gebhart/patrepeval huggingface dataset:
Data from Overexpression of Class III β-Tubulin Predicts Good Response to Taxane-Based Chemotherapy in Ovarian Clear Cell Adenocarcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Of the various microtubule-associated molecules, β-tubulin III has been reported to be closely associated with the therapeutic efficacy of taxane-based chemotherapy against ovarian cancer. Stathmin and microtubule-associated protein 4 (MAP4) have been reported to play an important role in microtubule stabilization. In this study, we investigated whether expression of these microtubule-associated factors affects the therapeutic efficacy of taxane-based chemotherapy in ovarian clear cell adenocarcinoma.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Drug sensitivity of paclitaxel or cisplatin was assessed in ovarian cancer cell lines treated with small interfering RNA of tubulin isoforms, MAP4, and stathmin. We examined 94 surgically resected ovarian clear cell adenocarcinoma specimens from patients treated with taxane-containing regimens (&lt;i&gt;n&lt;/i&gt; = 44) and with taxane-free regimens (&lt;i&gt;n&lt;/i&gt; = 50), using immunohistochemistry to detect expression of β-tubulin III, stathmin, and MAP4.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Knockdown of β-tubulin III and IV specifically conferred drug resistance to paclitaxel in one ovarian cancer cell line, but not to other molecules. Estimated overall survival revealed a significant synergistic effect between taxane and β-tubulin III in patients with ovarian clear cell adenocarcinoma. Of three microtubule-related molecules, among the taxane-based chemotherapy group, cases with higher β-tubulin III expression were associated with a significantly more favorable prognosis compared with those having lower β-tubulin III expression. By contrast, there was no statistical significance in the synergistic relationships between stathmin and taxane or between MAP4 and taxane.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Taxane-based chemotherapy was effective for patients with ovarian clear cell adenocarcinomas who were positive for β-tubulin III but not for those who were negative for these proteins.&lt;/p&gt;&lt;/div&gt;
Mapping chromosomal breakpoints of Burkitt's t(8;14) translocations far upstream of c-myc. (1992)

To analyze the region upstream of c-myc, a number of novel probes were established. These were generated by chromosomal walking starting from the breakpoint of the chromosomal translocation of the B-cell line 380 and by cloning the breakpoint of the translocation of the Burkitt lymphoma cell line IARC/BL72. Using the newly isolated probes a detailed physical map of 500 kilobases of the region upstream of c-myc was established applying pulsed-field gel electrophoresis. The chromosomal breakpoint of IARC/BL72 cells was mapped to a site 55 kilobases 5' of c-myc. A region 20 kilobases in length and containing the breakpoints of 380, EW36, P3HR-1, and Daudi cells was identified 170-190 kilobases upstream of c-myc. In addition the HPV18 integration site in HeLa cells was located between 340 and 500 kilobases 5' of c-myc. The probes were used to define the c-myc amplification units in Colo320-HSR and HL60 cells as well as in four cases of small cell lung cancer. Evidence is provided that the amplicon of HL60 cells is discontinuously organized.
Sparse Representations and Efficient Sensing of Data (Dagstuhl Seminar 11051) (2011)

This report documents the program and the outcomes of Dagstuhl Seminar 11051 ``Sparse Representations and Efficient Sensing of Data''. The scope of the seminar was twofold. First, we wanted to elaborate the state of the art in the field of sparse data representation and corresponding efficient data sensing methods. Second, we planned to explore and analyze the impact of methods in computational science disciplines that serve these fields, and the possible resources allocated for industrial applications.
OODB Bulk Loading Revisited: The Partitioned-List Approach (1995)

Object-oriented and object-relational databases (OODB) need to be able to load the vast quantities of data that OODB users bring to them. Loading OODB data is significantly more complicated than loading relational data due to the presence of relationships, or references, in the data; the presence of these relationships means that naive loading algorithms are slow to the point of being unusable. In our previous work, we presented the late-invsort algorithm, which performed significantly better than naive algorithms on all the data sets we tested. Unfortunately, further experimentation with the late-invsort algorithm revealed that for large data sets (ones in which a critical data structure of the load algorithm does not fit in memory), the performance of late-invsort rapidly degrades to where it, too, is unusable. In this paper we propose a new algorithm, the partitioned-list algorithm, whose performance almost matches that of late-invsort for smaller data sets but does not degrade for ...
Reproducible fabrication and characterization of diamond membranes for photonic crystal cavities (2016)

Single crystal diamond has turned out to be a promising material for applications in quantum information processing for its ability to host color centers with optimal properties such as narrow emission lines or long-lived spin states. However, the mechanical properties of diamond like its hardness and chemical resistance make the fabrication of photonic devices challenging up to date. In this article, a method is presented to produce thin, free-standing single crystal diamond membranes. These membranes are characterized with four different techniques complementing one another and detecting defects or thickness variations in the diamond films with high accuracy. The precise characterization allows for reproducible fabrication of two-dimensional photonic crystal cavities by focused ion beam milling in the as-produced membranes. Furthermore, optimizations in focused ion beam milling are presented, reducing imperfections of the fabricated photonic crystal cavities. Together with post-processing and implantation of color centers, these diamond nanostructures are a building block for cavity coupling experiments toward reliable spin–photon interfaces or optomechanical devices.
Reducing the efficiency droop by lateral carrier confinement in InGaN/GaN quantum-well nanorods (2014)

Efficiency droop is a major obstacle facing high-power application of InGaN/GaN quantum-well (QW) light-emitting diodes (LEDs). In this paper, we report the suppression of efficiency droop induced by the process of density-activated defect recombination in nanorod structures of a-plane InGaN/GaN QWs. In the high carrier density regime, the retained emission efficiency in a dry-etched nanorod sample is observed to be over two times higher than that in its parent QW sample. We further argue that such improvement is a net effect that the lateral carrier confinement overcomes the increased surface trapping introduced during fabrication.
Ionic liquids based on the imidazolium cation in platinum and titanium electropolishing (2011)

For the first time, the anodic behavior of platinum and titanium in ionic liquids (ILs) based on the imidazolium cation was investigated. ILs were established to possess a set of advantages compared with the traditional sulfuric acid electrolytes. It isn't necessary to maintain both a particular temperature and to use environmentally-harmful reagents, such as methanol or hydrofluoric acid, when electropolishing metals in IL media. The addition of propylene glycol to BMImCl (1 : 1) results in the formation of layers of titanium dioxide nanotubes on the metal surface.
Activation of phosphatidylinositol 3-kinase is necessary for differentiation of FDC-P1 cells following stimulation of type III receptor tyrosine kinases. (1998)

Signaling molecules that are responsible for proliferation and differentiation of hematopoietic cells following ectopic expression of receptor tyrosine kinases (RTKs) were investigated in the interleukin 3 (IL-3)-dependent hematopoietic cell line, FDC-P1. Cells were transfected with human platelet-derived growth factor receptor (PDGF-R), macrophage colony stimulating factor-1 receptor (CSF-1R), epidermal growth factor receptor (EGF-R), and chimeras consisting of the extracellular domain of EGF-R and the transmembrane and cytoplasmic domains of either HER2 (HER1-2) or c-kit (EK-R). All FDC-P1 transfectants proliferated in response to the corresponding growth factor in the absence of IL-3. However, only cells expressing PDGF-R, CSF-1R, and EK-R (type III RTKs) differentiated along the monocyte-macrophage lineage after treatment with their activating ligands. Analysis of proteins from these RTK-expressing cells revealed that a Mr 85,000 protein showed in vitro phosphorylation, and V8 protease peptide mapping showed that this protein was p85, the regulatory subunit of phosphatidylinositol 3-kinase (PI3-kinase). Accordingly, activation of PDGF-R-, CSF-1R-, and EK-R-expressing cells led to an increase in PI3-kinase activity. Expression of EK-R mutant Y721F, which lacked the known p85 binding site, blocked differentiation and activation of PI3-kinase, without affecting proliferation. Last, addition of wortmannin to cells expressing PDGF-R, CSF-1R, and EK-R blocked ligand-induced differentiation in a concentration-dependent manner, and this effect correlated with wortmannin's ability to inhibit PI3-kinase. Thus, ectopic expression of both type I and III RTKs could stimulate FDC-P1 proliferation in the absence of IL-3; however, only activation of type III RTKs led to differentiation via selective coupling to p85 and PI3-kinase activation.
Precision Heart Rate Estimation Using a PPG Sensor Patch Equipped with New Algorithms of Pre-Quality Checking and Hankel Decomposition (2023)

A new method for accurately estimating heart rates based on a single photoplethysmography (PPG) signal and accelerations is proposed in this study, considering motion artifacts due to subjects' hand motions and walking. The method comprises two sub-algorithms: pre-quality checking and motion artifact removal (MAR) via Hankel decomposition. PPGs and accelerations were collected using a wearable device equipped with a PPG sensor patch and a 3-axis accelerometer. The motion artifacts caused by hand movements and walking were effectively mitigated by the two aforementioned sub-algorithms. The first sub-algorithm utilized a new quality-assessment criterion to identify highly noise-contaminated PPG signals and exclude them from subsequent processing. The second sub-algorithm employed the Hankel matrix and singular value decomposition (SVD) to effectively identify, decompose, and remove motion artifacts. Experimental data collected during hand-moving and walking were considered for evaluation. The performance of the proposed algorithms was assessed using the datasets from the IEEE Signal Processing Cup 2015. The obtained results demonstrated an average error of merely 0.7345 ± 8.1129 beats per minute (bpm) and a mean absolute error of 1.86 bpm for walking, making it the second most accurate method to date that employs a single PPG and a 3-axis accelerometer. The proposed method also achieved the best accuracy of 3.78 bpm in mean absolute errors among all previously reported studies for hand-moving scenarios.
Broadband instantaneous frequency measurement based on stimulated Brillouin scattering (2017)

A technique for the instantaneous frequency measurement (IFM) of broadband signals is proposed based on stimulated Brillouin scattering (SBS) in a single-mode optical fiber. The instantaneous frequency and amplitude information is obtained by the narrowband filtering of the acoustic-optic interaction in the SBS process. Through sideband management of the optical-modulation, the IFM bandwidth can be far beyond the Brillouin frequency shift (i.e. ~11 GHz in 1550 nm). Proof-of-concept experiments for both the linearly frequency modulated pulse and frequency Costas coded pulse are carried out to verify the feasibility of the IFM.
Inhibition of estrogen-independent mammary carcinogenesis by disruption of growth hormone signaling (2006)

Clinical trials and laboratory-based studies indicate that the growth hormone/insulin-like growth factor-I axis may affect the development of breast cancer. The purpose of the present investigation was to develop a genetic model of mammary cancer to test the hypothesis that downregulation of GH signaling can substantially retard mammary cancer progression. We crossed the Laron mouse, in which the gene for the GH receptor/binding protein has been disrupted, with the C3(1)/TAg mouse, which develops estrogen receptor alpha negative mammary cancers. All mice used in our experiments were heterozygous for the large T antigen (TAg) and either homozygous wild-type for GHR (Ghr+/+) or null for GHR (Ghr-/-). Compared with the TAg/Ghr+/+ mice, the TAg/Ghr-/- mice showed delayed mammary cancer latency with significantly decreased multiplicity (9.8 +/- 1.4 versus 3.2 +/- 1.2) and volume (776.1 +/- 284.4 versus 50.5 +/- 8.9 mm3). Furthermore, the frequency of mammary hyperplasias was significantly reduced in the TAg/Ghr-/- mice (15.0 +/- 1.7 versus 6.8 +/- 1.7). To establish that these mammary cancers were estrogen-independent, 12-week-old TAg/Ghr+/+ mice, which lack visible hyperplasia, were either ovariectomized (ovx) or sham operated (sham). Compared with the sham group, ovariectomy resulted in no difference in the frequency of mammary hyperplasia, mammary tumor latency, incidence, multiplicity or tumor size. Together, these data demonstrate that the disruption of GH signaling significantly retards TAg-driven mammary carcinogenesis, and suggest that disrupting GH signaling may be an effective strategy to inhibit the progression of estrogen-independent breast cancer.
Spin-Noise-Detected Two-Dimensional Fourier-Transform NMR Spectroscopy (2013)

We introduce two-dimensional NMR spectroscopy detected by recording and processing the noise originating from nuclei that have not been subjected to any radio frequency excitation. The method relies on cross-correlation of two noise blocks that bracket the evolution and mixing periods. While the sensitivity of the experiment is low in conventional NMR setups, spin-noise-detected NMR spectroscopy has great potential for use with extremely small numbers of spins, thereby opening a way to nanoscale multidimensional NMR spectroscopy.
Plasma-Enhanced Atomic Layer Deposition of TiAlN: Compositional and Optoelectronic Tunability (2019)

Titanium nitride (TiN) is a unique refractory plasmonic material, the nanocomposites and alloys of which provide further opportunities to tailor its optical and photonic properties. We prepare TiAlN films of continuously variable compositions through the systematic variation of TiN versus AlN cycle ratio in plasma-enhanced atomic layer deposition (PEALD) and investigate the resulting thin-film composition, crystallinity, and optical properties. The resulting properties of TiAlN films are not simple linear combinations of the TiN and AlN films, which exhibit distinct metallic and dielectric properties, but instead are dramatically influenced by the local chemical environment of neighboring constituents. In situ spectroscopic ellipsometry further enables measurement of the varying optical properties of TiAlN films, which evolve over 10 s of nm of film thickness. The tunable optoelectronic properties of TiAlN films enable durable coatings of variable electrical resistance as well as high-temperature diffusion barriers and optical coatings with application to selective solar absorbers and emitters.
SARS-CoV-2-Mediated Lung Edema and Replication Are Diminished by Cystic Fibrosis Transmembrane Conductance Regulator Modulators (2023)

Coronaviruses (CoVs) of genera α, β, γ, and δ encode proteins that have a PDZ-binding motif (PBM) consisting of the last four residues of the envelope (E) protein (PBM core). PBMs may bind over 400 cellular proteins containing PDZ domains (an acronym formed by the combination of the first letter of the names of the three first proteins where this domain was identified), making them relevant for the control of cell function. Three highly pathogenic human CoVs have been identified to date: severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. The PBMs of the three CoVs were virulence factors. SARS-CoV mutants in which the E protein PBM core was replaced by the E protein PBM core from virulent or attenuated CoVs were constructed. These mutants showed a gradient of virulence, depending on whether the alternative PBM core introduced was derived from a virulent or an attenuated CoV. Gene expression patterns in the lungs of mice infected with SARS-CoVs encoding each of the different PBMs were analyzed by RNA sequencing of infected lung tissues. E protein PBM of SARS-CoV and SARS-CoV-2 dysregulated gene expression related to ion transport and cell homeostasis. Decreased expression of cystic fibrosis transmembrane conductance regulator (CFTR) mRNA, essential for alveolar edema resolution, was shown. Reduced CFTR mRNA levels were associated with edema accumulation in the alveoli of mice infected with SARS-CoV and SARS-CoV-2. Compounds that increased CFTR expression and activity, significantly reduced SARS-CoV-2 growth in cultured cells and protected against mouse infection, suggesting that E protein virulence is mediated by a decreased CFTR expression. <b>IMPORTANCE</b> Three highly pathogenic human CoVs have been identified: SARS-CoV, MERS-CoV, and SARS-CoV-2. The E protein PBMs of these three CoVs were virulence factors. Gene expression patterns associated with the different PBM motifs in the lungs of infected mice were analyzed by deep sequencing. E protein PBM motif of SARS-CoV and SARS-CoV-2 dysregulated the expression of genes related to ion transport and cell homeostasis. A decrease in the mRNA expression of the cystic fibrosis transmembrane conductance regulator (CFTR), which is essential for edema resolution, was observed. The reduction of CFTR mRNA levels was associated with edema accumulation in the lungs of mice infected with SARS-CoV-2. Compounds that increased the expression and activity of CFTR drastically reduced the production of SARS-CoV-2 and protected against its infection in a mice model. These results allowed the identification of cellular targets for the selection of antivirals.
Next generation perpendicular systems (2001)

Using 3D modeling, guidelines for ultra-high density perpendicular recording were defined. The concepts developed to choose dimensions and materials were verified experimentally using MFM and spin-stand experiments with a 60 nm wide focused ion beam (FIB) trimmed head.
Measurement and analysis of musical vibrato parameters (2015)

Vibrato is a fundamental feature of many musical sounds, with vocal, stringed instrument, and many wind instrumental performances employing vibrato as a principal device for conveying musical expression. In this paper, we describe a signal processing toolbox for extracting and analyzing vibrato-related parameters from audio recordings. In our method, sonic partials of a musical sound are separated first, followed by tracking of the instantaneous amplitude and frequency of each partial. A number of parameters that characterize vibrato can then be extracted from the tracked partials; these include the common frequency of the amplitude modulation (AM) and the frequency modulation (FM), the modulation depths, the relative phase between the AM and FM components of each partial, and the harmonic contents of the modulation components. This then enables a detailed comparison of the vibrato of various musical sounds, for example the relative amounts of AM and FM, the rate of vibrato, the correlation and phase between AM and FM vibrato components, and many other features. This framework provides a useful tool for applications such as music performance pedagogy and musicological studies.
Comparaison des lois de commande pour convertisseurs DC-DC. Application au convertisseur SEPIC (2010)

International audience
Aryl Hydrocarbon Receptor-Induced Adrenomedullin Mediates Cigarette Smoke Carcinogenicity in Humans and Mice (2012)

Cigarette smoking (CS) is a leading cause of death worldwide. The aryl hydrocarbon receptor (AHR) is partially responsible for tobacco-induced carcinogenesis although the underlying mechanisms involving early effector genes have yet to be determined. Here, we report that adrenomedullin (ADM) significantly contributes to the carcinogenicity of tobacco-activated AHR. CS and AHR activating ligands induced ADM in vitro and in vivo but not in AHR-deficient fibroblasts and mice. Ectopic transfection of AHR rescued ADM expression in AHR(-/-) fibroblasts whereas AHR blockage with siRNA in wild type cells significantly decreased ADM expression. AHR regulates ADM expression through two intronic xenobiotic response elements located close to the start codon in the ADM gene. Using tissue microarrays we showed that ADM and AHR were coupregulated in lung tumor biopsies from smoker patients. Microarray meta-analysis of 304 independent microarray experiments showed that ADM is elevated in smokers and smokers with cancer. In addition, ADM coassociated with a subset of AHR responsive genes and efficiently differentiated patients with lung cancer from nonsmokers. In a novel preclinical model of CS-induced tumor progression, host exposure to CS extracts significantly elevated tumor ADM although systemic treatment with the ADM antagonist NSC16311 efficiently blocked tobacco-induced tumor growth. In conclusion, ADM significantly contributes the carcinogenic effect of AHR and tobacco combustion products. We suggest that therapeutics targeting the AHR/ADM axis may be of clinical relevance in the treatment of tobacco-induced pulmonary malignancies.
Datagram Transport Layer Security (DTLS) as Transport for Session Traversal Utilities for NAT (STUN) (2014)

This document specifies the usage of Datagram Transport Layer Security (DTLS) as a transport protocol for Session Traversal Utilities for NAT (STUN). It provides guidance on when and how to use DTLS with the currently standardized STUN usages. It also specifies modifications to the STUN and Traversal Using Relay NAT (TURN) URIs and to the TURN resolution mechanism to facilitate the resolution of STUN and TURN URIs into the IP address and port of STUN and TURN servers supporting DTLS as a transport protocol. This document updates RFCs 5389 and 5928.