gebhart/patrepeval huggingface dataset:
Minimum complexity regression estimation with weakly dependent observations (1996)

The minimum complexity regression estimation framework (Barron, 1991; Barron and Cover, 1991 and Rissanen, 1989) is a general data-driven methodology for estimating a regression function from a given list of parametric models using independent and identically distributed (i.i.d.) observations. We extend Barron's regression estimation framework to m-dependent observations and to strongly mixing observations. In particular, we propose abstract minimum complexity regression estimators for dependent observations, which may be adapted to a particular list of parametric models, and establish upper bounds on the statistical risks of the proposed estimators in terms of certain deterministic indices of resolvability. Assuming that the regression function satisfies a certain Fourier-transform-type representation, we examine minimum complexity regression estimators adapted to a list of parametric models based on neural networks and by using the upper bounds for the abstract estimators, we establish rates of convergence for the statistical risks of these estimators. Also, as a key tool, we extend the classical Bernstein inequality from i.i.d. random variables to m-dependent processes and to strongly mixing processes.
Effective treatment of SIVcpz-induced immunodeficiency in a captive western chimpanzee (2017)

These data demonstrate that SIVcpz can cause immunodeficiency and other hallmarks of AIDS in captive chimpanzees, including P. t. verus apes that are not naturally infected with this virus. Moreover, SIVcpz-associated immunodeficiency can be effectively treated with antiretroviral therapy, although sufficiently high plasma concentrations must be maintained to prevent the emergence of drug resistance. These findings extend a growing body of evidence documenting the immunopathogenicity of SIVcpz and suggest that experimentally infected chimpanzees may benefit from clinical monitoring and therapeutic intervention.
Stationary Positron Emission Tomography and Its Image Reconstruction (1986)

Feasibility of stationary positron emission tomography (PET) using discrete detectors has been investigated by simulation studies. To enable full utilization of detector resolution, a "bank array" of detectors is proposed and an EM algorithm is adopted for image reconstruction. The bank array consists of an odd number of detector banks arranged on a circular ring with a gap equal to one half the detector width. The EM algorithm [11] is used with some modifications for reducing the quantity of computation, improving the convergence speed, and suppressing statistical noise, so as to meet the present purpose. Simulation studies involving several phantoms show that the stationary PET with the new detector array provides image quality which is good enough for clinical applications. For fast dynamic studies with low spatial resolution, the convolution-backprojection method is efficient, but for high-resolution static imaging, resolution enhancement by an iterative method is required. Problems arising in the corrections for attenuation of photons and detector sensitivity, etc., are also discussed. A totally stationary PET avoids the mechanical problems associated with accurate movement of heavy assemblies and is particularly advantageous in gated cardiac imaging or in fast dynamic studies. Elimination of a scan along the detector plane allows a quick scan in the axial direction to achieve three-dimensional imaging with a small number of detector rings.
Effects of Chromophore Functionalization and Physical Aging during Poling on Chromophore Orientational Dynamics in Poly(arylene ether)s for Second-Order Nonlinear Optics (1996)

The structure/property relationships including the effects of chromophore functionalization and physical aging during poling on the chromophore orientational dynamics and intermolecular cooperativity in a class of poly(arylene ether)s are discussed. Second-order nonlinear optics is used to examine the thermal and temporal stability of chromophore orientation in the poled polymer films as a function of processing.
Exomic Sequencing of Four Rare Central Nervous System Tumor Types (2013)

A heterogeneous population of uncommon neoplasms of the central nervous system (CNS) cause significant morbidity and mortality. To explore their genetic origins, we sequenced the exomes of 12 pleomorphic xanthoastrocytomas (PXA), 17 non-brainstem pediatric glioblastomas (PGBM), 8 intracranial ependymomas (IEP) and 8 spinal cord ependymomas (SCEP). Analysis of the mutational spectra revealed that the predominant single base pair substitution was a C:G>T:A transition in each of the four tumor types. Our data confirm the critical roles of several known driver genes within CNS neoplasms, including TP53 and ATRX in PGBM, and NF2 in SCEPs. Additionally, we show that activating BRAF mutations play a central role in both low and high grade glial tumors. Furthermore, alterations in genes coding for members of the mammalian target of rapamycin (mTOR) pathway were observed in 33% of PXA. Our study supports the hypothesis that pathologically similar tumors arising in different age groups and from different compartments may represent distinct disease processes with varied genetic composition.
TUNABLE MICROSTRIP FILTERS USING SELECTIVELY ETCHED FERROELECTRIC THIN-FILM VARACTORS FOR COUPLING (2010)

ABSTRACT We report on the use of patterned ferroelectric films to fabricate proof of concept tunable one-pole microstrip filters with excellent transmission and mismatch/reflection properties at frequencies up to 24 GHz. By controlling the electric field distribution within the coupling region between the resonator and input/output lines, sufficiently high loaded and unloaded Q values are maintained so as to be useful for microstrip filter design, with low mismatch loss. In the 23–24 GHz region, the filter was tunable over a 100 MHz range, the loaded and unloaded Q values were 29 and 68, respectively, and the reflection losses were below −16 dB, which demonstrates the suitability of these films for practical microwave applications.
Removal and Sequestration of Iodide From Alkaline Solutions Using Silver-Doped Carbon Nanotubes (2011)

The long-lived radioactive isotope iodine-129 that is associated with nuclear fuel cycle processes is becoming an increasing concern to human health and the environment due to difficulties in separating it from other nuclear wastes and the projected long- term risks. We have investigated the reaction of iodide in alkaline solutions with silver doped carbon nanotubes (Ag-CNTs) as a means of addressing concerns associated with this radioisotope. An in situ CNT doping technique, where the silver is added to the CNT during the chemical vapor deposition process, and a chemical filling process, where silver is added to the CNTs by solution contact followed by reduction under heat, were used to synthesize the Ag-CNTs. The iodide adsorption behavior of the Ag-CNTs appeared to be largely controlled by the silver content of the CNTs. In situ doping techniques resulted in silver contents of <0.0025 percent by weight, whereas chemical filling resulted in silver contents of almost 20 percent by weight. These chemically filled Ag-CNTs exhibited a sorption capacity of 458 ± 73 mg iodide/g CNT that was an order of magnitude greater than commercially available silver impregnated activated carbon tested in this study. Leaching of iodine from the reacted Ag-CNTs was below the method detection limit when a molar excess of silver was present and is consistent with an iodide release that is controlled by the sparingly soluble silver iodide solid. The properties of high sorption capacity and small iodine leaching of these Ag-CNTs make this material a potentially useful sorbent for application in nuclear waste separation processes and waste disposal systems.
Varying Assay Geometry to Emulate Connective Tissue Planes in an In Vitro Model of Acupuncture Needling (2010)

During traditional acupuncture, fine needles are inserted subcutaneously and rotated, which causes loose fascial tissue to wind around the needle. This coupling is stronger at acupuncture points, which tend to fall above intermuscular fascial planes, than control points, which lay above skeletal muscle. These different anatomical constraints may affect the mechanical coupling. Fascia at acupuncture points is bounded on two sides by skeletal muscle, but at control points is essentially unbounded. These differences were approximated in simple in vitro models. To emulate the narrower boundary within the intermuscular plane, type I collagen was cast in circular gels of different radii. To model the channel-like nature of these planes, collagen was cast in elliptical gels with major and minor axes matching the large and small circular gels, respectively, and in planar gels constrained on two sides. Acupuncture needles were inserted into the gels and rotated via a computer-controlled motor while capturing the evolution of fiber alignment under cross-polarization. Small circular gels aligned faster, but failed earlier than large circular gels. Rotation in elliptical and planar gels generated more alignment-per-revolution than circular gels. Planar gels were particularly resistant to failure. Fiber alignment in circular gels was isotropic, but was stronger in the direction of the minor axis in elliptical and planar gels. In fibroblast-populated gels, cells followed the alignment of the collagen fibers, and also became denser in regions of stronger alignment. These results suggest that the anatomy at acupuncture points provides unique boundaries that accentuate the mechanical response to needle manipulation.
Jacques Banchereau, PhD: A Conversation with Michael Ramsay, MD, President of Baylor Research Institute (2006)

Dr. Jacques Banchereau (Figure ​(Figure11) is director of the Baylor Institute for Immunology Research (BIIR) and holds the Caruth Chair for Transplantation Immunology Research. He received his PhD in biochemistry from the University of Paris in 1980 and later served as director of the Schering-Plough Laboratory for Immunological Research in Dardilly, near Lyon, France. While there, he discovered, with his colleagues at DNAX in California, a large panel of novel interleukins, molecules that assist in regulating T-cell functions. He was among the first to discover how to grow human dendritic cells (Figure ​(Figure22). Dr. Banchereau came to Baylor in 1996 to develop BIIR. He has served on the National Institutes of Health's (NIH's) Experimental Immunology Study Section, Center for Scientific Review. He has authored or coauthored more than 260 papers in major international journals and 160 book chapters and reviews; many of his publications are highly cited. Dr. Banchereau is a frequent speaker at national and international scientific conferences. His research interests focus on human immunology, particularly dendritic cell biology, genomic approaches to the diagnosis of human diseases, the pathophysiology of autoimmune diseases and cancer, and the design of novel vaccines.
Effect of imaging parameters on the echoes from ultrasonic contrast agents (2002)

High-resolution contrast-assisted techniques would facilitate differentiation of tissue and microbubble echoes. The authors have found that for the same transmitted time-averaged intensity, the wideband transmission produces an equal or higher received echo intensity from the contrast agent. Thus a wideband imaging scheme could be as effective as the more traditional narrowband technique. In addition, the transmission of wideband high intensity pulses is shown to produce a consistent time domain echo from the microbubbles. This echo is the same whether the bubbles break or remain intact over several pulses. A change in the phase of the transmitted pulse is shown to leave the polarity of the received signal unchanged under a set of experimental conditions.
Modeling of OxRAM variability from low to high resistance state using a stochastic trap assisted tunneling-based resistor network (2015)

In this work, a model is proposed to explain the variability of OxRAM devices, both in their high and low resistive states. This model is based on the calculation of a 3D resistance network, using trap assisted tunneling current. The stochastic nature of the resistance is captured by random placement of traps within a specific spatial distribution.
Differential Production of Interleukin 10 during Human Immunodeficiency Virus Infection (1996)

Interleukin 10, a product of T and B cells and monocytes, displays many Th2-like properties through inhibition of Th1 cell functions. Interleukin 10 is thought to play a major role in the immune dysfunction seen in HIV-infected individuals. In this study, we evaluated in detail the production of IL-10 during HIV infection. Although the constitutive production of IL-10 did not differ in PBMCs from healthy donors and HIV-infected individuals, IL-10 was differentially produced in response to polyclonal activators. The overall plasma IL-10 levels were similar in 32 controls and 67 patients at different stages of the disease and receiving different antiretroviral drugs. However, patients with low CD4 T cell count (< 200/mm3) secreted approximately three-fold more IL-10 than did patients with high CD4 T cell count (> 500/mm3). Competitive/quantitative PCR revealed similar levels of mRNA expression in PBMCs from controls and HIV-infected individuals. In vitro HIV infection rapidly and transiently induced IL-10 production in PBMCs and monocytes, and the low level of endogenously secreted IL-10 failed to inhibit HIV replication in acutely infected monocytes. On the other hand, HIV infection of selected CD4+ T cell clones generated in a Th1- or Th2-like environment, differentially up-regulated IL-10 production, with significantly higher production by Th2 clones. Together, our data indicate that IL-10 production is more complex than previously thought, and may depend on several factors such as producer cells, nature of the stimuli, as well as viral isolates.
Femtomole Detection of Proteins Using a Label-Free Nanostructured Porous Silicon Interferometer for Perspective Ultrasensitive Biosensing (2016)

Nanostructured porous silicon (PS) is a promising material for label-free optical detection of biomolecules, though it currently suffers of limited clinical diagnostic applications due to insufficient sensitivity. In this regard, here we introduce an ultrasensitive and robust signal processing strategy for PS biosensors that relies on the calculation of the average value over wavelength of spectral interferograms, namely IAW, obtained on PS interferometer by subtraction (wavelength by wavelength) of reflection spectra acquired after adsorption of biomolecules inside the nanopores from a reference reflection spectrum recorded in acetate buffer. As a case study, we choose to monitor bovine serum albumin (BSA) unspecific adsorption, which has been often employed in the literature as a model for proof-of-concept studies of perspective biosensing applications. The proposed IAW signal processing strategy enables reliable detection of BSA at concentrations in the range from 150 pM to 15 μM (down to 3 orders of magnitude lower than those targeted in the current literature) using a PS interferometer operating in label-free mode without any amplification strategies, with good sample-to-sample reproducibility over the whole range of tested concentrations (%CV = 16% over 5 replicates) and good signal-to-noise ratio also at the lowest tested concentration (S/N ≈ 4.6 at 150 pM). A detection limit (DL) of 20 pM (20 femtomoles, 1 mL) is estimated from the sigmoidal function best fitting (R(2) = 0.989) IAW experimental data over the whole range of tested concentrations. This is the lowest DL that has been reported in the literature since the seminal paper of Sailor and co-workers (1997) on the use of PS interferometer for biosensing, and lowers of 4 orders of magnitude DL attained with label-free PS interferometers using conventional effective optical thickness (EOT) calculation through reflective interferometric Fourier transform spectroscopy. Accordingly, the IAW signal processing strategy envisage bringing PS optical transduction at the forefront of ultrasensitive label-free biosensing techniques, especially for point-of-care clinical analysis where low analyte concentrations have to be detected in a small amount of biological samples.
Self-forming diffusion barrier layer in Cu–Mn alloy metallization (2005)

Advancement of semiconductor devices requires the realization of an ultrathin diffusion barrier layer between Cu interconnect and insulating layers. The present work investigated the possibility of the self-forming barrier layer in Cu–Mn alloy thin films deposited directly on SiO2. After annealing at 450 °C for 30 min, a Mn containing amorphous oxide layer of 3–4 nm in thickness was formed uniformly at the interface. Residual Mn atoms were removed to form a surface oxide layer, leading to a drastic resistivity decrease of the film. No interdiffusion was detected between Cu and SiO2 within the detection limit of x-ray energy dispersive spectroscopy.
Flow Cytometric Detection and Quantitation of Cell–Cell Electrofusion Products (2003)

Cell-cell electrofusion (CCE) is a process that involves forcing cells into close juxtaposition and then inducing fusion by delivering electric pulses to the cells. CCE has proven to have many practical applications. It has been used for monoclonal antibody (Mab) production (4,5), hybridoma production (1–3), and membrane surface marker transfer (6). Many other applications are described in this volume. In addition, the study of membrane fusion mechanisms has been the focus of some researchers (7–12). Electrofusion techniques seldom result in 100% yields between fusion partners. Therefore, a major aspect of all CCE applications is the ability to detect and quantitate fusion products.
A General Solution Route toward Metal Boride Nanocrystals (2011)

Eine Frage der Einstellung: Ein Ionothermalprozess unter relativ milden Bedingungen (500–900 °C) ergibt die erste vielseitige Route zu Metallhexaboriden, -tetraboriden und -diboriden sowie niedrigeren Metallboriden (siehe Bild; M=Ca, Ce, Mo, Nb, Hf, Fe, Mn). Durch gezielte Einstellung der Nanopartikelgröße und Materialstrukturierung gelingt die Feineinstellung dieser Funktionsmaterialien. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ERSFQ 4-to-16 Decoder for Energy-Efficient RAM (2014)

We designed, fabricated, and demonstrated an energy-efficient ERSFQ 4-bit decoder. The first version of the decoder is designed and fabricated using HYPRES legacy 1.0-μm four-layer 4.5-kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> process. It occupies an area of 700 μm × 1800 μm, which is to be reduced to 160 μm × 400 μm once fabricated using HYPRES's RIPPLE-2 0.25-μm six-layer process. The decoder features ±13% dc bias current operating margins and below 70-aJ energy consumption per one address select operation. We report test results of the decoder and discuss its future implementation in cryogenic random access memory devices, including magnetic memory devices.
Deregulation of the spindle assembly checkpoint is associated with paclitaxel resistance in ovarian cancer (2018)

We have generated model systems to explore drug resistance in ovarian cancer, which have revealed a key pathway related to the spindle assembly checkpoint underlying paclitaxel resistance in ovarian cell lines.
A phase-synchronization and random-matrix based approach to multichannel time-series analysis with application to epilepsy (2011)

We present a general method to analyze multichannel time series that are becoming increasingly common in many areas of science and engineering. Of particular interest is the degree of synchrony among various channels, motivated by the recognition that characterization of synchrony in a system consisting of many interacting components can provide insights into its fundamental dynamics. Often such a system is complex, high-dimensional, nonlinear, nonstationary, and noisy, rendering unlikely complete synchronization in which the dynamical variables from individual components approach each other asymptotically. Nonetheless, a weaker type of synchrony that lasts for a finite amount of time, namely, phase synchronization, can be expected. Our idea is to calculate the average phase-synchronization times from all available pairs of channels and then to construct a matrix. Due to nonlinearity and stochasticity, the matrix is effectively random. Moreover, since the diagonal elements of the matrix can be arbitrarily large, the matrix can be singular. To overcome this difficulty, we develop a random-matrix based criterion for proper choosing of the diagonal matrix elements. Monitoring of the eigenvalues and the determinant provides a powerful way to assess changes in synchrony. The method is tested using a prototype nonstationary noisy dynamical system, electroencephalogram (scalp) data from absence seizures for which enhanced cortico-thalamic synchrony is presumed, and electrocorticogram (intracranial) data from subjects having partial seizures with secondary generalization for which enhanced local synchrony is similarly presumed.
A novel EGR‐1 dependent mechanism for YB‐1 modulation of paclitaxel response in a triple negative breast cancer cell line (2016)

Chemotherapy with taxanes such as paclitaxel (PTX) is a key component of triple negative breast cancer (TNBC) treatment. PTX is used in combination with other drugs in both the adjuvant setting and in advanced breast cancer. Because a proportion of patients respond poorly to PTX or relapse after its use, a greater understanding of the mechanisms conferring resistance to PTX is required. One protein shown to be involved in drug resistance is Y-box binding protein 1 (YB-1). High levels of YB-1 have previously been associated with resistance to PTX in TNBCs. In this study, we aimed to determine mechanisms by which YB-1 confers PTX resistance. We generated isogenic TNBC cell lines that differed by YB-1 levels and treated these with PTX. Using microarray analysis, we identified EGR1 as a potential target of YB-1. We found that low EGR1 mRNA levels are associated with poor breast cancer patient prognosis, and that EGR1 and YBX1 mRNA expression was inversely correlated in a TNBC line and in a proportion of TNBC tumours. Reducing the levels of EGR1 caused TNBC cells to become more resistant to PTX. Given that PTX targets cycling cells, we propose a model whereby high YB-1 levels in some TNBC cells can lead to reduced levels of EGR1, which in turn promotes slow cell cycling and resistance to PTX. Therefore YB-1 and EGR1 levels are biologically linked and may provide a biomarker for TNBC response to PTX.