gebhart/patrepeval huggingface dataset:
A skull segmentation method for brain MR images based on multiscale bilateral filtering scheme (2010)

We present a novel automatic segmentation method for the skull on brain MR images for attenuation correction in
combined PET/MRI applications. Our method transforms T1-weighted MR images to the Radon domain and then
detects the feature of the skull. In the Radon domain we use a bilateral filter to construct a multiscale images series. For
the repeated convolution we increase the spatial smoothing at each scale and make the cumulative width of the spatial
and range Gaussian doubled at each scale. Two filters with different kernels along the vertical direction are applied along
the scales from the coarse to fine levels. The results from a coarse scale give a mask for the next fine scale and supervise
the segmentation in the next fine scale. The method is robust for noise MR images because of its multiscale bilateral
filtering scheme. After combining the two filtered sinogram, the reciprocal binary sinogram of the skull is obtained for
the reconstruction of the skull image. We use the filtered back projection method to reconstruct the segmented skull
image. We define six metrics to evaluate our segmentation method. The method has been tested with brain phantom data,
simulated brain data, and real MRI data. Evaluation results showed that our method is robust and accurate, which is
useful for skull segmentation and subsequently for attenuation correction in combined PET/MRI applications.
Acetate-Bridged Platinum(III) Complexes Derived from Cisplatin (2012)

Oxidation of the acetate-bridged half-lantern platinum(II) complex cis-[Pt(II)(NH(3))(2)(μ-OAc)(2)Pt(II)(NH(3))(2)](NO(3))(2), [1](NO(3))(2), with iodobenzene dichloride or bromine generates the halide-capped platinum(III) species cis-[XPt(III)(NH(3))(2)(μ-OAc)(2)Pt(III)(NH(3))(2)X](NO(3))(2), where X is Cl in [2](NO(3))(2) or Br in [3](NO(3))(2), respectively. These three complexes, characterized structurally by X-ray crystallography, feature short (≈2.6 Å) Pt-Pt separations, consistent with formation of a formal metal-metal bond upon oxidation. Elongated axial Pt-X distances occur, reflecting the strong trans influence of the metal-metal bond. The three structures are compared to those of other known dinuclear platinum complexes. A combination of (1)H, (13)C, (14)N, and (195)Pt NMR spectroscopy was used to characterize [1](2+)-[3](2+) in solution. All resonances shift downfield upon oxidation of [1](2+) to [2](2+) and [3](2+). For the platinum(III) complexes, the (14)N and (195)Pt resonances exhibit decreased line widths by comparison to those of [1](2+). Density functional theory calculations suggest that the decrease in the (14)N line width arises from a diminished electric field gradient at the (14)N nuclei in the higher valent compounds. The oxidation of [1](NO(3))(2) with the alternative oxidizing agent bis(trifluoroacetoxy)iodobenzene affords the novel tetranuclear complex cis-[(O(2)CCF(3))Pt(III)(NH(3))(2)(μ-OAc)(2)Pt(III)(NH(3))(μ-NH(2))](2)(NO(3))(4), [4](NO(3))(4), also characterized structurally by X-ray crystallography. In solution, this complex exists as a mixture of species, the identities of which are proposed.
Direct-write orientation of charge-transfer liquid crystals enables polarization-based coding and encryption (2020)

Optical polarizers encompass a class of anisotropic materials that pass-through discrete orientations of light and are found in wide-ranging technologies, from windows and glasses to cameras, digital displays and photonic devices. The wire-grids, ordered surfaces, and aligned nanomaterials used to make polarized films cannot be easily reconfigured once aligned, limiting their use to stationary cross-polarizers in, for example, liquid crystal displays. Here we describe a supramolecular material set and patterning approach where the polarization angle in stand-alone films can be precisely defined at the single pixel level and reconfigured following initial alignment. This capability enables new routes for non-binary information storage, retrieval, and intrinsic encryption, and it suggests future technologies such as photonic chips that can be reconfigured using non-contact patterning.
Fluorinated Nanodiamond as a Wet Chemistry Precursor for Diamond Coatings Covalently Bonded to Glass Surface (2005)

The chemical reaction between fluoro-nanodiamond (F-ND) powder, solubilized in o-dichlorobenzene, and a glass surface, functionalized with the silane coupling agent, 3-aminopropyltriethoxysilane (APTES), was found to proceed under heating at 130 degrees C for 24-40 h and to result in covalent bonding of F-ND particles to a glass substrate, forming a 10-40 nm thick nanocrystalline film. The observed process presents a novel and cost-effective approach to fabrication of diamond coatings on glass by using wet chemistry instead of CVD and can be extended to other materials.
Scanning Electrochemical Microscopy: High‐Resolution Deposition and Etching of Metals (1989)

Electrochemical methods for the high resolution etching of metals as well as the deposition of metals in polymer films and on conducting substrates are presented. These faradaic processes were carried out with a scanning electrochemical microscope (SECM) (similar in design to the scanning tunneling microscope) and different ionically conducting polymer films such as Nafion, poly(4‐vinylpyridine), and poly(bis‐(methoxyethoxyethoxide)phosphazene) on the substrate. Continuous patterns of silver, gold, copper, and palladium were deposited, and copper, silver, and gold were etched with widths in the submicron range. The use of polymer‐coated substrate electrodes to deposit and etch metals is compared to depositions and etchings performed in electrolyte solutions.
Endothelial cell-derived, secreted long non-coding RNAs <i>Gadlor1</i> and <i>Gadlor2</i> aggravate pathological cardiac remodeling via intercellular crosstalk (2022)

Abstract Background Pathological overload triggers maladaptive myocardial remodeling that leads to heart failure. Recent studies have shown that long non-coding RNAs (lncRNAs) regulate cardiac remodeling. This study investigates two recently discovered, secreted lncRNAs, Gadlor1 and Gadlor2 ( Gadlor 1/2 ). Methods We generated compound Gadlor 1/2 knock-out (KO) mice and compared their response to pressure overload by transverse aortic constriction (TAC) to that of wild-type (WT) littermates. Endothelial cells, fibroblasts and cardiomyocytes were isolated from the hearts of both genotypes after TAC and their transcriptome was investigated by RNA sequencing. Gadlor target proteins were identified by RNA antisense purification coupled with mass spectrometry (RAP-MS) in cardiomyocytes. In addition, we investigated the effects of cardiac overexpression of Gadlor1 / 2 . Results Gadlor1/2 are jointly upregulated in failing mouse hearts as well as in the myocardium of heart failure patients. Cardiac overexpression of Gadlor1 and Gadlor2 aggravated myocardial dysfunction and enhanced hypertrophic and fibrotic remodeling in mice exposed to pressure overload. Compound Gadlor1/2 KO mice, in turn, exerted markedly reduced myocardial hypertrophy, fibrosis and dysfunction, but more angiogenesis during short and long-standing pressure overload. Paradoxically, Gadlor1/2 KO mice suffered from sudden death during prolonged overload, possibly due to cardiac arrhythmia. Gadlor1 and Gadlor2 , which are mainly expressed in endothelial cells (ECs) in the heart, where they inhibit pro-angiogenic gene-expression, are strongly secreted within extracellular vesicles (EVs). These EVs transfer Gadlor lncRNAs to cardiomyocytes, where they bind and activate calmodulin-dependent kinase II, induce pro-hypertrophic gene-expression and enhance calcium re-uptake into the sarcoplasmic reticulum. Conclusion Gadlor1 and Gadlor2 are lncRNAs that are mainly enriched in EC-derived EVs and are jointly upregulated in mouse and human hearts during pathological overload. We reveal a crucial endothelial cell-cardiomyocyte crosstalk, which aims at restoring calcium homeostasis in cardiomyocytes during overload at the cost of aggravated hypertrophy and fibrosis.
Privacy-Preserving Musical Database Matching (2007)

In this paper we present an illustratory process which allows privacy-preserving transactions in the context of musical databases. In particular we address the problem of matching a piece of music audio to a service database in such a way such that the database provider will not directly observe the query, nor its result, thereby preserving the privacy of the inquirer. We formulate this process within the field of secure multiparty computation and show how such a transaction can be achieved once we derive secure versions of basic signal processing operations.
BER Estimation in Optical Fiber Transmission Systems Employing All-Optical 2R Regenerators (2004)

A bit error rate estimation method for optical fiber transmission systems employing all-optical 2R regenerators is presented. The method is based on the linearization of the nonlinear transfer function of the regenerators in three sections. Using this linearized three-section model, the impact of 2R regeneration on the system performance as a function of the extinction ratio, the clamping factor, and the steepness of the transfer function is studied.
Mobile one‐time passwords: two‐factor authentication using mobile phones (2011)

ABSTRACT Static password authentication has security drawbacks. In two‐factor authentication (2FA,) each user carries a device, called token, to generate passwords that are valid only one time. 2FA based on one‐time passwords (OTPs) provides improved protection because users are prompted to provide something they know (i.e., PIN) and something they have (i.e., token). Many systems have satisfied the 2FA requirements by sending an OTP through an SMS to the user's phone device. Unfortunately, international roaming, and SMS costs, delays, and security put restrictions on this system reliability. Also, time synchronous‐based solutions are not applicable for mobile phones. In this paper, we present a novel 2FA scheme whereby multiple OTPs are being produced by utilizing an initial seed and two different nested hash chains: one dedicated to seed updating and the other used for OTP production. We overcome all the restrictions that come from other techniques. We analyze our proposal from the viewpoint of security and performance compared with the other algorithms. Copyright © 2011 John Wiley & Sons, Ltd.
Shock Electrodeposition in Charged Porous Media (2015)

It is shown that surface conduction in porous media can drastically alter the stability and morphology of electrodeposition at high rates, above the diffusion-limited current. Copper electrodeposits are visualized by scanning electron microscopy and energy dispersive spectroscopy in cellulose nitrate membranes, whose pores are coated with positive or negative charged polymers. Above the limiting current, surface conduction inhibits growth in the positive membrane and produces irregular dendrites, while it enhances growth and suppresses dendrites behind a deionization shock in the negative membrane. The discovery of uniform growth contradicts quasi-steady leaky membrane models, which are in the same universality class as unstable Laplacian growth, and indicates the importance of transient electro-diffusion or electro-osmotic dispersion. Shock electrodeposition could be exploited for high-rate recharging of metal batteries or manufacturing of metal matrix composite coatings.
Temperature Effect on NMR Surface Relaxation in Rocks for Well Logging Applications (2002)

We present nuclear spin-relaxation experiments, at various temperatures and Larmor frequencies for water and oil confined in a series of calibrated porous media and various natural rocks. The temperature and frequency dependencies of the longitudinal nuclear spin relaxation rates 1/T1 are interpreted with an original model of surface diffusion taking into account the solid−liquid interactions with the pore surface. Depending of the strength of such interactions, one observes an anomalous temperature dependence of the transverse 1/T2 and longitudinal 1/T1 nuclear spin-relaxation rates for water in silica and various sandstones and a normal temperature behavior for water-saturated calcium carbonate surfaces. The model supports also the normal temperature dependence observed for oil saturated porous media at proximity of silica, sandstone, and carbonate surfaces. The potential impact of this study for NMR well logging applications is also discussed.
The Efficacy of a<i>Salmonella typhi</i>Vi Conjugate Vaccine in Two-to-Five-Year-Old Children (2001)

The Vi-rEPA conjugate typhoid vaccine is safe and immunogenic and has more than 90 percent efficacy in children two to five years old. The antibody responses and the efficacy suggest that this vaccine should be at least as protective in persons who are more than five years old.
Device Placement Optimization with Reinforcement Learning (2017)

The past few years have witnessed a growth in size and computational requirements for training and inference with neural networks. Currently, a common approach to address these requirements is to use a heterogeneous distributed environment with a mixture of hardware devices such as CPUs and GPUs. Importantly, the decision of placing parts of the neural models on devices is often made by human experts based on simple heuristics and intuitions. In this paper, we propose a method which learns to optimize device placement for TensorFlow computational graphs. Key to our method is the use of a sequence-to-sequence model to predict which subsets of operations in a TensorFlow graph should run on which of the available devices. The execution time of the predicted placements is then used as the reward signal to optimize the parameters of the sequence-to-sequence model. Our main result is that on Inception-V3 for ImageNet classification, and on RNN LSTM, for language modeling and neural machine translation, our model finds non-trivial device placements that outperform hand-crafted heuristics and traditional algorithmic methods.
Development of androgen resistance in mouse mammary tumor cells can be prevented by the antiandrogen flutamide (1987)

As has been clearly demonstrated in prostate and breast cancer, progression to hormone insensitivity is a major problem responsible for the usually partial and short-lived response to antihormonal therapy. Preincubation of androgen-sensitive Shionogi mouse carcinoma cells for 15 days in the absence of androgens causes the development of complete resistance of cell growth to androgens. Of potentially important therapeutic significance is the finding that androgen sensitivity can be maintained not only by the androgen dihydrotestosterone (DHT) but also by incubation with the pure antiandrogen Flutamide-OH in the absence of androgens. Since androgen resistance is one of the main problems facing the treatment of prostate cancer, the possibility of avoiding or at least delaying the development of androgen resistance with a pure antiandrogen could well provide the basis for improving the success of therapy for this disease.
Cardiac Abnormalities in Diabetic Patients With Neuropathy (2004)

OBJECTIVE—The goal of this study was to determine whether treatment with an aldose reductase inhibitor (ARI) has beneficial effects on asymptomatic cardiac abnormalities in diabetic patients with neuropathy. RESEARCH DESIGN AND METHODS—Diabetic subjects with neuropathy (n = 81) with either a low diastolic peak filling rate or impaired augmentation of left ventricular (LV) ejection fraction (LVEF) during maximal bicycle exercise were identified by gated radionuclide ventriculography. Coronary artery disease, left ventricular hypertrophy, and valvular heart disease were excluded by clinical evaluation, myocardial perfusion imaging, and echocardiography. Subjects were randomized to receive blinded treatment with either the placebo or the ARI zopolrestat 500 or 1,000 mg daily for 1 year. RESULTS—After 1 year of ARI treatment, there were increases in resting LVEF (P &lt; 0.02), cardiac output (P &lt; 0.03), LV stroke volume (P &lt; 0.004), and exercise LVEF (P &lt; 0.001). In placebo-treated subjects, there were decreases in exercise cardiac output (P &lt; 0.03), stroke volume (P &lt; 0.02), and end diastolic volume (P &lt; 0.04). Exercise LVEF increased with ARI treatment independent of blood pressure, insulin use, or the presence of baseline abnormal heart rate variability. There was no change in resting diastolic filling rates in either group. CONCLUSIONS—Diabetic patients with neuropathy have LV abnormalities that can be stabilized and partially reversed by ARI treatment.
Perturbation of Lipopolysaccharide (LPS) Micelles by Sushi 3 (S3) Antimicrobial Peptide (2004)

S3 peptide, derived from the Sushi 3 domain of Factor C, which is the lipopolysaccharide (LPS)-sensitive serine protease of the horseshoe crab coagulation cascade, was shown previously to harbor antimicrobial activity against Gram-negative bacteria. However, the mechanism of action remains poorly understood at the molecular level. Here we demonstrate that the intermolecular disulfide bonding of S3 resulting in S3 dimers is indispensable for its interaction with LPS. The binding properties of the S3 monomer and dimer to LPS were analyzed by several approaches including enzyme-linked immunosorbent assay (ELISA)-based assay, surface plasmon resonance, and fluorescence correlation spectroscopy (FCS). It is evident that the S3 dimer exhibits stronger binding to LPS, demonstrating 50% LPS-neutralizing capability at a concentration of 1 mum. Circular dichroism spectrometry revealed that the S3 peptide undergoes conformational change in the presence of a disulfide bridge, transitioning from a random coil to beta-sheet structure. Using a fluorescence correlation spectroscopy monitoring system, we describe a novel approach for examining the mechanism of peptide interaction with LPS in the native environment. The strategy shows that intermolecular disulfide bonding of S3 into dimers plays a critical role in its propensity to disrupt LPS micelles and consequently neutralize LPS activity. S3 dimers display detergent-like properties in disrupting LPS micelles. Considering intermolecular disulfide bonds as an important parameter in the structure-activity relationship, this insight provides clues for the future design of improved LPS-binding and -neutralizing peptides.
Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus (2018)

The methodological pipeline described here is adequate to characterize in-depth mutant spectra of HCV populations, and it provides a tool to understand HCV diversification and treatment failures. The pipeline can be periodically extended in the event of HCV diversification into new genotypes or subtypes, and provides a framework applicable to other RNA viral pathogens, with potential to couple detection of drug-resistant mutations with treatment planning.
Tuberculosis Subunit Vaccination Provides Long-Term Protective Immunity Characterized by Multifunctional CD4 Memory T Cells (2009)

Improved vaccines capable of promoting long-term cellular immunity are urgently required for a number of diseases that remain global health problems. In the present study, we demonstrate that a tuberculosis subunit vaccine, Ag85B-ESAT-6/CAF01 (where ESAT-6 is early secreted antigenic target of 6 kDa and CAF01 is cationic adjuvant formulation 01), induces very robust memory CD4 T cell responses that are maintained at high levels for >1 year postvaccination. This long-term, vaccine-induced memory response protects against a challenge with Mycobacterium tuberculosis at levels that are comparable to or better than those of bacillus Calmette-Guérin. Characterization of the CD4 memory T cells by multicolor flow cytometry demonstrated that the long-lived memory population consisted almost exclusively of TNF-alpha(+)IL-2(+) and IFN-gamma(+)TNF-alpha(+)IL-2(+) multifunctional T cells. In addition, memory cells isolated >1 year postvaccination maintained a strong, vaccine-specific proliferative potential. Long-term memory induced by the BCG vaccine contained fewer multifunctional T cells and was biased toward effector cells mainly of the TNF-alpha(+)IFN-gamma(+)-coexpressing subset. Ag85B-ESAT-6/CAF01 vaccination very efficiently sustained multifunctional CD4 T cells that accumulated at the site of infection after M. tuberculosis challenge, whereas the response in unvaccinated animals was characterized by CD4 effector T cells. Our data demonstrate that adjuvanted subunit vaccines can promote long-term protective immune responses characterized by high levels of persisting multifunctional T cells and that the quality and profile of this response is sustained postinfection.
A Human Pluripotent Stem Cell-Based Screen for Smooth Muscle Cell Differentiation and Maturation Identifies Inhibitors of Intimal Hyperplasia (2019)

Contractile to synthetic phenotypic switching of smooth muscle cells (SMCs) contributes to stenosis in vascular disease and vascular transplants. To generate more contractile SMCs, we performed a high-throughput differentiation screen using a MYH11-NLuc-tdTomato human embryonic stem cell reporter cell line. We identified RepSox as a factor that promotes differentiation of MYH11-positive cells by promoting NOTCH signaling. RepSox induces SMCs to exhibit a more contractile phenotype than SMCs generated using PDGF-BB and TGF-β1, two factors previously used for SMC differentiation but which also cause intimal hyperplasia. In addition, RepSox inhibited intimal hyperplasia caused by contractile to synthetic phenotypic switching of SMCs in a rat balloon injury model. Thus, in addition to providing more contractile SMCs that could prove useful for constructing artificial blood vessels, this study suggests a strategy for identifying drugs for inhibiting intimal hyperplasia that act by driving contractile differentiation rather than inhibiting proliferation non-specifically.
On-chip Test Acceleration for Advanced Technologies (2021)

A novel on-chip test acceleration method was developed to speed up addressable test chip measurements. Co-optimized with tester hardware, a sustained test speed of up to 40,000 items per second was achieved, corresponding to 30X of a traditional test setup. This method was employed to address critical test challenges during both technology development and mass production phases of advanced technologies.
Sublocalization of the human interferon-gamma receptor accessory factor gene and characterization of accessory factor activity by yeast artificial chromosomal fragmentation. (1994)

A chromosomal fragmentation procedure was employed to produce a deletion set of yeast artificial chromosomes (YACs) from a parental YAC, GART D142H8, known to map to human chromosome 21q and to encode the human interferon-gamma receptor (Hu-IFN-gamma R) accessory factor gene as well as the phosphoribosylglycinamide formyltransferase (GART) gene. When expressed in Chinese hamster ovary cells, these deleted YACs retain accessory factor activity, as judged by major histocompatibility complex class I antigen inducibility, until the deletions from the acentric end exceed 390 kilobases (kb). Therefore, the accessory factor (AF-1) gene can be localized to a 150-kb region at the left (centric) end of the parental 540-kb GART YAC. Cells containing functional YACs are also able to induce the ISGF3 gamma and gamma-activated factor (GAF) transcription factors, but were not protected against encephalomyocarditis virus (EMCV) upon treatment with Hu-IFN-gamma. Therefore, the Hu-IFN-gamma R and the AF-1 are sufficient for some, but not all, of the actions of Hu-IFN-gamma. We postulate that an additional accessory factor (AF-2) required for antiviral activity against EMCV is encoded on chromosome 21q.