gebhart/patrepeval huggingface dataset:
Rare calcium oxalate monohydrate calculus attached to the wall of the renal pelvis (2011)

Most renal calculi can be classified using well-established criteria in a manner that reflects both composition and fine structure under specific pathophysiological conditions. However, when a large patient population is considered, rare renal calculi invariably appear, some of which have never been classified; careful study is required to establish stone etiology in such cases. The patient in the present case report formed two types of calculi. One was attached on the wall of the renal pelvis near the ureter and part of the calculus was embedded inside pelvic renal tissue. The calculus developed on an ossified calcification located in the pelvis tissue. Current knowledge on the development of calcification in soft tissues suggests a pre-existing injury as an inducer of its development. A mechanism of calculus formation is proposed. The second stone was a typical jack-stone calculus.
Differentiation of Inflammation-Responsive Astrocytes from Glial Progenitors Generated from Human Induced Pluripotent Stem Cells (2017)

Astrocyte dysfunction and neuroinflammation are detrimental features in multiple pathologies of the CNS. Therefore, the development of methods that produce functional human astrocytes represents an advance in the study of neurological diseases. Here we report an efficient method for inflammation-responsive astrocyte generation from induced pluripotent stem cells (iPSCs) and embryonic stem cells. This protocol uses an intermediate glial progenitor stage and generates functional astrocytes that show levels of glutamate uptake and calcium activation comparable with those observed in human primary astrocytes. Stimulation of stem cell-derived astrocytes with interleukin-1β or tumor necrosis factor α elicits a strong and rapid pro-inflammatory response. RNA-sequencing transcriptome profiling confirmed that similar gene expression changes occurred in iPSC-derived and primary astrocytes upon stimulation with interleukin-1β. This protocol represents an important tool for modeling in-a-dish neurological diseases with an inflammatory component, allowing for the investigation of the role of diseased astrocytes in neuronal degeneration.
A High-Frequency Power Factor Correction Stage With Low Output Voltage (2019)

Single-phase power factor correction (PFC) stages would ideally have three features-operation over the entire line cycle, soft switching at high frequency for all powers and voltages, and a reasonably low output voltage. These features permit high power factor, high combination of density and efficiency, and reduced stress on subsequent stages. Most PFC stages, including the most commonly used, achieve only a subset of these features. Here, we present control innovations to allow a PFC stage to operate from universal input (90-265 V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ac</sub> ) over the entire line cycle with zero-voltage switching (ZVS) with a reduced output voltage. These features are verified with a prototype with very high power factor (> 0.99), high efficiency (98%), and high density (80 W/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ). The PFC can provide an output of 200 V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dc</sub> from the entire universal input voltage range which greatly reduces the conversion stress required from subsequent stages. The proposed PFC control consists of a blended feedforward/feedback method that provides additional advantages like guaranteed soft switching, the ability to correct for input capacitance, and the ability to interface with a high-ripple output bus. Therefore, the proposed PFC provides advantages in efficiency and density both for the PFC stage and the overall system.
Characterization of amorphous hydrogenated carbon nitride films prepared by plasma-enhanced chemical vapor deposition using a helical resonator discharge (1997)

Amorphous hydrogenated carbon nitride thin films (a-CNx:H) have been prepared by plasma-enhanced chemical vapor deposition of N2 and CH4 gases using a helical resonator discharge. The structural and optical properties of the deposited a-CNx:H films have been systematically studied as a function of the substrate temperature and radio frequency (rf) substrate bias. The chemical structure and elemental composition of the a-CNx:H films were characterized by Fourier transform infrared spectroscopy (FT-IR), x-ray photoelectron spectroscopy (XPS), and Raman spectroscopy. The optical properties of the films were evaluated using transmission ultraviolet–visible spectroscopy. The morphology of the films was investigated by scanning electron microscopy and atomic force microscopy. The FT-IR and XPS studies demonstrate the presence of carbon–nitrogen bonds with hydrogenated components in the films. The film composition ratio N/C was found to vary from 0.127 to 0.213 depending on the deposition conditions. The Raman spectra, showing the G and D bands, indicate that the a-CNx:H films have a graphitic structure. It can be found that the optical band-gap Eg of a-CNx:H films is associated with graphitic clusters, while the decrease in Eg is correlated with an increase in the size and number of graphitic clusters. Combining the results of Raman and optical measurements, it can be concluded that a progressive graphitization of the films occurs with increasing the substrate temperature and rf substrate bias power, corresponding to bias voltage.
Topological cell clustering in the ATLAS calorimeters and its performance in LHC Run 1 (2017)

The reconstruction of the signal from hadrons and jets emerging from the proton-proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting <i>topological cell clusters</i> have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS.
Alkyl halides in conjunction with inorganic salt for the initiation of the polymerization and graft copolymerization of heterocycles (1976)

Abstract When certain alkyl halides react with suitable inorganic salts in the presence of a heterocyclic monomer, polymerization ensues. Appropriate alkyl halides include allylic, tertiary, and benzylic chlorides, bromides, and possibly iodides. If the halide is a small organic molecule, a homopolymer is formed; if it is a polymer halide, a graft copolymer results. Soluble silver salts with counterions such as SO 3 CF 3 − , BF 4 − , PF 6 − , SbF 6 − , and ClO 4 − are most suitable, but LiPF 6 and NaClO 4 can also be used. So far, nine heterocycles have been polymerized by this method, e.g., tetrahydrofuran, 7‐oxabicyclo[2·2·1]heptane, propylene oxide, styrene oxide, dioxolane, trioxane, ε‐caprolactone, and thietane. To date, no effort has been made to optimize conditions for each monomer, but the preliminary data suggest that many of the expected side reactions are operative. Graft copolymers have been prepared from seven backbones: poly(vinyl chloride), neoprene, chlorinated EPDM, chlorobutyl rubber, bromobutyl rubber, chlorinated butadiene, and chlorinated butadiene‐styrene copolymer. In the most thoroughly examined cases with polytetrahydrofuran as the grafted copolymer and silver triflate as the inorganic salt, current data indicate that no unreacted backbone remains and no homopolymer forms. With some of the other monomers, homopolymer is formed in addition to graft during the grafting process.
Endocrine regulation of hepatic somatomedin C (IGF1) production in young calves (1988)

International audience
An Analysis of Binocular Slant Contrast (1999)

When a small frontoparallel surface (a test strip) is surrounded by a larger slanted surface (an inducer), the test strip is perceived as slanted in the direction opposite to the inducer. This has been called the depth-contrast effect, but we call it the slant-contrast effect. In nearly all demonstrations of this effect, the inducer's slant is specified by stereoscopic signals; and other signals, such as the texture gradient, specify that it is frontoparallel. We present a theory of slant estimation that determines surface slant via linear combination of various slant estimators; the weight of each estimator is proportional to its reliability. The theory explains slant contrast because the absolute slant of the inducer and the relative slant between test strip and inducer are both estimated with greater reliability than the absolute slant of the test strip. The theory predicts that slant contrast will be eliminated if the signals specifying the inducer's slant are consistent with one another. It also predicts reversed slant contrast if the inducer's slant is specified by nonstereoscopic signals rather than by stereo signals. These predictions were tested and confirmed in three experiments. The first showed that slant contrast is greatly reduced when the stereo-specified and nonstereo-specified slants of the inducer are made consistent with one another. The second showed that slant contrast is eliminated altogether when the stimulus consists of real planes rather than images on a display screen. The third showed that slant contrast is reversed when the nonstereo-specified slant of the inducer varies and the stereo-specified slant is zero. We conclude that slant contrast is a byproduct of the visual system's reconciliation of conflicting information while it attempts to determine surface slant.
The Effects of Glia on the Tensile Properties of the Spinal Cord (2008)

Glia, the primary non-neuronal cells of the central nervous system, were initially believed to bind or glue neurons together and/or provide a supporting scaffold [1, 2]. It is now recognized that these cells provide specialized and essential biological and regulatory functions. Still, their contributions to the overall mechanical properties would also strongly influence the tissue’s tolerance to loading conditions experienced during trauma and potentially regulate of function and growth in neurons and glia [3, 4]. White matter represents an intriguing tissue to appreciate the role of glia in tissue and cellular mechanics. White matter consists of bundles of axons aligned in parallel, which are myelinated by oligodendrocytes, and a network of astrocytes, which interconnect axons and the vascular supply. In this study, we selectively interfered with the glial network during chick embryo development and evaluated the tensile properties of the spinal cord. Myelination was suppressed by injecting ethidium bromide (EB), which is cytotoxic to dividing cells and kills oligodendrocytes and astrocytes, or an antibody against galactocerebroside (αGalC) with serum complement, which interferes with oligodendrocytes during the myelination process without affecting astrocytes.
High Dynamic Range Fluorescence Imaging (2018)

Fluorescence acquisition and image display over a high dynamic range is highly desirable. However, the limited dynamic range of current photodetectors and imaging CCDs impose a limit on the fluorescence intensities that can be simultaneously captured during a single image acquisition. This is particularly troublesome when imaging biological samples, where protein expression fluctuates considerably. As a result, biological images will often contain regions with signal that is either saturated or hidden within background noise, causing information loss. In this manuscript we summarize recent work from our group and others, to extended conventional to high dynamic range fluorescence imaging. These strategies have many biological applications, such as mapping of neural connections, vascular imaging, bio-distribution studies or pharmacologic imaging at the single cell and organ level.
Protein design-scapes generated by microfluidic DNA assembly elucidate domain coupling in the bacterial histidine kinase CpxA (2021)

The randomization and screening of combinatorial DNA libraries is a powerful technique for understanding sequence-function relationships and optimizing biosynthetic pathways. Although it can be difficult to predict a priori which sequence combinations encode functional units, it is often possible to omit undesired combinations that inflate library size and screening effort. However, defined library generation is difficult when a complex scan through sequence space is needed. To overcome this challenge, we designed a hybrid valve- and droplet-based microfluidic system that deterministically assembles DNA parts in picoliter droplets, reducing reagent consumption and bias. Using this system, we built a combinatorial library encoding an engineered histidine kinase (HK) based on bacterial CpxA. Our library encodes designed transmembrane (TM) domains that modulate the activity of the cytoplasmic domain of CpxA and variants of the structurally distant "S helix" located near the catalytic domain. We find that the S helix sets a basal activity further modulated by the TM domain. Surprisingly, we also find that a given TM motif can elicit opposing effects on the catalytic activity of different S-helix variants. We conclude that the intervening HAMP domain passively transmits signals and shapes the signaling response depending on subtle changes in neighboring domains. This flexibility engenders a richness in functional outputs as HKs vary in response to changing evolutionary pressures.
Photoluminescence and scintillation properties GaN (2021)

Photoluminescence (PL) and scintillation properties of GaN film deposited on Al2O3 substrate were evaluated. In PL and X-ray induced scintillation spectra, two emission bands at 400 and 550 nm were observed. The X-ray induced scintillation decay curve demonstrated two decay components of 1.6 and 8.4 ns. Upon 55Fe 5.9 keV X-ray and 241Am 5.5 MeV α-ray excitation, the GaN film showed a higher scintilaltion light yield than ZnO, which was a common semiconductor scintillator.
The Acute Promyelocytic Leukemia-Oncoprotein PML-Raralpha Blocks Senescence and Disrupts The Atrx/Daxx Chromatin Remodeling Complex To Promote Leukemia (2013)

Abstract Although Acute Promyelocytic Leukemia (APL) has become a curable disease due to in-depth understanding of the underlying molecular processes, its investigation has provided unique and valuable insights into the processes involved in leukemogenesis. Therefore we use it as a model disease. 99% of APL-patients express a PML-RAR fusion protein. While involvement of RAR has proven indispensable for oncogenicity, the role of the PML domain is far less clear. In our previous study (Sternsdorf et al., Cancer Cell, 2006) we found that substitution of PML with heterologous self-interaction domains suffices to induce leukemias, but drastically decreases oncogenic potency of the resulting fusion proteins. In this study, we have chosen the inverse strategy: we have modified the PML domain to create a more active artificial model oncoprotein by adapting PR to its biological environment: As the typical model organism for APL studies is the mouse, we have replaced the human PML domain with the murine PML domain. This oncoprotein (mPR) creates APL-type leukemias in mice with higher penetrance and shorter latency than its human counterpart, hPR. We have used this system to study immediate early effects of expression of the model oncoprotein. While proliferating murine bone marrow cells go into senescence ex vivo, expression of mPR prevents this and robustly immortalizes murine bone marrow from every mouse strain tested so far. Senescence-associated upregulation of the cell-cycle regulators p21 and p19 was efficiently blocked by mPR expression. In mouse cells, mPR exhibits higher potency in disrupting the PML-associated Daxx/ATRX complex than hPR. Knockdown of ATRX, but not Daxx ameliorated ATRA-induced growth suppression and p21 upregulation in the human APL model cell line NB4. These data suggest, that PML-RAR promotes leukemogenesis by disrupting the Daxx/ATRX complex, which assembles at PML nuclear bodies during the onset of senescence. Disclosures: No relevant conflicts of interest to declare.
14 Medisch-immunologische diagnostiek (2016)

De laatste decennia is de kennis van immunologische aandoeningen (auto-immuunziekten, allergie, aangeboren immunodeficiënties, proliferaties en maligniteiten van het immuunsysteem, immunologische problematiek rondom transplantatie en transfusie) aanzienlijk toegenomen. Deze toename in kennis heeft ook geleid tot een toename in mogelijkheden voor diagnostisch onderzoek op het gebied van immuunziekten. Voor dergelijke immunologische diagnostiek bestaat er een apart laboratoriumspecialisme, de medische immunologie.
A Decompilation Approach to Partitioning Software for Microprocessor/FPGA Platforms (2005)

We present a software compilation approach for microprocessor/FPGA platforms that partitions a software binary onto custom hardware implemented in the FPGA. Our approach imposes fewer restrictions on software tool flow than previous compiler approaches, allowing software designers to use any software language and compiler. Our approach uses a back-end partitioning tool that utilizes decompilation techniques to recover important high-level information, resulting in performance comparable to high-level compiler-based approaches.
Digital optical signal processing using ultrashort optical pulse. (1987)

Merits and existing problems of using pulsed semiconductor lasers as optical clock for optoelectronic integrate circuits (OEIC) are discussed. Examples are taken from the research efforts of the author's group on opto-electronic demultiplexing and multiplexing based either on fast photoconductive switch or on bistable semiconductor laser. Importance of developing optical circuit technology enabling multiple input/output optical connection is pointed out.
Mouse models of angiogenesis, arterial stenosis, atherosclerosis and hemostasis (1998)

The development of efficient transgenic technologies in mice has allowed the study of the consequences of genetic alterations on cardiovascular (patho)physiology, although the development of such models have been hampered by size limitation of species resulting in time-consuming, labor-intensive and costly analyses. This overview summarizes the murine models currently available for studying or manipulating angiogenesis, arterial stenosis, atherosclerosis, transplant arteriopathy, thrombosis, thrombolysis and bleeding and addresses techniques to evaluate vascular development during embryogenesis.
Insights into the Water Transport Mechanism in Polymeric Membranes from Neutron Scattering (2020)

Polymeric membranes are ubiquitous in transport applications including gas separation, water desalination, solid-state batteries, and fuel cells. The transport mechanism in certain classes of membranes is well understood. It is generally believed that polymeric membranes used in gas separation follow the solution–diffusion model. However, the transport mechanism in other membranes such as the ones used in water desalination is less clear as both the solution–diffusion and hydrodynamic models have been proposed. In this contribution, we study the structure as well as the water and polymer dynamics of several polymeric membranes using small-angle and quasi-elastic neutron scattering. We demonstrate that on the scale of a few nanometers, water appears to diffuse through a desalination membrane at a rate comparable to bulk water, while water diffuses at a rate that is a factor of 2 slower in an anion-exchange membrane. These results illustrate the importance of studying both the structure and dynamics of membrane materials and have important implications in understanding the transport mechanisms that differentiate the different types of polymeric membranes.
Drug resistance-associated mutations in antiretroviral treatment-naïve and -experienced patients in Kuwait (2018)

The identification of human immunodeficiency virus (HIV) mutations leading to drug resistance enables patient-specific adaptation of the treatment regimen and predicts the risk of transmission of drug-resistant HIV. In this study, we report for the first time the prevalence in Kuwait of non-polymorphic resistance-associated mutations (RAMs) in patients under first-line antiretroviral therapy. Viral RNA was extracted from plasma samples of 64 treatment-naïve (untreated) and 64 treatment-experienced patients. The HIV-1 load was determined by real-time RT-PCR. The protease- and reverse transcriptase-encoding regions were analyzed by subtyping, and for drug resistance. The HIV-1 load at sampling in treatment-naïve patients ranged from 1.61 x 104 to 1.91 x 106 copies/ml, whereas that in treatment-experienced patients ranged from bitors (PIs) and NNRTIs. These results necessitate efforts to be made for reducing emergence of resistance-associated mutations in treated patients, and highlight the need for continuous monitoring of drug resistance patterns in Kuwait.
Selective electrochemical reduction of CO2 to CO with a cobalt chlorin complex adsorbed on multi-walled carbon nanotubes in water (2015)

Electrocatalytic reduction of CO2 occurred efficiently using a glassy carbon electrode modified with a cobalt(II) chlorin complex adsorbed on multi-walled carbon nanotubes at an applied potential of -1.1 V vs. NHE to yield CO with a Faradaic efficiency of 89% with hydrogen production accounting for the remaining 11% at pH 4.6.
Function-led design of new porous materials (2015)

Porous solids are important as membranes, adsorbents, catalysts, and in other chemical applications. But for these materials to find greater use at an industrial scale, it is necessary to optimize multiple functions in addition to pore structure and surface area, such as stability, sorption kinetics, processability, mechanical properties, and thermal properties. Several different classes of porous solids exist, and there is no one-size-fits-all solution; it can therefore be challenging to choose the right type of porous material for a given job. Computational prediction of structure and properties has growing potential to complement experiment to identify the best porous materials for specific applications.
Regularized Latent Class Model for Joint Analysis of High-Dimensional Longitudinal Biomarkers and a Time-to-Event Outcome (2018)

Although many modeling approaches have been developed to jointly analyze longitudinal biomarkers and a time-to-event outcome, most of these methods can only handle one or a few biomarkers. In this article, we propose a novel joint latent class model to deal with high dimensional longitudinal biomarkers. Our model has three components: a class membership model, a survival submodel, and a longitudinal submodel. In our model, we assume that covariates can potentially affect biomarkers and class membership. We adopt a penalized likelihood approach to infer which covariates have random effects and/or fixed effects on biomarkers, and which covariates are informative for the latent classes. Through extensive simulation studies, we show that our proposed method has improved performance in prediction and assigning subjects to the correct classes over other joint modeling methods and that bootstrap can be used to do inference for our model. We then apply our method to a dataset of patients with idiopathic pulmonary fibrosis, for whom gene expression profiles were measured longitudinally. We are able to identify four interesting latent classes with one class being at much higher risk of death compared to the other classes. We also find that each of the latent classes has unique trajectories in some genes, yielding novel biological insights.