gebhart/patrepeval huggingface dataset:
Techno-Economic Analysis of Integrated Gasification Fuel Cell Systems (2014)

This report presents the results of an updated Pathway Study for coal-based, integrated gasification fuel cell (IGFC) power systems with carbon capture and storage (CCS). The results quantify the performance and cost benefits for a series of projected gains made through the development of advanced technologies or improvements in plant operation and maintenance. The results represent the potential future benefits of IGFC technology development. They also provide DOE with a basis to select the most appropriate development path for IGFC, and to measure and prioritize the contribution of its R&D program to future power systems technology.
CO2 Capture from Cement Plants and Steel Mills Using Membranes (2018)

Carbon dioxide capture, utilization, and storage (CCUS) has been identified as an effective method of mitigating anthropogenic CO2 emissions. To date, most research and development has centered on capturing CO2 emitted from coal power plants, as they are the largest point source emitters globally. However, cement and steel plants also emit large amounts of CO2 and are potentially easier targets for a CO2 capture process because the CO2 in their flue gas tends to be more concentrated. In this paper, the feasibility of capturing CO2 from cement and steel plants is examined using currently available membrane technology. Coal power plant flue gas contains 13–15% CO2; cement and steel plant flue gas contains 20–30% CO2; this higher CO2 concentration is useful for all separation technologies, but especially for membranes where separation is strongly dependent on the partial pressure driving force. Membrane-based systems can capture 80% of the CO2 emitted from cement or steel production processes at costs of $40 to $50/tonne of CO2 captured. Lower costs are possible if lower capture rates are considered. This makes CO2 capture from these gas streams an attractive first application for commercial membranes recently developed for flue gas treatment.
Binary Assembly of PbS and Au Nanocrystals: Patchy PbS Surface Ligand Coverage Stabilizes the CuAu Superlattice (2019)

Self-assembly of two sizes of nearly spherical colloidal nanocrystals (NCs) capped with hydrocarbon surface ligands has been shown to produce more than 20 distinct phases of binary nanocrystal superlattices (BNSLs). Such structural diversity, in striking contrast to binary systems of micron-sized colloidal beads, cannot be rationalized by models assuming entropy-driven crystallization of simple spheres. In this work, we show that the PbS ligand binding equilibrium controls the relative stability of two closely related BNSL structures featuring alternating layers of PbS and Au NCs. At an intermediate size ratio, as-prepared PbS NCs assemble with Au NCs into CuAu BNSLs featuring orientational coherence of PbS NCs across the lattice. Measurement of interparticle separations within CuAu and modeling of the structure reveal that PbS inorganic cores are nearly in contact through (100) NC surfaces in the square tiling of the CuAu basal plane. On the other hand, AlB<sub>2</sub> BNSLs with PbS NCs packed in random orientations were found to be the dominant self-assembly product when the same binary NC solution was evaporated in the presence of added oleic acid (OAH). Solution nuclear magnetic resonance titration experiments confirmed that added OAH binds to PbS NCs, implicating ligand surface coverage as an important factor influencing the relative stability of CuAu and AlB<sub>2</sub> BNSLs at the experimental size ratio. From these results, we conclude that as-prepared PbS NCs feature sparsely covered (100) surfaces and thus effectively flat patches along NC x-, y-, and z-directions. Such anisotropic PbS-PbS interactions can be efficiently screened by restoring effectively spherical NC shape via addition of OAH to the binary assembly solution. Our findings underscore the important contribution of NC surfaces to superlattice phase stability and offer a strategy for targeted BNSL assembly.
Advanced Software Architectures and Technologies in High Performance Computing and Data Centers (2020)

This paper reviews advanced software architectures and technologies that support in-networking computing and improve the overall performance of data centers and high-performance computing clusters; the ability to converge software and hardware allows for new solutions, such as artificial intelligence, to be deployed massively.
Use of cell type‐specific transcriptome to identify genes specifically involved in Müller glia differentiation during retinal development (2013)

Retinal progenitor cells alter their properties over the course of development, and sequentially produce different sub-populations of retinal cells. We had previously found that early and late retinal progenitor cell populations can be distinguished by their surface antigens, SSEA-1 and c-kit, respectively. Using DNA microarray analysis, we examined the transcriptomes of SSEA-1 positive cells at E14, and c-kit positive, and c-kit negative cells at P1. By comparing data, we identified genes specifically expressed in c-kit positive late retinal progenitor cells. The previous literature suggests that most of the c-kit positive cell-specific genes are related to glia differentiation in brain or are expressed in Müller glia. Since Notch signaling promotes Müller glia differentiation in retina, we examined the effects of gain- and loss-of-Notch signaling on expression of these genes and found that all the genes were positively affected by Notch signaling. Finally, we screened the genes for their function in retinal development by shRNA-based suppression in retinal explants. In about half the genes, Müller glia differentiation was perturbed when their expression was suppressed. Taken together, these results show that at P1, c-kit positive retinal progenitor cells, which include Müller glia precursor cells, are enriched for genes related to glial differentiation. We propose analysis of purified subsets of retinal cells as a powerful tool to elucidate the molecular basis of retinal development.
A roadmap for gene drives: using institutional analysis and development to frame research needs and governance in a systems context (2017)

The deployment of gene drives is emerging as an alternative for protecting endangered species, controlling agricultural pests, and reducing vector-borne diseases. This paper reports on a workshop held in February 2016 to explore the complex intersection of political, economic, ethical, and ecological risk issues associated with gene drives. Workshop participants were encouraged to use systems thinking and mapping to describe the connections among social, policy, economic, and ecological variables as they intersect within governance systems. In this paper, we analyze the workshop transcripts and maps using the Institutional Analysis and Development (IAD) framework to categorize variables associated with gene drive governance and account for the complexities of socio-ecological systems. We discuss how the IAD framework can be used in the future to test hypotheses about how features of governance systems might lead to certain outcomes and inform the design of research programs, public engagement, and anticipatory governance of gene drives. Keywords: Gene drive; governance; risk; systems; IAD; genetic engineering
Evolution of Hydrogen-Bond Networks in Protonated Water Clusters H+(H2O)n (n = 1 to 120) Studied by Cryogenic Ion Mobility-Mass Spectrometry (2014)

Cryogenic (80 K) ion mobility-mass spectrometry (cryo-IM-MS) is employed to study structural transitions of protonated water clusters in both the small, H(+)(H2O)n (n = 1 to 30), and large, (n = 31 to ∼120), size regions. In agreement with previous studies, we find compelling evidence of regions of uniform cluster decay in the small size region, accompanied by sharp transition points whereby the loss of a single water monomer induces a different H-bonding motif. The investigation of the isomeric distribution of each species at 80 K reveals experimental evidence supporting the notion that H(+)(H2O)n (n = 6) is the smallest system to possess both Eigen- (H3O(+)) and Zundel- (H5O2(+)) centered structures. Cryo-IM-MS is particularly well-suited for studying clusters in the large size region, for which previous spectroscopic experimental studies are scarce.
Posttraumatic Phycomycosis of the Anterior Segment (1978)

Keratomycosis and infection of the anterior chamber with a Rhizopus sp (phycomycosis, mucormycosis) developed in a 24-year-old man following a perforating injury of the cornea with a soil-contaminated screwdriver. The infection was documented by positive cultures of the corneal wound and of the anterior chamber and by histopathologic studies. Phycomycosis of the eye usually occurs in the setting of systemically impaired host resistance. The patient had no underlying disease that wound predispose him to this infection but the treatment with topical 0.1% dexamethasone and triamcinolone acetonide suspension injected into the sub-Tenon's space following the injury may have impaired his local immunologic defenses. Excisional keratoplasty played an important role in the successful management of this case.
PQL: Protein Query Language (2012)

This paper introduces a Protein Query Language (PQL) for querying protein structures in an expressive yet concise manner. One of the objectives of the paper is to demonstrate how such a language would be beneficial to protein researchers to obtain in-depth protein data from a relational database without extensive SQL knowledge. The language features options such as limiting query results by key protein characteristics such as methyl donated hydrogen bond interactions, minimum and maximum phi and psi angles, repulsive forces, CH/Pi calculations, and other pertinent factors. A backend data model was designed to support storage and retrieval of protein primary and secondary sequences, atomic-level data, as well as calculations on said data. A relational DBMS is used as the persistent storage backend, with every effort made to ensure transparent portability to most relational database systems. In addition, front end applications can be developed to support retrieving, transforming, and preprocessing of information from the Research Collaboratory for Structural Bioinformatics (RCSB) into the backend data repository. The new language and associated architecture allow users to load additional protein files from RCSB into the database, issue standard queries to download pertinent data in user-friendly formats including CSV files, issue non-standard queries against secondary structures via the protein query language, and run error-detection routines against data in the database. Query results may include normalized or denormalized data, model and chain data, residue data, atom detail data, and primary as well as secondary structure data.
Bioactivity of Autologous Irradiated Renal Cell Carcinoma Vaccines Generated by Ex Vivo Granulocyte-Macrophage Colony-Stimulating Factor Gene Transfer (1998)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) gene-transduced, irradiated tumor vaccines induce potent, T-cell-mediated antitumor immune responses in preclinical models. We report the initial results of a Phase I trial evaluating this strategy for safety and the induction of immune responses in patients with metastatic renal cell carcinoma (RCC). Patients were treated in a randomized, double-blind dose-escalation study with equivalent doses of autologous, irradiated RCC vaccine cells with or without ex vivo human GM-CSF gene transfer. The replication-defective retroviral vector MFG was used for GM-CSF gene transfer. No dose-limiting toxicities were encountered in 16 fully evaluable patients. GM-CSF gene-transduced vaccines were equivalent in toxicity to nontransduced vaccines up to the feasible limits of autologous tumor vaccine yield. No evidence of autoimmune disease was observed. Biopsies of intradermal sites of injection with GM-CSF gene-transduced vaccines contained distinctive macrophage, dendritic cell, eosinophil, neutrophil, and T-cell infiltrates similar to those observed in preclinical models of efficacy. Histological analysis of delayed-type hypersensitivity responses in patients vaccinated with GM-CSF-transduced vaccines demonstrated an intense eosinophil infiltrate that was not observed in patients who received nontransduced vaccines. An objective partial response was observed in a patient treated with GM-CSF gene-transduced vaccine who displayed the largest delayed-type hypersensitivity conversion. No replication-competent retrovirus was detected in vaccinated patients. This Phase I study demonstrated the feasibility, safety, and bioactivity of an autologous GM-CSF gene-transduced tumor vaccine for RCC patients.
The grapevine flagellin receptor VvFLS2 differentially recognizes flagellin‐derived epitopes from the endophytic growth‐promoting bacterium Burkholderia phytofirmans and plant pathogenic bacteria (2013)

• The role of flagellin perception in the context of plant beneficial bacteria still remains unclear. Here, we characterized the flagellin sensing system flg22-FLAGELLIN SENSING 2 (FLS2) in grapevine, and analyzed the flagellin perception in the interaction with the endophytic plant growth-promoting rhizobacterium (PGPR) Burkholderia phytofirmans. • The functionality of the grapevine FLS2 receptor, VvFLS2, was demonstrated by complementation assays in the Arabidopsis thaliana fls2 mutant, which restored flg22-induced H₂O₂ production and growth inhibition. Using synthetic flg22 peptides from different bacterial origins, we compared recognition specificities between VvFLS2 and AtFLS2. • In grapevine, flg22-triggered immune responses are conserved and led to partial resistance against Botrytis cinerea. Unlike flg22 peptides derived from Pseudomonas aeruginosa or Xanthomonas campestris, flg22 peptide derived from B. phytofirmans triggered only a small oxidative burst, weak and transient defense gene induction and no growth inhibition in grapevine. Although, in Arabidopsis, all the flg22 epitopes exhibited similar biological activities, the expression of VvFLS2 into the fls2 background conferred differential flg22 responses characteristic for grapevine. • These results demonstrate that VvFLS2 differentially recognizes flg22 from different bacteria, and suggest that flagellin from the beneficial PGPR B. phytofirmans has evolved to evade this grapevine immune recognition system.
Spatial frequencies from human periosteum at different depths using two-photon microscopic images (2014)

The outer layer of human bone, the periosteum, was studied using two-photon (2P) fluorescence microscopy. This layer of the periosteum is composed mostly of fibrous collagen. The inner cambium layer has less collagen and contains osteoblasts necessary for bone remodeling. The spatial frequencies from the layers of the periosteum of human bone at different depths were investigated using images acquired with two-photon excitation microscopy. This 2P spectroscopic method offers deeper depth penetration into samples, high fluorescence collection efficiency, and a reduction in photobleaching and photodamage. Using 130 femtosecond pulses with an 800 nm wavelength excitation, a 40&times; microscope objective, and a photomultiplier tube (PMT) detector, high contrast images of the collagen present in the periosteum at various micrometers depths from the surface were obtained. Fourier transform analysis of the 2P images was used to assess the structure of the periosteum at different depths in terms of spatial frequencies. The spatial frequency spectra from the outer and inner periosteal regions show significant spectral peak differences which can provide information on the structure of the layers of the periosteum. One may be able to use spatial frequency spectra for optical detection of abnormalities of the periosteum which can occur in disease.
Metrology and inspection for process control during bonding and thinning of stacked wafers for manufacturing 3D SIC's (2011)

New challenges for wafer metrology solutions have evolved with 3D-IC manufacturing technology. 3D-IC technology allows stacking single chips, electrically connecting them in the vertical direction, and then forming a chip structure with significant advantages over traditional chips. However, before the 3D-stacking of IC's becomes a mainstream process numerous metrology issues need to be solved. In this paper we discuss the critical in-line metrology needs during bonding and thinning of the device wafers before stacking. We show how TSV depth variations, glue layer defects and grinding issues require monitoring for a successful 3D integration.
Recent Progress on Organic Electrodes Materials for Rechargeable Batteries and Supercapacitors (2019)

Rechargeable batteries are essential elements for many applications, ranging from portable use up to electric vehicles. Among them, lithium-ion batteries have taken an increasing importance in the day life. However, they suffer of several limitations: safety concerns and risks of thermal runaway, cost, and high carbon footprint, starting with the extraction of the transition metals in ores with low metal content. These limitations were the motivation for an intensive research to replace the inorganic electrodes by organic electrodes. Subsequently, the disadvantages that are mentioned above are overcome, but are replaced by new ones, including the solubility of the organic molecules in the electrolytes and lower operational voltage. However, recent progress has been made. The lower voltage, even though it is partly compensated by a larger capacity density, may preclude the use of organic electrodes for electric vehicles, but the very long cycling lives and the fast kinetics reached recently suggest their use in grid storage and regulation, and possibly in hybrid electric vehicles (HEVs). The purpose of this work is to review the different results and strategies that are currently being used to obtain organic electrodes that make them competitive with lithium-ion batteries for such applications.
Cantleyoside-dimethyl-acetal and Other Iridoid Glucosides from Pterocephalus perennis – Antimicrobial Activities (2002)

Cantleyoside-dimethyl-acetal (6), was isolated from the endemic Greek plant Pterocephalus perennis subsp. perennis in addition to five other known iridoid glucosides, loganin, loganic acid, cantleyoside, secologanin, and secologanin-dimethyl-acetal. The structure of these compounds was determined by all spectroscopic means mainly by NMR and MS techniques. The above compounds as well as their acetyl derivatives were tested against six Gram positive and negative bacteria and three pathogenic fungi.
Al-2.39 Doctor Blading (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Risk of Colorectal Neoplasia in Individuals With Self-Reported Family History: A Prospective Colonoscopy Study from 16 Asia-Pacific Regions (2016)

The risk of colorectal neoplasia was similar among subjects with different FDRs affected. These findings do not support the need to discriminate proband identity in screening participants with affected FDRs when their risks of colorectal neoplasia were estimated.
Methodology for the preparation of olive oil open ring secoiridoids (2012)

Olive oil (OO) as an important component of the Mediterranean diet has been extensively studied and correlated with NSAID properties, simulating the ones of ibuprofen. The phenolic content of OO includes open ring secoiridoids such as oleacein (2), closely related to oleuropein (1). The latter is easily isolated from olive tree leaves and can be used as a natural synthon. Herein, it is proposed that the opening of the oleuropein secoiridoid ring can afford a series of secoiridoid dialdehydes similar to oleacein. This methodology can be expanded to various secoiridoid conjugates providing a tool for the synthesis of a number of analogues. Project was carried out under the scope of OLITEC (IAAP 230763).
Direct integrated strain sensors for robust temperature behaviour (2015)

We have investigated the fundamental behavior of strain sensitive transistors with respect to different transistor parameters. Therefore, the transistors have been simulated by using a modified BSIM3.3 model. The simulations showed an increase of drain current between 3.5 % and 5.8 % at 60 MPa stress, an acceptable shift of threshold voltage, and almost no increase of leakage current. For basic characterization, pressure sensitive silicon membranes have been fabricated as strain inducing elements. Measurements with elongated membranes confirmed the simulation results regarding the transistor parameters and the robust temperature behaviour.
Activation of a Plasma Membrane–Associated Neutral Sphingomyelinase and Concomitant Ceramide Accumulation During IgG-Dependent Phagocytosis in Human Polymorphonuclear Leukocytes (1998)

Abstract The sphingomyelin cycle, which plays an important role in regulation of cell growth, differentiation, and apoptosis, involves the formation of ceramide by the action of a membrane-associated, Mg2+-dependent, neutral sphingomyelinase and/or a lysosomal acid sphingomyelinase. In human polymorphonuclear leukocytes (PMNs), ceramide production correlates with and plays a role in the regulation of functional responses such as oxidant release and Fcγ receptor-mediated phagocytosis. To increase our understanding of the sphingomyelin cycle in human PMNs, the cellular location of neutral and acid sphingomyelinases was investigated in resting, formylmethionylleucylphenylalanine (FMLP)-activated, and FMLP-activated PMNs engaged in phagocytosis. In resting PMNs, a Mg2+-dependent, neutral sphingomyelinase was the predominant activity and was localized to the plasma membrane fractions along with the majority of ceramide. Upon FMLP-activation, there was a 1.9-fold increase in this neutral, Mg2+-dependent sphingomyelinase activity, which increased to 2.7-fold subsequent to phagocytosis of IgG opsonized targets. This increase in sphingomyelinase activity was restricted to the plasma membrane fractions, which were also the site of increased ceramide levels. Phospholipase D (PLD) activity, which is a target of ceramide action and is required for phagocytosis, was also found primarily in the plasma membrane fractions of FMLP-activated and phagocytosing PMNs. Our findings indicate that in human PMNs engaged in phagocytosis, the sphingomyelin cycle is restricted to the plasma membrane where intracellular targets of ceramide action, such as PLD, are localized.