gebhart/patrepeval huggingface dataset:
Annular Oligomeric Amyloid Intermediates Observed by in Situ Atomic Force Microscopy (2004)

Amyloidoses and related protein deposition diseases involve the transformation of normally soluble proteins into insoluble deposits, usually fibrillar in nature. Although it was originally assumed that the fibrils were the toxic species, this assumption has recently been called into question. Accumulating evidence in several systems suggests that oligomeric intermediates on the aggregation pathway may be toxic. In the present study we used in situ atomic force microscopy to monitor aggregation in aqueous solution in real time. The sample used was an amyloidogenic immunoglobulin light chain, involved in AL or light chain amyloidosis. The nature of the observed oligomeric intermediates was dependent on the conditions of incubation, especially pH and ionic strength. Several different aggregation intermediates with a variety of morphologies, including annular or torus-shaped species, were observed. The data indicate that protein aggregation can be very complex, involving a variety of different oligomeric intermediates whose population will be determined by the kinetic and thermodynamic competition between them.
Carrot solution culture bioproduction of uniformly labeled 13C-lutein and in vivo dosing in non-human primates (2016)

Lutein is a xanthophyll abundant in nature and most commonly present in the human diet through consumption of leafy green vegetables. With zeaxanthin and meso-zeaxanthin, lutein is a component of the macular pigment of the retina, where it protects against photooxidation and age-related macular degeneration. Recent studies have suggested that lutein may positively impact cognition throughout the lifespan, but outside of the retina, the deposition, metabolism, and function(s) of lutein are poorly understood. Using a novel botanical cell culture system ( Daucus carota), the present study aimed to produce a stable isotope lutein tracer for use in future investigations of dietary lutein distribution and metabolism. Carrot cultivars were initiated into liquid solution culture, lutein production conditions optimized, and uniformly labeled <sup>13</sup>C-glucose was provided as the sole media carbon source for four serial growth cycles. Lutein yield was 2.58 ± 0.24 µg/g, and mass spectrometry confirmed high enrichment of <sup>13</sup>C: 64.9% of lutein was uniformly labeled and 100% of lutein was labeled on at least 37 of 40 possible carbons. Purification of carrot extracts yielded a lutein dose of 1.92 mg with 96.0 ± 0.60% purity. <sup>13</sup>C-lutein signals were detectable in hepatic extracts of an adult rhesus macaque monkey ( Macaca mulatta) dosed with <sup>13</sup>C-lutein, but not in hepatic samples collected from control animals. This novel botanical biofactory approach can be used to produce sufficient quantities of highly enriched and pure <sup>13</sup>C-lutein doses for use in tracer studies investigating lutein distribution, metabolism, and function.
Sensing an Oxygen Sensor: Development and Application of Activity-Based Assays Directly Monitoring HIF Heterodimerization (2021)

Conventionally, hypoxia-inducible factor (HIF) activation by prolyl hydroxylase domain enzyme (PHD) inhibition is monitored by gene reporter assays. The principle relies on the monitoring of an upstream event (HIF stabilization) by the downstream transcriptional activity. Here, we developed a novel approach to directly sense HIF activation by monitoring the heterodimerization of the HIFα/HIFβ subunits, constituting the functional HIF transcription factor. Two live cell-based biosensor assay setups were designed, utilizing functional complementation of split-nanoluciferase as a tool to measure HIFα/HIFβ protein-protein interaction resulting from the stabilization of HIF1α or HIF2α. The assay setup in a 96-well format was optimized for a duration of 2 h, and a HEK293T transfection protocol was introduced for the optimal configuration of HIFα/HIFβ-fusion proteins. These new bioassays outperformed hypoxia response element-based gene reporter assay, the current state-of-the-art assay, in terms of sensitivity. Applicability was demonstrated using a panel of PHD inhibitors, including roxadustat, molidustat, daprodustat, desidustat, vadadustat, and FG-2216, for which concentration-response curves were generated, allowing for the derivation of potency (EC<sub>50</sub>) and efficacy (<i>E</i><sub>max</sub>) data. The broad applicability of the biosensors was established via applying hypoxia mimetic CoCl<sub>2</sub>, iron chelator desferrioxamine, proteasome inhibitor MG-132, and 2-OG mimetic dimethyloxalylglycine on the assays, indicating concentration-dependent effects.
A new modular synthesis of deoxypyridinoline, a primary reference material for monitoring bone metabolism (1999)

P. Allevi, A. Longo and M. Anastasia, J. Chem. Soc., Perkin Trans. 1, 1999, 2867 DOI: 10.1039/A907248I
Analysis of Factors That Affect FlgM-Dependent Type III Secretion for Protein Purification with Salmonella enterica Serovar Typhimurium (2014)

The FlgM protein is secreted in response to flagellar hook-basal body secretion and can be used as a secretion signal to direct selected protein secretion via the flagellar type III secretion (T3S) system [H. M. Singer, M. Erhardt, A. M. Steiner, M. M. Zhang, D. Yoshikami, G. Bulaj, B. M. Olivera, and K. T. Hughes, mBio 3(3):e00115-12, 2012, http://dx.doi.org/10.1128/mBio.00115-12]. Conditions known to affect flagellar gene expression, FlgM stability, and flagellar T3S were tested either alone or in combination to determine their effects on levels of secreted FlgM. These conditions included mutations that affect activity of the flagellar FlhD4C2 master regulatory protein complex or the FlgM T3S chaperone σ(28), the removal of Salmonella pathogenicity island 1 (Spi1), the removal of flagellar late secretion substrates that could compete with FlgM for secretion, and changes in the ionic strength of the growth medium. Conditions that enhanced FlgM secretion were combined in order to maximize levels of secreted FlgM. An optimized FlgM secretion strain was used to secrete and isolate otherwise difficult-to-produce proteins and peptides fused to the C terminus of FlgM. These include cysteine-rich, hydrophobic peptides (conotoxins δ-SVIE and MrVIA), nodule-specific, cysteine-rich antimicrobial peptides (NCR), and a malaria surface antigen domain of apical membrane antigen AMA-1.
Introduction to the Special Issue on the Practical Salinity Scale 1978 (1980)

This paper outlines the work done at the five laboratories which provided, at the request of the Joint Panel on Oceanographic Tables and Standards (JPOTS), the basic data for the new Practical Salinity Scale 1978, Interlaboratory agreement of a very high order was achieved. The new scale is in process of acceptance by all major oceanographic societies, at which time it will be officially recommended for all future reporting of oceanographic data.
How power wheelchair users choose computing devices (2013)

People with motor impairments experience a range of challenges when interacting with computers. While much prior research has explored the effects of motor impairments on accessing computer input devices, such as keyboards, mice, and touch screens, we know relatively little about how real world use of a wheelchair affects why people in power wheelchairs choose specific computing devices, and how they switch between such devices. We interviewed 8 power wheelchair users about their use of computers and mobile devices. We found that participants often had difficulty switching between the various devices in their life, and that technology use was especially challenging on the go. Our findings suggest that there are numerous opportunities to make computing more wheelchair-friendly, by consolidating devices, improving reachability and portability of devices, and by creating technology that is robust to the challenges of moving around in a wheelchair.
A multicenter phase II study of vorinostat in patients (pts) with relapsed or refractory indolent B-cell non-Hodgkin lymphoma (B-NHL) or mantle cell lymphoma (MCL). (2012)

8029 Background: Most pts with indolent B-NHL relapse even after rituximab-containing chemotherapy. Vorinostat is an orally active histone deacetylase (HDAC) inhibitor, and is under investigation as monotherapy or in combination regimens in various hematologic malignancies. It has been reported that the histone acetyltransferase genes (EP300 and CREBBP) are frequently mutated in NHL, suggesting the potential usefulness of HDAC inhibitors in its treatment. Methods: We conducted a phase 2 study to investigate the efficacy, safety and tolerability of vorinostat in pts with indolent B-NHL or MCL with the overall response rate (ORR) against follicular lymphoma (FL) as the primary endpoint. The primary hypothesis was to demonstrate the efficacy in FL pts as measured by the ORR. Assuming the true ORR with vorinostat of 50% and without vorinostat of less than 25%, 39 pts will provide 90% power to demonstrate an ORR&gt;25%. Vorinostat was administered at the dose of 200 mg BID for 14 consecutive days in a 21-day cycle. The ORR and PFS were determined by an independent review panel in the Full Analysis Set (FAS) population. Results: A total of 56 pts with a median age of 60 years (range: 33 - 75) were enrolled, and 50 of them (39 with FL, 11 with other subtypes of indolent B-NHL or MCL) were included in the FAS population. The number of prior therapeutic regimens was 2 (range: 1 - 4) and 41 pts have previously received rituximab-based regimens.. The percentages of pts with FLIPI at low risk, intermediate risk and high risk were 41%, 39%, and 21%, respectively. The ORR in 39 pts with FL was 49% (95% CI: 32, 65), and the pre-specified statistical success criterion was met. The median PFS in 39 pts with FL was 17.5 months (range: 2, 22+), especially the median PFS in 19 responders with FL has not yet been reached. The major toxicities were hematologic and gastrointestinal ones, which were reversible and manageable. Grade 3/4 infection was observed in 2%. Conclusions: This phase 2 study demonstrated that oral vorinostat is an agent with sustained antitumor activity in pts with relapsed or refractory indolent B-NHL, with acceptable safety profiles, warranting further investigations.
Optical property of a novel (111)-oriented quantum structure (1997)

A novel hetero tensile-unstrained-tensile-unstrained-tensile (t-u-t-u-t) quantum structure, which consists of multiple quantum wells in the unstrained (u) regions, lattice matched to a (111)-oriented substrate, and sandwiched between tensile-strained epitaxial layers (t), is proposed. The energy band configuration modified by the strain-induced piezoelectric field and the distribution of the built-in internal electric field within this hetero t-u-t-u-t quantum structure were theoretically deduced and found to be consistent with the experimental results. It was demonstrated that some nonlinear optical properties such as the energy blue shift observed in the excitation-power-dependent photoluminescence spectra are strongly dependent on the distribution of the strain-induced built-in electric field within this quantum structure and quite comparable to the analogous values for the existing quantum structures.
Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil (2016)

Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.
Planters and their Components: Types, attributes, functional requirements, classification and description (2006)

A major constraint to adoption of improved resource-conserving cropping systems in developing countries is the lack of simple planting equipment. This manual provides a valuable reference for research and extension personnel engaged in the selection, adaptation and/or construction of complete planters appropriate to specific soil, crop, climate and residue conditions.&#13;\n&#13;\n&#13;\n
Exact inductive parasitic extraction for analysis of IGBT parallel switching including DCB-backside eddy currents (2002)

This paper deals with the parallel switching process of IGBTs in a power module. It is shown experimentally and by simulation that eddy currents in the direct copper bonding (DCB) ceramics backside metallization have an important influence on switching behaviour. An effective simulation tool based on the partial element equivalent circuit (PEEC) method is used to extract all inductive couplings for circuit modeling.
Frequently Asked Questions about Color (1997)

www.inforamp.net/~poynton poynton@poynton.com This FAQ is intended to clarify aspects of color that are important to color image coding, computer graphics, image processing, video, and the transfer of digital images to print. I assume that you are familiar with intensity, luminance (CIE Y), lightness (CIE L*), and the nonlinear relationship between CRT voltage and luminance – that is, gamma. To learn more about these topics, please read the companion Frequently Asked Questions about Gamma. This document is available on the Internet from Toronto at: I retain copyright to this note. You have permission to use it, but you may not publish it.
Revision of tissue‐maximum ratio and scatter‐maximum ratio concepts for cobalt 60 and higher energy x‐ray beams (1980)

The concept of tissue-maximum ratios (TMR) as a basis of dose computations has posed problems when applied to a whole range of clinically used megavoltage beams. Another problem is the definition of scatter-maximum ratio (SMR) which assumes a value of zero at the depth of maximum dose. This paper describes new methods of measuring collimator and phantom scatter correction factors. The definitions of TMR and SMR are modified in order to compute phantom scatter at any depth, including depth of maximum dose. The revised concept is basic and general enough that it can be applied to x-ray beams of any energy fields of any shape and isocentric as well as non-isocentric modes of treatment.
THE DETERMINATION OF THE BOUNDARIES BETWEEN CONTINUOUS AND DISCONTINUOUS CONDUCTION AS POWER FACTOR PREREGULATORS MODES IN PWM DC-TO-DC CONVERTERS USED (1992)

The deterniinafion of the bounduries between borh modes of conduction (continuous and disconrinuous) in P WM de-to-dc switching converters used as Power Fucfor Prerregulators is studied in this paper. When U de-to-de switching converter works CIS Power Factor Prereguluror, irs operation point is constantly changing due ro the facr that both the de voltage conversion ratio and the loud setti by the converter are constantly changing in each hay-sinusoide of the line voltage (input voltage of the converter). In rhese conditions, the conduction mode cannot be directly determined. In this paper, the bounduries between borh conducrion niodes in each angle of rhc half-sinusoidul input voltuge hus been determined. The condirions io alwuys operur in continuous or in disconrinuous conduction modes huw hren derermined as well. Finully. these results have been Lvrifified in several prototypes and simulations.
Lesestörungen (2000)

Die nachfolgenden Ausführungen betreffen den gesamten — sich überlappenden — Bereich der Lese- und Rechtschreibstörungen. Sie reflektieren allerdings in erster Linie eine Betrachtungsweise, wie sie im angloamerikanischen Raum üblich ist (d.h. Lesestörung im Vordergrund), während im deutschsprachigen Raum eher die Rechtschreibstörungen im Blickfeld sind. Neben gewissen, allen Sprachen gemeinsamen Aspekten sind die jeweiligen muttersprachlichen Besonderheiten zu beachten (z. B. visuelle und auditorische Gewichtung).
OrthoMap: Homeomorphism-guaranteeing normal-projection map between surfaces (2004)

Consider two (n 1)-dimensional manifolds, S and S # in . We say that they are projection-homeomorphic when the closest projection of each one onto the other is a homeomorphism. We give tight conditions under which S and S # are projection-homeomorphic. These conditions involve the local feature size for S and for S # and the Hausdor# distance between them. Our results hold for arbitrary n.
Sequence and Binding Activity of the Autolysin-Adhesin Ami from Epidemic Listeria monocytogenes 4b (2004)

Ami is an autolytic amidase from Listeria monocytogenes that is targeted to the bacterial surface via its C-terminal cell wall anchoring (CWA) domain. We recently showed that the CWA domain from Ami of L. monocytogenes EGD (serovar 1/2a) (Ami 1/2a) mediated bacterial binding to mammalian cells. Here we studied the sequence and binding properties of Ami from CHUT 82337 (serovar 4b) (Ami 4b). The Ami 4b polypeptide is predicted to be 770 amino acids long (compared with the 917 amino acids of Ami 1/2a from EGD). Ami 1/2a and Ami 4b are almost identical in the N-terminal enzymatic domain (approximately 98% amino acid identity), but the sequence is poorly conserved in the C-terminal CWA domain, with only approximately 54% amino acid identity and eight GW modules in Ami 1/2a compared with six GW modules in Ami 4b. The purified Ami 4b CWA domain efficiently bound serovar 4b bacterial cells and only poorly bound serovar 1/2a bacterial cells. The Ami 4b CWA domain was also significantly less able to bind Hep-G2 human hepatocytic cells than the Ami 1/2a CWA domain. We sequenced the ami regions encoding CWA domains of reference strains belonging to the 12 L. monocytogenes serovars. The phylogenic tree constructed from the sequences yielded a binary division into group I (serovars 1/2a, 1/2b, 1/2c, 3a, 3b, 3c, and 7) and group II (serovars 4a, 4b, 4c, 4d, and 4e). This is the first direct evidence of divergence between serovars 1/2a and 4b in a gene involved in the adhesion of L. monocytogenes to mammalian cells, as well as the first demonstration of allelic polymorphism correlated with the somatic antigen in this species.
Radiation-engineered multifunctional nanogels: a versatile platform with theranostic capabilities for cancer (2018)

Under a rational desing, combining biologically active molecules, ligand to specific cell receptors and fluorescent, radioactive or paramagnetic labels into a single nano-object can bride the unique properties of the individual components and impruve conventional sensing, imaging and therapeutic efficaces.
Development of a Wireless Computer Vision Instrument to Detect Biotic Stress in Wheat (2014)

Knowledge of crop abiotic and biotic stress is important for optimal irrigation management. While spectral reflectance and infrared thermometry provide a means to quantify crop stress remotely, these measurements can be cumbersome. Computer vision offers an inexpensive way to remotely detect crop stress independent of vegetation cover. This paper presents a technique using computer vision to detect disease stress in wheat. Digital images of differentially stressed wheat were segmented into soil and vegetation pixels using expectation maximization (EM). In the first season, the algorithm to segment vegetation from soil and distinguish between healthy and stressed wheat was developed and tested using digital images taken in the field and later processed on a desktop computer. In the second season, a wireless camera with near real-time computer vision capabilities was tested in conjunction with the conventional camera and desktop computer. For wheat irrigated at different levels and inoculated with wheat streak mosaic virus (WSMV), vegetation hue determined by the EM algorithm showed significant effects from irrigation level and infection. Unstressed wheat had a higher hue (118.32) than stressed wheat (111.34). In the second season, the hue and cover measured by the wireless computer vision sensor showed significant effects from infection (p = 0.0014), as did the conventional camera (p < 0.0001). Vegetation hue obtained through a wireless computer vision system in this study is a viable option for determining biotic crop stress in irrigation scheduling. Such a low-cost system could be suitable for use in the ﬁeld in automated irrigation scheduling applications.
Influence of microwave irradiation on enzymatic properties: applications in enzyme chemistry (2007)

Although microwave-assisted reactions are widely applied in various domains of organic chemistry, their use in the area of enzyme chemistry has been rather limited, due to the high temperatures associated with the microwave heating: Because current technology, allows a good control of reaction parameters, several examples of microwave-assisted enzyme chemistry have been reported, using stable and effective biocatalysts (modified enzymes). The purpose of this review is to highlight the applications and studies on the influence of microwave irradiation on enzymatic properties and their application in enzyme chemistry.
Virus diseases of orchids (2022)

Orchids are known for their exquisite beauty, novelty and long vase life. Availability and affordability have made the orchid sector one of the most economically important for the indoor plant market. Orchids are susceptible to a large number of abiotic and biotic agents that can affect their development and decrease the quality of their flowers and leaves. Viruses are one of the most important biotic agents and more than 58 viruses are known to infect orchids with Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV) are the most prevalent and economically important viruses worldwide. In India, so far 10 viruses have been reported to infect different orchids viz: Cymbidium mosaic virus (CymMV), Odontoglossum ringspot virus (ORSV), Calanthe mild mosaic virus (CalMMV), Ground nut bud necrosis virus (GBNV), Orchid fleck virus (OFV), Vanilla necrosis virus, (VNV), Cymbidium ringspot virus, (CyRSV), Cucumber mosaic virus, (CMV), Bean yellow mosaic virus, (BYMV) and Vanilla mosaic virus.
A hybrid model for time series forecasting (2012)

For time series, the problem that we often encounter is how to extract the patterns hidden in the real world data for forecasting its future values. A single linear or nonlinear model is inadequate in modeling and forecasting the time series, because most of them usually contain both linear and nonlinear patterns. This study constructs a hybrid forecasting model that combines autoregressive integrated moving average (ARIMA) with Elman artificial neural network (ANN) for short-term forecasting of time series. The proposed approach considers the linear and nonlinear patterns in the real data simultaneously so that it can mine more precise characteristics to describe the time series better. Finally, the forecasting results of the hybrid model are adjusted with the knowledge from text mining and expert system. The empirical results on the container throughput forecast of Tianjin Port show that the forecasts by the hybrid model are superior to those of ARIMA model and Elman network.