gebhart/patrepeval huggingface dataset:
HBsAg seroclearance in chronic hepatitis B in the Chinese: Virological, histological, and clinical aspects (2004)

Few studies have examined Chinese patients with chronic hepatitis B who exhibit hepatitis B surface antigen (HBsAg) seroclearance. We comprehensively studied the biochemical, virological, histological, and clinical aspects of 92 patients with HBsAg seroclearance (median follow-up, 126 months). Ninety-two HBsAg-positive controls matched for age, sex, and duration of follow-up were also recruited. Liver biochemistry, serum hepatitis B virus (HBV) DNA levels, and development of clinical complications were monitored. Intrahepatic total and covalently closed circular (ccc) HBV DNA were measured quantitatively in 16 patients. HBV genotype was determined in 30 patients. The mean age at HBsAg seroclearance was 48.8 (+ 13.81) years. There was a significant improvement in serum alanine aminotransferase levels after HBsAg seroclearance (p<0.0001). Patients with genotype B had a higher chance of HBsAg seroclearance than those with genotype C (P =.014). Ninety-eight percent of patients had undetectable serum HBV DNA. Thirty-seven percent of patients had low titer of intrahepatic HBV DNA, mainly in the form of cccDNA (71%-100%). All 14 patients with liver biopsies had near normal histology. There was no difference in the risk of development of hepatocellular carcinoma (HCC) between patients with and without HBsAg seroclearance. However, the mean age of HBsAg seroclearance was significantly older in patients with HCC than in patients without HCC (P =.016). In conclusion, patients with HBsAg seroclearance had favorable biochemical, virological, and histological parameters. Intrahepatic HBV DNA level was low and predominantly in the form of cccDNA. However, HCC could still develop, particularly in patients with cirrhosis who had HBsAg seroclearance at an older age.
Detail-Preserving Variational Surface Design With Multiresolution Constraints (2005)

Abstract We present a variational framework for rapid shape prototyping. The modeled shape is represented as a Catmull-Clark multiresolution subdivision surface which is interactively deformed by direct user input. Free-form design goals are formulated as constraints on the shape and the modeling problem is cast into a constrained optimization one. The focus of this paper is on handling multiresolution constraints of different kinds and on preserving surface details throughout the deformation process. Our approach eliminates the need for an explicit decomposition of the input model into frequency bands and the overhead associated with saving and restoring high-frequency detail after global shape fairing. Instead, we define a deformation vector field over the model and we optimize its energy. Surface details are considered as part of the rest shape and are preserved during free-form model editing. We explore approximating the solution of the optimization problem to various degrees to balance trade-offs between interactivity and accuracy of the results.
Quantitatively Profiling Nanoparticle Plasmons with Sub-10-nm Resolution by Molecular Molding (2010)

International audience
Dietary bisphenol A prevents ovarian degeneration and bone loss in female mice lacking the aromatase gene (Cyp19 ) (2002)

We previously generated mice lacking aromatase activity by targeted disruption of Cyp19 (ArKO mice), and reported phenotypes of the female mice, showing hemorrhage formation and follicular depletion in the ovary, diminution in uterine size, and bone loss. In the present study, we examined the influence of dietary bisphenol A (BPA), a monomer used for the production of polycarbonate and known to have estrogenic activity, on these phenotypes of the ArKO mice. When ArKO mice were fed chow diets supplemented with 0.1% or 1% (w/w) BPA for 5 months, they were protected from ovarian degeneration, uterine diminution and bone loss in a dose-dependent manner. Northern blot analyses of ovarian RNA of ArKO mice showed differences in the expression levels of insulin-like growth factor (IGF)-I, IGF-I receptor, growth differentiation factor 9 and bone morphogenetic protein 15 as compared with those in the ovaries of wild-type mice. The differences in the expression levels were restored by dietary BPA. In the ArKO uteri, expression of progesterone receptor and vascular endothelial growth factor mRNAs was diminished, and was restored by BPA to the levels in wild-type mice. In contrast, BPA had little effect on the ovarian, uterine and skeletal structures of wild-type mice. In conclusion, estrogenic effects of BPA on the reproductive tract as well as skeletal tissue were evident in adult female ArKO mice. These results suggest that the ArKO mouse is an animal model suitable for studying effects of estrogenic chemicals as well as estrogen in vivo.
Accurate Modelling of Liquid Crystal-Based Microwave Devices (2015)

Liquid crystal substrates have been shown to provide the means to develop low-cost, reconfigurable, adaptive and tuneable microwave devices for mobile and wireless communication systems. In order to take maximum advantage of the possibilities that these materials offer and to design LC-based devices appropriately, techniques for the characterisation of the liquid crystal dielectric properties are needed. Similarly, appropriate modelling methods are required to simulate accurately the switching behaviour of the liquid crystal and the characteristics of the wave propagation through the devices, taking full consideration of the point-by-point variation of the material tensor permittivity.
Wideband-tunable highly pure 40 GHz picosecond soliton train generation by short comb-like profiled fiber (2004)

We demonstrated generation of low-noise 40 GHz CS-RZ 3 ps pulse train with wideband tunability of wider than 20 nm through adiabatic soliton compression in 1.8 km-long comb-like profiled fiber.
Data on characterization of nano- and micro-structures resulting from glycine betaine surfactant/kappa-carrageenan interactions by Laser Scanning Confocal Microscopy and Transmission Electron Microscopy (2016)

This article contains data on the Laser Scanning Confocal Microscopy (LSCM) and Transmission Electron Microscopy (TEM) images related to multi-scaled self-assemblies resulting from 'green' cationic glycine betaine surfactant/anionic kappa-carrageenan interactions. These data gave clear evidence of the evolution of the micron-, nano-sized structures obtained at two surfactant/polymer molar ratios (3.5 and 0.8) and after the dilution of the aqueous dispersions with factors of 5 and 10 times. This data article is related to the research article entitled, "Monitoring the architecture of anionic ĸ-carrageenan/cationic glycine betaine amide surfactant assemblies by dilution: A multiscale approach" (Gaillard et al., 2017) [1].
Hardware-efficient multi-redundancy superposed trellis coded modulation on 16QAM constellation (2015)

We propose multi-redundancy optical coded modulation using superposed trellis. We experimentally prove that our scheme enables fine adaptive SE control and high coding gain of 7.1dB for 3-bit redundant 16QAM with quarterly reduced circuit complexity.
Optimizing HANS Color Separation: Meet the CMY Metamers (2011)

HANS &#x2013; the Neugebauer Primary based color separation and halftoning print control approach &#x2013; was presented in broad terms at CIC18. The present paper provides an in&#x2013;depth look at how HANS color separation can be optimized, what level of variety it provides access to and how it can be used for direct optimization of print attributes. The results show that even in the case of having only three colorants &#x2013; CMY, where current approaches lead to unique solutions, HANS provides significant metamer sets that lead to variety in print attributes such as the 12.7% ink use range show in the results.
CHIP attenuates lipopolysaccharide‐induced cardiac hypertrophy and apoptosis by promoting NFATc3 proteasomal degradation (2019)

Carboxyl-terminus of Hsc70 interacting protein (CHIP) is a chaperone-dependent E3-ubiquitin ligase with important function in protein quality control system. In the current research endeavor, we have investigated the putative role of CHIP in lipopolysaccharides (LPS)-induced cardiomyopathies. Basically, H9c2 cardiomyoblasts were transfected with CHIP for 24 hr, and thereafter, treated with LPS for 12 hr. Concomitantly, western blot analysis, actin staining, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, and coimmunoprecipitation studies were performed to investigate the underlying intricacies. Interestingly, western blot analysis revealed that the expression of hypertrophy and apoptosis-related proteins were considerably reduced following overexpression of CHIP. Moreover, Actin staining and TUNEL assay further ascertained the attenuation of cardiac hypertrophy and apoptosis following overexpression of CHIP respectively. These aspects instigate the role of CHIP in attenuation of LPS-induced cardiomyopathies. Additionally and importantly, co-immunoprecipitation and western blot studies revealed that CHIP plausibly promotes degradation of nuclear factor of activated T cells 3 (NFATc3) through ubiquitin-proteasomal pathway. Taken together, our study reveals that CHIP attenuates LPS-induced cardiac hypertrophy and apoptosis perhaps by promoting NFATc3 proteasomal degradation.
Intravascular optical coherence tomography [Invited] (2017)

Shortly after the first demonstration of optical coherence tomography for imaging the microstructure of the human eye, work began on developing systems and catheters suitable for intravascular imaging in order to diagnose and investigate atherosclerosis and potentially to monitor therapy. This review covers the driving considerations of the clinical application and its constraints, the major engineering milestones that enabled the current, high-performance commercial imaging systems, the key studies that laid the groundwork for image interpretation, and the clinical research that traces intravascular optical coherence tomography (OCT) from early human pilot studies to current clinical trials.
A Dynamic Nonlinear Impedance Model of a Single Photon Avalanche Diode (2023)

A nonlinear LCR parallel circuit model of a single photon avalanche diode (SPAD) is derived from a Lienard-type nonlinear differential equation. The resistance and the inductance associated with avalanche multiplication (AM) are time-dependent and governed by the avalanche time constant due to the impact ionization ratio. Time dependences of current, voltage, resistance, and inductance in the model are analyzed by numerically solving the equation. During the initial generation of a Geiger-mode pulse, when the voltage reaches the breakdown voltage, the resistance diverges to limit the maximum current and the inductance reduces to give the maximum speed of the voltage variation with the avalanche time constant. In the frequency domain, avalanche impedance (AI) spectra are obtained as a ratio of voltage and current spectra calculated as Fourier transforms of the time domain signals. The AI spectra exhibit a negative-resistance and an inductance. An analytic expression for the impedance is derived and found to comprise only a quenching resistance and a stray capacitance as indicated by a constant radius of a Nyquist plot. Finally, the present model is shown to incorporate the models of impact-ionization-avalanche transit-time (IMPATT) diodes when a very small-signal limit is assumed.
Review of Mechanisms by Which Electrical Stimulation Alters the Transmembrane Potential (1999)

Electrical stimuli pace, cardiovert, or defibrillate the heart by changing transmembrane potential (deltaVm). Recent simulation studies provide insights into mechanisms by which stimuli establish deltaVm. This review attempts a nonmathematical description of these mechanisms. We start with the cable model in which the intracellular core conductor is bounded by a highly resistive and capacitive membrane that separates the intracellular and extracellular spaces. Intracellular and extracellular resistances are assumed to vary linearly with position. Although this model predicts anodal extracellular stimuli hyperpolarize adjacent tissue and cathodal extracellular stimuli depolarize that tissue, it fails to reproduce regions of opposite deltaVm distant from the electrodes. We then consider the sawtooth model in which microscopic discontinuities in intracellular resistance represent gap junctions. While model studies with such discontinuities demonstrate large deltaVm at cell ends, experimental validation of such deltaVm remains elusive. Extending the analysis to the two- and three-dimensional syncytium, we also consider the bidomain model in which intracellular, extracellular, and interstitial currents are explicitly characterized. Differences in resistance to these currents gives rise to virtual electrodes, which are experimentally observed regions of large deltaVm that arise distant from the stimulating electrode. Distant deltaVm regions are also evident when macroscopic discontinuities in intracellular resistance are introduced into the bidomain model. Such discontinuities are associated with clefts or scars that give rise to "secondary sources." Albeit the cable model offers remarkable insight the bidomain model and the concept of secondary sources provide a more complete understanding of membrane excitation, especially when combined into a unifying activating function.
Supplementary Figure S1 from Small-Molecule ONC201/TIC10 Targets Chemotherapy-Resistant Colorectal Cancer Stem–like Cells in an Akt/Foxo3a/TRAIL–Dependent Manner (2023)

&lt;p&gt;Representative flow cytometry images for CD133 and CD44 TRAIL staining.&lt;/p&gt;
Variants of a mouse myeloma cell line that synthesize immunoglobulin heavy chains having an altered serotype. (1975)

Cells of the MPC-11 mouse myeloma cell line, which produces an IgG2b immunoglobulin, were subjected to mutagenesis with Melphalan or with ICR-191, after which they were cloned in soft agar. Approximately 0.5 percent of the clones produced altered heavy chains that: (i) were the same size as or larger than the parent; (ii) no longer recognized by antibody specific for the parent gamma2b subclass; (iv) were recognized by antibody against the Fab (NH2-terminal half) of the parental immunoglobulin, but lacked some of the antigenic determinants of the Fc (COOH-terminal half) of the heavy chain; (v) lacked many of the tryptic/chymotryptic peptides found in the parent; (vi) contained tryptic/chymotryptic peptides that were not present in the parent but were present in an unrelated gamma2a myeloma heavy chain; and (vii) assembled with light chains by a pathway typical of IgG2a myelomas.
Advanced on-chip test technology for RSFQ circuits (1997)

We have developed an advanced version of on-chip test system with new high-speed clock generation and control. For high-speed clock generation, a novel wide-bandwidth ring generator is designed using circular Josephson transmission lines with an inductively coupled trigger. The generator is capable of producing SFQ clock pulses in the range of from 15 to 55 GHz using a 1 kA/cm/sup 2/ Nb fabrication process. For clock control, we have designed two different types of clock-controller circuits based on programmable shift-register and counter. Using the on-chip test system, we have successfully tested a parallel multiplier module up to 15 GHz with 16% dc bias margins.
Characterization of Alu Repeats That Are Associated with Trinucleotide and Tetranucleotide Repeat Microsatellites (1997)

The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of microsatellites with families of Alu elements was used to facilitate the development of genetic markers. Sequences containing Alu repeats were eliminated because unique primers could not be designed. Various classes of microsatellites are associated with different classes of Alu repeats. Very abundant and poly(A)-rich microsatellite classes (ATA, AATA) are frequently associated with an evolutionarily older subclass of Alu repeats, AluSx, whereas most of GATA and CA microsatellites are associated with a recent Alu subfamily, AluY. Our observations support all three possible mechanisms for the association of Alu repeats to microsatellites. Primers designed using a set of sequences from a particular microsatellite class showed higher homology with more sequences of that class than probes designed for other classes. We developed an efficient method of prescreening GGAA and ATA microsatellite clones for Alu repeats with probes designed in this study. We also showed that Alu probes labeled in a single reaction (multiplex labeling) could be used efficiently for prescreening of GGAA clones. Sequencing of these prescreened GGAA microsatellites revealed only 5% Alu repeats. Prescreening with primers designed for ATA microsatellite class resulted in the reduction of the loss of markers from approximately 50% to 10%. The new Alu probes that were designed have also proved to be useful in Alu-Alu fingerprinting.
ChemInform Abstract: Asymmetric Conjugate Additions of an Hydroxyethyl Carbanion Equivalent. Synthesis of (+)‐A Factor. (1988)

Abstract The chiral tolylsulfinylbutenolide (S)‐(+)‐(IV) is coupled with the lithiated bisether which is prepared from benzyloxymethyl chloride (I) and the hydroxymethylstannane (II) by lithium tin exchange.
CFD Analysis inside a CO2 Rotary Compressor Shell to Improve Oil Separation and Reduce the Shell Size (2012)

A CO2 rotary compresspr uses refrigeration oil to lubricate and cool sliding parts and to seal the cylinder. It is difficult to separate the oil inside the shell at high pressure from CO2 gas, whose difference in density from the oil is small. It remains an issue to retain high efficiency with the same shell size as a present hydro fluorocarbon (HFC) compressor. We explored an improvement in the oil separation by use of CFD analysis and identified two effective measures. One measure is to flatten a lower balance weight of the rotor to prevent the oil mist from moving up through the motor flow paths. Another measure is to set up a rotating disc over a protruding balance weight at the top of the rotor to increase the pressure in the upper space and allow the oil over the stator to return to the lower space by gravity. Experiments with an actual compressor verify that oil separation is improved to the target value.
Figure S5 from PET Reporter Gene Imaging and Ganciclovir-Mediated Ablation of Chimeric Antigen Receptor T Cells in Solid Tumors (2023)

&lt;p&gt;Figure S5 shows flow cytometry of spleens at 9 days following the final GCV treatment&lt;/p&gt;
Expanding Access to Remdesivir via an Improved Pyrrolotriazine Synthesis: Supply Centered Synthesis (2020)

Pyrrolotriazine <b>1</b> is an important precursor to remdesivir. Initial results toward an efficient synthesis are disclosed consisting of sequential cyanation, amination, and triazine formation beginning from pyrrole. This route makes use of highly abundant, commoditized raw material inputs. The yield of triazine was doubled from 31% to 59%, and the synthetic step count was reduced from 4 to 2. These efforts help to secure the remdesivir supply chain.
DNA-Encoded Multivalent Display of Protein Tetramers on Phage: Synthesis and In Vivo Aplications (2021)

Abstract Phage display links phenotype of displayed polypeptides with DNA sequence in phage genome and offers a universal method for discovery of proteins with novel properties. Injection of phage-displayed libraries in living organisms further provides a unique and powerful approach to optimize biochemical, pharmacological and biological properties of the displayed peptides, antibodies and other proteins in vivo . However, over 60% of the proteome is comprised of multi-domain proteins, and display of large multi-subunit proteins on phages remains a challenge. Majority of protein display systems are based on monovalent phagemid constructs but methods for robust display of multiple copies of large proteins are scarce. Here, we describe a DNA-encoded display of a ∼200 kDa tetrameric protein tetrameric L-asparaginase on M13 phage produced by ligation of SpyCatcher-Asparaginase fusion (ScA) to prospectively barcoded phage clones displaying SpyTag peptide. Starting from the SpyTag display on p3 minor coat protein or p8 major coat protein yielded constructs with five copies of ScA displayed on p3 (ScA 5 -phage) and 50 copies of ScA on p8 protein (ScA 50 -phage). ScA remained active after conjugation. It could be easily produced directly from lysates of bacteria that express ScA. Display constructs of different valency can be injected into mice and analyzed by deep-sequencing of the DNA barcodes associated phage clones. In these multiplexed studies, we observed a density-dependent clearance rate in vivo . A known clearance mechanism of L-asparaginase is endocytosis by phagocytic cells. Our observations, thus, link the increase in density of the displayed protein with the increased rate of the endocytosis by cells in vivo . In conclusion, we demonstrate that a multivalent display of L-asparaginase on phage could be used to study the circulation life of this protein in vivo and such approach opens the possibility to use DNA sequencing to investigate multiplexed libraries of other multi-subunit proteins in vivo . Abstract Graphic
The Application of Engineered Glucose Dehydrogenase to a Direct Electron–Transfer‐Type Continuous Glucose Monitoring System and a Compartmentless Biofuel Cell (2006)

Abstract Continuous glucose monitoring (CGM) is expected to become an ideal way to monitor glycemic levels in diabetic patients. On the other hand, biofuel cells can be used as an alternative energy source in future implantable devices, such as implantable glucose sensors in the artificial pancreas. Glucose dehydrogenase from Acinetobacter calcoaceticus, which harbors pyrroloquinoline quinone as the prosthetic group (PQQGDH), is one of the enzymes most attractive as a glucose sensor constituent and as the anode enzyme in biofuel cells, due to its high catalytic activity and insensitivity to oxygen. However, the application of PQQGDH for these purposes is inherently limited because an electron mediator is required for the electron transfer to the electrode. We have recently reported on the development of an engineered enzyme, quinohemoprotein glucose dehydrogenase (QH‐GDH), in which the cytochrome c domain of the quinohemoprotein ethanol dehydrogenase (QH‐EDH) was fused with PQQGDH, to enable electron transfer to the electrode in the absence of an artificial mediator. In this study, we constructed a direct electron‐transfer‐type CGM system employing QH‐GDH. This CGM system showed sufficient current response and high operational stability. Furthermore, we successfully constructed a compartmentless biofuel cell employing QH‐GDH. Keywords: Fuel cellsglucose dehydrogenasecontinuous glucose monitoringdirect electron transfercytochrome c domain