gebhart/patrepeval huggingface dataset:
From master slave interferometry to complex master slave interferometry: theoretical work (2018)

A general theoretical framework is described to obtain the advantages and the drawbacks of two novel Fourier Domain Optical Coherence Tomography (OCT) methods denoted as Master/Slave Interferometry (MSI) and its extension denoted as Complex Master/Slave Interferometry (CMSI). Instead of linearizing the digital data representing the channeled spectrum before a Fourier transform can be applied to it (as in OCT standard methods), channeled spectrum is decomposed on the basis of local oscillations. This replaces the need for linearization, generally time consuming, before any calculation of the depth profile in the range of interest. In this model two functions, g and h, are introduced. The function g describes the modulation chirp of the channeled spectrum signal due to nonlinearities in the decoding process from wavenumber to time. The function h describes the dispersion in the interferometer. The utilization of these two functions brings two major improvements to previous implementations of the MSI method. The paper details the steps to obtain the functions g and h, and represents the CMSI in a matrix formulation that enables to implement easily this method in LabVIEW by using parallel programming with multi-cores.
Abstract LB-192: Circulating tumor cell clusters are precursors of breast cancer metastasis (2014)

Abstract The metastatic spread of breast cancer, typically to bone, lung, liver and brain, accounts for the vast majority of cancer-related deaths. Breast cancer metastases are thought to be derived primarily from individual migratory cancer cells, reaching distant sites through the bloodstream and initiating proliferation within distant organs. In addition to these single circulating tumor cells (CTCs), CTC-clusters have been detected in the blood of patients with cancer. In patients with breast cancer, we find that presence of such CTC-clusters is correlated with decreased progression-free survival. To study their functional role, we used mouse models, demonstrating that breast cancer cells injected intravascularly as clusters are more prone to survive and colonize the lungs than similarly injected single cancer cells. Primary orthotopic mammary tumors comprised of differentially tagged cells give rise to oligoclonal CTC-clusters, with 40-fold increased metastatic potential to the lung, compared with single CTCs. Using in vivo flow cytometry, we show that CTC-clusters are rapidly cleared from peripheral vessels, consistent with their trapping in small capillaries. Together, our observations suggest that primary tumor cells break off into the vasculature as CTC-clusters, and exhibit greatly enhanced metastatic propensity. Citation Format: Nicola Aceto, Aditya Bardia, Joel A. Spencer, Ben S. Wittner, Min Yu, Maria C. Donaldson, Adam Pely, Amanda Engstrom, Huili Zhu, Brian W. Brannigan, Ravi Kapur, Shannon L. Stott, Toshi Shioda, Sridhar Ramaswamy, David T. Ting, Charles P. Lin, Mehmet Toner, Daniel A. Haber, Shyamala Maheswaran. Circulating tumor cell clusters are precursors of breast cancer metastasis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-192. doi:10.1158/1538-7445.AM2014-LB-192
Protective Effect of Vaccine Promoted Neutralizing Antibodies against the Intracellular Pathogen Chlamydia trachomatis (2017)

There is an unmet need for a vaccine to control <i>Chlamydia trachomatis</i> (<i>C.t</i>.) infections. We have recently designed a multivalent heterologous immuno-repeat 1 (Hirep1) vaccine construct based on major outer membrane protein variable domain (VD) 4 regions from <i>C.t</i>. serovars (Svs) D-F. Hirep1 administered in the Cationic Adjuvant Formulation no. 1 (CAF01) promoted neutralizing antibodies in concert with CD4<sup>+</sup> T cells and protected against genital infection. In the current study, we examined the protective role of the antibody (Ab) response in detail. Mice were vaccinated with either Hirep1 or a vaccine construct based on a homologous multivalent construct of extended VD4's from SvF (extVD4<sup>F</sup>*4), adjuvanted in CAF01. Hirep1 and extVD4<sup>F</sup>*4 induced similar levels of Ab and cell-mediated immune responses but differed in the fine specificity of the B cell epitopes targeted in the VD4 region. Hirep1 induced a strong response toward a neutralizing epitope (LNPTIAG) and the importance of this epitope for neutralization was demonstrated by competitive inhibition with the corresponding peptide. Immunization with extVD4<sup>F</sup>*4 skewed the response to a non-neutralizing epitope slightly upstream in the sequence. Vaccination with Hirep1 as opposed to extVD4<sup>F</sup>*4 induced significant protection against infection in mice both in short- and long-term vaccination experiments, signifying a key role for Hirep1 neutralizing antibodies during protection against <i>C.t</i>. Finally, we show that passive immunization of Rag1 knockout mice with Hirep1 antibodies completely prevented the establishment of infection in 48% of the mice, demonstrating an isolated role for neutralizing antibodies in controlling infection. Our data emphasize the role of antibodies in early protection against <i>C.t</i>. and support the inclusion of neutralizing targets in chlamydia vaccines.
Miniaturized strongly coupled magnetic resonant systems for wireless power transfer (2016)

Compact design on Conformal Strongly Coupled Magnetic Resonant (CSMCR) systems for wireless power transfer (WPT) are proposed and summarized in this paper. Operating frequencies can be tuned to lower frequencies based on the properties of planar CSCMR systems, therefore the system volume will shrink. In addition, methods for miniaturized CSCMR systems based on novel topology and high permeability substrate are proposed. Compared to one traditional CSCMR system, the proposed methods shift the operating frequency from 83 MHz to 33 MHz and 54 MHz, with efficiencies of 67.8% and 84.0%, respectively.
<i>Toxoplasma gondii</i> GRA8-derived peptide immunotherapy improves tumor targeting of colorectal cancer (2020)

Targeted tumor and efficient, specific biological drug delivery <i>in vivo</i> has been one of the main challenges in protein-based cancer-targeted therapies. Mitochondria are potential therapeutic targets for various anti-cancer drugs. We have previously reported that protein kinase Cα-mediated phosphorylation of <i>Toxoplasma gondii</i> GRA8 is required for mitochondrial trafficking and regulating the interaction of the C-terminal of GRA8 with ATP5A1/SIRT3 in mitochondria. Furthermore, SIRT3 facilitates ATP5A1 deacetylation, mitochondrial activation, and subsequent antiseptic activity <i>in vivo</i>. Herein we developed a recombinant acidity-triggered rational membrane (ATRAM)-conjugated multifunctional GRA8 peptide (rATRAM-G8-M/AS) comprising ATRAM as the cancer-targeting cell-penetrating peptide, and essential/minimal residues for mitochondrial targeting or ATP5A1/SIRT3 binding. This peptide construct showed considerably improved potency about cancer cell death via mitochondria activity and biogenesis compared with rGRA8 alone in HCT116 human carcinoma cells, reaching an IC<sub>50</sub> value of up to 200-fold lower <i>in vitro</i> and 500-fold lower <i>in vivo</i>. Notably, rATRAM-G8-M/AS treatment showed significant therapeutic effects in a mouse xenograft model through mitochondrial metabolic resuscitation, and it produced negligible immunogenicity and immune responses <i>in vivo</i>. Thus, these results demonstrate that rATRAM-G8-M/AS represents a useful therapeutic strategy against tumors, particularly colon cancer. This strategy represents an urgently needed paradigm shift for therapeutic intervention.
A novel coil array for combined TMS/fMRI experiments at 3 T (2014)

The novel coil array is safe, strongly improves signal-to-noise ratio in concurrent TMS/fMRI experiments, enables parallel imaging, and allows for flexible positioning of the TMS on the head while ensuring efficient TMS stimulation due to its ultraslim design.
Enhanced Expression of Anti-CD19 Chimeric Antigen Receptor in piggyBac Transposon-Engineered T Cells (2017)

Adoptive T cell therapy using chimeric antigen receptor (CAR)-modified T cells is a promising cancer immunotherapy. We previously developed a non-viral method of gene transfer into T cells using a <i>piggyBac</i> transposon system to improve the cost-effectiveness of CAR-T cell therapy. Here, we have further improved our technology by a novel culture strategy to increase the transfection efficiency and to reduce the time of T cell manufacturing. Using a CH2CH3-free CD19-specific CAR transposon vector and combining irradiated activated T cells (ATCs) as feeder cells and virus-specific T cell receptor (TCR) stimulation, we achieved 51.4% ± 14% CAR<sup>+</sup> T cells and 2.8-fold expansion after 14 culture days. Expanded CD19.CAR-T cells maintained a significant fraction of CD45RA<sup>+</sup>CCR7<sup>+</sup> T cells and demonstrated potent antitumor activity against CD19<sup>+</sup> leukemic cells both <i>in vitro</i> and <i>in vivo</i>. Therefore, <i>piggyBac</i>-based gene transfer may provide an alternative to viral gene transfer for CAR-T cell therapy.
Synthesis of (+)-Vinblastine and Its Analogues (2007)

A synthetic route to vinblastine and its analogues with an ethynyl group, which features a stereoselective coupling of an 11-membered key intermediate with vindoline, is described. Transformations of the alkynyl moiety including a partial reduction as well as a Sonogashira coupling furnished a variety of analogues.
Anthropogenic Chemical Carbon Cycle for a Sustainable Future (2011)

Nature's photosynthesis uses the sun's energy with chlorophyll in plants as a catalyst to recycle carbon dioxide and water into new plant life. Only given sufficient geological time, millions of years, can new fossil fuels be formed naturally. The burning of our diminishing fossil fuel reserves is accompanied by large anthropogenic CO(2) release, which is outpacing nature's CO(2) recycling capability, causing significant environmental harm. To supplement the natural carbon cycle, we have proposed and developed a feasible anthropogenic chemical recycling of carbon dioxide. Carbon dioxide is captured by absorption technologies from any natural or industrial source, from human activities, or even from the air itself. It can then be converted by feasible chemical transformations into fuels such as methanol, dimethyl ether, and varied products including synthetic hydrocarbons and even proteins for animal feed, thus supplementing our food chain. This concept of broad scope and framework is the basis of what we call the Methanol Economy. The needed renewable starting materials, water and CO(2), are available anywhere on Earth. The required energy for the synthetic carbon cycle can come from any alternative energy source such as solar, wind, geothermal, and even hopefully safe nuclear energy. The anthropogenic carbon dioxide cycle offers a way of assuring a sustainable future for humankind when fossil fuels become scarce. While biosources can play a limited role in supplementing future energy needs, they increasingly interfere with the essentials of the food chain. We have previously reviewed aspects of the chemical recycling of carbon dioxide to methanol and dimethyl ether. In the present Perspective, we extend the discussion of the innovative and feasible anthropogenic carbon cycle, which can be the basis of progressively liberating humankind from its dependence on diminishing fossil fuel reserves while also controlling harmful CO(2) emissions to the atmosphere. We also discuss in more detail the essential stages and the significant aspects of carbon capture and subsequent recycling. Our ability to develop a feasible anthropogenic chemical carbon cycle supplementing nature's photosynthesis also offers a new solution to one of the major challenges facing humankind.
Optimization MRI Cylindrical Coils Using Discretized Stream Function With High Order Smoothness (2011)

The design of coil for magnetic resonance image (MRI) application is an optimization problem, in which a specified distribution of the magnetic field inside a region of interest is generated by choosing the optimal distribution of current density on a specified non-intersecting design surface. This paper proposes an iterative optimization method for designing MRI coils on a cylindrical surface by using a piecewise discretized scalar stream function as design variable. The surface current density is accurately calculated using piecewise interpolation with smoothness based on the developable property for a cylindrical surface. MRI coils are designed by choosing bi-objective functions and pseudo-Newton sensitivity analysis. The smoothness of the coil are maintained by adjusting the value of derivative degrees of freedom of design variables which are used to interpolate the stream function. Pareto points provide more flexible choices between the two complementary objectives.
Discovery and Characterization of Potent Thiazoles versus Methicillin- and Vancomycin-Resistant <i>Staphylococcus aureus</i> (2014)

Methicillin- and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA) infections are growing global health concerns. Structure-activity relationships of phenylthiazoles as a new antimicrobial class have been addressed. We present 10 thiazole derivatives that exhibit strong activity against 18 clinical strains of MRSA and VRSA with acceptable PK profile. Three derivatives revealed an advantage over vancomycin by rapidly eliminating MRSA growth within 6 h, and no derivatives are toxic to HeLa cells at 11 μg/mL.
A parallel-detection electron spectrometer using quadrupole lenses (1986)

Serial detection systems that are standardly employed in electron energy loss spectrometry (EELS) only examine one energy channel at a time and are therefore inherently inefficient. Parallel detection systems using either photodiode arrays or charge-coupled devices (CCDs) promise to remove this inefficiency. However, to completely replace the serial detection systems, they will need 1) a detective quantum efficiency (DQE) approaching 100%, 2) a dynamic range sufficient to cover the range of intensities encountered in the energy loss spectra (about 10 6 ), and 3) ability to operate without any loss in energy resolution. We have constructed and tested a parallel detection system which incorporates three quadrupole lenses placed after the magnetic sector prism of the Gatan 607 spectrometer, a single crystal YAG scintillator, and a fiber-optically coupled linear photodiode array. The quadrupoles magnify the small dispersion (1.8μm per eV at 100kV primary voltage) of the spectrum produced by the magnetic sector to as high as 1 mm per eV without producing any spectrum rotation and with small power requirements.
Variational path profiling (2005)

Current profiling techniques are good at identifying where time is being spent during program execution. These techniques are not as good at pinpointing exactly where in the execution there are definite opportunities a programmer can exploit with optimization. In this paper we present a new type of profiling analysis called variational path profiling (VPP). VPP pinpoints exactly where in the program there are potentially significant optimization opportunities for speedup. VPP finds the acyclic control flow paths that vary the most in execution time (the time it takes to execute each occurrence of the path). This is calculated by sampling the time it takes to execute frequent paths using hardware performance counters. The motivation for concentrating on a path with a high net variation in its execution time is that it can potentially be optimized so that most or all executions of that path have the minimal execution time seen during profiling. We present a profiling and analysis approach to find these variational paths, so that they can be communicated back to a programmer to guide optimization. Our results show that this variation accounts for a significant fraction of overall program execution time and a small number of paths account for a large fraction of this variation. By applying straight forward prefetching optimizations to these variational paths we see 8.5% speedups on average.
A battery node for power plant monitoring systems (2002)

Valve regulated lead acid batteries have become the dominant battery for outside plant power system applications. As the usage mushroomed due to tremendous advantages over flooded cells, complaints about short life, unexpected failures, unplanned service calls and general capacity loss have surfaced. This paper presents a "battery node" proposal which strategically monitors and controls up to four strings of batteries. The battery node is targeted to be "online" with full time data acquisition, status calculations and reserve time and life prediction, yet maintain a minimal cost impact by design to the user.
Molecular Subtyping reveals Immune Alterations associated with Progression of Bronchial Premalignant Lesions (2018)

Abstract Bronchial premalignant lesions (PMLs) are precursors of lung squamous cell carcinoma, but have variable outcome, and we lack tools to identify and treat PMLs at highest risk for progression to invasive cancer. Profiling endobronchial biopsies of PMLs obtained from high-risk smokers by RNA-Seq identified four PML subtypes with differences in epithelial and immune processes. One molecular subtype ( Proliferative ) is enriched with dysplastic lesions and exhibits up-regulation of metabolic and cell cycle pathways and down-regulation of ciliary processes. RNA-Seq profiles from normal-appearing uninvolved large airway brushings could identify subjects with Proliferative lesions with high specificity. Expression of interferon signaling and antigen processing/presentation pathways are decreased in progressive/persistent Proliferative lesions and immunofluorescence indicates a depletion of innate and adaptive immune cells in these lesions. Molecular biomarkers measured in PMLs or the uninvolved airway can enhance histopathological grading and suggests that immunoprevention strategies may be effective in intercepting the progression of PMLs to lung cancer.
SU‐FF‐T‐309: Laser‐Accelerated Proton Therapy: Target Chamber Design and Shielding Requirements (2006)

Purpose: Recent advances in laser technology have facilitated proton (light ion) acceleration using laser‐induced plasmas. In this work, we investigate target chamber designs and their shielding requirements for a laser‐proton therapy system. Method and Materials: This new therapy system employs laser‐accelerated protons. If successfully developed, it may provide a compact and cost‐effective solution to energy‐ and intensity‐modulated proton therapy (EIMPT). Since laser‐accelerated protons have broad energy and angular distributions, which are not suitable for radiotherapy applications directly, we have designed a compact particle selection and beam collimating system for EIMPT beam delivery. The target chamber contains the laser focusing and target assembles and is connected to the proton beam collimation and particle selection device. Monte Carlo simulations using MCNPX and FLUKA have been performed to verify the shielding walls for the experimental setup, which consist of stainless steel, polystyrene and lead. Results: The primary particles resulting from the laser‐target interaction are protons and electrons. Our particle in cell simulation predicted energy spectra with 300 MeV maximum energy for protons and 20 MeV for electrons for a laser intensity of 10 21 W/cm 2 . The maximum number was 10 11 and 10 12 per pulse for protons and electron, respectively. Our Monte Carlo simulations showed that a combination of 1/4″ 304 stainless steel, 6″ polystyrene and 3″ lead will reduce the combined leakage dose equivalent to 0.32 μSv (0.032 mrem) per laser pulse at 1 m from the chamber, which included the effect of all primary and secondary particles. Conclusion: We have designed an experimental setup to accommodate the laser focusing mirror, the target assemblies, the beam collimator and the particle selection system. Different shielding walls are designed to ensure the leakage dose equivalent to within 20 μSv (2 mrem)/week.
Phase Transition Characteristics and Device Performance of Sn-doped Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub> in Phase Change Random Access Memory (2006)

Sn was employed in Ge2Sb2Te5 to accelerate operation speed of phase change random access memory (PRAM). Crystallized Sn-doped Ge2Sb2Te5 showed face centered cubic (fcc) or hexagonal close packed (hcp) structures upon heat treatment, which was similar to that of Ge2Sb2Te5. However, Sn doping increased the phase transformation temperature to hcp of Ge2Sb2Te5. 17 at. % Sn-doped Ge2Sb2Te5 had an accelerated crystallization under laser irradiation and moreover, showed decreased operation time of PRAM compared to that of Ge2Sb2Te5. In addition, 17 at. % Sn-doped Ge2Sb2Te5 showed stable and reversible device performance.
One-year Efficacy and Safety Results of Secukinumab in Patients With Rheumatoid Arthritis: Phase II, Dose-finding, Double-blind, Randomized, Placebo-controlled Study (2014)

Patients with active RA who failed to respond to DMARD and other biologics showed an improvement after longterm treatment with 150 mg of secukinumab. The frequency of AE remained stable over time and secukinumab had a consistent safety profile over 60 weeks.
PMOS: A Complete and Coarse-Grained Incremental Garbage Collector for Persistent Object Stores. (1996)

Traditional garbage collection techniques designed for language systems operating over transient data do not readily migrate to a persistent context. The size, complexity, and permanence characteristics of a persistent object store mean that an automatic storage reclamation system, in addition to ensuring that all unreachable and only unreachable data is reclaimed, must also maintain store consistency while limiting I/O overhead when collecting secondary-memory data. Research has shown that careful selection of which area of a store to collect can significantly increase the amount of reclaimed storage while reducing the I/O costs. Many garbage collectors for existing stores, however, either are off-line or rely on reclaiming space in a predefined order. This paper presents a new incremental garbage collection algorithm specifically designed for reclaiming persistent object storage. The collector extends the Mature Object Space algorithm to ensure incrementality in a persistent context, to achieve recoverability, and to impose minimum constraints on the order of collection of areas of the persistent address space.