gebhart/patrepeval huggingface dataset:
Disease-associated mutation in <i>SRSF2</i> misregulates splicing by altering RNA-binding affinities (2015)

Serine/arginine-rich splicing factor 2 (SRSF2) is an RNA-binding protein that plays important roles in splicing of mRNA precursors. SRSF2 mutations are frequently found in patients with myelodysplastic syndromes and certain leukemias, but how these mutations affect SRSF2 function has only begun to be examined. We used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 nuclease to introduce the P95H mutation to SRSF2 in K562 leukemia cells, generating an isogenic model so that splicing alterations can be attributed solely to mutant SRSF2. We found that SRSF2 (P95H) misregulates 548 splicing events (<1% of total). Of these events, 374 involved the inclusion of cassette exons, and the inclusion was either increased (206) or decreased (168). We detected a specific motif (UCCA/UG) enriched in the more-included exons and a distinct motif (UGGA/UG) in the more-excluded exons. RNA gel shift assays showed that a mutant SRSF2 derivative bound more tightly than its wild-type counterpart to RNA sites containing UCCAG but bound less tightly to UGGAG sites. Thus in most cases the pattern of exon inclusion or exclusion correlated with stronger or weaker RNA binding, respectively. We further show that the P95H mutation does not affect other functions of SRSF2, i.e., protein-protein interactions with key splicing factors. Our results thus demonstrate that the P95H mutation positively or negatively alters the binding affinity of SRSF2 for cognate RNA sites in target transcripts, leading to misregulation of exon inclusion. Our findings shed light on the mechanism of the disease-associated SRSF2 mutation in splicing regulation and also reveal a group of misspliced mRNA isoforms for potential therapeutic targeting.
Non-linear electrical property of composite materials with two kinds of filler (2002)

Electrical property of the composite made with resin as a binder resin and SiC and/or Fe/sub 3/O/sub 4/ as filler has been studied. It is found that the critical volume fraction of Fe/sub 3/O/sub 4/ in the composite made with resin and Fe/sub 3/O/sub 4/ differs from that in the composite made with resin, Fe/sub 3/O/sub 4/ and SiC. The nonlinear behavior of resistivity for electric field is controlled by percolating paths formed by SiC particles. It. is also found that the appearance of the non-linear property shifts to higher electric fields by adding Fe/sub 3/O/sub 4/ as a filler to the composite made with resin and SiC particles.
High-speed variable-focus optical system for extended depth of field (2009)

A high-speed camera is essential for observing dynamic phenomena. Such a camera needs a bright lens with large aperture due to the short exposure time. Since the depth of field (DOF) becomes shallow when using a bright lens, there is a demand for a high-speed camera with an extended depth of field. One commonly used technique to extend the DOF is to synthesize images captured at various focus positions. However, this method cannot be applied to a high-speed camera because no conventional mechanism can shift the focus position quickly enough. In this paper, we propose a new high-speed variable-focus optical system for extending the DOF. The proposed optical system is based on a high-speed variable-focus liquid lens with millisecond-order response time that was developed by our group. We show that our proposed system results in better light intensity than the method involving decreasing the diameter of the aperture stop. Furthermore, our experiment demonstrated that a 1000-fps movie with extended DOF was successfully acquired using the high-speed variable-focus optical system in combination with the image synthesizing technique.
Multiphoton in vivo flow cytometry (2005)

Flow cytometry using two-photon excitation is demonstrated for detection of particles and cells circulating in the blood stream of a live mouse. With appropriate dye labeling, two-photon excitation enables quantitative cytometry in vivo.
An Acetobacter xylinum insertion sequence element associated with inactivation of cellulose production (1991)

An insertion sequence (IS) element, IS1031, caused insertions associated with spontaneous cellulose deficient (Cel-) mutants of Acetobacter xylinum ATCC 23769. The element was discovered during hybridization analysis of DNAs from Cel- mutants of A. xylinum ATCC 23769 with pAXC145, an indigenous plasmid from a Cel- mutant of A. xylinum NRCC 17005. An IS element, IS1031B, apparently identical to IS1031, was identified on pAXC145. IS1031 is about 950 bp. DNA sequencing showed that the two elements had identical termini with inverted repeats of 24 bp containing two mismatches and that they generated 3-bp target sequence duplications. The A. xylinum ATCC 23769 wild type carries seven copies of IS1031. Southern hybridization showed that 8 of 17 independently isolated spontaneous Cel- mutants of ATCC 23769 contained insertions of an element homologous to IS1031. Most insertions were in unique sites, indicating low insertion specificity. Significantly, two insertions were 0.5 kb upstream of a recently identified cellulose synthase gene. Attempts to isolate spontaneous cellulose-producing revertants of these two Cel- insertion mutants by selection in static cultures were unsuccessful. Instead, pseudorevertants that made waxlike films in the liquid-air interface were obtained. The two pseudorevertants carried new insertions of an IS1031-like element in nonidentical sites of the genome without excision of the previous insertions. Taken together, these results suggest that indigenous IS elements contribute to genetic instability in A. xylinum. The elements might also be useful as genetic tools in this organism and related species.
Wavelength division multiplexed sensor network using Bragg fibre reflection gratings (1992)

A new wavelength division multiplexed data gathering network is proposed and demonstrated. The sensor multiplexing architecture operaters in the 1.5 μm fibre transmission window using a broadband superfluorescent erbium doped fibre source and fibre Bragg reflection gratings.
A Critical Reassessment of the Role of Mitochondria in Tumorigenesis (2005)

The role of mitochondria in tumorigenesis remains unclarified. Our findings of laboratory errors in many contributions would represent only the tip of the iceberg since most published studies do not provide the raw sequence data for inspection, thus hindering a posteriori evaluation of the results. There is no precedent for such a concatenation of errors and misconceptions affecting a whole subfield of medical research.
Glycoprotein methods and protocols :the mucins (2000)

Anthony P. Corfield and a group of hands-on expermentalists bring together in Glycoprotein Methods and Protocols: The Mucins a state-of-the-art collection of reliable and tested methods for the study of all aspects of mucins. These powerful methods range from the preparation of mucins to their detection and quantitation with molecular biological and biochemical reagents. Also included are methods for the assessment of mucin peptide and carbohydrate, of mucin biosynthesis and degradation, and of mucin bacteriology and cell biology. The techniques take advantage of the latest improvements in sensitivity and specificity of detection, and in the preparation of new reagents for specific biochemical detection. Glycoprotein Methods and Protocols: The Mucins offers today's researchers a complete range of readily reproducible analytical techniques for studying mucins. Its powerful techniques constitute a launching pad for those entering the field for the first time and a state-of-the-art collection for those already active in mucin research
Toll-like receptors, chemokine receptors and death receptor ligands responses in SARS coronavirus infected human monocyte derived dendritic cells (2009)

The upregulation of chemokines and CCRs may facilitate DC migration from the infection site to the lymph nodes, whereas the increase of TRAIL may induce lymphocyte apoptosis. These findings may explain the increased lung infiltrations and lymphoid depletion in SARS patients. Further explorations of the biological significance of these findings are warranted.
Formation Combined with Intercalation of Ni and Its Alloy Nanoparticles within Mesoporous Silica for Robust Catalytic Reactions (2018)

Intercalation of silica-supported nickel nanoparticles within mesoporous silica has been achieved through chemical reduction of nickel silicate with mesoporous silica ( mSiO<sub>2</sub>) coated on inner and outer surfaces. Formation of nickel nanoparticles was controlled at nickel silicate-silica interface and was well-confined by mSiO<sub>2</sub> coating. Doping of other transition metals has been accomplished at the stage of nickel silicate formation, because of similarity in critical stability constants of respective metal salts. Doped nickel silicates were able to produce nickel-based bimetallic and trimetallic alloy nanoparticles within the final dual-shell configuration. This type of catalyst has been tested for both liquid- and gas-phase reactions, all showing good activity and selectivity. Ni nanoparticles could serve as the active catalyst or activity enhancer to other alloyed metals for different reactions. Especially for selective hydrogenation of trans-cinnamaldehyde, 100% selectivity toward hydrocinnamaldehyde at full conversion has been achieved without using noble metals. Spent catalysts in all cases showed no changes in terms of morphology and crystal structure, indicating this type of catalyst was robust under such reaction conditions, including gas-solid reaction systems.
Effect of human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein on HIV-1 reverse transcriptase activity in vitro. (1970)

Conversion of human immunodeficiency virus type 1 (HIV-1) genomic RNA to viral DNA is a requisite step in the virus life cycle. This conversion is catalyzed by reverse transcriptase (RT) associated with a large nucleoprotein complex composed of several viral proteins including nucleocapsid (NC). To better characterize the biochemical mechanisms of viral DNA synthesis, we overexpressed and purified recombinant HIV-1 NC and studied its effect on the activity and processivity of HIV-1 RT during polymerization of HIV-1 template sequences in vitro. The effect of NC on steady-state RT activity was dependent on the order of addition of reaction components. Addition of NC prior to formation of RT-primer.template-dNTP ternary complexes inhibited primer extension and reduced total product yields by slowing steady-state RT turnover. In contrast, addition of NC to preformed ternary complexes resulted in efficient primer extension and increased RT processivity at specific DNA template sites. NC stimulated polymerization (2-4 times) through eight of 13 sites examined in the cRRE region of HIV-1 env and increased the rate of polymerization through the D3/CTS region of HIV-1 pol 10 times. The data suggest that NC affects RT processivity by facilitating polymerization through regions of template secondary structure. Thus, NC functions as a single-strand binding (SSB)-like accessory replication factor for RT in vitro and may be part of a multicomponent retroviral replication complex.
Nonlinear regularization of iterative weighted filtered backprojection for helical cone-beam CT (2008)

We report on experiments on combining iterative weighted filtered backprojection with nonlinear regularization. The resulting methods allow for contrast dependent resolution. In combination with improved geometrical modeling of the acquisition process, they have the potential to improve high contrast resolution while preserving low contrast image properties.
Mesoionic compounds. XXXIII. Thermal rearrangement of 4H-1,3-thiazinium betaines to 4-quinolones (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMesoionic compounds. XXXIII. Thermal rearrangement of 4H-1,3-thiazinium betaines to 4-quinolonesK. T. Potts, R. Ehlinger, and W. M. NicholsCite this: J. Org. Chem. 1975, 40, 18, 2596–2600Publication Date (Print):September 1, 1975Publication History Published online1 May 2002Published inissue 1 September 1975https://pubs.acs.org/doi/10.1021/jo00906a005https://doi.org/10.1021/jo00906a005research-articleACS PublicationsRequest reuse permissionsArticle Views104Altmetric-Citations25LEARN 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
Penalized-likelihood reconstruction for sparse data acquisitions with unregistered prior images and compressed sensing penalties (2011)

This paper introduces a general reconstruction technique for using unregistered prior images within model-based penalized- likelihood reconstruction. The resulting estimator is implicitly defined as the maximizer of an objective composed of a likelihood term that enforces a fit to data measurements and that incorporates the heteroscedastic statistics of the tomographic problem; and a penalty term that penalizes differences from prior image. Compressed sensing (p-norm) penalties are used to allow for differences between the reconstruction and the prior. Moreover, the penalty is parameterized with registration terms that are jointly optimized as part of the reconstruction to allow for mismatched images. We apply this novel approach to synthetic data using a digital phantom as well as tomographic data derived from a conebeam CT test bench. The test bench data includes sparse data acquisitions of a custom modifiable anthropomorphic lung phantom that can simulate lung nodule surveillance. Sparse reconstructions using this approach demonstrate the simultaneous incorporation of prior imagery and the necessary registration to utilize those priors.
Dielectric Metasurface Analogue of Electromagnetically Induced Transparency (2015)

We present an experimental demonstration of a metasurface analogue of electromagnetically induced transparency based on silicon instead of lossy plasmonic metal, therefore achieved a record-high quality factor of 483 and a sensing figure-of-merit of 103.
Ultrafast Spin-Motion Entanglement and Interferometry with a Single Atom (2013)

We report entanglement of a single atom's hyperfine spin state with its motional state in a time scale of less than 3 ns. We engineer a short train of intense laser pulses to impart a spin-dependent momentum transfer of ± 2 ħk. Using pairs of momentum kicks, we create an atomic interferometer and demonstrate collapse and revival of spin coherence as the motional wave packet is split and recombined. The revival after a pair of kicks occurs only when the second kick is delayed by an integer multiple of the harmonic trap period, a signature of entanglement and disentanglement of the spin with the motion. Such quantum control opens a new regime of ultrafast entanglement in atomic qubits.
Assays for Determination of Protein Concentration (2007)

Biochemical analysis of proteins relies on accurate quantitation of protein concentration. This appendix describes how to perform commonly used protein assays, e.g., Lowry, Bradford, BCA, and UV spectroscopic protein assays. The primary focus of the appendix is assay selection, emphasizing sample and buffer compatibility. Protein assay standard curves and data processing fundamentals are discussed in detail. This appendix also details high-throughput adaptations of the commonly used protein assays, and also contains a protocol for BCA assay of total protein in SDS-PAGE sample buffer that is used for equal loading of SDS-PAGE gels, which is reliable, inexpensive, and quick.
The Negative Mode Proteome with Activated Ion Negative Electron Transfer Dissociation (AI-NETD) (2015)

The field of proteomics almost uniformly relies on peptide cation analysis, leading to an underrepresentation of acidic portions of proteomes, including relevant acidic posttranslational modifications. Despite the many benefits negative mode proteomics can offer, peptide anion analysis remains in its infancy due mainly to challenges with high-pH reversed-phase separations and a lack of robust fragmentation methods suitable for peptide anion characterization. Here, we report the first implementation of activated ion negative electron transfer dissociation (AI-NETD) on the chromatographic timescale, generating 7,601 unique peptide identifications from Saccharomyces cerevisiae in single-shot nLC-MS/MS analyses of tryptic peptides-a greater than 5-fold increase over previous results with NETD alone. These improvements translate to identification of 1,106 proteins, making this work the first negative mode study to identify more than 1,000 proteins in any system. We then compare the performance of AI-NETD for analysis of peptides generated by five proteases (trypsin, LysC, GluC, chymotrypsin, and AspN) for negative mode analyses, identifying as many as 5,356 peptides (1,045 proteins) with LysC and 4,213 peptides (857 proteins) with GluC in yeast-characterizing 1,359 proteins in total. Finally, we present the first deep-sequencing approach for negative mode proteomics, leveraging offline low-pH reversed-phase fractionation prior to online high-pH separations and peptide fragmentation with AI-NETD. With this platform, we identified 3,467 proteins in yeast with trypsin alone and characterized a total of 3,730 proteins using multiple proteases, or nearly 83% of the expressed yeast proteome. This work represents the most extensive negative mode proteomics study to date, establishing AI-NETD as a robust tool for large-scale peptide anion characterization and making the negative mode approach a more viable platform for future proteomic studies.
Polymer film formulations for the preparation of enteric pharmaceutical capsules (2010)

Selected formulations from this study have potential for use as delayed release capsules.
The Effect of Aluminium on Graphitization of Cast Iron Treated with Cerium Mixture (2014)

Abstract The work determined the influence of aluminium in the amount from about 0.6% to about 8% on graphitization of cast iron with relatively high silicon content (3.4%-3.9%) and low manganese content (about 0.1%). The cast iron was spheroidized with cerium mixture and graphitized with ferrosilicon. It was found that the degree of graphitization increases with an increase in aluminium content in cast iron up to 2.8%, then decreases. Nodular and vermicular graphite precipitates were found after the applied treatment in cast iron containing aluminium in the amount from about 1.9% to about 8%. The Fe 3 AlC x carbides, increasing brittleness and deteriorating the machinability of cast iron, were not found in cast iron containing up to about 6.8% Al. These carbides were revealed only in cast iron containing about 8% Al.
Photo-injection p-i-n diode switch for high-power RF switching (2002)

The high RF power-switching properties of the photo-injection p-i-n switch (PIPINS), an optically controlled RF switch, are investigated. Proper functioning of a PIPINS as a low insertion-loss RF switch requires that it operates as a photoconductor, where the photo-injected charge is much greater than the RF sweep out charge. Insertion loss using 650-mW optical power was <0.4 dB at RF (VHF-UHF) power in excess of 200 W, and devices successfully standoff 200-W incident RF power with the series isolation being determined by the device capacitance (e.g., 225 fF). PIPINS hot-switching measurements are reported for the first time, with output RF power up to 180 W at low duty cycle, rise times of 1 ps, and fall times for a series shunt switch of /spl ap/2.5 /spl mu/s. The RF power for hot switching a PIPINS is limited by a latch-on effect, which is dependent on a variety of parameters, including duty cycle and repetition period, consistent with thermally generated carriers contributing to the latch-on effect. The switching properties of PIPINS make them a candidate for high RF power applications such as reconfigurable antennas, where electromagnetic isolation of the switch and control lines are critical.
PMM-Lab – A community resource for integrated Predictive Microbial Modelling (PMM) (2013)

The prediction of growth and inactivation of microorganisms in food matrices is a field of intensive research with increasing relevance to food safety professionals and public authorities. Today, large quantities of experimental and quality control data are available in comprehensive
public or proprietary databases. Parallel to this, the mathematical foundation for the generation of predictive microbial models has been developed and is now available. Nevertheless, there is a gap in easy-to-use and transparent software solutions that enable food safety professionals to apply state-of-the art mathematical modeling concepts to their proprietary data. Furthermore, an integrated infrastructure for information management on raw data and generated models is missing. The software PMM-Lab has been specifically designed to address these gaps. It has been outlined right from the beginning as a community resource to allow broad application and joint development. PMM-Lab already provides many valuable data analysis and modeling features including modules to create, visualize, analyze, save, import, export and deploy
predictive microbial models based on experimental data. Moreover, it allows consistent data management for the analyzed experimental data and generated models due to the integrated database. Technically, PMM-Lab is an extension of the open-source data integration and
analysis platform KNIME (www.knime.org ) from which it inherits highly beneficial properties like modularity, flexibility, scalability and extensibility. PMM-Lab is designed to be used by laboratory scientists, food safety specialists or even modeling experts who wish to distribute their methods to a broad community. Users trying to answer fundamental research questions based on experimental data collections or looking for structure in their growing data and model collection will also find value in this software. The possible application areas are numerous and include the prediction of shelf life and food spoilage. PMM-Lab has been developed by the Federal Institute for Risk Assessment, Germany and is available for free at http://sourceforge.net/projects/pmmlab/ under the GNU public license.