gebhart/patrepeval huggingface dataset:
A Novel Type of Influenza Vaccine: Safety and Immunogenicity of Replication‐Deficient Influenza Virus Created by Deletion of the Interferon Antagonist NS1 (2009)

BACKGROUND. The nonstructural protein NS1 of influenza virus counteracts the interferon-mediated immune response of the host. By deleting the open reading frame of NS1, we have generated a novel type of influenza vaccine. We studied the safety and immunogenicity of an influenza strain lacking the NS1 gene (DeltaNS1-H1N1) in healthy volunteers. METHODS. Healthy seronegative adult volunteers were randomized to receive either a single intranasal dose of the DeltaNS1-H1N1 A/New Caledonia vaccine at 1 of 5 dose levels (6.4, 6.7, 7.0, 7.4, and 7.7 log(10) median tissue culture infective dose) (n = 36 recipients) or placebo (n = 12 recipients). RESULTS. Intranasal vaccination with the replication-deficient DeltaNS1-H1N1 vaccine was well tolerated. Rhinitis-like symptoms and headache were the most common adverse events identified during the 28-day observation period. Adverse events were similarly distributed between the treatment and placebo groups. Vaccine-specific local and serum antibodies were induced in a dose-dependent manner. In the highest dose group, vaccine-specific antibodies were detected in 10 of 12 volunteers. Importantly, the vaccine also induced neutralizing antibodies against heterologous drift variants. CONCLUSIONS. We show that vaccination with an influenza virus strain lacking the viral interferon antagonist NS1 induces statistically significant levels of strain-specific and cross-neutralizing antibodies despite the highly attenuated replication-deficient phenotype. Further studies are warranted to determine whether these results translate into protection from influenza virus infection. TRIAL REGISTRATION. ClinicalTrials.gov identifier: NCT00724997 .
Proximity (2012)

We describe a method for determining coordination requirements in collaborative software development. Our method uses "live" data based on developer activity rather than relying on historical data such as source code commits which is prevalent in existing methods. We introduce proximity, a measure of the strength of the work dependencies that lead to coordination requirements among members of a software development organization. Our proximity measure relies on a tool which captures the interactions of a developer with her IDE. It quantifies the similarity between records of interactions of developers as they work on their assigned tasks. We describe an algorithm that measures proximity between pairs of tasks or pairs of developers. Through an empirical study on an open source project that routinely records environment interaction data, we show how proximity accurately determines coordination requirements. The proximity measure thus enables proactive detection of coordination requirements and makes possible real time intervention and coordination facilitation via management-, design- and team-related decisions.
Analysis of Cholesterol in All Lipoprotein Classes by Single Vertical Ultracentrifugation of Fingerstick Blood and Controlled-Dispersion Flow Analysis (1992)

This new, highly sensitive analytical system, based on controlled dispersion of the flowing sample, gives a rapid, continuous, and direct analysis for cholesterol in all lipoprotein classes, separated by single vertical-spin density-gradient ultracentrifugation. In this Vertical Auto Profile-II fingerstick system, designated VAP-IIfs, a narrow-bore Teflon coil serves as the reactor with no segmentation of the analytical stream by air bubbles, in contrast to the Technicon AutoAnalyzer used in the VAP-I method. Concentrations of high-, low-, intermediate-, and very-low-density lipoprotein cholesterol and lipoprotein(a) cholesterol are determined by decomposing the spectrophotometric absorbance curve for the continuous analysis of the centrifuged sample, with use of software developed in this laboratory. Total cholesterol is determined from the total area under the absorbance curve. For assaying total cholesterol, the CV between aliquots within a rotor ranged from 1.35% to 3.15%; the CV between rotors was 2.45%. Because only 18 microL of sample is required, VAP-IIfs can be readily adapted to analysis for lipoprotein cholesterol profiles in capillary blood samples. Total cholesterol values by VAP-IIfs for fingerstick and venous samples from 23 subjects agreed well: slope = 1.01 (SD 0.03), intercept = -21 (SD 51) mg/L, Sy/x = 50 mg/L, and r = 0.992. Results by VAP-IIfs also correlated highly with results for duplicate samples analyzed at the Northwest Lipid Research Laboratories.
CU-LTE: Spectrally-efficient and fair coexistence between LTE and Wi-Fi in unlicensed bands (2016)

To cope with the increasing scarcity of spectrum resources, researchers have been working to extend LTE/LTE-A cellular systems to unlicensed bands, leading to so-called unlicensed LTE (U-LTE). However, this extension is by no means straightforward, primarily because the radio resource management schemes used by LTE and by systems already deployed in unlicensed bands are incompatible. Specifically, it is well known that coexistence with scheduled systems like LTE degrades considerably the throughput of Wi-Fi networks that are based on carrier-sense medium access schemes. To address this challenge, we propose for the first time a cognitive coexistence scheme to enable spectrum sharing between U-LTE and Wi-Fi networks, referred to as CU-LTE. The proposed scheme is designed to jointly determine dynamic channel selection, carrier aggregation and fractional spectrum access for U-LTE networks, while guaranteeing fair spectrum access for Wi-Fi based on a newly designed cross-technology fairness criterion. We first derive a mathematical model of the spectrum sharing problem for the coexisting networks; we then design a solution algorithm to solve the resulting fairness constrained mixed integer nonlinear optimization problem. The algorithm, based on a combination of branch and bound and convex relaxation techniques, maximizes the network utility with guaranteed optimality precision that can be set arbitrarily to 1 at the expense of computational complexity. Performance evaluation indicates that near-optimal spectrum access can be achieved with guaranteed fairness between U-LTE and Wi-Fi. Issues regarding implementation of CU-LTE are also discussed.
Layout optimization of the secondary coils for wireless power transfer systems (2015)

Due to the complexity of wireless power transfer systems, little literature to date has addressed the development of systematic and efficient design framework for determining the optimal layout of coils. In this paper, introducing the concepts of fixed grid-based coil representation and effective turns, a novel layout optimization is proposed to determine the optimal layout of the secondary coils when the primary coils are given. Using the proposed method, the secondary-coil layouts are successfully determined to maximize the induced voltages while satisfying mass constraints. The optimized layouts are then validated through the experiments under the same conditions.
MicroRNAs as novel immunotherapeutics (2013)

A large unmet need exists for cost-effective, widely available antineoplastic immunotherapeutic agents with a robust translational potential. MicroRNAs (miRNAs) that regulate tumor-mediated immunosuppression or immune checkpoints can induce robust therapeutic immune responses, indicating that miRNAs may ultimately become part of the portfolio of anticancer immunotherapeutics.
Global-to-local Memory Pointer Networks for Task-Oriented Dialogue (2019)

End-to-end task-oriented dialogue is challenging since knowledge bases are usually large, dynamic and hard to incorporate into a learning framework. We propose the global-to-local memory pointer (GLMP) networks to address this issue. In our model, a global memory encoder and a local memory decoder are proposed to share external knowledge. The encoder encodes dialogue history, modifies global contextual representation, and generates a global memory pointer. The decoder first generates a sketch response with unfilled slots. Next, it passes the global memory pointer to filter the external knowledge for relevant information, then instantiates the slots via the local memory pointers. We empirically show that our model can improve copy accuracy and mitigate the common out-of-vocabulary problem. As a result, GLMP is able to improve over the previous state-of-the-art models in both simulated bAbI Dialogue dataset and human-human Stanford Multi-domain Dialogue dataset on automatic and human evaluation.
Broadband Raman Amplifiers (2002)

Internet traffic has been increasing at a rate faster than what one would expect on the basis of Moore’s law, generating an urgent need for the development of technologies that can serve as an alternative to conventional WDM transmission based on erbium-doped fiber amplifiers (EDFAs). Since the percentage of data traffic exceeds the percentage of voice traffic, networks worldwide must evolve from voice-centric systems to data-centric systems. The trend translates into a need for higher capacity and longer distance transmission than can be supplied by conventional WDM.
An emerging micro-scale immuno-analytical diagnostic tool to see the unseen. Holding promise for precision medicine and P4 medicine B Analytical technologies in the biomedical and life sciences (2016)

Over the years, analytical chemistry and immunology have contributed significantly to the field of clinical diagnosis by introducing quantitative techniques that can detect crucial and distinct chemical, biochemical and cellular biomarkers present in biosamples. Currently, quantitative two-dimensional hybrid immuno-analytical separation technologies are emerging as powerful tools for the sequential isolation, separation and detection of protein panels, including those with subtle structural changes such as variants, isoforms, peptide fragments, and post-translational modifications. One such technique to perform this challenging task is immunoaffinity capillary electrophoresis (IACE), which combines the use of antibodies and/or other affinity ligands as highly selective capture agents with the superior resolving power of capillary electrophoresis. Since affinity ligands can be polyreactive, i.e., binding and capturing more than one molecule, they may generate false positive results when tested under mono-dimensional procedures; one such application is enzyme-linked immunosorbent assay (ELISA). IACE, on the other hand, is a two-dimensional technique that captures (isolation and enrichment), releases, separates and detects (quantification, identification and characterization) a single or a panel of analytes from a sample, when coupled to one or more detectors simultaneously, without the presence of false positive or false negative data. This disruptive technique, capable of preconcentrate on-line results in enhanced sensitivity even in the analysis of complex matrices, may change the traditional system of testing biomarkers to obtain more accurate diagnosis of diseases, ideally before symptoms of a specific disease manifest.In this manuscript, we will present examples of the determination of biomarkers by IACE and the design of a miniaturized multi-dimensional IACE apparatus capable of improved sensitivity, specificity and throughput, with the potential of being used as a point-of-care instrument and holding promise for precision medicine and P4 medicine.
On the geometry of stabilizer states (2014)

Large-scale quantum computation is likely to require massive quantum error correction (QEC). QEC codes and circuits are described via the stabilizer formalism, which represents stabilizer states by keeping track of the operators that preserve them. Such states are obtained by stabilizer circuits (consisting of CNOT, Hadamard and Phase gates) and can be represented compactly on conventional computers using Θ(n2) bits, where n is the number of qubits [18]. As an additional application, the work in [1, 2] suggests the use of superpositions of stabilizer states to represent arbitrary quantum states. To aid in such applications and improve our understanding of stabilizer states, we characterize and count nearest-neighbor stabilizer states, quantify the distribution of angles between pairs of stabilizer states, study succinct stabilizer superpositions and stabilizer bivectors, explore the approximation of non-stabilizer states by single stabilizer states and short linear combinations of stabilizer states, develop an improved inner-product computation for stabilizer states via synthesis of compact canonical stabilizer circuits, propose an orthogonalization procedure for stabilizer states, and evaluate several of these algorithms empirically.
Solid component evaluation in mixed ground glass nodules (2007)

Multi-Slice Computed Tomography (MSCT) imaging of the lungs allow for detection and follow-up of very small lesions including solid and ground glass nodules (GGNs). However relatively few computer-based methods have been implemented for GGN segmentation. GGNs can be divided into pure GGNs and mixed GGNs, which contain both nonsolid and solid components (SC). This latter category is especially of interest since some studies indicate a higher likelihood of malignancy in GGNs with SC. Due to their characteristically slow growth rate, GGNs are typically monitored with multiple follow-up scans, making measurement of the volume of both solid and non-solid component especially desirable. We have developed an automated method to estimate the SC percentage within a segmented GGN. First, the SC algorithm uses a novel method to segment out the solid structures, while excluding any vessels passing near or through the nodule. A gradient distribution analysis around solid structures validates the presence or absence of SC. We tested 50 GGNs, split between three groups: 15 GGNs with SC, 15 GGNs with a solid nodule added to simulate SC, and 20 GGNs without SC. With three defined satisfaction levels for the segmentation (A: succeed, B: acceptable, C: failed), the first group resulted in 60% with score A, 40% with score B, 0% with score C. The second group resulted in 66.7% with score A and 33.3% with score B. In testing the first and 3rd groups, the algorithm correctly detected SC in all cases where it was present (sensitivity of 100%) and correctly determined absence of SC in 15 out of 20 cases (specificity 75%).
Mechanically-Assisted Electrochemical Production of Graphene Oxide (2016)

Graphene oxide (GO) is promising for a variety of applications due to its excellent dispersibility and processability. However, current chemical oxidation routes have several drawbacks, including the use of explosive oxidizing agents, residual metal ions contaminations, and the creation of irreparable hole defects on the GO sheet. The electrochemical exfoliation and oxidation of graphite is a potentially greener approach without the need for extensive purification steps. Most reported electrochemical methods employ a single preformed bulk graphite as electrode, which limits their scalability, reproducibility, and degree of oxidation. Herein, we reported a novel mechanically assisted electrochemical method to produce graphene oxide directly from graphite flakes. The electrochemically derived graphene oxide (EGO) shows a good degree of oxidation but with less physical defects than chemically derived graphene oxide (CGO). EGO has good dispersibility in water and various solvents and, in particular, displays better long-term stability in ethanol when compared with CGO. Notably, unlike conventional CGO, EGO can undergo facile thermal conversion at 200 °C in air to conductive thermally processed EGO, which is highly desirable for heat/chemical-sensitive applications.
High -gain inner-shell photoionization laser in Cd vapor pumped by soft-x-ray radiation from a laser-produced plasma source (1983)

A soft-x-ray-pumped inner-shell photoionization laser has been produced in Cd vapor at 4416 and 3250 A. A gain of 5.6 cm(-1) has been measured at 4416 A, and a reasonably high-energy storage of 0.2 mJ/cm(3) in the upper laser states has been obtained.
Abstract 1818: ERBB3/HER2 signaling limits the effectiveness of EGFR blockade in head and neck and colorectal cancer models (2014)

Abstract Introduction: EGFR blocking antibodies are approved for the treatment of colorectal cancer (CRC) and head and neck squamous cell carcinoma (HNSCC). However, responses to single agent EGFR blocking antibodies are relatively infrequent and transient. Thus, there is a clear need for agents that can enhance the benefit of EGFR blockade. While ERBB3 signaling has been proposed to limit the effectiveness of EGFR inhibitors, the underlying molecular mechanisms are not fully understood. In this report, we employ blocking antibodies against ERBB3 (REGN1400) and EGFR (REGN955), as well as a HER2 blocking antibody, to investigate the role of ERBB3 in modulating the response to EGFR inhibition. Experimental procedures and results: We show that EGFR and ERBB3 are co-activated in multiple HNSCC cell lines and that combined blockade of EGFR and ERBB3 inhibits the growth of these cell lines more effectively than blockade of either receptor alone. Western blotting analysis shows that REGN955 strongly inhibits activation of ERK, but not Akt, while REGN1400 strongly inhibits activation of Akt, but not ERK, consistent with the more potent effect of the combination on cell growth. In addition, using a colorectal cancer cell line with low endogenous ERBB3 activity, we show that neuregulin 1 treatment significantly increases ERBB3 phosphorylation and reverses the inhibitory effect of REGN955 on cell growth. To further understand the mechanism of ERBB3 activation, we employed a HER2 blocking antibody to show that ERBB3 phosphorylation in HNSCC and CRC cells is strictly dependent on association with HER2, but not EGFR, and that neuregulin 1 activates ERBB3/HER2 signaling to reverse the effect of EGFR blockade on CRC cell growth. Finally, while REGN1400 and REGN955 as single agents slowed the growth of HNSCC and CRC xenografts, the combination of REGN1400 plus REGN955 caused significant tumor regression. Summary and conclusion: Our findings demonstrate that ERBB3 partners with HER2 to activate the Akt survival pathway and to limit the effect of EGFR blockade on the growth of HNSCC and CRC cell lines and tumor xenografts. These findings suggest that REGN1400, which is currently in a Phase 1 clinical trial, could provide clinical benefit when combined with EGFR blocking antibodies. Citation Format: Li Zhang, Carla Castanaro, Bo Luan, Katie Yang, Amy Fan, John Rudge, Nicholas Papadopoulos, Gavin Thurston, Christopher Daly. ERBB3/HER2 signaling limits the effectiveness of EGFR blockade in head and neck and colorectal cancer models. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1818. doi:10.1158/1538-7445.AM2014-1818
Antibiosis‐type insect resistance in transgenic plants expressing a teratocyte secretory protein (TSP14) gene from a hymenopteran endoparasite (<i>Microplitis croceipes</i>) (2003)

We have isolated a teratocyte secretory protein (TSP14) gene product from a hymenopteran endoparasite that disrupts the growth of lepidopteran insect larvae. To evaluate the insecticidal activity of TSP14 for the protection of crops from insect damage, chimeric gene constructs of TSP14 were expressed in transgenic plants. The coding sequence of the TSP14 gene, with and without its native signal peptide, was placed between the modified peanut chlorotic streak virus (PClSV) full-length transcript (FLt) promoter with duplicated enhancer domains and the terminator sequence from the rbcSE9 gene. These chimeric genes, expressed in transgenic tobacco (Nicotiana tabacum cv. Samsun NN) were stably inherited in successive plant generations (R0, R1 and R2 progeny) as shown by molecular analysis. A Western blot analysis of plant extracts showed the presence of a polypeptide of the expected size that cross-reacted with TSP14-specific antibodies. Larvae of the tobacco budworm (Heliothis virescens) and tobacco hornworm (Manduca sexta) which were fed with several independent homozygous transgenic plant lines (R2 progeny) exhibited mortality and reduced growth rates compared to those fed with plants transformed by a vector control. Our results demonstrate the potential for introduction of the TSP14 gene into plants in order to achieve protection against lepidopteran pests.
Automated glycan assembly of a <i>S. pneumoniae</i> serotype 3 CPS antigen (2016)

Vaccines against S. pneumoniae, one of the most prevalent bacterial infections causing severe disease, rely on isolated capsular polysaccharide (CPS) that are conjugated to proteins. Such isolates contain a heterogeneous oligosaccharide mixture of different chain lengths and frame shifts. Access to defined synthetic S. pneumoniae CPS structures is desirable. Known syntheses of S. pneumoniae serotype 3 CPS rely on a time-consuming and low-yielding late-stage oxidation step, or use disaccharide building blocks which limits variability. Herein, we report the first iterative automated glycan assembly (AGA) of a conjugation-ready S. pneumoniae serotype 3 CPS trisaccharide. This oligosaccharide was assembled using a novel glucuronic acid building block to circumvent the need for a late-stage oxidation. The introduction of a washing step with the activator prior to each glycosylation cycle greatly increased the yields by neutralizing any residual base from deprotection steps in the synthetic cycle. This process improvement is applicable to AGA of many other oligosaccharides.
ChemInform Abstract: Catalytic Enantioselective Olefin Metathesis Reactions (2011)

Abstract Review: 112 refs.
Synthesis and Cytostatic and Antiviral Profiling of Thieno-Fused 7-Deazapurine Ribonucleosides (2017)

Two isomeric series of new thieno-fused 7-deazapurine ribonucleosides (derived from 4-substituted thieno[2',3':4,5]pyrrolo[2,3-d]pyrimidines and thieno[3',2':4,5]pyrrolo[2,3-d]pyrimidines) were synthesized by a sequence involving Negishi coupling of 4,6-dichloropyrimidine with iodothiophenes, nucleophilic azidation, and cyclization of tetrazolopyrimidines, followed by glycosylation and cross-couplings or nucleophilic substitutions at position 4. Most nucleosides (from both isomeric series) exerted low micromolar or submicromolar in vitro cytostatic activities against a broad panel of cancer and leukemia cell lines and some antiviral activity against HCV. The most active were the 6-methoxy, 6-methylsulfanyl, and 6-methyl derivatives, which were highly active to cancer cells and less toxic or nontoxic to fibroblasts.
Development of the first well-defined tungsten oxo alkyl derivatives supported on silica by SOMC: towards a model of WO<sub>3</sub>/SiO<sub>2</sub> olefin metathesiscatalyst (2010)

A well-defined, silica-supported tungsten oxo alkyl species prepared by the surface organometallic chemistry approach displays high and sustained activity in propene metathesis. Remarkably, its catalytic performances outpace those of the parent imido derivative, underlining the importance of the oxo ligand in the design of robust catalysts.