gebhart/patrepeval huggingface dataset:
Rapid Isothermal Amplification and Portable Detection System for SARS-CoV-2 (2020)

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay details and primer sequences become widely known, many laboratories could perform diagnostic tests using methods such as RT-PCR or isothermal RT-LAMP amplification. A key advantage of RT-LAMP based approaches compared to RT-PCR is that RT-LAMP is known to be robust in detecting targets from unprocessed samples. In addition, RT-LAMP assays are performed at a constant temperature enabling speed, simplicity, and point-of-use testing. Here, we provide the details of an RT-LAMP isothermal assay for the detection of SARS-CoV-2 virus with performance comparable to currently approved tests using RT-PCR. We characterize the assay by introducing swabs in virus spiked synthetic nasal fluids, moving the swab to viral transport medium (VTM), and using a volume of that VTM for performing the amplification without an RNA extraction kit. The assay has a Limit-of-Detection (LOD) of 50 RNA copies/μL in the VTM solution within 20 minutes, and LOD of 5000 RNA copies/μL in the nasal solution. Additionally, we show the utility of this assay for real-time point-of-use testing by demonstrating detection of SARS-CoV-2 virus in less than 40 minutes using an additively manufactured cartridge and a smartphone-based reader. Finally, we explore the speed and cost advantages by comparing the required resources and workflows with RT-PCR. This work could accelerate the development and availability of SARS-CoV-2 diagnostics by proving alternatives to conventional laboratory benchtop tests.
Cryogen Free High Temperature Superconducting Magnets for 94 GHz Gyroklystron‐Powered Radar Applications (1998)

ABSTRACT There is current interest within the Navy to develop high average power gyroklystron amplifiers to generate millimeter wave electromagnetic radiation for enhanced performance W‐band (94 GHz) radar applications. These applications include high resolution imaging, precision tracking, and cloud physics studies. Notwithstanding the relatively high atmospheric absorption in the high frequency millimeter wave bands, the development of radars in these frequency bands can solve many pressing problems, provided sufficient power levels can be obtained. Gyroklystron amplifiers are vacuum electronic amplifiers which are capable of providing more than an order of magnitude increase in power over conventional coupled‐cavity TWTs in these bands. One current frequency of interest is in the 94 GHz range which requires an external magnetic field of ˜3.4 Tesla in order for the gyroklystron to operate. The most efficient means for generating this magnetic field level is through the use of superconducting magnets. With the continued development of high temperature superconductors (HTS) and a corresponding progress in cryo‐cooler technology, it is now possible to consider utilizing cryo‐cooled HTS in this application. Operating in the 10 K to 25 K range with a cryo‐cooler, we are currently developing a prototype cryogen free HTS magnet system for this radar application.
V<inf>T</inf> statistics on nanoscale NAND Flash arrays (2011)

This paper presents a compact model allowing the investigation of the variability effects in nanoscale NAND Flash arrays. The proposed model describes the NAND string current in the readout conditions, including parasitic capacitive couplings among neighboring cells, and also the cell programming and erase operations. Changing the model parameters to account for their physical fluctuation in a Monte Carlo fashion, the impact of each variability source on the statistical dispersion of the cell threshold-voltage is obtained for state-of-the-art and next generation technology nodes. Good agreement between simulations and experimental results and the low computational load make the proposed methodology a valid solution for the assessment of variability constraints on NAND technology design.
Promoting social cohesionImplications for policy and evaluation (2011)

Abstract This book makes a forthright case for a shift in policy focus from ‘community cohesion’ to the broader notion of social cohesion, and is distinctive in its focus on evaluation. It constitutes a valuable source both for practitioners involved in social-cohesion interventions and for researchers and students studying theory-based evaluation and the policy areas highlighted: housing, intergenerational issues, the recession, education, communications, and community development.
Generation of Filter Bank-Based Multicarrier Waveform Using Partial Synthesis and Time Domain Interpolation (2010)

Recently, multirate filter banks have been recognized as high performance signal processing tools that could significantly enhance the efficiency and flexibility of future wireless communications. Filter bank-based multicarrier (FBMC) modulation allows increasing the spectral efficiency of high data rate transmission, both through the lack of time domain guard periods and the reduced frequency domain guard bands. Further, the inherent frequency selectivity is regarded as a vital characteristic, which enables high quality radio scene analysis, necessary for successful deployment of dynamic spectrum access in the context of cognitive radio technology. When applied to multicarrier communications, the filter banks are operated in the so-called transmultiplexer configuration where typically equal-size synthesis and analysis filter banks are utilized at the transmitter and receiver, respectively. This paper presents a new approach to generate an FBMC signal waveform. We focus on contiguous narrowband subcarrier allocation, which is often encountered in uplink transmission. Instead of using a full-size <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> -subchannel synthesis filter bank, the proposed scheme relies on a cascade of a <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</i> -subchannel synthesis bank (P ≪ <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> ), time domain interpolation, and a user-specific frequency shift. This method allows constructing a transmitter-receiver pair using synthesis and analysis filter banks of different sizes. The presented approach is shown to provide notable computational complexity savings over a wide range of practical user bandwidth allocations, when compared to the conventional implementation consisting of equally sized filter banks. Therefore, this novel scheme provides flexible and low-complexity synthesis of spectrally well-localized FBMC uplink waveforms, which show strong potential for future broadband mobile communications.
Anisotropy of Electronic Structure and Transport Properties of Oxide Superconductors (1998)

Abstract High temperature superconductivity in cuprates has become a fairly mature field now that more than a decade has passed by since its discovery. While scientific appeal of the field continues, the technological implications have faced harsh realities. Although the transition temperatures are high, the coherence length in oxide superconductors is awfully short and thus inhomegeneity or perturbation at the length scale of a few nanometers proves extremely detrimental to their properties, especially transport. Further, slight changes in the oxygen stoichiometry in cuprates have a profound effect on their superconducting properties and it is often not clear whether the nonstoichiometry at defect sites (e.g. grain boundaries- GBs) is intrinsic or extrinsic. The anisotropy of electronic structure is well reflected in low loss EELS spectra of these materials. Figure 1 shows low loss EELS spectra from Y124: one taken with momentum transfer confined to the Cu-02 planes, and the other normal to them. These observations are in accord with the fact that conduction is predominantly along the ab-planes, within single crystals.
Abstract 11181: Discovery of Neurovascular Reactivity During a Standard 5-minute Arm-cuff Reactive Hyperemia - Data From 7105 Patient Registry (2019)

Background: Endothelial function testing using a 5-minute arm-cuff occlusion have always focused on hemodynamic measures from the occluded arm. No publication is found in PubMed (as of May 2019) on...
High group birefringence in air-core photonic bandgap fibers (2005)

A numerical investigation of group birefringence is carried out on a recently reported highly birefringent hollow-core photonic bandgap fiber by use of an efficient vector finite-element method. The hollow fiber core has an area as large as that of approximately four airholes in the cladding region and assumes a rhombic shape with round corners, and the airholes in the cladding region are hexagonal and provide a high air-filling fraction. Numerical results show very high group birefringence of the order of 10(-2) and phase birefringence of the order of 10(-3).
On Data Importance Analysis (2011)

Accidents of information leakage and insider threats by malicious employee are major issues in enterprise IT system. Data importance analysis methods can resolve this issue, the importance of data is automatically analyzed by the method and confirms whether the operation suits the security policy for the level of importance of the data. Insider threads are also protected by analyzing data importance and data flows. A mechanism to ascertain data importance via automatic analysis is useful for avoiding human error. The mechanism finds the appropriate category for user sent data in terms of data importance, highly secret, important, and unclassified. In this paper, we presented an analysis method and discussed its application. It will apply to information leakage by both human error and insider threads. The method is a combination of data diagnosis and data categorization, and it can analyze whether the transaction to send the data compiles with the security policy.
Parallel Synthesis of N‐Arylpiperazines Using Polymer‐Assisted Reactions. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Synthesis and Self-Assembly of Globotriose Derivatives:  A Model System for Studies of Carbohydrate−Protein Interactions (2002)

Self-assembled monolayers (SAMs) on gold exposing α-d-Galp-(1→4)-β-d-Galp-(1→4)-β-d-Glcp (globotriose) are described. A synthetic pathway for the preparation of the bioactive carbohydrate globotriose coupled directly to bis(16-hydroxyhexadecanyl) disulfide ((HOC16H32S)2), as well as via tetra- or di(ethylene glycol) spacers, was developed. The SAMs were characterized by ellipsometry, contact angle goniometry, infrared reflection−absorption spectroscopy, and by their interactions with monoclonal antibodies. The ellipsometry measurements of mixed SAMs revealed thicknesses between 22 and 40 Å, depending on the ratio between carbohydrate and non-carbohydrate disulfides in the preparation solution. When the solution contained 10% or more of the carbohydrate adsorbate, the modified gold substrates displayed total wetting. Infrared reflection−absorption spectroscopy conferred well-ordered SAMs with a high degree of crystallinity. Furthermore, two monoclonal antibodies (IgM, MAHI 419 and IgG, MAHI 5) showed different affinity for mixed SAMs depending on the fraction and the structure of the carbohydrate component used (globotriose or globotriose tetra(ethylene glycol)), with the largest amount of protein bound for MAHI 419 at 1−10% of surface carbohydrate. These results demonstrate the usefulness of the SAM approach to explore molecular details such as the effect of a spacer or antigen distribution on antibody interactions at interfaces.
A WAVEGUIDE HORN ANTENNA WITH COUPLED RESONATOR NOTCH FILTER DESIGNED BY THE LAGRANGIAN FORMULATION FOR METAMATERIALS (2016)

This paper presents the design and analysis of guided wave notch filters using the Lagrangian formulation for metamaterials. It is shown that the application of the Lagrangian is a convenient and effective way to select an appropriate filtering structure and determine the necessary configuration for desired filter performance. A WR-187 waveguide horn antenna is investigated with notch filters composed of broadside coupled and gap coupled split ring resonators. It is shown that broadside coupling offers significant tunability in a compact size. The filter exhibits an operational bandwidth from approximately 3.9-5.7 GHz with 40-150 MHz of instantaneous bandwidth. The fabrication of the horn antenna and split ring resonators is presented along with simulated and measured data that confirms the approach.
A Randomized Phase II/III Trial of 3 Weekly Intraperitoneal versus Intravenous Carboplatin in Combination with Intravenous Weekly Dose-dense Paclitaxel for Newly Diagnosed Ovarian, Fallopian Tube and Primary Peritoneal Cancer (2010)

Retrospective studies and a Phase II trial demonstrated the promising efficacy and safety of intraperitoneal administration of carboplatin in ovarian, fallopian tube and primary peritoneal cancer. A Japanese Gynecologic Oncology Group 3016 randomized Phase III trial for these cancers showed dose-dense weekly administration of paclitaxel significant improvement of progression-free survival and overall survival over every 3-week administration. From June 2010, we have been conducting a randomized Phase II/III trial of intravenous versus intraperitoneal administration of carboplatin every 3 week in combination with dose-dense weekly administration of paclitaxel. The purpose of this trial is to prove the superiority of intraperitoneal administration of carboplatin over intravenous administration. Primary endpoint is progression-free survival and secondary endpoints include overall survival, quality of life assessment and cost-benefit. The first 120 patients will be evaluated for the feasibility of intraperitoneal arm and a total of 746 patients will be enrolled in a Phase III study.
Synthesis of Polystyrene by Dispersion Polymerization in 1,1,1,2-Tetrafluoroethane (R134a) Using Inexpensive Hydrocarbon Macromonomer Stabilizers (2003)

We describe here the use of inexpensive poly(vinyl acetate) (PVAc) macromonomer stabilizers for the free radical dispersion polymerization of styrene in 1,1,1,2-tetrafluoroethane (R134a). PVAc was identified from a wide range of polymers as being highly soluble in R134a at low pressures (<10 bar). The phase behavior of PVAc (Mw = 12 000−500 000 g/mol) in R134a was studied over a range of temperatures and pressures. It was found that PVAc exhibits LCST phase behavior in R134a. Based on the results of these solubility studies, PVAc macromonomer stabilizers were synthesized for use in dispersion polymerization. The dispersion polymerization of styrene in R134a gave rise to polystyrene microspheres (4−5 μm diameter) in good yields (up to 95%) with number-average molecular weights as high as 42 000 g/mol. The polystyrene microspheres could be redispersed in neat R134a after isolation and purification.
Review of Quanta Image Sensors for Ultralow-Light Imaging (2022)

The quanta image sensor (QIS) is a photon-counting image sensor that has been implemented using different electron devices, including impact ionization-gain devices, such as the single-photon avalanche detectors (SPADs), and low-capacitance, high conversion-gain devices, such as modified CMOS image sensors (CIS) with deep subelectron read noise and/or low noise readout signal chains. This article primarily focuses on CIS QIS, but recent progress of both types is addressed. Signal processing progress, such as denoising, critical to improving apparent signal-to-noise ratio, is also reviewed as an enabling coinnovation.
High Health-Related Quality of Life During Dendritic Cell Vaccination Therapy in Patients With Castration-Resistant Prostate Cancer (2020)

Patients with asymptomatic or minimally symptomatic CRPC show high HRQoL throughout DC-based immunotherapy. This is a clinically relevant finding in this older-aged patient population with advanced prostate cancer.
Crack‐Interface Interactions in a Tungsten‐Yttria‐Stabilized‐Zirconia Directionally Solidified Eutectic (1996)

A directionally solidified eutectic (DSE) of W‐ZrO 2 (Y 2 O 3 ) consists of faceted fibers of tungsten embedded in yttriastabilized cubic zirconia. The W‐ZrO 2 interfaces in this system are devoid of any impurity phases or a reaction product. Microindentation‐induced cracks and their interactions with interphase interfaces are investigated using scanning and transmission electron microscopy. Crack‐interface interactions are found to fall into one of four categories: propagation along the metal‐ceramic interface, deflection away from the interface, crack‐interface bridging, and shearing of tungsten fibers. Further crack propagation is investigated in situ in a TEM with a propagation induced by local electron beam heating. These crack path selections are analyzed within the framework of phenoin‐enological understanding of crack‐interface interactions in composites.
A Multisite Molecular Mechanism for Baeyer–Villiger Oxidations on Solid Catalysts Using Environmentally Friendly H2O2 as Oxidant (2005)

The molecular mechanism of the Baeyer-Villiger oxidation of cyclohexanone with hydrogen peroxide catalyzed by the Sn-beta zeolite has been investigated by combining molecular mechanics, quantum-chemical calculations, spectroscopic, and kinetic techniques. A theoretical study of the location of Sn in zeolite beta was performed by using atomistic force-field techniques to simulate the local environment of the active site. An interatomic potential for Sn/Si zeolites, which allows the simulation of zeolites containing Sn in a tetrahedral environment, has been developed by fitting it to the experimental properties of quartz and SnO2(rutile). The tin active site has been modeled by means of a Sn(OSiH3)3OH cluster, which includes a defect in the framework that provides the flexibility necessary for the interaction between the adsorbates and the Lewis acid center. Two possible reaction pathways have been considered in the computational study, one of them involving the activation of the cyclohexanone carbonyl group by Sn (1) and the other one involving hydrogen peroxide being activated through the formation of a tin-hydroperoxo intermediate (2). Both the quantum-chemical results and the kinetic study indicate that the reaction follows mechanism 1, and that the catalyst active site consists of two centers: the Lewis acid Sn atom to which cyclohexanone has to coordinate, and the oxygen atom of the Sn-OH group that interacts with H2O2 forming a hydrogen bond.
Tumor-Infiltrating Lymphocytes and Prognosis: A Pooled Individual Patient Analysis of Early-Stage Triple-Negative Breast Cancers (2019)

This pooled data analysis confirms the strong prognostic role of sTILs in early-stage TNBC and excellent survival of patients with high sTILs after adjuvant chemotherapy and supports the integration of sTILs in a clinicopathologic prognostic model for patients with TNBC. This model can be found at www.tilsinbreastcancer.org .
A cell-surface β-hydroxylase is a biomarker and therapeutic target for hepatocellular carcinoma (2014)

These studies suggest that the enzymatic activity of ASPH is important for hepatic oncogenesis. Reduced β-hydroxylase activity generated by the SMI MO-I-1100 leads to antitumor effects through inhibiting Notch signaling cascade in HCC. ASPH promotes the generation of an HCC malignant phenotype and represents an attractive molecular target for therapy of this fatal disease.
Efficient Implementation of Gaussian Belief Propagation Solver for Large Sparse Diagonally Dominant Linear Systems (2012)

We present an implementation-oriented algorithm for the recently developed Gaussian Belief Propagation solver that demonstrates 17× speedup over the prior algorithm for diagonally dominant matrices generated by typical Finite Elements applications. Compared to the diagonally-preconditioned conjugate gradient method, our algorithm demonstrates empirical improvements up to 6× in iteration count and speedups up to 1.8× in execution time. Also we present a new flexible scheduling scheme of the algorithm that is aimed for implementation on parallel architectures by reducing the iteration count of parallel GaBP and achieving better hardware parallelism.
ChemInform Abstract: Solvent Effects on the Ring Opening of Cyclopropanones to Oxyallyls: A Combined ab initio and Monte Carlo Study. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Generalized Framework for Network Component Analysis (2005)

The authors recently introduced a framework, named Network Component Analysis (NCA), for the reconstruction of the dynamics of transcriptional regulators' activities from gene expression assays. The original formulation had certain shortcomings that limited NCA's application to a wide class of network dynamics reconstruction problems, either because of limitations in the sample size or because of the stringent requirements imposed by the set of identifiability conditions. In addition, the performance characteristics of the method for various levels of data noise or in the presence of model inaccuracies were never investigated. In this article, the following aspects of NCA have been addressed, resulting in a set of extensions to the original framework: 1) The sufficient conditions on the a priori connectivity information (required for successful reconstructions via NCA) are made less stringent, allowing easier verification of whether a network topology is identifiable, as well as extending the class of identifiable systems. Such a result is accomplished by introducing a set of identifiability requirements that can be directly tested on the regulatory architecture, rather than on specific instances of the system matrix. 2) The two-stage least square iterative procedure used in NCA is proven to identify stationary points of the likelihood function, under Gaussian noise assumption, thus reinforcing the statistical foundations of the method. 3) A framework for the simultaneous reconstruction of multiple regulatory subnetworks is introduced, thus overcoming one of the critical limitations of the original formulation of the decomposition, for example, occurring for poorly sampled data (typical of microarray experiments). A set of monte carlo simulations we conducted with synthetic data suggests that the approach is indeed capable of accurately reconstructing regulatory signals when these are the input of large-scale networks that satisfy the suggested identifiability criteria, even under fairly noisy conditions. The sensitivity of the reconstructed signals to inaccuracies in the hypothesized network topology is also investigated. We demonstrate the feasibility of our approach for the simultaneous reconstruction of multiple regulatory subnetworks from the same data set with a successful application of the technique to gene expression measurements of the bacterium Escherichia coli.