gebhart/patrepeval huggingface dataset:
Lysosomal Targeting Enhancement by Conjugation of Glycopeptides Containing Mannose-6-phosphate Glycans Derived from Glyco-engineered Yeast (2018)

Many therapeutic enzymes for lysosomal storage diseases require a high content of mannose-6-phosphate (M6P) glycan, which is important for cellular uptake and lysosomal targeting. We constructed glyco-engineered yeast harboring a high content of mannosylphosphorylated glycans, which can be converted to M6P glycans by uncapping of the outer mannose residue. In this study, the cell wall of this yeast was employed as a natural M6P glycan source for conjugation to therapeutic enzymes. The extracted cell wall mannoproteins were digested by pronase to generate short glycopeptides, which were further elaborated by uncapping and α(1,2)-mannosidase digestion steps. The resulting glycopeptides containing M6P glycans (M6PgPs) showed proper cellular uptake and lysosome targeting. The purified M6PgPs were successfully conjugated to a recombinant acid α-glucosidase (rGAA), used for the treatment of Pompe disease, by two-step reactions using two hetero-bifunctional crosslinkers. First, rGAA and M6PgPs were modified with crosslinkers containing azide and dibenzocyclooctyne, respectively. In the second reaction using copper-free click chemistry, the azide-functionalized rGAA was conjugated with dibenzocyclooctyne-functionalized M6PgPs without the loss of enzyme activity. The M6PgP-conjugated rGAA had a 16-fold higher content of M6P glycan than rGAA, which resulted in greatly increased cellular uptake and efficient digestion of glycogen accumulated in Pompe disease patient fibroblasts.
Surface of cellulosic materials modified with functionalized polyethylene coupling agents (2003)

Abstract The interfacial adhesion between a wood fiber and a plastic matrix strongly influences the performance of wood‐fiber‐reinforced thermoplastic composites. Fiber surface modification with coupling agents is generally needed to induce bond formation between the fiber and polymer matrix. This study investigated the chemical reactions between cellulosic materials and functionalized polyethylene coupling agents. Both wood flour and cotton cellulose powder were treated with acrylic acid‐functionalized polyethylene and maleic anhydride‐functionalized polyethylene (maleated polyethylene) for surface modifications, and chemical changes resulting from these treatments were followed by a study of the Fourier transform infrared and X‐ray photoelectron spectroscopy spectra. Variations in the band intensities, oxygen‐to‐carbon ratios, and concentrations of unoxidized carbon atoms were related to changes that occurred on the surfaces of modified cellulosic materials. The experimental results indicated that chemical bonds between the hydroxyl groups of the cellulosic materials and the functional groups of the coupling agents occurred through esterification reactions. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 278–286, 2003
A Hemicyanine-Conjugated Copolymer as a Highly Sensitive Fluorescent Thermometer (2008)

A simple-structured copolymer, poly(NIPAM-co-HC), consisting of N-isopropylacrylamide (NIPAM) and 4-(4-dimethylaminostyryl)pyridine (hemicyanine, HC) units as thermoresponsive and fluorescent signaling parts, respectively, has been synthesized. This copolymer dissolved in water shows very weak fluorescence at <25 degrees C, while showing fluorescence enhancement at >25 degrees C. The fluorescence intensity increases with a rise in temperature and saturates at >40 degrees C, enabling temperature detection at 25-40 degrees C. The fluorescence enhancement is driven by a heat-induced phase transition of the polymer from coil to globule state. The HC units within the coil state polymer exist as the nonfluorescent benzenoid form; however, the less polar domain formed inside the globule state polymer leads to transformation of the HC unit to the fluorescent quinoid form, resulting in heat-induced fluorescence enhancement. The fluorescence intensity measured at 40 degrees C is >20-fold higher than the intensity at <25 degrees C, which is the highest enhancement value among the fluorescent thermometers proposed so far. The polymer shows reversible fluorescence enhancement/quenching, regardless of the heating/cooling process. In addition, the polymer shows high reusability with a simple recovery process.
Role of Hydrocarbon Deposits in the Enhanced Performance of Direct-Oxidation SOFCs (2003)

We have examined the changes that occur in the performance of solid oxide fuel cells (SOFCs) with Cu-ceria-yttria-stabilized zirconia anodes at 973 K following exposure to various hydrocarbon fuels, including methane, propane, n-butane, n-decane, and toluene. For cells with Cu contents of 20 wt % or less, large increases were observed in the power densities for operation in after the anode had been exposed to any of the hydrocarbons except methane. The increased performance is completely reversible upon oxidation of the anode and subsequent reduction in The enhancement decreases with increasing Cu content, implying that the deposits improve the connectivity of the metallic phase in the anode. Impedance spectra taken on cells before and after exposure to hydrocarbon fuels confirm that the conductivity of the anode improves after exposure. Temperature-programmed oxidation and weight changes were used to show that the deposits that enhance performance correspond to of the anode and are probably not graphitic. Measurements of the open-circuit voltages in hydrocarbon fuels suggest that equilibrium is established with partial oxidation products and that the chemical structure of the deposits change upon current flow. Finally, the implications of these results for operation of SOFC on hydrocarbons without added steam and with low copper contents are discussed. © 2003 The Electrochemical Society. All rights reserved.
Antiviral Activity of Type I, II, and III Interferons Counterbalances ACE2 Inducibility and Restricts SARS-CoV-2 (2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), is a recently emerged respiratory coronavirus that has infected >23 million people worldwide with >800,000 deaths. Few COVID-19 therapeutics are available, and the basis for severe infections is poorly understood. Here, we investigated properties of type I (β), II (γ), and III (λ1) interferons (IFNs), potent immune cytokines that are normally produced during infection and that upregulate IFN-stimulated gene (ISG) effectors to limit virus replication. IFNs are already in clinical trials to treat COVID-19. However, recent studies highlight the potential for IFNs to enhance expression of host angiotensin-converting enzyme 2 (ACE2), suggesting that IFN therapy or natural coinfections could exacerbate COVID-19 by upregulating this critical virus entry receptor. Using a cell line model, we found that beta interferon (IFN-β) strongly upregulated expression of canonical antiviral ISGs, as well as ACE2 at the mRNA and cell surface protein levels. Strikingly, IFN-λ1 upregulated antiviral ISGs, but ACE2 mRNA was only marginally elevated and did not lead to detectably increased ACE2 protein at the cell surface. IFN-γ induced the weakest ISG response but clearly enhanced surface expression of ACE2. Importantly, all IFN types inhibited SARS-CoV-2 replication in a dose-dependent manner, and IFN-β and IFN-λ1 exhibited potent antiviral activity in primary human bronchial epithelial cells. Our data imply that type-specific mechanisms or kinetics shape IFN-enhanced ACE2 transcript and cell surface levels but that the antiviral action of IFNs against SARS-CoV-2 counterbalances any proviral effects of ACE2 induction. These insights should aid in evaluating the benefits of specific IFNs, particularly IFN-λ, as repurposed therapeutics.<b>IMPORTANCE</b> Repurposing existing, clinically approved, antiviral drugs as COVID-19 therapeutics is a rapid way to help combat the SARS-CoV-2 pandemic. Interferons (IFNs) usually form part of the body's natural innate immune defenses against viruses, and they have been used with partial success to treat previous new viral threats, such as HIV, hepatitis C virus, and Ebola virus. Nevertheless, IFNs can have undesirable side effects, and recent reports indicate that IFNs upregulate the expression of host ACE2 (a critical entry receptor for SARS-CoV-2), raising the possibility that IFN treatments could exacerbate COVID-19. Here, we studied the antiviral- and ACE2-inducing properties of different IFN types in both a human lung cell line model and primary human bronchial epithelial cells. We observed differences between IFNs with respect to their induction of antiviral genes and abilities to enhance the cell surface expression of ACE2. Nevertheless, all the IFNs limited SARS-CoV-2 replication, suggesting that their antiviral actions can counterbalance increased ACE2.
Hypoxia Preconditioning of Human MSCs: a Direct Evidence of HIF-1α and Collagen Type XV Correlation (2018)

These results add useful information to understand the role of a still little investigated collagen such as ColXV, and identify ColXV as a marker of successful hypoxia preconditioning. As a whole, our data give further evidence that hypoxia preconditioned hMSCs have greater osteopotency than normal hMSCs, and that the effects of hypoxic regulation of hMSCs activities should be considered before they are clinically applied.
Mesoporous Silica Nanoparticles End‐Capped with Collagen: Redox‐Responsive Nanoreservoirs for Targeted Drug Delivery (2010)

If the cap fits: Attachment of collagen (Col) to silica nanoparticles (MSN) by a disulfide linker, followed by introduction of lactobionic acid (LA, a cell-specific targeting moiety), results in a redox-responsive system for cell-specific intracellular drug delivery and efficient endocytosis (see picture). Controlled release of a model drug (fluorescein isothiocyanate, FITC) was achieved by cleavage of the disufide bonds. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Investigating Macrophage and Malignant Cell Interactions In Vitro (2009)

Within most human and murine cancers there is an abundant macrophage population, attracted to the tumor microenvironment by cytokines and chemokines such as CSF-1 (M-CSF) and CCL2 (MCP-1) (Cell 124:263-266, 2006). Despite their intrinsic antitumor activity there is usually, but not always, a positive association between the extent of the macrophage infiltrate in tumors and a bad prognosis (Cell 124:263-266, 2006; Nat Rev Cancer 4:71-78, 2004). According to Condeelis and Pollard (Nat Rev Cancer 4:71-78, 2004), tumor-associated macrophages are obligate partners for malignant cell migration, invasion, and metastasis. These conclusions are based not only on association studies, but also on experiments demonstrating that ablation of macrophage function, or their infiltration into experimental tumors, inhibits growth and metastasis (J Exp Med 193:727-740, 2001). While it has become well appreciated that the extensive macrophage infiltrate of tumors can correlate with tumor progression, there is little understanding of the precise nature of interactions between malignant cells and macro-phages and the mechanisms by which these promote cancer. There are several experimental approaches to study the interactions between macrophages and tumor cells in vitro, which we will describe here.
AlGaN layers grown on AlGaN buffer layer and GaN buffer layer using strain-relief interlayers (2007)

We investigated AlGaN layers grown by metalorganic chemical vapor deposition (MOCVD) on high temperature (HT-)GaN and AlGaN buffer layers. On GaN buffer layer, there are a lot of surface cracking because of tensile strain in subsequent AlGaN epilayers. On HT-AlGaN buffer layer, not only cracks but also high densities rounded pits present, which is related to the high density of coalescence boundaries in HT-AlGaN growth process. The insertion of interlayer (IL) between AlGaN and the GaN pseudosubstrate can not only avoid cracking by modifying the strain status of the epilayer structure, but also improved Al incorporation efficiency and lead to phase-separation. And we also found the growth temperature of IL is a critical parameter for crystalline quality of subsequent AlGaN epilayer. Low temperature (LT-) AlN IL lead to a inferior quality in subsequent AlGaN epilayers.
Perovskite-perovskite tandem photovoltaics with optimized band gaps (2016)

We demonstrate four- and two-terminal perovskite-perovskite tandem solar cells with ideally matched band gaps. We develop an infrared-absorbing 1.2-electron volt band-gap perovskite, FA<sub>0.75</sub>Cs<sub>0.25</sub>Sn<sub>0.5</sub>Pb<sub>0.5</sub>I<sub>3</sub>, that can deliver 14.8% efficiency. By combining this material with a wider-band gap FA<sub>0.83</sub>Cs<sub>0.17</sub>Pb(I<sub>0.5</sub>Br<sub>0.5</sub>)<sub>3</sub> material, we achieve monolithic two-terminal tandem efficiencies of 17.0% with >1.65-volt open-circuit voltage. We also make mechanically stacked four-terminal tandem cells and obtain 20.3% efficiency. Notably, we find that our infrared-absorbing perovskite cells exhibit excellent thermal and atmospheric stability, not previously achieved for Sn-based perovskites. This device architecture and materials set will enable "all-perovskite" thin-film solar cells to reach the highest efficiencies in the long term at the lowest costs.
Collaborative Aspects of Information Retrieval Tools: Summarising Three Action Case Studies (2000)

Information retrieval (IR) tools are engaged to find information in electronic form, in databases, digital libraries, and networks. However, the advent of the web technology has boosted the amount of information available to us way beyond our cognitive capacity. The importance of good IR tools has thus increased and the tools have become natural focal points for organisational information seeking. This situation offers a possibility to exploit the collaborative efforts of the individual users. However, is the opportunity utilised? In action case studies of a search engine, a notifier program, and a recommender system on a corporate intranet, this study seeks the answer to that question. The conclusion is that most IR tools have neglected to incorporate support for collaborative action, or allowing awareness of other users with similar information needs. By integrating functionality from all three tools, according to the design implications presented here, future systems sh...
Introduction (2018)

This introduction presents an overview of the key concepts discussed in the subsequent chapters of this book. The book focuses on actual threats, the risks of those threats, and the actors' perceptions and expectations of those risks and responses. Nationalism is a polysemous concept, but this chapter uses it in its broadest sense. Tensions and conflicts are evident in various channels of interaction, especially in legal and policy arenas, namely the regulatory environment, accounting practice, corporate law, anti-trust law and, above all, taxation law. In particular, the subject of international taxation has been studied by international business scholars and legal scholars. As taxes on companies are levied within the legal frameworks of individual sovereign states, the premise underlying the actions undertaken by firms to cope with the political risks associated with taxation was that it was possible to distinguish between those jurisdictions which offered favourable conditions.
Multi-resolution panoramic modeling based on spherical projective geometry (2012)

Panorama image can provide 360 degrees view in one hotspot, which could solve the traditional three-dimensional expression of inadequate authenticity, difficult data acquisition as well as laborious and time-consuming modeling. However, there is usually only one single resolution of panoramic images in websides, if it amplified by the certain extent, it shows vagueness, having poor texture detail. So, we propose a kind of multi-resolution panoramic geometric modeling based on spherical projective geometry in this paper with many advantages: realtime dynamic geometric data representation divided by quadtree subdivision; panoramic images of multi-resolution organization with the visualization needs of being transferred, having the deformation as small as possible in the process of that being mapped to the sphere, moreover, the current image has the highest clarity. And something useful is obtained.
Comparison of different follow-up lung registration methods with and without segmentation (2004)

In modern multi slice CT scanners the increasing amount of data also increases the demand on image processing methods that assist the diagnosis. For the detection and classification of lung nodules in a follow up study it is very helpful to have the slices of a previous scan aligned with the slices of the current scan. This is a typical problem of image registration, for which different types of solutions exist. We investigated the accuracy and computation times of a rigid body, an affine, and a spline based elastic registration approach on the complete data set, and compared the results to a method where the registration was preceded by a segmentation of the lung volume. The registration quality was determined on a ground truth of previously determined lung nodule locations by measuring the average distance of corresponding nodules. It was found that an affine registration is slightly better than a rigid body registration, and that both are much faster than the elastic registration, which in turn showed the best registration quality. A good compromise was the affine registration on a previously segmented lung volume, which in total is not much slower than the registration without segmentation, but shows better alignment and higher robustness.
Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond (2017)

Data on hundreds or thousands of single nucleotide polymorphisms (SNPs) provide detailed information about the relationships between individuals, but currently few tools can turn this information into a multigenerational pedigree. I present the r package sequoia, which assigns parents, clusters half-siblings sharing an unsampled parent and assigns grandparents to half-sibships. Assignments are made after consideration of the likelihoods of all possible first-, second- and third-degree relationships between the focal individuals, as well as the traditional alternative of being unrelated. This careful exploration of the local likelihood surface is implemented in a fast, heuristic hill-climbing algorithm. Distinction between the various categories of second-degree relatives is possible when likelihoods are calculated conditional on at least one parent of each focal individual. Performance was tested on simulated data sets with realistic genotyping error rate and missingness, based on three different large pedigrees (N = 1000-2000). This included a complex pedigree with overlapping generations, occasional close inbreeding and some unknown birth years. Parentage assignment was highly accurate down to about 100 independent SNPs (error rate <0.1%) and fast (<1 min) as most pairs can be excluded from being parent-offspring based on opposite homozygosity. For full pedigree reconstruction, 40% of parents were assumed nongenotyped. Reconstruction resulted in low error rates (<0.3%), high assignment rates (>99%) in limited computation time (typically <1 h) when at least 200 independent SNPs were used. In three empirical data sets, relatedness estimated from the inferred pedigree was strongly correlated to genomic relatedness.
Enantioselective Synthesis of α-Substituted Ketones by Asymmetric Addition of Chiral Zinc Enamides to 1-Alkenes (2003)

A zinc enamide of a chiral imine derived from a ketone and (S)-valinol or (S)-t-leucinol undergoes addition to 1-alkene to generate a gamma-zincioimine intermediate, which reacts with a carbon electrophile to give upon hydrolysis an optically active alpha-substituted ketone in good yield. The stereoselectivity of the addition reaction may reach 99% for the reaction of a cyclohexanone imine with ethylene.
Drying of the Silica/PVA Suspension: Effect of Suspension Microstructure (2009)

The particle/polymer/solvent suspension system shows complicated microstructure. When the suspension system experiences an industrial process such as coating and drying, the system experiences microstructural change. In this study, we investigated the microstructural change during the drying of a silica/polyvinyl alcohol (PVA) suspension, with an emphasis on suspension stability. We controlled the amount of PVA adsorption on the silica surface by adjusting the pH (1.5, 3.6, and 9) of the silica/PVA suspension. The amount of adsorption was measured to increase with decreasing pH, and the degree of flocculation in the silica/PVA suspension became stronger with decreasing pH. However, through the measurement of stress development during drying and the observation of film microstructure after drying, we found that the more strongly flocculated suspension became a more disperse, close-packed film after drying. By evaluating the potential energy, we could suggest the role of adsorbed polymers in structural change during the drying of the silica/PVA suspension. As pH decreases, the adsorbed polymers could bridge the particles and lead to a flocculated suspension before drying. As the solvent evaporates during drying, the adsorbed polymers introduce steric repulsion between approaching particles, leading to a change from flocculated to dispersed microstructure. This implies that the required silica/PVA film performance and the microstructure of the silica/PVA suspension can be tailored through controlling the polymer adsorption in suspension.
Molecular changes in carbohydrate antigens associated with cancer (1990)

Oncogenic transformation is often associated with aberrant glycosylation in experimental and human tumors. The carbohydrate epitopes, resulting either from incomplete synthesis or neosynthesis, accumulate in high density, possibly in a novel conformation, at the tumor cell surface. A variety of monoclonal antibodies have been developed that recognize tumor-associated carbohydrate antigens and their aberrant organization at the cell surface. These carbohydrate epitopes and the antibodies specific to these structures are being exploited to develop novel diagnostic tools and therapeutic strategies for cancer.