gebhart/patrepeval huggingface dataset:
Electrical and Optical Characterization of Core-Shell InGaN/GaN Nanowire Solar Cells on Si (111) (2014)

We present electrical and optical characterization of InGaN/GaN nanowires on silicon with a goal to develop an intermediate band solar cell based on this novel material system. We demonstrate current-voltage characteristics illuminated with up to 16 suns AM 1.5G illumination, and the improved photoluminescence properties of InGaN/GaN quantum dots inside GaN nanowireswith an AlGaN shell. A sub-bandgap contribution to the quantum efficiency is observed, demonstrating the use of InGaN/GaN quantum dots as a possible route towards efficiency beyond the Shockley-Queisser limit.
Identification of LOS in Time-Varying, Frequency Selective Radio Channels (2008)

A method is proposed to identify the existence of line-of-sight (LOS) for time-varying, frequency selective radio channels. The proposed method considers the second-order statistical characteristics of underlying process in the channel taps. Identification is established by comparing the autocorrelation coefficients of the first tap with those of any other tap when the other tap reaches its coherence time. Numerical results and related discussions are presented considering several practical scenarios.
Gaussian Processes for Analyzing Positioned Trajectories in Sports (2019)

Kernel-based machine learning approaches are gaining increasing interest for exploring and modeling large dataset in recent years. Gaussian process (GP) is one example of such kernel-based approaches, which can provide very good performance for nonlinear modeling problems. In this work, we first propose a grey-box modeling approach to analyze the forces in cross country skiing races. To be more precise, a disciplined set of kinetic motion model formulae is combined with data-driven Gaussian process regression model, which accounts for everything unknown in the system. Then, a modeling approach is proposed to analyze the kinetic flow of both individual and clusters of skiers. The proposed approaches can be generally applied to use cases where positioned trajectories and kinetic measurements are available. The proposed approaches are evaluated using data collected from the Falun Nordic World Ski Championships 2015, in particular the Men's cross country $4\times10$ km relay. Forces during the cross country skiing races are analyzed and compared. Velocity models for skiers at different competition stages are also evaluated. Finally, the comparisons between the grey-box and black-box approach are carried out, where the grey-box approach can reduce the predictive uncertainty by $30\%$ to $40\%$.
Comprehensive Guide to Extracting and Expressing Fungal Secondary Metabolites with Aspergillus fumigatus as a Case Study (2021)

Fungal secondary metabolites (SMs) have captured the interest of natural products researchers in academia and industry for decades. In recent years, the high rediscovery rate of previously characterized metabolites is making it increasingly difficult to uncover novel compounds. Additionally, the vast majority of fungal SMs reside in genetically intractable fungi or are silent under normal laboratory conditions in genetically tractable fungi. The fungal natural products community has broadly overcome these barriers by altering the physical growth conditions of the fungus and heterologous/homologous expression of biosynthetic gene cluster regulators or proteins. The protocols described here summarize vital methodologies needed when researching SM production in fungi. We also summarize the growth conditions, genetic backgrounds, and extraction protocols for every published SM in Aspergillus fumigatus, enabling readers to easily replicate the production of previously characterized SMs. Readers will also be equipped with the tools for developing their own strategy for expressing and extracting SMs from their given fungus or a suitable heterologous model system. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Making glycerol stocks from spore suspensions Alternate Protocol 1: Creating glycerol stocks from non-sporulating filamentous fungi Basic Protocol 2: Activating spore-suspension glycerol stocks Basic Protocol 3: Extracting secondary metabolites from Aspergillus spp grown on solid medium Alternate Protocol 2: Extracting secondary metabolites from Aspergillus spp using ethyl acetate Alternate Protocol 3: High-volume metabolite extraction using ethyl acetate Alternate Protocol 4: Extracting secondary metabolites from Aspergillus spp in liquid medium Support Protocol: Creating an overlay culture Basic Protocol 4: Extracting DNA from filamentous fungi Basic Protocol 5: Creating a DNA construct with double-joint PCR Alternate Protocol 5: Creating a DNA construct with yeast recombineering Basic Protocol 6: Transformation of Aspergillus spp Basic Protocol 7: Co-culturing fungi and bacteria for extraction of secondary metabolites.
Isolation and Structure of New Isocoumarins (1977)

Journal Article Isolation and Structure of New Isocoumarins Get access Yoshio Furutani, Yoshio Furutani Institute of Microbial Chemistry, 3–14–23, Kamiosaki, Shinagawa-ku, Tokyo, Japan Present address: Research Center, Mitsui Toatsu Chemicals, Inc., 1190, Kasama-cho, Tbtsuka-ku, Yokohama, Japan. Search for other works by this author on: Oxford Academic Google Scholar Hiroshi Naganawa, Hiroshi Naganawa Institute of Microbial Chemistry, 3–14–23, Kamiosaki, Shinagawa-ku, Tokyo, Japan Search for other works by this author on: Oxford Academic Google Scholar Tomio Takeuchi, Tomio Takeuchi Institute of Microbial Chemistry, 3–14–23, Kamiosaki, Shinagawa-ku, Tokyo, Japan Search for other works by this author on: Oxford Academic Google Scholar Hamao Umezawa Hamao Umezawa Institute of Microbial Chemistry, 3–14–23, Kamiosaki, Shinagawa-ku, Tokyo, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 41, Issue 7, 1 July 1977, Pages 1179–1183, https://doi.org/10.1080/00021369.1977.10862645 Published: 01 July 1977 Article history Received: 23 December 1976 Published: 01 July 1977
Iridovirus infection of cell cultures from the Diaprepes root weevil, Diaprepes abbreviatus (2003)

We here report the development and viral infection of a Diaprepes root weevil cell culture. Embryonic tissues of the root weevil were used to establish cell cultures for use in screening viral pathogens as potential biological control agents. Tissues were seeded into a prepared solution of insect medium and kept at a temperature of 24 degrees C. The cell culture had primarily fibroblast-like morphology with some epithelial monolayers. Root weevil cells were successfully infected in vitro with a known insect virus, Invertebrate Iridescent Virus 6. Potential uses of insect cell cultures and insect viruses are discussed.
Finite element analysis of microstrip line on ferroelectric (Ba-Sr)TiO/sub 3/ substrate (2002)

The characteristics of microstrip line on ferroelectric (Ba-Sr)TiO/sub 3/ substrate is analyzed. The static field analysis is performed iteratively to obtain the position-dependent dielectric constant in BST substrate with DC bias voltage. On the assumption of small AC field compared to DC field, the propagation constant and the characteristic impedance of the microstrip line on such a biased BST substrate is found by edge-based finite element method. The results can be used for the accurate design of various devices using BST such as dielectric phase shifter, voltage controlled resonators, etc.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Feature Selection for Scene Categorization Using Support Vector Machines (2008)

Categorization of scenes is a fundamental process of human vision that allows us to efficiently and rapidly analyze our surroundings. Scene classification, the classification of images into semantic categories (e.g., coast, mountains, highways and streets) is a challenging and important problem nowadays. This paper is classifying the scenes using support vector machine with radial basis kernel with p1=5. This work is double folded as to classify the scenes using support vector machine and to find better feature extraction method among the ones which have been used by the research community often i.e., wavelet features, invariant moments and co-occurrences matrix. The sample images are taken from the real world dataset.
Biosynthesis and Intracellular Targeting of the CLN3 Protein Defective in Batten Disease (1998)

Batten disease (juvenile-onset neuronal ceroid lipofuscinosis, JNCL), the most common neurodegenerative disorder of childhood, is caused by mutations in a recently identified gene ( CLN3 ) localized to chromosome 16p11.2-12.1. To elucidate the biosynthesis and localization of the CLN3 protein, we expressed CLN3 cDNA in COS-1 and HeLa cell lines. In vitro translation, immunoprecipitation and Western blotting analyses detected an approximately 43 kDa polypeptide. Pulse-chase experiments indicated that the CLN3 protein is synthesized as an N -glycosylated single-chain polypeptide, which was not detected in growth medium. Confocal immunofluorescence microscopy revealed that the CLN3 protein is localized to the lysosomal compartment. These results provide evidence that Batten disease can be classified as a member of lysosomal diseases.
The First Total Synthesis of (−) and (+)-2-Hydroxy-24-oxooctacosanolide Using an Effective Lactonization (2006)

[structure: see text] An effective method for the total synthesis of 2-hydroxy-24-oxooctacosanolide, a defensive salivary secretion of the African termite Pseudacanthotermes spiniger, has been developed. The key lactonization to form a 29-membered ring lactone core is performed using 2-methyl-6-nitrobenzoic anhydride with a catalytic amount of 4-(dimethylamino)pyridine N-oxide.
Requirement of CTLA-4 counter receptors for IL-4 but not IL-10 elevations during a primary systemic in vivo immune response. (1995)

The CD28/CTLA-4 costimulatory signal is required for TCR-mediated T cell activation resulting in increased IL-2 production in vitro, but its role in IL-4 production is unclear and few studies have examined the function of CTLA-4/CD28 in the in vivo immune response. We have examined the in vivo effects of blocking the interaction of B7 with its ligands, CTLA-4 and CD28, in an IL-4 dominant in vivo immune response to goat anti-mouse IgD. This response is characterized by elevations in serum Igs preceded by elevations in IL-2 and the Th2 cytokines: IL-4, IL-9, and IL-10. The fusion protein CTLA4-Ig administered during the in vivo immune response to goat anti-mouse IgD caused an inhibition in elevations of IL-2, IL-4, and IL-9 gene expression at both day 3 and day 6 after immunization. In contrast, IL-10 cytokine gene expression as late as day 6 after immunization was not decreased. Cell sorting analysis demonstrated that TCR-alpha beta +, CD4+ T cells were the primary source of the elevated IL-10, suggesting that T cell activation leading to IL-10 gene expression may not require CTLA-4 ligand interactions. Similarly CTLA4-Ig completely blocked elevations in the number of IL-4- but not IL-10-secreting cells, as measured by ELISPOT, in both unsorted splenic cells and sorted CD4+, TCR-alpha beta+ T cells. In situ staining of spleen sections also showed inhibition of IL-4-producing cells. These results suggest that, with the notable exception of IL-10, interaction, of B7 with its ligands is required for elevated Th2 cytokine gene expression and secretion during a primary systemic IL-4-dominant response.
Increased frequency of aberrant V(D)J recombination products in core RAG-expressing mice (2004)

RAG1 and RAG2 play a central role in V(D)J recombination, a process for antigen receptor gene assembly. The truncated 'core' regions of RAGs are sufficient to catalyze the recombination reaction, although with lower joining efficiency than full-length proteins. To investigate the role of the non-core regions of RAGs in the end-joining phase of antigen receptor rearrangement, we analyzed recombination products isolated from core RAG1 and core RAG2 knock-in mice. Here, we report that the truncation of RAGs increases the frequency of aberrant recombination in vivo. Signal joints (SJs) associated with V-to-D recombination of core RAG1 knock-in mice were normal, whereas those of core RAG2 knock-in mice were highly imprecise, containing large deletions and additions, and in some cases coding sequences. In contrast, we found an elevated level of imprecise D-to-J associated SJs for both core RAG1- and RAG2-expressing mice. Likewise, sequences of coding joints (CJs) were also affected by the expression of core RAGs. Finally, sequences found at the junctions of rearranged T-cell receptor loci were highly influenced by differences in rearranging recombination signal sequence pairs. We provide the first evidence that the non-core regions of RAGs have critical functions in the proper assembly and resolution of recombination intermediates in endogenous antigen receptor loci.
Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma (2020)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
An Evolved Mxe GyrA Intein for Enhanced Production of Fusion Proteins (2014)

Expressing antibodies as fusions to the non-self-cleaving Mxe GyrA intein enables site-specific, carboxy-terminal chemical modification of the antibodies by expressed protein ligation (EPL). Bacterial antibody-intein fusion protein expression platforms typically yield insoluble inclusion bodies that require refolding to obtain active antibody-intein fusion proteins. Previously, we demonstrated that it was possible to employ yeast surface display to express properly folded single-chain antibody (scFv)-intein fusions, therefore permitting the direct small-scale chemical functionalization of scFvs. Here, directed evolution of the Mxe GyrA intein was performed to improve both the display and secretion levels of scFv-intein fusion proteins from yeast. The engineered intein was shown to increase the yeast display levels of eight different scFvs by up to 3-fold. Additionally, scFv- and green fluorescent protein (GFP)-intein fusion proteins can be secreted from yeast, and while fusion of the scFvs to the wild-type intein resulted in low expression levels, the engineered intein increased scFv-intein production levels by up to 30-fold. The secreted scFv- and GFP-intein fusion proteins retained their respective binding and fluorescent activities, and upon intein release, EPL resulted in carboxy-terminal azide functionalization of the target proteins. The azide-functionalized scFvs and GFP were subsequently employed in a copper-free, strain-promoted click reaction to site-specifically immobilize the proteins on surfaces, and it was demonstrated that the functionalized, immobilized scFvs retained their antigen binding specificity. Taken together, the evolved yeast intein platform provides a robust alternative to bacterial intein expression systems.
VEHICLE ACTION LIGHTS: AN APPROACH TO INTERSECTION CRASH AVOIDANCE (2000)

Purpose: Motor vehicle crashes at intersections and driveways are an important area of safety. This study presents a crash avoidance concept using Vehicle Action Lights (VAL), which enhances the conspicuity of driver brake and throttle action for oncoming or crossing traffic. This gives others an earlier indication of vehicle motion. Method: A vehicle was modified with VAL on the front corners so that brake action is shown by a red light and throttle action is displayed by a series of eight white lights which are sequenced in a four-light roll. The lights are visible to oncoming and crossing traffic. Results: As a driver approaches an intersection and applies the brakes, the front corners show a red light. As the driver's foot is moved off the brake to the throttle, the red light goes off. It takes more than 0.4 s to move to the throttle. Once the throttle is pushed, a white-light sequence starts and steps forward using a four-light roll. This indicates that the vehicle is accelerating forward. There is about 0.2 s delay between depressing the throttle and the vehicle moving. A driving simulator study was conducted with 24 volunteers. About 1.2 s advanced warning is provided by VAL for on-coming and crossing traffic. Conclusion: An earlier warning of actions by another driver enables emergency evasive action or yielding of right of way, which may prevent or lessen the severity of vehicle crashes.
PIM kinases as therapeutic targets against advanced melanoma (2016)

Therapeutic strategies for the treatment of metastatic melanoma show encouraging results in the clinic; however, not all patients respond equally and tumor resistance still poses a challenge. To identify novel therapeutic targets for melanoma, we screened a panel of structurally diverse organometallic inhibitors against human-derived normal and melanoma cells. We observed that a compound that targets PIM kinases (a family of Ser/Thr kinases) preferentially inhibited melanoma cell proliferation, invasion, and viability in adherent and three-dimensional (3D) melanoma models. Assessment of tumor tissue from melanoma patients showed that PIM kinases are expressed in pre- and post-treatment tumors, suggesting PIM kinases as promising targets in the clinic. Using knockdown studies, we showed that PIM1 contributes to melanoma cell proliferation and tumor growth in vivo; however, the presence of PIM2 and PIM3 could also influence the outcome. The inhibition of all PIM isoforms using SGI-1776 (a clinically-available PIM inhibitor) reduced melanoma proliferation and survival in preclinical models of melanoma. This was potentiated in the presence of the BRAF inhibitor PLX4720 and in the presence of PI3K inhibitors. Our findings suggest that PIM inhibitors provide promising additions to the targeted therapies available to melanoma patients.
Understanding and Modelling the Mechanical and Corrosion Properties of 6056 for Aerospace Applications (2000)

Alloys of the Al-Mg-Si-Cu series like AA6056 are good candidates for welded fuselage panels. The first part of the paper recalls the main metallurgical influences on final properties (mechanical strength, damage tolerance and intergranular corrosion resistance). Starting from these principles, the properties of AA6056 type alloys were rationalised using metallurgical modelling. Clear relationships between measured properties and metallurgical calculations are found. An illustration of such an approach is given, leading to an optimised version of AA6056.
Precaution: Open gene drive research (2017)

In their Policy Forum “Precaution and governance of emerging technologies” (11 November 2016, p. [710][1]), G. E. Kaebnick and colleagues convincingly assert that precaution is consistent with support for science. However, they overlook one way to improve safety while hastening discovery: Make
Sketch2Manga: Sketch-based manga retrieval (2014)

We propose a sketch-based method for manga image retrieval, in which users draw sketches via a Web browser that enables the automatic retrieval of similar images from a database of manga titles. The characteristics of manga images are different from those of naturalistic images. Despite the widespread attention given to content-based image retrieval systems, the question of how to retrieve manga images effectively has been little studied. We propose a fine multi-scale edge orientation histogram (FMEOH) whereby a number of differently sized squares on a page can be indexed efficiently. Our experimental results show that FMEOH can achieve greater accuracy than a state-of-the-art sketch-based retrieval method [1].
Intelligent Prediction for Rock Porosity While Drilling Complex Lithology in Real Time (2021)

Rock porosity is an important parameter for the formation evaluation, reservoir modeling, and petroleum reserve estimation. The conventional methods for determining the rock porosity are considered costly and time-consuming operations during the well drilling. This paper aims to predict the rock porosity in real time while drilling complex lithology using machine learning. In this paper, two intelligent models were developed utilizing the random forest (RF) and decision tree (DT) techniques. The drilling parameters include weight on bit, torque, standpipe pressure, drill string rotation speed, rate of penetration, and pump rate. Two datasets were employed for building the models (3767 data points) and for validating the developed models (1676 data points). Both collected datasets have complex lithology of carbonate, sandstone, and shale. Sensitivity and optimization on different parameters for each technique were conducted to ensure optimum prediction. The models' performance was checked by four performance indices which are coefficient of determination (<i>R</i> <sup>2</sup>), average absolute percentage error (AAPE), variance account for (VAF), and a20 index. The results indicated the strong porosity prediction capability for the two models. DT model showed <i>R</i> <sup>2</sup> of 0.94 and 0.87 between the predicted and actual porosity values with AAPE of 6.07 and 9% for training and testing, respectively. Generally, RF provided a higher level of strong prediction than DT as RF achieved <i>R</i> <sup>2</sup> of 0.99 and 0.90 with AAPE of 1.5 and 7% for training and testing, respectively. The models' validation proved a high prediction performance as DT achieved <i>R</i> <sup>2</sup> of 0.88 and AAPE of 8.58%, while RF has <i>R</i> <sup>2</sup> of 0.92 and AAPE of 6.5%.
Ultrasmall silicon nanoparticles as a promising platform for multimodal imaging (2019)

Bimodal systems for nuclear and optical imaging are currently being intensively investigated due to their comparable detection sensitivity and the complementary information they provide. In this perspective, we have implemented both modalities on biocompatible ultrasmall silicon nanoparticles (Si NPs). Such nanoparticles are particularly interesting since they are highly biocompatible, have covalent surface functionalization and demonstrate very fast body clearance. We prepared monodisperse citrate-stabilized Si NPs (2.4 ± 0.5 nm) with more than 40 accessible terminal amino groups per particle and, for the first time, simultaneously, a near-infrared dye (IR800-CW) and a radiolabel (64Cu-NOTA = 1,4,7-triazacyclononane-1,4,7-triacetic acid) have been covalently linked to the surface of such Si NPs. The obtained nanomaterials have been fully characterized using HR-TEM, XPS, UV-Vis and FT-IR spectroscopy. These dual-labelled particles do not exhibit any cytotoxicity in vitro. In vivo studies employing both positron emission tomography (PET) and optical imaging (OI) techniques revealed rapid renal clearance of dual-labelled Si NPs from mice.