gebhart/patrepeval huggingface dataset:
Abstract 24061: Targeting Trpv4 Channels Protects Heart From Pathological Remodeling Following Myocardial Infarction (2017)

Heart failure is one of the leading causes of death which is often characterized by pathological fibrosis. Cardiac remodeling following myocadial infarction is a multiphase reparative process which involves replacement of damaged tissue with physiological (reparative) fibrosis to form scar that limit the expansion of the infarct. Myofibroblasts are critical mediator of this reparative fibrosis, however, hyperactivation of these cells can cause pathological fibrosis leading to heart failure. We have previously demonstrated that the mechanosensitive ion channel TRPV4 (transient receptor potential vanilloid channel 4) regulates cardiac fibroblast differentiation into myofibroblasts. However, the physiological or translational significance of TRPV4 in cardiac remodeling following MI is unknown. To explore this, we have induced MI (permanent LAD ligation) in WT and TRPV4KO mice and measured cardiac function for 8 weeks. Separately, WT mice were given an orally active TRPV4 antagonist GSK2193874, immediately after MI surgery and followed for 5 weeks. 2D-echocardiography revealed that the cardiac function (ejection fraction and fractional shortening) is preserved post-MI in both TRPV4KO and GSK2193874-treated WT mice compared to either WT or vehicle treated mice. Further, we found reduced cardiac fibrosis at infarcted and remote zones in TRPV4KO and GSK2193874-treated WT mice compared to their MI counter parts. Furthermore, TRPV4KO hearts exhibited decreased cardiomyocyte apoptosis (TUNEL assay) and increased capillary density (CD31 staining) post-MI compared to WT hearts. Our results thus suggest that targeting TRPV4 protects heart from myocardial infarction-induced damage by preserving cardiac structure and function via reduced myocyte apoptosis, diminished fibrosis and increased revascularization, and identifies TRPV4 as a novel therapeutic target for heart failure.
Multi-label Connectionist Temporal Classification (2019)

The Connectionist Temporal Classification (CTC) loss function [1] enables end-to-end training of a neural network for sequence-to-sequence tasks without the need for prior alignments between the input and output. CTC is traditionally used for training sequential, single-label problems; each element in the sequence has only one class. In this work, we show that CTC is not suitable for multi-label tasks and we present a novel Multi-label Connectionist Temporal Classification (MCTC) loss function for multi-label, sequence-to-sequence classification. Multi-label classes can represent meaningful attributes of a single element; for example, in Optical Music Recognition (OMR), a music note can have separate duration and pitch attributes. Our approach achieves state-of-the-art results on Joint Handwritten Text Recognition and Name Entity Recognition, Asian Character Recognition, and OMR.
pandas: a Foundational Python Library for Data Analysis and Statistics (2011)

In this paper we will discuss pandas, a Python library of rich data structures and tools for working with structured data sets common to statistics, finance, social sciences, and many other fields. The library provides integrated, intuitive routines for performing common data manipulations and analysis on such data sets. It aims to be the foundational layer for the future of statistical computing in Python. It serves as a strong complement to the existing scientific Python stack while implementing and improving upon the kinds of data manipulation tools found in other statistical programming languages such as R. In addition to detailing its design and features of pandas, we will discuss future avenues of work and growth opportunities for statistics and data analysis applications in the Python language.
Computed Crystal Energy Landscapes for Understanding and Predicting Organic Crystal Structures and Polymorphism (2008)

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible structures. Indeed, we have observed that systems with many almost equi-energetic structures that contain a common interchangeable motif correlate with a tendency to disorder and problems with control of the crystallization product. Thus, contrasting the computed crystal energy landscape with the known crystal structures of a given molecule provides a valuable complement to solid form screening, and the examination of the low-energy structures often leads to a rationalization of the forms found.
Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry (2004)

Among the methods used to unravel protein interaction surfaces, chemical cross-linking followed by identification of the cross-linked peptides by mass spectrometry has proven especially useful in dynamic and complex systems. During the signal recognition particle (SRP)-dependent targeting of proteins to the bacterial plasma membrane, the specific interaction between Ffh (the protein component of SRP) and FtsY (the SRP receptor) is known to be essential for the efficiency and fidelity of this process. In this work, we studied the Escherichia coli and Thermus aquaticus Ffh.FtsY complexes by using chemical cross-linking and tandem mass spectrometry to identify nine intermolecular cross-linked peptides. This information was used in conjunction with a previously undescribed model-building approach that combines geometric restraint optimization with macromolecular docking. The resulting model of the Ffh.FtsY complex is in good agreement with the crystal structure solved shortly thereafter. Intriguingly, four of the cross-linked pairs involve the M domain of Ffh, which is absent from the crystal structure, providing previously undocumented experimental evidence that the M domain is positioned in close proximity to the Ffh.FtsY interface in the complex.
Mountains of Data (2012)

A famous mountaineer and Microsoft researchers are blending images, data, and computer models to document how changing climate is affecting the Himalaya.
A passenger vehicle onboard computer system for engine fault diagnosis, performance measurement and control (1987)

This paper describes a microprocessor based on-board instrumentation system with applications to engine fault diagnosis, performance measurement and control. A non contacting measurement of engine angular position, taken at the flywheel by means of a magnetic sensor, provides a signal proportional to crankshaft angular velocity. The signal is then appropriately digitized and interfaced to a microprocessor, along with timing information regarding engine position. Suitable processing of the signal by the microprocessor provides information in real time regarding crankshaft speed and torque nonuniformity, which is employed to detect engine faults and to yield a measure of engine performance. Experimental verification of a prototype instrument has been carried out on the road in a number of vehicles, with very successful results. A variety of experiments have confirmed the usefulness of the system for applications in fault diagnosis and performance measurement, and the potential of the system for some aspects of engine control.
Raman spectra of graphene exfoliated on insulating crystalline substrates (2011)

We have investigated single layer, bilayer and few-layer graphene exfoliated on SiO2 and on single crystal surfaces of SrTiO3, Al2O3 and TiO2 using Raman spectroscopy. The typical 'fingerprint' 2D peak turns out to be indicative of the number of graphene layers independent of the substrate material. The morphological quality of the graphene is as good as on SiO2 substrates for all the materials. We find evidence for substrate-induced changes due to doping. With most substrates, hole doping is observed, but with SrTiO3 we have identified a dielectric substrate with which electron accumulation in graphene can be achieved.
Tissue oxygen debt as a determinant of lethal and nonlethal postoperative organ failure (1988)

The aim of this study was to evaluate the concept that tissue oxygen debt reflected by inadequate oxygen consumption (VO2) in the intraoperative and immediate postoperative periods is a common determinant of multisystem organ failure and death. We measured the cumulative tissue oxygen debt during and immediately after 100 consecutive high-risk surgical operations in 98 patients and correlated these data with the subsequent development of lethal and nonlethal organ failure complications. The tissue VO2 deficit was calculated as the measured VO2 minus the estimated VO2 requirements corrected for both temperature and anesthesia; the net cumulative VO2 deficit was calculated as the integrated area under the VO2 deficit-time curve. The maximum cumulative VO2 deficit averaged 33.5 +/- 36.9 (SD) L/m2 in nonsurvivors, 26.8 +/- 32.1 L/m2 in survivors with organ failure, and 8.0 +/- 10.9 L/m2 in survivors without organ failure. The time postoperatively to reach the maximal cumulative VO2 deficit and the duration of the VO2 deficit was greatest in nonsurvivors, less in survivors with organ failure, and least in survivors without organ failure. Although many associated clinical conditions as well as innumerable physiologic mechanisms and biochemical mediators play important roles in tissue injury, tissue oxygen debt reflected by insufficient VO2 appears to be the primary event as well as a major determinant of organ failure and outcome.
Formation of condensed metallic deuterium lattice and nuclear fusion (2002)

It was confirmed that nanometer-sized metal powder (atom clusters or simply clusters) can absorb an extremely large amount of deuterium/hydrogen atoms more than 300% against the number density of host metal. Within such clusters, the bonding potential widely changes from the center region to peripheral ones, so that the zig•zag atom-chains are always formed dynamically around the average position of atoms and the degree of filling up of the constituent atoms for the fcc type metal reduces to about 0.64 from 0.74 in bulk metal, i.e., vacant space increases to 0.36 from 0.26. As a result, a large amount of deuterium /hydrogen atoms are instantly dissolved into such host-clusters at room temperature. Furthermore, “metallic deuterium lattice”(or hydrogen one) including locally the“deuterium-lump”with the ultrahigh density is formed with body centered cuboctahedral structure which belongs to a unit cell of the host lattice, while such event cannot be realized at all within bulk metals. It seems that nuclear fusion in solid (“solid fusion”) takes place in the highly condensed“deuterium-lump”inside each unit cell of the“metallic deuterium lattice”(or mixed hydrogen one) which is formed inside each cell of the host metal lattice. It is considered, therefore, that each unit cell of the host lattice corresponds to minimum units of“solid fusion reactor”. In order to achieve“solid fusion”, just the generation of the ultrahigh density“deuterium-lump”(simply“pycnodeuterium-lump”) coagulated locally inside unit cell of the host lattice and/or the highly condensed metallic deuterium lattice should be an indispensable condition.
Identification of new probe substrates for human CYP20A1 (2019)

CYP20A1 is a well-conserved member of the human cytochrome P450 enzyme family for which no endogenous or xenobiotic substrate is known. We have recently shown that this enzyme has moderate activity towards two proluciferin probe substrates. In order to facilitate the search for physiological substrates we have tested nine additional proluciferins in this study and identified three such probe substrates that give much higher product yields. Using one of these probes, we demonstrate inhibition of CYP20A1 activity by 1-benzylimidazole, ketoconazole and letrozole. Finally, we show that the combination of two common single nucleotide polymorphisms (SNPs) of CYP20A1 leads to an enzyme (CYP20A1Leu97Phe346) with reduced activity.
Charge Transfer in Donor Polymer-Acceptor Polymer Mixtures (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCharge Transfer in Donor Polymer-Acceptor Polymer MixturesTheodore Sulzberg and Robert J. CotterCite this: Macromolecules 1968, 1, 6, 554–555Publication Date (Print):November 1, 1968Publication History Published online1 May 2002Published inissue 1 November 1968https://pubs.acs.org/doi/10.1021/ma60006a020https://doi.org/10.1021/ma60006a020research-articleACS PublicationsRequest reuse permissionsArticle Views103Altmetric-Citations21LEARN 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
High Affinity Heme Binding to a Heme Regulatory Motif on the Nuclear Receptor Rev-erbβ Leads to Its Degradation and Indirectly Regulates Its Interaction with Nuclear Receptor Corepressor (2015)

Rev-erbα and Rev-erbβ are heme-binding nuclear receptors (NR) that repress the transcription of genes involved in regulating metabolism, inflammation, and the circadian clock. Previous gene expression and co-immunoprecipitation studies led to a model in which heme binding to Rev-erbα recruits nuclear receptor corepressor 1 (NCoR1) into an active repressor complex. However, in contradiction, biochemical and crystallographic studies have shown that heme decreases the affinity of the ligand-binding domain of Rev-erb NRs for NCoR1 peptides. One explanation for this discrepancy is that the ligand-binding domain and NCoR1 peptides used for in vitro studies cannot replicate the key features of the full-length proteins used in cellular studies. However, the combined in vitro and cellular results described here demonstrate that heme does not directly promote interactions between full-length Rev-erbβ (FLRev-erbβ) and an NCoR1 construct encompassing all three NR interaction domains. NCoR1 tightly binds both apo- and heme-replete FLRev-erbβ·DNA complexes; furthermore, heme, at high concentrations, destabilizes the FLRev-erbβ·NCoR1 complex. The interaction between FLRev-erbβ and NCoR1 as well as Rev-erbβ repression at the Bmal1 promoter appear to be modulated by another cellular factor(s), at least one of which is related to the ubiquitin-proteasome pathway. Our studies suggest that heme is involved in regulating the degradation of Rev-erbβ in a manner consistent with its role in circadian rhythm maintenance. Finally, the very slow rate constant (10(-6) s(-1)) of heme dissociation from Rev-erbβ rules out a prior proposal that Rev-erbβ acts as an intracellular heme sensor.
Second-Order Blind Separation of First- and Second-Order Cyclostationary Sources—Application to AM, FSK, CPFSK, and Deterministic Sources (2004)

Most of the second-order (SO) and higher order (HO) blind source separation (BSS) methods developed this last decade aim at blindly separating statistically independent sources that are assumed zero-mean, stationary, and ergodic. Nevertheless, in many situations of practical interest, such as in radiocommunications contexts, the sources are nonstationary and very often cyclostationary (digital modulations). The behavior of the current SO and fourth-order (FO) cumulant-based BSS methods in the presence of cyclostationary sources has been analyzed, recently, in a previous paper by Ferre/spl acute/ol and Chevalier, assuming zero-mean sources. However, some cyclostationary sources used in practical situations are not zero-mean but have a first-order (FIO) cyclostationarity property, which is, in particular, the case for some amplitude modulated (AM) signals and for some nonlinearly modulated digital sources such as frequency shift keying (FSK) or some continuous phase frequency shift keying (CPFSK) sources. For such sources, the results presented in the previous paper by Ferre/spl acute/ol and Chevalier no longer hold, and the purpose of this paper is to analyze the behavior and to propose adaptations of the current SO BSS methods for sources that are both FIO and SO cyclostationary and cyclo-ergodic. An extension for deterministic sources is also proposed in the paper.
A novel UPS using high-frequency switch-mode rectifier and high-frequency PWM inverter (2003)

An uninterruptible power supply (UPS) resorting to high-frequency switch-mode rectifier (SMR) techniques and high-frequency pulse-width-modulated inverter techniques has been developed. The input current of UPS is controlled to maintain a sinusoidal waveform by SMR, and the output voltage waveform distortion is suppressed to a low level by instantaneous voltage control. This UPS is suitable for a protector of computer-applied equipment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Substrate specificities of tyrosine-specific protein kinases toward cytoskeletal proteins in vitro. (1986)

We have previously reported that fodrin (beta subunit), tubulin (alpha subunit) and microtubule-associated proteins (MAPs; MAP2 and tau) are good substrates for the purified insulin receptor kinase (Kadowaki, T., Nishida, E., Kasuga, M., Akiyama, T., Takaku, F., Ishikawa, M., Sakai, H., Kathuria, S., and Fujita-Yamaguchi, Y. (1985) Biochem. Biophys. Res. Commun. 127, 493-500 and Kadowaki, T., Fujita-Yamaguchi, Y., Nishida, E., Takaku, F., Akiyama, T., Kathuria, S., Akanuma, Y., and Kasuga, M. (1985) J. Biol. Chem. 260, 4016-4020). In this study, to investigate the substrate specificities of tyrosine kinases, we have examined the actions of the purified epidermal growth factor (EGF) receptor kinase and Rous sarcoma virus src kinase on purified microfilament- and microtubule-related proteins. Among microfilament-related proteins examined, the purified EGF receptor kinase phosphorylated the beta subunit, but not the alpha subunit, of fodrin on tyrosine residues with a Km below the micromolar range. The fodrin phosphorylation by the EGF receptor kinase was markedly inhibited by F-actin. In contrast, the purified src kinase preferentially phosphorylated the alpha subunit of fodrin on tyrosine residues. Fodrin phosphorylation by the src kinase was not inhibited by F-actin. Among microtubule proteins examined, MAP2 was the best substrate for the EGF receptor kinase. By contrast, src kinase favored phosphorylation of tubulin as compared to MAP2. The peptide mapping of MAP2 phosphorylated by the EGF receptor kinase and by the insulin receptor kinase produced very similar patterns of phosphopeptides, while that of MAP2 phosphorylated by the src kinase gave a distinctly different pattern. When the phosphorylation of the tubulin subunits was examined, the EGF receptor kinase preferred beta subunit to alpha subunit, but the src kinase phosphorylated both alpha and beta subunits to a similar extent. These results, together with our previous results, indicate that the substrate specificities of the EGF receptor kinase and the insulin receptor kinase are very similar, but not identical, while that of the src kinase is distinctly different from that of these growth factor receptor kinases.
Text graphic separation in Indian newspapers (2013)

Digitization of newspaper article is important for registering historical events. Layout analysis of Indian newspaper is a challenging task due to the presence of different font size, font styles and random placement of text and non-text regions. In this paper we propose a novel framework for learning optimal parameters for text graphic separation in the presence of complex layouts. The learning problem has been formulated as an optimization problem using EM algorithm to learn optimal parameters depending on the nature of the document content.
The Helical MreB Cytoskeleton in Escherichia coli MC1000/pLE7 Is an Artifact of the N-Terminal Yellow Fluorescent Protein Tag (2012)

Based on fluorescence microscopy, the actin homolog MreB has been thought to form extended helices surrounding the cytoplasm of rod-shaped bacterial cells. The presence of these and other putative helices has come to dominate models of bacterial cell shape regulation, chromosome segregation, polarity, and motility. Here we use electron cryotomography to show that MreB does in fact form extended helices and filaments in Escherichia coli when yellow fluorescent protein (YFP) is fused to its N terminus but native (untagged) MreB expressed to the same levels does not. In contrast, mCherry fused to an internal loop (MreB-RFP(SW)) does not induce helices. The helices are therefore an artifact of the placement of the fluorescent protein tag. YFP-MreB helices were also clearly distinguishable from the punctate, "patchy" localization patterns of MreB-RFP(SW), even by standard light microscopy. The many interpretations in the literature of such punctate patterns as helices should therefore be reconsidered.
Separation of Water into Its Ortho and Para Isomers (2002)

Polyatomic molecules can exist as nuclear spin isomers. For example, the ortho and para hydrogen spin isomers are characterized by different values of specific heat, boiling point, heat of vapor formation, and so forth (1). Hydrogen has been the only substance whose spin modifications are well studied and available for practical use.