gebhart/patrepeval huggingface dataset:
Geometrical Theory of Electromagnetic Nonreciprocity (2023)

Recent advances in electromagnetic nonreciprocity raise the question of how to engineer the nonreciprocal electromagnetic response with geometrical approaches. In this Letter, we examine this problem by introducing generalized electromagnetic continua consisting structured points, which carry extra degrees of freedom over coordinate transformation. We show that general nonreciprocal media have a unique time-varying Riemannian metric structure with local spinning components. It is demonstrated that the nonreciprocity can be alternatively identified as the torsion tensor of a Riemann-Cartan space, which could provide analytic expressions for the magneto-optical effect and the axionic magnetoelectric coupling. Our theory not only gives a deeper insight into the fundamental understanding of electromagnetic nonreciprocity but also provides a practical principle to geometrically design nonreciprocal devices through frame transformation.
Joint Sidelobe Suppression and PAPR Reduction in OFDM Using Partial Transmit Sequences (2013)

Orthogonal frequency-division multiplexing (OFDM) waveform is known for its drawbacks that affect application in practice: high out-of-band (OOB) radiation and high peak-to-average power ratio (PAPR). In this paper, we propose a three-stage technique for the joint reduction of OOB radiation and PAPR, therefore minimizing the spectral regrowth after the power amplifier as well as signal distortion. In the first and the second stages, the OFDM data vector is partitioned into contiguous blocks that are naturally suited for PAPR reduction using partial transmit sequences (PTS). Since edge blocks/subcarriers have more impact on the OOB radiation, each edge block is further divided into smaller interleaved sub-blocks, and optimized phase rotations are applied to each sub-block to suppress the spectral sidelobes. Following the frequency domain techniques, optimum phase rotation for the time domain OFDM symbol is calculated to achieve smoother transition with the previous symbol, which further reduces the OOB spectrum. The proposed method improves the joint containment in frequency and power dimensions, along which the OFDM signal suffers from high spreading.
The CC Chemokine I-309 Inhibits CCR8-dependent Infection by Diverse HIV-1 Strains (1998)

Using a chemokine receptor model based on known receptor sequences, we identified several members of the seven transmembrane domain G-protein superfamily as potential chemokine receptors. The orphan receptor ChemR1, which has recently been shown to be a receptor for the CC chemokine I-309, scored very high in our model. We have confirmed that I-309, but not a number of other chemokines, can induce a transient Ca2+ flux in cells expressing CCR8. In addition, the human erythroleukemic cell line K562 responded chemotactically in a dose-responsive manner to this chemokine. Since several chemokine receptors have been shown to be required as coreceptors for HIV-1 infection, we asked whether human immunodeficiency virus type 1 (HIV-1) could efficiently utilize CCR8. Here we show that the CCR8 receptor can serve as a coreceptor for diverse T-cell tropic, dual-tropic, and macrophage-tropic HIV-1 strains and that I-309 was a potent inhibitor of HIV-1 envelope-mediated cell-cell fusion and virus infection. Furthermore, we show by flow cytometry and immunohistochemistry that antibodies generated against the CCR8 receptor amino-terminal peptide cross-reacted with U-87 MG cells stably expressing CCR8, THP-1 cells, HL-60 cells, and human monocytes, a target cell for HIV-1 infectivity in vivo.
Protease treatment of nuclear extracts distinguishes between class II MHC X1 box DNA-binding proteins in wild-type and class II-deficient B cells (1993)

The X box region is critical for directing the expression of class II major histocompatibility complex genes in B lymphocytes. Although several class II promoter-specific DNA binding factors have been described, only the X box region factor, RFX, shows a genetic correlation with class II expression, being deficient in some B cell lines derived from patients with class II-deficient congenital immunodeficiency. To further evaluate the role of X box DNA-binding proteins in class II gene expression, the role of the X box region was examined in both class II-positive and -negative lymphoid cells. In addition to the wild-type B cell line Raji, two class II transcriptional mutant cell lines, SJO and RJ2.2.5, and Jurkat, a class II negative T cell line, were examined. In contrast to wild-type B cells, neither of the class II mutant cell lines could use the X box region to direct the expression of a transiently transfected reporter gene, indicating that the X box-dependent transcriptional pathway is defective in these cells. The binding activity of the X1 box DNA-binding protein RFX was examined and found to be present in wild-type B cells and the mutant RJ2.2.5 but was absent in SJO and Jurkat. However, other X1 box-specific activities were detected in all these cell lines. To determine whether these different X1 box activities represented distinct DNA binding proteins or multimeric forms of the same factor(s), protease treatment of the crude nuclear extracts followed by DNA-binding assays were carried out and demonstrated that B cell extracts contain at least two X1-specific factors. One of these cleaved products (band 1 pk) correlates with RFX activity. A similar comparison with protease-treated extracts prepared from Jurkat cells demonstrated the presence of the band 1pk activity despite an absence of the native RFX activity. In contrast, protease treatment and analysis of SJO extracts showed no detectable levels of the band 1pk activity. These results demonstrate that multiple X1 box-specific DNA-binding activities exist in all lymphoid cells, but the presence of an actively binding RFX species correlates with class II transcription.
Correlation of abnormal RB, p16ink4a, and p53 expression with 3p loss of heterozygosity, other genetic abnormalities, and clinical features in 103 primary non-small cell lung cancers. (1999)

This study was performed to determine the frequency of inactivation and clinical correlates in non-small cell lung cancer (NSCLC) of three known tumor suppressor genes [TSGs; RB, MTS1/CDKN2 (p16), and p53] and various regions of 3p loss of heterozygosity (LOH) as other major potential TSG sites. Paraffin sections from 103 resected NSCLCs were analyzed for expression of pRB, p16, and p53 by immunohistochemistry, whereas DNA from tumor and normal tissue were tested for LOH at 3p25-26, 3p21, and 3p14. Previously published LOH data for 5q, 11p, 17q, and 18q were also available. Loss of pRB or p16 expression and overexpression of p53 were considered abnormal. The immunohistochemical and LOH data were correlated with a variety of clinical parameters including stage, age, sex, smoking history, and survival. With respect to pRB, p16, and p53, the tumors could be grouped into four categories: normal for all three proteins (21%); abnormal for pRB or p16 and normal for p53 (30%); normal for pRB and p16 and abnormal for p53 (20%); and abnormal in both pathways (28%). Aberrant expression of pRB, p16, p53, and 3p LOH, either individually or in combination, was not associated with survival differences or any other clinical parameters, with the exception that pRB/pl6 abnormalities were more common in older patients (P = 0.0005). pRB and p16 expression showed a strong inverse correlation (P = 0.002), whereas there was no correlation between expression of pRB, p16, and p53. Abnormal expression of any of the three genes inversely correlated with K-ras codon 12 mutations (P = 0.004), but not with 3p LOH or LOH at other TSG loci. We conclude that resectable NSCLCs show distinct patterns of TSG inactivation, but that no clear clinical correlates exist either alone or in combination for pRB, p16, p53, and 3p abnormalities.
A microflow cytometer on a chip (2010)

A rapid, automated, multi-analyte Microflow Cytometer is being developed as a portable, field-deployable sensor for onsite diagnosis of biothreat agent exposure and environmental monitoring. The technology relies on a unique method for ensheathing a sample stream in continuous flow past an interrogation region where optical fibers provide excitation and collect emission. This approach efficiently focuses particles in the interrogation region of the fluidic channel, avoids clogging and provides for subsequent separation of the core and sheath fluids in order to capture the target for confirmatory assays and recycling of the sheath fluid. Fluorescently coded microspheres provide the capability for highly multiplexed assays. Optical analysis at four different wavelengths identified six sets of the coded microspheres recognizing Escherichia coli, Listeria, and Salmonella as well as cholera toxin, staphylococcal enterotoxin B (SEB), and ricin, and assay results were compared with those of a commercial Luminex analysis system.
Strained silicon: A dielectric-response calculation (1992)

Strain-induced birefringence is calculated with crystalline silicon for pressure applied along the [001] and [111] directions of the crystal. Results for the dielectric function and its change under hydrostatic strain are also given. The results are calculated for photon energies in the range 0--3.25 eV, i.e., below the direct band gap. We have made a fully-self-consistent Kohn-Sham local-density-approximation calculation, in the pseudopotential, plane-wave scheme, with a self-energy correction in the form of a rigid shift of the conduction bands of magnitude \ensuremath{\Delta}=0.9 eV. Agreement with experiment is very good in the static limit, considering disagreements among the experimental values. Values of the photoelastic tensor for [001] strain are ${\mathit{p}}_{11}$-${\mathit{p}}_{12}$=-0.118 (theory) and -0.111\ifmmode\pm\else\textpm\fi{}0.005, -0.127\ifmmode\pm\else\textpm\fi{}0.005 (expt.). For [111] strain, we obtain ${\mathit{p}}_{44}$=-0.050 (theory) and -0.051\ifmmode\pm\else\textpm\fi{}0.002, -0.051\ifmmode\pm\else\textpm\fi{}0.002 [sic] (expt.); for hydrostatic distortions, ${\mathit{p}}_{11}$+2${\mathit{p}}_{12}$=-0.067 (theory) and -0.055\ifmmode\pm\else\textpm\fi{}0.006, -0.070\ifmmode\pm\else\textpm\fi{}0.008 (expt.). For the static dielectric constant, we obtain 10.9, compared to 11.7 and 11.4 (0 K) (expt.). All experiments quoted are at room temperature, except as noted. Above 2 eV, the calculation predicts less dispersion than seen by the experiments. Thermal effects and electron-hole interactions are estimated to resolve some of the discrepancies with experiment. The experimental data for [001] strains is not consistent with a single-oscillator model, and is therefore suspect.
Jitter transfer characteristics of delay-locked loops - theories and design techniques (2003)

This paper presents analyses and experimental results on the jitter transfer of delay-locked loops (DLLs). Through a z-domain model, we show that in a widely used DLL configuration, jitter peaking always exists and high-frequency jitter does not get attenuated as previous analyses suggest. This is true even in a first-order DLL and an overdamped second-order DLL. The amount of jitter peaking is shown to trade off with the tracking bandwidth and, therefore, the acquisition time. Techniques to reduce jitter amplification by loop filtering and phase filtering are discussed. Measurements from a prototype chip incorporating the discussed techniques confirm the prediction of the analytical model. In environments where the reference clock is noisy or where multiple timing circuits are cascaded, this jitter amplification effect should be carefully evaluated.
Transfer of Low-Molecular Weight Single-Stranded DNA through the Membrane of a High-Flux Dialyzer (2014)

This study establishes that significant transfer across the dialyzer may occur with single-stranded DNA in the size range of 20-bases or less. These findings need to be confirmed with an in vitro whole blood model and with clinical investigations. Previous studies have described the clinical benefits of achieving high-purity dialysate. Precautions are warranted to minimize the presence of these DNA compounds in fluids utilized for hemodialysis treatment.
Supplementary Figure 5A-B from NVP-AUY922: A Novel Heat Shock Protein 90 Inhibitor Active against Xenograft Tumor Growth, Angiogenesis, and Metastasis (2023)

Supplementary Figure 5A-B from NVP-AUY922: A Novel Heat Shock Protein 90 Inhibitor Active against Xenograft Tumor Growth, Angiogenesis, and Metastasis
Enabling Smart Grid Features by Enhanced Utilization of Actual Advanced Metering Infrastructure (2019)

The behaviour of Low Voltage (LV) grids is undergoing a transition from a load leaded passive role to a more active one [1], arising technical challenges such as sudden voltage dips and swells, bidirectional power flows, etc. Besides, these events are not automatically reported at the Distribution System Operator (DSO) control center, and mitigation actions (in case of abnormal conditions or outages) take relatively long time and a lot of manpower [2]. However, the undergoing deployment of Advanced Metering Infrastructures (AMI) in Europe appears promising for addressing these operational challenges. Nevertheless, the actual performance of the existing AMI is given by an architecture mainly designed for billing purposes, where the potential of the systems is not fully exploited. This paper aims to provide, an overview of the actual architecture, performance and utilization of the AMI. Additionally, alternative approaches on the utilization of actual AMI are discussed, in the frame of the ongoing research project PSO-RemoteGrid, in concordance with the needs reported by DSOs in Europe. Practical aspects such as the required system architecture supporting the implementation of smart grid functionalities are also discussed. This paper aims to increase the awareness of smart grid actors on existing capabilities and unused potential of current AMI.
MVsnaclec, a novel C-type lectin protein from Macrovipera lebetina venom, inhibits proliferation, induces apoptosis and suppresses migration in SK-MEL-28 human melanoma cells (2017)

International audience
Photorefractive amplification at high frequencies (2011)

Photorefractive optical amplification, while useful, is a slow process. Under some circumstances, however, it amplifies optical signals effectively even when one is modulated at a relatively high frequency. We determine the reasons for this capability (what we have called the "Fast Photorefractive Effect") and analyze its enhanced bandwidth, improvements over standard photorefractivity, and limitations.
Serum mass-spectrometry test in first-line advanced NSCLC patients treated with standard chemotherapy regimens. (2014)

e19090 Background: The mass-spectrometry based serum test VeriStrat (VS) was shown to be prognostic in various therapies and predictive of differential overall survival (OS) benefit for erlotinib vs. chemotherapy (CT) in second line NSCLC setting. Performance of the test in CT is of clinical interest. We investigated the role of VS in first-line advanced NSCLC patients (pts) treated with Cisplatin (Cis) or Carboplatin (Carbo) plus Pemetrexed (P). Methods: VS classification was available for 55 eligible stage IV, pts with non-squamous histology; pts were classified as VS Good (VSG) or VS Poor (VSP), VS testing of pretreatment serum samples was done blinded to clinical data. OS and progression-free survival (PFS) were analyzed by Kaplan-Meier method and compared using log-rank p-values; Cox models were used in multivariate analysis. Association with categorical variables was analyzed by Fisher’s exact test. Results: 36 (65%) pts were classified as VSG and 19 (35%) as VSP. In the overall population, median PFS was 5.7 months (mo) for VSG vs.1.4 mo for VSP (hazard ratio (HR) 0.37 [0.19-0.72], p=0.002 ); adjusted HR (AHR) 0.38 [0.17-0.86], p=0.021). Median OS was 10.8 mo for VSG vs. 3.4 mo for VSP (HR 0.23 [0.11-0.51], p < 0.001; AHR 0.12 [0.04-0.37], p<0.001). A similar relationship was found in both treatments: In CarboP median PFS in VSG and VSP was 3.8 mo and 2.0 mo respectively (HR 0.38 [0.15-0.94], p=0.030); median OS was 10.8 mo in VSG and 3.4 mo in VSP (HR 0.26 [0.09-0.72], p=0.006). In CisP median PFS was 6.1 mo in VSG and 1.2 mo in VSP (HR 0.40 [0.14-1.12], p=0.070), median OS was 12.3 mo in VSG, 3.8 mo in VSP (HR 0.17 [0.04-0.69], p=0.005).When compared within VS groups, no statistically significant differences between CarboP and CisP was found either for PFS (VSG: p=0.508, VSP: p=0.718) or OS (VSG: p=0.466 , VSP: p=0.522). VS was significantly associated with disease control rate (p=0.003) and trended towards significance for objective response (p=0.085). Conclusions: In Platinum-based doublet CT, VSP pts had much shorter PFS and OS than VSG. The behavior was similar in CisP and CarboP arms. Further research is needed to find alternative treatments to improve outcomes for VSP pts. ClinicalTrials.gov Identifier NCT02055144.
Evaluating the sensitivity of deep learning to inter-reader variations in lesion delineations on bi-parametric MRI in identifying clinically significant prostate cancer (2022)

Deep learning based convolutional neural networks (CNNs) for prostate cancer (PCa) risk stratification employ radiologist delineated regions of interest (ROIs) on MRI. These ROIs contain the reader’s interpretation of the region of PCa. Variations in reader annotations change the features that are extracted from the ROIs, which may in turn affect classification performance of CNNs. In this study, we sought to analyze the effect of variations in inter-reader delineations of PCa ROIs on training of CNNs with regards to distinguishing clinically significant (csPCa) and insignificant PCa (ciPCa). We employed 180 patient studies (n=274 lesions) from 3 cohorts who underwent 3T multi-parametric MRI followed by MRI-targeted biopsy and/or radical prostatectomy. ISUP Gleason grade groups (GGG) obtained from pathology were used to determine csPCa (GGG&ge;2) and ciPCa (GGG=1). 5 experienced radiologists, with over 5 years of experience in prostate imaging, delineated PCa ROIs on bi-parametric MRI (bpMRI including T2 weighted (T2W) and diffusion weighted (DWI) sequences) within the training set (n<sub>1</sub>=160 lesions) using targeted biopsy locations. Patches were extracted using the ROIs which were then used to train individual CNNs (N<sub>1</sub>-N<sub>5</sub>) using the SqueezeNet architecture. The average volume for readerdelineated ROIs used for training varied greatly, ranging between 1106 and 2107 mm across all readers. The resulting networks showed no significant difference in classification performance (AUC= 0.82 &plusmn; 0.02) indicating that they were relatively robust to inter-reader variations in ROI. These models were evaluated on independent test sets (n<sub>2</sub>=85 lesions, n<sub>3</sub>=29 lesions) where ROIs were obtained by co-registration of MRI with post-surgical pathology, unaffected by inter-reader variations in ROIs. Network performance across D<sub>2</sub> and D<sub>3</sub> was 0.80&plusmn;0.02 and 0.62 &plusmn; 0.03, respectively. The CNN predictions were moderately consistent, with ICC(2,1) scores across D<sub>2</sub> and D<sub>3</sub> being 0.74 and 0.54, respectively. Higher agreement in ROI overlap produced higher correlation in predictions on external test sets (R = 0.89, p &lt; 0.05). Furthermore, higher average ROI volume produced greater AUC scores on D<sub>3</sub>, indicating that comprehensive ROIs may provide more features for DL networks to use in classification. Inter-reader variations in ROIs on MRI may influence the reliability and generalizability of CNNs trained for PCa risk stratification.
Cripto-1 Is a Cell Surface Marker for a Tumorigenic, Undifferentiated Subpopulation in Human Embryonal Carcinoma Cells (2010)

Deregulation of stem cells is associated with the generation and progression of malignant tumors. In addition, genes that are associated with early embryogenesis are frequently expressed in cancer. Cripto-1 (CR-1), a glycosylphosphatidylinositol-linked glycoprotein, is expressed during early embryogenesis and in various human carcinomas. We demonstrated that human embryonal carcinoma (EC) cells are heterogeneous for CR-1 expression and consist of two distinct subpopulations: a CR-1(High) and a CR-1(Low) population. By segregating CR-1(High) and CR-1(Low) populations of NTERA2/D1 EC cells by fluorescence-activated cell sorting, we demonstrated that CR-1(High) cells were more tumorigenic than CR-1(Low) cells by an in vitro tumor sphere assay and by in vivo xenograft formation. The CR-1(High) population was enriched in mRNA expression for the pluripotent embryonic stem (ES) cell genes Oct4, Sox2, and Nanog. CR-1 expression in NTERA2/D1 cells was regulated by a Smad2/3-dependent autocrine loop, by the ES cell-related transcription factors Oct4/Nanog, and partially by the DNA methylation status of the promoter region. These results demonstrate that CR-1 expression is enriched in an undifferentiated, tumorigenic subpopulation and is regulated by key regulators of pluripotent stem cells.
Multiaxial Lenticular Stress-Strain Relationship of Native Myocardium is Preserved by Infarct-Induced Natural Heart Regeneration in Neonatal Mice (2020)

Neonatal mice exhibit natural heart regeneration after myocardial infarction (MI) on postnatal day 1 (P1), but this ability is lost by postnatal day 7 (P7). Cardiac biomechanics intricately affect long-term heart function, but whether regenerated cardiac muscle is biomechanically similar to native myocardium remains unknown. We hypothesized that neonatal heart regeneration preserves native left ventricular (LV) biomechanical properties after MI. C57BL/6J mice underwent sham surgery or left anterior descending coronary artery ligation at age P1 or P7. Echocardiography performed 4 weeks post-MI showed that P1 MI and sham mice (n = 22, each) had similar LV wall thickness, diameter, and ejection fraction (59.6% vs 60.7%, p = 0.6514). Compared to P7 shams (n = 20), P7 MI mice (n = 20) had significant LV wall thinning, chamber enlargement, and depressed ejection fraction (32.6% vs 61.8%, p < 0.0001). Afterward, the LV was explanted and pressurized ex vivo, and the multiaxial lenticular stress-strain relationship was tracked. While LV tissue modulus for P1 MI and sham mice were similar (341.9 kPa vs 363.4 kPa, p = 0.6140), the modulus for P7 MI mice was significantly greater than that for P7 shams (691.6 kPa vs 429.2 kPa, p = 0.0194). We conclude that, in neonatal mice, regenerated LV muscle has similar biomechanical properties as native LV myocardium.