gebhart/patrepeval huggingface dataset:
Validation of Hemoglobin Concentration Imaging of Breast Tumors Through Comparison with Pathological Assessment (2002)

Pathologically determined percentage vessel density measurement is used to compare with the percent blood volume, in order to estimate the validity of local hemoglobin concentrations reconstructed by near-infrared tomography of human breast cancer tumors.
Molecular Basis for the Unique Role of the AAA+ Chaperone ClpV in Type VI Protein Secretion (2011)

Ring-forming AAA(+) ATPases act in a plethora of cellular processes by remodeling macromolecules. The specificity of individual AAA(+) proteins is achieved by direct or adaptor-mediated association with substrates via distinct recognition domains. We investigated the molecular basis of substrate interaction for Vibrio cholerae ClpV, which disassembles tubular VipA/VipB complexes, an essential step of type VI protein secretion and bacterial virulence. We identified the ClpV recognition site within VipB, showed that productive ClpV-VipB interaction requires the oligomeric state of both proteins, solved the crystal structure of a ClpV N-domain-VipB peptide complex, and verified the interaction surface by mutant analysis. Our results show that the substrate is bound to a hydrophobic groove, which is formed by the addition of a single α-helix to the core N-domain. This helix is absent from homologous N-domains, explaining the unique substrate specificity of ClpV. A limited interaction surface between both proteins accounts for the dramatic increase in binding affinity upon ATP-driven ClpV hexamerization and VipA/VipB tubule assembly by coupling multiple weak interactions. This principle ensures ClpV selectivity toward the VipA/VipB macromolecular complex.
Evaluation of Differences in Temporal Synchrony Between Brain Regions in Individuals With Autism and Typical Development (2018)

Whereas the magnitude of functional connectivity in autism is variable across brain regions, participant samples, and development, prolonged temporal synchrony of functional connections is reproducibly observed in autism, suggesting a potential mechanism for core symptoms.
A Multiscale Statistical Evaluation of DRAM Variable Retention Time (2021)

This paper presents a multiscale physics-based approach for evaluating DRAM cell retention time including variable retention time effects. The flow goes from ab-initio DFT simulation to high-sigma SPICE analysis, allowing for the evaluation of the causes and retention time related failure states for DRAM technologies.
Scaffold Topologies. 2. Analysis of Chemical Databases (2008)

We have systematically enumerated graph representations of scaffold topologies for up to eight-ring molecules and four-valence atoms, thus providing coverage of the lower portion of the chemical space of small molecules (Pollock et al. J. Chem. Inf. Model., this issue). Here, we examine scaffold topology distributions for several databases: ChemNavigator and PubChem for commercially available chemicals, the Dictionary of Natural Products, a set of 2742 launched drugs, WOMBAT, a database of medicinal chemistry compounds, and two subsets of PubChem, "actives" and DSSTox comprising toxic substances. We also examined a virtual database of exhaustively enumerated small organic molecules, GDB (Fink et al. Angew. Chem., Int. Ed. 2005, 44, 1504-1508), and we contrast the scaffold topology distribution from these collections to the complete coverage of up to eight-ring molecules. For reasons related, perhaps, to synthetic accessibility and complexity, scaffolds exhibiting six rings or more are poorly represented. Among all collections examined, PubChem has the greatest scaffold topological diversity, whereas GDB is the most limited. More than 50% of all entries (13 000 000+ actual and 13 000 000+ virtual compounds) exhibit only eight distinct topologies, one of which is the nonscaffold topology that represents all treelike structures. However, most of the topologies are represented by a single or very small number of examples. Within topologies, we found that three-way scaffold connections (3-nodes) are much more frequent compared to four-way (4-node) connections. Fused rings have a slightly higher frequency in biologically oriented databases. Scaffold topologies can be the first step toward an efficient coarse-grained classification scheme of the molecules found in chemical databases.
Immunogenicity of novel mRNA COVID-19 vaccine MRT5500 in mice and non-human primates (2020)

Summary An effective vaccine to address the global pandemic of coronavirus disease 2019 (COVID-19) is an urgent public health priority 1 . Novel synthetic mRNA and vector-based vaccine technologies offer an expeditious development path alternative to traditional vaccine approaches. Here we describe the efforts to utilize an mRNA platform for rational design and evaluations of mRNA vaccine candidates based on Spike (S) glycoprotein of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus causing COVID-19. Several mRNA constructs expressing various structural conformations of S-protein, including wild type (WT), a pre-fusion stabilized mutant (2P), a furin cleavage-site mutant (GSAS) and a double mutant form (2P/GSAS), were tested in a preclinical animal model for their capacity to elicit neutralizing antibodies (nAbs). The lead 2P/GSAS candidate was further assessed in dose-ranging studies in mice and Cynomolgus macaques. The selected 2P/GSAS vaccine formulation, now designated MRT5500, elicited potent nAbs as measured in two types of neutralization assays. In addition, MRT5500 elicited T H 1-biased responses in both mouse and non-human primate species, a result that helps to address a hypothetical concern regarding potential vaccine-associated enhanced respiratory diseases associated with T H 2-biased responses. These data position MRT5500 as a viable vaccine candidate for clinical development against COVID-19.
Field evaluation of a Pan-Lassa rapid diagnostic test during the 2018 Nigerian Lassa fever outbreak (2020)

Lassa virus (LASV) is the causative agent of Lassa fever (LF), an often-fatal hemorrhagic disease. LF is endemic in Nigeria, Sierra Leone and other West African countries. Diagnosis of LASV infection is challenged by the genetic diversity of the virus, which is greatest in Nigeria. The ReLASV Pan-Lassa Antigen Rapid Test (Pan-Lassa RDT) is a point-of-care, in vitro diagnostic test that utilizes a mixture of polyclonal antibodies raised against recombinant nucleoproteins of representative strains from the three most prevalent LASV lineages (II, III and IV). We compared the performance of the Pan-LASV RDT to available quantitative PCR (qPCR) assays during the 2018 LF outbreak in Nigeria. For patients with acute LF (RDT positive, IgG/IgM negative) during initial screening, RDT performance was 83.3% sensitivity and 92.8% specificity when compared to composite results of two qPCR assays. 100% of samples that gave Ct values below 22 on both qPCR assays were positive on the Pan-Lassa RDT. There were significantly elevated case fatality rates and elevated liver transaminase levels in subjects whose samples were RDT positive compared to RDT negative.
Improved Carbonylation of Heterocyclic Chlorides and Electronically Challenging Aryl Bromides (2004)

[reaction: see text] Optimized conditions are described that effect the carbonylation of diverse heterocyclic chlorides to yield the desired alkyl esters. In addition, bromoanilines and bromoanisoles, which normally are poor substrates under standard carbonylation protocols, were efficiently converted to the desired products under these new conditions. The nature of the metal bidentate ligand complex was found to be critical. Specifically, a correlation between ligand bite angle and catalytic efficiency is documented.
How many tiers? (2011)

ISPs are increasingly selling "tiered" contracts, which offer Internet connectivity to wholesale customers in bundles, at rates based on the cost of the links that the traffic in the bundle is traversing. Although providers have already begun to implement and deploy tiered pricing contracts, little is known about how to structure them. While contracts that sell connectivity on finer granularities improve market efficiency, they are also more costly for ISPs to implement and more difficult for customers to understand. Our goal is to analyze whether current tiered pricing practices in the wholesale transit market yield optimal profits for ISPs and whether better bundling strategies might exist. In the process, we deliver two contributions: 1) we develop a novel way of mapping traffic and topology data to a demand and cost model, and 2) we fit this model on three large real-world networks: an European transit ISP, a content distribution network, and an academic research network, and run counterfactuals to evaluate the effects of different bundling strategies. Our results show that the common ISP practice of structuring tiered contracts according to the cost of carrying the traffic flows (e.g., offering a discount for traffic that is local) can be suboptimal and that dividing contracts based on both traffic demand and the cost of carrying it into only three or four tiers yields near-optimal profit for the ISP.
Impact of Nitridation on Negative and Positive Charge Buildup in SiC Gate Oxides (2008)

We report on the effect of nitridation on the negative and positive charge buildup in SiC gate oxides during carrier injection. We observe that the incorporation of nitrogen at the SiO2/SiC interface can enhance the reliability of the interface by suppressing the generation of interface states upon electron injection but that it can also degrade the oxide by creating additional hole traps. We relate these phenomena to the passivation of atomic-level defects by nitrogen.
An instrumental variable approach to non-linear model-based adaptive control of engine speed (2005)

An instrumental variable approach to non-linear model-based adaptive control of engine speed regulation was investigated and implemented on a spark ignition internal combustion engine. A four-step version of instrumental variable parameter estimation is used to identify a bias-free and noise tolerant model of the engine dynamics from the by-pass air valve voltage input to the output engine speed. The parametric model representing the engine dynamics is a truncated Volterra series structure. Model-based adaptive control is accomplished through a partitioned non-linear model inversion of the engine model. The desired throttle response and disturbance rejection dynamics are introduced via a two-degree-of-freedom control structure. Performance of the non-linear model-based adaptive control algorithm has been verified experimentally.
N Th-Generation Product Ion (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Power Applications (2015)

Power cables are the technology of choice for supplying and distributing electrical power in densely populated areas where the ground is covered with buildings and traffic routes. Superconducting (SC) materials have the capability to transport extremely high currents nearly without resistance. There are two fundamental designs of high-temperature superconductor (HTS)-cables: warm dielectric cables and cold dielectric cables. The use of superconducting devices requires that electric current be supplied to low-temperature devices. These devices typically include large superconducting magnets and particle accelerator magnets that are made with low-temperature superconductors (LTSs). The superconducting fault current limiters (SFCLs) could be divided into the following two major categories: resistive and inductive SFCLs. This chapter discusses technological issues for the manufacture of reliable SC transformers. Two types of storage technology rely on superconductivity namely, superconducting magnetic energy storage (SMES), and flywheel energy storage system (FESS) based on superconducting magnetic bearings (SMBs).
Package size effects on the gains of patch antennas and finite patch arrays (2013)

This paper discusses the package size effect on a patch or patch array, particularly on antenna gain variations which are important for phased array applications. Study indicates choosing the package size properly can minimize the variation.
Delivery of Cytokines by Liposomes. I. Preparation and Characterization of Interleukin-2 Encapsulated in Long-Circulating Sterically Stabilized Liposomes (1994)

In an attempt to enhance the therapeutic efficacy of interleukin-2 (IL-2), recombinant human IL-2 was encapsulated either in large conventional liposomes or in small (mean diameter 65 nm), unilamellar, long-circulating, extravasating liposomes [referred to as sterically stabilized liposomes (SSLs)]. The SSL-IL-2 activity was assessed in vitro and in mice in comparison with soluble IL-2, IL-2 in conventional liposomes (non-SSL-IL-2), and pegilated IL-2 (PEG-IL-2). The main observations were as follows: (a) SSLs were far better carriers than conventional liposomes with regard to encapsulation efficiency and pharmacokinetics; (b) > 85% of IL-2 biological activity was consistently encapsulated in SSLs; (c) SSL-IL-2 was much more stable than soluble IL-2 at 4 and 37 degrees C; (d) SSL-IL-2, but not "empty" liposomes, bound in vitro to IL-2 receptor-bearing T-cells, indicating that the domain of the cytokine molecule involved in binding to the receptor is exposed on the outer liposome membrane; (e) release of IL-2 from the liposomes was not required for its in vitro biological activity; (f) plasma half-lives (t1/2 alpha, t1/2 beta) and area under the curve (AUC) of SSL-IL-2 were 10-30 times greater than those of soluble IL-2 and similar to those of PEG-IL-2; and (g) IL-2 is released from the SSLs in vivo with a t1/2 of approximately 40 min, although the SSL-IL-2s retained their steric stabilization in the plasma for > 4 h, with little liposome accumulation in the reticuloendothelial system. These data, together with the improved immunomodulatory and antitumor activity of SSL-IL-2 in mice, suggest that SSL-IL-2 might be a therapeutic agent superior to soluble IL-2.
The performance of adaptive frequency allocation in an environment of non-cooperative interference (2005)

WLAN technology is likely to be a part of future wireless broadband communication systems. As the wireless unlicensed radio traffic increases, the need for good solutions to co-existence problems caused by interference becomes apparent. In this paper the performance of a hypothetical WLAN operating at 17 GHz, using decentralized dynamic channel allocation, is assessed in regard to its susceptibility to external interference. Three different interference cases are studied. The first case is narrowband static interference. The second case is wideband interference, similar to the interference caused by a spread spectrum system. The third case is agile interference caused by a frequency hopping system. In all cases the WLAN and the interferers are located in the same geographical location. The results suggest that the chosen channel allocation algorithm, adaptive frequency allocation, provides excellent channel plans within seconds from start-up as long as the interference is static. It is however not, as it is defined here, able to perform well when the interfering devices use frequency hopping technology.
Microwave frequency beating between monolithically integrated quantum-dot ring lasers (2007)

The fabrication of quantum-dot-based optoelectronic integrated circuits incorporating twin ring diode lasers, waveguides, directional couplers, a Y-junction mixer, and photodetectors, is reported. Microwave frequency beating between longitudinal modes from individual ring diode lasers as well as beat notes between integrated twin ring diode lasers are demonstrated.
Rigid Partitioning Techniques for Efficiently Generating 3D Reconstructions from Images (2004)

This thesis explores efficient techniques for generating 3D reconstructions from imagery. Non-linear optimization is one of the core techniques used when computing a reconstruction and is a computational bottleneck for large sets of images. Since non-linear optimization requires a good initialization to avoid getting stuck in local minima, robust systems for generating reconstructions from images build up the reconstruction incrementally. A hierarchical approach is to split up the images into small subsets, reconstruct each subset independently and then hierarchically merge the subsets. Rigidly locking together portions of the reconstructions reduces the number of parameters needed to represent them when merging, thereby lowering the computational cost of the optimization.\n\nWe present two techniques that involve optimizing with parts of the reconstruction rigidly locked together. In the first, we start by rigidly grouping the cameras and scene features from each of the reconstructions being merged into separate groups. Cameras and scene features are then incrementally unlocked and optimized until the reconstruction is close to the minimum energy. This technique is most effective when the influence of the new measurements is restricted to a small set of parameters.\n\nMeasurements that stitch together weakly coupled portions of the reconstruction, though, tend to cause deformations in the low error modes of the reconstruction and cannot be efficiently incorporated with the previous technique. To address this, we present a spectral technique for clustering the tightly coupled portions of a reconstruction into rigid groups. Reconstructions partitioned in this manner can closely mimic the poorly conditioned, low error modes, and therefore efficiently incorporate measurements that stitch together weakly coupled portions of the reconstruction. We explain how this technique can be used to scalably and efficiently generate reconstructions from large sets of images.
Recent developments linking retroviruses to human breast cancer: infectious agent, enemy within or both? (2014)

Evidence is accumulating that one or more beta-retrovirus is associated with human breast cancer. Retroviruses can exist as an infectious (exogenous) virus or as a part of the genetic information of cells due to germline integration (endogenous). An exogenous virus with a genome that is highly homologous to mouse mammary tumour virus is gaining acceptance as possibly being associated with human breast cancer, and recently furnished evidence is discussed in this article, as is the evidence for involvement of an endogenous human beta-retrovirus, HERV-K. Modes of interaction are also reviewed and linkages to the APOBEC3 family are suggested.
Lung response to low-frequency underwater sound (1999)

The response of the lung to exposure to low-frequency underwater sound was investigated for frequencies of 100–500 Hz. Several different experimental and theoretical approaches demonstrated that the lung responds to low-frequency underwater sound as a resonant structure. Measurements of acoustic scattering near murine and rat lung indicated that the response of the lung to low-frequency acoustic fields can be described well by the theory of linear oscillations of a bubble in water. The measured mean resonance frequency was 325 Hz for adult mice (30 g), 420 Hz for young mice (10 g), and 175 Hz for rats (320 g). Noninvasive measurements of the displacement amplitude of the lung using an ultrasonic pulse-echo ranging technique confirmed that the lung oscillates in response to exposure near the resonance frequency. At the resonance frequency the response of the lung is maximized and the thresholds for damage to the lung and surrounding tissues (such as liver) were lowest. For exposure of adult mice at the resonance frequency, the threshold for lung hemorrhage and for liver hemorrhage was ∼184 dB re: 1 μPa (i.e., 1.6 kPa).
Isolation of Aurantiamide Acetate fromArisaema erubescens (1996)

Aurantiamide acetate (N-benzoyl-1-phenylalanyl-1-pheylalaninol acetate) has been isolated by chromatographic separation of a methanol extract of Arisaema erubescens and its structure confirmed by synthesis.
Enhancing phytoremediation through the use of transgenics and endophytes (2008)

In the last decade, there has been an increase in research on improving the ability of plants to remove environmental pollution. Genes from microbes, plants, and animals are being used successfully to enhance the ability of plants to tolerate, remove, and degrade pollutants. Through expression of specific bacterial genes in transgenic plants, the phytotoxic effects of nitroaromatic pollutants were overcome, resulting in increased removal of these chemicals. Overexpression of mammalian genes encoding cytochrome P450s led to increased metabolism and removal of a variety of organic pollutants and herbicides. Genes involved in the uptake or detoxification of metal pollutants were used to enhance phytoremediation of this important class of pollutants. Transgenic plants containing specific bacterial genes converted mercury and selenium to less toxic forms. In addition to these transgenic approaches, the use of microbes that live within plants, termed endophytes, also led to improved tolerance to normally phytotoxic chemicals and increased removal of the pollutants. Bacteria that degraded a herbicide imparted resistance to the herbicide when inoculated into plants. In another study, plants harboring bacteria capable of degrading toluene were more tolerant to normally phytotoxic concentrations of the chemical, and transpired less of it into the atmosphere. This review examines the recent advances in enhancing phytoremediation through transgenic plant research and through the use of symbiotic endophytic microorganisms within plant tissues.
Research Guides: Wagner College Archive: Digital Collections (2012)

The Wagner Archive is dedicated to collecting and preserving materials documenting the history and legacy of Wagner College.
Fabrication and Characterization of a Yellow-Emitting BCNO Phosphor for White Light-Emitting Diodes (2009)

A yellow-emitting phosphor comprised of boron, carbon, nitrogen, and oxygen (BCNO) atoms without any rare-earth ions as luminescence centers was successfully synthesized using a facile process at low temperature and atmospheric pressure. The synthesized BCNO powders showed a broad emission spectrum centered at under excitation at due to the radiation transitions of local luminescence provided in the species. Further analysis revealed that the BCNO yellow phosphor exhibited a high external quantum efficiency (60%) having a hexagonal-BN crystalline structure mixed with cubic-. The synthesized yellow-emitting BCNO phosphor is promising for high-efficiency phosphor conversion-based white light-emitting diodes.
Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease (2017)

In this hypothesis-generating analysis, gene expression networks in relation to asthma severity provided potentially new insight into biological mechanisms associated with the development of SA and its phenotypes.