gebhart/patrepeval huggingface dataset:
Translation of mRNA for human lymphotoxin in microinjected Xenopus oocytes (1984)

Synthesis and secretion of biologically active human lymphotoxin (LT) can be detected in Xenopus laevis oocytes following their inoculation with poly(A+) RNA from human stimulated peripheral blood lymphocytes, but not in oocytes inoculated with RNA from unstimulated lymphocytes or from fibroblastoid cells. In size-fractionating mRNA of stimulated lymphocytes most LT activity is found to be coded for by RNA with an approximate sedimentation value of 19 S.
Contextual hidden Markov models for wavelet-domain signal processing (2002)

Wavelet-domain hidden Markov models (HMMs) provide a powerful new approach for statistical modeling and processing of wavelet coefficients. In addition to characterizing the statistics of individual wavelet coefficients, HMMs capture some of the key interactions between wavelet coefficients. However, as HMMs model an increasing number of wavelet coefficient interactions, HMM-based signal processing becomes increasingly complicated. In this paper, we propose a new approach to HMMs based on the notion of context. By modeling wavelet coefficient inter-dependencies via contexts, we retain the approximation capabilities of HMMs, yet substantially reduce their complexity. To illustrate the power of this approach, we develop new algorithms for signal estimation and for efficient synthesis of nonGaussian, long-range-dependent network traffic.
A Prospective Virtual Screening Study: Enriching Hit Rates and Designing Focus Libraries To Find Inhibitors of PI3Kδ and PI3Kγ (2016)

Here, we report a high-throughput virtual screening (HTVS) study using phosphoinositide 3-kinase (both PI3Kγ and PI3Kδ). Our initial HTVS results of the Janssen corporate database identified small focused libraries with hit rates at 50% inhibition showing a 50-fold increase over those from a HTS (high-throughput screen). Further, applying constraints based on "chemically intuitive" hydrogen bonds and/or positional requirements resulted in a substantial improvement in the hit rates (versus no constraints) and reduced docking time. While we find that docking scoring functions are not capable of providing a reliable relative ranking of a set of compounds, a prioritization of groups of compounds (e.g., low, medium, and high) does emerge, which allows for the chemistry efforts to be quickly focused on the most viable candidates. Thus, this illustrates that it is not always necessary to have a high correlation between a computational score and the experimental data to impact the drug discovery process.
Association of Surgical Left Atrial Appendage Occlusion With Subsequent Stroke and Mortality Among Patients Undergoing Cardiac Surgery (2018)

Among patients undergoing cardiac surgery, concurrent surgical LAAO, compared with no surgical LAAO, was associated with reduced risk of subsequent stroke and all-cause mortality. Further research, including from randomized clinical trials, is needed to more definitively determine the role of surgical LAAO.
Streptococcus bovis endocarditis as a presenting manifestation of idiopathic ulcerative colitis (1992)

Streptococcus bovis bacteraemia and endocarditis have been associated with several gastrointestinal diseases, mainly malignant or potentially malignant tumours, and less commonly non-malignant gastrointestinal disorders. We describe a 73 year old man in whom Streptococcus bovis endocarditis developed, and was the presenting manifestation of undiagnosed quiescent ulcerative colitis. Such an association has not been described previously.
Improving Early Robotics Education Using a Line-Following Robot Simulator (2018)

Line-following robots have the ability to recognize and follow a line drawn on a surface. Elements of their operating principles could be used in the evelopment of numerous autonomous technologies, with applications in education and industry. A simulator has been developed to aide in performing several trials in order to validate a project. By taking the Pololu 3pi Robot as the model, the proposed solution simulates its physical structure, behavior, and operations - being able to read lines on surfaces - enabling the user to observe the robot following the line according to the code used. This paper aims to validate the developed simulator as an alternative to ease the process of learning to use the 3pi platform applied in both educational and competitive environments.
Mechanistic aspects of the ligand-assisted nucleophilic addition reaction (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanistic aspects of the ligand-assisted nucleophilic addition reactionKevin A. Swiss, Dennis C. Liotta, and Cynthia A. MaryanoffCite this: J. Am. Chem. Soc. 1990, 112, 25, 9393–9394Publication Date (Print):December 1, 1990Publication History Published online1 May 2002Published inissue 1 December 1990https://pubs.acs.org/doi/10.1021/ja00181a051https://doi.org/10.1021/ja00181a051research-articleACS PublicationsRequest reuse permissionsArticle Views549Altmetric-Citations50LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Block sparsity and sampling over a union of subspaces (2009)

Sparse signal representations have gained wide popularity in recent years. In many applications the data can be expressed using only a few nonzero elements in an appropriate expansion. In this paper, we study a block-sparse model, in which the nonzero coefficients are arranged in blocks. To exploit this structure, we redefine the standard (NP-hard) sparse recovery problem, based on which we propose a convex relaxation in the form of a mixed lscr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> =lscr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> program. Isometry-based analysis is used to prove equivalence of the solution to that of the optimal program, under certain mild conditions. We further establish the robustness of our algorithm to mismodeling and bounded noise. We then present theoretical arguments and numerical experiments demonstrating the improved recovery performance of our method in comparison with sparse reconstruction that does not incorporate a block structure. The results are then applied to two related problems. The first is that of simultaneous sparse approximation. Our results can be used to prove isometry-based equivalence properties for this setting. In addition, we propose an alternative approach to acquire the measurements, that leads to performance improvement over standard methods. Finally, we show how our results can be used to sample signals in a finite structured union of subspaces, leading to robust and efficient recovery algorithms.
Expression and characterization of RNase III and Era proteins. Products of the rnc operon of Escherichia coli. (1990)

The synthesis rates of ribonuclease III (RNase III) and Era proteins are relatively low, and expression of the era gene is translationally coupled with expression of the rnc gene. Expression of both genes is negatively controlled by RNase III itself. We have constructed plasmids that overproduce RNase III and/or Era proteins under the control of the lambda PL promoter. A plasmid with the rnc gene under PL control expresses RNase III at levels greater than 40% of total cellular protein. Another plasmid with the era gene under PL control and a modified translation-initiation signal produces up to 80% of total cell protein as Era. Each protein has been purified using simple and rapid procedures. Purified RNase III protein specifically processes mRNA transcripts containing known RNase III sites. The purified Era protein binds GDP and GTP and has GTPase activity. Kinetic analysis shows that one molecule of GTP or GDP is bound/Era peptide with a Kd of 5.5 microM for GTP binding and 1.0 microM for GDP binding. The Km of the Era GTPase is 9.0 microM, and the maximum catalyzed rate of GTP hydrolyzed/min/mol of Era protein at 37 degrees C is 9.8 mmol.
An Exciting Year Ahead for ACS Sensors (2018)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTAn Exciting Year Ahead for ACS SensorsJ. Justin Gooding, Antonella Mazur, Michael Sailor, Maarten Merkx, Shana Kelley, Nongjian Tao, Yitao Long, and Eric BakkerView Author Information The University of New South Wales, Sydney, Australia ACS Publications, Washington, DC, United States University of California, San Diego, California United States Technische Universiteit Eindhoven, Eindhoven, The Netherlands The University of Toronto, Toronto, Ontario Canada Arizona State University, Tempe, Arizona, United States East China University of Science and Technology, Shanghai, China The University of Geneva, Geneva, SwitzerlandCite this: ACS Sens. 2018, 3, 1, 1–2Publication Date (Web):January 26, 2018Publication History Received5 January 2018Published online26 January 2018Published inissue 26 January 2018https://pubs.acs.org/doi/10.1021/acssensors.8b00013https://doi.org/10.1021/acssensors.8b00013editorialACS PublicationsCopyright © 2018 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1173Altmetric-Citations-LEARN 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 PDF (696 KB) Get e-AlertscloseSUBJECTS:Sensors Get e-Alerts
Railroad Bridge Instrumentation with Fiber Optic Sensors (1997)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text W. Lee, J. Lee, C. Henderson, H. F. Taylor, R. James, C. E. Lee, V. Swenson, W. N. Gibler, R. A. Atkins, and W. G. Gemeiner, "Railroad Bridge Instrumentation with Fiber Optic Sensors," in 12th International Conference on Optical Fiber Sensors, Vol. 16 of 1997 OSA Technical Digest Series (Optica Publishing Group, 1997), paper OThC2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
The nature of the capturable singlet trimethylenemethane intermediate in the decomposition of 7-isopropylidene-2,3-diazanorbornene (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe nature of the capturable singlet trimethylenemethane intermediate in the decomposition of 7-isopropylidene-2,3-diazanorborneneMatthew S. Platz, Donald R. Kelsey, Jerome A. Berson, Nicholas J. Turro, and Manfred MirbachCite this: J. Am. Chem. Soc. 1977, 99, 6, 2009–2010Publication Date (Print):March 1, 1977Publication History Published online1 May 2002Published inissue 1 March 1977https://pubs.acs.org/doi/10.1021/ja00448a071https://doi.org/10.1021/ja00448a071research-articleACS PublicationsRequest reuse permissionsArticle Views27Altmetric-Citations10LEARN 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
Finite Element-Based Personalized Simulation of Duodenal Hydrogel Spacer: Spacer Location Dependent Duodenal Sparing and a Decision Support System for Spacer-Enabled Pancreatic Cancer Radiation Therapy (2022)

A duodenal spacer simulator platform was developed and used to systematically study the dosimetric effect of spacer location. Further, L1cc is an informative anatomical feedback to guide the DSS to indicate the spacer efficacy, optimum location, and expected improvement.
Energy efficient inverters for wind energy applications (2013)

In this paper, efficiency and standby mode of operation of power conversion unit for wind power application is investigated. Mathematical model to calculate the power losses in three phase voltages source inverters, LCL filters, DC link capacitors and disconnect switches are presented. A comparison of inverter losses with sinusoidal pulse width modulation (PWM), space vector PWM and discontinuous PWM (DPWM) is discussed. Selection of power modules based on switching frequency, effect of modulation and gate resistance are presented. Techniques to improve the efficiency of the power conversion units are provided. The standby mode of operation is proposed to saves energy during unavailability of wind power. Efficiency of power conversion unit is calculated based on mathematical model and compare it with actual measurement.
Tissue‐Engineered Fibrin‐Based Heart Valve with Bio‐Inspired Textile Reinforcement (2016)

The mechanical properties of tissue-engineered heart valves still need to be improved to enable their implantation in the systemic circulation. The aim of this study is to develop a tissue-engineered valve for the aortic position - the BioTexValve - by exploiting a bio-inspired composite textile scaffold to confer native-like mechanical strength and anisotropy to the leaflets. This is achieved by multifilament fibers arranged similarly to the collagen bundles in the native aortic leaflet, fixed by a thin electrospun layer directly deposited on the pattern. The textile-based leaflets are positioned into a 3D mould where the components to form a fibrin gel containing human vascular smooth muscle cells are introduced. Upon fibrin polymerization, a complete valve is obtained. After 21 d of maturation by static and dynamic stimulation in a custom-made bioreactor, the valve shows excellent functionality under aortic pressure and flow conditions, as demonstrated by hydrodynamic tests performed according to ISO standards in a mock circulation system. The leaflets possess remarkable burst strength (1086 mmHg) while remaining pliable; pronounced extracellular matrix production is revealed by immunohistochemistry and biochemical assay. This study demonstrates the potential of bio-inspired textile-reinforcement for the fabrication of functional tissue-engineered heart valves for the aortic position.
TenDSuR: Tensor-Based 4D Sub-Nyquist Radar (2018)

We propose tensor-based four-dimensional sub-Nyquist radar that samples in spectral, spatial, Doppler, and temporal domains at sub-Nyquist rates while simultaneously recovering the target's direction, Doppler velocity, and range without loss of native resolutions. We formulate the radar signal model wherein the received echo samples are represented by a partial third-order tensor. We then apply compressed sensing in the tensor domain and use our tensor-orthogonal matching pursuit (OMP) and tensor completion algorithms for signal recovery. Our numerical experiments demonstrate joint estimation of all three target parameters at the same native resolutions as a conventional radar but with reduced measurements. Furthermore, tensor completion methods show enhanced performance in off-grid target recovery with respect to tensor-OMP.
In vivo regulation of gene expression and T helper type 17 differentiation by RORγt inverse agonists (2015)

The orphan nuclear receptor, retinoic acid receptor-related orphan nuclear receptor γt (RORγt), is required for the development and pathogenic function of interleukin-17A-secreting CD4(+) T helper type 17 (Th17) cells. Whereas small molecule RORγt antagonists impair Th17 cell development and attenuate autoimmune inflammation in vivo, the broader effects of these inhibitors on RORγt-dependent gene expression in vivo has yet to be characterized. We show that the RORγt inverse agonist TMP778 acts potently and selectively to block mouse Th17 cell differentiation in vitro and to impair Th17 cell development in vivo upon immunization with the myelin antigen MOG35-55 plus complete Freund's adjuvant. Importantly, we show that TMP778 acts in vivo to repress the expression of more than 150 genes, most of which fall outside the canonical Th17 transcriptional signature and are linked to a variety of inflammatory pathologies in humans. Interestingly, more than 30 genes are related with SMAD3, a transcription factor involved in the Th17 cell differentiation. These results reveal novel disease-associated genes regulated by RORγt during inflammation in vivo, and provide an early read on potential disease indications and safety concerns associated with pharmacological targeting of RORγt.
Poly(ethylene glycol)-Supported Enzyme Inactivators. Efficient Identification of the Site of Covalent Attachment to α-Chymotrypsin by PEG-TPCK (2004)

A new methodology utilizing an enzyme inactivator covalently attached to poly(ethylene glycol) (PEG) is described in which the PEG affords facile and mild quantification, isolation, and identification of the site of enzyme inactivation. As proof of concept, the known affinity labeling agent for alpha-chymotrypsin, N-tosyl-L-phenylalanine chloromethyl ketone (TPCK), was linked to PEG. The synthesis of the PEG-bound inactivator PEG-TPCK was carried out in good yields using standard solution-phase chemistry. Inactivation of alpha-chymotrypsin with PEG-TPCK was monitored via UV-vis spectroscopy in aqueous conditions, which resulted in less than 3% remaining activity, indicating that 97% of the alpha-chymotrypsin was covalently modified with PEG-TPCK. The MALDI-TOF mass spectrum showed only one new peak that was distinct in shape and corresponded to the mass of PEG-TPCK-alpha-chymotrypsin. Following proteolytic digestion, the PEG-TPCK-peptide was easily discernible from the rest of the digest in a HPLC trace because of its characteristic prolonged retention time and broad polymer shape. MALDI-TOF MS was used to determine the mass of the PEGylated peptide. Without prior removal of the PEG, the amino acid site to which PEG-TPCK covalently bound was determined via Edman sequencing. In comparison to other methods, the PEG-supported inactivator system is significantly cheaper and safer than the synthesis of radiolabeled compounds; furthermore, isolation of the PEGylated peptide is milder and more selective than standard affinity binding columns. Edman sequencing provides an exact determination of the site of inactivator covalent attachment without extensive, tedious LC-MS analysis of a complex peptide mixture. The method described here could be applied to a variety of enzymes as an alternative to current techniques.
UNcleProt (Universal Nuclear Protein database of barley): The first nuclear protein database that distinguishes proteins from different phases of the cell cycle (2016)

Proteins are the most abundant component of the cell nucleus, where they perform a plethora of functions, including the assembly of long DNA molecules into condensed chromatin, DNA replication and repair, regulation of gene expression, synthesis of RNA molecules and their modification. Proteins are important components of nuclear bodies and are involved in the maintenance of the nuclear architecture, transport across the nuclear envelope and cell division. Given their importance, the current poor knowledge of plant nuclear proteins and their dynamics during the cell's life and division is striking. Several factors hamper the analysis of the plant nuclear proteome, but the most critical seems to be the contamination of nuclei by cytosolic material during their isolation. With the availability of an efficient protocol for the purification of plant nuclei, based on flow cytometric sorting, contamination by cytoplasmic remnants can be minimized. Moreover, flow cytometry allows the separation of nuclei in different stages of the cell cycle (G1, S, and G2). This strategy has led to the identification of large number of nuclear proteins from barley (Hordeum vulgare), thus triggering the creation of a dedicated database called UNcleProt, http://barley.gambrinus.ueb.cas.cz/ .
On the Analysis and Optimization of Fast Conditional Handover With Hand Blockage for Mobility (2023)

Although frequency range 2 (FR2) systems are an essential part of 5G-Advanced and future 3GPP releases, the mobility performance of multi-panel user equipment (MPUE) with hand blockage is still an area open for research and standardization. In this article, a comprehensive study on the mobility performance of MPUE with hand blockage is performed for conditional handover (CHO) and its potential enhancement denoted by fast conditional handover (FCHO). In contrast to CHO, in FCHO the MPUE can reuse earlier target cell preparations after each handover to autonomously execute subsequent handovers. This saves both the signaling overhead associated with the reconfiguration and re-preparation of target cells after each handover and reduces mobility failures. Results have shown that FCHO offers considerable mobility performance gains as compared to CHO for different hand blockage cases that are dependent on the hand position around the MPUE. For the worst-case hand blockage scenario, it is seen that mobility failures reduce by 10.5% and 19.3% for the 60 km/h and 120 km/h mobility scenarios, respectively. This gain comes at the expense of reserving the handover resources of an MPUE for a longer time given that the target cell configurations are not necessarily released after each handover. In this article, the longer resource reservation problem in FCHO is analysed and three different resource reservation optimization techniques are introduced. Results have shown that these optimization techniques not only reduce the resource reservation time but also significantly reduce the signaling overhead at the possible expense of a tolerable degradation in mobility performance.