gebhart/patrepeval huggingface dataset:
Restoration of domain folding and interdomain assembly by second‐site suppressors of the ΔF508 mutation in CFTR (2010)

Deletion of PHE508 (DeltaF508) from the first nucleotide-binding domain (NBD1) of CFTR, which causes most cystic fibrosis, disrupts the folding and assembly of the protein. Although the folding pathways and yield of isolated NBD1 are altered, its global structure is not, and details of the changes in the rest of the protein remain unclear. To gain further insight into how the whole mutant protein is altered, we have determined the influence of known second-site suppressor mutations in NBD1 on the conformation of this domain and key interfaces between domains. We found that the suppressors restored maturation of only those processing mutations located in NBD1, but not in other domains, including those in the C-terminal cytoplasmic loop of the second membrane-spanning domain, which forms an interface with the NBD1 surface. Nevertheless, the suppressors promoted the formation of this interface and others in the absence of F508. The suppressors restored maturation in a DeltaF508 construct from which NBD2 was absent but to a lesser extent than in the full-length, indicating that DeltaF508 disrupts interactions involving NBD2, as well as other domains. Rescue of DeltaF508-CFTR by suppressors required the biosynthesis of the entire full-length protein in continuity, as it did not occur when N- and C-terminal "halves" were coexpressed. Simultaneous with these interdomain perturbations, DeltaF508 resulted in suppressor reversed alterations in accessibility of residues both in the F508-containing NBD1 surface loop and in the Q loop within the domain core. Thus, in the context of the full-length protein, DeltaF508 mutation causes detectable changes in NBD1 conformation, as well as interdomain interactions.
High temperature superconductors having planar magnetic flux pinning centers and methods for making the same (2023)

Superconductor wires or layers having improved properties and methods for making the same are described. The superconducting layer includes a rare earth element-alkaline earth element-transition metal oxide having an average stacking fault density that is greater than about 0.01 nm−1, wherein two or more rare earth cations form the rare earth element. To form the superconductor layer of the present invention, a layer having a rare earth element-alkaline earth element-transition metal oxide substantially in a first crystal structure can be provided to a substrate where two or more rare earth cations form the rare earth element. The layer can then be heated at a temperature that is greater than 550° C. under oxidizing conditions to form a high-temperature superconducting layer substantially in a second crystal structure.
libdft (2012)

Dynamic data flow tracking (DFT) deals with tagging and tracking data of interest as they propagate during program execution. DFT has been repeatedly implemented by a variety of tools for numerous purposes, including protection from zero-day and cross-site scripting attacks, detection and prevention of information leaks, and for the analysis of legitimate and malicious software. We present libdft, a dynamic DFT framework that unlike previous work is at once fast, reusable, and works with commodity software and hardware. libdft provides an API for building DFT-enabled tools that work on unmodified binaries, running on common operating systems and hardware, thus facilitating research and rapid prototyping. We explore different approaches for implementing the low-level aspects of instruction-level data tracking, introduce a more efficient and 64-bit capable shadow memory, and identify (and avoid) the common pitfalls responsible for the excessive performance overhead of previous studies. We evaluate libdft using real applications with large codebases like the Apache and MySQL servers, and the Firefox web browser. We also use a series of benchmarks and utilities to compare libdft with similar systems. Our results indicate that it performs at least as fast, if not faster, than previous solutions, and to the best of our knowledge, we are the first to evaluate the performance overhead of a fast dynamic DFT implementation in such depth. Finally, libdft is freely available as open source software.
Characterizing time decay of bibenzyl scintillator using time correlated single photon counting (2012)

The time decay of several scintillation materials has been measured using the time correlated single photon counting method and a new organic crystal with a highly suppressed delayed light has been identified. Results comparing the light decay of the bibenzyl crystal with a xylene based detector, which is currently installed at National Ignition Facility will be presented.
Performance Evaluation of a Transmission Scintillator-Based Lens-Coupled 4K CCD Camera for Use in Low-Dose Electron Cryo-Tomography (2004)

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.
Strong optical nonlinearities in dispersive dielectric chirped mirrors below the damage threshold (2020)

We experimentally characterized an unexpectedly-strong nonlinear response in dispersive dielectric multilayer mirrors below the known damage threshold. We observed a strong reflectivity decrease, local heating, transient spectral modifications, and time-dependent absorption of the incident pulse.
Development and characterization of a monoclonal antibody specific for Listeria monocytogenes and Listeria innocua (1991)

BALB/c mice were immunized with crude cell surface proteins of Listeria monocytogenes V7. Approximately 1,680 hybridomas were generated after two fusions, and the monoclone C11E9 was selected and used for further characterization. The monoclonal antibody (MAb) produced by C11E9 was immunoglobulin subclass G2b with kappa light chains. Dot and colony blot results indicated that MAb C11E9 was reactive to all the L. monocytogenes (34 of 34) and Listeria innocua (6 of 6) isolates without any cross-reaction to other organisms tested. Western blot (immunoblot) analysis of crude cell surface proteins in native polyacrylamide gel electrophoresis (PAGE) indicated that MAb C11E9 reacts with a single band in each species, with a molecular mass of 174 kDa for L. monocytogenes and 182 kDa for L. innocua. The MAb reacted with one major protein band in Western blot from acid-urea PAGE for both L. monocytogenes and L. innocua. Isoelectric focusing results indicated two immunoreactive protein bands with pIs of 8.1 and 7.4 for L. monocytogenes. Sodium dodecyl sulfate (SDS)-PAGE and Western blot analysis indicated several proteins with molecular masses of 76, 66, 56, and 52 kDa for L. monocytogenes and 66, 56, and 52 kDa for L. innocua. Reaction of MAb C11E9 to washed live cells indicated the possible binding of antibody to cell surface antigen. These cell surface antigens could be removed by 1 N HCl plus 9 M urea, 2% SDS-0.5% beta-mercaptoethanol, or 4 M guanidine-HCl. The epitope of MAb C11E9 binding site was shown to be protein in nature. Periodic acid-Schiff staining and glycoprotein immunoassay indicated that carbohydrate was absent in the epitope. The cellular locations of the MAb C11E9-reactive antigens were calculated to be 76 and 90% outside and 24 and 10% inside the cell membranes of L. monocytogenes and L. innocua, respectively, for 12- to 14-h cultures.
In vitro 3D evaluation of penetrability of SRJ09, a semisynthetic anticancer agent (1048.4) (2014)

The inability of anticancer drugs to penetrate through the tumor within their respective pharmacokinetic lifespan to destroy all the tumor cells is recognized as one of the factors that lead to poor outcome of chemotherapy. SRJ09 (3,19‐(2‐bromobenzylidene)andrographolide) has been identified as a lead anticancer agent on the basis of its selectivity towards breast and colon cancer cell line panels (Jada et al (2008) Br J Pharmacol, 155(5):641‐54). In our recent landmark study (Hocker et al (2013), PNAS, 110(25):10201‐6), we showed that the compound disrupts mutant K‐Ras activity by binding to it. In this present investigation, the penetrability of SRJ09 through the DLD‐1 colon cancer multi cell layer (MCL) was evaluated. DLD‐1 MCL is established by culturing the cells in collagen‐coated plastic insert. The amount of SRJ09 that penetrated through MCL was quantitated by utilizing high performance liquid chromatography (HPLC). Histopathological staining was used to visualize the morphology of MCL. Chemosensitivity assay was performed to assess the anticancer activity of SRJ09 in DLD‐1 cells. SRJ09 was able to penetrate through 3D tumor and is inversely proportional with the MCL thickness. Furthermore, the compound has better penetrability compared with doxorubicin, a clinical anticancer drug. Subsequent histopathological analysis revealed that the integrity of the MCL was retained and no visible damage was inflicted on the cell membrane, confirming the penetration of SRJ09 is by diffusion. Chemosensitivity assay demonstrated that SRJ09 was able to achieve IC50 value of 40.7 µM upon 1 hour exposure time on DLD‐1 cells which was approximately 4 folds lower than andrographolide, the parent compound of SRJ09. In conclusion, SRJ09 successfully penetrated through DLD‐1 MCL by diffusion and could be potentially developed as a clinically relevant anti‐colon cancer drug. This study was funded by Universiti Putra Malaysia Research University Grant Scheme (04‐01‐09‐0713RU; 04‐02‐12‐2017RU).
Miscibility and cocrystallization in homopolymer-segmented block copolymer blends (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMiscibility and cocrystallization in homopolymer-segmented block copolymer blendsK. P. Gallagher, X. Zhang, J. P. Runt, G. Huynh-Ba, and J. S. LinCite this: Macromolecules 1993, 26, 4, 588–596Publication Date (Print):February 1, 1993Publication History Published online1 May 2002Published inissue 1 February 1993https://pubs.acs.org/doi/10.1021/ma00056a006https://doi.org/10.1021/ma00056a006research-articleACS PublicationsRequest reuse permissionsArticle Views213Altmetric-Citations35LEARN 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
Global Copyright Protest? A Comparison of DeCSS Posting in the People's Republic of China, Hong Kong, and the European Union (2005)

This study explored the differences in DeCSS posting between EU member nations, the PRC, and Hong Kong. In particular, it sought to investigate the degree to which website authors in the EU, the PRC, and Hong Kong used DeCSS to protest changes in copyright law brought about by the World Intellectual Property Organization (WIPO) Internet Treaties. Data were drawn from a country-restrict based sample of websites from the Google index in Spring 2004 and content analysis was conducted on each website. Results found little evidence of protest posting in PRC, some evidence in Hong Kong, and substantial evidence in the EU. Taken as a whole, the results do not provide strong evidence of global posting of DeCSS on websites in order to protest changes to copyright law. Rather, results suggest the value and meaning of DeCSS varies across different nations.
Feasibility study of a passive smart self-healing cementitious composite (1998)

The basic concept of a passive smart-healing cementitious composite has been demonstrated, in the laboratory, to be feasible. The basic elements of this smart material include the sensors and actuators in the form of controlled microcracks and hollow glass fibers carrying air-curing chemicals. Controlled microcracking is offered by a strain-hardening engineered cementitious composite developed previously. The mechanisms of sensing and actuation are revealed through in situ environmental scanning electron microscopy observations. The self-healing effectiveness is confirmed by measurement of the elastic modulus of the composite. The elastic modulus is found to regain its original value in a repeat loading subsequent to damage in a first load cycle.
Characterization of volatile metabolites taken up by or released from Streptococcus pneumoniae and Haemophilus influenzae by using GC-MS (2012)

Volatile organic compounds (VOCs) released from or taken up by Streptococcus pneumoniae and Haemophilus influenzae cultures were analysed by means of GC-MS after adsorption of headspace samples on multi-bed sorption tubes. Sampling was performed at different time points during cultivation of bacteria to follow the dynamics of VOC metabolism. VOCs were identified not only by spectral library match but also based on retention times of native standards. As many as 34 volatile metabolites were released from S. pneumoniae and 28 from H. influenzae, comprising alcohols, aldehydes, esters, hydrocarbons, ketones and sulfur-containing compounds. For both species, acetic acid, acetaldehyde, methyl methacrylate, 2,3-butanedione and methanethiol were found in strongly elevated concentrations and 1-butanol and butanal in moderately elevated concentrations. In addition, characteristic volatile biomarkers were detected for both bacterial species and exclusively for S. pneumoniae, also catabolism of aldehydes (3-methylbutanal and hexanal) was found. The results obtained provide important input into the knowledge about volatile bacterial biomarkers, which may become particularly important for detection of pathogens in upper airways by breath-gas analysis in the future.
PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine (2017)

Supplementary data are available at Bioinformatics online.
Ultrasonic wave propagation and scattering in cancellous bone (2004)

Theoretical models and experimental data describing the interaction between ultrasound and cancellous bone will be discussed. Ultrasonic attenuation in cancellous bone is much greater than that for soft tissues and varies approximately linearly with frequency between 400 kHz and 1.7 MHz. Speed of sound in cancellous bone is slightly higher than that for soft tissues and decreases gradually with frequency at diagnostic frequencies (between 300 and 700 kHz). The dependence of phase velocity on porosity may be predicted from theory of acoustic propagation in fluid-filled porous solids. The negative dispersion can be explained using a stratified two-component model. At diagnostic frequencies, scattering varies approximately as frequency to the nth power where 3&amp;lt;n&amp;lt;3.5. This may be explained either by a continuous or discrete scattering model. The latter represents trabeculae as small finite-length cylindrical scatterers. The frequency dependence of scattering, along with the anisotropy of scattering and attenuation, implies that absorption is a greater source of attenuation than scattering. [Funding from the FDA Office of Women’s Health is gratefully acknowledged.]
Advanced code sequences design for pedestrian detection in millimeter-wave pulse-compression radar system (2012)

The paper proposes code sequences with an optimized criterion for precisely detecting pedestrians in the presence of vehicles in millimeter-wave pulse-compression radar system. The criterion named FR (Floor-Ratio) focuses on the maximum of sidelobes. The code sequences based on FR attain higher maximum sidelobe suppression compared to the ones based on conventional criterion. Computer simulation and experimental measurement have been done for verification. Consequently, our work proves the effectiveness of the proposed code sequences with the criterion for next generation millimeter-wave radar systems.
Measurement of the photon field on Sandia`s Z facility (1998)

The Z Facility at Sandia National Laboratories utilizes z-pinch implosions to produce up to 2 MJ of X-rays. On Z, bremsstrahlung radiation is produced as a product of both power flow electrons and those accelerated in the pinch region. An understanding of the energy spectra and intensity of this radiation is important to both the explanation of the z-pinch physics and the design of new diagnostics. This paper describes the techniques and results used to date for mapping the bremsstrahlung radiation in the vacuum section of the Z Accelerator.
Bipolar Electrochemical Analysis of Chirality in Complex Media through Miniaturized Stereoselective Light-Emitting Systems (2023)

Environmentally relevant contaminants endowed with chirality may include pharmaceutical compounds, flame retardants, perfluoroalkyl chemicals, pesticides, and polychlorinated biphenyls. Despite having similar physicochemical properties, enantiomers may differ in their biochemical interactions with enzymes, receptors, and other chiral molecules leading to different biological responses. In this work, we have designed a wireless miniaturized stereoselective light-emitting system able to qualitatively detect a chiral contaminant (3,4-dihydroxyphenylalanine, DOPA) dissolved in reduced volumes (in the microliters range), through bipolar electrochemistry. The diastereomeric environment was created by mixing the enantiomers of an inherently chiral inductor endowed with helical shape (7,8-dipropyltetrathia[7]helicene) and the chiral probe (DOPA) in micro-solutions of a commercial ionic liquid. The synergy between the inductor, the applied electric field, and the chiral pollutant was transduced by the light emission produced from a miniaturized light-emitting diode (LED) exploited in such an approach as a bipolar electrode.
Imaging Heterogeneous Electrocatalyst Stability and Decoupling Degradation Mechanisms in Operating Hydrogen Fuel Cells (2021)

The proliferation of hydrogen fuel cell systems is hindered by a degradation of the platinum catalyst. Here, we provide a device-level assessment of the catalyst degradation phenomena and its coupling to nanoscale hydration gradients, using advanced operando X-ray scattering tomography tailored for device-scale imaging. Gradients formed inside the fuel cell produce a heterogeneous degradation of the catalyst nanostructure, which can be linked to the flow field design and water distribution in the cell. Striking differences in catalyst degradation are observed between operating fuel cell devices and the liquid cell routinely used for catalyst stability studies, highlighting the crucial impact of the complex operating environment on the catalyst degradation phenomena. This degradation knowledge gap accentuates the necessity of multimodal, in situ characterization of real devices when assessing the performance and durability of electrocatalysts and, more generally, electrochemically active phases used in energy conversion and storage technologies.
Crystalline Retinopathy From Primary Hyperoxaluria (2012)

Yuan, Alex MD, PhD; Ehlers, Justis P. MDEditor(s): Toth, Cynthia A.; Martel, Joseph; Yiu, Glenn Author Information
Degradation of recombinant proteins by CHO host cell proteases is prevented by Matriptase-1 knock-out (2018)

An increasing number of non-antibody format proteins are entering the clinical development. However, one of the major hurdles for the production of non-antibody glycoproteins is host cell-related proteolytic degradation, which can drastically impact developability and timelines of pipeline projects. 
Chinese hamster ovary (CHO) cells are the preferred production host for recombinant therapeutic proteins. Using protease inhibitors, transcriptomics and genetic knockdowns we have identified, out of the more than 700 known proteases in rodents, Matriptase-1 as the major protease involved in degradation of recombinant proteins expressed in CHO-K1 cells. Subsequently Matriptase-1 was deleted in CHO-K1 cells using “Transcription Activator-Like Effector Nucleases” (TALENs) as well as zinc-finger nucleases (ZFNs). This resulted in a superior CHO-K1 matriptase knockout (KO) cell line with strongly reduced or no proteolytic degradation activity towards a panel of recombinantly-expressed proteins. 
The matriptase KO cell line was evaluated in spike-in experiments, and showed little or no degradation of proteins incubated in conditioned medium derived from the KO cells. This effect was confirmed when the same proteins were recombinantly expressed in the KO cell line.
In summary, the combination of novel cell line engineering tools, next generation sequencing screening methods and the recently published Chinese hamster genome has enabled the development of this novel matriptase KO CHO cell line capable of improving expression yields of intact therapeutic proteins.
Joint Intent Detection and Slot Filling with Convolutional Neural Networks (2013)

We describe a joint model for intent detection and slot filling based on convolutional neural networks (CNN). The proposed architecture can be perceived as a neural network (NN) version of the triangular CRF model (TriCRF), in which the intent label and the slot sequence are modeled jointly and their dependencies are exploited. Our slot filling component is a globally normalized CRF style model, as opposed to left-to-right models in recent NN based slot taggers. Its features are automatically extracted through CNN layers and shared by the intent model. We show that our slot model component generates state-of-the-art results, outperforming CRF significantly. Our joint model outperforms the standard TriCRF by 1% absolute for both intent and slot. On a number of other domains, our joint model achieves 0.7 – 1%, and 0.9 – 2.1% absolute gains over the independent modeling approach for intent and slot respectively.
ChemInform Abstract: Reaction of 2,5‐Bis(trifluoromethyl)‐1,3,4‐oxadiazole with Hydrazine. The Synthesis of 4‐Amino‐3,5‐bis(trifluoromethyl)‐4H‐1,2,4‐triazole. (1989)

Abstract The oxadiazole (I) is cleaved with anhydrous hydrazine (II), yielding the hydrazonic acid hydrazide (III).
ChemInform Abstract: The Chemistry of Cyclic Vinyl Ethers. Part 6. Total Synthesis of Polyether Ionophore Antibiotics of the Calcimycin (A‐23187) Class. (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.
Ideas for Next-Generation ASR (2003)

Examines future directions for automatic speech recognition, including modeling the whole speech signal and handling mixtures.