gebhart/patrepeval huggingface dataset:
Heteroepitaxial devitrification of silica to integrate functional oxide nanostructures on silicon (2014)

26-30 Mai 2014
2A Proteinase of Human Rhinovirus Cleaves Cytokeratin 8 in Infected HeLa Cells (2000)

Rhino- and enteroviruses encode two proteinases, 2A and 3C, which are responsible for the processing of the viral polyprotein and for cleavage of several cellular proteins. To identify further targets of the 2A proteinase of human rhinovirus serotype 2 (HRV2), an in vitro cleavage assay followed by two-dimensional electrophoresis was employed. Cytokeratin 8, a member of the intermediate filament group of proteins, was found to be proteolytically cleaved in vitro by the 2A proteinase of HRV2 and of coxsackievirus B4 and in vivo during HRV2 infection of HeLa cells. The cleavage results in removal of 14 amino acids from the N-terminal head domain of cytokeratin 8. However, other intermediate filament proteins (cytokeratins 7 and 18 and vimentin) were not cleaved in the course of the HRV2 infection. Compared with the processing of the eucaryotic translation initiation factors 4GI and 4GII, cleavage of cytokeratin 8 occurs late in the infection cycle at the time of the onset of the cytopathic effect.
Production and secretion of functional full-length SARS-CoV-2 spike protein in Chlamydomonas reinhardtii (2021)

Abstract The spike protein is the major protein on the surface of coronaviruses. It is therefore the prominent target of neutralizing antibodies and consequently the antigen of all currently admitted vaccines against SARS-CoV-2. Since it is a 1273-amino acids glycoprotein with 22 N-linked glycans, the production of functional, full-length spike protein was limited to mammalian and insect cells, requiring complex culture media. Here we report the production of full-length SARS-CoV-2 spike protein – lacking the C-terminal membrane anchor – as a secreted protein in the prefusion-stabilized conformation in the unicellular green alga Chlamydomonas reinhardtii . We show that the spike protein is efficiently cleaved at the furin cleavage site during synthesis in the alga and that cleavage is abolished upon mutation of the multi-basic cleavage site. We could enrich the spike protein from culture medium by ammonium sulfate precipitation and demonstrate its functionality based on its interaction with recombinant ACE2 and ACE2 expressed on human 293T cells. Chlamydomonas reinhardtii is a GRAS organism that can be cultivated at low cost in simple media at a large scale, making it an attractive production platform for recombinant spike protein and other biopharmaceuticals in low-income countries.
UCLID-Net: Single View Reconstruction in Object Space (2020)

Most state-of-the-art deep geometric learning single-view reconstruction approaches rely on encoder-decoder architectures that output either shape parametrizations or implicit representations. However, these representations rarely preserve the Euclidean structure of the 3D space objects exist in. In this paper, we show that building a geometry preserving 3-dimensional latent space helps the network concurrently learn global shape regularities and local reasoning in the object coordinate space and, as a result, boosts performance. We demonstrate both on ShapeNet synthetic images, which are often used for benchmarking purposes, and on real-world images that our approach outperforms state-of-the-art ones. Furthermore, the single-view pipeline naturally extends to multi-view reconstruction, which we also show.
Understanding Dimethyl Methylphosphonate Adsorption and Decomposition on Mesoporous CeO2 (2021)

The increased risk of chemical warfare agent usage around the world has intensified the search for high-surface-area materials that can strongly adsorb and actively decompose chemical warfare agents. Dimethyl methylphosphonate (DMMP) is a widely used simulant molecule in laboratory studies for the investigation of the adsorption and decomposition behavior of sarin (GB) gas. In this paper, we explore how DMMP interacts with the as-synthesized mesoporous CeO<sub>2</sub>. Our mass spectroscopy and <i>in situ</i> diffuse reflectance infrared Fourier transform spectroscopy measurements indicate that DMMP can dissociate on mesoporous CeO<sub>2</sub> at room temperature. Two DMMP dissociation pathways are observed. Based on our characterization of the as-synthesized material, we built the pristine and hydroxylated (110) and (111) CeO<sub>2</sub> surfaces and simulated the DMMP interaction on these surfaces with density functional theory modeling. Our calculations reveal an extremely low activation energy barrier for DMMP dissociation on the (111) pristine CeO<sub>2</sub> surface, which very likely leads to the high activity of mesoporous CeO<sub>2</sub> for DMMP decomposition at room temperature. The two reaction pathways are possibly due to the DMMP dissociation on the pristine and hydroxylated CeO<sub>2</sub> surfaces. The significantly higher activation energy barrier for DMMP to decompose on the hydroxylated CeO<sub>2</sub> surface implies that such a reaction on the hydroxylated CeO<sub>2</sub> surface may occur at higher temperatures or proceed after the pristine CeO<sub>2</sub> surfaces are saturated.
Interference between GSM mobile phones and pace-makers: in vitro evaluation of interaction mechanisms (2005)

Aim of this study was to in-vitro evaluate the effectiveness of the filtered feedthrough assembly used to filter out the electromagnetic interference at the Input stage of Implantable pace-makers. We used three modified pace-makers of the same model, with an electrical connection to the output of the input sensing amplifier. The pace-makers differed for the level of protection against electromagnetic interference. We used a dual-band mobile phone. For each pace-maker the output of the sensing amplifier was monitored in 4 status: 1) no inhibition signal; 2) inhibition signal with amplitude 50% greater than the sensing threshold; 3) inhibition signal slightly lower than the sensing threshold; 4) inhibition signal slightly greater than the sensing threshold. For each pace-maker, evaluation has been performed in basal condition (no radiated power), during ringing and during talking. We found that the PMK with only the block capacitor shows asynchronous pacing and inhibition, while the other two PMKs do not interfere with the mobile phone, in any stage and for any mobile status.
Applications of a non-interferometric x-ray phase contrast imaging method with both synchrotron and conventional sources (2013)

We have developed a totally incoherent, non-interferometric x-ray phase contrast imaging (XPCI) method. This is based on the edge illumination (EI) concept developed at the ELETTRA synchrotron in Italy in the late `90s. The method was subsequently adapted to the divergent beam generated by a conventional source, by replicating it for every detector line through suitable masks. The method was modelled both with the simplified ray-tracing and with the more rigorous wave-optics approach, and in both cases excellent agreement with the experimental results was found. The wave-optics model enabled assessing the methods' coherence requirements, showing that they are at least an order of magnitude more relaxed than in other methods, without this having negative consequences on the phase sensitivity. Our masks have large pitches (up to 50 times larger than in grating interferometry, for example), which allows for manufacturing through standard lithography, scalability, cost-effectiveness and easiness to align. When applied to a polychromatic and divergent beam generated by a conventional source, the method enables the detection of strong phase effects also with uncollimated, unapertured sources with focal spots of up to 100 μm, compatible with the state-of-the-art in mammography. When used at synchrotrons, it enables a contrast increase of orders of magnitude over other methods. Robust phase retrieval was proven for both coherent and incoherent sources, and additional advantages are compatibility with high x-ray energies and easy implementation of phase sensitivity in two directions simultaneously. This paper briefly summarizes these achievements and reviews some of the key results.
Specific In Vivo Deletion of B-Cell Subpopulations Expressing Human Immunoglobulins by the B-Cell Superantigen Protein L (2004)

Some pathogens have evolved to produce proteins, called B-cell superantigens, that can interact with human immunoglobulin variable regions, independently of the combining site, and activate B lymphocytes that express the target immunoglobulins. However, the in vivo consequences of these interactions on human B-cell numbers and function are largely unknown. Using transgenic mice expressing fully human immunoglobulins, we studied the consequences of in vivo exposure of protein L of Peptostreptococcus magnus with human immunoglobulins. In the mature pool of B cells, protein L exposure resulted in a specific reduction of splenic marginal-zone B cells and peritoneal B-1 cells. Splenic B cells exhibited a skewed light-chain repertoire consistent with the capacity of protein L to bind specific kappa gene products. Remarkably, these two B-cell subsets are implicated in innate B-cell immunity, allowing rapid clearance of pathogens. Thus, the present study reveals a novel mechanism that may be used by some infectious agents to subvert a first line of the host's immune defense.
Fieldwork In Human Geography (2010)

Introduction: Fieldwork for Human Geographers PART ONE: APPROACHING THE FIELD Getting the Most out of Fieldwork Justifying the Cost: Your Degree and Your Job Prospects Before You Go: Research Design and Preparation Ethics: Positioning Yourself and Encountering Others Working in Groups and Travelling Together PART TWO: METHODS AND CONTEXTS Reading the Landscape: Describing and Interpreting Field Sites Interviewing for Fieldwork Participant Observation and Participatory Geographies How to Be an Explorer: Rediscovering Your Curiosity
Self-Assembly of Mammalian-Cell Membranes on Bioelectronic Devices with Functional Transmembrane Proteins (2020)

Transmembrane proteins (TMPs) regulate processes occurring at the cell surface and are essential gatekeepers of information flow across the membrane. TMPs are difficult to study, given the complex environment of the membrane and its influence on protein conformation, mobility, biomolecule interaction, and activity. For the first time, we create mammalian biomembranes supported on a transparent, electrically conducting polymer surface, which enables dual electrical and optical monitoring of TMP function in its native membrane environment. Mammalian plasma membrane vesicles containing ATP-gated P2X2 ion channels self-assemble on a biocompatible polymer cushion that transduces the changes in ion flux during ATP exposure. This platform maintains the complexity of the native plasma membrane, the fluidity of its constituents, and protein orientation critical to ion channel function. We demonstrate the dual-modality readout using microscopy to characterize protein mobility by single-particle tracking and sensing of ATP gating of P2X2 using electrical impedance spectroscopy. This measurement of TMP activity important for pain sensing, neurological activity, and sensory activity raises new possibilities for drug screening and biosensing applications.
Structure of Type IIL Restriction-Modification Enzyme MmeI in Complex with DNA Has Implications for Engineering New Specificities (2016)

The creation of restriction enzymes with programmable DNA-binding and -cleavage specificities has long been a goal of modern biology. The recently discovered Type IIL MmeI family of restriction-and-modification (RM) enzymes that possess a shared target recognition domain provides a framework for engineering such new specificities. However, a lack of structural information on Type IIL enzymes has limited the repertoire that can be rationally engineered. We report here a crystal structure of MmeI in complex with its DNA substrate and an S-adenosylmethionine analog (Sinefungin). The structure uncovers for the first time the interactions that underlie MmeI-DNA recognition and methylation (5'-TCCRAC-3'; R = purine) and provides a molecular basis for changing specificity at four of the six base pairs of the recognition sequence (5'-TCCRAC-3'). Surprisingly, the enzyme is resilient to specificity changes at the first position of the recognition sequence (5'-TCCRAC-3'). Collectively, the structure provides a basis for engineering further derivatives of MmeI and delineates which base pairs of the recognition sequence are more amenable to alterations than others.
Application of Synergism and Variation in Ionic Compatibilities within a Hydrophilic Polymeric Sodium Starch Glycolate-Kappa-Carrageenan Combination: Textural Profiling of the Suspension Behavior (2006)

The advantages of starch-carrageenan gel systems have been demonstrated in numerous applications. The exploitation of this functional synergism could provide improvements in the textural properties of a pharmaceutical suspension when prepared employing a combination of the two polymers rather than use of either one alone. This study characterized the influence of kappa-carrageenan (C) on the textural properties of sodium starch glycolate (SSG) through analysis of the textural profiles following force-displacement testing. The effect of gel-inducing or gel-strengthening cations on the textural behavior of SSG-C gel systems was also elucidated. The determination of the rate of gelation, as well as the final viscosity of the SSG-C systems was conducted and correlated with the textural properties of the systems. The presence of C in the gel systems significantly increased several textural properties, such as, compressibility (p 0.002), adhesivity (p 0.001) and the final viscosity (p 0.021) of the gels. These properties can be exploited through C’s function as a suspending and gelling agent to improve the textural and gel-forming properties of soluble starches, such as, SSG through the establishment of a three-dimensional gel network. Because of the availability of sodium ions in SSG, its combination with C may confer the additional advantage of promoting helix formation and gelation. Neither the presence of gel-inducing nor gel-strengthening cations significantly improved the textural properties of the gel systems (p 0.050). The resultant systems, particularly those incorporating the gel-inducing potassium cation, had a heterogenous consistency; they were dense, turbid gels exhibiting water expulsion or syneresis.
Infographic: Total hip arthroplasty component wear and stability (2019)

TEST 02 - Elsevier's Scopus, the largest abstract and citation database of peer-reviewed literature. Search and access research from the science, technology, medicine, social sciences and arts and humanities fields.
Self-Es (2017)

Email has been central to online communication for the past two decades. Through constant use, new information flows are being defined around users' interactions with emails. Alongside traditional messages, the email inbox is an always-available repository of to-do lists, reminders, files and notes. In this paper, we investigate the use of self-addressed emails (self-Es) as an information management tool, by analysing both: (i) responses to a survey about email use; and (ii) a collection of user donated self-addressed emails. Our results show that sending self-Es is a frequent behaviour among the users we questioned. In addition, we find that to-dos and reminders are the most popular type of information contained in emails-to-self. Our findings have direct implications for the development of systems that support novel interactions with information flows centred around email.
Figure S1 from Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA <i>In Situ</i> Hybridization Assay (2023)

&lt;p&gt;Representative microphotographs of samples showing different MCPyV RNA in situ hybridization (RNA-ISH) intensity (400X magnification)&lt;/p&gt;
Enantioselective Synthesis of Biarylphenylglycines and Their Use as Chiral Ligands in the Lewis Acid Catalyzed Diels-Alder Reaction (1998)

The enantioselective syntheses of naphthyl-substituted-N-tosylphenylglycines are described. These unnatural amino acids were tested as ligands for the chiral oxazaborolidine catalyzed Diels-Alder reaction between cyclopentadiene and 2-bromoacrolein.
Unsupervised Domain Adaptation of Contextual Embeddings for Low-Resource Duplicate Question Detection (2019)

Answering questions is a primary goal of many conversational systems or search products. While most current systems have focused on answering questions against structured databases or curated knowledge graphs, on-line community forums or frequently asked questions (FAQ) lists offer an alternative source of information for question answering systems. Automatic duplicate question detection (DQD) is the key technology need for question answering systems to utilize existing online forums like StackExchange. Existing annotations of duplicate questions in such forums are community-driven, making them sparse or even completely missing for many domains. Therefore, it is important to transfer knowledge from related domains and tasks. Recently, contextual embedding models such as BERT have been outperforming many baselines by transferring self-supervised information to downstream tasks. In this paper, we apply BERT to DQD and advance it by unsupervised adaptation to StackExchange domains using self-supervised learning. We show the effectiveness of this adaptation for low-resource settings, where little or no training data is available from the target domain. Our analysis reveals that unsupervised BERT domain adaptation on even small amounts of data boosts the performance of BERT.
ChemInform Abstract: Synthesis and Evaluation of α‐(((2‐Haloethyl)amino)methyl)‐2‐ nitro‐1H‐imidazole‐1‐ethanols as Prodrugs of α‐((1‐Aziridinyl) methyl)‐2‐nitro‐1H‐imidazole‐1‐ethanol (RSU‐1069) and Its Analogues which are Radiosensitizers and Bioreductively Activated Cytotoxins. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Non-causal encoding of predictively coded samples (2014)

We study the INTRA-prediction operation employed in hybrid video coders where sample values to be compressed are predicted using previously-decoded context values and the prediction errors are transform coded. Given the context values this procedure can be argued to be rate-distortion optimal for Gaussian signals. Yet natural images and video contain many structures that do not readily fit into Gaussian signal assumptions. Targeting such structures we propose a technique that predicts each sample using the context values and samples that are jointly transform coded with the predicted sample. We show that this joint, non-causal encoding can be represented with a nonorthogonal transform whose form and parameters we derive. We augment the HEVC standard with our work and show significant compression improvements on images/video that contain directional structures.
Xenogenomics: genomic bioprospecting in indigenous and exotic plants through EST discovery, cDNA microarray-based expression profiling and functional genomics: Conference Papers (2005)

To date, the overwhelming majority of genomics programs in plants have been directed at model or crop plant species, meaning that very little of the naturally occurring sequence diversity found in plants is available for characterization and exploitation. In contrast, ‘xenogenomics’ refers to the discovery and functional analysis of novel genes and alleles from indigenous and exotic species, permitting bioprospecting of biodiversity using high-throughput genomics experimental approaches. Such a program has been initiated to bioprospect for genetic determinants of abiotic stress tolerance in indigenous Australian flora and native Antarctic plants. Uniquely adapted Poaceae and Fabaceae species with enhanced tolerance to salt, drought, elevated soil aluminium concentration, and freezing stress have been identified, based primarily on their eco-physiology, and have been subjected to structural and functional genomics analyses. For each species, EST collections have been derived from plants subjected to appropriate abiotic stresses. Transcript profiling with spotted unigene cDNA micro-arrays has been used to identify genes that are transcriptionally modulated in response to abiotic stress. Candidate genes identified on the basis of sequence annotation or transcript profiling have been assayed in planta and other in vivo systems for their capacity to confer novel phenotypes. Comparative genomics analysis of novel genes and alleles identified in the xenogenomics target plant species has subsequently been undertaken with reference to key model and crop plants. Copyright © 2005 John Wiley & Sons, Ltd.
Isomeric trimesogens exhibiting modulated nematic mesophases (2017)

A simple deprotection/etherification strategy enables us to prepare oligomeric liquid-crystalline materials with ease, and unearth a potentially new mesophase.
Structure and tunneling dynamics of malonaldehyde. A theoretical study (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure and tunneling dynamics of malonaldehyde. A theoretical studyJozef Bicerano, Henry F. Schaefer III, and William H. MillerCite this: J. Am. Chem. Soc. 1983, 105, 9, 2550–2553Publication Date (Print):May 1, 1983Publication History Published online1 May 2002Published inissue 1 May 1983https://pubs.acs.org/doi/10.1021/ja00347a005https://doi.org/10.1021/ja00347a005research-articleACS PublicationsRequest reuse permissionsArticle Views279Altmetric-Citations99LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts