gebhart/patrepeval huggingface dataset:
Laser Capture Microdissection and Protein Microarray Analysis of Human Non-small Cell Lung Cancer (2008)

Little is known about lung carcinoma epidermal growth factor (EGF) kinase pathway signaling within the context of the tissue microenvironment. We quantitatively profiled the phosphorylation and abundance of signal pathway proteins relevant to the EGF receptor within laser capture microdissected untreated, human non-small cell lung cancer (NSCLC) (n = 25) of known epidermal growth factor receptor (EGFR) tyrosine kinase domain mutation status. We measured six phosphorylation sites on EGFR to evaluate whether EGFR mutation status in vivo was associated with the coordinated phosphorylation of specific multiple phosphorylation sites on the EGFR and downstream proteins. Reverse phase protein array quantitation of NSCLC revealed simultaneous increased phosphorylation of EGFR residues Tyr-1148 (p < 0.044) and Tyr-1068 (p < 0.026) and decreased phosphorylation of EGFR Tyr-1045 (p < 0.002), HER2 Tyr-1248 (p < 0.015), IRS-1 Ser-612 (p < 0.001), and SMAD Ser-465/467 (p < 0.011) across all classes of mutated EGFR patient samples compared with wild type. To explore which subset of correlations was influenced by ligand induction versus an intrinsic phenotype of the EGFR mutants, we profiled the time course of 115 cellular signal proteins for EGF ligand-stimulated (three dosages) NSCLC mutant and wild type cultured cell lines. EGFR mutant cell lines (H1975 L858R) displayed a pattern of EGFR Tyr-1045 and HER2 Tyr-1248 phosphorylation similar to that found in tissue. Persistence of phosphorylation for AKT Ser-473 following ligand stimulation was found for the mutant. These data suggest that a higher proportion of the EGFR mutant carcinoma cells may exhibit activation of the phosphatidylinositol 3-kinase/protein kinase B (AKT)/mammalian target of rapamycin (MTOR) pathway through Tyr-1148 and Tyr-1068 and suppression of IRS-1 Ser-612, altered heterodimerization with ERBB2, reduced response to transforming growth factor beta suppression, and reduced ubiquitination/degradation of the EGFR through EGFR Tyr-1045, thus providing a survival advantage. This is the first comparison of multiple, site-specific phosphoproteins with the EGFR tyrosine kinase domain mutation status in vivo.
Influenza hemagglutinin: kinetic control of protein function In response to decreased pH, influenza hemagglutinin changes to a more stable conformation. Such changes, which can be controlled thermodynamically or kinetically, are the method by which many biological 'switches' are thrown. (1994)

Many enveloped viruses such as influenza virus entercells through receptor-mediated endocytosis. Once inthe endosome, the low pH triggers the fusion of the viraland endosomal membranes allowing efficient delivery ofthe viral genome into the cytoplasm [1,2]. In the case ofinfluenza virus, cell surface binding and membranefusion are mediated by a single protein, called hemagglu-tinin (HA), whose high-resolution structure was deter-mined by the Wiley lab in 1981 [3]. As a consequence ofthis early progress, HA has served as a model system forunderstanding the general processes of viral entry andmembrane fusion.Recent studies, culminating in the stunning paper byBullough et al., which appeared recently in Nature [4],indicate that dramatic and irreversible conformationalchanges in HA are fundamental to the mechanism ofHA-mediated membrane fusion. Here we will try tosummarize these findings and to consider the results fromthe perspective of novel mechanisms for regulatingprotein function.Native HA is a 200 kDa trimer of identical subunits;each subunit consists of two chains, HA
A new cardo bisphenol monomer containing pendant azido group and the resulting aromatic polyesters (2019)

ABSTRACT Expanding on our strategy to synthesize aromatic step‐growth polymers containing pendant clickable azido groups via functional monomer approach, we have now designed and synthesized a new cardo bisphenol, viz., 2‐(2‐azidoethyl)‐3, 3‐bis(4‐hydroxyphenyl) isoindolin‐1‐one (PPH‐N 3 ). PPH‐N 3 was conveniently synthesized starting from commercially available phenolphthalein by a three‐step route in an overall yield of 65% using simple organic transformations. Aromatic (co)polyesters bearing pendant azido groups were synthesized by low‐temperature solution polycondensation of PPH‐N 3 or different molar ratios of PPH‐N 3 and bisphenol‐A (BPA) with aromatic diacid chlorides in dry dichloromethane in the presence of triethylamine (TEA) as a base. The formation of medium to reasonably high‐molecular‐weight (co)polyesters was evidenced from intrinsic viscosity and number‐average molecular‐weight measurements that were in the range 0.52–0.85 dL/g and 16,700–28,200, respectively. Tough, transparent, and flexible films could be cast from chloroform solutions of these (co)polyesters. (Co)polyesters were characterized using FTIR, 1 H NMR, 13 C NMR spectroscopy, XRD, and TGA. The thermal curing reaction of (co)polyesters involving decomposition of azido groups was studied by DSC analysis. The chemical modification of a representative copolyester containing pendant azido groups was carried out quantitatively using catalyst‐free azide‐maleimide cycloaddition reaction with two maleimides, namely, N ‐methylmaleimide and N ‐hexylmaleimide. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019, 57, 1516–1526
Optical Phase Contrast Mapping of Highly Focused Ultrasonic Fields (2013)

The most common method of measuring an ultrasonic pressure field is a hydrophone scan. However, this method has a long scanning time and disturbs the acoustic field. In this study, we used an optical phase contrast method for the measurement. Because this method uses light, fast and noninvasive measurement can be performed. The projections of an ultrasonic pressure field were obtained with a charge-coupled device (CCD) camera, and the three-dimensional (3D) acoustic pressure field was reconstructed using a computed tomography (CT) algorithm from these projections. The result was compared with that of hydrophone measurement and demonstrated the successful reconstruction of a focal ultrasonic pressure field.
Critical Incidents Associated with Intraoperative Exchanges of Anesthesia Personnel (1983)

Bioengineering Unit, Department of Anesthesia, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
Overexpression of Arabidopsis Ceramide Synthases Differentially Affects Growth, Sphingolipid Metabolism, Programmed Cell Death, and Mycotoxin Resistance (2015)

Ceramide synthases catalyze an N-acyltransferase reaction using fatty acyl-coenzyme A (CoA) and long-chain base (LCB) substrates to form the sphingolipid ceramide backbone and are targets for inhibition by the mycotoxin fumonisin B1 (FB1). Arabidopsis (Arabidopsis thaliana) contains three genes encoding ceramide synthases with distinct substrate specificities: LONGEVITY ASSURANCE GENE ONE HOMOLOG1 (LOH1; At3g25540)- and LOH3 (At1g19260)-encoded ceramide synthases use very-long-chain fatty acyl-CoA and trihydroxy LCB substrates, and LOH2 (At3g19260)-encoded ceramide synthase uses palmitoyl-CoA and dihydroxy LCB substrates. In this study, complementary DNAs for each gene were overexpressed to determine the role of individual isoforms in physiology and sphingolipid metabolism. Differences were observed in growth resulting from LOH1 and LOH3 overexpression compared with LOH2 overexpression. LOH1- and LOH3-overexpressing plants had enhanced biomass relative to wild-type plants, due in part to increased cell division, suggesting that enhanced synthesis of very-long-chain fatty acid/trihydroxy LCB ceramides promotes cell division and growth. Conversely, LOH2 overexpression resulted in dwarfing. LOH2 overexpression also resulted in the accumulation of sphingolipids with C16 fatty acid/dihydroxy LCB ceramides, constitutive induction of programmed cell death, and accumulation of salicylic acid, closely mimicking phenotypes observed previously in LCB C-4 hydroxylase mutants defective in trihydroxy LCB synthesis. In addition, LOH2- and LOH3-overexpressing plants acquired increased resistance to FB1, whereas LOH1-overexpressing plants showed no increase in FB1 resistance, compared with wild-type plants, indicating that LOH1 ceramide synthase is most strongly inhibited by FB1. Overall, the findings described here demonstrate that overexpression of Arabidopsis ceramide synthases results in strongly divergent physiological and metabolic phenotypes, some of which have significance for improved plant performance.
Scaffold-Based Therapies: Proceedings of the International Consensus Meeting on Cartilage Repair of the Ankle (2018)

Level V, expert opinion.
Alteration of endothelial function markers in women with gestational diabetes and their fetuses (2012)

These data suggest that the molecular mechanisms behind oxidative stress in women with GDM and their fetuses appear similar to those hypothesized for non-pregnant adults with type 2 diabetes mellitus (DM).
On Localizing a Camera from a Single Image (2020)

Public cameras often have limited metadata describing their attributes. A key missing attribute is the precise location of the camera, using which it is possible to precisely pinpoint the location of events seen in the camera. In this paper, we explore the following question: under what conditions is it possible to estimate the location of a camera from a single image taken by the camera? We show that, using a judicious combination of projective geometry, neural networks, and crowd-sourced annotations from human workers, it is possible to position 95% of the images in our test data set to within 12 m. This performance is two orders of magnitude better than PoseNet, a state-of-the-art neural network that, when trained on a large corpus of images in an area, can estimate the pose of a single image. Finally, we show that the camera's inferred position and intrinsic parameters can help design a number of virtual sensors, all of which are reasonably accurate.
Kallikrein Content of Rat Pancreatic Acinar Cells or Islets by Direct Radioimmunoassay (1980)

Recent reports have suggested that kallikreins may enzymatically convert proinsulin to insulin. The quantity of rat pancreatic kallikrein in isolated Islets of Langerhans, acinar cells and in whole pancreatic extracts was measured by direct radioimmunoassay and bioassay. Immunoreactive kallikrein content in acinar cells was 813 +/- 111 ng/mg protein (mean +/- S.E.M.). In whole pancreatic homogenates, it was 1303 +/- 213 ng/mg protein. Appreciable quantities of the enzyme were not detected in islets. Kallikrein activity as measured with a rat uterine bioassay had similar distribution. Because of the localization of kallikrein, it is unlikely that the enzyme is involved in the in vivo conversion of proinsulin to insulin.
Fighting against diffraction: apodization and near field diffraction structures (2011)

Abstract Diffraction is a natural phenomenon, which occurs when waves propagate or encounter an obstacle. Diffraction is also a fundamental aspect of modern optics: all imaging systems are diffraction systems. However, like a coin has two sides, diffraction also leads to some unfavorable effects, such as an increase in the size of a beam during propagation, and a limited minimal beam size after focusing. To overcome these disadvantages set by diffraction, many techniques have been developed by various groups, including apodization techniques to reduce the divergence of a laser beam and increase the resolution, and time reversal, STED microscopy, super lenses and optical antennas to obtain resolution down to nano‐scale. This review concentrates on the diffraction of electromagnetic waves, and the ways to overcome beam divergence and the diffraction limit.
Isolation and characterization of a cDNA from Trichoderma harzianum P1 encoding a 14-3-3 protein homolog (1996)

A full-length cDNA close, Th1433, (GenBank accession No. U24158), was isolated and characterized from the filamentous fungus, Trichoderma harzianum. The deduced amino acid (aa) sequence showed an acidic 30-kDa protein homologous to the 14-3-3 proteins, a family of putative kinase regulators originally characterized in mammalian brain tissue. The greatest homology, 71% identical aa, was found to BMH1, the corresponding protein from Saccharomyces cerevisiae and to the epsilon isoform from sheep brain. Southern analysis of genomic DNA indicated that Th1433 is a member of a small genomic family. At least two genes encoding 14-3-3-like proteins exist in T. harzianum. Northern analysis showed the highest level of expression during the first day after inoculation of the culture with conidial spores.
Neurodegenerative Disease Transmission and Transgenesis in Mice (2017)

Although the discovery of the prion protein (PrP) resulted from its co-purification with scrapie infectivity in Syrian hamsters, work with genetically defined and genetically modified mice proved crucial for understanding the fundamental processes involved not only in prion diseases caused by PrP misfolding, aggregation, and spread but also in other, much more common, neurodegenerative brain diseases. In this review, we focus on methodological and conceptual approaches used to study scrapie and related PrP misfolding diseases in mice and how these approaches have advanced our understanding of related disorders including Alzheimer's and Parkinson's disease.
Tuning the donor–acceptor interactions in phase-segregated block molecules (2021)

The assembly of donor-acceptor molecules <i>via</i> charge transfer (CT) interactions gives rise to highly ordered nanomaterials with appealing electronic properties. Here, we present the synthesis and bulk co-assembly of pyrene (Pyr) and naphthalenediimide (NDI) functionalized oligodimethylsiloxanes (oDMS) of discrete length. We tune the donor-acceptor interactions by connecting the pyrene and NDI to the same oligomer, forming a heterotelechelic block molecule (NDI-oDMSPyr), and to two separate oligomers, giving Pyr and NDI homotelechelic block molecules (Pyr-oDMS and NDI-oDMS). Liquid crystalline materials are obtained for binary mixtures of Pyr-oDMS and NDI-oDMS, while crystallization of the CT dimers occurred for the heterotelechelic NDI-oDMS-Pyr block molecule. The synergy between crystallization and phase-segregation coupled with the discrete length of the oDMS units allows for perfect order and sharp interfaces between the insulating siloxane and CT layers composed of crystalline CT dimers. We were able to tune the lamellar domain spacing and donor-acceptor CT interactions by applying pressures up to 6 GPa on the material, making the system promising for soft-material nanotechnologies. These results demonstrate the importance of the molecular design to tune the CT interactions and stability of a CT material.
A Permanent Magnet Brushless Doubly Fed Electric Machine for Variable-Speed Constant-Frequency Wind Turbines (2022)

A permanent magnet (PM) brushless doubly fed electric machine is presented in this article. This machine is developed for variable-speed constant-frequency (VSCF) wind energy generation applications. Differing from conventional doubly fed electric machines based on induction machines, a PM rotor provides the magnetic field excitations for both the control winding and the power winding in the presented machine. The operating principle of the presented machine for the VSCF operation is revealed in detail. Compared to a counterpart machine, the presented machine exhibits significantly improved back-electromotive force, torque/power density, torque per magnet volume, efficiency, etc. Finally, a proof-of-concept prototype of the presented machine is fabricated, and the corresponding experimental results are provided to verify the fact that the presented machine is capable of achieving the VSCF function.
Speed Limit for Triplet-Exciton Transfer in Solid-State PbS Nanocrystal-Sensitized Photon Upconversion (2017)

Hybrid interfaces combining inorganic and organic materials underpin the operation of many optoelectronic and photocatalytic systems and allow for innovative approaches to photon up- and down-conversion. However, the mechanism of exchange-mediated energy transfer of spin-triplet excitons across these interfaces remains obscure, particularly when both the macroscopic donor and acceptor are composed of many separately interacting nanoscopic moieties. Here, we study the transfer of excitons from colloidal lead sulfide (PbS) nanocrystals to the spin-triplet state of rubrene molecules. By reducing the length of the carboxylic acid ligands on the nanocrystal surface from 18 to 4 carbon atoms, thinning the effective ligand shell from 13 to 6 Å, we are able to increase the characteristic transfer rate by an order of magnitude. However, we observe that the energy transfer rate asymptotes for shorter separation distances (≤10 Å) which we attribute to the reduced Dexter coupling brought on by the increased effective dielectric constant of these solid-state devices when the aliphatic ligands are short. This implies that the shortest ligands, which hinder long-term colloidal stability, offer little advantage for energy transfer. Indeed, we find that hexanoic acid ligands are already sufficient for near-unity transfer efficiency. Using nanocrystals with these optimal-length ligands in an improved solid-state device structure, we obtain an upconversion efficiency of (7 ± 1)% with excitation at λ = 808 nm.
Thermal Cyclization of Ketene Dithioacetals: A Convenient Synthetic Route to Substituted 2(1H)-Quinolinones and 2(1H)-Pyridones (1992)

Acyl(arylcarbamoyl)ketene dithioacetals 2 and acyl(1-alkenylcarbamoyl)ketene dithioacetals 5 obtained from the corresponding ß-oxo amides 1, 4 were thermally cyclized to give various 3-acyl-4-alkylthio-2(1H)-quinolinones 3, and 3-acyl-4-alkylthio-5-aryl-2(1H)-pyridones 6, respectively, depending on the substituent of the amide group.
Standard Cell and Custom Circuit Optimization using Dummy Diffusions through STI Width Stress Effect Utilization (2007)

Starting at the 65 nm node, stress engineering to improve performance of transistors has been a major industry focus. An intrinsic stress source - shallow trench isolation - has not been fully utilized up to now for circuit performance improvement. In this paper, we present a new methodology that enables the exploitation of STI stress for performance improvement of standard cells and custom integrated circuits. We start with process simulation of a 65 nm STI technology, and generate mobility models for STI stress based on these simulations. Based on these models, we are able to perform STI stress-aware modeling and simulation using SPICE. We then present our optimization of STI stress in standard-cell and custom designs using active-layer (dummy) fill insertion to alter the STI widths. Circuit level experimental results are based on a miscellaneous ring oscillator, which is known to correlate well to silicon. Using a generic 65 nm cell library, we show that the STI-optimized designs provide up to 8% improvement in clock frequency. The frequency improvement through exploitation of STI stress comes at practically zero cost with respect to area and wire length.
Incidence of malignant pleural mesothelioma in coastal and continental Croatia: epidemiological study. (2002)

Assuming that the information obtained by the poll on the occupation of diseased subjects was a true characterization of all recorded cases of pleural mesothelioma, more than two-thirds of subjects with the studied tumor had an occupational exposure to asbestos. Uneven distribution of the tumor, with higher rate in men in the coastal area, may be related to shipbuilding and other industrial sources of asbestos exposure in that part of the country.
Superconducting Optoelectronic Neurons III: Synaptic Plasticity. (2018)

As a means of dynamically reconfiguring the synaptic weight of a superconducting optoelectronic loop neuron, a superconducting flux storage loop is inductively coupled to the synaptic current bias of the neuron. A standard flux memory cell is used to achieve a binary synapse, and loops capable of storing many flux quanta are used to enact multi-stable synapses. Circuits are designed to implement supervised learning wherein current pulses add or remove flux from the loop to strengthen or weaken the synaptic weight. Designs are presented for circuits with hundreds of intermediate synaptic weights between minimum and maximum strengths. Circuits for implementing unsupervised learning are modeled using two photons to strengthen and two photons to weaken the synaptic weight via Hebbian and anti-Hebbian learning rules, and techniques are proposed to control the learning rate. Implementation of short-term plasticity, homeostatic plasticity, and metaplasticity in loop neurons is discussed.
Diesel Generator Model Parameterization for Microgrid Simulation Using Hybrid Box-Constrained Levenberg-Marquardt Algorithm (2020)

Existing generator parameterization methods, typically developed for large turbine generator units, are difficult to apply to small kW-level diesel generators in microgrid applications. This article presents a model parameterization method that estimates a complete set of kW-level diesel generator parameters simultaneously using only load-step-change tests with limited measurement points. This method provides a more cost-efficient and robust approach to achieve high-fidelity modeling of diesel generators for microgrid dynamic simulation. A two-stage hybrid box-constrained Levenberg-Marquardt (H-BCLM) algorithm is developed to search the optimal parameter set given the parameter bounds. A heuristic algorithm, namely Generalized Opposition-based Learning Genetic Algorithm (GOL-GA), is applied to identify proper initial estimates at the first stage, followed by a modified Levenberg-Marquardt algorithm designed to fine tune the solution based on the first-stage result. The proposed method is validated against dynamic simulation of a diesel generator model and field measurements from a 16kW diesel generator unit.