gebhart/patrepeval huggingface dataset:
Structures of a Human Papillomavirus (HPV) E6 Polypeptide Bound to MAGUK Proteins: Mechanisms of Targeting Tumor Suppressors by a High-Risk HPV Oncoprotein (2007)

Human papillomavirus (HPV) E6 oncoprotein targets certain tumor suppressors such as MAGI-1 and SAP97/hDlg for degradation. A short peptide at the C terminus of E6 interacts specifically with the PDZ domains of these tumor suppressors, which is a property unique to high-risk HPVs that are associated with cervical cancer. The detailed recognition mechanisms between HPV E6 and PDZ proteins are unclear. To understand the specific binding of cellular PDZ substrates by HPV E6, we have solved the crystal structures of the complexes containing a peptide from HPV18 E6 bound to three PDZ domains from MAGI-1 and SAP97/Dlg. The complex crystal structures reveal novel features of PDZ peptide recognition that explain why high-risk HPV E6 can specifically target these cellular tumor suppressors for destruction. Moreover, a new peptide-binding loop on these PDZs is identified as interacting with the E6 peptide. Furthermore, we have identified an arginine residue, unique to high-risk HPV E6 but outside the canonical core PDZ recognition motif, that plays an important role in the binding of the PDZs of both MAGI-I and SAP97/Dlg, the mutation of which abolishes E6's ability to degrade the two proteins. Finally, we have identified a dimer form of MAGI-1 PDZ domain 1 in the cocrystal structure with E6 peptide, which may have functional relevance for MAGI-1 activity. In addition to its novel insights into the biochemistry of PDZ interactions, this study is important for understanding HPV-induced oncogenesis; this could provide a basis for developing antiviral and anticancer compounds.
The Casing Deformation During Shale Gas Hydraulic Fracturing: Why it is so Serious in Weiyuan-Changning, China? (2018)

Abstract Casing deformation turned out to be serious during hydraulic fracturing of shale gas wells in Weiyuan-Channing, where the ratio of casing deformation was more than 30%. Nevertheless, there were no such phenomenon in America and other shale gas producing areas. Why there were so many horizontal wells casing deformation in Weiyuan-Changning, China? There maybe kinds of factors. The authors mainly analyze the effect to casing deformation from operations factors during well drilling and completion, including dogleg angle, loss of cement sheath integrity and APD effect; as well as effect the geologic characteristics such as faults and natural fracture zones, lithologic interface, shale bedding. The results show that: Firstly, though the casing strength gradually decreased as the dogleg angle increasing, the casing collapsing strength drops off only 3.8% with average 2.7°/30m dogleg angle in the casing deformation zone, which showed that it can not lead casing deformation directly. Then, though the influence of temperature and loss of cement sheath integrity will significantly reduce the safety factor of the casing, it cannot be excluded that the local cement sheath can be always damaged after hydraulic fracturing, which suggested the APD effect was not the main factor leading to casing deformation. Finally, the original stress balance near wellbore can be destroyed during multistage hydraulic fracturing leading to non-uniform in-situ stress, which can active the fault, natural fractures, lithologic interface, shale bedding to slip. Therefore there were high probability of casing deformation in the formation with faults, natural fracture zones and strong heterogeneity. The above analysis can be used to explain why there is serious casing deformation in Weiyuan and Changning of China. Perforating far away from the point where casing deformation occurred easily and design the proper fracturing scheme can help us avoid casing deformation rather than simply raising steel grade and wall thickness of casing.
RelNN: A Deep Neural Model for Relational Learning (2018)

Statistical relational AI (StarAI) aims at reasoning and learning in noisy domains described in terms of objects and relationships by combining probability with first-order logic. With huge advances in deep learning in the current years, combining deep networks with first-order logic has been the focus of several recent studies. Many of the existing attempts, however, only focus on relations and ignore object properties. The attempts that do consider object properties are limited in terms of modelling power or scalability. In this paper, we develop relational neural networks (RelNNs) by adding hidden layers to relational logistic regression (the relational counterpart of logistic regression). We learn latent properties for objects both directly and through general rules. Back-propagation is used for training these models. A modular, layer-wise architecture facilitates utilizing the techniques developed within deep learning community to our architecture. Initial experiments on eight tasks over three real-world datasets show that RelNNs are promising models for relational learning.
Protecting Privacy and Security of Genomic Data in i2b2 with Homomorphic Encryption and Differential Privacy (2018)

Re-use of patients' health records can provide tremendous benefits for clinical research. Yet, when researchers need to access sensitive/identifying data, such as genomic data, in order to compile cohorts of well-characterized patients for specific studies, privacy and security concerns represent major obstacles that make such a procedure extremely difficult if not impossible. In this paper, we address the challenge of designing and deploying in a real operational setting an efficient privacy-preserving explorer for genetic cohorts. Our solution is built on top of the i2b2 (Informatics for Integrating Biology and the Bedside) framework and leverages cutting-edge privacy-enhancing technologies such as homomorphic encryption and differential privacy. Solutions involving homomorphic encryption are often believed to be costly and immature for use in operational environments. Here, we show that, for specific applications, homomorphic encryption is actually a very efficient enabler. Indeed, our solution outperforms prior work by enabling a researcher to securely compute simple statistics on more than 3,000 encrypted genetic variants simultaneously for a cohort of 5,000 individuals in less than 5 seconds with commodity hardware. To the best of our knowledge, our privacy-preserving solution is the first to also be successfully deployed and tested in a operation setting (Lausanne University Hospital).
Killing of Avian and Swine Influenza Virus by Natural Killer Cells (2010)

Today, global attention is focused on two influenza virus strains: the current pandemic strain, swine origin influenza virus (H1N1-2009), and the highly pathogenic avian influenza virus, H5N1. At present, the infection caused by the H1N1-2009 is moderate, with mortality rates of less <1%. In contrast, infection with the H5N1 virus resulted in high mortality rates, and ca. 60% of the infected patients succumb to the infection. Thus, one of the world greatest concerns is that the H5N1 virus will evolve to allow an efficient human infection and human-to-human transmission. Natural killer (NK) cells are one of the innate immune components playing an important role in fighting against influenza viruses. One of the major NK activating receptors involved in NK cell cytotoxicity is NKp46. We previously demonstrated that NKp46 recognizes the hemagglutinin proteins of B and A influenza virus strains. Whether NKp46 could also interact with H1N1-2009 virus or with the avian influenza virus is still unknown. We analyzed the immunological properties of both the avian and the H1N1-2009 influenza viruses. We show that NKp46 recognizes the hemagglutinins of H1N1-2009 and H5 and that this recognition leads to virus killing both in vitro and in vivo. However, importantly, while the swine H1-NKp46 interactions lead to the direct killing of the infected cells, the H5-NKp46 interactions were unable to elicit direct killing, probably because the NKp46 binding sites for these two viruses are different.
Magnetic anisotropy in Ni/Fe artificial lattice film (1988)

This paper presents an experimental investigation on the magnetic anisotropy and heat stability in Ni/Fe artificial lattice films. Magnetic anisotropy is found to increase as the lattice period and the Fe layer thickness decrease. The annealing of Ni/Fe films is shown to decrease hard-axis coercivity to 0.3 Oe. However, annealing at temperatures above 400 °C causes an increase in coercivity, perfect alloying of the Ni/Fe film, and recovery of the crystallinity of the Fe layer sandwiched between Ni layers. In the Ni/Fe (2/10 nm) film, very small magnetostriction and large saturation magnetization are maintained up to 350°C. A prototype thin-film head with a Ni/Fe yoke shows stable conventionally reproduced signals for small write currents, superior overwrite properties, and good heat stability at annealing temperatures below 300 °C.
Use of WN&lt;tex&gt;$_ X$&lt;/tex&gt;as the Diffusion Barrier for Interconnect Copper Metallization of InGaP–GaAs HBTs (2004)

Use of WN/sub X/ as the diffusion barrier for interconnect copper metallization of InGaP-GaAs heterojunction bipolar transistors (HBTs) was studied. The WN/sub X/ (40 nm) and Cu (400 nm) films were deposited sequentially on the InGaP-GaAs HBT wafers as the diffusion barrier and interconnect metallization layer, respectively, using the sputtering method. As judged from the data of scanning electron microscopy, X-ray diffraction, Auger electron spectroscopy, and sheet resistance, the Cu--WN/sub X/--SiN and Cu--WN/sub X/--Au structures were very stable up to 550/spl deg/C and 400/spl deg/C annealing, respectively. Current accelerated stress test was conducted on the Cu--WN/sub X/ metallized HBTs with V/sub CE/=2 V, J/sub C/=140 kA/cm/sup 2/ and stressed for 55 h, the current gain (/spl beta/) of these HBTs showed no degradation and was still higher than 100 after the stress test. The Cu--WN/sub X/ metallized HBTs were also thermally annealed at 250/spl deg/C for 25 h and showed no degradation in the device characteristics after the annealing. For comparison, HBTs with Au interconnect metallization were also processed, and these two kinds of devices showed similar characteristics after the stress tests. From these results, it is demonstrated that WN/sub X/ is a good diffusion barrier for the interconnection copper metallization of GaAs HBTs.
M-TUBE: a fabrication-free microfluidic device for large-volume bacterial electroporation requiring minimal assembly (2022)

Abstract Conventional cuvette-based and microfluidics-based bacterial electroporation approaches have distinct advantages, but they are typically limited to relatively small sample volumes, reducing their utility for applications requiring high throughput such as the generation of mutant libraries. Here, we present a disposable, user-friendly microfluidic electroporation device capable of processing large volume bacterial samples yet requiring minimal device fabrication and straightforward operation. We demonstrate that the proposed device can outperform conventional cuvettes in a range of situations, including across Escherichia coli strains with a range of electroporation efficiencies, and we use its large-volume bacterial electroporation capability to generate a library of transposon mutants in the anaerobic gut commensal Bifidobacterium longum .
Textual Spaces, Social Identities and Race in Singapore Advertising (2003)

Advertising in Singapore contests certain notions that prevail in much of the current advertising theory - notions of the advertisement as `commodity sign', removed from the real particularities of social contexts, in order to interpellate consumer readers into a uniform set of `symbolic exchange values'. The influence of Marxist thought in such theory is clear. However, this method of analysis is not remunerative in the Singapore context, chiefly because of its small size, highly multiracial and multicultural society and strong degree of governance. These are manifested in a number of ways: indirectly, for example, in the creation of so-called `Asian values' which are meant to resist `western influence'; and directly in the form of media and advertising regulations and government advertising campaigns that create signs quite different from the commodity signs touted by neo-Marxist theory. In addition, racial and cultural sensitivities are registered in textual dialogics which interrogate both this theory as well as the constructed identities (whether commodified or governanced) in advertising texts.
Diagnostic tests and algorithms used in the investigation of haematuria: systematic reviews and economic evaluation (2006)

There are insufficient data currently available to derive an evidence-based algorithm of the diagnostic pathway for haematuria. A hypothetical algorithm based on the opinion and practice of clinical experts in the review team, other published algorithms and the results of economic modelling is presented in this report. This algorithm is presented, for comparative purposes, alongside current US and UK guidelines. The ideas contained in these algorithms and the specific questions outlined should form the basis of future research. Quality assessment of the diagnostic accuracy studies included in this review highlighted several areas of deficiency.
Real time quantitative amplification detection on a microarray: towards high multiplex quantitative PCR (2012)

Quantitative real-time polymerase chain reaction (qrtPCR) is widely used as a research and diagnostic tool. Notwithstanding its many powerful features, the method is limited in the degree of multiplexing to about 6 due to spectral overlap of the available fluorophores. A new method is presented that allows quantitative amplification detection at higher multiplexing by the integration of amplification in solution and monitoring via hybridization to a microarray in real-time. This method does not require any manipulation of the PCR product and runs in a single closed chamber. Employing labeled primers, one of the main challenges is to measure surface signals against a high fluorescence background from solution. A compact, confocal scanner is employed, based on miniaturized optics from DVD technology and combined with a flat thermocycler for simultaneous scanning and heating. The feasibility of this method is demonstrated in singleplex with an analytical sensitivity comparable to routine qrtPCR.
Substrate perturbation alters the glycoside hydrolase activities and community composition of switchgrass‐adapted bacterial consortia (2011)

Bacteria modulate glycoside hydrolase expression in response to the changes in the composition of lignocellulosic biomass. The response of switchgrass-adapted thermophilic bacterial consortia to perturbation with a variety of biomass substrates was characterized to determine if bacterial consortia also responded to changes in biomass composition. Incubation of the switchgrass-adapted consortia with these alternative substrates produced shifts in glycoside hydrolase activities and bacterial community composition. Substantially increased endoglucanase activity was observed upon incubation with microcrystalline cellulose and trifluororacetic acid-pretreated switchgrass. In contrast, culturing the microbial consortia with ionic liquid-pretreated switchgrass increased xylanase activity dramatically. Microbial community analyses of these cultures indicated that the increased endoglucanase activity correlated with an increase in bacteria related to Rhodothermus marinus. Inclusion of simple organic substrates in the culture medium abrogated glycoside hydrolase activity and enriched for bacteria related to Thermus thermophilus. These results demonstrate that the composition of biomass substrates influences the glycoside hydrolase activities and community composition of biomass-deconstructing bacterial consortia.
Syntactic Dependency Based N-grams in Rule Based Automatic English as Second Language Grammar Correction. (2013)

In this paper, we present a system for automatic English (L2) grammatical error correction. It participated in ConLL 2013 shared tasks. The system applies a set of simple rules for correction of grammatical errors. In some cases, it uses syntactic n-grams, i.e., n-grams that are constructed in a syntactic metric: namely, by following paths in dependency trees, i.e., there is special procedure that allows obtaining syntactic n-grams. Note that in general case syntactic n-grams permit introducing syntactic information into machine learning methods, because syntactic n-grams have all properties of traditional n-grams. The system is simple, practically does not use additional linguistic resources and was constructed in two months. Due to its simplicity it does not obtain better scores as compared to more sophisticated systems that use many resources, the Internet and machine learning methods, but it can be positioned as a baseline system for the task. 1
Solubility of Methane in Methyldiethanolamine (2006)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSolubility of Methane in MethyldiethanolamineFang-Yuan Jou and Alan E. MatherView Author Information Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2G6, Canada Cite this: J. Chem. Eng. Data 2006, 51, 4, 1429–1430Publication Date (Web):May 11, 2006Publication History Received13 March 2006Published online11 May 2006Published inissue 1 July 2006https://pubs.acs.org/doi/10.1021/je060118ghttps://doi.org/10.1021/je060118gresearch-articleACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views444Altmetric-Citations16LEARN 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 SUBJECTS:Hydrocarbons,Mixtures,Solubility,Solution chemistry,Solvents Get e-Alerts
Synthesis of fullerene@gold core–shell nanostructures (2011)

A "direct encapsulation" method was developed for the synthesis of highly stable water-soluble fullerene@gold core-shell nanostructures, with gold nanoshells showing either closed or porous morphology. This gold nano-shell coating formed a "nano-oven", capable of decomposing encapsulated fullerene molecules rapidly when irradiated by laser. We envisaged this being a useful tool for chemical reactions as well as a novel scaffold for nano-material synthesis.
Binding of quercetin with human serum albumin: A critical spectroscopic study (2003)

Flavonols are plant pigments that are ubiquitous in nature. Quercetin (3,3',4',5,7-pentahydroxyflavone) and other related plant flavonols have come into recent prominence because of their usefulness as anticancer, antitumor, anti-AIDS, and other important therapeutic activities of significant potency and low systemic toxicity. Quercetin is intrinsically weakly fluorescent in aqueous solution, showing an emission maximum at approximately 538 nm. Upon binding to human serum albumin (HSA), quercetin undergoes dramatic enhancement in its fluorescence emission intensity, along with the appearance of dual emission behavior, consisting of normal and excited-state proton transfer (ESPT) fluorescence. In addition, the occurrence of a third emitting species has been noted for the first time. This is attributed to a electronic ground-state complex formed in the protein environment. High values of the fluorescence anisotropy (r) are obtained in the presence of HSA for the ESPT tautomer (r = 0.18), as well as the complex species (r = 0.37) of quercetin, indicating that the precursor ground-state molecules for both these emitting species of quercetin molecules are located in the motionally constrained sites of HSA. The steady-state emission data suggest that quercetin binds to two distinct sites in HSA from which the emissions from the normal tautomer and complex species take place. The preliminary results of studies on emission decay kinetics are also reported herein. Studies by far-UV circular dichroism spectroscopy reveal that binding of quercetin induces no significant perturbation in the secondary structure of HSA.
Water mediated synthesis of substituted quinolines - A new green approach to the friedländer annulation (2006)

A new green approach to the Friedländer Quinoline synthesis is described for the preparation of polysubstituted quinolines from o-amino aryl ketones and carbonyl compounds containing active methylene group mediated by water and catalysed by KHSO4 in good yields.
Identification of the carboxy terminus as important for the isoform-specific subcellular targeting of glucose transporter proteins. (1993)

Differential trafficking of glucose transporters contributes significantly to the establishment of a cell's capacity for hormone-regulatable hexose uptake. In the true insulin-sensitive peripheral target tissues, muscle and adipose, the transporter isoform GLUT1 residues on the cell surface and interior of the cell whereas the highly homologous isoform GLUT4 displays virtually exclusive intracellular sequestration, allowing the latter to redistribute to the cell surface in response to hormone. These patterns are equally pronounced in cells into which the transporters have been introduced by DNA-mediated gene transfer, suggesting that signals for isoform-specific sorting are recognized in diverse cell types. To determine the primary sequences responsible for the characteristic distributions, chimeric transporters were constructed in which reciprocal domains were exchanged between GLUT1 and GLUT4. In addition, a non-disruptive, species-specific epitope "tag" was introduced into a neutral region of the transporter to allow analysis of reciprocal chimeras using a single antibody. These recombinant transporters were stably expressed in HIH 3T3 and PC12 cells by retrovirus-mediated gene transfer, and were localized by indirect immunofluorescence and laser scanning confocal microscopy, as well as by staining of plasma membrane sheets prepared from these cells. The results indicate that the carboxy-terminal 30 amino acids are primarily responsible for the differential targeting of the glucose transporter isoforms GLUT1 and GLUT4, though there is a lesser additional contribution by the amino-terminal 183 amino acids.