gebhart/patrepeval huggingface dataset:
Initial performance of Los Alamos Advanced Free-Electron Laser (2002)

Many industrial and research applications can benefit from the availability of a compact, turn-key laser that puts out 100 watts or more of tunable light. Free-electron lasers are inherently capable of generating light over a wide wavelength band with high average powers, In the past, FELs have been typically large and complex machines. Over the past three years, Los Alamos has sponsored an engineering effort to design, build and test a compact and versatile free-electron laser called the Advanced FEL. The design of this compact FEL is based on integration of a number of advanced technologies that have emerged over the last ten years such as the photoinjector, the high-gradient linear accelerator, and the pulsed electromagnet microwiggler. These enabling technologies allow us to shrink the size of the Advanced FEL so that it will fit in a small laboratory, yet still be capable of providing high average powers in the near-ir, visible or even ultraviolet. The compact beamline is made up of permanent magnet components that do not require cooling or power sources. The entire beamline and the FEL resonator fit on a 6-ft by 10-ft vertical optical table.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Graphene As a Tunnel Barrier: Graphene-Based Magnetic Tunnel Junctions (2012)

Graphene has been widely studied for its high in-plane charge carrier mobility and long spin diffusion lengths. In contrast, the out-of-plane charge and spin transport behavior of this atomically thin material have not been well addressed. We show here that while graphene exhibits metallic conductivity in-plane, it serves effectively as an insulator for transport perpendicular to the plane. We report fabrication of tunnel junctions using single-layer graphene between two ferromagnetic metal layers in a fully scalable photolithographic process. The transport occurs by quantum tunneling perpendicular to the graphene plane and preserves a net spin polarization of the current from the contact so that the structures exhibit tunneling magnetoresistance to 425 K. These results demonstrate that graphene can function as an effective tunnel barrier for both charge and spin-based devices and enable realization of more complex graphene-based devices for highly functional nanoscale circuits, such as tunnel transistors, nonvolatile magnetic memory, and reprogrammable spin logic.
Validation of a Blocking Enzyme-Linked Immunosorbent Assay for Detection of Antibodies against Porcine Reproductive and Respiratory Syndrome Virus (2004)

Porcine reproductive and respiratory syndrome (PRRS) continues to be one of the most significant diseases of swine. IDEXX HerdChek PRRS, a commercially available enzyme-linked immunosorbent assay (ELISA), has become the industry standard for the detection of antibodies against PRRS virus (PRRSV). The need to accurately determine the PRRSV serostatus of herds and individual animals has prompted the development of several follow-up assay methods. A highly specific and repeatable blocking ELISA (bELISA) was developed on the basis of the use of an expressed PRRSV nucleocapsid (N) protein as the antigen and a biotinylated monoclonal antibody. Validation of the bELISA used sera from 316 animals experimentally and naturally infected with North American PRRSV and sera from 370 uninfected animals. Receiver operating characteristic analysis of the data calculated a diagnostic sensitivity of 97.8% and a diagnostic specificity of 100%. The between-run coefficient of variation of an internal quality control serum was 4.24%. The bELISA was able to detect seroconversion as well as the IDEXX ELISA and the indirect fluorescent antibody (IFA) assay; kappa values were 0.94 and 0.96, respectively. A collection of 133 serum samples with unexpected positive IDEXX ELISA results was obtained from 4,038 diagnostic samples submitted from farms from which PRRS-negative results were expected. The bELISA identified 97% of the samples as PRRS seronegative, while the IFA identified 100% as seronegative. The anticipated use of the bELISA is as a follow-up test to the IDEXX ELISA for determining the PRRSV serostatus of individual animals with unexpected positive test results from swine herds from which negative results are expected.
Production of citramalate by metabolically engineered <i>Escherichia coli</i> (2016)

Citramalic acid (citramalate) is a five carbon hydroxy-dicarboxylic acid and potential precursor for the production of methacrylic acid from renewable resources. We examined citramalate production in Escherichia coli expressing the citramalate synthase gene cimA. Although, knockouts in ldhA coding lactate dehydrogenase and glcB/aceB coding malate synthase did not benefit citramalate accumulation, knockouts in gltA coding citrate synthase, and ackA coding acetate kinase significantly increased citramalate accumulation compared to the control strain. A fed-batch process in a controlled fermenter using a glucose feed resulted in 46.5 g/L citramalate in 132 h with a yield of 0.63 g/g, over 75% of the theoretical maximum yield from glucose of 0.82 g/g. Biotechnol. Bioeng. 2016;113: 2670-2675. © 2016 Wiley Periodicals, Inc.
Abnormal Hyperphosphorylation of Tau: Sites, Regulation, and Molecular Mechanism of Neurofibrillary Degeneration (2012)

Microtubule associated protein tau is a phosphoprotein which potentially has 80 serine/threonine and 5 tyrosine phosphorylation sites. Normal brain tau contains 2-3 moles of phosphate per mole of the protein. In Alzheimer's disease brain, tau is abnormally hyperphosphorylated to a stoichiometry of at least three-fold greater than normal tau, and in this altered state it is aggregated into paired helical filaments forming neurofibrillary tangles, a histopathological hallmark of the disease. The abnormal hyperphosphorylation of tau is also a hallmark of several other related neurodegenerative disorders, called tauopathies. The density of neurofibrillary tangles in the neocortex correlates with dementia and, hence, is a rational therapeutic target and an area of increasing research interest. Development of rational tau-based therapeutic drugs requires understanding of the role of various phosphorylation sites, protein kinases and phosphatases, and post-translational modifications that regulate the phosphorylation of this protein at various sites, as well as the molecular mechanism by which the abnormally hyperphosphorylated tau leads to neurodegeneration and dementia. In this article we briefly review the progress made in these areas of research.
A link based alternative routing scheme for network restoration under failure (2002)

We present an alternative routing scheme which ensures that the network restores itself under any single link failure. In addition, our scheme has the advantage that restoration of the network occurs immediately on discovery of failure (without waiting for time consuming exchange of messages). An efficient heuristic algorithm, based on maximal-flow algorithm, is first used to partition the network into two parts (one carries the regular or primary traffic and the other is reserved to carry re-routed traffic in the event of failure). Then, we show how to use the results of the algorithm to actually find the alternative routes for a given call at the time of call setup.
Resistive Address Decoder (2017)

Hardwired dynamic NAND address decoders are widely used in random access memories to decode parts of the address. Replacing wires by resistive elements allows storing and reprogramming the addresses and matching them to an input address. The resistive address decoder thus becomes a content addressable memory, while the read latency and dynamic energy remain almost identical to those of a hardwired address decoder. One application of the resistive address decoder is a fully associative TLB with read latency and energy consumption similar to those of a one-way associative TLB. Another application is a many-way associative cache with read latency and energy consumption similar to those of a direct mapped one. A third application is elimination of physical addressing and using virtual addresses throughout the entire memory hierarchy by introducing the resistive address decoder into the main memory.
Performance and application of a superlattice infrared photodetector with a blocking barrier (2002)

An infrared photodetector that contains a superlattice structure and a blocking barrier was investigated. The photodetector shows advantages including a low operating voltage (&lt;0.7 V), wide detection bandwidth, flexible miniband engineering, and in particular, voltage-tunable spectral responsivity. The blocking barrier not only prohibits the dark current but also acts as a high-pass energy filter to tune the spectral responsivity. The zero background peak detectivity of our detector is 3.7×109 cm Hz0.5/W (9.7 μm) at −0.5 V and 2.2×1010 cm Hz0.5/W (6.7 μm) at −0.1 V. Since the spectral responsivity at different biases is independent, temperature sensing is feasible by taking the ratio of the measured photocurrent at different biases. A demonstration of temperature sensing by using our superlattice infrared photodetector with a blocking barrier is also shown in this article. Those results show the superlattice is a simple and efficient structure for the design of a multicolor infrared photodetector.
A Downlink Index-Modulation Based Nonorthogonal Multiple Access Scheme (2020)

Massive connectivity and spectral efficiency are among the main defining terms of the future communications era. Therefore, revolutionary technologies are required to keep up with the connectivity and spectrum demands. Non-orthogonal multiple access (NOMA) and Index modulation (IM) techniques have emerged as promising candidates to satisfy the spectral efficiency and capacity demands. In this paper, a novel downlink multiple access scheme, called IM-NOMA, is proposed reaping the advantages of both NOMA and IM. In IM-NOMA, the bit block to be sent to each user is divided into two sub-blocks. While the first sub-block is modulated, the second sub-block determines a subset from the available set of channels to carry the modulated symbol. As in power-domain NOMA, the base station (BS) superimposes the modulated symbols carried by the same frequency carrier after a proper power allocation. In such, spectral efficiency is boosted by the extra bits carried by the indexes of the used carriers and the error performance is improved by spreading the users' signals in power domain as well as diversifying the symbols of each user over multiple channels. An upper bound on the average BER is derived in a closed form expression under maximum likelihood (ML) detection method and Rayleigh fading channel. Simulation results show a significant improvement in the BER of the proposed IM-NOMA as compared to the conventional NOMA scheme.
Cord Blood CD4+CD25+ Derived T Regulatory Cell Lines Express FoxP3 Protein and Manifest Potent Suppressor Function. (2004)

Abstract CD4+CD25+ T regulatory (Treg) cells have been shown to critically regulate self and more recently allograft tolerance in mice. Studies of human Treg have been hindered by the presence of CD25-dim conventional T cells that copurify during Treg isolation. We compared adult and cord blood sources for Treg, with the hypothesis that cord blood should lack significant numbers of memory cells or environmentally reactive T cells. We found that cord blood was a superior source for Treg isolation compared to adult blood. CD4+CD25+ cells were readily purified, and generated cell lines that consistently exhibited potent suppressor activity, with >95% suppression of allogeneic MLR (29/30 donors). The cells could markedly suppress an allo-MLR at a 1/16-1/32 suppressor/responder cell ratio. The cultured Treg cells blocked cytokine accumulation in MLR, with a less robust inhibition of chemokine production. Cultured Treg uniformly expressed CD25, CD62L, CCR7, CD27, and intracellular CTLA4. Upon re-stimulation with anti-CD3/CD28 beads, the cultured Treg produced minimal cytokines (IL2, IFN-gamma, and IL10), and preferentially expressed TGF-beta latency associated protein on the cell surface, while conventional CD4+CD25− derived cell lines did not. Cytokine production however, could be largely restored by stimulation with PMA/ionomycin. Abundant FoxP3 mRNA was detected in fresh, cultured, and anti-CD3/CD28 bead restimulated CD4+CD25+ cells (approximately 2–4 fold less than cyclophillin A). Low amounts of FoxP3 mRNA were present in fresh CD25− cells, and they increased 32 fold on culture. However, FoxP3 protein, as assessed by western blot, was specifically expressed in the CD25+ derived cell lines, and was not detected in the CD25− derived cell lines. Restimulation with anti-CD3/CD28 beads led to increased expression of FoxP3 protein in CD25+ derived cell lines, but not in CD25− derived cell lines. Cord blood derived cultured suppressor cells were not cytolytic in chromium release assays, and mediated suppression of alloreactivity that was cell contact dependent and predominantly independent of IL10 and TGF-beta. Antibodies to GITR, GITR-L, OX40, OX40-L, CTLA4, and PD1 did not significantly affect suppression of the culture activated Treg cells. These results demonstrate virtually pure populations of potent suppressor cells can be cultured from cord blood, and these cell lines form an ideal model system for the evaluation of suppressor cell biology and mechanisms of action.
Characterization of the Opsonic and Protective Activity against <i>Staphylococcus aureus</i> of Fully Human Monoclonal Antibodies Specific for the Bacterial Surface Polysaccharide Poly- <i>N</i> -Acetylglucosamine (2006)

Carbohydrate antigens are important targets of the immune system in clearing bacterial pathogens. Although the immune system almost exclusively uses antibodies in response to foreign carbohydrates, there is still much to learn about the role of different epitopes on the carbohydrate as targets of protective immunity. We examined the role of acetyl group-dependent and -independent epitopes on the staphylococcal surface of polysaccharide poly-N-acetylated glucosamine (PNAG) by use of human monoclonal antibodies (MAbs) specific for such epitopes. We utilized hybridoma technology to produce fully human immunoglobulin G2 (IgG2) MAbs from B cells of an individual post-Staphylococcus aureus infection and cloned the antibody variable regions to produce an IgG1 form of each original MAb. Specificity and functionality of the purified MAbs were tested in vitro using enzyme-linked immunosorbent assays, complement deposition, and opsonophagocytic assays. We found that a MAb (MAb F598) that bound the best to nonacetylated or backbone epitopes on PNAG had superior complement deposition and opsonophagocytic activity compared to two MAbs that bound optimally to PNAG that was expressed with a native level (>90%) of N-acetyl groups (MAbs F628 and F630). Protection of mice against lethality due to S. aureus strains Mn8 and Reynolds further showed that the backbone-specific MAb had optimal protective efficacy compared with the acetate-specific MAbs. These results provide evidence for the importance of epitope specificity in inducing the optimal protective antibody response to PNAG and indicate that MAbs to the deacetylated form of PNAG could be immunotherapeutic agents for preventing or treating staphylococcal infections.
<title>Embeddable sensor for corrosion measurement</title> (1999)

The design of a microinstrument for corrosion monitoring in reinforced concrete is presented and the performance of the prototype device discussed. Sensors for the measurement of corrosion rate, corrosion potential, chloride concentration, and concrete conductivity have been developed and tested inside of model concrete slabs. The tests include electrochemical chloride driving as a method for test acceleration and wet/dry cycling. The corrosion rate and conductivity sensors perform very well, as do all aspects of the electronics. Work continues on the chloride sensor and reference electrode.
Accurate Deep Direct Geo-Localization from Ground Imagery and Phone-Grade GPS (2018)

One of the most critical topics in autonomous driving or ride-sharing technology is to accurately localize vehicles in the world frame. In addition to common multi-view camera systems, it usually also relies on industrial grade sensors, such as LiDAR, differential GPS, high precision IMU, and etc. In this paper, we develop an approach to provide an effective solution to this problem. We propose a method to train a geo-spatial deep neural network (CNN+LSTM) to predict accurate geo-locations (latitude and longitude) using only ordinary ground imagery and low accuracy phone-grade GPS. We evaluate our approach on the open dataset released during ACM Multimedia 2017 Grand Challenge. Having ground truth locations for training, we are able to reach nearly lane-level accuracy. We also evaluate the proposed method on our own collected images in San Francisco downtown area often described as "downtown canyon" where consumer GPS signals are extremely inaccurate. The results show the model can predict quality locations that suffice in real business applications, such as ride-sharing, only using phone-grade GPS. Unlike classic visual localization or recent PoseNet-like methods that may work well in indoor environments or small-scale outdoor environments, we avoid using a map or an SFM (structure-from-motion) model at all. More importantly, the proposed method can be scaled up without concerns over the potential failure of 3D reconstruction.
Energy Efficient Allocation of Virtual Machines in Cloud Data Centers (2010)

Rapid growth of the demand for computational power has led to the creation of large-scale data centers. They consume enormous amounts of electrical power resulting in high operational costs and carbon dioxide emissions. Moreover, modern Cloud computing environments have to provide high Quality of Service (QoS) for their customers resulting in the necessity to deal with power-performance trade-off. We propose an efficient resource management policy for virtualized Cloud data centers. The objective is to continuously consolidate VMs leveraging live migration and switch off idle nodes to minimize power consumption, while providing required Quality of Service. We present evaluation results showing that dynamic reallocation of VMs brings substantial energy savings, thus justifying further development of the proposed policy.
Reflectance modulator based on tandem Fabry-Perot resonators (1991)

We present calculations and data on a novel, electrically tunable reflector structure consisting of tandem Fabry–Perot resonators grown as a single epitaxial device. The device consists of three mirrors (quarter-wave stacks of AlGaAs and AlAs) separated by two cavities (one an AlGaAs alloy and the other a GaAs/AlGaAs superlattice) on a GaAs substrate. The tandem cavities produce a characteristic double-dipped reflectance spectrum which can be modulated by tunable electro-optic effects in the superlattice cavity. Our demonstration device has a modulation depth of ≳10% over a 20 nm bandwidth with &lt;4 V of bias swing.
Gold Nanoparticle-Assisted Laser Therapy for the Disruption of Methicillin-Resistant Staphylococcus aureus Biofilms (2016)

Abstract : The purpose of this study was to develop a method to destroy bacterial biofilms using energy absorbing gold nanoparticles (GNPs) in combination with pulsed laser irradiation. Methicillin-resistant Staphylococcus aureus (MRSA) biofilms were cultured in vitro for 24 hours and then treated with 0, 62.5, 125, 250, or 500 micro g/mL of GNPs for 1 to 5 hours. Biofilms were then exposed to 10 to 110 laser pulses (532 nm, 8 ns, 1 Hz) or sham exposed. The crystal violet assay for biofilm biomass revealed that optimal dispersion of MRSA biofilms was achieved after treatment with 500 micro g/mL of GNPs for 5 h followed by 50 laser pulses. Treatment of the biofilms with a combination of GNPs and laser irradiation led to a 63 +/- 8% reduction in colony forming units (CFUs) relative to controls and a 79 +/- 10% dispersion of biofilms as evidenced by confocal microscopy. Conversely, biofilms treated with 50 laser pulses alone or GNPs alone showed no discernible dispersion or reduction in CFUs compared to untreated controls. These results demonstrate the use of GNP-assisted laser therapy as a potential strategy to disrupt biofilms and, therefore, enhance the therapeutic efficacy of mainstay antibiotic regimens.
Penalized maximum likelihood reconstruction for x-ray differential phase-contrast tomography (2015)

Although the proposed cost function is inherently nonconvex, it can be used to reconstruct images with less aliasing artifacts and less streak artifacts than reconstruction methods based on phase retrieval. Furthermore, the proposed method can be used to reconstruct images of sliding window acquisitions with negligible smearing artifacts.
New approach to growth of high-quality GaAs layers on Si substrates (1987)

GaAs films were grown by molecular beam epitaxy (MBE) on Si (100) substrates using a two-step growth process of a 300 °C GaAs buffer layer followed by a 600 °C device layer. The films were examined by Rutherford backscattering and x-ray diffraction methods. A significant reduction in the defect density near the GaAs/Si interface and in the bulk of these films was observed when the buffer layer was deposited by alternately supplying Ga atoms and As4 molecules to the substrate, rather than applying conventional MBE. Possible reasons for this reduction of crystal defects are discussed.
Generating topic maps from XML/XSD documents (2013)

Over the years, XML has become a prominent standard for data exchange on the Web. Although XML can support syntactic inter-operability, problems arise when data sources represented as XML documents are needed to be integrated. The reason is that XML does not support sharing of concepts. This issues can be overcome by having suitable ontology representations of XML documents. The Semantic Web languages can play an important role here as they support ontology representation. Topic Map is a Semantic Web formalism (an ISO standard) for knowledge representation and interchange with an emphasis on navigation and retrieval of information. In this work we propose a framework for automatically generating Topic Map ontology from XML. We make use of XQuery and Tolog to validate our method. We illustrate our technique on examples. We also provide performance measures of our approach on some standard data sets.
Spinal codes (2012)

Spinal codes are a new class of rateless codes that enable wireless networks to cope with time-varying channel conditions in a natural way, without requiring any explicit bit rate selection. The key idea in the code is the sequential application of a pseudo-random hash function to the message bits to produce a sequence of coded symbols for transmission. This encoding ensures that two input messages that differ in even one bit lead to very different coded sequences after the point at which they differ, providing good resilience to noise and bit errors. To decode spinal codes, this paper develops an approximate maximum-likelihood decoder, called the bubble decoder , which runs in time polynomial in the message size and achieves the Shannon capacity over both additive white Gaussian noise (AWGN) and binary symmetric channel (BSC) models. Experimental results obtained from a software implementation of a linear-time decoder show that spinal codes achieve higher throughput than fixed-rate LDPC codes, rateless Raptor codes, and the layered rateless coding approach of Strider, across a range of channel conditions and message sizes. An early hardware prototype that can decode at 10 Mbits/s in FPGA demonstrates that spinal codes are a practical construction.