gebhart/patrepeval huggingface dataset:
Genome‐wide microRNA analysis of HPV‐positive self‐samples yields novel triage markers for early detection of cervical cancer (2018)

Offering self-sampling for HPV testing improves the effectiveness of current cervical screening programs by increasing population coverage. Molecular markers directly applicable on self-samples are needed to stratify HPV-positive women at risk of cervical cancer (so-called triage) and to avoid over-referral and overtreatment. Deregulated microRNAs (miRNAs) have been implicated in the development of cervical cancer, and represent potential triage markers. However, it is unknown whether deregulated miRNA expression is reflected in self-samples. Our study is the first to establish genome-wide miRNA profiles in HPV-positive self-samples to identify miRNAs that can predict the presence of CIN3 and cervical cancer in self-samples. Small RNA sequencing (sRNA-Seq) was conducted to determine genome-wide miRNA expression profiles in 74 HPV-positive self-samples of women with and without cervical precancer (CIN3). The optimal miRNA marker panel for CIN3 detection was determined by GRridge, a penalized method on logistic regression. Six miRNAs were validated by qPCR in 191 independent HPV-positive self-samples. Classification of sRNA-Seq data yielded a 9-miRNA marker panel with a combined area under the curve (AUC) of 0.89 for CIN3 detection. Validation by qPCR resulted in a combined AUC of 0.78 for CIN3+ detection. Our study shows that deregulated miRNA expression associated with CIN3 and cervical cancer development can be detected by sRNA-Seq in HPV-positive self-samples. Validation by qPCR indicates that miRNA expression analysis offers a promising novel molecular triage strategy for CIN3 and cervical cancer detection applicable to self-samples.
Hyperactive pectoralis reflex as an indicator of upper cervical spinal cord compression (1997)

Myelopathy from cervical spondylosis is often accompanied by hyperreflexia of the upper-extremity deep tendon reflexes (DTRs). Reflexes such as the pectoralis jerk and the deltoid jerk may only be apparent in the context of hyperreflexia. Although the nerve roots involved in the reflex arcs are well described, levels of cervical spinal cord compression that lead to the hyperreflexia are not as clear. This is of particular significance for patients with multilevel cervical spondylosis in determining the levels responsible for their symptoms. The authors examined 15 consecutive patients who presented for treatment of cervical myelopathy. The clinical examination was then correlated with levels of cervical spinal cord compression by cervical magnetic resonance imaging or computerized tomography with intrathecal contrast enhancement. The presence of a prominent pectoralis jerk was seen only in patients with spinal cord compression at the C2-3 and/or C3-4 levels (nine patients). No patient with compression at or below the C4-5 disc space without coexisting compression at a higher level had hyperactive pectoralis reflexes. This association between the C3-4 level and a hyperactive pectoralis reflex was significant (p < 0.004, Fisher's exact test). The deltoid reflex was tested in the last nine consecutive patients. It was present in patients with compression of the upper spinal cord at levels C3-4 and C4-5 (four of five patients) but appeared in only one of four patients with compression below C4-5. This association did not attain statistical significance. The presence of a hyperactive pectoralis reflex is specific for lesions of the upper cervical spinal cord. Examination of upper-extremity DTRs may be helpful in planning the appropriate levels for surgical decompression in patients with multilevel spondylosis and myelopathy.
A 200 Line MATLAB Code for Inverse Design in Photonics by Topology Optimization (2020)

We provide a compact 200 line MATLAB code demonstrating how Topology Optimization as an inverse design tool may be used in photonics, targeting the design of two-dimensional dielectric metalenses and a metallic reflector as examples. The physics model is solved using the finite element method and the code utilizes MATLABs \textit{fmincon} algorithm to solve the optimization problem. In addition to presenting the code itself, we briefly discuss a number of extensions and provide the code required to implement some of these. The MATLAB software is freely available along with the paper and may be downloaded from \url{http://www.topopt.dtu.dk}.
Link layer multicasting with smart antennas: No client left behind (2008)

Wireless link layer multicast is an important service primitive for emerging applications, such as live video, streaming audio, and other content telecasts. The broadcast nature of the wireless channel is amenable to multicast because a single packet transmission may be received by all clients in the multicast group. However, in view of diverse channel conditions at different clients, the rate of such a transmission is bottlenecked by the rate of the weakest client. Multicast throughput degrades severely. Attempts to increase the data rate result in lower reliability and higher unfairness. This paper utilizes smart beamforming antennas to improve multicast performance in wireless LANs. The main idea is to satisfy the stronger clients with a high-rate omnidirectional transmission, followed by high-rate directional transmission(s) to cover the weaker ones. By selecting an optimal transmission strategy (using dynamic programming), we show that the multicast throughput can be maximized while achieving a desired delivery ratio at all the clients. We use testbed measurements to verify our main assumptions. We simulate our protocol in Qualnet, and observe consistent performance improvements over a range of client topologies and time-varying channel conditions.
Adaptive Quantization in Multispectral Image Compression for Equalizing Visual Error Distribution (2002)

This article proposes an adaptive nonlinear quantization method for multispectral image compression. When linear scalar quantization is applied for multispectral image compression, extremely large error is perceived in low-luminance colors due to the nonlinear phenomenon of human vision. In the proposed method, quantization tables are switched pixel by pixel depending on the corresponding luminance. The switching rule is determined according to the relationship between the luminance and the error in the uniform color space. As a result, distribution of the error in the uniform color space can be equalized and the error in the low-luminance pixels is suppressed. Experimental results using a 16-band multispectral image of an oil painting shows the effectiveness of the proposed method.
Synthesis and structure-function study of artificial nucleases on the basis of hemin conjugates with peptide fragments of cell differentiation factor HLDF (2006)

A series of octa-hexapeptide fragments of HLDF and their conjugates with hemin were obtained by solid phase peptide synthesis. A relationship between the structure and the nuclease activity of the compounds was established. The effect of various factors (medium pH, the presence of metal ions, complexons, reducers, and buffer composition) on DNA destruction with hemin peptides was studied. Preliminary information confirming an oxidative mechanism of this process was obtained. The cleavage of plasmid DNA under the action of hemin peptides was studied by the methods of electron microscopy, gel electrophoresis, and atomic force microscopy.
Spectroelectrochemistry and Dimerization Equilibria of Chloro(terpyridine)platinum(II). Nature of the Reduced Complexes (1996)

[Pt(tpy)Cl]+ (tpy is 2,2‘:6‘,2‘‘-terpyridine) undergoes reversible one-electron reductions in 0.1 M TBAH/DMF (TBAH is tetrabutylammonium hexafluorophosphate) at E° ‘+/0 = −0.74 V and E° ‘0/- = −1.30 V (vs AgCl (1.0 M KCl)/Ag). The first reduction couple is substantially positive of those observed for other M(II)−tpy complexes (for example, E° ‘0/- = −1.36 V for [Zn(tpy)Cl2]), a finding that suggests there is coupling between the empty 6pz orbital of square planar Pt(II) and the π* orbital of tpy, stabilizing the (π*)1 radical state. The dimerization constants of both [Pt(tpy)Cl]+ and [Pt(tpy)Cl] in 0.1 M TBAH/DMF were determined spectroelectrochemically and found to be 8(1) × 10 and 10(4) × 10 M-1, respectively. On the basis of variable-concentration studies, a species observed at an intermediate level of reduction is formulated as the mixed-valence dimer [(Pt(tpy)Cl)2]+, with Kmix = [(Pt(tpy)Cl)2+]/([Pt(tpy)Cl+][Pt(tpy)Cl]) = 18(4) × 10 M-1. Analysis of variable-temperature EPR spectra indicates that the first reduction is ligand-centered (2B2) with substantial contributions from Pt(II) 5dyz (4−6%) and 6pz (3−4%). The second reduction is tentatively assigned as metal-centered; 5dx2-y2 is the likely acceptor orbital.
Overexpression of a Metallothionein 2A Gene from Date Palm Confers Abiotic Stress Tolerance to Yeast and Arabidopsis thaliana (2019)

Although the date palm tree is an extremophile with tolerance to drought and certain levels of salinity, the damage caused by extreme salt concentrations in the soil, has created a need to explore stress-responsive traits and decode their mechanisms. Metallothioneins (MTs) are low-molecular-weight cysteine-rich proteins that are known to play a role in decreasing oxidative damage during abiotic stress conditions. Our previous study identified date palm metallothionein 2A (<i>PdMT2A</i>) as a salt-responsive gene, which has been functionally characterized in yeast and <i>Arabidopsis</i> in this study. The recombinant PdMT2A protein produced in <i>Escherichia coli</i> showed high reactivity against the substrate 5'-dithiobis-2-nitrobenzoic acid (DTNB), implying that the protein has the property of scavenging reactive oxygen species (ROS). Heterologous overexpression of <i>PdMT2A</i> in yeast (<i>Saccharomyces cerevisiae</i>) conferred tolerance to drought, salinity and oxidative stresses. The <i>PdMT2A</i> gene was also overexpressed in <i>Arabidopsis</i>, to assess its stress protective function in planta. Compared to the wild-type control, the transgenic plants accumulated less Na<sup>+</sup> and maintained a high K<sup>+</sup>/Na<sup>+</sup> ratio, which could be attributed to the regulatory role of the transgene on transporters such as HKT, as demonstrated by qPCR assay. In addition, transgenic lines exhibited higher chlorophyll content, higher superoxide dismutase (SOD) activity and improved scavenging ability for reactive oxygen species (ROS), coupled with a better survival rate during salt stress conditions. Similarly, the transgenic plants also displayed better drought and oxidative stress tolerance. Collectively, both in vitro and in planta studies revealed a role for <i>PdMT2A</i> in salt, drought, and oxidative stress tolerance.
Processing and Testing Re 2 Si 2 O 7 Matrix Composites (2012)

This chapter contains sections titled: Introduction Experimental Results and Discussion Summary and Conclusions
The Maize Single myb histone 1 Gene, Smh1, Belongs to a Novel Gene Family and Encodes a Protein That Binds Telomere DNA Repeats in Vitro (2003)

We screened maize (Zea mays) cDNAs for sequences similar to the single myb-like DNA-binding domain of known telomeric complex proteins. We identified, cloned, and sequenced five full-length cDNAs representing a novel gene family, and we describe the analysis of one of them, the gene Single myb histone 1 (Smh1). The Smh1 gene encodes a small, basic protein with a unique triple motif structure of (a) an N-terminal SANT/myb-like domain of the homeodomain-like superfamily of 3-helical-bundle-fold proteins, (b) a central region with homology to the conserved H1 globular domain found in the linker histones H1/H5, and (c) a coiled-coil domain near the C terminus. The Smh-type genes are plant specific and include a gene family in Arabidopsis and the PcMYB1 gene of parsley (Petroselinum crispum) but are distinct from those (AtTRP1, AtTBP1, and OsRTBP1) recently shown to encode in vitro telomere-repeat DNA-binding activity. The Smh1 gene is expressed in leaf tissue and maps to chromosome 8 (bin 8.05), with a duplicate locus on chromosome 3 (bin 3.09). A recombinant full-length SMH1, rSMH1, was found by band-shift assays to bind double-stranded oligonucleotide probes with at least two internal tandem copies of the maize telomere repeat, TTTAGGG. Point mutations in the telomere repeat residues reduced or abolished the binding, whereas rSMH1 bound nonspecifically to single-stranded DNA probes. The two DNA-binding motifs in SMH proteins may provide a link between sequence recognition and chromatin dynamics and may function at telomeres or other sites in the nucleus.
A DESCRIPTION OF SIX NEW RHINOVIRUSES OF HUMAN ORIGIN1 (1965)

Journal Article A DESCRIPTION OF SIX NEW RHINOVIRUSES OF HUMAN ORIGIN Get access M. A. MUFSON, M. A. MUFSON Search for other works by this author on: Oxford Academic PubMed Google Scholar R. KAWANA, R. KAWANA Search for other works by this author on: Oxford Academic PubMed Google Scholar H. D. JAMES, JR., H. D. JAMES, JR. Search for other works by this author on: Oxford Academic PubMed Google Scholar L. W. GAULD, L. W. GAULD Search for other works by this author on: Oxford Academic PubMed Google Scholar H. H. BLOOM, H. H. BLOOM Search for other works by this author on: Oxford Academic PubMed Google Scholar R. M. CHANOCK R. M. CHANOCK Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 81, Issue 1, January 1965, Pages 32–43, https://doi.org/10.1093/oxfordjournals.aje.a120495 Published: 01 January 1965 Article history Received: 29 June 1964 Published: 01 January 1965
Heterogeneous or Homogeneous? A Case Study Involving Palladium‐Containing Perovskites in the Suzuki Reaction (2005)

Abstract The utility of a series of palladium‐containing perovskite catalysts in the Suzuki reaction is described; turnover numbers of up to 400,000 are reported. A detailed investigation into the mode of action of these catalysts encompassing kinetic studies, catalyst poisoning, microscopy and three‐phase tests demonstrate that these heterogeneous materials are pre‐catalysts that operate by a solution‐phase mechanism
100 Amp, 1000 Volt Class 4H-Silicon Carbide MOSFET Modules (2009)

The development of large area, up to 70m/1kV (0.45cm x 0.45cm) 4H-SiC vertical DMOSFETs is presented. DC and switching characteristics of high-current, 100Amp All-SiC power switching modules are demonstrated using 0.45cm x 0.225cm DMOSFET die and commercial Schottky diodes. The switching performance from room temperature up to T=200°C of the All-SiC modules is presented, with as much as ten times lower losses than co-fabricated Si-based modules using commercial IGBTs.
ARTISTE: Automatic Generation of Hybrid Data Structure Signatures from Binary Code Executions (2012)

Data structure signatures can be used for finding instances of data structures holding sensitive data in memory, a crucial capability for many security applications such as memory forensics, rootkit detection, online games cheat analysis, reverse engineering, and virtual machine introspection. Manually generating data structure signatures is a tedious and error-prone process. Prior work automatically generates data structure signatures from the type definitions in the program’s source code, but unfortunately for many programs their source code is not publicly available. In this paper we present ARTISTE, the first tool for automatically generating data structure signatures without access to the program’s source code or debugging symbols. The salient features of ARTISTE are: (1) it generates hybrid signatures that minimize false positives during scanning by combining points-to relationships, value invariants, and cycle invariants; (2) it uses a novel dynamic shape analysis to recover recursive data structures, classifying them by their shapes (e.g., doubly linkedlist or tree); (3) it identifies data structures of the same type allocated at different program points; and (4) it accumulates data structure information over multiple executions, increasingly improving its accuracy. Our experimental results on a number of binary programs show that the hybrid signatures generated by ARTISTE accurately identify instances of the data structures in memory with no false positives or false negatives in 80% of the programs, while prior signature types produce large false positive rates.
Magnetic resonance imaging quantification of left ventricular dysfunction following coronary microembolization (2008)

Microembolization is common after coronary interventions, and therefore this MRI study aimed to quantify the effect of coronary microembolization on left ventricular (LV) function. The left anterior descending artery (LAD) was selectively catheterized in an XMR suite (Philips Medical Systems, Best, The Netherlands) in eight pigs to deliver MR contrast media to measure the LAD territory using first-pass perfusion and for intracoronary delivery of the embolic agent. Cine, tagged, and delayed contrast-enhanced MRI (DCE-MRI) was performed to assess LV volumes, ejection fraction, radial and circumferential strain, and viability at baseline, 1 h, and 1 week after microembolization. Histopathology and histochemical staining were used to characterize and measure the extent of microinfarction. The LAD territory was 35% +/- 2% LV mass. Patchy microinfarction on DCE-MRI at 1 week was 22.0% +/- 3.6% LAD territory (7.5% LV mass). Microembolization caused persistent decline in ejection fraction (baseline = 49% +/- 1%, 1 h = 29% +/- 1%, P = 0.02 and 1 week = 36% +/- 1%, P = 0.03) and increased end-diastolic (79.6 +/- 3.9 ml, 85.5 +/- 4.5 ml, P = 0.03 and 92.4 +/- 6.2 ml, P = 0.06, respectively) and end-systolic (40.8 +/- 2.1 ml, 60.2 +/- 3.4 ml, P = 0.02 and 59.3 +/- 4.8 ml, P = 0.03, respectively) volumes. The microembolized territory was manifested as dysfunctional regions for 1 week on cine and tagged MRI. Histopathology revealed occlusive microemboli surrounded by necrotic tissue undergoing repair. Microinfarction was visualized after coronary microembolization and caused LV dysfunction disproportionate to the size of myocardial damage. It also changed LV geometry and decreased radial and circumferential strain over the course of 1 week.
Online Spatiotemporal Popularity Learning via Variational Bayes for Cooperative Caching (2020)

Herein, we focus on an end-to-end design of a proactive cooperative caching strategy for a multi-cell network. The design is challenging as it involves two interrelated problems: the ability to predict future content popularity and to meet network operation characteristics. To this end, we first formulate a cooperative content caching in order to optimize the aggregated network cost for delivering contents to users. An efficient proactive caching policy requires an accurate prediction of time-varying content popularity. Content popularity has temporal and spatial dependencies and therefore, we develop a probabilistic dynamical model for content popularity prediction by exploiting its spatiotemporal correlations. To achieve an accurate tracking and prediction of content popularity evolution, the proposed dynamical model is non-linear and incorporates non-Gaussian distributions. We use Variational Bayes (VB) approach for estimating the model parameters. The VB provides mathematical tractability. We then develop an online VB method that works with streaming data where content request arrives sequentially. Using extensive simulations study on a real-world dataset, we show that our online VB based dynamical model provides improved performance compared to conventional content caching policies.
High-brightness 975-nm pumps with ultra-stable wavelength stabilization (2012)

The majority of fiber laser volume applications are price sensitive. Therefore, the availability, quality and cost of singleemitter- based pumps will have decisive impact on the breadth of further fiber lasers' acceptance. Availability and cost should not come in expense of further improvement in pumps' performance and reliability. Here we report on optimized high-power and high-brightness wavelength stabilized CW devices. Performance of CW pumps rated for 100W and 50W power is discussed. Pumps launch over 98% output power into a spectral window of 975±0.5nm at driving currents ranging from 2A to 12A and the heatsink temperature variation from 20°C to 50°C. Such performance qualifies these wavelength-stabilized pumps for use in many air-cooled and special applications.
267: Effects of Steroidal and Non-Steroidal Antiandrogens on Wild-Type and Mutant Androgen Receptors (2007)

You have accessJournal of UrologyModerated Poster 10, Sunday, May 20, 2007, 10:00 am - 12:00 pm1 Apr 2007267: Effects of Steroidal and Non-Steroidal Antiandrogens on Wild-Type and Mutant Androgen Receptors Masayasu Urushibara, Yukio Kageyama, Junichiro Ishioka, Yotsuo Higashi, Shuntaro Hara, Kazunori Kihara, Pratap Singh, and John T. Isaacs Masayasu UrushibaraMasayasu Urushibara More articles by this author , Yukio KageyamaYukio Kageyama More articles by this author , Junichiro IshiokaJunichiro Ishioka More articles by this author , Yotsuo HigashiYotsuo Higashi More articles by this author , Shuntaro HaraShuntaro Hara More articles by this author , Kazunori KiharaKazunori Kihara More articles by this author , Pratap SinghPratap Singh More articles by this author , and John T. IsaacsJohn T. Isaacs More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)30532-9AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "267: Effects of Steroidal and Non-Steroidal Antiandrogens on Wild-Type and Mutant Androgen Receptors." The Journal of Urology, 177(4S), pp. 89–90 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 89-90 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Masayasu Urushibara More articles by this author Yukio Kageyama More articles by this author Junichiro Ishioka More articles by this author Yotsuo Higashi More articles by this author Shuntaro Hara More articles by this author Kazunori Kihara More articles by this author Pratap Singh More articles by this author John T. Isaacs More articles by this author Expand All Advertisement Loading ...
Efficient PSoC Implementation of Modular Multiplication and Exponentiation Based on Serial-Parallel Combination (2019)

This paper presents an FPGA implementation of the most critical operations of Public Key Cryptography (PKC), namely the Modular Exponentiation (ME) and the Modular Multiplication (MM). Both operations are integrated as Programmable System on Chip (PSoC) where the processor Microblaze of Xilinx is used for flexibility. Our objective is to achieve a best trade-off between time execution, occupied area and flexibility. The implementation of these operations on such environment requires taking into account several criteria. Indeed, the Hardware (HW) architectures data bus should be smaller than the input data length. The design must be scalable to support different security levels. The implementation achieves optimums execution time and HW resources number. In order to satisfy these constraints, Montgomery Power Ladder (MPL) and Montgomery Modular Multiplication (MMM) algorithms are utilized for the ME and the MM implementations as HW accelerators, respectively. Our implementation approach is based on the digit-serial method for performing the basic arithmetic operations. Efficient parallel and pipeline strategies are developed at the digit level for the optimization of the execution times. The application for 1024-bits data length shows that the MMM run in 6.24[Formula: see text][Formula: see text]s and requires 647 slices. The ME is executed in 6.75[Formula: see text]ms using 2881 slices.