by inhalation of 3% saline. The specimens obtained were stained with Giemsa stain and examined for Pneumocystis carinii. Smears of sputum were also appropriately stained and examined for acid-fast organisms and fungi, as well as cultured for these organisms. Patients whose sputum did not contain P. carinii had bronchoscopy within 24 h of sputum induction. Twenty-five of the 32 patients were ultimately determined to have P. carinii pneumonia. Of these, 14 were detected by examination of sputum (sensitivity, 56%). Of 18 patients whose sputum did not contain P. carinii, 11 had the organism detected in specimens obtained by bronchoscopy (negative predictive value, 39%). There were no clinical features that identified patients more likely to have a positive sputum examination. No additional treatable lung pathogens appeared to be missed by sputum examination. In this select population, examination of induced sputum establishes the diagnosis of P. carinii pneumonia in a significant proportion of patients, thereby decreasing the need for more invasive procedures.
The Aging Eye: Common Degenerative Mechanisms Between the Alzheimer's Brain and Retinal Disease (2013)

Alzheimer's disease (AD) is a common, incurable, and progressive dementia, characterized by loss of learning and memory and the neuropathologic accumulation of amyloid plaques and neurofibrillary tangles in the brain. A number of similarities between AD pathology and several distinct retinal degenerations have been described, particularly with respect to either glaucoma or age-related macular degeneration (AMD), each a leading cause of vision loss and blindness worldwide. Although comparisons between these diseases may provide important new insights into their pathogenic mechanisms, glaucoma and AMD result in markedly different degenerations. Therefore, analyses of the differences and the similarities between these conditions may prove equally productive. Common mechanisms that appear to underlie all three diseases are explored here, as well as potential use of the retina as a biomarker for AD diagnosis and progression. Based on this comparison, past and current efforts to transfer therapeutic strategies between diseases are discussed.