gebhart/patrepeval huggingface dataset:
Elevated HERV-K Expression in Soft Tissue Sarcoma Is Associated with Worsened Relapse-Free Survival (2018)

A wide variety of endogenous retroviral sequences has been demonstrated in the human genome so far, divided into several different families according to the sequence homology to viral strains. While increased expression of human endogenous retrovirus (HERV) elements has already been linked to unfavorable prognosis in hepatocellular carcinoma, breast cancer, and ovarian carcinoma yet less is known about the impact of the expression of different HERV elements on sarcomagenesis in general as well as the outcome of soft tissue sarcoma (STS) patients. Therefore, in this study the association between expression of HERV-K and HERV-F and the clinicopathological characteristics in a cohort of STSs as well as the patients' prognosis was evaluated. HERV-K and HERV-F expression was assessed by quantitative real-time PCR in 120 patient specimens. HERV-K and HERV-F expression was significantly correlated (<i>r</i><sub>S</sub> = 0.5; <i>p</i> = 6.4 × 10<sup>-9</sup>; Spearman's rank bivariate correlation). Also, tumor diameter exhibited a significant negative association to HERV-K and HERV-F expression. Levels of several hypoxia-related RNAs like HIF-1α and miR-210 showed a significant positive correlation with both HERV-K and HERV-F expression. Although in survival analyses no impact of HERV expression on disease-specific survival could be detected, patients with elevated HERV-K expression had a significantly shorter relapse-free survival (<i>p</i> = 0.014, log-rank analysis). In conclusion, we provide evidence for the first time that the increased expression of HERV-K in tumors is associated with STS patients' prognosis.
Characterizing process semiconductor thin films with a confocal micro X-ray fluorescence microscope (2006)

The versatility of confocal micro X-ray fluorescence (MXRF) in analyzing thin films on semiconductor wafers is demonstrated. Unlike conventional MXRF, confocal MXRF can depth profile sample layers and reduce spectral background. Nondestructive quantification of the silicon dioxide concentration in hafnium silicate thin films is an example of one application demonstrating the advantage of confocal MXRF. Additionally, the growth of titanium nitride films on various high- k gate dielectric substrates was analyzed with confocal MXRF due to its ability to detect sub-nm film thickness changes.
An expanded analysis framework for multivariate GWAS connects inflammatory biomarkers to functional variants and disease (2019)

ABSTRACT Multivariate methods are known to increase the statistical power of association detection, but they have lacked essential follow-up analysis tools necessary for understanding the biology underlying these associations. We developed a novel computational workflow for multivariate GWAS follow-up analyses, including fine-mapping and identification of the subset of traits driving associations (driver traits). Many follow-up tools require univariate regression coefficients which are lacking from multivariate results. Our method overcomes this problem by using Canonical Correlation Analysis to turn each multivariate association into its optimal univariate Linear Combination Phenotype (LCP). This enables an LCP-GWAS, which in turn generates the statistics required for follow-up analyses. We implemented our method on 12 highly correlated inflammatory biomarkers in a Finnish population-based study. Altogether, we identified 11 associations, four of which ( F5, ABO, C1orf140 and PDGFRB ) were not detected by biomarker-specific analyses. Fine-mapping identified 19 signals within the 11 loci and driver trait analysis determined the traits contributing to the associations. A phenome-wide association study on the 19 putative causal variants from the signals in 176,899 individuals from the FinnGen study revealed 53 disease associations (p &lt; 1×10 -4 ). Several reported pQTLs in the 11 loci provided orthogonal evidence for the biologically relevant functions of the putative causal variants. Our novel multivariate analysis workflow provides a powerful addition to standard univariate GWAS analyses by enabling multivariate GWAS follow-up and thus promoting the advancement of powerful multivariate methods in genomics.
Electrophoresis of the nucleic acids (1964)

Abstract A zone electrophoresis apparatus using ultraviolet, optics has been constructed to study nucleic acids at concentration less than 0.004%. Native DNA has a mobility about 15% higher than denatured DNA over a range of conditions of pH and ionic strength. DNA's from different sources have closely similar mobilities. A study of a molecular weight series of DNA indicates that the mobility is constant in the molecular weight range of 2.5 × 10 5 to 1.3 × 10 8 . DNA mobilities change in the expected way with pH but the fractional change in mobility is less than the change in charge calculated by titration curves. A small decrease in mobility accompanies an increase in ionic strength. RNA's from various sources have mobilities slightly lower than denatured DNA except for s‐RNA which travels slightly faster.
Design and Integration: Chip- and System-Level Challenges (2003)

In this special issue, guest edited by Alberto Sangiovanni-Vincentelli and Luciano Lavagno, the readers get an excellent view of the issues, challenges, and trends in on-chip integration within the emerging field of complex system-ona-chip (SOC) design. These articles come from presentations at a Project Madess workshop in Rome. Madess stands for Materiali e Dispositivi per l’Elettronica dello Stato Solido (materials and devices for solid-state electronics); it is a special initiative managed by Italy’s Council of National Research (CNR). An ambitious multiyear project, Madess has sought to promote the cooperation of industry and academia in microelectronics development (http://www. madess.cnr.it/summary.htm). These articles cover challenges presented by
Combination of light-induced effect and gate bias stress in organic phototransistors (2016)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation R. Liguori, W. C. Sheets, E. Bezzeccheri, A. Facchetti, A. Rubino; Combination of light-induced effect and gate bias stress in organic phototransistors. AIP Conference Proceedings 18 May 2016; 1736 (1): 020167. https://doi.org/10.1063/1.4949742 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Sparse τ-p Z-noise attenuation for ocean-bottom data (2012)

In ocean-bottom seismic data processing, while the pressure component P is in general of good quality, high levels of noise are often observed on the vertical component Z. Nonetheless, Z is needed to achieve complete pre-stack wavefield separation and also to drive processes such as mirror imaging and up-down deconvolution. We propose a new method to address this problem, based on upgoing and downgoing wavefield properties and pressure-particle velocity relationships. The sparse τ-p domain playsa key role in this 3D method, allowing for better signal-noise discrimination than other domains. The application of the proposed algorithm to a deep-water ocean-bottom survey effectively attenuates noise while preserving amplitudes.
Electronic Effects on the β-Alkyl Migratory Insertion Reaction of para-Substituted Styrene Methyl Palladium Complexes (1996)

The β-methyl migratory insertion chemistry of a series of cis-coordinated styrene methyl complexes of palladium [(phen)Pd(CH3)(p-X-C6H4CHCH2)+Ar'4B- (2X) (phen = 1,10-phenanthroline; X = CF3, Cl, H, CH3, OCH3; Ar' = 3,5-(CF3)2C6H3)] has been investigated. Complexes 2X are prepared in situ from the addition of p-X-styrene to CD2Cl2 solutions of (phen)Pd(CH3)(OEt2)+Ar'4B- (1). The X-ray structure of 1 has been determined [P21/c; a = 16.460(4) Å, b = 18.911(3) Å, c = 17.374(3) Å; β = 117.996(14)°; V = 4775.2(15) Å3; Z = 4] at −78 °C. The rearrangement of 2X, via β-CH3 migratory insertion then arene coordination, to yield (phen)Pd(η3-CH(CH2CH3)(C6H4-p-X)+Ar'4B- (3X) has been studied by 1H NMR spectroscopy. The rearrangement is accelerated by electron-withdrawing groups; a Hammett analysis at −29.2 °C reveals that log k values are best fit by σp parameters: ρp = 1.1 ± 0.1, r = 0.992. The anti-isomer of 3H has been structurally characterized: P21/n; a = 13.950(4) Å, b = 15.582(5) Å, c = 24.004(8) Å; β = 101.961(24)°; V = 5105(3) Å3; Z = 4. Complex 3H reacts further with styrene to form (phen)Pd(η3-CH(CH3)(C6H5)+Ar'4B- (4) and (E)-β-methylstyrene; kinetic and isotopic labeling experiments have been employed to determine the mechanism of this benzyl exchange reaction. The relative binding affinities of the p-X-styrenes of 2X have been determined for the equilibria p-X-C6H4CHCH2 + 2H ⇌ C6H5CHCH2 + 2X at −66 °C. The electron-rich styrenes bind tightest to Pd; a Hammett plot of these equilibrium constants yields ρp = −2.2 ± 0.1 and r = 0.999. The kinetic and thermodynamic data indicate that both the ground and transition-states are stabilized by electron-rich styrenes and, of the two, the substituent effects are greatest in the ground-states. Since the relative rates are determined by the relative differences in energy of the ground and transition states, the migratory insertion reaction of 2X is accelerated by styrenes bearing electron-withdrawing substituents.
Production of Cyclic Tetrasaccharide with 6-.ALPHA.-Glucosyltransferase and .ALPHA.-Isomaltosyltransferase (2004)

Cyclic tetrasaccharide (CTS; cyclo{→6)-α-D-Glcp-(1→3)-α-D-Glcp-(1→6)-α-D-Glcp-(1→3)-α-D-Glcp-(1→}) is a cyclic oligosaccharide four D-glucosyl residues linked in an alternating α-1,3- and α-1,6-fashion. CTS has been reported for enzymatic synthesis from alternan, an α-(1→3)-α-(1→6)-D-glucan synthesized from sucrose by Leuconostoc mesenteroides NRRL B-1355 alternansucrase, by endo-glucanase (alternanase) from Bacillus sp. NRRL B-21195. While searching for nonreducing oligosaccharides that can be produced from α-1,4-glucan as the substrate, we screened bacteria isolated from soil in our own way, and obtained Bacillus globisporus C11, which produces CTS from starch. Two kinds of glycosyltransferase, 6-α-glucosyltransferase (6GT) and α-isomaltosyltransferase (IMT), were purified from the culture supernatant of this strain. It was found that CTS is produced by the sequential action of both enzymes. The genes for IMT (CtsY) and 6GT (CtsZ) were linked together on the chromosome, forming ctsYZ. Both of the gene products showed similarities to α-glucosidases belonging to glycoside hydrolase family 31 and conserved two aspartic acids corresponding to the putative catalytic residues of these enzymes. CtsYZ and four open reading frames upstream of ctsYZ form a gene cluster, ctsUVWXYZ. The reaction conditions for CTS synthesis were examined using 6GT and IMT from B. globisporus C11. The optimum reaction conditions to obtain CTS from Pinedex #100 (partial hydrolyzate of starch, 1.3%-hydrolysis) were the following: substrate concentration, 3%; pH, 6-7; temperature, 30°C; enzyme dosages, 1 U/g-dry solid 6GT, 10 U/g-dry solid IMT. In these optimum conditions the CTS yields reached 62% at the reaction time of 48 h. A mass-production method of highly purified CTS crystals at a reasonable cost was established, and the functions and characteristics of CTS were studied.
Synthesis and anti-HIV activity of 1,3-dithiolane nucleosides (1999)

N. Nguyen-Ba, W. L. Brown, L. Chan, N. Lee, L. Brasili, D. Lafleur and B. Zacharie, Chem. Commun., 1999, 1245 DOI: 10.1039/A901927H
Fiber-Nonlinearity-Tolerant Superchannel Transmission via Nonlinear Noise Squeezing and Generalized Phase-Conjugated Twin Waves (2013)

We present fiber-nonlinearity-tolerant transmission of polarization-division multiplexed binary phase-shift keying (PDM-BPSK) through a nonlinear noise squeezing (NLNS) effect that is achieved by optimized digital electronic dispersion precompensation. With the improved nonlinear tolerance, a 406.6-Gb/s superchannel consisting of eight 37.5-GHz-spaced 32-Gbaud Nyquist-filtered PDM-BPSK signals is transmitted over a 12800-km (160 × 80-km) EDFA-only amplified dispersion-unmanaged nonzero-dispersion-shifted fiber link. We establish a connection between the beneficial NLNS effect and the recently reported phase-conjugated twin wave (PCTW) concept and further generalize the PCTW concept to vector twin waves that are traveling through a fiber link along orthogonal dimensions such as time and space. Moreover, we apply the PCTW concept to wavelength-division-multiplexed (WDM) superchannel transmission by treating the entire WDM superchannel as a twin wave to further mitigate interchannel nonlinear effects. Through numerical simulations, we show that the generalized PCTW technique can effectively mitigate interchannel nonlinear impairments, in addition to mitigating intrachannel nonlinear impairments.
THz-Driven Ultrafast Spin-Lattice Scattering in Amorphous Metallic Ferromagnets (2016)

We use single-cycle THz fields and the femtosecond magneto-optical Kerr effect to, respectively, excite and probe the magnetization dynamics in two thin-film ferromagnets with different lattice structures: crystalline Fe and amorphous CoFeB. We observe Landau-Lifshitz-torque magnetization dynamics of comparable magnitude in both systems, but only the amorphous sample shows ultrafast demagnetization caused by the spin-lattice depolarization of the THz-induced ultrafast spin current. Quantitative modeling shows that such spin-lattice scattering events occur on similar time scales than the conventional spin conserving electronic scattering (∼30 fs). This is significantly faster than optical laser-induced demagnetization. THz conductivity measurements point towards the influence of lattice disorder in amorphous CoFeB as the driving force for enhanced spin-lattice scattering.
Identification of Vaccinia Virus Inhibitors and Cellular Functions Necessary for Efficient Viral Replication by Screening Bioactives and FDA-Approved Drugs (2020)

Four decades after the eradication of smallpox, poxviruses continue to threaten the health of humans and other animals. Vaccinia virus (VACV) was used as the vaccine that successfully eradicated smallpox and is a prototypic member of the poxvirus family. Many cellular pathways play critical roles in productive poxvirus replication. These pathways provide opportunities to expand the arsenal of poxvirus antiviral development by targeting the cellular functions required for efficient poxvirus replication. In this study, we developed and optimized a secreted Gaussia luciferase-based, simplified assay procedure suitable for high throughput screening. Using this procedure, we screened a customized compound library that contained over 3200 bioactives and FDA (Food and Drug Administration)-approved chemicals, most having known cellular targets, for their inhibitory effects on VACV replication. We identified over 140 compounds that suppressed VACV replication. Many of these hits target cellular pathways previously reported to be required for efficient VACV replication, validating the effectiveness of our screening. Importantly, we also identified hits that target cellular functions with previously unknown roles in the VACV replication cycle. Among those in the latter category, we verified the antiviral role of several compounds targeting the janus kinase/signal transducer and activator of transcription-3 (JAK/STAT3) signaling pathway by showing that STAT3 inhibitors reduced VACV replication. Our findings identify pathways that are candidates for use in the prevention and treatment of poxvirus infections and additionally provide a foundation to investigate diverse cellular pathways for their roles in poxvirus replications.
Drug Targeting of alpha-Synuclein Oligomerization in Synucleinopathies. (2008)

The heterogeneity of symptoms and disease progression observed in synucleinopathies, of which Parkinson's disease (PD) is the most common representative, poses large problems for the discovery of novel therapeutics. The molecular basis for pathology is currently unclear, both in familial and in sporadic cases. While the therapeutic effects of L-DOPA and dopamine receptor agonists constitute good options for symptomatic treatment in PD, the development of neuroprotective and/or neurorestorative treatments for PD and other synucleinopathies faces significant challenges due to the poor knowledge of the putative targets. Recent experimental evidence strongly suggests a central role for neurotoxic alpha-synuclein oligomeric species in neurodegeneration. The events leading to protein oligomerization, as well as the oligomeric species themselves, are likely amenable to modulation by small molecules, which are beginning to emerge in high throughput compound screens in a variety of model organisms. The therapeutic potential of small molecule modulators of oligomer formation demands further exploration and validation in cellular and animal disease models in order to accelerate human drug development.
Magnetic measurements of hydrogen desorption from palladium hydride PdH0.64 prepared by severe plastic deformation (2020)

Hydrogen absorption and desorption through diffusive processes and the accompanying phase transformations in hydrogen storage materials have been investigated by x-ray diffraction, thermogravimetry, pressure-composition-temperature isotherms, and electrical resistance measurements. We use time- and temperature-dependent magnetic measurements to gain a detailed understanding of these phenomena in palladium hydride PdH0.64 prepared by severe plastic deformation via the high-pressure torsion method. The concept of our method is pursuing an increase in the ratio of the paramagnetic α-phase Pd+H to the diamagnetic β-phase PdH. An antiferromagnetic correlation appears between the paramagnetic moments of Pd at a low temperature and a huge discrete change in magnetization appears due to collective H desorption above room temperature. It is also verified that H diffusion and its desorption can be changed with the accumulation of the severe lattice strain.
Advancing Near-Infrared Phosphorescence with Heteroleptic Iridium Complexes Bearing a Single Emitting Ligand: Properties and Organic Light-Emitting Diode Applications (2022)

Cyclometalated iridium complexes, emitters of choice in organic light-emitting diodes (OLEDs), hold great potential for near-infrared (NIR) applications. Upon increasing the conjugation size and chemical complexity of the ligands, as required to push the emission toward the NIR), overall high-molecular-weight complexes (both homoleptic and heteroleptic β-diketonate ones) are obtained, posing related issues in OLED processing. One, so far barely explored, question arises: “Why endow Ir(III) with three or two emissive ligands when one might work just as well?” Herein, as proof of concept for OLED technology, we disclose three novel deep-red to NIR emitters of formula Ir(C^N)2(iqbt), with a single iqbt (1-(benzo[b]thiophen-2-yl)-isoquinolinate) ligand responsible for the emission in the NIR range. (C^N) are cyclometalated ligands with higher triplet energy than that of iqbt. We demonstrate that the presence of a single iqbt ligand is sufficient to enable efficient phosphorescence matching that of homoleptic Ir(iqbt)3; moreover, the Ir(C^N)2(iqbt) based OLEDs display efficiency exceeding the one of Ir(iqbt)3. These compounds offer several important benefits: (i) advantageous synthetic protocols limiting to the last step of the use of novel and synthetic costly NIR ligands (implying a lower amount of ligand required), (ii) commercially available (C^N) to prepare the starting Ir chloro-dimers, and (iii) lower molecular weight of the complexes compared to that of the homoleptic parent ones fruitful for easier vacuum thermal processing of the emitters.
An Empirical Study Of Semi-Supervised Chinese Word Segmentation Using Co-Training (2013)

In this paper we report an empirical study on semi-supervised Chinese word segmentation using co-training.We utilize two segmenters: 1) a word-based segmenter leveraging a word-level language model, and 2) a character-based segmenter using characterlevel features within a CRF-based sequence labeler.These two segmenters are initially trained with a small amount of segmented data, and then iteratively improve each other using the large amount of unlabelled data.Our experimental results show that co-training captures 20% and 31% of the performance improvement achieved by supervised training with an order of magnitude more data for the SIGHAN Bakeoff 2005 PKU and CU corpora respectively.
Strain-specific and common epitopes of gonococcal pili. (1984)

The antigenic structure of gonococcal pilin, strain MS11 (Tr), was investigated by assaying the binding of antisera engendered by intact pili from strains MS11 and R10 and their two major cyanogen bromide-generated fragments, CNBr-2 (residues 9-92) and CNBr-2 (residues 93-159), to synthetic peptides corresponding to the amino acid sequence of MS11 pilin. Four peptides were synthesized corresponding to regions of sequence variation between MS11 and R10 gonococcal pilin. Antisera against the homologous pilus filament and against its CNBr-3 fragment bind peptides equivalent to residues 121-134 and 135-151, which comprise the 30 amino acid disulfide loop near the carboxyl terminus of the protein. Heterologous pili antisera did not bind these peptides. Absorption studies proved that each peptide contained an independent, strain-specific epitope. Synthetic peptides corresponding to regions of identical sequence between MS11 and R10 pilin were used in similar binding experiments to localize a weakly immunogenic, common determinant between residues 48 and 60. less than 15% of the antibodies raised against intact pili were directed at this site. Antisera raised against MS11 or R10 CNBr-2 bind a separate peptide, residues 69-80. This region is immunogenic only as a fragment, not in the intact pilus filament.