gebhart/patrepeval huggingface dataset:
DNA methylation on N6-adenine in mammalian embryonic stem cells (2020)

It has been widely accepted that 5-methylcytosine is the only form of DNA methylation in mammalian genomes. Here we identify N6-methyladenine as another form of DNA modification in mouse embryonic stem cells. Alkbh1 encodes a demethylase for N6-methyladenine. An increase of N6-methyladenine levels in Alkbh1-deficient cells leads to transcriptional silencing. N6-methyladenine deposition is inversely correlated with the evolutionary age of LINE-1 transposons; its deposition is strongly enriched at young (<1.5 million years old) but not old (>6 million years old) L1 elements. The deposition of N6-methyladenine correlates with epigenetic silencing of such LINE-1 transposons, together with their neighbouring enhancers and genes, thereby resisting the gene activation signals during embryonic stem cell differentiation. As young full-length LINE-1 transposons are strongly enriched on the X chromosome, genes located on the X chromosome are also silenced. Thus, N6-methyladenine developed a new role in epigenetic silencing in mammalian evolution distinct from its role in gene activation in other organisms. Our results demonstrate that N6-methyladenine constitutes a crucial component of the epigenetic regulation repertoire in mammalian genomes.
Benign and malignant prostatic diseases. (1991)

The risk of prostatic diseases and disorders increases with age. Symptomatic benign prostatic hyperplasia is often treated with transurethral resection of the prostate. Antibiotic therapy is generally effective in bacterial prostatitis, but both chronic bacterial prostatitis with recurrent urinary tract infection and nonbacterial prostatitis remain difficult to treat. Early diagnosis of prostate cancer improves survival. Therapeutic options include surgery, radiotherapy and hormone therapy.
Recombinant Human Erythropoietin in the Treatment of Anemia Associated with Human Immunodeficiency Virus (HIV) Infection and Zidovudine Therapy (1992)

Therapy with r-HuEPO can increase the mean hematocrit and decrease the mean transfusion requirement in anemic patients with AIDS who are receiving zidovudine and have endogenous low erythropoietin levels (< or equal to 500 IU/L). Such therapy is of no apparent benefit in patients whose endogenous erythropoietin levels are higher than 500 IU/L.
Thermal Conductivity of Nanoparticle - Fluid Mixture (1999)

Effective thermal conductivity of mixtures of e uids and nanometer-size particles is measured by a steady-state parallel-plate method. The tested e uids contain two types of nanoparticles, Al 2O3 and CuO, dispersed in water, vacuum pump e uid, engine oil, and ethylene glycol. Experimental results show that the thermal conductivities of nanoparticle ‐e uid mixtures are higher than those of the base e uids. Using theoretical models of effective thermal conductivity of a mixture, we have demonstrated that the predicted thermal conductivities of nanoparticle ‐e uid mixtures are much lower than our measured data, indicating the dee ciency in the existing models when used for nanoparticle ‐e uid mixtures. Possible mechanisms contributing to enhancement of the thermal conductivity of the mixtures are discussed. A more comprehensive theory is needed to fully explain the behavior of nanoparticle ‐e uid mixtures. Nomenclature cp = specie c heat k = thermal conductivity L = thickness Pe = Peclet number P q = input power to heater 1 r = radius of particle S = cross-sectional area T = temperature U = velocity of particles relative to that of base e uids ® = ratio of thermal conductivity of particle to that of base liquid ¯ = .® i 1/=.® i 2/ ° = shear rate of e ow Ω = density A = volume fraction of particles in e uids Subscripts
IL-4 Suppresses Dendritic Cell Response to Type I Interferons (2007)

Cytokines play an important role in modulating the development and function of dendritic cells (DCs). Type I IFNs activate DCs and drive anti-viral responses, whereas IL-4 is the prototype of a Th2 cytokine. Evidence suggests that type I IFNs and IL-4 influence each other to modulate DC functions. We found that two type I IFNs, IFN-alpha and IFN-beta, stimulated a similar costimulatory profile in myeloid resting DCs. IL-4 suppressed the response of myeloid DCs to both type I IFNs in vitro and in vivo by impairing the up-regulation of MHC and costimulatory molecules and the production of cytokines, such as IL-6 and IL-15, and anti-viral genes, such as Mx-1, upon type I IFN stimulation. In dissecting the mechanism underlying this inhibition, we characterized the positive feedback loop that is triggered by IFN-alpha in primary DCs and found that IL-4 inhibited the initial phosphorylation of STAT1 and STAT2 (the transducers of signaling downstream of IFN-alpha and -beta receptors (IFNARs)) and reduced the up-regulation of genes involved in the amplification of the IFN response such as IRF-7, STAT1, STAT2, IFN-beta, and the IFNARs in vitro and in vivo. Therefore, IL-4 renders myeloid DCs less responsive to paracrine type I IFNs and less potent in sustaining the autocrine positive loop that normally amplifies the effects of type I IFNs. This inhibition could explain the increased susceptibility to viral infections observed during Th2-inducing parasitoses.
Fractographical Analysis on Fracture Mechanism of Stainless Steel Having Harmonic Microstructure (2012)

Mechanically milled stainless steel powder was applied to hot roll sintering (HRS) or hot isostatic pressing (HIP) processes. The mechanically milled powder has a bimodal structure with a severely deformed surface domain which is named as “Shell”, and an inner domain which is named as “Core”. The shell and core microstructure in the milled powder can be maintained even after sintering. As a result, microstructure of the HRS and HIP materials consists of a shell and core bimodal microstructure. Because severe plastic deformation mainly concentrates to the shell domain, a nano grain structure forms in the shell, while a coarse (meso) grain structure form in the core. Such a nano / meso harmonic structured material demonstrated not only superior strength but also a large elongation. The mechanical properties of the HRS and HIP materials were strongly influenced by the nano/meso harmonic microstructure, such as grain size of the shell/core and shell volume fraction. The shell had role of strengthening and core has role of ductility. Thus, the nano/meso harmonic microstructure has been proved to be very effective to improve mechanical properties of structure materials. In present study, a fracture and deformation mechanism of the harmonic microstructure stainless steel have been investigated through a delicate SEM observation. It was confirmed that fracture was initiated at second phase particles and then propagated along the shell/core interface.
Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague (2013)

Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19(th) and 20(th) centuries, during which plague was spread around the world, and the second pandemic of the 14(th)-17(th) centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6(th)-8(th) centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics.
The complete mitogenome and plastome of the haptophyte Pavlova lutheri NIVA-4/92 (2020)

The complete mitochondrial and plastid genomes of the microalga <i>Pavlova lutheri</i> strain NIVA-4/92 are reported. The circular-mapping mitogenome is 36,202 bp in length, contains 22 protein-coding genes, 24 <i>tRNAs</i>, and has a GC content of 37.5%. Like other haptophytes the mitogenome contains a single large, complex repeat region of approximately 5.4 kbp. The plastome is 95,281 bp in length and has a GC content of 35.6%. It contains 111 protein-coding genes and 27 tRNAs.
Two‐Photon Fluorescent Imaging of Myelination in the Spinal Cord (2012)

Myelination is a fundamental biological process in the vertebrate nervous system. Damage to or malformation of myelin can lead to various neurological diseases; for example, demyelination in the spinal cord is a major cause of paralysis of patients suffering from multiple sclerosis and related diseases. The ability to directly track myelin levels in the spinal cord is needed in order to assess the efficacy of therapeutics in promoting myelin repair. To address this unmet need, 4-((E)-4-((E)-4-aminostyryl)-2,5-dimethoxystyryl)-N-methylaniline, known as Case Imaging Compound (CIC), has been developed as a myelin-targeted fluorescent imaging agent that selectively binds to myelin. CIC was synthesized via an improved route and evaluated as a fluorescent probe for two-photon fluorescent imaging of myelin in the spinal cord in both demyelinated and dysmyelinated models. In vitro and ex vivo tissue staining both suggest that CIC selectively binds to in animal models. Further evaluation in animal models indicated that CIC is sensitive to differences in myelin content in healthy versus pathological myelin. CIC could potentially be useful in the development and evaluation of novel therapies for multiple sclerosis and other demyelinating diseases.
Nonlinear optical properties of polymeric materials (1987)

Abstract In this paper we discuss the molecular and macroscopic requirements for large second order nonlinear optical effects in polymeric systems. A new enhancement mechanism attributable to cooperative interactions between dipoles in polar polymer chains is proposed and tested by the synthesis and characterization of asymmetric condensation copolymers derived from p‐oxy‐α‐cyanocinnimate derivatives. An enhancement of a factor of 20 in electric field induced second harmonic generation relative to an equivalent concentration of chemically identical nonpolymerized chromophores in solution is obtained. Conformational and perhaps alignment restrictions in the rubbery state result in a reduction in alignment relative to what would be expected for an equivalent concentration of the polymerized chromophores in a moderately viscous medium. A model is proposed to account for the enhancement factors.
Accumulation of regulatory oxysterols, 32-oxolanosterol and 32-hydroxylanosterol in mevalonate-treated cell cultures. (1987)

In a previous publication (Saucier, S.E., A.A., Taylor, F.R., Spencer, T.A., Phirwa, S., and Gayen, A.K., J. Biol. Chem. (1985) 260, 14571-14579), we demonstrated that cultured Chinese hamster lung (Dede) cells contain 24(S),25-epoxycholesterol and 25-hydroxycholesterol in cellular concentrations within the range required to repress 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase. In this paper, we show that the addition to the culture medium of a concentration of mevalonate high enough to repress the reductase by 90% resulted in the appearance of two new regulatory oxysterols. The two new sterols are believed to be 32-oxolanosterol and 32-hydroxylanosterol on the basis of high performance liquid chromatography (HPLC) retention times and mass spectrometric and nuclear magnetic resonance spectroscopic data and by NaBH4 reduction of the putative aldehyde to material which had the HPLC retention time of the putative alcohol. The cellular concentrations of 24(S),25-epoxycholesterol and 25-hydroxycholesterol were not significantly changed by the presence of mevalonate. However, there was approximately a 30% increase in total HMG-CoA reductase repressor units which can be ascribed to the 32-oxolanosterol and 32-hydroxylanosterol, where 1 unit equals the repressor activity of 1 ng of 25-hydroxycholesterol. These results support the idea that the level of HMG-CoA reductase activity in growing cell cultures is determined by intracellular oxysterol metabolites and that relatively small changes in their numbers or concentrations can alter the level of HMG-CoA reductase activity.
Protein Cargo Encapsulation by Virus-Like Particles: Strategies and Applications (2022)

Viruses and the recombinant protein cages assembled from their structural proteins, known as virus-like particles (VLPs), have gained wide interest as tools in biotechnology and nanotechnology. Detailed structural information and their amenability to genetic and chemical modification make them attractive systems for further engineering. This review describes the range of non-enveloped viruses that have been co-opted for heterologous protein cargo encapsulation and the strategies that have been developed to drive encapsulation. Spherical capsids of a range of sizes have been used as platforms for protein cargo encapsulation. Various approaches, based on native and non-native interactions between the cargo proteins and inner surface of VLP capsids, have been devised to drive encapsulation. Here we outline the evolution of these approaches, discussing their benefits and limitations. Like the viruses from which they are derived, VLPs are of interest in both biomedical and materials applications. The encapsulation of protein cargo inside VLPs leads to numerous uses in both fundamental and applied biocatalysis and biomedicine, some of which are discussed herein. The applied science of protein encapsulating VLPs is emerging as a research field with great potential. Developments in loading control, higher order assembly, and capsid optimization are poised to realize this potential in the near future.
Why is the internet traffic bursty in short time scales? (2005)

Internet traffic exhibits multifaceted burstiness and correlation structure over a wide span of time scales. Previous work analyzed this structure in terms of heavy-tailed session characteristics, as well as TCP timeouts and congestion avoidance, in relatively long time scales. We focus on shorter scales, typically less than 100-1000 milliseconds. Our objective is to identify the actual mechanisms that are responsible for creating bursty traffic in those scales. We show that TCP self-clocking, joint with queueing in the network, can shape the packet interarrivals of a TCP connection in a two-level ON-OFF pattern. This structure creates strong correlations and burstiness in time scales that extend up to the Round-Trip Time (RTT) of the connection. This effect is more important for bulk transfers that have a large bandwidth-delay product relative to their window size. Also, the aggregation of many flows, without rescaling their packet interarrivals, does not converge to a Poisson stream, as one might expect from classical superposition results. Instead, the burstiness in those scales can be significantly reduced by TCP pacing. In particular, we focus on the importance of the minimum pacing timer, and show that a 10-millisecond timer would be too coarse for removing short-scale traffic burstiness, while a 1-millisecond timer would be sufficient to make the traffic almost as smooth as a Poisson stream in sub-RTT scales.
Interferometric Measurement of Vibration Amplitudes (1963)

As part of an investigation of contact-stress problems, it became necessary to build an interferometer to calibrate certain strain transducers. The strain under investigation was produced by simple harmonic stresses with loads consisting of internal energy dissipation. The calibration was performed under unloaded conditions. The results of this calibration gave confidence in the validity of the method used. The disappearing Fizeau fringe technique was used in the interferometric measurement of vibration amplitudes.
Tatouage perceptuel et adaptatif d'images fixes (2002)

National audience
Elegant studies of transplant-derived repair of cognitive performance (1995)

Abstract Cholinergic-rich grafts have been shown to be effective in restoring maze-learning deficits in rats with lesions of the forebrain cholinergic projection system. However, the relevance of those studies to developing novel therapies for Alzheimer's disease is questioned.
Globally Optimal Affine and Metric Upgrades in Stratified Autocalibration (2007)

We present a practical, stratified autocalibration algorithm with theoretical guarantees of global optimality. Given a projective reconstruction, the first stage of the algorithm upgrades it to affine by estimating the position of the plane at infinity. The plane at infinity is computed by globally minimizing a least squares formulation of the modulus constraints. In the second stage, the algorithm upgrades this affine reconstruction to a metric one by globally minimizing the infinite homography relation to compute the dual image of the absolute conic (DIAC). The positive semidefiniteness of the DIAC is explicitly enforced as part of the optimization process, rather than as a post-processing step. For each stage, we construct and minimize tight convex relaxations of the highly non-convex objective functions in a branch and bound optimization framework. We exploit the problem structure to restrict the search space for the DIAC and the plane at infinity to a small, fixed number of branching dimensions, independent of the number of views. Experimental evidence of the accuracy, speed and scalability of our algorithm is presented on synthetic and real data. MATLAB code for the implementation is made available to the community.
Separability of Density Matrices and Conditional Information Transmission (2000)

We give necessary and sufficient conditions under which a density matrix acting on a two-fold tensor product space is separable. Our conditions are given in terms of quantum conditional information transmission.
A light down conversion infrared scene projector (2015)

An infrared scene projector is described in this paper which based on light down conversion. The film transducer is the key device of the projector which is a free standing substrate and coated on one side with an absorbing optical black. The optical black coating absorbs the visible light and emits the infrared light. The emission spectrum is similar with the blackbody. The single pixel which is 25×25μm in sizes and 35um at intervals in a film transducer is realized by MEMS technology. The array size of the film transducer is more than 1024×1024 in a transducer of 76.2mm (3 inch) diameter. Illuminated by a visible light projector with different intensities, the gray scale is more than 200 and the equivalent black body temperature of the transducer could be varied in the range of 293K to 573K.
Supplementary Figure S2 from Targeting CD20<sup>+</sup> Aggressive B-cell Non–Hodgkin Lymphoma by Anti-CD20 CAR mRNA-Modified Expanded Natural Killer Cells <i>In Vitro</i> and in NSG Mice (2023)

&lt;p&gt;Supplementary Fig.S2: nucleofection of anti-CD20 CAR mRNA does not affect the expression of endogenous receptors on exPBNK cells PBNK cells were expanded ex vivo by co-culturing PBMC with irradiated geK562 feeder cell lines in the presence of 40 IU/mL IL-2 for 14 days and isolated by depleting CD3+ T cells. The expanded NK cells were nucleofected with anti-CD20 CAR mRNA (CAR) or without anti-CD20 CAR mRNA (mock). CAR exPBNK or MOCK exPBNK cells were stained with indicated monoclonal antibodies. The expression of receptors on viable exPBNK Cells were compared by flow cytometry analysis.&lt;/p&gt;
Evaluation of Seismic Performance Factors of Diagrid Structural System (2010)

As a new structural system, the diagrid system resists both gravity and lateral loads with diagonal columns. In current seismic design provisions, however, the response modification factor for a new structural system is not provided yet. ATC-63 provides a new methodology for defining various seismic performance factors, including the response modification factor. ATC-63 includes the collapse margin ratio in modifying the response modification factor, which can vary with many structural systems. In this paper, a non-linear static analysis and a dynamic analysis were conducted for four different diagrid models with 4-to 36-story heights. From these analyses, the response modification factor of the diagrid system was evaluated.
Novel Deep Glass Etched Microring Resonators Based on Silica-on-Silicon Technology (2006)

Microring resonators fabricated in silica-on-silicon technology using deep glass etching are demonstrated. The fabrication procedures are introduced and the transmission spectrum of a resonator is presented.
Visible light-degradable supramolecular gels comprising cross-linked polyrotaxanes capped with trithiocarbonate groups (2021)

Visible light-degradable supramolecular gels were designed using polyrotaxanes (PRXs) containing bulky trithiocarbonate groups as stopper molecules that are cleaved by visible light irradiation.
Supported CuO/Ce1−x Zr x O2 catalysts for the preferential oxidation of CO in H2-rich gases (2006)

The catalytic properties of CuO supported on ceria or ceria-zirconia mixed oxides have been investigated in the preferential oxidation of CO in H2-rich gases. CuO/CeO2 shows very high activity towards the oxidation of CO with a light-off temperature of about 70°C. This catalyst is very selective for the oxidation of CO rather than of H2 in the low temperature region (70–120°C), while at higher temperatures, the oxidation of hydrogen begins, causing of a maximum of CO conversion to arise with increasing temperature.
Cycloadditionsreaktionen mit α.β‐diheterosubstituierten Olefinen, I Reaktionen mit Sulfonylisocyanaten (1969)

Abstract Sulfonylisocyanate reagieren mit α.β‐disauerstoffsubstituierten Olefinen unter 1.2‐Addition zu 1‐Sulfonyl‐3.4‐dialkoxy‐azetidinon‐(2)‐Verbindungen 3 . Daneben bilden sich durch Substitution α.β‐ungesättigte N ‐Sulfonyl‐carbonsäureamid‐Verbindungen 4 . Mit Schwefel‐und Stickstoff‐substituierten Olefinen wird eine Azetidinon‐Bildung IR‐spektroskopisch nachgewiesen. Reaktionsweisen sowie kinetische Untersuchungen zur Bildung der β‐Lactam‐Derivate 3 werden beschrieben.