gebhart/patrepeval huggingface dataset:
Correction to High Sensitivity Detection and Quantitation of DNA Copy Number and Single Nucleotide Variants with Single Color Droplet Digital PCR (2015)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrection to High Sensitivity Detection and Quantitation of DNA Copy Number and Single Nucleotide Variants with Single Color Droplet Digital PCRLaura Miotke, Billy T. Lau, Rowza T. Rumma, and Hanlee P. Ji*Cite this: Anal. Chem. 2015, 87, 5, 3114Publication Date (Web):February 12, 2015Publication History Published online12 February 2015Published inissue 3 March 2015https://doi.org/10.1021/acs.analchem.5b00061Copyright © 2015 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views740Altmetric-Citations7LEARN 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 InReddit PDF (162 KB) Get e-Alerts Get e-Alerts
Randomness Efficient Fast-Johnson-Lindenstrauss Transform with Applications in Differential Privacy and Compressed Sensing (2014)

The Johnson-Lindenstrauss property ({\sf JLP}) of random matrices has immense application in computer science ranging from compressed sensing, learning theory, numerical linear algebra, to privacy. This paper explores the properties and applications of a distribution of random matrices. Our distribution satisfies {\sf JLP} with desirable properties like fast matrix-vector multiplication, sparsity, and optimal subspace embedding. We can sample a random matrix from this distribution using exactly $2n+n \log n$ random bits. We show that a random matrix picked from this distribution preserves differential privacy under the condition that the input private matrix satisfies certain spectral property. This improves the run-time of various differentially private mechanisms like Blocki {\it et al.} (FOCS 2012) and Upadhyay (ASIACRYPT 13). Our final construction has a bounded column sparsity. Therefore, this answers an open problem stated in Blocki {\it et al.} (FOCS 2012). Using the results of Baranuik {\it et al.} (Constructive Approximation: 28(3)), our result implies a randomness efficient matrices that satisfies the Restricted-Isometry Property of optimal order for small sparsity with exactly linear random bits. We also show that other known distributions of sparse random matrices with the {\sf JLP} does not preserves differential privacy; thereby, answering one of the open problem posed by Blocki {\it et al.} (FOCS 2012). Extending on the works of Kane and Nelson (JACM: 61(1)), we also give unified analysis of some of the known Johnson-Lindenstrauss transform. We also present a self-contained simplified proof of an inequality on quadratic form of Gaussian variables that we use in all our proofs.
A Type I Peritrophic Matrix Protein from the Malaria VectorAnopheles gambiae Binds to Chitin (1998)

Upon feeding, mosquito midguts secrete the peritrophic matrix (PM), an extracellular chitin-containing envelope that completely surrounds the blood meal. Because the malaria parasite must cross the PM to complete its life cycle in the mosquito, the PM is a potential barrier for malaria transmission. By antibody screening of an expression library we have identified and partially characterized a cDNA encoding a putative PM protein, termed Anopheles gambiae adult peritrophin 1 (Ag-Aper1). Ag-Aper1 is the first cloned PM gene from a disease vector. Northern analysis detected an abundant Ag-Aper1 transcript only in the adult gut, and not in any other tissues or at any other stages of development. The predicted amino acid sequence indicates that it has two tandem chitin-binding domains that share high sequence similarity with each other and also with the chitin-binding domain of an adult gut-specific chitinase from the same organism. The presumed ability of Ag-Aper1 to bind chitin was verified by a functional assay with the baculovirus-expressed recombinant protein. Ag-Aper1 did bind to chitin but not to cellulose, indicating that Ag-Aper1 binds chitin specifically. The double chitin-binding domain organization of Ag-Aper1 suggests that each protein molecule is able to link two chitin polymer chains. Hence, this protein is likely to act as a molecular linker that connects PM chitin fibrils into a three-dimensional network.
ADENOVIRUS E1A PROTEINS AND TRANSFORMATION (REVIEW) (1994)

The E1A gene region of human adenovirus can cooperate with a second gene such as adenovirus E1B or activated ras to transform rodent cells oncogenically. On its own, E1A induces quiescent cells to divide, represses cellular differentiation, induces programmed cell death and affects gene expression. E1A acts through its products, two similar nuclear proteins of 289 and 243 residues, which bind to cellular proteins, particularly p300 and a group of interrelated proteins, p130, p107 and pRb. This review describes what is known of the ways E1A interferes with growth regulation by these and other cellular proteins, such as cyclins and transcription factors, so as to bring about oncogenic transformation.
Alteration of Platelet-Associated Membrane Glycoproteins During Extracorporeal Apheresis of Peripheral Blood Progenitor Cells (1997)

In extracorporeal circulation, blood is affected by artificial biomaterials and shear forces. We investigated the effects of peripheral blood progenitor cell (PBPC) apheresis on the kinetics and level of platelet membrane antigen expression in 11 breast cancer and 13 testicular cancer patients. After mobilization with rhG-CSF, continuous-flow apheresis was performed. Expression of structural antigens CD41a and CD42b and activation-dependent antigens CD62p, CD63, and fibrinogen was analyzed by flow cytometry at fixed time intervals. Initial changes occurred in all of the antigens within minutes, followed by a progressive increase in the mean channel fluorescence intensities (MCFI) of CD62p from 26 +/- 8 (mean +/- SD) to 73 +/- 29 (p < 0.05), CD63 from 22 +/- 5 to 51 +/- 16 (p < 0.05) and antifibrinogen from 120 +/- 20 to 356 +/- 154 (p < 0.05). In contrast, CD41a and CD42b fluorescence decreased during apheresis (p < 0.05 for both). The more rapid sequestration of P-selectin-expressing platelets known to occur during extracorporeal PBPC apheresis suggests that platelet activation may be associated with the loss of platelets during this procedure. In addition, alteration of platelet surface antigens increases thrombogenic potential and may reduce the in vivo efficacy of the platelet hemostatic potential.
Temporal development of hard and soft x-ray emission from a gas-puff Z pinch (1986)

Previous time- and space-resolved x-ray measurements on a small gas-puff Z pinch indicated the presence of bursts of energetic electron beam and related ‘‘hot spots’’—high-temperature, high-density plasma regions. Spectra taken from these hot spots are consistent with a plasma of electron density about 1022–1023 cm−3 and electron temperature of 500 eV. Here we present time correlation of the hard x-ray emission from the anode with large fluctuations in İ and with short bursts of intense soft x rays. These soft x-ray bursts originating from the hot spots are shown always to be preceded by hard x-ray emissions. Using suitable apertures, the plasma is shown to be a source of hard x rays, &amp;lt;2.5 Å. This is confirmed by x-ray pinhole photographs. By varying the Z of the anode the electron beam associated with hard x-ray emission is found to be of low energy (10 keV) agreeing with previous measurements. In particular a plastic, PTFE (Teflon), is shown to be a suitable material for the anode, with superior lifetime performance compared with conventional metallic substances.
Charting the Progress of PV Power Plant Energy Generating Costs to Unsubsidized Levels, Introducing the PV - LCOE Framework (2011)

Fundamental to the widespread global deployment of photovoltaic (PV) power plants is reducing the levelized cost of electricity (LCOE) to levels that make systems economically attractive without incentives. In recent years substantial progress has been made to this end with significant reductions seen in all aspects of PV power plant costs. When speaking of PV power plant economics the industry focuses around three critical metrics: the PV panel and balance of system (BOS) costs and the cost of energy as measured by LCOE. The PV and BOS costs and LCOE are valuable tools to track industry progress, but have some limitations that make it desirable to establish a modified approach to track PV power plant energy generation economics. This paper proposes a new framework for categorizing and calculating PV power plant energy generating costs using a system called the PV-LCOE. The PV-LCOE framework combines a cost taxonomy, performance metrics, operating costs, and a simple energy generating cost (LCOE) equation to chart PV power plant cost reduction. The major value of this framework will be to simplify the calculation, identify key assumptions, and enable apples for apples comparisons from one plant to another.
Relationship between Glycolysis and Exopolysaccharide Biosynthesis in Lactococcus lactis (2001)

The relationships between glucose metabolism and exopolysaccharide (EPS) production in a Lactococcus lactis strain containing the EPS gene cluster (Eps(+)) and in nonproducer strain MG5267 (Eps(-)) were characterized. The concentrations of relevant phosphorylated intermediates in EPS and cell wall biosynthetic pathways or glycolysis were determined by (31)P nuclear magnetic resonance. The concentrations of two EPS precursors, UDP-glucose and UDP-galactose, were significantly lower in the Eps(+) strain than in the Eps(-) strain. The precursors of the peptidoglycan pathway, UDP-N-acetylglucosamine and UDP-N-acetylmuramoyl-pentapeptide, were the major UDP-sugar derivatives detected in the two strains examined, but the concentration of the latter was greater in the Eps(+) strain, indicating that there is competition between EPS synthesis and cell growth. An intermediate in biosynthesis of histidine and nucleotides, 5-phosphorylribose 1-pyrophosphate, accumulated at concentrations in the millimolar range, showing that the pentose phosphate pathway was operating. Fructose 1,6-bisphosphate and glucose 6-phosphate were the prominent glycolytic intermediates during exponential growth of both strains, whereas in the stationary phase the main metabolites were 3-phosphoglyceric acid, 2-phosphoglyceric acid, and phosphoenolpyruvate. The activities of relevant enzymes, such as phosphoglucose isomerase, alpha-phosphoglucomutase, and UDP-glucose pyrophosphorylase, were identical in the two strains. (13)C enrichment on the sugar moieties of pure EPS showed that glucose 6-phosphate is the key metabolite at the branch point between glycolysis and EPS biosynthesis and ruled out involvement of the triose phosphate pool. This study provided clues for ways to enhance EPS production by genetic manipulation.
In Vivo Micro-Image Mosaicing (2010)

Recent advances in optical imaging have led to the development of miniature microscopes that can be brought to the patient for visualizing tissue structures in vivo. These devices have the potential to revolutionize health care by replacing tissue biopsy with in vivo pathology. One of the primary limitations of these microscopes, however, is that the constrained field of view can make image interpretation and navigation difficult. In this paper, we show that image mosaicing can be a powerful tool for widening the field of view and creating image maps of microanatomical structures. First, we present an efficient algorithm for pairwise image mosaicing that can be implemented in real time. Then, we address two of the main challenges associated with image mosaicing in medical applications: cumulative image registration errors and scene deformation. To deal with cumulative errors, we present a global alignment algorithm that draws upon techniques commonly used in probabilistic robotics. To accommodate scene deformation, we present a local alignment algorithm that incorporates deformable surface models into the mosaicing framework. These algorithms are demonstrated on image sequences acquired in vivo with various imaging devices including a hand-held dual-axes confocal microscope, a miniature two-photon microscope, and a commercially available confocal microendoscope.
A flexible spread-spectrum multi-carrier multiple-access system for multi-media applications (2002)

This paper presents a novel multiple access scheme designed for mobile multi-media applications. The scheme is referred to as spread-spectrum multi-carrier multiple-access (SS-MC-MA) and exploits the advantages given by the combination of the spread-spectrum technique with multi-carrier modulation, known from multi-carrier code division multiple access (MC-CDMA) schemes. In contrast to MC-CDMA, the SS-MC-MA separates the users' signals according to an FDMA scheme on the sub-carrier level. Thus, the novel scheme avoids multiple access interference (MAI) within a cell. SS-MC-MA can use the same radio interface for the up- and the down-link. Its bandwidth efficiency is comparable to the high bandwidth efficiency achievable with MC-CDMA in the down-link. By providing a high degree of flexibility, this system can be a good candidate for the future Universal Mobile Telecommunications Systems (UMTS).
On the shortest spanning subtree of a graph and the traveling salesman problem (1956)

7. A. Kurosh, Ringtheoretische Probleme die mit dem Burnsideschen Problem uber periodische Gruppen in Zussammenhang stehen, Bull. Acad. Sei. URSS, Ser. Math. vol. 5 (1941) pp. 233-240. 8. J. Levitzki, On the radical of a general ring, Bull. Amer. Math. Soc. vol. 49 (1943) pp. 462^66. 9. -, On three problems concerning nil rings, Bull. Amer. Math. Soc. vol. 49 (1943) pp. 913-919. 10. -, On the structure of algebraic algebras and related rings, Trans. Amer. Math. Soc. vol. 74 (1953) pp. 384-409.
Biomaterials for Vascular Tissue Engineering (2009)

Cardiovascular disease is the leading cause of mortality in the USA. The limited availability of healthy autologous vessels for bypass grafting procedures has led to the fabrication of prosthetic vascular conduits. While synthetic polymers have been extensively studied as substitutes in vascular engineering, they fall short of meeting the biological challenges at the blood-material interface. Various tissue engineering strategies have emerged to address these flaws and increase long-term patency of vascular grafts. Vascular cell seeding of scaffolds and the design of bioactive polymers for in situ arterial regeneration have yielded promising results. This article describes the advances made in biomaterials design to generate suitable materials that not only match the mechanical properties of native vasculature, but also promote cell growth, facilitate extracellular matrix production and inhibit thrombogenicity.
Induction of apoptosis in cisplatin-sensitive and -resistant human ovarian cancer cell lines. (1997)

In this study, we have assessed the mechanism of cytotoxicity in a series of cisplatin-sensitive and -resistant ovarian carcinoma cells following treatment with equitoxic concentrations of cisplatin. The specific proteolytic degradation and the enzymatic activities of the DNA-dependent protein kinase (DNA-PK) were assessed in the cisplatin-sensitive A2780 cell line and two resistant derivative cell lines, CP70 and C30. Forty-eight h following cisplatin treatment, unattached, apoptotic A2780 cells demonstrated a 20-30% decrease in DNA-PK phosphorylation activity. The resistant CP70 and C30 cell lines showed greater decreases in activity approaching 80 and 90%, respectively. The decreases in kinase activity were attributed to proteolytic degradation of the catalytic subunit of DNA-PK (DNA-PKcs). The extent of degradation mimicked the loss of DNA-PK activity, with the resistant cell lines showing the greatest portion of degraded DNA-PKcs. At the same time point, the ability of the DNA-PK Ku subunits to bind DNA was decreased in apoptotic, unattached cells compared to untreated controls, with the decrease in binding activity being attributed to decreased expression of the Ku subunits. In addition to DNA-PKcs cleavage, specific proteolytic cleavage of the poly(ADP-ribose)polymerase and generation of nucleosome-length DNA ladders was observed in all cell lines following cisplatin treatment. These data suggest that cell death via the accumulation of cisplatin-damaged DNA occurs via apoptosis in both the cisplatin-resistant and -sensitive ovarian cancer cells.
Solid-State [4 + 2] Cycloaddition of Fullerene C60 with Condensed Aromatics Using a High-Speed Vibration Milling Technique (1999)

The solid-state reaction using a high-speed vibration milling (HSVM) technique has been applied to the [4 + 2] cycloaddition of fullerene C(60) with condensed aromatics such as anthracenes, tetracene, pentacene, and naphtho[2,3-a]pyrene. From the reaction with anthracene, [4 + 2] cycloadduct 1 was obtained in better yield than the reaction in solution. Despite such heterogeneous solid-state reaction conditions, an equilibrium state appears to be attained between the reactants (C(60) and anthracene) and products (mono- and bisadducts) since essentially the same product mixture was obtained starting either from the reactants or from the monoadduct after 30 min of the HSVM reaction. The reaction with pentacene gave double C(60) adduct 4 with two C(60) cages attached to a pentacene molecule, which cannot be obtained in the reaction in toluene solution, in addition to symmetrical monoadduct 3. The HSVM treatment of C(60) with 9,10-dimethylanthracene, tetracene, or naphtho[2,3-a]pyrene also gave the corresponding [4 + 2] cycloadducts in fair yields. The redox properties of these adducts were investigated by the use of cyclic voltammetry.
Porphyrin dimers as photosensitizers in photodynamic therapy (1990)

Porphyrin dimers 9 with either linkages and possible isomers bis[1-[6,7-bis[2-(methoxycarbonyl)ethyl]-1,3,5,8-tetramethyl-2- vinylporphin-4-yl]ethyl] ether (10) bis[1-[6,7-bis[2-(methoxycarbonyl)ethyl]-1,3,5,8-tetramethyl-4- vinylporphin-2-yl]ethyl] ether (11), and 1-[6,7-bis[2-(methoxycarbonyl)ethyl]-1,3,5,8-tetramethyl-2-vinylporph in- 4-yl]ethyl 1-[6,7-bis[2-(methoxycarbonyl)ethyl]-1,3,5,8-tetramethyl-4-vinylporph in- 2-yl]ethyl ether (12) were synthesized from the corresponding (1-hydroxyethyl)vinyldeuteroporphyrin IX dimethyl esters (Hvd). The pure Hvd isomers 2-(1-hydroxyethyl)-4-vinyldeuteroporphyrin IX dimethyl ester (7) and 4-(1-hydroxyethyl)-2-vinyldeuteroporphyrin IX dimethyl ester (8) were obtained from 2-acetyl-4-(1-hydroxyethyl) deuteroporphyrin IX dimethyl ester (3) and 4-acetyl-2-(1-hydroxyethyl)deuteroporphyrin IX dimethyl ester (4). Porphyrins 3 and 4 were prepared either by partial reduction of 2,4-diacetyldeuteroporphyrin IX dimethyl ester (2) or by oxidation of hematoporphyrin IX dimethyl ester (1) by using tetra-n-propylammonium perruthenate (Prn4N)(RuO4) with N-methylmorpholine N-oxide as an oxidizing agent. The in vivo photosensitizing ability and therapeutic ratios of dimers 9-12 were compared with that of Photofrin II in the SMT-F tumor growing subcutaneously in DBA/2 Ha mice. These dimers were found to have better tumoricidal activity than Photofrin II with reduced skin phototoxicity.
The UK National External Quality Assessment Scheme for Heritable Bleeding Disorders (2014)

Molecular genetic analysis of families with hemophilia and other heritable bleeding disorders is a frequently requested laboratory investigation. In the United Kingdom, laboratories undertaking genetic testing must participate in a recognized external quality assessment scheme for formal accreditation. The UK National External Quality Assessment Scheme (UK NEQAS) for heritable bleeding disorders was established in its current format in 2003, and currently has 27 registered participants in the United Kingdom, the European Union (EU), and the non-EU countries. Two exercises per annum are circulated to participants comprising either whole blood or DNA isolated from cell lines, and laboratories are allowed 6 weeks to analyze the samples and generate a report. Reports are assessed by a panel comprising clinicians and scientists with expertise in this area. Samples to date have involved analysis of the F8 gene (10 exercises), the F9 gene (4 exercises), and the VWF gene (3 exercises) and have comprised a wide spectrum of mutations representing the routine workload encountered in the molecular genetics laboratory. The majority of laboratories in each exercise passed, but a small number did not and reasons for failing included clerical errors, genotyping inaccuracies, and a failure to correctly interpret data. Overall we have seen an improvement in quality of reports submitted for assessment, with a more concise format that will be of value to referring clinicians and counsellors. Informal feedback from participants has been very positive.
Formation of multiply charged ions from large molecules using massive‐cluster impact (1994)

Massive-cluster impact is demonstrated to be an effective ionization technique for the mass analysis of proteins as large as 17 kDa. The design of the cluster source permits coupling to both magnetic-sector and quadrupole mass spectrometers. Mass spectra are characterized by the almost total absence of chemical background and a predominance of multiply charged ions formed from 100% glycerol matrix. The number of charge states produced by the technique is observed to range from +3 to +9 for chicken egg lysozyme (14,310 Da). The lower m/z values provided by higher charge states increase the effective mass range of analyses performed with conventional ionization by fast-atom bombardment or liquid secondary ion mass spectrometry.
Interleukin-12 induces relapse in experimental allergic encephalomyelitis in the Lewis rat. (1997)

Acute, monophasic experimental allergic encephalomyelitis (EAE) in the Lewis rat shows pathological similarities to the human disease multiple sclerosis (MS). Rats that recover from EAE are essentially resistant to disease reinduction, unlike MS in which relapses are frequently associated with common bacterial and viral infections. As macrophage-derived interleukin (IL)-12 is a critical component of innate resistance to bacterial infection and appears to directly activate encephalitogenic T cells in vivo, the ability of this cytokine to reinduce paralysis in EAE was examined. Paralytic disease was exacerbated by intraperitoneal IL-12 administration and could be reinduced up to 1 week after recovery from the primary clinical episode. Concomitant with worsening of initial clinical signs and relapse was an increase in the ratio of macrophages to T cells in brain stem perivascular cuffs and the expression of inducible nitric oxide synthase in cells with both macrophage and microglial morphology. These findings suggest that IL-12 may contribute to macrophage-mediated disease exacerbation and relapse in patients with MS.