gebhart/patrepeval huggingface dataset:
Large-scale Metabolomic Profiling Identifies Novel Biomarkers for Incident Coronary Heart Disease (2014)

Analyses of circulating metabolites in large prospective epidemiological studies could lead to improved prediction and better biological understanding of coronary heart disease (CHD). We performed a mass spectrometry-based non-targeted metabolomics study for association with incident CHD events in 1,028 individuals (131 events; 10 y. median follow-up) with validation in 1,670 individuals (282 events; 3.9 y. median follow-up). Four metabolites were replicated and independent of main cardiovascular risk factors [lysophosphatidylcholine 18∶1 (hazard ratio [HR] per standard deviation [SD] increment = 0.77, P-value<0.001), lysophosphatidylcholine 18∶2 (HR = 0.81, P-value<0.001), monoglyceride 18∶2 (MG 18∶2; HR = 1.18, P-value = 0.011) and sphingomyelin 28∶1 (HR = 0.85, P-value = 0.015)]. Together they contributed to moderate improvements in discrimination and re-classification in addition to traditional risk factors (C-statistic: 0.76 vs. 0.75; NRI: 9.2%). MG 18∶2 was associated with CHD independently of triglycerides. Lysophosphatidylcholines were negatively associated with body mass index, C-reactive protein and with less evidence of subclinical cardiovascular disease in additional 970 participants; a reverse pattern was observed for MG 18∶2. MG 18∶2 showed an enrichment (P-value = 0.002) of significant associations with CHD-associated SNPs (P-value = 1.2×10-7 for association with rs964184 in the ZNF259/APOA5 region) and a weak, but positive causal effect (odds ratio = 1.05 per SD increment in MG 18∶2, P-value = 0.05) on CHD, as suggested by Mendelian randomization analysis. In conclusion, we identified four lipid-related metabolites with evidence for clinical utility, as well as a causal role in CHD development.
Lack of transforming growth factor-beta 1 expression in benign skin tumors of p53null mice is prognostic for a high risk of malignant conversion. (1994)

Expression of transforming growth factor beta 1 (TGF beta 1) protein was examined in chemically induced benign skin tumors with genetically defined empirical risks for malignant conversion. Benign tumors induced in mice which have both alleles of the p53 gene deleted have a malignant conversion frequency of approximately 50%, whereas similar tumors induced in wildtype and heterozygous p53 mice have conversion probabilities of 3 and 8%, respectively (Kemp et al., Cell, 74: 813-822, 1993). The TGF beta 1 antibody, anti-CC (1-30-1), was shown to stain either the proliferative keratinocyte compartment of the tumor or the tumor stroma, whereas another TGF beta 1 antibody, anti-LC (1-30-1), stained highly differentiated granular cells of the tumors. A strong correlation was found between staining of the proliferative keratinocyte compartment of tumors with the anti-CC (1-30-1) antibody and tumor genotype. Only 18% (6 of 32) of homozygous p53 null tumors showed any basal keratinocyte staining with this antibody, whereas over 80% (32 of 38) of heterozygous and wild-type tumors showed positive staining. Additionally, in most tumors examined, the spatial distribution of staining for the proliferating cell nuclear antigen appeared to be mutually exclusive with that of TGF beta 1 on adjacent serial sections. This suggests that, in these cases, tumor keratinocytes are sensitive to negative growth regulation by TGF beta. TGF beta 1 protein staining in benign tumors is thus prognostic for a low probability of malignant conversion, and its expression may be mechanistically involved in limiting malignant conversion since, at the benign tumor stage examined, keratinocytes are still sensitive to growth inhibition by TGF beta 1.
Foliar Silicon and Titanium Applications Influence Growth and Quality Characteristics of Annual Bedding Plants (2014)

This study investigated the effects of foliar Si and Ti applications on annual bedding plant growth and quality in soilless media. The five annual plant species selected were geranium (Pelargonium x hortorum 'Elite Cherry'), impatiens (Impatiens walleriana 'Accent White'), pansy (Viola x wittrockiana 'Delta Premium Marina'), petunia (Petunia x hybrid 'Celebrity White') and snapdragon (Antirrhinum majus 'Montego Purple'). Sodium silicate (NaSiO 3 ) supplied foliar treatments of 0, 50, 100, 150 and 200 mg SiL -1 and Ti-ascorbate (Tytanit ) supplied foliar treatments of 0, 25, 50, 75 and 100 mg TiL -1 . Silicon treatments affected plant height for all five species, while Ti treatments only affected plant height for geranium, petunia and snapdragon. Snapdragon plant height increased linearly in response to Si and Ti treatments. Plant height increased, then decreased quadratically for geranium with Ti treatments and pansy with Si treatments. The number of days to flower for petunias exhibited a linear decrease with Ti treatments while impatiens exhibited a linear increase with Si and Ti treatments. Geranium responded with a quadratic decrease, then increase for the number of days to flower with increasing Ti treatments. The chlorophyll SPAD content of impatiens exhibited a linear decrease in response to Ti treatments, while geranium had the same response to Si treatments. Silicon and Ti supplementations were found to affect growth and quality characteristics of annual bedding plants. However, this response was species specific and further research is needed to assess the specific impacts of Si and Ti on additional annual crop species and varieties grown in soilless media.
A Multi-Platform Optical Sensor for In Vivo and In Vitro Algae Classification (2017)

Differentiation among major algal groups is important for the ecological and biogeochemical characterization of water bodies, and for practical management of water resources. It helps to discern the taxonomic groups that are beneficial to aquatic life from the organisms causing harmful algal blooms. An LED-induced fluorescence (LEDIF) instrument capable of fluorescence, absorbance, and scattering measurements; is used for in vivo and in vitro identification and quantification of four algal groups found in freshwater and marine environments. Aqueous solutions of individual and mixed dissolved biological pigments relevant to different algal groups were measured to demonstrate the LEDIF's capabilities in measuring extracted pigments. Different genera of algae were cultivated and the cell counts of the samples were quantified with a hemacytometer and/or cellometer. Dry weight of different algae cells was also measured to determine the cell counts-to-dry weight correlations. Finally, in vivo measurements of different genus of algae at different cell concentrations and mixed algal group in the presence of humic acid were performed with the LEDIF. A field sample from a local reservoir was measured with the LEDIF and the results were verified using hemacytometer, cellometer, and microscope. The results demonstrated the LEDIF's capabilities in classifying and quantifying different groups of live algae.
Encoding the \ell_p Ball from Limited Measurements (2006)

We address the problem of encoding signals which are sparse, i.e. signals that are concentrated on a set of small support. Mathematically, such signals are modeled as elements in the /spl lscr//sub p/ ball for some p < 1. We describe a strategy for encoding elements of the /spl lscr//sub p/ ball which is universal in that 1) the encoding procedure is completely generic, and does not depend on p (the sparsity of the signal), and 2) it achieves near-optimal minimax performance simultaneously for all p < 1. What makes our coding procedure unique is that it requires only a limited number of nonadaptive measurements of the underlying sparse signal; we show that near-optimal performance can be obtained with a number of measurements that is roughly proportional to the number of bits used by the encoder. We end by briefly discussing these results in the context of image compression.
Epitaxial liftoff of AlAs/GaAs double barrier resonant tunnelling diodes (1991)

For the first time, the successful removal of AlAs/GaAs double barrier resonant tunnelling diodes from the substrate using the epitaxial liftoff technique is reported. Ohmic contacts were formed to the top and bottom of the devices, using indium-alloyed ohmic contacts for the backside of the lifted-off diodes. Room temperature peak-to-valley ratios of 3.4 with peak current densities of 50 kA/cm2 were obtained.
Cholecystokinin‐8 regulation of NGF concentrations in adult mouse brain through a mechanism involving CCK<sub>A</sub> and CCK<sub>B</sub> receptors (1998)

1. Nerve growth factor (NGF), a powerful agent for the growth, differentiation and regeneration of lesioned cells of the central and peripheral nervous systems, has in recent years been indicated as a potential therapeutic agent capable of reversing the processes of cell damage in neurodegenerative events in man. Since NGF does not cross the blood-brain barrier and central NGF administration requires invasive surgical procedures, the discovery of substances modulating in vivo NGF synthesis in the brain will be extremely useful for a possible clinical use of NGF. 2. The aim of the present study to analyse if the content of NGF in the brain of adult mice can be affected by peripheral administration of cholecystokinin-8 (CCK-8), a well known neuropeptide which has stimulant actions on neurons in the brain and promotes a variety of neurobehavioural effects both in man and rodents. 3. The dose-response and time course effects of an i.p. injection of CCK-8 on the NGF concentrations in the hippocampus, cortex, hypothalamus and pituitary of adult male mice were analysed by use of a sensitive immunoenzymatic assay for NGF. The effects of pretreatment with selective CCK(A) and CCK(B) receptor antagonists and atropine on the NGF response to CCK injection were also studied. 4. The effects of CCK-8 were dose- and time-dependent and the injection of 8 nmol kg(-1) resulted in a 3 fold increase of NGF levels in the hypothalamus and pituitary, and about a 60% increase in the hippocampus. No effects were observed in the cortex. Pretreatment with a selective CCK(A) receptor antagonist blocked the CCK-induced NGF increase in the hypothalamus and pituitary. In the hippocampus the same effect was obtained with a CCK(B) receptor antagonist. Pretreatment with atropine suppressed the CCK-induced effects on NGF levels in all the brain regions examined. 5. Our results showing that i.p. injection with CCK-8 can modulate NGF levels in the brain through a mechanism which seems, in part, to be mediated via the vagal afferents, indicate that this neuropeptide may represent a useful pharmacological approach to enhance endogenous NGF levels in neuropathologies associated with a neurotrophin deficit.
Vagal Cardiac Activity in Essential Hypertension: The Effects of Metoprolol and Ramipril (1998)

Cardiovascular parasympathetic activity is attenuated in essential hypertension. Both beta-adrenoceptor antagonists and angiotensin converting enzyme inhibitors have been reported to increase vagal modulation of heart rate and baroreflex sensitivity, but the relations between the antihypertensive and vagal cardiac effects of these drugs have remained unclear in essential hypertension. In the present study we evaluated the effects of a 4-week crossover monotherapy with metoprolol and ramipril on spectrum analysis indices of heart rate variability in the supine rest and head-up tilted positions, baroreflex sensitivity (phenylephrine method), and 24-h ambulatory blood pressure (BP) in 12 formerly untreated stage 1-2 essential hypertensive patients. Compared to the pretreatment values, both drugs decreased BP similarly and significantly. However, the drugs showed different effects on cardiac vagal activity: metoprolol increased significantly mean R-R interval, R-R interval total, and high-frequency variability at supine rest and baroreflex sensitivity, but ramipril did not significantly affect these variables. The metoprolol-induced decrease in ambulatory BP correlated with the prolongation of the R-R interval and the increase of high-frequency variability at supine rest. The present data show that 4-week treatment with metoprolol increases tonic and reflex vagal cardiac activity, whereas ramipril does not affect vagal cardiac control in essential hypertension. Increase in vagal activity may contribute to the BP-lowering effect of metoprolol in hypertensive patients.
Characterization of multi-bit soft error events in advanced SRAMs (2004)

Error correction code schemes are being implemented in memories and microprocessor caches in response to SER increases which result from increasing bit counts and technology scaling. These methods can be rendered ineffective by multi-bit error events. An exhaustive characterization of multi-bit errors in 90/130 nm SRAMs is presented to support bit interleaving rules that make the impact of multi-bit errors negligible.
In Vivo Transduction of Cerebellar Purkinje Cells Using Adeno-Associated Virus Vectors (2000)

We investigated whether adenovirus or adeno-associated virus vectors can transduce cerebellar Purkinje cells (PCs) in vivo. Mice were injected in the deep cerebellar nuclei (DCN) with lacZ-transducing adenovirus (Ad.RSV-betagal) or a recombinant AAV serotype 2 (rAAV2) vector (vTR-CMVbeta) mixed with wild-type adenovirus type 5 (Ad5). One week later, Ad.RSV-betagal transduced cells were found throughout the cerebellar white matter in a dose-dependent manner, but few transduced PCs were evident. In contrast, vTR-CMVbeta with Ad5 transduced several hundred PCs throughout the injected hemisphere. Using an rAAV2 vector transducing a CMV-regulated green fluorescent protein gene, we again found PC transduction, but only with Ad5 coinjection. To assess the effect of injection site and to determine whether the apparent requirement for Ad5 coinfection is observed with other promoters, a beta-actin-regulated vector was injected with or without Ad5 to DCN or cerebellar cortical sites. Thousands of transduced PCs were observed under each condition. Cortical injection yielded greater numbers of transduced cells. Injection of rAAV2 without Ad5 led to greater specificity for PC transduction. We conclude that injection of rAAV2 vectors into the cerebellum is an effective means for transferring genes into substantial numbers of Purkinje cells in vivo.
Exploration of the Effects of High Hydrostatic Pressure on Microbial Growth, Physiology and Survival: Perspectives from Piezophysiology (2007)

The discovery of piezophiles (previously referred to as barophiles) prompted researchers to investigate the survival strategies they employ in high-pressure environments. There have been innovative high-pressure studies on biological processes applying modern techniques of genetics and molecular biology in bacteria and yeasts as model organisms. Recent advanced studies in this field have shown unexpected outcomes in microbial growth, physiology and survival when living cells are subjected to high hydrostatic pressure. The effects are conceptually dependent on the sign and magnitude of volume changes associated with any chemical reaction in the cells. Nevertheless, it is difficult to explain the pressure effects on complex metabolic networks based on a simple volume law. The challenges in piezophysiology are to discover whether the physiological responses of living cells to high pressure are relevant to their growth and to identify the critical factors in cell viability and lethality under high pressure from the general and organism-specific viewpoints.
Pneumotonometry versus Goldmann tonometry after laser in situ keratomileusis for myopia1 (1999)

Postoperatively, there was a decrease in IOP measured by central GAT that was statstically significant. Differences in pneumotonometry were less substantial, with greater reliability of pneumotonometry than GAT after LASIK.
A flow cytometer for the measurement of Raman spectra (2008)

Multiparameter measurements in flow cytometry are limited by the broad emission spectra of fluorescent labels. By contrast, Raman spectra are notable for their narrow spectral features. To increase the multiparameter analysis capabilities of flow cytometry, we investigated the possibility of measuring Raman signals in a flow cytometry-based system. We constructed a Raman Spectral Flow Cytometer, substituting a spectrograph and CCD detector for the traditional mirrors, optical filters, and photomultiplier tubes. Excitation at 633 nm was provided by a HeNe laser, and forward-angle light scatter is used to trigger acquisition of complete spectra from individual particles. Microspheres were labeled with nanoparticle surface enhanced Raman scattering (SERS) tags and measured using the RSFC. Fluorescence and Raman spectra from labeled microspheres were acquired using the Raman Spectral Flow Cytometer. SERS spectral intensities were dependent on integration time, laser power, and detector pixel binning. Spectra from particles labeled with one each of four different SERS tags could be distinguished by either a virtual bandpass approach using commercial flow cytometry data analysis software or by principal component analysis. Raman flow cytometry opens up new possibilities for highly multiparameter and multiplexed measurements of cells and other particles using a simple optical design and a single detector and light source.
Temporal click model for sponsored search (2010)

Previous studies on search engine click modeling have identified two presentation factors that affect users' behavior: (1) position bias: the same result will get a different number of clicks when displayed in different positions and (2) externalities: the same result might get more clicks when displayed with results of relatively lower quality than when shown with higher quality results. In this paper we focus on analyzing the sequence of user actions to model users' click behavior on sponsored listings shown on the search results page. We first show that temporal click sequences are good indicators of externalities in the advertising domain. We then describe the positional rationality hypothesis to explain both the position bias and the externalities, and based on this hypothesis we further propose the temporal click model (TCM), a Bayesian framework that is scalable and computationally efficient. To the best of our knowledge, this is the first attempt in the literature to estimate positional bias, externalities and unbiased user-perceived ad quality from user click logs in a combined model. We finally evaluate the proposed model on two real datasets, each containing over 100 million ad impressions obtained from a commercial search engine. The experimental results show that TCM outperforms two other competitive methods at click prediction.
Comparison of Levator Ani Muscle Defects and Function in Women With and Without Pelvic Organ Prolapse (2007)

II.
Effects of Hypoxic Cell Radiosensitizer Doranidazole (PR-350) on the Radioresponse of Murine and Human Tumor Cells in vitro and in vivo (2005)

We have investigated the radiosensitizing effect of doranidazole, a hypoxic cells radiosensitizer, using SCCVII tumor cells of C3H mice and CFPAC-1 and MIA PaCa-2 human pancreatic tumor cells. The radiosensitivity of hypoxic SCCVII cells in vitro increased with 1 mM doranidazole by a factor of 1.34 and 1.68, when determined by clonogenic survival and micronucleus (MN) formation, respectively. The radiation-induced growth delay of SCCVII tumors was significantly enhanced and the TCD(50/120) was reduced by a factor of 1.33 when 200 mg/kg doranidazole was injected, i.v., 20 min prior to tumor irradiation. The in vivo-in vitro excision assay showed that radiosensitivity of SCCVII cells in vivo increased by a factor of 1.47 with 200 mg/kg doranidazole. The radiation-induced growth delay of CFPAC-1 xenografts in nude mice was significantly enhanced and the TCD(50/90) was reduced by a factor of 1.30 by 200 mg/kg doranidazole. On the other hand, 200 mg/kg of doranidazole exerted no influence on the radiation-induced growth delay in MIA PaCa-2 xenografts. The tumor oxygenation status, as determined with an oxygen sensitive needle probe and the immunohistological study using pimonidazole, indicated that MIA PaCa-2 tumors are better oxygenated than CFPAC-1 tumors. The relatively well-oxygenated status in MIA PaCa-2 tumor may account for the lack of radiosensitization by doranidazole. It is concluded that the magnitude of radiosensitization of tumors by doranidazole is dependent on the oxygenation status of the tumors and that doranidazole may be useful in increasing the response of hypoxic human pancreatic tumor to IORT.
Importance of Catheter Contact Force During Irrigated Radiofrequency Ablation: Evaluation in a Porcine <i>Ex Vivo</i> Model Using a Force‐Sensing Catheter (2010)

Catheter contact force has an important impact on both ablation lesion size and the incidence of pops.
Biased random mutagenesis of peptides: determination of mutation frequency by computer simulation (1995)

Cassette mutagenesis is a method of protein engineering which generates a wide diversity of genetic variants that can be subjected to either selection or screening. As long as the target sequence to be modified is kept short (corresponding to four to six amino acids), complete combinatorial libraries can be produced. A major problem arises when longer peptides are to be engineered for desired functions. In such situations the production of a limited collection of variants can be helpful; thus, biased random mutagenesis and 'doping schemes' have been reported previously. Here we describe a computer algorithm that enables the determination of the degree of phosphoramidite contamination of nucleotide precursor reservoirs. Through simulation of biological translation, the algorithm allows the prediction of the effect of contamination levels on the number of mutations to occur for any given peptide sequence. In this study the cholinergic binding site was used as a model sequence (22 amino acids). Considerations, based on the computer program, are discussed regarding the efficient design of phage-display combinatorial libraries.
Glycosylation, Hypogammaglobulinemia, and Resistance to Viral Infections (2014)

Genetic defects in MOGS, the gene encoding mannosyl-oligosaccharide glucosidase (the first enzyme in the processing pathway of N-linked oligosaccharide), cause the rare congenital disorder of glycosylation type IIb (CDG-IIb), also known as MOGS-CDG. MOGS is expressed in the endoplasmic reticulum and is involved in the trimming of N-glycans. We evaluated two siblings with CDG-IIb who presented with multiple neurologic complications and a paradoxical immunologic phenotype characterized by severe hypogammaglobulinemia but limited clinical evidence of an infectious diathesis. A shortened immunoglobulin half-life was determined to be the mechanism underlying the hypogammaglobulinemia. Impaired viral replication and cellular entry may explain a decreased susceptibility to infections.