gebhart/patrepeval huggingface dataset:
μChIP: Chromatin Immunoprecipitation for Small Cell Numbers (2009)

Chromatin immunoprecipitation (ChIP) is a technique of choice for studying protein-DNA interactions. ChIP has been used for mapping the location of modified histones on DNA, often in relation to transcription or differentiation. Conventional ChIP protocols, however, require large number of cells, which limits the applicability of ChIP to rare cell samples. ChIP assays for small cell numbers (in the range of 10,000-100,000) have been recently reported; however, these remain lengthy. Our laboratory has elaborated fast ChIP assays suitable for small cell numbers (100-100,000) and for the immunoprecipitation of histone proteins or transcription factors under cross-linking conditions. We describe here a rapid micro (micro)ChIP assay suited for multiple parallel ChIPs from a single chromatin batch from 1,000 cells. The assay is also applicable to a single immunoprecipitation from 100 cells.
NAP (Davunetide) Provides Functional and Structural Neuroprotection (2011)

NAP (davunetide) is an eight amino acid peptide (NAPVSIPQ) that has been shown to provide potent neuroprotection, in vitro and in vivo. In human clinical trials, NAP has been shown to increase memory scores in patients suffering from amnestic mild cognitive impairment, a precursor to Alzheimer's disease and to enhance functional daily behaviors in schizophrenia patients. NAP is derived from activity-dependent neuroprotective protein (ADNP) a molecule that is essential for brain formation, interacting with chromatin associated protein alpha and the chromatin remodeling complex SWI/SNF and regulating >400 genes during embryonic development. Partial loss in ADNP results in cognitive deficits and pathology of the microtubule associated protein tau (tauopathy) that is ameliorated in part by NAP replacement therapy. Recent studies increased the scope of NAP neuroprotection and provided further insights into the NAP mechanisms of action. Thus, it has been hypothesized that the presence of tau on axonal microtubules renders them notably less sensitive to the microtubule-severing protein katanin, and NAP was shown to protect microtubules from katanin disruption in the face of reduced tau expression. Parallel studies showed that NAP reduced the number of apoptotic neurons through activation of PI-3K/Akt pathway in the cortical plate or both PI-3K/Akt and MAPK/MEK1 kinases in the white matter. The interaction of these disparate yet complementary pathways is the subject of future studies toward human brain neuroprotection in the clinical scenario.
Lymphatic Intervention for Various Types of Lymphorrhea: Access and Treatment (2016)

Traumatic lymphorrhea is a rare but potentially life-threatening complication. Postoperative lymphorrhea is the leading cause of traumatic lymphorrhea and can arise anywhere within the lymphatic system. Leaks arising from the aortoiliac region to the thoracic duct (TD) and from hepatic lymphatics can be identified with intranodal lymphangiography and transhepatic lymphangiography, respectively. Therefore, an appropriate lymphangiography technique is essential for identifying the sources of leaks. Chylothorax resulting from damage to the TD can be serious because the TD transports large amounts of lymphatic fluid from the gastrointestinal, hepatic, and aortoiliac regions. Percutaneous TD embolization-comprising access to the TD followed by embolization-has recently become a minimally invasive alternative to surgical TD ligation for high-output chylothorax. The selection of access routes to the TD depends on its anatomy. If the TD cannot be approached by such means, other options include TD needle interruption or drainage of lymphatic fluid adjacent to the leakage point followed by sclerotherapy. Most cases of abdominal lymphorrhea arise from the aorta-iliac lymphatic system, and lymphangiography alone or computed tomography-guided sclerotherapy might be useful. Rarely, leakage may arise from hepatic lymphatics due to a damaged gastroduodenal ligament and can be visualized and embolized transhepatically. This article comprehensively reviews clinically relevant anatomic TD variations, lymphangiography techniques and criteria for their selection, and treatment strategies for lymphorrhea. <sup>©</sup>RSNA, 2016.
Study in Jealousy (1991)

. . . eyes . . . The windows’ lower halves were smeared, only heads poked out. Pale, eyes sunken, women pressed up against the glass, trying to get a look at theirs. Today was signout day. Brakes screeched on arriving cars, reception room doors slammed. Pavel had already reported to his wife, and now, as she buttoned up the umpteenth item of apparel, he paced back and forth in the courtyard, swinging his bouquet like a cudgel. How should he act? First option: smile like nothing’s wrong, give her a kiss, hand her the flowers, receive the child ... or first receive the child, then hand her the flowers? Damned if he knew how it was done, and that was beside the point anyway. So, second option: Lilya, don’t think you can kid me—and he chuckled despite himself: that’s exactly what she was doing—kidding me. But if she thinks I think the kid is mine, she’s got a surprise in store for her. So: Lilya, don’t think you can kid . . . No, that’s impossible. Just like that, out of the blue. The nurse or nanny’s going to be right there. No, that’s out. Third option: exceedingly gracious, zero emotion—greeted, gave, received, put in car, not a word en route, polite nod to the neighbor women, door locked in room, and—the whole truth, from day one, the facts, the figures, the lies, the certificate from the hospital, the note—yes, yes, the note too, written in her own hand. Sure, she was going to try to deny it, there might be tears, even hysterics, she’d call him the scum of the earth— let her! let her! The main thing was to get at the whole truth, quietly but firmly, to reach the point where, cry as you might, we’re not going to live together. Help you out in the beginning? Gladly. Whatever you need—my pleasure: diapers, food, bottles, stroller, playpen . . . but the playpen’s already bought, I picked it up yesterday, and I got paper diapers, thirty of them, your whole family could wet the bed—in general, any services, but that’s what they are, services, understand, no sloppy sentimentality, no fatherly feeling, and in a month—that’s it, we cut our ties, I go to my parents in Tushino (my father will have a heart attack; my mother will pass out), and . . . “Pasha!” He shuddered and turned. Lilya was standing on the landing, holding onto the railing. Next to her a nurse’s aide was puffing and holding something large and square-shaped, tied up in a blue ribbon. “Pasha, what’s the matter with you?” shouted Lilya. “I’ve been calling you and calling you, and you act like you’ve gone deaf. ”
Distributed Temperature Sensing in Polymer Optical Fiber by BOFDA (2014)

Distributed temperature measurements in a perfluorinated graded-index polymer optical fiber (POF) with 50- μm core diameter are reported for the first time, to the best of our knowledge. Brillouin optical frequency-domain analysis is shown to be able to resolve spatially the temperature-dependent Brillouin frequency shift profile along a 20-m POF fiber sample, at a nominal spatial resolution of 4 m. The results indicate that POFs are potentially useful for distributed temperature measurements based on stimulated Brillouin scattering.
Solvent-free microwave-assisted Meyers’ lactamization (2010)

Microwave solvent-free conditions developed for Meyers’ lactamization, a typical bielectrophile-binucleophile reaction that produces quaternary centers in a stereoselective manner, give access to Meyers’ chiral lactams in good yield and high diastereoselectivity in short times.
Coarsening of monodisperse wet microfoams (2004)

We report experiments on the aging of monodisperse wet microfoams. We use the flow focusing technique to produce perfectly monodisperse microbubbles from 50 to 80 μm in diameter. This results in a foam of spherical bubbles of the same size ordered in random ordered lattices like “crystal grains” above the foam/liquid interface. We observe two different behaviors while the foam drains without any interference. At early times, the foam bubble size is almost constant from 10 to 20 min depending on the initial diameter of the bubbles. For longer times, the foam reaches a scaling state where the bubbles mean diameter growth agrees with the theoretical prediction t1/3.
Frequency Domain Analysis for Detecting Pipeline Leaks (2005)

This paper introduces leak detection methods that involve the injection of a fluid transient into the pipeline, with the resultant transient trace analyzed in the frequency domain. Two methods of leak detection using the frequency response of the pipeline are proposed. The inverse resonance method involves matching the modeled frequency responses to those observed to determine the leak parameters. The peak-sequencing method determines the region in which the leak is located by comparing the relative sizes between peaks in the frequency response diagram. It was found that a unique pattern was induced on the peaks of the frequency response for each specific location of the leak within the pipeline. The leak location can be determined by matching the observed pattern to patterns generated numerically within a lookup table. The procedure for extracting the linear frequency response diagram, including the optimum measurement position, the effect of unsteady friction, and the way in which the technique can be extended into pipeline networks, are also discussed within the paper.
Fundamentals of gas turbines (1984)

History of the Gas Turbine. Thermodynamics. Fluid Mechanics. Combustion. Shaft--Power Gas Turbines. Gas Turbines for Aircraft Propulsion. Compressors. Turbines. Inlets, Combustion Chambers, and Nozzles. Component Matching. Environmental Considerations. Appendix. Index.
Preventing lost messages in event-driven programming (2006)

Abstract. The event-driven programming style is pervasive as an efficient method for interacting with the environment. Unfortunately, the event-driven style severely complicates program maintenance and understanding, as it requires each logical flow of control to be fragmented across multiple independent callbacks. We propose a backward-compatible extension to Java, called TaskJava, which supports lightweight, interleaved computations without foregoing standard control mechanisms like procedures and exceptions. At the same time, TaskJava programs can be automatically translated into efficient event-based code. This technical report presents, in detail, a formalization of TaskJava. We formalize the operational semantics, typing rules, and modular compilation strategy for a core sublanguage. We then prove a number of properties of this core language, including type soundness, observational equivalence of translated programs, and freedom from certain classes of bugs. 1
The diverse family of <scp>M</scp>mp<scp>L</scp> transporters in mycobacteria: from regulation to antimicrobial developments (2017)

Summary Mycobacterial genomes contain large sets of loci encoding membrane proteins that belong to a family of multidrug resistance pumps designated Resistance‐Nodulation‐Cell Division (RND) permeases. Mycobacterial membrane protein Large (MmpL) transporters represent a subclass of RND transporters known to participate in the export of lipid components across the cell envelope. These surface‐exposed lipids with unusual structures play key roles in the physiology of mycobacteria and/or can act as virulence factors and immunomodulators. Defining the substrate specificity of MmpLs and their mechanisms of regulation helps understanding how mycobacteria elaborate their complex cell wall. This review describes the diversity of MmpL proteins in mycobacteria, emphasising their high abundance in a few opportunistic rapid‐growing mycobacteria. It reports the conservation of mmpL loci between Mycobacterium tuberculosis and non‐tuberculous mycobacteria, useful in predicting the role of MmpLs with unknown functions. Paradoxically, whereas MmpLs participate in drug resistance mechanisms, they represent also attractive pharmacological targets, opening the way for exciting translational applications. The most recent advances regarding structural/functional information are also provided to explain the molecular basis underlying the proton‐motive force driven lipid transport. Overall, this review emphasises the Janus‐face nature of MmpLs at the crossroads between antibiotic resistance mechanisms and exquisite vulnerability to drugs.
Physically based synthetic image generation for machine learning: a review of pertinent literature (2019)

The term deep learning is almost on everyone's lips these days, in the area of computer vision manly because of the great advances deep learning approaches have made amongst others in object detection and classification. For general object location or classification tasks there do exist several giant databases containing several millions of labeled images and several thousands of different labels like COCO and ImageNet. In contrast in industrial applications like quality inspection there do hardly ever exist such training data not only for reasons of confidentiality of trade secrets. An obvious way to remedy this deficiency is the synthetic creation of image data. Physically based rendering attempts to achieve photorealistic images by accurately simulating the ow of light of the real world according to various physical laws. Therefor multiple techniques like Ray Tracing and Path Tracing have been implemented and are becoming increasingly widespread as hardware performance increases. The intent of this article is to give a wide but nevertheless preferably comprehensive overview which approaches have been pursued in recent literature to generate realistic synthetic training images. The development of various rendering methods from rasterization to bidirectional Monte Carlo path tracing is outlined, as well as their differences and use. Along with the terminology a few mathematical foundations like the Bidirectional Reflectance Distribution Function (BRDF) are briefly described. Altogether specially concern is given to industrial data and quality control, comparing literature and the practical application of its results.
Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass (2011)

Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.
Unsupervised semantic clustering of Twitter hashtags (2014)

Social micro-blogging networks such as Twitter provide an enormous amount of information, and their automated and unsupervised analysis constitutes an exciting research challenge in Artificial Intelligence. This work presents a novel methodology, based on a semantic clustering of the set of hashtags, which permits to obtain automatically the topics associated to a given set of tweets. A case study on the field of Oncology shows how the main topics of interest are successfully discovered.
<scp>d</scp> -Alanine Deprivation of <i>Bacillus subtilis</i> Teichoic Acids Is without Effect on Cell Growth and Morphology But Affects the Autolytic Activity (1996)

Using insertional inactivation of the different genes of the dlt operon in Bacillus subtilis, we searched for metabolic and morphological changes caused by D-alanine ester deprivation of lipoteichoic acid and wall teichoic acid. There were no alterations of cell growth, basic metabolism, cellular content of phosphorus-containing compounds, ultrastructure, cell separation, and surface charge. The only alteration observed was an enhancement of endogenous and beta-lactam-induced cell lysis. Since this enhancement is doubtless correlated with the D-alanine ester deprivation of the teichoic acids, the present view based on in vitro experiments, that negatively charged LTA is inhibitory to autolysins, may be questioned. We propose that negatively charged lipoteichoic acid and/or wall teichoic acid serve in vivo to fix the cationic autolysins within the cell wall-membrane complex by electrostatic interaction. Positively charged D-alanine ester substituents decrease the binding capacity of the teichoic acids for autolysins by charge compensation.
Technique for joint balancing of IQ modulator-demodulator chains in wireless transmitters (2009)

This paper presents a technique to jointly balance an IQ modulator and demodulator chain in a wireless transmitter. A scheme is introduced for simultaneously extracting the amplitude and phase errors in these two cascaded RF devices based on the measurement of one or two calibrated delay lines depending on whether the delay line losses can be neglected. An analytic solution is obtained for the extraction of these parameters from the three measured K-matrices relating the modulator and demodulator in-phase and quadrature components. The algorithm was implemented in a FPGA testbed. It was first applied to behavioral IQ modulator and demodulator implemented with their K matrix and verified to extract the correct amplitude and phase errors. A final demonstration study was then carried out with an actual physical IQ modulator and demodulator operating at 3.5 GHz and correct results within the phase margin were obtained for these devices. This technique for balancing a modulator demodulator chain may find useful applications in the loop back chains for adaptive linearization.
Aldosteronism in Heart Failure: A Proinflammatory / Fibrogenic Cardiac Phenotype. Search for Biomarkers and Potential Drug Targets (2003)

Heart failure is a major health problem of epidemic proportions. Irrespective of its etiologic origins, a dysfunction of this normally efficient muscular pump is associated with systemic consequences, a progressive downhill clinical course and poor prognosis. Ventricular dysfunction is ultimately accompanied by neurohormonal system activation that accounts for: the congestive heart failure syndrome; an induction of oxi/nitrosative stress; adverse vascular remodeling; and activation of the immune system that contributes to a wasting syndrome known as cardiac cachexia. Circulating effector hormones of the renin-angiotensin-aldosterone system are an integral feature of this neurohormonal activation; they have systemic consequences. Insights into the pathophysiology of heart failure will identify improved methods of prevention, including biomarkers to aid in its detection and identification of risk, and to the development of specific drug targets. Herein we address one aspect of the neurohormonal profile of heart failure, namely that related to aldosteronism. Our focus is directed at the link between aldosteronism and its adverse influence on coronary vasculature structure, a proinflammatory/fibrogenic cardiac phenotype, which is based on an immunostimulatory state that includes activated peripheral blood mononuclear cells.
Calcium Signaling and c-Fos Gene Expression via M3 Muscarinic Acetylcholine Receptors in Human T- and B-Cells (2000)

We previously showed that blood acetylcholine (ACh) originates mainly from T-lymphocytes, and that stimulation of muscarinic ACh receptors (mAChRs) induces Ca2+ oscillations and up-regulates c-fos gene expression in both T- and B-lymphocytes. In the present study, we investigated which mAChR subtypes are involved in Ca2+ signaling and c-fos gene expression in human T- (CEM) and B- (Daudi) cells. Stimulation of mAChRs with 100 microM oxotremorine-M, an M1/M3 agonist, increased levels of intracellular free Ca2+ ([Ca2+]i) and c-fos mRNA expression in both cell lines. 4-DAMP, an M3 antagonist, more effectively blocked the oxotremorine-M-induced increase in [Ca2+]i than pirenzepine and telenzepine, M1-receptor antagonists; AF-DX 116, an M2 antagonist; hexahydrosiladifenidol, a weak M3 antagonist; or hexamethonium and d-tubocurarine, nicotinic receptor antagonists. McN-A-343 (100 microM), a partial M1-receptor agonist, had no apparent effect on [Ca2+]i in either cell line. The oxotremorine-M-induced up-regulation of c-fos transcription was inhibited by 4-DAMP, but not by pirenzepine or AF-DX 116. Our findings thus suggest that ACh released from T-lymphocytes acts as an autocrine/paracrine factor, transmitting a Ca2+-dependent signal to the nuclei of T- and B-lymphocytes via M3 receptors.
Beyond morphological size distribution (2009)

In the field of digital image processing, the description of image content is one of the most crucial tasks. Indeed, it is a mandatory step for various applications, such as industrial vision, medical imaging, content-based image retrieval, etc. The description of the image content is achieved through the computation of some predefined features, which can be performed at different scales. Among global features that describe the content of the whole image, the gray level histogram focuses on the distribution of gray levels within the image, while morphological features (e.g., the pattern spectrum) measure the distribution of object sizes in the image. Despite their broad interest, such morphological size-distribution features are limited due to their monodimensional nature. Our goal is to review multidimensional extensions of these features able to deal with complementary information (such as shape, orientation, spectral, intensity, or spatial information). Moreover, we illustrate each multidimensional feature by an illustrative example that shows their relevance compared to the standard morphological size distribution. These features can be seen as relevant solutions when the standard monodimensional features fail to accurately represent the image content.
Sterilization of bacterial endospores by an atmospheric-pressure argon plasma jet (2007)

Argon plasma jets penetrate deep into ambient air and create a path for oxygen radicals to sterilize microbes. A sterilization experiment with bacterial endospores indicates that an argon-oxygen plasma jet very effectively kills endospores of Bacillus atrophaeus (ATCC 9372), thereby demonstrating its capability to clean surfaces and its usefulness for reinstating contaminated equipment as free from toxic biological warfare agents. However, the spore-killing efficiency of the atmospheric-pressure argon-oxygen jet depends very sensitively on the oxygen concentration in the argon gas.