gebhart/patrepeval huggingface dataset:
Generalized unmixing model for multispectral flow cytometry utilizing nonsquare compensation matrices (2013)

Multispectral and hyperspectral flow cytometry (FC) instruments allow measurement of fluorescence or Raman spectra from single cells in flow. As with conventional FC, spectral overlap results in the measured signal in any given detector being a mixture of signals from multiple labels present in the analyzed cells. In contrast to traditional polychromatic FC, these devices utilize a number of detectors (or channels in multispectral detector arrays) that is larger than the number of labels, and no particular detector is a priori dedicated to the measurement of any particular label. This data-acquisition modality requires a rigorous study and understanding of signal formation as well as unmixing procedures that are employed to estimate labels abundance. The simplest extension of the traditional compensation procedure to multispectral data sets is equivalent to an ordinary least-square (LS) solution for estimating abundance of labels in individual cells. This process is identical to the technique employed for unmixing spectral data in various imaging fields. The present study shows that multispectral FC data violate key assumptions of the LS process, and use of the LS method may lead to unmixing artifacts, such as population distortion (spreading) and the presence of negative values in biomarker abundances. Various alternative unmixing techniques were investigated, including relative-error minimization and variance-stabilization transformations. The most promising results were obtained by performing unmixing using Poisson regression with an identity-link function within a generalized linear model framework. This formulation accounts for the presence of Poisson noise in the model of signal formation and subsequently leads to superior unmixing results, particularly for dim fluorescent populations. The proposed Poisson unmixing technique is demonstrated using simulated 8-channel, 2-fluorochrome data and real 32-channel, 6-fluorochrome data. The quality of unmixing is assessed by computing absolute and relative errors, as well as by calculating the symmetrized Kullback-Leibler divergence between known and approximated populations. These results are applicable to any flow-based system with more detectors than labels where Poisson noise is the dominant contributor to the overall system noise and highlight the fact that explicit incorporation of appropriate noise models is the key to accurately estimating the true label abundance on the cells. © 2013 International Society for Advancement of Cytometry.
Deep energy levels in CdTe and CdZnTe (1998)

The deep levels present in semiconducting CdTe and semi-insulating CdTe:Cl and Cd0.8Zn0.2Te have been investigated by means of cathodoluminescence, deep level transient spectroscopy (DLTS), photo-induced current transient spectroscopy, and photo-DLTS. The latter two methods, which can be applied to semi-insulating materials, allow to characterize the deep traps located up to midgap and can determine whether they are hole or electron traps. We have identified 12 different traps, some common to all the investigated samples, some peculiar to one of them. A comparison of the results obtained from the various materials is given and the status of defect models is reviewed.
Detecting and targetting oncogenic fusion proteins in the genomic era (2015)

The advent of widespread cancer genome sequencing has accelerated our understanding of the molecular aberrations underlying malignant disease at an unprecedented rate. Coupling the large number of bioinformatic methods developed to locate genomic breakpoints with increased sequence read length and a deeper understanding of coding region function has enabled rapid identification of novel actionable oncogenic fusion genes. Using examples of kinase fusions found in liquid and solid tumours, this review highlights major concepts that have arisen in our understanding of cancer pathogenesis through the study of fusion proteins. We provide an overview of recently developed methods to identify potential fusion proteins from next-generation sequencing data, describe the validation of their oncogenic potential and discuss the role of targetted therapies in treating cancers driven by fusion oncoproteins.
Both-faces hindered porphyrins. Part 2. Synthesis and characterization of internally five-co-ordinated iron(II) basket-handle porphyrins derived from 5,10,15,20-tetrakis(o-hydroxyphenyl)porphyrin (1985)

Compounds (9), so-called ether ‘hanging base’ porphyrins, derived from 5,10,15,20-tetrakis(o-hydroxyphenyl) porphyrin in which one of the faces is hindered by a pyridine-3,5-diylbisalkylene bridge and the other face is protected by an alkylene or an p-arylenebisalkylene chain have been synthesized following the concept of the ‘basket handle’ porphyrins (BHP). From an analysis of the 1H n.m.r. spectra of their iron(II) derivatives (20) at 34 °C, it has been determined that ca. 85% were high-spin five-co-ordinated complexes (s= 2). Despite the steric hindrance of the distal face, bimolecular associations typical for this class of compounds have been detected except for the most hindered (20c). An additional bispyridine ‘basket handle’ porphyrin (21) has been synthesized in order to study the dynamics of the pyridine chain.
Drug-Eluting Stents in Preclinical Studies (2008)

Coronary drug-eluting stents are commonplace in clinical practice with acceptable safety and efficacy. Preclinical evaluation of novel drug-eluting stent technologies has great importance for understanding safety and possibly efficacy of these technologies, and well-defined preclinical testing methods clearly benefit multiple communities within the developmental, testing, and clinical evaluation chain. An earlier consensus publication enjoyed widespread adoption but is in need of updating. This publication is an update, presenting an integrated view for testing drug-eluting technologies in preclinical models, including novel devices such as bioabsorbable coatings, totally bioabsorbable stents, bifurcation stents, and stent-free balloon-based drug delivery. This consensus document was produced by preclinical and translational scientists and investigators engaged in interventional technology community. The United States Food and Drug Administration (USFDA) recently issued a Draft Guidance for Industry Document for Drug-Eluting Stents. This expert consensus document is consistent with the Food and Drug Administration guidance. The dynamic nature of this field mandates future modifications and additions that will be added over time.
Android Apps Security (2012)

<p><em>Android Apps Security</em> provides guiding principles forÂ how to best design and develop Android apps with security in mind.Â It explores concepts that can be used to secure apps and howÂ developers can use and incorporate these security features into their apps.<br> <br> This book will provide developers with the information they need to design useful, high-performing, and secure apps that expose end-users to as little risk as possible.Â </p> <ul> <li>Overview of Android OS versions, features, architecture and security.Â </li> <li>Detailed examination of areas where attacks on applications can take place and what controls should be implemented to protect private user data </li> <li>In-depth guide to data encryption, authentication techniques, enterprise security and applied real-world examples of these concepts </li> </ul>
Advanced courses in high-school chemistry (1926)

ADVERTISEMENT RETURN TO ISSUEPREVLetterNEXTAdvanced courses in high-school chemistryWalter S. Taylor Cite this: J. Chem. Educ. 1926, 3, 2, 213Publication Date (Print):February 1, 1926Publication History Received3 August 2009Published online1 February 1926Published inissue 1 February 1926https://doi.org/10.1021/ed003p213.1RIGHTS & PERMISSIONSArticle Views85Altmetric-Citations-LEARN 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 (441 KB) Get e-Alerts Get e-Alerts
Reconstruction of complex environments by robust pre-aligned ICP (2002)

This paper proposes a technique for three-dimensional reconstruction of an underwater environment from range views acquired by an acoustic camera. The final target of the work lies in improving the understanding of a human operator driving an underwater remotely operated vehicle floating close to an offshore structure. Due to the narrow field of view and the absence of control of the sensor position, no information is available about the degree of over-lapping between the range images; further, speckle noise and low resolution make more difficult the registration process. In this paper, we propose a preprocessing method which gives a coarse alignment of range images prior to running the Iterative Closest Point (ICP) algorithm for the accurate registration of views pairs. The pre-alignment is based on the matching between the three-dimensional skeletons extracted from the images. A comparative analysis is presented where our method is compared with plain ICP, and with a technique based on principal components analysis.
Visual transcripts (2015)

Blackboard-style lecture videos are popular, but learning using existing video player interfaces can be challenging. Viewers cannot consume the lecture material at their own pace, and the content is also difficult to search or skim. For these reasons, some people prefer lecture notes to videos. To address these limitations, we present Visual Transcripts , a readable representation of lecture videos that combines visual information with transcript text. To generate a Visual Transcript, we first segment the visual content of a lecture into discrete visual entities that correspond to equations, figures, or lines of text. Then, we analyze the temporal correspondence between the transcript and visuals to determine how sentences relate to visual entities. Finally, we arrange the text and visuals in a linear layout based on these relationships. We compare our result with a standard video player, and a state-of-the-art interface designed specifically for blackboard-style lecture videos. User evaluation suggests that users prefer our interface for learning and that our interface is effective in helping them browse or search through lecture videos.
Synthesis and Diastereoselective Complexation of Enantiopure Sulfinyl Dienes:  The Preparation of Sulfinyl Iron(0) Dienes (1997)

The preparation of a diverse array of enantiomerically pure 1- and 2-sulfinyl dienes has been achieved via Stille coupling of halovinyl sulfoxides and vinyl stannanes, hydrogenation of 1-sulfinyl-1-en-3-ynes, or vinylcupration of 1-sulfinyl alkynes. Formation of the corresponding sulfinyl diene iron(0) tricarbonyl complexes was accomplished by utilizing Fe(CO)5/NMO or (bda)Fe(CO)3 as iron(0) tricarbonyl transfer reagents. Installation of the iron(0) tricarbonyl fragment was shown to be highly diastereoselective (10−16:1) for (R)-(1Z)-1-sulfinyl dienes, most likely as a result of allylic 1,3-strain. The synthesis of a 1-sulfinyl-1,3,8,10-tetraene is also described.
Multi-user Receiver Using Conjugate Gradient Method for Wideband CDMA (2005)

The paper describes a new scheme for a multi-user receiver to improve the capacity of wideband CDMA systems. The scheme is obtained by applying a conjugate gradient method (CGM) based on a mathematical approach. CGM gives an iterative solution of a large-scale matrix under multiple access interference environments. The relation between the transmitted and received signals is represented by a sparse matrix, which has diagonal components almost equal to one and other components approaching 0. This matrix equation is expected to be solved effectively by using CGM. The proposed scheme has been shown to have three times enhancement in capacity compared to single user receiver.
Circulating T lymphocyte subsets in coeliac disease (CoD) patients and healthy family members (1998)

Increased proportions of circulating antigen-primed CD45RO+ TCR gammadelta cells have been found in untreated CoD patients. As certain immunological features are now found in both CoD and healthy persons carrying the HLA DQ2 heterodimer, we sought to establish whether healthy members of the families of CoD patients who are positive for HLA DQ2 and also have increased densities of TCR gammadelta intraepithelial lymphocytes (IEL) in their small bowel mucosa have elevated levels of circulating TCR gammadelta memory cells. Peripheral blood T cells were analysed by flow cytometry in 22 patients with CoD and 16 healthy family members. Untreated CoD patients had higher percentages of circulating CD45RO+ TCR gammadelta cells and CD45RO+ Vdelta1+ cells than healthy family members. On the other hand, the amount of circulating Vdelta1+ lymphocytes was lower in patients with CoD compared with healthy family members. In contrast, no differences were found between HLA DQ2+ and HLA DQ2- healthy family members in respect of circulating TCR gammadelta cell subsets. The change in circulating TCR gammadelta cell subsets found in patients with CoD is thus a consequence of an ongoing immunological process which diminishes on a gluten-free diet rather than a phenomenon directly caused by DQ2. These changes in peripheral blood are not found in healthy individuals who have the same HLA alleles DQA1*0501 and DQB1*0201 encoding the HLA DQ2 and who also have increased densities of TCR gammadelta IEL in their otherwise normal jejunal mucosa.
Synthesis and biological properties of pinane-thromboxane A2, a selective inhibitor of coronary artery constriction, platelet aggregation, and thromboxane formation. (1979)

Pinane-thromboxane A2 (PTA2, [1alpha,2 beta(Z),-3 alpha (1E,3R*),5 alpha]-7-(3-(3-hydroxy-1-octenyl)-6,6-dimethylbicyclo[3.1.1]hept-2-yl)-5-heptenoic acid) has been synthesized and tested for biological activity in systems responsive to thromboxane A2, stable prostaglandin endoperoxide (PGH2) analogs, and prostatacyclin (PGI2). At low concentrations, PTA2 inhibited cat coronary artery constriction induced by stable prostaglandin endoperoxide analogs, and it stabilized liver lysosomes. At slightly higher concentrations, it inhibited platelet aggregation. At still higher concentrations, PTA2 inhibited thromboxane synthetase, but it had no effect on prostacyclin synthetase. The analog also had no effect on the inhibition of platelet aggregation by PGI2 or prostaglandin D2. It is suggested that PTA2 has a suitable biochemical profile for use as an antithrombotic agent.
Assessment of Similarity Measures for Accurate Deformable Image Registration (2012)

Purpose: Deformable image registration is widely used in radiation therapy applications. There are several different algorithms for deformable image registration. The purpose of this study was to evaluate the optimal similarity measures needed to obtain accurate deformable image registration by using a phantom.
Relevance of Interleukin-1 Receptor Antagonist Intron-2 Polymorphism in Ischemic Stroke (2003)

Evidence of inflammatory phenomena associated with atherosclerotic plaques is extensive. Interleukin-1 (IL-1) is one of the key modulators of the inflammatory response, and its activity is critically regulated by its receptor antagonist (IL-1Ra). A variable number of tandem repeats (VNTR) in intron 2 of the human IL-1Ra shows a common polymorphism that has been related to different production of IL-1Ra and IL-1 proteins. In monocytes, the less common allele 2 has been associated with an increased production of IL-1Ra and a decreased production of IL-1. Moreover, a cooperative effect with a C to T polymorphism in the promoter of IL-1beta gene (C(-511)-->T) has been described. In the present study, we investigated the frequency of these polymorphisms in 110 subjects who survived an ischemic stroke, in 101 healthy age-matched individuals, and in a population-based sample of 1,303 healthy Italians. The frequency of the IL- 1Ra 1/1 genotype was significantly higher in stroke survivors with respect to age-matched controls (77.2 and 45.5%, respectively; p < 0.001), and to the wide group of healthy Italians (77.2 and 51.9%, respectively; p < 0.001). As expected, the estimated frequency of the IL-1Ra allele 1 (Ra*1 allele) in stroke survivors was higher than in age-matched controls (0.851 and 0.664, respectively; p < 0.001) and in healthy Italians (0.851 and 0.717, respectively; p < 0.001). Thus, ischemic stroke survivors that carry the Ra*1 allele showed a strong association with the disease with respect to age-matched controls [odds ratio (OR) = 3.905; 95% confidence interval (CI), 2.110-7.229] and healthy Italians [OR = 3.256 (95% CI, 1.971-5.379)]. No significant association was seen for the IL-1beta (C(-511)-->T) polymorphism. However, in stroke survivors, an association between the Ra*1 allele and the C allele of the IL-1beta (-511) polymorphism was found (p < 0.001). Our results implicate the IL-1Ra gene in the susceptibility to ischemic stroke, and suggest that IL-1Ra genotyping may be useful in the identification of patient subgroups for pharmacological intervention in IL-1 production or actions.
DAAODV: A Secure Ad Hoc Routing Protocol Based on Direct Anonymous Attestation (2009)

Many approaches have been proposed to secure various ad hoc routing protocols. However, many attacks such as wormhole attacks, vertex cut attacks, and traffic-analysis based attacks are still not well addressed. In this paper, we propose a novel secure routing protocol DAAODV which is based on ad-hoc on-demand distance vector routing (AODV). DAAODV takes full advantage of trusted computing technology, particularly the direct anonymous attestation (DAA) and property-based attestation (PBA) protocols. DAAODV is an anonymous protocol without requirement of trusted third party (TTP). Moreover, we propose an efficient signing and verification scheme to overcome the potential DoS attacks triggered by the low efficiency of DAA and PBA. In the simulation, the results show that DAAODV is still efficient in discovering secure routes compared with AODV protocol.
Growth of Al oxide layers on GaAs (100) by reaction with condensed molecular oxygen (1990)

An Al oxide-GaAs (100) interface fabricated by the reactive deposition of Al into a molecular oxygen overlayer on a gallium terminated GaAs (100) surface at T=49 K is studied by synchrotron radiation photoemission. Al forms a stable oxide layer by reaction with O2 until all the oxygen is consumed. Limited oxidation of surface As atoms (≊20%) is observed during the initial deposition of Al, but further Al deposition reduces the AsO bond. The well-known exchange reaction between Al and Ga when Al is directly deposited on GaAs (100) is not observed.
Bioluminescence-Based Neuraminidase Inhibition Assay for Monitoring Influenza Virus Drug Susceptibility in Clinical Specimens (2013)

The QFlu prototype bioluminescence-based neuraminidase (NA) inhibition (NI) assay kit was designed to detect NA inhibitor (NAI)-resistant influenza viruses at point of care. Here, we evaluated its suitability for drug susceptibility assessment at a surveillance laboratory. A comprehensive panel of reference viruses (n = 14) and a set of 90 seasonal influenza virus A and B isolates were included for testing with oseltamivir and/or zanamivir in the QFlu assay using the manufacturer-recommended protocol and a modified version attuned to surveillance requirements. The 50% inhibitory concentrations (IC50s) generated were compared with those of NI assays currently used for monitoring influenza drug susceptibility, the fluorescent (FL) and chemiluminescent (CL) assays. To provide proof of principle, clinical specimens (n = 235) confirmed by real-time reverse transcription (RT)-PCR to contain influenza virus A(H1N1)pdm09 and prescreened for the oseltamivir resistance marker H275Y using pyrosequencing were subsequently tested in the QFlu assay. All three NI assays were able to discriminate the reference NA variants and their matching wild-type viruses based on the difference in their IC50s. Unless the antigenic types were first identified, certain NA variants (e.g., H3N2 with E119V) could be detected among seasonal viruses using the FL assays only. Notably, the QFlu assay identified oseltamivir-resistant A(H1N1)pdm09 viruses carrying the H275Y marker directly in clinical specimens, which is not feasible with the other two phenotypic assays, which required prior virus culturing in cells. Furthermore, The QFlu assay allows detection of the influenza virus A and B isolates carrying established and potential NA inhibitor resistance markers and may become a useful tool for monitoring drug resistance in clinical specimens.
High-purity silicon sensor array for imaging soft X-ray and infrared radiation (2003)

A 256-element radiation sensor array with separate x- and y-readout addresses, fabricated on high-purity silicon (4 k Omega -cm) utilizing only standard integrated-circuit processing technologies, is presented. The design of the 16*16 array of 250*250 mu m/sup 2/ elements emulates that of successful precursors. The principle of operation of the sensor is based on the capacitive coupling of the elements in a matrix of sensing diodes. Two-dimensional position resolution is achieved through the direct collection of radiation-generated charge in the x-dimension and through the indirect capacitive coupling of this charge in the y-dimension. The design is an improvement over its predecessor (see S.A. Audet et al., 1989), which utilized polysilicon structures to resistively couple the columnar elements. Optimization of the readout electronics resulted in a charge-collection deficit of less than 1% at the x-addressed outputs, eliminating the need for the polysilicon structures and improving the energy and position resolutions of the modified sensor array. Experimental results demonstrated good sensor characteristics and confirmed two-dimensional position resolution of incident radiation with minimal crosstalk.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>