gebhart/patrepeval huggingface dataset:
SARS-CoV-2 Nucleocapsid Protein Interacts with RIG-I and Represses RIG-Mediated IFN-β Production (2020)

SARS-CoV-2 is highly pathogenic in humans and poses a great threat to public health worldwide. Clinical data shows a disturbed type I interferon (IFN) response during the virus infection. In this study, we discovered that the nucleocapsid (N) protein of SARS-CoV-2 plays an important role in the inhibition of interferon beta (IFN-β) production. N protein repressed IFN-β production induced by poly(I:C) or upon Sendai virus (SeV) infection. We noted that N protein also suppressed IFN-β production, induced by several signaling molecules downstream of the retinoic acid-inducible gene I (RIG-I) pathway, which is the crucial pattern recognition receptor (PRR) responsible for identifying RNA viruses. Moreover, our data demonstrated that N protein interacted with the RIG-I protein through the DExD/H domain, which has ATPase activity and plays an important role in the binding of immunostimulatory RNAs. These results suggested that SARS-CoV-2 N protein suppresses the IFN-β response through targeting the initial step, potentially the cellular PRR-RNA-recognition step in the innate immune pathway. Therefore, we propose that the SARS-CoV-2 N protein represses IFN-β production by interfering with RIG-I.
Changes in EEG Cross-Frequency Coupling During Cognitive Behavioral Therapy for Social Anxiety Disorder (2011)

Coupling between EEG delta and beta oscillations is enhanced among anxious and healthy individuals during anticipatory anxiety. EEG coupling patterns associated with psychotherapy have not yet been quantified in socially anxious individuals. In this study, we used a double baseline, repeated measures design, in which 25 adults with a principal diagnosis of social anxiety disorder completed 12 weekly sessions of standardized group cognitive behavioral therapy and four EEG assessments: two at pretreatment, one at midtreatment, and one at posttreatment. Treatment was associated with reductions in symptom severity across multiple measures and informants, as well as reductions in delta-beta coupling at rest and during speech anticipation. Moreover, the clinical group exhibited greater coupling at pretreatment than did post hoc control participants with low social anxiety. The EEG cross-frequency profiles in the clinical group normalized by the posttreatment assessment. These findings provide evidence of concomitant improvement in neural and behavioral functioning among socially anxious adults undergoing psychotherapy.
Recombinant rabbit hemorrhagic disease virus capsid protein expressed in baculovirus self-assembles into viruslike particles and induces protection (1994)

VP60, the unique component of rabbit hemorrhagic disease virus capsid, was expressed in the baculovirus system. The recombinant VP60, released in the supernatant of infected insect cells, assembled without the need of any other viral component to form viruslike particles (VLPs), structurally and immunologically indistinguishable from the rabbit hemorrhagic disease virion. Intramuscular vaccination of rabbits with the VLPs conferred complete protection in 15 days; this protection was found to be effective from the fifth day after VLP injection and was accompanied by a strong humoral response.
Component adaptation and assembly using interface relations (2010)

Software's expense owes partly to frequent reimplementation of similar functionality and partly to maintenance of patches, ports or components targeting evolving interfaces. More modular non-invasive approaches are unpopular because they entail laborious wrapper code. We propose Cake, a rule-based language describing compositions using interface relations. To evaluate it, we compare several existing wrappers with reimplemented Cake versions, finding the latter to be simpler and better modularised.
A Two-Tier Distributed Electronic Design Framework (2002)

We present the concept of a distributed, web-based electronic design framework. The salient feature of our system is the extension of the client-server architecture to two-tiers, with the web server serving client requests whilst acting as client to the tool servers. In the sample application of the framework, developed in Java, any of the servers can be based on Linux, MS Windows or SunSPARC server. The web server that has been used to demonstrate the framework for on-line access to VAMS (a VHDL-AMS parser) and Avant! HSPICE is currently available for Linux but has been developed with a truly platform independent implementation in mind.
Splatting without the blur (1999)

Splatting is a volume rendering algorithm that combines efficient volume projection with a sparse data representation: Only voxels that have values inside the iso-range need to be considered, and these voxels can be projected via efficient rasterization schemes. In splatting, each projected voxel is represented as a radially symmetric interpolation kernel, equivalent to a fuzzy ball. Projecting such a basis function leaves a fuzzy impression, called a footprint or splat, on the screen. Splatting traditionally classifies and shades the voxels prior to projection, and thus each voxel footprint is weighted by the assigned voxel color and opacity. Projecting these fuzzy color balls provides a uniform screen image for homogeneous object regions, but leads to a blurry appearance of object edges. The latter is clearly undesirable, especially when the view is zoomed on the object. In this work, we manipulate the rendering pipeline of splatting by performing the classification and shading process after the voxels have been projected onto the screen. In this way, volume contributions outside the iso-range never affect the image. Since shading requires gradients, we not only splat the density volume, using regular splats, but we also project the gradient volume, using gradient splats. However, alternative to gradient splats, we can also compute the gradients on the projection plane, using central differencing. This latter scheme cuts the number of footprint rasterization by a factor of four, since only the voxel densities have to be projected. Our new method renders objects with crisp edges and well-preserved surface detail. Added overhead is the calculation of the screen gradients and the per-pixel shading. Both of these operations, however, may be performed using fast techniques employing lookup tables.
Near-infrared diode laser airborne hygrometer (1994)

We describe a new laser-based hygrometer for ambient water vapor monitoring which uses a fiber-optic coupled, near-infrared diode laser in conjunction with high frequency wavelength modulation spectroscopy. The instrument operates unattended, uses little power, can be extremely compact, and exhibits high detection sensitivity. This instrument was flown on a KC-135 aircraft for a period of six months and measured frost points at altitudes between 10 000 and 40 000 ft. The water detection sensitivity corresponds to a volume mixing ratio of 8 ppm V. Further improvements including the use of newly designed near-infrared lasers are expected to realize frost points below −100 °C.
A novel family of hemicellulolytic α‐glucuronidase (2009)

Investigation of the xylanolytic enzyme system of the xylose-fermenting yeast Pichia stipitis resulted in the discovery of an extracellular alpha-glucuronidase efficiently debranching hardwood glucuronoxylan. This activity is not exhibited by more extensively investigated alpha-glucuronidases of glycoside hydrolase (GH) family 67, operating on substrates in which the uronic acid is linked to the non-reducing xylopyranosyl residues of main chain fragments. The N-terminus of the purified enzyme corresponded exactly to the P. stipitis gene ABN67901 coding for a protein of unknown function. BLAST search revealed the presence of similar genes in genomes of other microorganisms. These results lead to the emergence of a new family of alpha-glucuronidases.
The oxidation-reduction potentials of compound I/compound II and compound II/ferric couples of horseradish peroxidases A2 and C. (1979)

The reversibility of the stepwise reduction of Compound I to the ferric state via Compound II was confirmed in horseradish peroxidases A2 and C. The values of E'o (compound I/Compound II) and E'O (Compound II/ferric) were measured from equilibrium data coupled with the K2IrCl6-K3IrCl6 system in a narrow region of pH near 6.3. The ferric enzymes were also oxidized by ferricyanide to Compound II at alkaline pH and the values of E'O (Compound II/ferric) were measured from the equilibrium data. The pH dependence of E'O (Compound II/ferric) was in accord with the equation: E'O = EO + 0.058 log (Kr[H+] + [H+]2)/(KO + [H+]), where Kr and KO are proton dissociation constants in the ferric enzyme and Compound II, respectively. The pH-E'O (Compound I/Compound II) curves were likewise obtained from the equation, E'O = EO + 0.058 log (Kr + [H+]), where Kr is the proton dissociation constant in Compound II. The forward and backward rate constants were measured in each of one-electron transfer reactions of the peroxidases with the K2IrCl6-K3IrCl6 system at various pH values. The E'O values calculated on the assumption that the ratio of the rate constants equals the equilibrium constant were compared with those obtained from the equilibrium data.
Quantitative characterization of biotic iron oxides by analytical electron microscopy (2002)

Hydrous ferric oxides (HFO) play a tremendous role in the environment, and as a result, they have often been analyzed for their bulk chemical and mineralogical composition, but rarely at the particle level. This study used a combination of transmission electron microscopy (TEM), parallel electron energy loss spectroscopy (TEM-PEELS), and selected area electron diffraction (TEM-SAED), to determine the morphology, stoichiometry, and mineralogy of synthetic biotic HFO and assess the effect of specimen preparation (i.e., dehydration) on their overall chemical composition. A mixture of synthetic lepidocrocite (γ-FeOOH) and goethite (α-FeOOH) was used as reference material for all TEM analyses. HFO were formed by the oxidation of Fe2+ (pH = 8) in the presence of <em>Bacillus subtilis</em> (bacteria without extracellular polymers) and <em>Bacillus licheniformis</em> cells (with extracellular polymers). Biotic Fe-oxides occurred as small particles (5–10 nm diameter) on the bacterial cell walls and associated exopolymers and were identified as 2-line ferrihydrite by TEM-SAED. Quantitative TEM-PEELS results showed that (1) freeze-dried abiotic samples had an Fe/O atomic ratio of 0.54 ± 0.03, whereas the Fe/O ratio of the biotic ferrihydrite formed in the presence of <em>B. licheniformis</em> and <em>B. subtilis</em> was 0.48 ± 0.06 and 0.54 ± 0.08, respectively; (2) air-dried biotic ferrihydrite possessed an Fe/O ratio close to 0.30, whereas the ratio of the abiotic air-dried HFO samples remained unchanged (i.e., 0.51 ± 0.04). These results indicate that quantitative TEM-PEELS can be used for the chemical characterization of Fe-oxides, since the measured Fe/O atomic ratios of the reference HFO are in agreement with their known stoichiometry (i.e., 0.50 for FeOOH). Our results also suggest that ferrihydrite dehydrates during freeze-drying and that specimen preparation is very important when assessing chemical composition.
Study of blood charring precursor states using backscattering at 663 nm from blood and optical window boundary (2012)

The transient optical changes in blood prior to charring may be caused by changes in the morphology of RBCs on the optical window surface. Backscattering light power measurements may be a practical method to detect the precursor state of charring.
Macroautophagy is deregulated in murine and human lupus T lymphocytes (2012)

Macroautophagy was recently shown to regulate both lymphocyte biology and innate immunity. In this study we sought to determine whether a deregulation of autophagy was linked to the development of autoimmunity. Genome-wide association studies have pointed out nucleotide polymorphisms that can be associated with systemic lupus erythematosus, but the potential role of autophagy in the initiation and/or development of this syndrome is still unknown. Here, we provide first clues of macroautophagy deregulation in lupus. By the use of LC3 conversion assays and electron microscopy experiments, we observed that T cells from two distinct lupus-prone mouse models, i.e., MRL (lpr/lpr) and (NZB/NZW)F1, exhibit high loads of autophagic compartments compared with nonpathologic control CBA/J and BALB/c mice. Unlike normal mice, autophagy increases with age in murine lupus. In vivo lipopolysaccharide stimulation in CBA/J control mice efficiently activates T lymphocytes but fails to upregulate formation of autophagic compartments in these cells. This argues against a deregulation of autophagy in lupus T cells solely resulting from an acute inflammation injury. Autophagic vacuoles quantified by electron microscopy are also found to be significantly more frequent in T cells from lupus patients compared with healthy controls and patients with non-lupus autoimmune diseases. This elevated number of autophagic structures is not distributed homogeneously and appears to be more pronounced in certain T cells. These results suggest that autophagy could regulate the survival of autoreactive T cell during lupus, and could thus lead to design new therapeutic options for lupus.
Bismuth Telluride Hexagonal Nanoplatelets and Their Two-Step Epitaxial Growth (2005)

We report a synthesis of discrete, single-crystal, defect-free, and hexagonal Bi2Te3 nanoplatelets using a high-temperature organic solution approach, and we demonstrate a two-step epitaxial growth of the cylindrical strings of Bi2Te3 nanoplatelets on the surface of the Te rod by packing them along c-axis in a top-bottom-top-bottom sequence. This type of building-up provides additional opportunity for the exploration of novel thermoelectric properties from such quantum-confined materials, in which the boundary scattering of phonons is anticipated to enhance.
Randomness Amplification under Minimal Fundamental Assumptions on the Devices (2016)

Recently, the physically realistic protocol amplifying the randomness of Santha-Vazirani sources producing cryptographically secure random bits was proposed; however, for reasons of practical relevance, the crucial question remained open regarding whether this can be accomplished under the minimal conditions necessary for the task. Namely, is it possible to achieve randomness amplification using only two no-signaling components and in a situation where the violation of a Bell inequality only guarantees that some outcomes of the device for specific inputs exhibit randomness? Here, we solve this question and present a device-independent protocol for randomness amplification of Santha-Vazirani sources using a device consisting of two nonsignaling components. We show that the protocol can amplify any such source that is not fully deterministic into a fully random source while tolerating a constant noise rate and prove the composable security of the protocol against general no-signaling adversaries. Our main innovation is the proof that even the partial randomness certified by the two-party Bell test [a single input-output pair (u^{*}, x^{*}) for which the conditional probability P(x^{*}|u^{*}) is bounded away from 1 for all no-signaling strategies that optimally violate the Bell inequality] can be used for amplification. We introduce the methodology of a partial tomographic procedure on the empirical statistics obtained in the Bell test that ensures that the outputs constitute a linear min-entropy source of randomness. As a technical novelty that may be of independent interest, we prove that the Santha-Vazirani source satisfies an exponential concentration property given by a recently discovered generalized Chernoff bound.
Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini (2007)

Individual posttranslational modifications (PTMs) on histones have well established roles in certain biological processes, notably transcriptional programming. Recent genomewide studies describe patterns of covalent modifications, such as H3 methylation and acetylation at promoters of specific target genes, or "bivalent domains," in stem cells, suggestive of a possible combinatorial interplay between PTMs on the same histone. However, detection of long-range PTM associations is often problematic in antibody-based or traditional mass spectrometric-based analyses. Here, histone H3 from a ciliate model was analyzed as an enriched source of transcriptionally active chromatin. Using a recently developed mass spectrometric approach, combinatorial modification states on single, long N-terminal H3 fragments (residues 1-50) were determined. The entire modification status of intact N termini was obtained and indicated correlations between K4 methylation and H3 acetylation. In addition, K4 and K27 methylation were identified concurrently on one H3 species. This methodology is applicable to other histones and larger polypeptides and will likely be a valuable tool in understanding the roles of combinatorial patterns of PTMs.
Passive and active probe arrays for dip-pen nanolithography (2002)

The development of passive and active atomic force microscope (AFM) probe arrays is reported in this paper. The devices are specifically designed to work with Dip-Pen Nanolithography and are fabricated using MEMS micromachining techniques. These devices can generate sub-100 nm patterns in a high speed, parallel, and controllable fashion.
Antibiotic resistance: a rundown of a global crisis (2018)

The advent of multidrug resistance among pathogenic bacteria is imperiling the worth of antibiotics, which have previously transformed medical sciences. The crisis of antimicrobial resistance has been ascribed to the misuse of these agents and due to unavailability of newer drugs attributable to exigent regulatory requirements and reduced financial inducements. Comprehensive efforts are needed to minimize the pace of resistance by studying emergent microorganisms, resistance mechanisms, and antimicrobial agents. Multidisciplinary approaches are required across health care settings as well as environment and agriculture sectors. Progressive alternate approaches including probiotics, antibodies, and vaccines have shown promising results in trials that suggest the role of these alternatives as preventive or adjunct therapies in future.
Synthesis of Diode Molecules and Their Sequential Assembly to Control Electron Transport (2004)

A sequential deprotection and immobilization procedure was enabled by the synthesis of two thiophene–thiazole diblock oligomers with two different thiol protection groups. Investigation of the I/V behaviors of these diblock molecules between two gold electrodes (see picture) showed that the rectifying direction was controlled by their orientation between the electrodes.
Hand-foot Syndrome in a Patient with Multiple Fire Ant Stings (2004)

The case is reported of an elderly patient with known previous exposure to fire ant stings, and who presented with hand-foot syndrome (HFS) in the setting of multiple fire ant stings to the lower extremities. Both hands and both feet were red, swollen, and mildly tender. Treatment was with fluocinonide cream, and all symptoms resolved as the classic fire ant skin lesions regressed. HFS was initially reported in association with acute crisis in sickle cell anemia and thalassemia and more recently as a common toxicity of chemotherapy administration. This is the first report of its occurrence in the setting of fire ant envenomization. Although recent literature may indicate a potential therapeutic benefit from COX-2 antagonists, the process appears to be self-limited, and requires only conservative treatment.
Reactions of Ammonium Polyphosphates with Soil Minerals (1967)

Abstract When suspended in solutions of ammonium pyro‐ or tripoly‐phosphates at room temperature, calcium and magnesium carbonates reacted rapidly and clay minerals and hydrous oxides of iron and aluminum reacted slowly. The precipitated solid products of the reactions included calcium and magnesium ammonium pyro‐ and tripolyphosphates and iron and aluminum ammonium pyrophosphates but no tripolyphosphates; no solid orthophosphates were formed. The condensed phosphates were much less reactive with the soil minerals than are orthophosphates.
High‐Efficiency Orange and Tandem White Organic Light‐Emitting Diodes Using Phosphorescent Dyes with Horizontally Oriented Emitting Dipoles (2014)

Tandem white organic light-emitting diodes (WOLEDs) using horizontally oriented phosphorescent dyes in an exciplex-forming co-host are presented, along with an orange OLED. A high external quantum efficiency of 32% is achieved for the orange OLED at 1000 cd m(-2) and the tandem WOLEDs exhibit a high maximum EQE of 54.3% (PE of 63 lm W(-1)).
Low energy electron-beam proximity projection lithography: Discovery of a missing link (1999)

Low energy electron(e)-beam proximity projection lithography is proposed for integrated circuit lithography for minimum feature sizes ⩽0.1 μm. This new e-beam lithography is similar to optical projection lithography except that photons are replaced by low energy electrons of 2 kV. The low e-beam energy permits the use of single crystal 0.5 μm thick silicon membrane masks without an absorbing metal layer of high atomic number. This membrane mask is thick enough for good heat conduction and thin enough for feature sizes ⩽0.1 μm. The mask distortion caused by the fabrication can be corrected by a fine-tuning deflector. Therefore the mask is allowed to have a residual distortion of more than 100 nm. The proposed system does not suffer from the space charge effect in the electron optics column nor the proximity effect with respect to both the wafer and mask writings, and it is fundamentally a low power lithography which needs no special cooling system. The analysis shows that the e-beam column can be made entirely of electrostatic components to achieve sufficient resolution. For an appropriate resist process for this low energy e-beam we propose a bilayer process which consists of a chemically amplified thin deep ultraviolet photoresist and a thick antireflective layer. We estimated a throughput of 30 12 in. wafers per hour and a resolution of less than 50 nm.
Capacity analysis of automated material handling systems in semiconductor fabs (2004)

A critical aspect of semiconductor manufacturing is the design and analysis of material handling and production control polices to optimize fab performance. As wafer sizes have increased, semiconductor fabs have moved toward the use of automated material handling systems (AMHS). However, the behavior of AMHS and the effects of AMHS on fab productivity is not well understood. This research involves the development of a design and analysis methodology for evaluating the throughput capacity of AMHS. A set of simulation experiments is used to evaluate the throughput capacity of an AMHS and the effects on fab performance measures. The analysis uses SEMATECH fab data for full semiconductor fabs to evaluate the AMHS throughput capacity.