gebhart/patrepeval huggingface dataset:
Recombinant scrapie-like prion protein of 106 amino acids is soluble (1996)

The N terminus of the scrapie isoform of prion protein (PrPSc) can be truncated without loss of scrapie infectivity and, correspondingly, the truncation of the N terminus of the cellular isoform, PrPC, still permits conversion into PrPSc. To assess whether additional segments of the PrP molecule can be deleted, we previously removed regions of putative secondary structure in PrPC; in the present study we found that deletion of each of the four predicted helices prevented PrPSc formation, as did deletion of the stop transfer effector region and the C178A mutation. Removal of a 36-residue loop between helices 2 and 3 did not prevent formation of protease-resistant PrP; the resulting scrapie-like protein, designated PrPSc106, contained 106 residues after cleavage of an N-terminal signal peptide and a C-terminal sequence for glycolipid anchor addition. Addition of the detergent Sarkosyl to cell lysates solubilized PrPSc106, which retained resistance to digestion by proteinase K. These results suggest that all the regions of proposed secondary structure in PrP are required for PrPSc formation, as is the disulfide bond stabilizing helices 3 and 4. The discovery of PrPSc106 should facilitate structural studies of PrPSc, investigations of the mechanism of PrPSc formation, and the production of PrPSc-specific antibodies.
Parametric study of a room-temperature metal vapor laser (1988)

We have demonstrated laser operation at room temperature on the Cui (511,578 nm) and Aui (312,628 nm) transitions and obtained specific pulse energies for the Cui 511 nm and Aui 628 nm lines of about 5 and 2 μJ cm−3, respectively, from a single-section tube. A simple theoretical model has been used to show that the reduced outputs for the Cui 578 nm and Aui 312 nm lines are due to the significantly smaller fraction of the working volume in saturation in each case. The metal vapor column of length 20 cm and local ground-state concentration in the 1014–1015 cm−3 range is produced on demand in a single-section tube in less than 10 ms. The highest output power obtained is for a 90% He in an Ar/He mixture at a total flowrate of 1.8 ℓ min−1, the tube pressure being 20 mbar. A specific sputtering discharge energy of approximately 600 mJ cm−3 is needed to obtain a peak power of 1 kW on either the Cui 511 nm or Aui 628 nm lines.
Alignment tolerant stripline directional couplers (2002)

The design methodology for a new type of alignment tolerant, broadside coupled, stripline, directional coupler is developed. The coupler uses an even number of cascaded, asymmetric, broadside coupled line stages that are electrically short (</spl lambda//sub g//8) and have been alternately inverted to achieve nearly symmetric coupling and return loss at all ports. The results demonstrate layer to layer alignment insensitivity that enables coupler designs where misalignment between layers is a critical parameter. Measured S-parameter results for 3 dB and 10 dB coupler designs are presented and agree well with theory. Coupling range variations less than 0.5 dB are achieved for a 3 dB alignment tolerant coupler design compared to 0.9 dB for a standard, symmetric 3 dB design with misalignments of +/-0.25 mm (+/-0.010"). An 8.4 dB alignment tolerant directional coupler displays a variation of 0.3 dB over the same layer to layer alignment range compared to an equivalent 10 dB standard design that has a coupling variation of 4.9 dB with similar misalignment between layers.
Concentric circle scanning system for large-area and high-precision imaging (2015)

Large-area manufacturing surfaces containing micro- and nano-scale features and large-view biomedical targets motivate the development of large-area, high-resolution and high-speed imaging systems. Compared to constant linear velocity scans and raster scans, constant angular velocity scans can significantly attenuate transient behavior while increasing the speed of imaging. In this paper, we theoretically analyze and evaluate the speed, acceleration and jerks of concentric circular trajectory sampling (CCTS). We then present a CCTS imaging system that demonstrates less vibration and lower mapping errors than raster scanning for creating a Cartesian composite image, while maintaining comparably fast scanning speed for large scanning area.
Combined differential and static pressure sensor based on a double-bridged structure (2005)

A combined differential and static silicon microelectromechanical system pressure sensor based on a double piezoresistive Wheatstone bridge structure is presented. The developed sensor has a conventional (inner) bridge on a micromachined diaphragm and a secondary (outer) bridge on the chip substrate. A novel approach is demonstrated with a combined measurement of outputs from the two bridges, which results in a combined deduction of both differential and static media pressure. Also following this new approach, a significant improvement in differential pressure sensor accuracy is achieved. Output from the two bridges depends linearly on both differential and absolute (relative to atmospheric pressure) media pressure. Furthermore, the sensor stress distributions involved are studied by three-dimensional finite-element (FE) stress analysis. Furthermore, the FE analysis evaluates current and other potential piezoresistor positions on the outer Wheatstone bridge.
Controlled Angiogenesis in Peptide Nanofiber Composite Hydrogels (2015)

Multidomain peptide (MDP) nanofibers create scaffolds that can present bioactive cues to promote biological responses. Orthogonal self-assembly of MDPs and growth-factor-loaded liposomes generate supramolecular composite hydrogels. These composites can act as delivery vehicles with time-controlled release. Here we examine the controlled release of placental growth factor-1 (PlGF-1) for its ability to induce angiogenic responses. PlGF-1 was loaded either in MDP matrices or within liposomes bound inside MDP matrices. Scaffolds showed expected rapid infiltration of macrophages. When released through liposomes incorporated in MDP gels (MDP(Lipo)), PlGF-1 modulates HUVEC VEGF receptor activation in vitro and robust vessel formation in vivo. These loaded MDP(Lipo) hydrogels induce a high level of growth-factor-mediated neovascular maturity. MDP(Lipo) hydrogels offer a biocompatible and injectable platform to tailor drug delivery and treat ischemic tissue diseases.
Masking the overhead of protocol layering (1996)

Protocol layering has been advocated as a way of dealing with the complexity of computer communication. It has also been criticized for its performance overhead. In this paper, we present some insights in the design of protocols, and how these insights can be used to mask the overhead of layering, in a way similar to client caching in a file system. With our techniques, we achieve an order of magnitude improvement in end-to-end message latency in the Horus communication framework. Over an ATM network, we are able to do a round-trip message exchange, of varying levels of semantics, in about 170 µseconds, using a protocol stack of four layers that were written in ML, a high-level functional language.
Differentially Expressed Genes in Hepatopancreas of Acute Hepatopancreatic Necrosis Disease Tolerant and Susceptible Shrimp (Penaeus vannamei) (2021)

Acute hepatopancreatic necrosis disease (AHPND) is a lethal disease in marine shrimp that has caused large-scale mortalities in shrimp aquaculture in Asia and the Americas. The etiologic agent is a pathogenic <i>Vibrio</i> sp. carrying binary toxin genes, <i>pir</i>A and <i>pir</i>B in plasmid DNA. Developing AHPND tolerant shrimp lines is one of the prophylactic approaches to combat this disease. A selected genetic line of <i>Penaeus vannamei</i> was found to be tolerant to AHPND during screening for disease resistance. The mRNA expression of twelve immune and metabolic genes known to be involved in bacterial pathogenesis were measured by quantitative RT-PCR in two populations of shrimp, namely P1 that showed susceptibility to AHPND, and P2 that showed tolerance to AHPND. Among these genes, the mRNA expression of chymotrypsin A (ChyA) and serine protease (SP), genes that are involved in metabolism, and crustin-P (CRSTP) and prophenol oxidase activation system 2 (PPAE2), genes involved in bacterial pathogenesis in shrimp, showed differential expression between the two populations. The differential expression of these genes shed light on the mechanism of tolerance against AHPND and these genes can potentially serve as candidate markers for tolerance/susceptibility to AHPND in <i>P. vannamei</i>. This is the first report of a comparison of the mRNA expression profiles of AHPND tolerant and susceptible lines of <i>P. vannamei</i>.
Quantitative GSTP1 Methylation and the Detection of Prostate Adenocarcinoma in Sextant Biopsies (2003)

Hypermethylation of the 5' promoter region of the glutathione S-transferase pi gene (GSTP1) occurs at a very high frequency in prostate adenocarcinoma. We compared the results of blinded histologic review of sextant biopsy samples from 72 excised prostates with those obtained using a quantitative methylation-specific polymerase chain reaction assay (QMSP) for GSTP1. Formal surgical pathologic review of the resected prostates was used to determine the number of patients with (n = 61) and without (n = 11) prostate cancer. Histology alone detected prostate carcinoma with 64% sensitivity (95% confidence interval [CI] = 51% to 76%) and 100% specificity (95% CI = 72% to 100%), whereas the combination of histology and GSTP1 QMSP at an assay threshold greater than 10 detected prostate carcinoma with 75% sensitivity (95% CI = 63% to 86%) and 100% specificity (95% CI = 72% to 100%), an 11% improvement (95% CI = 5% to 22%) in sensitivity over histology alone. The combination of histology and GSTP1 QMSP at an assay threshold greater than 5 detected prostate adenocarcinoma with 79% sensitivity (95% CI = 68% to 89%), a 15% improvement (95% CI = 7% to 26%) over histology alone. Thus, GSTP1 QMSP improved the sensitivity of histologic review of random needle biopsies for prostate cancer diagnosis. Further studies should determine whether detection of GSTP1 hypermethylation in a biopsy sample with normal histology indicates the need for an early repeat biopsy at the same site.
An optical fiber microprobe for surface-enhanced Raman scattering sensing with enhanced signal-to-background ratio (2019)

Surface-enhanced Raman scattering (SERS) is a highly sensitive and versatile analytical technique that can be implemented on an optical fiber platform for use in challenging environments. This work has sought to address a major factor limiting the use of optical fibers for SERS analytical applications, namely the silica Raman background generated inside the fiber can make it difficult to detect the target analyte. Two different approaches were investigated to address this problem. Firstly, double clad fiber (DCF) was found to increase the collection of Raman scattered signal from the analyte, giving up to twelve-fold improvement in the signal-to-background ratio (SBR). Secondly, a prototype microfilter was manufactured by femtosecond laser machining and attached directly to the DCF tip. Its performance in rejecting background signal was then evaluated. When taking the lengths of the optical fibers into account, the filtered DCF microprobe delivers 7.0 SBR.cm, while the bare DCF probe provided 3.0 SBR.cm. Therefore, the microfilter assembly more than doubled the performance of the SERS probe and, with further optimization in future, it shows great promise for ultra-compact SERS and Raman optical fiber probes.
Portable High-Voltage Power Supply and Electrochemical Detection Circuits for Microchip Capillary Electrophoresis (2003)

Miniaturized, battery-powered, high-voltage power supply, electrochemical (EC) detection, and interface circuits designed for microchip capillary electrophoresis (CE) are described. The dual source CE power supply provides +/- 1 kVDC at 380 microA and can operate continuously for 15 h without recharging. The amperometric EC detection circuit provides electrode potentials of +/-2 VDC and gains of 1, 10, and 100 nA/V. The CE power supply power is connected to the microchip through an interface circuit consisting of two miniature relays, diodes, and resistors. The microchip has equal length buffer and separation channels. This geometry allows the microchip to be controlled from only two reservoirs using fixed dc sources while providing a consistent and stable sample injection volume. The interface circuit also maintains the detection reservoir at ground potential and allows channel currents to be measured likewise. Data are recorded, and the circuits are controlled by a National Instruments signal interface card and software installed in a notebook computer. The combined size (4 in. x 6 in. x 1 in.) and weight (0.35 kg) of the circuits make them ideal for lab-on-a-chip applications. The circuits were tested electrically, by performing separations of dopamine and catechol EC and by laser-induced fluorescence visualization.
Sequence-to-Sequence Language Grounding of Non-Markovian Task Specifications (2018)

Often times, natural language commands issued to robots not only specify a particular target configuration or goal state but also outline constraints on how the robot goes about its execution. That is, the path taken to achieving some goal state is given equal importance to the goal state itself. One example of this could be instructing a wheeled robot to "go to the living room but avoid the kitchen," in order to avoid scuffing the floor. This class of behaviors poses a serious obstacle to existing language understanding for robotics approaches that map to either action sequences or goal state representations. Due to the non-Markovian nature of the objective, approaches in the former category must map to potentially unbounded action sequences whereas approaches in the latter category would require folding the entirety of a robot's trajectory into a (traditionally Markovian) state representation, resulting in an intractable decision-making problem. To resolve this challenge, we use a recently introduced probabilistic variant of Linear Temporal Logic (LTL) as a goal specification language for a Markov Decision Process (MDP). While demonstrating that standard neural sequence-to-sequence learning models can successfully ground language to this semantic representation, we also provide analysis that highlights generalization to novel, unseen logical forms as an open problem for this class of model. We evaluate our system within two simulated robot domains as well as on a physical robot, demonstrating accurate language grounding alongside a significant expansion in the space of interpretable robot behaviors.
Purification and Some Properties of a Trehalase from a Green Alga,<i>Lobosphaera</i>sp. (1994)

An unicellular green alga identified as Lobosphaera sp. by morphological observations was selected as a source of trehalase. The alga grew well heterotrophically and produced intracellular trehalase using Polypepton, yeast extract, and glycerol as nutrients. The enzyme was highly purified by ammonium sulfate fractionation, column chromatography on DEAE-Toyopearl, Sepharose CL-4B, and SP-Toyopearl. The molecular mass was estimated to be 400 kDa by gel filtration. SDS-PAGE indicated that the enzyme consisted of two subunits with a molecular mass range of 180-220 kDa and it contained carbohydrates. The enzyme was most active at pH 5.5 and at 65 degrees C and stable between pH 4-9 and below 65 degrees C. Fe3+ inactivated the enzyme. Sucrose was a competitive inhibitor with a Ki of 7.5 mM. The enzyme specifically hydrolyzed trehalase with a Km of 0.6 mM.
A robust background modeling and foreground object detection using color component analysis (2012)

Background modeling and foreground object detection are crucial techniques for embedded image surveillance systems. The popular and accurate methods are mostly pixel based, taking up more memory and requiring longer execution times. Thus, these techniques are not suitable for embedded platforms. This paper presents a block-based major color background modeling and a foreground detection algorithm that possesses efficient processing and low memory requirement in a complex scene, making them feasible for embedded platforms. Our proposed approach consumes 37% less memory and increases accuracy by at least 2.5% compared to other existing methods. Last, implementing the object detection algorithm on the 2.83GHz CPU, we can achieve 26 frames per second for the benchmark video with image size 768×576.
Content Bias in Online Health Search (2014)

Search engines help people answer consequential questions. Biases in retrieved and indexed content (e.g., skew toward erroneous outcomes that represent deviations from reality), coupled with searchers' biases in how they examine and interpret search results, can lead people to incorrect answers. In this article, we seek to better understand biases in search and retrieval, and in particular those affecting the accuracy of content in search results, including the search engine index, features used for ranking, and the formulation of search queries. Focusing on the important domain of online health search, this research broadens previous work on biases in search to examine the role of search systems in contributing to biases. To assess bias, we focus on questions about medical interventions and employ reliable ground truth data from authoritative medical sources. In the course of our study, we utilize large-scale log analysis using data from a popular Web search engine, deep probes of result lists on that search engine, and crowdsourced human judgments of search result captions and landing pages. Our findings reveal bias in results, amplifying searchers' existing biases that appear evident in their search activity. We also highlight significant bias in indexed content and show that specific ranking signals and specific query terms support bias. Both of these can degrade result accuracy and increase skewness in search results. Our analysis has implications for bias mitigation strategies in online search systems, and we offer recommendations for search providers based on our findings.
Characterization of Nda2, a Plastoquinone-reducing Type II NAD(P)H Dehydrogenase in Chlamydomonas Chloroplasts (2008)

Electron transfer pathways associated to oxygenic photosynthesis, including cyclic electron flow around photosystem I and chlororespiration, rely on non-photochemical reduction of plastoquinones (PQs). In higher plant chloroplasts, a bacterial-like NDH complex homologous to complex I is involved in PQ reduction, but such a complex is absent from Chlamydomonas plastids where a type II NAD(P)H dehydrogenase activity has been proposed to operate. With the aim to elucidate the nature of the enzyme-supporting non-photochemical reduction of PQs, one of the type II NAD(P)H dehydrogenases identified in the Chlamydomonas reinhardtii genome (Nda2) was produced as a recombinant protein in Escherichia coli and further characterized. As many type II NAD(P)H dehydrogenases, Nda2 uses NADH as a preferential substrate, but in contrast to the eukaryotic enzymes described so far, contains non-covalently bound FMN as a cofactor. When expressed at a low level, Nda2 complements growth of an E. coli lacking both NDH-1 and NDH-2, but is toxic at high expression levels. Using an antibody raised against the recombinant protein and based on its mass spectrometric identification, we show that Nda2 is localized in thylakoid membranes. Chlorophyll fluorescence measurements performed on thylakoid membranes show that Nda2 is able to interact with thylakoid membranes of C. reinhardtii by reducing PQs from exogenous NADH or NADPH. We discuss the possible involvement of Nda2 in cyclic electron flow around PSI, chlororespiration, and hydrogen production.
Selenium and Selenium–Sulfur Chemistry for Rechargeable Lithium Batteries: Interplay of Cathode Structures, Electrolytes, and Interfaces (2017)

In the search for a transformative new energy storage system, the rechargeable Li/sulfur battery is considered as one of the promising candidates due to its much higher energy density and lower cost than state-of-the-art lithium-ion batteries. However, the insulating nature of sulfur and the dissolution of intermediary polysulfides into the electrolyte significantly hinder its practical application. Very recently, selenium and selenium–sulfur systems have received considerable attention as cathode materials for rechargeable batteries owing to the high electronic conductivity (20 orders of magnitude higher than sulfur) and high volumetric capacity (3254 mAh/cm3) of selenium. In this Perspective, we present an overview of the implications of employing selenium and selenium–sulfur systems with different structures and compositions as electroactive materials for rechargeable lithium batteries. We also show how the cathode structures, electrolytes, and electrode–electrolyte interfaces affect the electrochemistry of Se- and Se–S -based cathodes. Furthermore, suggestions are provided on paths for future development of these cathodes.
Expression of a cassava granule‐bound starch synthase gene in the amylose‐free potato only partially restores amylose content (1999)

ABSTRACT Granule‐bound starch synthase I (GBSS I) is responsible for the synthesis of amylose in starch granules. A heterologous cassava GBSS I gene was tested for its ability to restore amylose synthesis in amylose‐free ( amf ) potato mutants. For this purpose, the cassava GBSS I was equipped with different transit peptides. In addition, a hybrid containing the potato transit peptide, the N‐terminal 89 amino acids of the mature potato GBSS I, and the C‐terminal part of cassava GBSS I was prepared. The transgenic starches were first analysed by iodine staining. Only with the hybrid could full phenotypic complementation of the amf mutation be achieved in 13% of the plants. Most transformants showed partial complementation, but interestingly the size of the blue core was similar in all granules derived from one tuber of a given plant. The amylose content was only partially restored, up to 60% of wild‐type values or potato GBSS I‐complemented plants; however, the GBSS activity in these granules was similar to that found in wild‐type ones. From this, and the observation that the hybrid protein (a partial potato GBSS I look‐alike) performs best, it was concluded that potato and cassava GBSS I have different intrinsic properties and that the cassava enzyme is not fully adapted to the potato situation.
An adaptive segment-based view synthesis optimization method for 3D-HEVC (2015)

This paper presents an adaptive segment-based view synthesis optimization (VSO) for depth map coding in 3D-HEVC. The original method skips lines of pixels where there is no change in depth data, and exhaustively renders pixels from all the rest of lines to get distortions from synthesized views. It brings unnecessary coding operations and ignores smaller regions which can also be skipped in VSO. The proposed method is designed to skip proper segments of pixels for the non-skipped lines based on both of the texture smoothness and depth data unchangeableness. Experimental results show that the proposed method can achieve low coding complexity without significant performance loss for the synthesized views.