gebhart/patrepeval huggingface dataset:
Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19 (2020)

Severe cases of coronavirus disease 2019 (COVID-19), caused by infection with SARS-Cov-2, are characterized by a hyperinflammatory immune response that leads to numerous complications. Production of proinflammatory neutrophil extracellular traps (NETs) has been suggested to be a key factor in inducing a hyperinflammatory signaling cascade, allegedly causing both pulmonary tissue damage and peripheral inflammation. Accordingly, therapeutic blockage of neutrophil activation and NETosis, the cell death pathway accompanying NET formation, could limit respiratory damage and death from severe COVID-19. Here, we demonstrate that synthetic glycopolymers that activate the neutrophil checkpoint receptor Siglec-9 suppress NETosis induced by agonists of viral toll-like receptors (TLRs) and plasma from patients with severe COVID-19. Thus, Siglec-9 agonism is a promising therapeutic strategy to curb neutrophilic hyperinflammation in COVID-19.<br>.
LRRK2 inhibitors induce reversible changes in nonhuman primate lungs without measurable pulmonary deficits (2020)

The kinase-activating mutation G2019S in leucine-rich repeat kinase 2 (LRRK2) is one of the most common genetic causes of Parkinson's disease (PD) and has spurred development of LRRK2 inhibitors. Preclinical studies have raised concerns about the safety of LRRK2 inhibitors due to histopathological changes in the lungs of nonhuman primates treated with two of these compounds. Here, we investigated whether these lung effects represented on-target pharmacology and whether they were reversible after drug withdrawal in macaques. We also examined whether treatment was associated with pulmonary function deficits. We conducted a 2-week repeat-dose toxicology study in macaques comparing three different LRRK2 inhibitors: GNE-7915 (30 mg/kg, twice daily as a positive control), MLi-2 (15 and 50 mg/kg, once daily), and PFE-360 (3 and 6 mg/kg, once daily). Subsets of animals dosed with GNE-7915 or MLi-2 were evaluated 2 weeks after drug withdrawal for lung function. All compounds induced mild cytoplasmic vacuolation of type II lung pneumocytes without signs of lung degeneration, implicating on-target pharmacology. At low doses of PFE-360 or MLi-2, there was ~50 or 100% LRRK2 inhibition in brain tissue, respectively, but histopathological lung changes were either absent or minimal. The lung effect was reversible after dosing ceased. Lung function tests demonstrated that the histological changes in lung tissue induced by MLi-2 and GNE-7915 did not result in pulmonary deficits. Our results suggest that the observed lung effects in nonhuman primates in response to LRRK2 inhibitors should not preclude clinical testing of these compounds for PD.
An experimental analysis of classifier ensembles for learning drifting concepts over time in autonomous outdoor robot navigation (2007)

Autonomous robot navigation in unstructured outdoor environments is a challenging area of active research and is currently unsolved. The navigation task requires identifying safe, traversable paths which allow the robot to progress toward a goal while avoiding obstacles. Stereo is an effective tool in the near field, but for smooth long-range trajectory planning or fast driving an approach is needed to understand far-field terrain as well. One approach is to apply Machine Learning techniques that accomplish near-to-far learning by augmenting near-field Stereo readings with learned classifications of the appearance of safe terrain and obstacles in the far field. A key problem with basic instantiations of this approach is that they are not able to identify obstacles in the far field unless there are examples of those obstacles in the near field within the same image, which is not always the case. This leads to a common failure mode in autonomous navigation where incorrect trajectories are followed by the robot as a result of short-sightedness. 
This thesis proposes to address this problem through the use of classifier ensembles which serve as a mechanism to store previously learned terrain models. Such ensembles are shown in the literature to improve predictive performance in both static environments and in the dynamic environments associated with the problem domain. In this domain, individual models are trained over time and added to an on-line model library as the robot navigates towards a goal. These stored models serve as memory and can be used for terrain classification of an incoming image. The key issues for this task are model selection of appropriate models from the library and the subsequent model combination of each selected model's output. 
Several methods for selecting and combining models from the library are proposed: choosing the best K models from the library, Bayesian Model Averaging, and a proposed adaptation of Ensemble Selection for use in dynamic environments. An extensive experimental evaluation is performed. This analysis is conducted on novel hand-labeled datasets taken directly from the problem domain, which are shown to contain drifting concepts. Several baselines are considered, including the one-model-per-image approach used in the most basic near-to-far learning. The experimental results uncover many important differences in the behavior of ensemble methods versus simpler approaches. In many scenarios, it is shown that the use of classifier ensembles increases far-field predictive performance compared to non-ensemble approaches, although this result was not shown to be statistically significant over all datasets and metrics in the analysis.
Isoprenoid synthesis in peppermint (Mentha x piperita): Development of a model system for measuring flux of intermediates through the mevalonic acid pathway in plants (1995)

Conference Article| May 01 1995 Isoprenoid synthesis in peppermint (Mentha x piperita): Development of a model system for measuring flux of intermediates through the mevalonic acid pathway in plants DAVID MCCASKILL; DAVID MCCASKILL 1Institute of Biological Chemistry, Washington State University, Pullman, WA, USA 99164–6340 Search for other works by this author on: This Site PubMed Google Scholar RODNEY CROTEAU RODNEY CROTEAU 1Institute of Biological Chemistry, Washington State University, Pullman, WA, USA 99164–6340 Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1995) 23 (2): 290S. https://doi.org/10.1042/bst023290s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation DAVID MCCASKILL, RODNEY CROTEAU; Isoprenoid synthesis in peppermint (Mentha x piperita): Development of a model system for measuring flux of intermediates through the mevalonic acid pathway in plants. Biochem Soc Trans 1 May 1995; 23 (2): 290S. doi: https://doi.org/10.1042/bst023290s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: FPP = farnesyl pyrophosphate, GPP = geranyl pyrophosphate, HMG-CoA = 3-hydroxy-3-methylglutaryl-CoA, IPP = isopentenyl pyrophosphate This content is only available as a PDF. © 1995 Biochemical Society1995 Article PDF first page preview Close Modal You do not currently have access to this content.
Simple, sensitive and quantitative bioluminescence assay for determination of malaria pre-patent period (2014)

A novel, simple, fast, and sensitive method to measure pre-patent period of malaria infection in rodents is described here. The sensitivity and accuracy of this new method is comparable to standard PCR and microscopy-based techniques, respectively.
Dynamics of Plasma Refill Rate and Intradialytic Hypotension During Hemodialysis: Retrospective Cohort Study With Causal Methodology (2023)

Key Points Directly studying plasma refill rate (PRR) during hemodialysis (HD) can offer insight into physiologic mechanisms that change throughout HD. PRR at the start and during HD is associated with intradialytic hypotension, independent of ultrafiltration rate. A rising PRR during HD may be an early indicator of compensatory mechanisms for impending circulatory instability. Background Attaining the optimal balance between achieving adequate volume removal while preserving organ perfusion is a challenge for patients receiving maintenance hemodialysis (HD). Current strategies to guide ultrafiltration are inadequate. Methods We developed an approach to calculate the plasma refill rate (PRR) throughout HD using hematocrit and ultrafiltration data in a retrospective cohort of patients receiving maintenance HD at 17 dialysis units from January 2017 to October 2019. We studied whether ( 1 ) PRR is associated with traditional risk factors for hemodynamic instability using logistic regression, ( 2 ) low starting PRR is associated with intradialytic hypotension (IDH) using Cox proportional hazard regression, and ( 3 ) time-varying PRR throughout HD is associated with hypotension using marginal structural modeling. Results During 180,319 HD sessions among 2554 patients, PRR had high within-patient and between-patient variability. Female sex and hypoalbuminemia were associated with low PRR at multiple time points during the first hour of HD. Low starting PRR has a higher hazard of IDH, whereas high starting PRR was protective (hazard ratio [HR], 1.26, 95% confidence interval [CI], 1.18 to 1.35 versus HR, 0.79, 95% CI, 0.73 to 0.85, respectively). However, when accounting for time-varying PRR and time-varying confounders, compared with a moderate PRR, while a consistently low PRR was associated with increased risk of hypotension (odds ratio [OR], 1.09, 95% CI, 1.02 to 1.16), a consistently high PRR had a stronger association with hypotension within the next 15 minutes (OR, 1.38, 95% CI, 1.30 to 1.45). Conclusions We present a straightforward technique to quantify plasma refill that could easily integrate with devices that monitor hematocrit during HD. Our study highlights how examining patterns of plasma refill may enhance our understanding of circulatory changes during HD, an important step to understand how current technology might be used to improve hemodynamic instability.
SAR Geolocation Using Range-Doppler Multilateration (2021)

Radar is by its basic nature a ranging instrument. If radar rang e and range-rate measurements from multiple directions can be made and a ssembled, then multilateration allows locating a feature common to the set of SAR images to an accurate 3-D coordinate. The ability to employ effective multilateration algorithms is highly dependent on the geom etry of the data collections, and the accuracy with which rela tive range measurements can be made. The problem can be cast as a least-squares exercise, and the concept of Dilution of Precision can describe the accuracy and precision with which a 3-D location can be made. - 4 - Acknowledgements This report is the result of an unf unded Research and Development effort. The authors thank their colleague Tim Bielek for his review of this report and much appreciated comments.
Treatment of experimental adjuvant arthritis with a novel folate receptor-targeted folic acid-aminopterin conjugate (2011)

EC0746 is the first high FR-binding dihydrofolate reductase inhibitor that demonstrates FR-specific anti-inflammatory activities both in vitro and in vivo. Our data reveal that a relatively toxic anti-inflammatory drug, such as aminopterin, can be targeted with folic acid to inflammatory macrophages and thereby relieve inflammatory symptoms with greatly reduced toxicity.
Continuous-flow dielectrophoretic sorting of particles via 3D silicon electrodes featuring castellated sidewalls (2015)

Continuous-flow dielectrophoretic sorting of particles has been demonstrated using a simple microfluidic design incorporating 3D electrodes with castellated sidewalls. Two variations of the design have been fabricated, slightly differing in their sidewall and separation junction profiles, through a single-mask process on silicon-based platforms. These 3D silicon electrodes have shown the capacity to segregate polystyrene beads into distinct flow layers along the channel depth while delivering them to separate outlets through a downstream junction of a specific design. The utility of either structure has been showcased by sorting a mixture of 1 and 10 µm beads based on their size continuously at a velocity of 1.5 mm/s.
<title>Rapid area coverage for unexploded ordnance using UAVs incorporating magnetic sensors</title> (2002)

Tensor magnetic gradiometry reports accurate direction and approximate range to an UXO using a single point measurement. Instead of using a sparse grid of points, a UAV can fly a series of adjacent tracks and acquire the data needed to locate all items. Some recent modeling suggests that normal UAV flight speeds can achieve an area coverage rate of 15 acres/minute. This contrasts sharply with total field magnetic techniques that require a much denser grid of sensor tracks. Synthetic data from equivalent surface-based measurements and simulations of real time processing substantiate the models.
Study on the Immunogenicity of Human Class-II-restricted T-cell Epitopes: Processing Constraints, Degenerate Binding, and Promiscuous Recognition (1989)

T lymphocytes recognize peptides derived from intracellular processing of antigens that have bound to major histocompatibility complex (MHC) molecules. Thus, the immunogenicity of a given epitope has three essential requirements: (1) The appropriate fragment must be generated by the processing machinery; (2) an MHC molecule must be present capable of binding this fragment; and (3) specific T cells must be available in the repertoire. Failure at any one of these steps results in failure to respond.
Hermes: a platform for context-aware enterprise communication (2006)

This paper describes our vision for next-generation context-aware enterprise communications that achieves the integration of backend business processes with user communications. We envision a new class of enterprise applications in which communications between users in response to a variety of enterprise events will be driven by an automated process in which an appropriate group of users will be selected for communicating at an appropriate time on an appropriate media. To achieve this goal, the applications must exploit a variety of context information such as enterprise knowledge, user knowledge and application knowledge. This paper describes our platform Hermes that enables the creation and execution of such context-aware applications. It briefly presents experiences with Hermes in several demonstrations
All-optical pulse compression of broadband microwave signal based on stimulated Brillouin scattering (2016)

Pulse compression processing based on stimulated Brillouin scattering (SBS) in an optical fiber is theoretically and experimentally demonstrated. Broadband microwave signal is electro-optically modulated onto the pump lightwave that is launched into one end of the fiber. Acoustic wave in the fiber inherits the amplitude and phase information of the pump lightwave and thus the coupling between the acoustic wave and pump lightwave leads to the auto-correlated process of the pump lightwave as well as the modulated microwave signal. Derivation of the SBS coupling equations shows that the short-pulse probe lightwave amplified by the pump lightwave possesses the nature of auto-correlation formula. All-optical pulse compression of the broadband microwave signal is implemented after a subtraction between the detected probe pulse with and without SBS. A proof-of-concept experiment is carried out. The pulse compression of a linear frequency-modulated microwave signal with 1 GHz sweep range at the carrier frequency of 4.3 GHz is successfully realized, which well matches the theoretical analysis.
Structure Determination of Mycolactone C via Total Synthesis (2004)

[structure: see text] By total synthesis, mycolactone C has been established as an approximately 1:1 mixture of Z-Delta4'5'- and E-Delta4'5'-geometric isomers of C12'-deoxymycolactones A and B.
Color-matched esophagus phantom for fluorescent imaging (2013)

We developed a stable, reproducible three-dimensional optical phantom for the evaluation of a wide-field endoscopic molecular imaging system. This phantom mimicked a human esophagus structure with flexibility to demonstrate body movements. At the same time, realistic visual appearance and diffuse spectral reflectance properties of the tissue were simulated by a color matching methodology. A photostable dye-in-polymer technology was applied to represent biomarker probed “hot-spot” locations. Furthermore, fluorescent target quantification of the phantom was demonstrated using a 1.2mm ultrathin scanning fiber endoscope with concurrent fluorescence-reflectance imaging.
Isotope exchange reactions of the hydrogen H-5 of selected pyrimidine derivatives and the preparation of tritium-labeled pyrimidines (2011)

The hydrogen-to-deuterium isotope exchange reaction of hydrogen in position 5 of pyrimidine derivatives was studied using NMR techniques. The dependence of the reaction rate on the pH and on the solvent composition was explored. In tracer experiments using tritiated water, the application of this exchange reaction was tested for the preparation of pyrimidine derivatives labeled by tritium.
Dual controlled delivery of squalenoyl-gemcitabine and paclitaxel using thermo-responsive polymeric micelles for pancreatic cancer (2018)

In this study we report the synthesis of a themroresponsive block copolymer by reversible addition fragmentation transfer polymerization comprising poly(2-ethylhexyl methacrylate)-b-poly[di(ethylene glycol)methyl ether methacrylate-co-oligo(ethylene glycol)methyl ether methacrylate] as hydrophobic and thermoresponsive blocks respectively. The polymer self-assembles into sub-50 micelles and can carry simultaneously two drug molecules, namely squalene-gemcitabine and paclitaxel. Both drugs can be released from the micellar compartment in a thermally controlled manner owing to the controllable disruption of the micellar corona above the lower critical solution temperature of the polymer. We demonstrate that the formulation augments synergistically the cytotoxicity of the two drugs in vitro against a model pancreatic cancer cell line. More importantly, it is shown that the polymer exerts a direct interaction with the cell membrane which further augments the cytotoxicity of the drug cargo in a thermally controlled manner.
CRMP3 is required for hippocampal CA1 dendritic organization and plasticity (2007)

In vitro studies have pointed to the collapsin response mediator proteins (CRMPs) as key regulators of neurite outgrowth and axonal differentiation. CRMP3 is expressed mostly in the nervous system during development but remains at high levels in the hippocampus of adults. To explore CRMP3 function in vivo, we generated mice with targeted disruption of the CRMP3 gene. Immunohistochemistry and Golgi staining of CA1 showed abnormal dendrite and spine morphogenesis in the hippocampus of CRMP3-deficient mice. Apical dendrites displayed an increase in undulation and a reduction in length and branching points. Basal dendrites also exhibited a reduction in length with an alteration in soma stem distribution and an increased number of thick dendrites localized in stratum oriens (SO). Long-term potentiation (LTP) was impaired in this area. These data indicate an important role for CRMP3 in dendrite arborization, guide-posts navigation, and neuronal plasticity.
?^(2) and ?^(3) harmonic generation at a critical power in inhomogeneous doubly resonant cavities (2007)

We derive general conditions for 100% frequency conversion in any doubly resonant nonlinear cavity, for both second- and third-harmonic generation via Chi?((2))and Chi((3)) nonlinearities. We find that conversion efficiency is optimized for a certain "critical" power depending on the cavity parameters, and assuming reasonable parameters we predict 100% conversion using milliwatts of power or less. These results follow from a semi-analytical coupled-mode theory framework which is generalized from previous work to include both Chi((2))and Chi((3))?media as well as inhomogeneous (fully vectorial) cavities, analyzed in the high-efficiency limit where down-conversion processes lead to a maximum efficiency at the critical power, and which is verified by direct finite-difference time-domain (FDTD) simulations of the nonlinear Maxwell equations. Explicit formulas for the nonlinear coupling coefficients are derived in terms of the linear cavity eigenmodes, which can be used to design and evaluate cavities in arbitrary geometries.
Microbial Safety of Fresh Produce (2009)

Section I: Microbial Contamination of Fresh Produce. Chapter 1. Enteric human pathogens associated with fresh produce: sources, transport and ecology (Robert E. Mandrell). Chapter 2. The origin and spread of human pathogens in fruit production systems (Susan Bach and Pescal Delaquis). Chapter 3. Internalization of Pathogens in Produce (Elliot T. Ryser, Jianjun Hao, and Zhinong Yan). Section II: Pre-harvest Strategies. Chapter 4. Produce safety in organic vs conventional crops (Francisco Diez-Gonzalez and Avik Mukherjee). Chapter 5. The Role of Good Agricultural Practices in Produce Safety (Robert B. Gravani). Chapter 6. Effective Managing through a Crisis (Will Daniels and Michael P. Doyle). Chapter 7. The Role of Water and Water testing in Produce Safety (Charles P. Gerba ). Chapter 8. Role of manure and compost in produce safety (Xiuping Jiang). Section III: Post-harvest Interventions. Chapter 9. Aqueous antimicrobial treatments to improve fresh and fresh-cut produce safety (Joy Herdt and Hao Feng). Chapter 10. Irradiation enhances quality and microbial safety of fresh and fresh-cut fruits and vegetables (Brendan A. Niemira and Xuetong Fan). Chapter 11. Biological control of human pathogens on produce (John Andrew Hudson, Craig Billington, and Lynn McIntyre). Chapter 12. Extension of Shelf-life and Control of Human Pathogens in Produce by Antimicrobial Edible Films and Coatings (Tara H. McHugh, Roberto J. Avena-Bustillos, and Wen-Xian Du). Chapter 13. Improving Microbial Safety of Fresh Produce Using Thermal Treatment (Xuetong Fan, Lihan Huang, Bassam Annous). Chapter 14. Enhanced Safety and Extended Shelf-life of Fresh Produce for the Military (Peter Setlow, Christopher J. Doona, Florence E. Feeherry, and Kenneth Kustin, Deborah Sisson, and Shubham Chandra). Section IV: Produce Safety during Processing and Handling. Chapter 15. Consumer and Food Service Handling of Fresh Produce (Christine M. Bruhn). Chapter 16. Plant Sanitation and Good Manufacturing Practices for Optimum Food Safety in Fresh-cut Produce (Edith Garrett). Chapter 17. Third party audit programs for the fresh produce industry (Kenneth S. Petersen). Chapter 18. Pathogen Detection in Produce using Applications of Immunomagnetic Beads and Biosensors (Shu-I Tu, Joseph Uknalis, Andrew Gehring, and Peter Irwin). Section V: Public, Legal, and Economic Perspectives. Chapter 19. Public Response to the 2006 Recall of Contaminated Spinach (William K. Hallman, Cara L. Cuite, Jocilyn E. Dellava, Mary L. Nucci, and Sarah C. Condry). Chapter 20. Produce in public: Spinach, safety and public policy (Douglas A. Powell, Casey J. Jacob and Benjamin Chapman). Chapter 21.Contaminated Fresh Produce and Product Liability: A Law-in-Action Perspective (Denis W. Stearns). Chapter 22. The Economics of Food Safety: The 2006 Foodborne Illness Outbreak Linked to Spinach (Linda Calvin, Helen H. Jensen and Jing Liang). Section VI: Research Challenges and Directions. Chapter 23. Research Needs and Future Directions (Brendan A. Niemira, Xuetong Fan, Christopher J. Doona, Florence E. Feeherry, Robert B. Gravani).