gebhart/patrepeval huggingface dataset:
Assessing cellular and circulating miRNA recovery: the impact of the RNA isolation method and the quantity of input material (2016)

MicroRNAs (miRNAs) have emerged as promising cancer biomarkers. However, exploiting their informative potential requires careful optimization of their detection. Here, we compared the efficiency of commonly used RNA extraction kits in miRNA recovery from cells, plasma and urine/plasma-derived exosomes, using single-gene RT-qPCR and miRNA profiling. We used increasing amounts of starting material to investigate the impact of the input material size on miRNA extraction. We showed that miRNA recovery was largely influenced by the isolation method and by the amount of input material. In particular, the miRCURY™ kit provided highly pure RNA. However, its columns poorly recovered miRNAs from limiting amounts of cells and plasma, and rapidly saturated by large RNA species and plasma components, thus impeding miRNA recovery from high input amounts. Overall, the miRNeasy® kit permitted a better miRNA detection despite a less pure extracted RNA. Nevertheless, some miRNAs were preferentially or exclusively isolated by either of the methods. Trizol® LS resulted in very low purity RNA which affected RT-qPCR efficiency. In general, miRCURY™ biofluids kit efficiently extracted miRNAs from plasma. A careful selection of the RNA isolation method and the consideration of the type and size of input material are highly recommended to avoid biased results.
Size-Dependent Optical Spectroscopy of a Homologous Series of CdSe Cluster Molecules (2001)

The optical properties and electronic structure of a homologous series of CdSe cluster molecules covering a size range between 0.7 and 2 nm are investigated. CdSe cluster molecules with 4, 8 10, 17, and 32 Cd atoms, capped by selenophenol ligands, were crystallized from solution and their structures determined by single-crystal X-ray diffraction. The cluster molecules are composed of a combination of adamanthane and barylene-like cages, the building blocks of the zinc blende and the wurtzite structures of the bulk CdSe. The onset of the room temperature absorption and low-temperature photoluminescence excitation spectra exhibit a systematic blue shift with reduced cluster size manifesting the quantum confinement effect down to the molecular limit of the bulk semiconductor. Blue-green emission, shifted substantially to lower energy from the absorption onset, is observed only at low temperature and its position is nearly independent of cluster size. The wavelength dependence of both photoluminescence and photoluminescence excitation was measured. The emission is assigned to forbidden transitions involving the cluster-molecule surface-capping ligands. This assignment is supported by the emission decay which exhibits distributed kinetics with microsecond time scale. The temperature dependence of the emission intensity is quantitatively explained by multiphonon-induced nonradiative relaxation mediated by low-frequency vibrations of the selenophenol capping ligands. Upon irradiation, the emission of all cluster molecules is quenched. Warming up and recooling leads to recovery of the emission (partial or complete) for all but the cluster molecule with 10 Cd atoms. This temporary darkening is assigned to the photoinduced charging of the cluster-molecule surface ligands, resembling the reversible on-off blinking of the emission observed for larger CdSe nanocrystals.
Non-disruptive collagen characterization in clinical histopathology using cross-modality image synthesis (2020)

The importance of fibrillar collagen topology and organization in disease progression and prognostication in different types of cancer has been characterized extensively in many research studies. These explorations have either used specialized imaging approaches, such as specific stains (e.g., picrosirius red), or advanced and costly imaging modalities (e.g., second harmonic generation imaging (SHG)) that are not currently in the clinical workflow. To facilitate the analysis of stromal biomarkers in clinical workflows, it would be ideal to have technical approaches that can characterize fibrillar collagen on standard H&E stained slides produced during routine diagnostic work. Here, we present a machine learning-based stromal collagen image synthesis algorithm that can be incorporated into existing H&E-based histopathology workflow. Specifically, this solution applies a convolutional neural network (CNN) directly onto clinically standard H&E bright field images to extract information about collagen fiber arrangement and alignment, without requiring additional specialized imaging stains, systems or equipment.
Nonlinear optical properties of neodymium yttrium aluminum borate crystals (1983)

An investigation was made of the linear and nonlinear optical properties of new neodymium yttrium aluminum borate crystals. These crystals were found to be suitable for use as multifunctional laser media and as nonlinear media capable of efficient frequency conversion of laser radiation.
Reactivity of diiron nonacarbonyl in tetrahydrofuran. I. Isolation and characterization of pyridinetetracarbonyliron and pyrazinetetracarbonyliron (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactivity of diiron nonacarbonyl in tetrahydrofuran. I. Isolation and characterization of pyridinetetracarbonyliron and pyrazinetetracarbonylironF. Albert Cotton and Jan M. TroupCite this: J. Am. Chem. Soc. 1974, 96, 11, 3438–3443Publication Date (Print):May 1, 1974Publication History Published online1 May 2002Published inissue 1 May 1974https://pubs.acs.org/doi/10.1021/ja00818a016https://doi.org/10.1021/ja00818a016research-articleACS PublicationsRequest reuse permissionsArticle Views1056Altmetric-Citations98LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
The role of filtration in preventing waterborne disease (1982)

Filtration is an important treatment process in the removal of pathogenic microorganisms and in the prevention of waterborne disease. Historical records indicate that filtration was responsible for reducing death and illness from waterborne disease in 1871 in Germany and for reducing morbidity and mortality from typhoid fever in the United States in the late 1800s‐early 1900s. After studying recent outbreaks of waterborne disease, the authors attribute the causes of these outbreaks to the lack of filtration or to faulty operation and maintenance of the process. Pilot‐plant data and results from full‐scale operation are presented to illustrate the effectiveness of various forms of filtration in reducing microbial populations to concentrations that are easily controlled by disinfection.
Molecular monitoring of minimal residual disease in patients in long-term complete remission after allogeneic stem cell transplantation for multiple myeloma (2000)

In the present study, we used a polymerase chain reaction–based (PCR-based) strategy to retrospectively analyze the presence of residual myeloma cells in serial posttransplant bone marrow samples obtained from 13 patients in remission after allogeneic hemopoietic stem cell transplantation (allo SCT). For this purpose, patient-specific primers were generated from complementarity determining regions 2 and 3 of the rearranged IgH gene. The level of sensitivity of the PCR-based assay ranged from 1 in 105 to 1 in 106 normal marrow cells. Following transplantation, 9 of 12 patients who attained stringently defined complete remission (CR) remained persistently PCR− for a median of 36 months, and 4 of the patients remained PCR− up to the latest analysis, which was performed at 48, 72, 72, and 120 months, respectively, after allo SCT. None of the patients in the PCR− subgroup experienced a disease relapse, and only 1 of 4 PCR+ patients experienced a relapse. It is concluded that allo SCT has the potential ability to induce sustained serological and molecular CR in selected patients with multiple myeloma.
Structure/Activity Relationships of Grandinol: a Germination Inhibitor in<i>Eucalyptus</i> (1985)

Structure/activity relationships of grandinol (1), which shows potent inhibition to cress germination, were examined by an activity comparison of many synthetic analogues. The result clearly indicates that a combination of two carbonyl functionalities on a phloroglucinol nucleus is necessary for inhibition. The presumptive site of action requires strict steric limitation of the ketonic side chain, which must be less than four carbon units in length. The alkyl substituent on the nucleus is not essential, although it may enhance the activity.
Thermal near-field radiative transfer between two spheres (2008)

Radiative energy transfer between closely spaced bodies is known to be significantly larger than that predicted by classical radiative transfer because of tunneling due to evanescent waves. Theoretical analysis of near-field radiative transfer is mainly restricted to radiative transfer between two half-spaces or spheres treated in the dipole approximation (very small sphere) or proximity force approximation (radius of sphere much greater than the gap). Sphere-sphere or sphere-plane configurations beyond the dipole approximation or proximity force approximation have not been attempted. In this work, the radiative energy transfer between two adjacent non-overlapping spheres of arbitrary diameters and gaps is analyzed numerically. For spheres of small diameter (compared to the wavelength), the results coincide with the dipole approximation. We see that the proximity force approximation is not valid for spheres with diameters much larger than the gap, even though this approximation is well established for calculating forces. From the numerical results, a regime map is constructed based on two nondimensional length scales for the validity of different approximations.
An environmentally benign and selective electrochemical oxidation of sulfides and thiols in a continuous-flow microreactor (2017)

A practical and environmentally benign electrochemical oxidation of thioethers and thiols in a commercially-available continuous-flow microreactor is presented.
SIZ1-Mediated Sumoylation of ICE1 Controls<i>CBF3/DREB1A</i>Expression and Freezing Tolerance in<i>Arabidopsis</i> (2007)

SIZ1 is a SUMO E3 ligase that facilitates conjugation of SUMO to protein substrates. siz1-2 and siz1-3 T-DNA insertion alleles that caused freezing and chilling sensitivities were complemented genetically by expressing SIZ1, indicating that the SIZ1 is a controller of low temperature adaptation in plants. Cold-induced expression of CBF/DREB1, particularly of CBF3/DREB1A, and of the regulon genes was repressed by siz1. siz1 did not affect expression of ICE1, which encodes a MYC transcription factor that is a controller of CBF3/DREB1A. A K393R substitution in ICE1 [ICE1(K393R)] blocked SIZ1-mediated sumoylation in vitro and in protoplasts identifying the K393 residue as the principal site of SUMO conjugation. SIZ1-dependent sumoylation of ICE1 in protoplasts was moderately induced by cold. Sumoylation of recombinant ICE1 reduced polyubiquitination of the protein in vitro. ICE1(K393R) expression in wild-type plants repressed cold-induced CBF3/DREB1A expression and increased freezing sensitivity. Furthermore, expression of ICE1(K393R) induced transcript accumulation of MYB15, which encodes a MYB transcription factor that is a negative regulator of CBF/DREB1. SIZ1-dependent sumoylation of ICE1 may activate and/or stabilize the protein, facilitating expression of CBF3/DREB1A and repression of MYB15, leading to low temperature tolerance.
Emerging high-speed access technologies (1999)

Networks are fast becoming the backbone of many businesses, but the technology behind them is probably the most complex and least understood IT subject. It's not enough to have a particular network in place-you must also keep data flowing from site to site and to and from the Internet at adequate speed. This is where the choice of access technologies-the various ways your enterprise can connect to larger networks-is crucial. Your choices have never been more diverse. After years of talk about how to upgrade the "last mile" (the connection from your location to a hub or central office), vendors now have products to offer. Some are relatively immature, having only recently become commercially available. Regardless, they can make an immediate difference in throughput. To benefit, you'll need to navigate some complex vendor options and keep an eye on future developments in technology and standards. To help guide your decision making, the authors present a brief overview of new network access technologies. Be aware that deployment depends on location and market: some of these technologies may be available in your area, others may not. The following are mentioned: phone line access; digital subscriber lines; cable modems; and direct broadcast satellites.
Selective adapter recruitment and differential signaling networks by VEGF vs. shear stress (2007)

Vascular endothelial cells are continuously exposed to mechanical and chemical stimuli, such as shear stress and VEGF, respectively. It is still not clear how cells perceive these stimuli and orchestrate their responses. Studying the molecular mechanism by which shear stress and VEGF regulate the signaling pathways in bovine endothelial aortic cells, we found that VEGF induced a rapid association of VEGF receptor 2 (Flk-1) with Nck beta, but shear stress did not have such an effect. SU1498 (a specific inhibitor of Flk-1) and Nck beta(nm) (a negative mutant of Nck beta) blocked the VEGF-induced ERK and JNK activities. Only SU1498, but not Nck beta(nm), inhibited the shear-induced ERK activity. Furthermore, neither SU1498 nor Nck beta(nm) had significant effects on the shear-induced JNK activity, which can be blocked by inhibitors of Src family kinase and ROCK kinase. Therefore, mechanical (shear stress) and chemical (VEGF) stimuli diverge at the receptor Flk-1 in terms of the recruitment of the adapter protein Nck beta, and they employ different components of the complex signaling network in regulating downstream molecules, e.g., ERK and JNK.
EXM eigen templates for detecting and classifying arbitrary junctions (2002)

A novel method for extracting parametric junction and corner features in images is presented. By treating each complex feature as a combination of elementary line and edge features, the method provides an efficient way to locate features of interest with reduced number of filtering operations. The expansion matching (EXM) method is used to design optimal detectors for a set of elementary model shape features. Next, the principal components of the Karhunen-Loeve (KL) representation of these model EXM detectors are used to filter the image and extract candidate interest points derived from the energy peaks of the eigen coefficients. The KL coefficients at these candidate points are then used to efficiently reconstruct the response and differentiate real junctions and corners from arbitrary features in the image. The method is robust to additive noise and is able to successfully extract, classify and find the myriad compositions of corner and junction features formed by combinations of two or more elementary edges or lines.
SOAPindel: Efficient identification of indels from short paired reads (2012)

We present a new approach to indel calling that explicitly exploits that indel differences between a reference and a sequenced sample make the mapping of reads less efficient. We assign all unmapped reads with a mapped partner to their expected genomic positions and then perform extensive de novo assembly on the regions with many unmapped reads to resolve homozygous, heterozygous, and complex indels by exhaustive traversal of the de Bruijn graph. The method is implemented in the software SOAPindel and provides a list of candidate indels with quality scores. We compare SOAPindel to Dindel, Pindel, and GATK on simulated data and find similar or better performance for short indels (<10 bp) and higher sensitivity and specificity for long indels. A validation experiment suggests that SOAPindel has a false-positive rate of ∼10% for long indels (>5 bp), while still providing many more candidate indels than other approaches.
Expression of Vascular Endothelial Growth Factor Promotes Colonization, Vascularization, and Growth of Transplanted Hepatic Tissues in the Mouse (1999)

A complex vascular network forms an important component of the liver architecture. This network is essential for the supply of oxygen and nutrients to cells and delivery of molecules for metabolic exchange. In this study, we attempted to construct a vascular network in transplanted hepatic tissues and examined the effect of such network on tissue formation. Primary hepatocytes of adult mice were transfected with vascular endothelial growth factor (VEGF) gene in vitro then transplanted with collagen beads intraperitoneally in mice. VEGF-transfected hepatocytes secreted sufficient protein of the transgene in vitro to induce proliferation of endothelial cells. In vivo, VEGF-transfected hepatocytes formed a large number of colonies and developed a significant vascular network in established tissues compared with control tissues. In addition, hepatocytes of VEGF-transfected, established tissues proliferated and formed a substantial parenchymal region. These hepatocytes were also functional as confirmed by the production of albumin. Our results suggested that VEGF expression conferred not only the formation of a vascular network but also promoted tissue formation. Our study showed that ex vivo gene transfection into hepatocytes is a useful method for the induction of liver reconstitution in vivo.
Regulation of cholesterol 7 alpha-hydroxylase in the liver. Purification of cholesterol 7 alpha-hydroxylase and the immunochemical evidence for the induction of cholesterol 7 alpha-hydroxylase by cholestyramine and circadian rhythm. (1990)

Two cholesterol 7 alpha-hydroxylase isozymes were purified from liver microsomes of cholestyramine-treated female rats by using anion exchange high performance liquid chromatography. These two cytochrome P-450 isozymes were similar in electrophoretic mobility, immunocross-reactivity, and Vmax but differed in Km for cholesterol, turnover number, and charges. Antibody against the major isozyme was raised in rabbit. This antibody specifically inhibited microsomal cholesterol 7 alpha-hydroxylase activity. Immunoblot of microsomal polypeptides indicated that microsomal cholesterol 7 alpha-hydroxylase enzyme levels were increased in parallel with cholesterol 7 alpha-hydroxylase activity upon the treatment of rats with diet supplemented with cholestyramine. Both cholesterol 7 alpha-hydroxylase activity and enzyme levels were drastically reduced immediately after the removal of cholestyramine from the diet. Cholesterol 7 alpha-hydroxylase activity was also detected in the microsomes of kidney, heart, and lung in about 7-27% of the level found in the liver. 3-Methylcholanthrene treatment induced cholesterol 7 alpha-hydroxylase activity and enzyme level. In contrast, pregnenolone-16 alpha-carbonitrile or dexamethasone treatment greatly depressed enzyme and activity in rats. Cholesterol 7 alpha-hydroxylase enzyme level was 2-3-fold higher in liver microsomes of rats maintained under the reversed light cycle than under the normal light cycle. In genetically obese Zucker rats, cholesterol 7 alpha-hydroxylase activity and enzyme level did not respond to the change in the light cycle, however, were induced to the same levels as in the lean rats by cholestyramine treatment. This study provided the first direct evidence that the bile acid feedback regulation and circadian rhythm of microsomal cholesterol 7 alpha-hydroxylase activity involved the induction of cholesterol 7 alpha-hydroxylase enzyme level.
Function and design of DOS/360 and TOS/360 (1967)

Prior to third-generation computers, few systems programmers had tried to implement full-function operating systems for small-storage computers. True, most installations had many of the functional requirements that justified operating systems, but storage limitations made it impractical to meet these needs on an integrated basis. At present, however, two forces are clearly at work to change the trend. First, the new computers bring with them a degree of device modularity and flexibility that intensifies the need for integrated operating systems, and second, these same computers possess a degree of efficiency that makes operating systems practical for smaller main-storage areas.
Pharmacological relevance and potential of sphingosine 1‐phosphate in the vascular system (2011)

Sphingosine-1-phosphate (S1P) was identified as a crucial molecule for regulating immune responses, inflammatory processes as well as influencing the cardiovascular system. S1P mediates differentiation, proliferation and migration during vascular development and homoeostasis. S1P is a naturally occurring lipid metabolite and is present in human blood in nanomolar concentrations. S1P is not only involved in physiological but also in pathophysiological processes. Therefore, this complex signalling system is potentially interesting for pharmacological intervention. Modulation of the system might influence inflammatory, angiogenic or vasoregulatory processes. S1P activates G-protein coupled receptors, namely S1P(1-5) , whereas only S1P(1-3) is present in vascular cells. S1P can also act as an intracellular signalling molecule. This review highlights the pharmacological potential of S1P signalling in the vascular system by giving an overview of S1P-mediated processes in endothelial cells (ECs) and vascular smooth muscle cells (VSMCs). After a short summary of S1P metabolism and signalling pathways, the role of S1P in EC and VSMC proliferation and migration, the cause of relaxation and constriction of arterial blood vessels, the protective functions on endothelial apoptosis, as well as the regulatory function in leukocyte adhesion and inflammatory responses are summarized. This is followed by a detailed description of currently known pharmacological agonists and antagonists as new tools for mediating S1P signalling in the vasculature. The variety of effects influenced by S1P provides plenty of therapeutic targets currently under investigation for potential pharmacological intervention.