gebhart/patrepeval huggingface dataset:
Antibody to Cardiolipin as a Predictor of Fetal Distress or Death in Pregnant Patients with Systemic Lupus Erythematosus (1985)

During a prospective study of pregnancies in women with systemic lupus erythematosus, we examined the relation between antibody to cardiolipin, measured by the enzyme-linked immunosorbent assay, and midpregnancy fetal distress, identified by abnormal results of antepartum fetal heart-rate testing or by fetal death. All of nine patients with lupus and this complication had abnormally high antibody levels (mean, 212.3 +/- 55.3 units), as compared with values in normal nonpregnant women (28.2 +/- 10.1 units). None of 12 pregnant patients with lupus but without this complication had antibody levels above 50 units (mean, 27.5 +/- 3.4 units; P less than 0.005 vs. women with lupus and fetal distress); 4 of 12 pregnant subjects without lupus had antibody levels above 50 units (mean, 42.5 +/- 11.0), and fetal death occurred in the subject with the highest level. The mean antibody level in 12 nonpregnant patients with lupus was 117.4 +/- 35.0 units. Two patients who had lupus anticoagulant but not clinical lupus, both with histories of prior fetal death, also had high antibody levels; fetal death occurred in one, and spontaneous fetal bradycardia in the other. Antibody to cardiolipin was loosely linked to a history, but not the simultaneous presence, of demonstrable lupus anticoagulant or thrombocytopenia, and could be detected as early in pregnancy as either anticoagulant or thrombocytopenia. We conclude that measurement of antibody to cardiolipin is the most sensitive assay to predict fetal distress or death in patients with systemic lupus erythematosus and may be of pathogenetic importance in this syndrome.
Topological events in polarization resolved angular patterns of nematic liquid crystal cells at varying ellipticity of incident wave (2008)

We study the angular structure of polarization of light transmitted through a nematic liquid crystal (NLC) cell by analyzing the polarization state as a function of the incidence angles and the polarization of the incident wave. The polarization resolved angular patterns emerging after the NLC cell illuminated by the convergent light beam are described in terms of the polarization singularities such as C-points (points of circular polarization) and L-lines (lines of linear polarization). For the homeotropically aligned cell, the Stokes polarimetry technique is used to measure the polarization resolved conoscopic patterns at different values of the ellipticity of the incident light impinging onto the cell. Using the exact analytical expressions for the transfer matrix we show that variations of the ellipticity induce transformations of the angular pattern exhibiting the effect of avoided L-line crossings and characterized by topological events such as creation and annihilation of the C-points. The predictions of the theory are found to be in good agreement with the experimental results.
A compact coaxial-type optical transceiver module using a half-transmittance photodiode for TCM optical access networks (1998)

A compact coaxial-type optical transceiver module has been developed without using a conventional 3 dB optical coupler. This transceiver is composed of a newly designed half-transmittance photodiode (HT-PD) and a 1.3-/spl mu/m-MQW-LD. An HT-PD is used both as a photodetector and as a window for LD light. Fiber output power of 1.15 mW at the drive current of 26 mA and responsivity of 0.48 A/W at the reverse-voltage of 5 V were obtained. Temperature dependence of responsivity is also reported.
Leveraging Memristive Systems in the Construction of Digital Logic Circuits (2011)

The recent emergence of the memristor has led to a great deal of research into the potential uses of the devices. Specifically, the innate reconfigurability of memristors can be exploited for applications ranging from multilevel memory, programmable logic, and neuromorphic computing, to name a few. In this work, memristors are explored for their potential use in dense programmable logic circuits. While much of the work is focused on Boolean logic, nontraditional styles including threshold logic and neuromorhpic computing are also considered. In addition to an analysis of the circuits themselves, computer-aided design (CAD) flows are presented which have been used to map digital logic functionality to dense complementary metal-oxide-semiconductor (CMOS)-memristive logic arrays. As exemplified through the circuits described here memristor-based digital logic holds great potential for high-density and energy-efficient computing.
Solar cycle 22 continues strong climb (1989)

Solar Cycle 22, which began in September 1986, continues to rise at a rate that rivals or exceeds that of all sunspot cycles in the record of direct sunspot observations. As measured by smoothed sunspot numbers and 10.7‐cm radio flux values, Cycle 22 remains ahead of all past cycles in the modern record except Cycle 19, which peaked during the late 1950s (see Figure 1). By other measures, such as the number of X ray flares or solar proton events, this cycle is running up to 30% higher than at the corresponding point in all previous cycles. In our previous report (“Solar and Geomagnetic Activity During Cycle 21 and Implications for Cycle 22,” Eos, 69 , 962, 1988) we presented early information on Cycle 22 and discussed some possible solar‐terrestrial effects of solar activity. Figure 1 updates that information to the present in sunspot number and 10.7‐cm radio flux values.
Clinical Spectroscopy: general discussion (2016)

Duncan Graham opened a general discussion of the paper by Pavel Matousek: Regarding the temperature measurements, how did you do them? Stokes/anti-Stokes measurement? The values are not what I'd expect and seem lower. What was the wavelength and power of the laser and did you calculate what you
Multifactorial Deep Learning Reveals Pan-Cancer Genomic Tumor Clusters with Distinct Immunogenomic Landscape and Response to Immunotherapy (2020)

Our study provides a proof for principle that deep learning modeling may have the potential to discover intrinsic statistical cross-modality correlations of multifactorial input data to dissect the molecular mechanisms underlying primary resistance to immunotherapy, which likely involves multiple factors from both the tumor and host at different molecular levels.
Heterogeneous integration of low power pH FinFET sensors with passive capillary microfluidics and miniaturized Ag/AgCl quasi-Reference Electrode (2016)

This work presents one of the first low power pH sensing microfluidic chip based on the heterogeneous integration of: (i) high-k FinFET sensors with liquid gate, (ii) miniaturized Ag/AgCl quasi-Reference Electrode and (iii) passive microfluidic. The integration of these three components provides a fully integrated and compact platform that could be exploited for ionic monitoring in biofluids for healthcare applications. We describe the full fabrication process for the microfluidic system with the embedded reference electrode. The electrical characterization of heterogeneously integrated pH FinFET sensor with the integrated reference electrode shows I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> -V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> characteristics with subthreshold swing SS~141mV/dec, low Ioff current and I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> /I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> > 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> . When applying a constant current operation scheme, a sensitivity of 8mV/pH of the output drain voltage is reported. Due to the biocompatibility of the selected materials and small size, the resulting microsystem-on-chip could be used as a noninvasive wearable sensor for continuous monitoring of pH in sweat.
ChemInform Abstract: PHOTOCYCLOADDITIONS TO 3‐PHENYL‐1,2‐BENZISOTHIAZOLE (1982)

Abstract Die Benzisothiazole (Ia) bis (Ic) liefern mit Vinylethylether (II) beim Bestrahlen in einer Einstufenreaktion jeweils nur ein Photoaddukt, die Thiazepine (IIIa), (IIIb) bzw. (IIIc), von denen (IIIa) zusätzlich röntgenstrukturanalytisch untersucht wird (RG: P2 1 /n, Z=8).
Radical Reactions: Part 1 (2004)

This chapter contains sections titled: Introduction Rearrangements Intramolecular Addition Fragmentation, Recombination, and Homolysis Atom Abstraction Reactions Addition Reactions Homolytic Substitution Reactivity Effects Stereoselectivity in Radical Reactions Redox Reactions Radical Ions Peroxides, Peroxyl, and Hydroxyl Radicals Biological Chemistry References
Treatment with Imiquimod enhances antitumor immunity induced by therapeutic HPV DNA vaccination (2010)

Thus, our data suggests that the combination of therapeutic HPV DNA vaccination with topical treatment with the TLR7 agonist imiquimod enhances the antitumor immunity induced by DNA vaccination. The current study has significant implications for future clinical translation.
Maximizing Wind Energy Capture for Speed-Constrained Wind Turbines During Partial Load Operation (2016)

With the development of wind turbine technology, more wind turbines operate in the partial load region, where one of the main objectives is to maximize captured wind energy. This paper presents the development of an optimal control framework to maximize wind energy capture for wind turbines with limited rotor speed ranges. Numerical optimal control (NOC) techniques were applied to search for the achievable maximum power coefficient, thus maximum wind energy capture. Augmentations of these optimal techniques significantly reduced the computational cost. Simulation results show that, in comparison with the traditional torque feedback and conventional optimal control algorithms, the proposed augmented optimal control algorithm increases the harvested energy while minimizing the computational expense for speed-constrained wind turbines during partial load operation.
ADAM10 mediates trastuzumab resistance and is correlated with survival in HER2 positive breast cancer (2014)

Trastuzumab prolongs survival in HER2 positive breast cancer patients. However, resistance remains a challenge. We have previously shown that ADAM17 plays a key role in maintaining HER2 phosphorylation during trastuzumab treatment. Beside ADAM17, ADAM10 is the other well characterized ADAM protease responsible for HER ligand shedding. Therefore, we studied the role of ADAM10 in relation to trastuzumab treatment and resistance in HER2 positive breast cancer. ADAM10 expression was assessed in HER2 positive breast cancer cell lines and xenograft mice treated with trastuzumab. Trastuzumab treatment increased ADAM10 levels in HER2 positive breast cancer cells (p ≤ 0.001 in BT474; p ≤ 0.01 in SKBR3) and in vivo (p ≤ 0.0001) compared to control, correlating with a decrease in PKB phosphorylation. ADAM10 inhibition or knockdown enhanced trastuzumab response in naïve and trastuzumab resistant breast cancer cells. Trastuzumab monotherapy upregulated ADAM10 (p ≤ 0.05); and higher pre-treatment ADAM10 levels correlated with decreased clinical response (p ≤ 0.05) at day 21 in HER2 positive breast cancer patients undergoing a trastuzumab treatment window study. Higher ADAM10 levels correlated with poorer relapse-free survival (p ≤ 0.01) in a cohort of HER2 positive breast cancer patients. Our studies implicate a role of ADAM10 in acquired resistance to trastuzumab and establish ADAM10 as a therapeutic target and a potential biomarker for HER2 positive breast cancer patients.
Supplementary Figure 1 from Genetic Variation That Predicts Platinum Sensitivity Reveals the Role of miR-193b* in Chemotherapeutic Susceptibility (2023)

&lt;p&gt;PDF file, 65K, The Pearson correlation coefficient distribution of gene pairs.&lt;/p&gt;
Impact of ultra-short pauses between stacked lesions with and without active esophageal cooling (2023)

Abstract Funding Acknowledgements Type of funding sources: Public Institution(s). Main funding source(s): Research reported in this abstract was supported by the National Heart, Lung, And Blood Institute of the National Institutes of Health under Award Number R44HL158375 (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health). Background Placing lesions at the same point (stacking lesions) in the left atrium during radiofrequency (RF) ablation can increase the risk of collateral injury. The use of active esophageal cooling has been shown to significantly reduce the risk of thermal injury to the esophagus, but stacking of lesions may overcome these protective effects. Longer pauses between lesions may reduce this risk, but the effect of very short pauses has not been previously quantified. Purpose To examine the impact of ultra-short pauses between stacked lesions with and without active esophageal cooling. Methods Using a computational model of the left atrium, we measured the effect of RF ablation in the left atrium on injury formation in the esophagus. Models with and without active esophageal cooling, using a dedicated esophageal cooling device, were created. Using a power of 50 W for 10 s, with up to 3 sequential lesions placed in the same location, we used the Arrhenius equation to quantify the fraction of damage (FOD) in the esophageal wall. The time between lesions was set to as short as 1 s, and results were compared to prior studies using longer pauses of up to 20 s. To account for thermal latency, measures of esophageal damage were taken both immediately after RF ablation, and again 90 s afterwards. Results With active cooling in place, esophageal injury was eliminated with active esophageal cooling after the first lesion placement, but reached 21% transmurality without cooling. Lesion transmurality increased after each lesion due to thermal latency, but active esophageal cooling prevented this effect when only one lesion was placed. Subsequent lesions resulted in esophageal injury when placed in the same location. After 3 lesions with 1 s pauses between each, esophageal injury transmurality reached 91% without cooling in place, and 22% with active cooling in place (Figure 1). In contrast, analysis of the intended lesions in the atrial wall demonstrated minimal effects from cooling (Figure 2). Conclusions Active esophageal cooling significantly reduces esophageal injury from RF ablation, but placing additional lesions at the same point can overcome the heat extraction capacity of a dedicated cooling device. Decreased time between lesions exacerbates this risk, with an ultra-short pause of one second posing the greatest risk.
Light Scattering Anomalies Analyzed Through the Eigen-Frequencies of Mie Scatterers (2020)

International audience
Functional and Structural Characterization of an IclR Family Transcription Factor for the Development of Dicarboxylic Acid Biosensors (2023)

Abstract Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work we characterize the PcaR TF belonging to the IclR family. We present in vitro functional analysis of PcaR’s ligand profile and construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae . We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this TF. This work provides key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors. Graphical Abstract Highlights PcaR is an IclR family transcription regulator responsive to dicarboxylic acids PcaR was established as an in vivo biosensor in yeast Crystal structure of PcaR in the apo form was solved Crystal structure with PcaR in complex with succinate was solved Sequence alignments unveil ligand-binding positions in the IclR family
Proteomic and single-cell landscape reveals novel pathogenic mechanisms of HBV-infected intrahepatic cholangiocarcinoma (2023)

Despite the epidemiological association between intrahepatic cholangiocarcinoma (ICC) and hepatitis B virus (HBV) infection, little is known about the relevant oncogenic effects. A cohort of 32 HBV-infected ICC and 89 non-HBV-ICC patients were characterized using whole-exome sequencing, proteomic analysis, and single-cell RNA sequencing. Proteomic analysis revealed decreased cell-cell junction levels in HBV-ICC patients. The cell-cell junction level had an inverse relationship with the epithelial-mesenchymal transition (EMT) program in ICC patients. Analysis of the immune landscape found that more CD8 T cells and Th2 cells were present in HBV-ICC patients. Single-cell analysis indicated that transforming growth factor beta signaling-related EMT program changes increased in tumor cells of HBV-ICC patients. Moreover, ICAM1<sup>+</sup> tumor-associated macrophages are correlated with a poor prognosis and contributed to the EMT in HBV-ICC patients. Our findings provide new insights into the behavior of HBV-infected ICC driven by various pathogenic mechanisms involving decreased cell junction levels and increased progression of the EMT program.
Image classification of coral reef components from underwater color video (2002)

The purpose of this study is to automate coral reef assessment, that is, to classify coral images into benthic categories from digitized underwater video using a computer-based classifier such that coral reef analysis becomes less subjective, less tedious and more precise. Corals exhibit a variety of color, texture and structure which are the visual cues used by marine scientists for their classification. In computer vision, color is a point property of a picture element while texture is a property of an area. Color and texture have been combined as color-texture which is a feature that describes the spatial organization of colors in an area. As inputs to a classifier, the authors extract color, texture and color-texture descriptors from coral images and measure recognition rates using each feature. Corals are 3D structures and, when imaged, are prone to varying resolutions, perspective projection and lighting conditions. Therefore, an additional objective of this study is to address the problem of illumination, rotation and scale invariance in pattern recognition of underwater images. Images were classified into one of five benthic categories: alive coral, dead coral, dead coral with algae, algae and abiotics. Overall, texture was found to be more discriminating than using color alone or color and texture combined. Dead coral was the most successfully recognized class using color features.
Engineering modular intracellular protein sensor-actuator devices (2018)

Understanding and reshaping cellular behaviors with synthetic gene networks requires the ability to sense and respond to changes in the intracellular environment. Intracellular proteins are involved in almost all cellular processes, and thus can provide important information about changes in cellular conditions such as infections, mutations, or disease states. Here we report the design of a modular platform for intrabody-based protein sensing-Actuation devices with transcriptional output triggered by detection of intracellular proteins in mammalian cells. We demonstrate reporter activation response (fluorescence, apoptotic gene) to proteins involved in hepatitis C virus (HCV) infection, human immunodeficiency virus (HIV) infection, and Huntington's disease, and show sensor-based interference with HIV-1 downregulation of HLA-I in infected T cells. Our method provides a means to link varying cellular conditions with robust control of cellular behavior for scientific and therapeutic applications.
Structure of Vps75 and implications for histone chaperone function (2008)

The vacuolar protein sorting 75 (Vps75) histone chaperone participates in chromatin assembly and disassembly at both active and inactive genes through the preferential binding to histone H3-H4. Vps75 is also one of two histone chaperones, along with antisilencing factor 1, that promotes histone H3-Lys-56 acetylation by the regulation of Ty1 transposition protein 109 (Rtt109) histone acetyltransferase. Here, we report the x-ray crystal structure of Vps75 and carry out biochemical studies to characterize its interaction with Rtt109. We find that the Vps75 structure forms a homodimeric "headphone" architecture that includes an extended helical dimerization domain and earmuff domains at opposite ends and sides of the dimerization domain. Despite the similar overall architecture with the yeast nucleosome assembly protein 1 and human SET/TAF-1beta/INHAT histone chaperones, Vps75 shows several unique features including the relative disposition of the earmuff domains to the dimerization domain, characteristics of the earmuff domains, and a pronounced cleft at the center of the Vps75 dimer. These differences appear to correlate with the unique function of Vps75 to interact with Rtt109 for histone acetylation. Our biochemical studies reveal that two surfaces on the earmuff domain of Vps75 participate in Rtt109 interaction with a stoichiometry of 2:1, thus leaving the pronounced central cleft of the Vps75 dimer largely accessible for histone binding. Taken together, our data provide a structural framework for understanding how Vps75 mediates both nucleosome assembly and histone acetylation by Rtt109.
Reversible Basenkoordination an ein Disilen (2012)

SiSi-Aktivierung: Die reversible Bildung eines Donor-Akzeptor-Komplexes zwischen einem N-heterocyclischen Carben und einem Cyclotrisilen mit C-Substituenten verschiebt die Elektronendichte der Doppelbindung und induziert somit eine starke Polarisierung, wie durch das signifikant pyramidale dreifachkoordinierte Siliciumatom verdeutlicht wird.
Facile synthesis of an electrically conductive polycarbazole–zirconium(<scp>iv</scp>)phosphate cation exchange nanocomposite and its room temperature ammonia sensing performance (2015)

An electrically conductive polycarbazole–zirconium(<sc>iv</sc>)phosphate nanocomposite based sensor was fabricated for sensing aqueous ammonia at room temperature.