gebhart/patrepeval huggingface dataset:
Identification of pathogenic fungi with an optoelectronic nose (2014)

Human fungal infections have gained recent notoriety following contamination of pharmaceuticals in the compounding process. Such invasive infections are a more serious global problem, especially for immunocompromised patients. While superficial fungal infections are common and generally curable, invasive fungal infections are often life-threatening and much harder to diagnose and treat. Despite the increasing awareness of the situation's severity, currently available fungal diagnostic methods cannot always meet diagnostic needs, especially for invasive fungal infections. Volatile organic compounds produced by fungi provide an alternative diagnostic approach for identification of fungal strains. We report here an optoelectronic nose based on a disposable colorimetric sensor array capable of rapid differentiation and identification of pathogenic fungi based on their metabolic profiles of emitted volatiles. The sensor arrays were tested with 12 human pathogenic fungal strains grown on standard agar medium. Array responses were monitored with an ordinary flatbed scanner. All fungal strains gave unique composite responses within 3 hours and were correctly clustered using hierarchical cluster analysis. A standard jackknifed linear discriminant analysis gave a classification accuracy of 94% for 155 trials. Tensor discriminant analysis, which takes better advantage of the high dimensionality of the sensor array data, gave a classification accuracy of 98.1%. The sensor array is also able to observe metabolic changes in growth patterns upon the addition of fungicides, and this provides a facile screening tool for determining fungicide efficacy for various fungal strains in real time.
C5a anaphylatoxin is a major regulator of activating versus inhibitory FcγRs in immune complex–induced lung disease (2002)

IgG Fc receptors (FcgammaRs, especially FcgammaRIII) and complement (in particular, C5a anaphylatoxin) are critical effectors of the acute inflammatory response to immune complexes (ICs). However, it is unknown whether and how these two key components can interact with each other in vivo. We use here a mouse model of the acute pulmonary IC hypersensitivity reaction to analyze their potential interaction. FcgammaRIII and C5aR are coexpressed on alveolar macrophages (AMs), and both FcgammaRIII and C5aR mutant mice display impaired immune responses. We find that recombinant human C5a (rhC5a) can control inverse expression of various FcgammaRs, and costimulation of ICs with rhC5a results in strong enhancement of FcgammaRIII-triggered cellular activation in vitro and in vivo. Moreover, we show here that early IC-induced bioactive C5a, and its interaction with C5aR, causes induction of activating FcgammaRIII and suppression of inhibitory FcgammaRII on AMs that appears crucial for efficient cytokine production and neutrophil recruitment in lung pathology. Therefore, C5a, which is a potent chemoattractant, has a broader critical function in regulating the inhibitory/activating FcgammaRII/III receptor pair to connect complement and FcgammaR effector pathways in immune inflammation.
A Framework for Robust Online Video Contrast Enhancement Using Modularity Optimization (2012)

We address the problem of video contrast enhancement. Existing techniques either do not exploit temporal information at all or do not exploit it correctly. This results in inconsistency that causes undesirable flash and flickering artifacts. Our method analyzes video streams and cluster frames that are similar to each other. Our method does not have omniscient information about the entire video sequence. It is an online process with a fixed delay. A sliding window mechanism successfully detects shot boundaries “on-the-fly” in a video. A graph-based technique called “modularity” performs automatic clustering of video frames without a priori information about clusters. For every cluster in the video, we extract key frames belonging to each cluster using eigen analysis and estimate enhancement parameters for only the key frame, then use these parameters to enhance frames belonging to that cluster, thus making our method robust. We evaluate the clustering method on video sequences from the TRECVid 2001 dataset and compare it with existing methods. We show reduction of flash artifacts in enhanced videos. We show statistically significant improvement in perceived video quality and validate that by conducting experiments on human observers. We show application of our clustering process to perform robust video segmentation.
High-performance liquid chromatography/thermospray mass spectrometry of eicosanoids and novel oxygenated metabolites of docosahexaenoic acid (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh-performance liquid chromatography/thermospray mass spectrometry of eicosanoids and novel oxygenated metabolites of docosahexaenoic acidJames A. Yergey, Hee Yong. Kim, and Norman. SalemCite this: Anal. Chem. 1986, 58, 7, 1344–1348Publication Date (Print):June 1, 1986Publication History Published online1 May 2002Published inissue 1 June 1986https://pubs.acs.org/doi/10.1021/ac00298a016https://doi.org/10.1021/ac00298a016research-articleACS PublicationsRequest reuse permissionsArticle Views150Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Temperature dependence of local segmental motion in polystyrene and its variation with molecular weight (2003)

Dielectric measurements are reported for the α-relaxation in polystyrene (PS) of varying molecular weights. Although the segmental relaxation dispersion was essentially invariant to Mw, the Tg-normalized temperature dependence (fragility) increases systematically with molecular weight. The latter result corroborates dynamic mechanical and light scattering studies, but is at odds with the reported (T−Tg) superpositioning of the shift factors for the recoverable creep compliance of PS. The failure of the dielectric relaxations time to superimpose when expressed as a function of T−Tg is consistent with the analysis of equation of state data for PS. We find that volume is not the dominant control variable, and in fact, temperature exerts a stronger influence on the relaxation times.
Chromosome painting in plants: in situ hybridization with a DNA probe from a specific microdissected chromosome arm of common wheat. (1994)

We report here on the successful painting of a specific plant chromosome within its own genome. Isochromosomes for the long arm of chromosome 5 of the wheat B genome (5BL) were microdissected from first meiotic metaphase spreads of a monoisosomic 5BL line of the common wheat Triticum aestivum cv. Chinese Spring. The dissected isochromosomes were amplified by degenerate oligonucleotide-primed PCR in a single tube reaction. The amplified DNA was used as a complex probe mixture for fluorescent in situ hybridization on first meiotic metaphase spreads of lines carrying 5BL as a distinctive marker. Hybridization signals were observed, specifically, along the entire 5BL. In some of the cells, labeling was also detected in two bivalents, presumably those of the 5B "homoeologues" (partial homologues) found in common wheat (5A and 5D). The probe also revealed discrete domains in tapetal nuclei at interphase, further supporting the probe's high specificity. These data suggest that chromosome and homoeologous group-specific sequences are more abundant in 5BL than genome-specific sequences. Chromosome-painting probes, such as the one described here for 5BL, can facilitate the study of chromosome evolution in polyploid wheat.
Oleuropein aglycone induces autophagy via the AMPK/mTOR signalling pathway: a mechanistic insight (2015)

The healthy effects of plant polyphenols, some of which characterize the so-called Mediterranean diet, have been shown to arise from epigenetic and biological modifications resulting, among others, in autophagy stimulation. Our previous work highlighted the beneficial effects of oleuropein aglycone (OLE), the main polyphenol found in the extra virgin olive oil, against neurodegeneration both in cultured cells and in model organisms, focusing, in particular, autophagy activation. In this study we investigated more in depth the molecular and cellular mechanisms of autophagy induction by OLE using cultured neuroblastoma cells and an OLE-fed mouse model of amylod beta (Aβ) deposition. We found that OLE triggers autophagy in cultured cells through the Ca2+-CAMKKβ-AMPK axis. In particular, in these cells OLE induces a rapid release of Ca2+ from the SR stores which, in turn, activates CAMKKβ, with subsequent phosphorylation and activation of AMPK. The link between AMPK activation and mTOR inhibition was shown in the OLE-fed animal model in which we found that decreased phospho-mTOR immunoreactivity and phosphorylated mTOR substrate p70 S6K levels match enhanced phospho-AMPK levels, supporting the idea that autophagy activation by OLE proceeds through mTOR inhibition. Our results agree with those reported for other plant polyphenols, suggesting a shared molecular mechanism underlying the healthy effects of these substances against ageing, neurodegeneration, cancer, diabetes and other diseases implying autophagy dysfunction.
Wavelets and Dilation Equations: A Brief Introduction (1989)

Wavelets are new families of basis functions that yield the representation $f(x) = \sum {b_{jk} W(2^j x - k)} $. Their construction begins with the solution $\phi (x)$ to a dilation equation with coefficients $c_k $. Then W comes from $\phi $, and the basis comes by translation and dilation of W. It is shown in Part 1 how conditions on the $c_k $ lead to approximation properties and orthogonality properties of the wavelets. Part 2 describes the recursive algorithms (also based on the $c_k $) that decompose and reconstruct f. The object of wavelets is to localize as far as possible in both time and frequency, with efficient algorithms
Cell-Autonomous Death of Cerebellar Purkinje Neurons with Autophagy in Niemann-Pick Type C Disease (2005)

Niemann-Pick type C is a neurodegenerative lysosomal storage disorder caused by mutations in either of two genes, npc1 and npc2. Cells lacking Npc1, which is a transmembrane protein related to the Hedgehog receptor Patched, or Npc2, which is a secreted cholesterol-binding protein, have aberrant organelle trafficking and accumulate large quantities of cholesterol and other lipids. Though the Npc proteins are produced by all cells, cerebellar Purkinje neurons are especially sensitive to loss of Npc function. Since Niemann-Pick type C disease involves circulating molecules such as sterols and steroids and a robust inflammatory response within the brain parenchyma, it is crucial to determine whether external factors affect the survival of Purkinje cells (PCs). We investigated the basis of neurodegeneration in chimeric mice that have functional npc1 in only some cells. Death of mutant npc1 cells was not prevented by neighboring wild-type cells, and wild-type PCs were not poisoned by surrounding mutant npc1 cells. PCs undergoing cell-autonomous degeneration have features consistent with autophagic cell death. Chimeric mice exhibited a remarkable delay and reduction of wasting and ataxia despite their substantial amount of mutant tissue and dying cells, revealing a robust mechanism that partially compensates for massive PC death.
Molecular mechanisms in the hormonal regulation of plasminogen activator activity in ovarian granulosa cells and cumulus-oocyte complexes. (1988)

Molecular mechanisms in the hormonal regulation of plasminogen activator activity in ovarian granulosa cells and cumulus-oocyte complexes.
Heterogeneous Catalysis by Heteropoly Compounds of Molybdenum and Tungsten (1987)

Abstract Heteropolyanions are polymeric oxoanions which are formed by the condensation of more than two different oxoanions [Eq. (1)l. Polyanions consisting of one kind of oxoanion are called isopolyanions [Eq. (2)]. Acidic elements such as Mo, W, V, Nb, and Ta are present as oxoanions in aqueous solutions and polymerize to form polyanions at low pH. Free acids (or acid forms) of these species are called heteropoly and isopoly acids, respectively. Here, the term “heteropoly compounds” is used for heteropoly acids and their salts.
Ubiquitin C‐terminal hydrolase‐L1 as a biomarker for ischemic and traumatic brain injury in rats (2010)

Ubiquitin C-terminal hydrolase-L1 (UCH-L1), also called neuronal-specific protein gene product 9.5, is a highly abundant protein in the neuronal cell body and has been identified as a possible biomarker on the basis of a recent proteomic study. In this study, we examined whether UCH-L1 was significantly elevated in cerebrospinal fluid (CSF) following controlled cortical impact (CCI) and middle cerebral artery occlusion (MCAO; model of ischemic stroke) in rats. Quantitative immunoblots of rat CSF revealed a dramatic elevation of UCH-L1 protein 48 h after severe CCI and as early as 6 h after mild (30 min) and severe (2 h) MCAO. A sandwich enzyme-linked immunosorbent assay constructed to measure UCH-L1 sensitively and quantitatively showed that CSF UCH-L1 levels were significantly elevated as early as 2 h and up to 48 h after CCI. Similarly, UCH-L1 levels were also significantly elevated in CSF from 6 to 72 h after 30 min of MCAO and from 6 to 120 h after 2 h of MCAO. These data are comparable to the profile of the calpain-produced alphaII-spectrin breakdown product of 145 kDa biomarker. Importantly, serum UCH-L1 biomarker levels were also significantly elevated after CCI. Similarly, serum UCH-L1 levels in the 2-h MCAO group were significantly higher than those in the 30-min group. Taken together, these data from two rat models of acute brain injury strongly suggest that UCH-L1 is a candidate brain injury biomarker detectable in biofluid compartments (CSF and serum).
Optisch aktive Amine durch Lipase-katalysierte Methoxyacetylierung (1997)

Optically Active Amines via Lipase-Catalyzed Methoxyacetylation Racemic amines can be efficiently resolved using ethylmethoxyacetate as acylating agent in a lipase-catalyzed reaction. The reaction of 1-phenyethylamine with ethylmethoxyacetate in the presence of a lipase from Burkholderia plantarii is presented. Excellent yields and selectivity and minimal amount of enzyme characterize this new process.
Coupled microcolumn size-exclusion liquid chromatography–capillary supercritical fluid chromatography (1991)

Fractions of the eluate from a packed capillary size-exclusion column were selectively transferred via a solvent-vented interface to an open tubular capillary supercritical fluid chromatography column. The system was evaluated for use with mixtures of polymers and additives, edible oils contaminated with polymer additives, and agrochemicals in natural products.
Steiner Surface Patches (1985)

Gain valuable insight into better geometric approaches to high- degree surface patches by studying the simple free-form Steiner patch.
Functional expression of the human CHIP28 water channel in a yeast secretory mutant (1995)

The temperature-sensitive Saccharomyces cerevisiae mutant strain NY17, deficient in the secretory pathway (sec6-4 mutation), is used for the heterologous expression of the human CHIP28 water channel. After a heat-shock, the protein is present in partially purified post-golgi secretory vesicles. Immunodetection and water transport studies, directly made on the vesicles, showed that CHIP28 is highly expressed and active in the yeast membranes.
A way-halting cache for low-energy high-performance systems (2004)

Caches contribute to much of a microprocessor system's power and energy consumption. We have developed a new cache architecture, called a way-halting cache, that reduces energy while imposing no performance overhead. Our way-halting cache is a four-way set-associative cache that stores the four lowest-order bits of all ways' tags into a fully associative memory, which we call the halt tag array. The lookup in the halt tag array is done in parallel with, and is no slower than, the set-index decoding. The halt tag array pre-determines which tags cannot match due to their low-order four bits mismatching. Further accesses to ways with known mismatching tags are then halted, thus saving power. Our halt tag array has an additional feature of using static logic only, rather than dynamic logic used in highly associative caches. We provide data from experiments on 17 benchmarks drawn from MediaBench and Spec 2000, based on our layouts in 0.18 micron CMOS technology. On average, 55% savings of memory-access related energy were obtained over a conventional four-way set-associative cache. We show that energy savings are greater than previous methods, and nearly twice that of highly-associative caches, while imposing no performance overhead and only 2% cache area overhead.
CD4+ T lymphocytes enumeration by an easy‐to‐use single platform image cytometer for HIV monitoring in resource‐constrained settings (2007)

The immunolabeling methods and the instrumentation are simple and easy-to-handle for less-trained operators. The SP ICM system is a good candidate for CD4(+) T lymphocytes enumeration in point-of-care settings of resource-constrained countries.
Small Stress Proteins as Novel Regulators of Apoptosis (1996)

Small stress protein expression enhances the survival of mammalian cells exposed to numerous injuries that induce necrotic cell death. The cell surface receptor Fas/APO-1 and its ligand have been recently identified as important mediators of apoptosis. Here, we show that constitutive expression of human heat shock protein (hsp)27 in murine L929 cells blocks Fas/APO-1-mediated cell death. Expression of human hsp27 prevented anti-APO-1-induced DNA fragmentation and morphological changes. These results strongly suggest that human hsp27 acts as a cellular inhibitor of Fas/APO-1-induced apoptosis. We also report that the expression of small stress proteins from different species, such as human hsp27, Drosophila Dhsp27, or human alphaB-crystallin, confers resistance to apoptotic cell death induced by staurosporine, a protein kinase C inhibitor. Hence, small stress proteins are novel regulators that are able to block apoptosis induced by different pathways.
Spatiotemporal Frequency Analysis of Ventricular Fibrillation in Explanted Human Hearts (2008)

Ventricular fibrillation (VF) is a medical condition that occurs due to rapid and irregular electrical activity of heart. If undiagnosed or untreated, VF leads to sudden cardiac death. VF has been studied by researchers for over 100 years to elucidate the mechanism that maintains VF, and thus to arrive at therapeutic options. VF is a nonstationary process, and it manifests into variations in the waveform morphology, phase, and frequency dynamics of the surface electrograms. Dominant frequency analysis (DF maps) and phase maps are two widely used complementary approaches in assessing the evolution of VF process. These techniques are applied to electrograms or fluorescence signals obtained with voltage-sensitive dyes. In spite of VF being a nonstationary process, most of the existing literature limits frequency analysis to a segmented, time-averaged spectral analysis, where valuable information on the instantaneous temporal evolution of the spectral characteristics is lost. In order to resolve this issue, in this paper, we present a joint time-frequency approach that is suited for VF analysis and demonstrate the application of instantaneous mean frequency (IMF) in interpreting VF episodes. Human VF sources are rarely anatomically stable and are migratory. Traditional DF techniques fail in tracking this migratory behavior. IMF, on the other hand, can deal with these migratory sources and conduction blocks better than DF approaches. Results of the analysis using the electrograms of 204 VF segments obtained from 13 isolated human hearts (explanted during cardiac transplantation) indicate that in 81% of the VF segments, there were significant changes in the spatiotemporal evolution of the frequency, suggesting that IMF provides better mechanistic insight of these signals. The IMF tool presented in this paper demonstrates potential for applications in tracking frequency patterns, conduction blocks, and arriving at newer therapies to modulate VF.
Plant Systems Biology (2009)

As a fairly new and expansive area of study, plant systems biology has been approached by scientists from fields as varied as plant physiology and astrophysics, creating a wide variety of techniques and methods to further this vital research. In Plant Systems Biology, expert investigators provide cutting-edge chapters dealing with diverse subjects such as systems biology of plant gene expression to analysis of networks, pathways, specific statistical issues and novel computational tools, imaging-based tools as well as chemical genetic, metabolomic and integrative methods that cannot be easily pigeonholed. As a volume in the highly successful Methods in Molecular Biology™ series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Authoritative and comprehensive, Plant Systems Biology is an ideal guide for all researchers who wish to contribute to the evolution of the vibrant field of plant biology
Immunological Discrimination of Intralysosomal, Cytosolic, and Two Membrane Sialidases Present in Rat Tissues1 (1990)

Cytosolic sialidase was purified from rat skeletal muscle, and the purified enzyme migrated as a single band of Mr 43,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. A polyclonal antibody raised against the enzyme inhibited and immunoprecipitated rat liver cytosolic sialidase as well as the muscle enzyme but failed to cross-react with the intralysosomal sialidase of rat liver and membrane sialidases I (synaptosomal) and II (lysosomal) of rat brain. The antibody against brain membrane sialidase I (anti-I) and that against sialidase II (anti-II), which could be useful to discriminate the two enzymes, did not cross-react with the intralysosomal and cytosolic sialidases of liver. Although more than 90% of liver plasma membrane sialidase was immunoprecipitated with anti-I, only 60% of liver lysosomal membrane sialidase was immunoprecipitated with anti-II, the remainder being immunoprecipitated with anti-I. In confirmation of these data, liver lysosomal membrane exhibited two peaks of ganglioside sialidase corresponding to the membrane sialidases I and II on Aminohexyl-Sepharose chromatography while only one peak of ganglioside sialidase corresponding to sialidase I was observed for liver plasma membrane. These results indicate that the four types of rat sialidase are proteins distinct from one another and that the three kinds of antisera described above are useful for discriminating these sialidases qualitatively and probably quantitatively.