gebhart/patrepeval huggingface dataset:
Detection of dsRNA from Cleistothecia and Conidia of the Grape Powdery Mildew Pathogen,Uncinula necator (1991)

Double-stranded RNA species ranging in molecular weight from 0.95 to 6.3 × 106 were detected in grapevines in New York. We recently showed that two of the species (Mr = 5.3 and 4.4 × 106) are associated with rupestris stem pitting disease. In this report, we show that the other eight detectable dsRNA species are associated with the powdery mildew fungus, Uncinula necator. These dsRNAs associated with the powdery mildew fungus were previously detected in leaves and epidermal stem tissue of grapevines infected with powdery mildew. The same dsRNA species were also detected from extracts of isolated cleistothecia and conidia of U. necator devoid of plant tissue. Isometric and rigid rodlike particles were observed in single cleistothecia preparations when examined under transmission electron microscopy.
Microgravity Studies of Cells and Tissues (2002)

Controlled in vitro studies of cells and tissues under the conditions of microgravity (simulated on Earth, or actual in space) can improve our understanding of gravity sensing, transduction, and responses in living cells and tissues. This paper discusses the scientific results and practical implications of three NASA-related biotechnology projects: ground and space studies of microgravity tissue engineering (JSC-Houston), and the development of the cell culture unit for use aboard the International Space Station (ARC-Ames).
Efficient Transfer Learning Method for Automatic Hyperparameter Tuning (2014)

We propose a fast and effective algorithm for automatic hyperparameter tuning that can generalize across datasets. Our method is an instance of sequential model-based optimization (SMBO) that transfers information by constructing a common response surface for all datasets, similar to Bardenet et al. (2013). The time complexity of reconstructing the response surface at every SMBO iteration in our method is linear in the number of trials (significantly less than previous work with comparable performance), allowing the method to realistically scale to many more datasets. Specifically, we use deviations from the per-dataset mean as the response values. We empirically show the superiority of our method on a large number of synthetic and real-world datasets for tuning hyperparameters of logistic regression and ensembles of classifiers.
Tumor spectrum in ARF-deficient mice. (1999)

The p19ARF product of the INK4a/ARF locus is induced in response to potentially oncogenic hyperproliferative signals and activates p53 by interfering with its negative regulator, Mdm2. Mice lacking ARF are highly prone to tumor development, and in this study, 80% of these animals spontaneously developed tumors and died within their first year of life. Mice that were heterozygous for ARF also developed tumors after a longer latency, whereas their wild-type littermates did not. In heterozygotes, tumor formation was accompanied by loss of the residual ARF allele and/or lack of ARF mRNA expression, implying that ARF can act as a canonical "two-hit" tumor suppressor gene. Tumors occurred earlier in life in ARF-null animals that were neonatally irradiated or given dimethylbenzanthrene, and several animals treated with carcinogen simultaneously developed multiple forms of malignancy arising from distinct cell lineages. Although p53-null mice primarily develop lymphomas and fibrosarcomas, the frequency of these two tumor types was inverted in ARF-null animals, with undifferentiated sarcomas predominating in a 3:2 ratio; 28% of ARF-null animals developed carcinomas and tumors of the nervous system, which have been rarely observed in untreated p53-null mice. The longer latency of tumor formation in ARF-null versus p53-null mice, therefore, appears to enable a broader spectrum of tumors to emerge.
An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli. (1985)

The expression of type 1 fimbriae (pili) of Escherichia coli is turned on and off at the transcriptional level at a high frequency (10(-3) per cell per generation) in a process termed phase variation. Using Southern blot and DNA sequence analysis, we have detected a genomic rearrangement in the switch region immediately upstream of the fimbrial structural gene. This rearrangement involves an invertible 314-base-pair segment of DNA whose alternating orientation apparently results in the on-and-off activation of a promoter that determines the state of fimbrial expression.
Seasonal variation of water‐soluble ions of the aerosol at the high‐alpine site Jungfraujoch (3580 m asl) (2003)

Within the Global Atmosphere Watch (GAW) Aerosol Program of the World Meteorological Organization (WMO), the aerosol chemical composition has been continuously measured since July 1999 at the Jungfraujoch (JFJ) of which the first 1.5‐year data set is presented. Sampling is performed in two size classes (total suspended particles (TSP) and particles with aerodynamic diameters smaller than 1 μm). The filters are analyzed for major ions, which constitute 30% of the total dry aerosol mass collected at this site. As annual mean, a total ion mass concentration of 1.04 μg m −3 was observed. Sulfate, ammonium, and nitrate were the major components of the fine aerosol fraction, while calcium and nitrate were two major water‐soluble components in the coarse mode. Single particle analysis confirmed the internal mixture of calcium and nitrate in the coarse mode. The total ion mass concentration showed strong seasonal differences, with 1.25, 1.62, 0.70, and 0.25 μg m −3 for spring, summer, fall, and winter, respectively. The variability was stronger for sulfate, ammonium, and nitrate than for calcium. The reason for this is believed to be local sources of calcium, which do not require vertical transport, along with Sahara dust episodes, which occur occasionally over the whole year, independent from the season.
Localization of T cell clonotypes using the Visium spatial transcriptomics platform (2022)

We present a protocol to localize T cell receptor clones using the Visium spatial transcriptomics platform. This approach permits simultaneous localization of both gene expression and T cell clonotypes in situ within tissue sections. T cell receptor sequences identified by this protocol are readily recapitulated by single-cell sequencing. This technique enables detailed studies of the spatial organization of the human T cell repertoire, such as the localization of infiltrating T cell clones within the tumor microenvironment. For complete details on the use and execution of this protocol, please refer to Sudmeier et al. (2022).
《大卫·科波菲尔》的托尔斯泰式解读 (1992)

托尔斯泰曾经指出:“假如你将世界一般文学予以筛选,狄更斯的作品将被保留;而筛选狄更斯的作品,《大卫·科波菲尔》将被存传。”在其五十余年来的日记与札记中,记载着他对狄更斯小说类似的褒誉。什么是艺术?他以为,《大卫·科波菲尔》才是艺术。在对他影响最大的诸如《圣经》及果戈理、卢梭等人的作品中,他显然认为狄更斯的《大卫·科波菲尔》是其中最重要的作品之一。
Effects of human HSS on hepatocyte and hepatoma cell proliferation and D-GAL induced acute liver failure. (1992)

Human hepatic stimulator substance (HSS), an organ-specific and heat-stable factor which differs from insulin, glucagon and EGF, has been partially purified from aborted human fetal livers. It was found to stimulate DNA synthesis of human hepatocytes. AH22 hepatoma cells responded dose-dependently. HSS was also found to enhance the survival of D-GAL intoxicated rats as compared to control (62.5% vs. 26.1%). Our results suggest that human HSS is very similar to that in animals.
Obstacles to the expansion of Eritrea's manufacturing sector (2002)

The Eritrea Investment Climate Assessment (ICA) is based primarily on a survey conducted by the Regional Program on Enterprise Development (Africa Private Sector Unit) in Spring 2002. The team covered manufacturing firms representing about 65 percent of total employment in manufacturing. The survey was designed to examine the cost of doing business and to generate cross-country comparisons of competitiveness and the investment climate. The recent efforts of the Government of Eritrea to promote private sector-led growth are grounded in a tradition of entrepreneurial spirit that has survived periods of conflict and other shocks. Eritrea's small economy has a GDP estimated in 2002 at $US 644 million. In 2001, industry as a whole accounted for 22.3 percent (only 7.8 percent of which was manufacturing). The government has recognized economic diversification, especially export diversification, as a key requirement for achieving sustainable, broad-based growth in the new century.
Uptake of amino acids and glucose by BHK 21 clone 13 suspension cells during cell growth. (1981)

The uptake of amino acids and glucose by BHK 21 clone 13 suspension cells grown in Modified Eagles Medium was monitored. The Growth Yields for sixteen amino acids and glucose were determined. Four "non essential" amino acids were utilised. Glutamine, glutamate, leucine and asparagine were used in greatest quantity by the cells which also utilised virtually all the cystine in the medium. The implications of these results are discussed.
Transfer of twelve charges is needed to open skeletal muscle Na+ channels. (1995)

Voltage-dependent Na+ channels are thought to sense membrane potential with fixed charges located within the membrane's electrical field. Measurement of open probability (Po) as a function of membrane potential gives a quantitative indication of the number of such charges that move through the field in opening the channel. We have used single-channel recording to measure skeletal muscle Na+ channel open probability at its most negative extreme, where channels may open as seldom as once per minute. To prevent fast inactivation from masking the voltage dependence of Po, we have generated a clone of the rat skeletal muscle Na+ channel that is lacking in fast inactivation (IFM1303QQQ). Using this mutant channel expressed in Xenopus oocytes, and the extra resolution afforded by single-channel analysis, we have extended the resolution of the hyperpolarized tail of the Po curve by four orders of magnitude. We show that previous measurements, which indicated a minimum of six effective gating charges, may have been made in a range of Po values that had not yet arrived at its limiting slope. In our preparation, a minimum of 12 charges must function in the activation gating of the channel. Our results will require reevaluation of kinetic models based on six charges, and they have major implications for the interpretation of S4 mutagenesis studies and structure/function models of the Na+ channel.
Efficacy of low‐dose dexamethasone in castration‐refractory prostate cancer (2007)

Low-dose dexamethasone has significant activity in CRPC. Subject to validation with more clinically meaningful endpoints, dexamethasone could become the corticosteroid of choice in the management of CRPC, and its potential for use in combination with novel agents should be explored.
Novel Antiasthmatic Agents with Dual Activities of Thromboxane A2 Synthetase Inhibition and Bronchodilation. VI. Indazole Derivatives. (1995)

Synthesis and pharmacological evaluation of novel indazole derivatives are described. These compounds were found to exhibit both thromboxane A2 (TXA2) synthetase-inhibitory and bronchodilatory activities. This observation supports the idea that the partial structure of the 3-pyridyl and phenyl groups with a methylene insertion is an important component for well-balanced activities.
Left‐Hemispheric Microstructural Abnormalities in Children With High‐Functioning Autism Spectrum Disorder (2014)

Current theories of the neurobiological basis of autism spectrum disorder (ASD) posit an altered pattern of connectivity in large-scale brain networks. Here we used diffusion tensor imaging to investigate the microstructural properties of the white matter (WM) that mediates interregional connectivity in 36 high-functioning children with ASD (HF-ASD) as compared with 37 controls. By employing an atlas-based analysis using large deformation diffeometric morphic mapping registration, a widespread but left-lateralized pattern of abnormalities was revealed. The mean diffusivity (MD) of water in the WM of HF-ASD children was significantly elevated throughout the left hemisphere, particularly in the outer-zone cortical WM. Across diagnostic groups, there was a significant effect of age on left-hemisphere MD, with a similar reduction in MD during childhood in both typically developing and HF-ASD children. The increased MD in children with HF-ASD suggests hypomyelination and may reflect increased short-range cortico-cortical connections subsequent to early WM overgrowth. These findings also highlight left-hemispheric connectivity as relevant to the pathophysiology of ASD and indicate that the spatial distribution of microstructural abnormalities in HF-ASD is widespread and left-lateralized. This altered left-hemispheric connectivity may contribute to deficits in communication and praxis observed in ASD.
Cyclin D1 Stimulation of Estrogen Receptor Transcriptional Activity Independent of cdk4† (1997)

Cyclin D1 plays an important role in the development of breast cancer and is required for normal breast cell proliferation and differentiation associated with pregnancy. We show that ectopic expression of cyclin D1 can stimulate the transcriptional activity of the estrogen receptor in the absence of estradiol and that this activity can be inhibited by 4-hydroxytamoxifen and ICI 182,780. Cyclin D1 can form a specific complex with the estrogen receptor. Stimulation of the estrogen receptor by cyclin D1 is independent of cyclin-dependent kinase 4 activation. Cyclin D1 may manifest its oncogenic potential in breast cancer in part through binding to the estrogen receptor and activation of the transcriptional activity of the receptor.
Rapid, fully automated measurement of plasma homocyst(e)ine with the Abbott IMx analyzer (1995)

We have developed a totally automated fluorescence polarization immunoassay for homocyst(e)ine with no pretreatment or chromatographic steps. Comparison with four well-established chromatographic methods yielded r values ranging from 0.980 to 0.997 and slopes from 1.030 to 1.493. Inter- and intraassay CVs ranged from 0.0% to 8.0% and from 0.0% to 6.4%, respectively. Imprecision (CV) of measuring six plasma samples on three instruments ranged from 6.3% to 10.2%. The assay was linear for plasma samples diluted with buffer from 0 to 8-fold. Mean recovery of homocysteine added to two plasma samples was 97.1% and 99.9%. The assay exhibited almost no cross-reactivity towards cysteine and methionine, and a batch of 20 samples can be processed in 60 min.
Cytokine mRNA expression in human epidermis after patch treatment with rhus and sodium lauryl sulfate (1999)

These preliminary results indicate differences in the steady state levels of cytokine mRNA in allergen versus vehicle and irritant treated sites at 24 hours after treatment.
Cell engineering with microfluidic squeezing preserves functionality of primary immune cells in vivo (2018)

The translational potential of cell-based therapies is often limited by complications related to effectively engineering and manufacturing functional cells. While the use of electroporation is widespread, the impact of electroporation on cell state and function has yet to be fully characterized. Here, we use a genome-wide approach to study optimized electroporation treatment and identify striking disruptions in the expression profiles of key functional transcripts of human T cells. These genetic disruptions result in concomitant perturbation of cytokine secretion including a 648-fold increase in IL-2 secretion (<i>P</i> < 0.01) and a 30-fold increase in IFN-γ secretion (<i>P</i> < 0.05). Ultimately, the effects at the transcript and protein level resulted in functional deficiencies in vivo, with electroporated T cells failing to demonstrate sustained antigen-specific effector responses when subjected to immunological challenge. In contrast, cells subjected to a mechanical membrane disruption-based delivery mechanism, cell squeezing, had minimal aberrant transcriptional responses [0% of filtered genes misregulated, false discovery rate (FDR) q < 0.1] relative to electroporation (17% of genes misregulated, FDR q < 0.1) and showed undiminished effector responses, homing capabilities, and therapeutic potential in vivo. In a direct comparison of functionality, T cells edited for PD-1 via electroporation failed to distinguish from untreated controls in a therapeutic tumor model, while T cells edited with similar efficiency via cell squeezing demonstrated the expected tumor-killing advantage. This work demonstrates that the delivery mechanism used to insert biomolecules affects functionality and warrants further study.
Activation of the Novel Estrogen Receptor G Protein-Coupled Receptor 30 (GPR30) at the Plasma Membrane (2007)

G protein-coupled receptor 30 (GPR30), a seven-transmembrane receptor (7TMR), is associated with rapid estrogen-dependent, G protein signaling and specific estrogen binding. At present, the subcellular site of GPR30 action is unclear. Previous studies using antibodies and fluorochrome-labeled estradiol (E2) have failed to detect GPR30 on the cell surface, suggesting that GPR30 may function uniquely among 7TMRs as an intracellular receptor. Here, we show that detectable expression of GPR30 on the surface of transfected HEK-293 cells can be selected by fluorescence-activated cell sorting. Expression of GPR30 on the cell surface was confirmed by confocal microscopy using the lectin concanavalin A as a plasma membrane marker. Stimulation of GPR30-expressing HEK-293 cells with 17beta-E2 caused sequestration of GPR30 from the cell surface and resulted in its codistribution with clathrin and mobilization of intracellular calcium stores. Evidence that GPR30 signals from the cell surface was obtained from experiments demonstrating that the cell-impermeable E2-protein conjugates E2-BSA and E2-horseradish peroxidase promote GPR30-dependent elevation of intracellular cAMP concentrations. Subcellular fractionation studies further support the plasma membrane as a site of GPR30 action with specific [3H]17beta-E2 binding and G protein activation associated with plasma membrane but not microsomal, or other fractions, prepared from HEK-293 or SKBR3 breast cancer cells. These results suggest that GPR30, like other 7TMRs, functions as a plasma membrane receptor.
Diode-laser absorption sensor for line-of-sight gas temperature distributions (2001)

Line-of-sight diode-laser absorption techniques have been extended to enable temperature measurements in nonuniform-property flows. The sensing strategy for such flows exploits the broad wavelength-scanning abilities (>1.7 nm approximately 30 cm(-1)) of a vertical cavity surface-emitting laser (VCSEL) to interrogate multiple absorption transitions along a single line of sight. To demonstrate the strategy, a VCSEL-based sensor for oxygen gas temperature distributions was developed. A VCSEL beam was directed through paths containing atmospheric-pressure air with known (and relatively simple) temperature distributions in the 200-700 K range. The VCSEL was scanned over ten transitions in the R branch of the oxygen A band near 760 nm and optionally over six transitions in the P branch. Temperature distribution information can be inferred from these scans because the line strength of each probed transition has a unique temperature dependence; the measurement accuracy and resolution depend on the details of this temperature dependence and on the total number of lines scanned. The performance of the sensing strategy can be optimized and predicted theoretically. Because the sensor exhibits a fast time response (~30 ms) and can be adapted to probe a variety of species over a range of temperatures and pressures, it shows promise for industrial application.
Lack of cell cycle regulation of telomerase activity in human cells (1997)

Conflicting reports have appeared concerning the cell cycle regulation of telomerase activity and its possible repression during quiescence and cell differentiation. We have reexamined these issues in an attempt to uncover the basis for the discrepancies. Variations in extracted telomerase activity during the cell cycle are not observed in cells sorted on the basis of DNA content. Variations are observed in cells synchronized using some biochemical cell cycle inhibitors, but only with those agents where cellular toxicity is evident. A progressive decline in telomerase activity is observed in cells whose growth rate is reduced from seven to eight population doublings per week to one to two doublings per week. Telomerase is largely absent in cells that truly exit the cell cycle and do not divide over the 7-day period. Although it is not necessary for all cell types to regulate telomerase in the same way, we conclude that in the immortal cultured cell lines examined, extracted telomerase activity does not change significantly during progression through the stages of the cell cycle. Telomerase activity generally correlates with growth rate and is repressed in cells that exit the cell cycle and become quiescent.
Algorithms for limited-view computed tomography: an annotated bibliography and a challenge (1985)

In many applications of computed tomography, it may not be possible to acquire projection data at all angles, as required by the most commonly used algorithm of convolution backprojection. In such a limited-data situation, we face an ill-posed problem in attempting to reconstruct an image from an incomplete set of projections. Many techniques have been proposed to tackle this situation, employing diverse theories such as signal recovery, image restoration, constrained deconvolution, and constrained optimization, as well as novel schemes such as iterative object-dependent algorithms incorporating a priori knowledge and use of multispectral radiation. We present an overview of such techniques and offer a challenge to all readers to reconstruct images from a set of limited-view data provided here.
Not all microseconds are equal (2010)

New applications such as algorithmic trading and high-performance computing require extremely low latency (in microseconds). Network operators today lack sufficient fine-grain measurement tools to detect, localize and repair performance anomalies and delay spikes that cause application SLA violations. A recently proposed solution called LDA provides a scalable way to obtain latency, but only provides aggregate measurements. However, debugging application-specific problems requires per-flow measurements, since different flows may exhibit significantly different characteristics even when they are traversing the same link. To enable fine-grained per-flow measurements in routers, we propose a new scalable architecture called reference latency interpolation (RLI) that is based on our observation that packets potentially belonging to different flows that are closely spaced to each other exhibit similar delay properties. In our evaluation using simulations over real traces, we show that RLI achieves a median relative error of 12% and one to two orders of magnitude higher accuracy than previous per-flow measurement solutions with small overhead.