gebhart/patrepeval huggingface dataset:
Sequencing, expression, and site-directed mutagenesis of aurone synthase, a novel polyphenol oxidase from Coreopsis grandiflora, involved in aurone formation (2015)

Auronsynthase ist ein neues und seltenes Beispiel fur ein Typ-3 Kupferenzym das die Oxidation des 6'-Deoxychalcons Butein zum 4-Deoxyauron Sulfuretin katalysiert und folglich an der 4-Deoxyauronbildung beteiligt ist. Somit ist die Auronsynthase verantwortlich fur die Bildung von gelben Pigmenten in den Blutenblattern des Madchenauges (Coreopsis grandiflora). Diese Arbeit prasentiert die Isolierung und Sequenzierung von drei neuen Genen, die fur Polyphenoloxidasen kodieren, und in der NCBI Gendatenbank veroffentlicht wurden. Genexpressionsstudien haben gezeigt, dass eines dieser Gene eine bestimmte physiologische Rolle in der Pigmentbildung spielt und wurde daher cgAUS1 genannt. Die anderen beiden Gene sind allelische Varianten bei der Pigmentbildung und wurden daher cgAUS2 a und b genannt. Die jeweiligen zugehorigen Proteine erhielten die Nomenklatur AUS1 beziehungsweise AUS2 a und b. Daher wurde auch das Proenzym AUS1 in E. coli kloniert, exprimiert, aufgereinigt und via massenspektrometrischen Methoden identifiziert. Gelelektrophorese und Aktivitatstests zeigten dass die Auronsynthase (AUS1) nur Diphenolase-Reaktionen katalysiert, wie es auch klassische Catecholoxidasen tun. Weiters zeigte sich, dass AUS1 einem anderen Mechanismus folgt als die fruher beschriebene Aureusidin synthase aus Lowenmaulchen (Antirrhinum majus), das beteiligt ist an der 4-Hydroxyauronbildung deren gelben Blutenblatter. Zielgerichtete Mutationen um die Kupfer A Bildungsstelle (CuA) von AUS1 zeigten, dass das Phenylalanin, das uber dem Kupfer A liegt, und das Cystein, das eine Thioetherbrucke mit einem der kupferkoordinierenden Histidine bildet, verantwortlich sind fur Aktivitat und damit Funktion des Enzyms, aber nicht am Kupfereinbau beteiligt sind. Mutationen der CuA koordinierenden Histidine zeigten, dass jedes einzelne Histidin erforderlich fur den Kupfereinbau ist und damit auch fur Funktion des Enzyms unentbehrlich sind.
Study of an Extensive Set of Eye Movement Features: Extraction Methods and Statistical Analysis (2018)

This work presents a study of an extensive set of 101 categories of eye movement features from three types of eye movement events: fixations, saccades, and post-saccadic oscillations. We present a unified framework of methods for the extraction of features that describe the temporal, positional and dynamic characteristics of eye movements. We perform statistical analysis of feature values by employing eye movement data from a normative population of 298 subjects, recorded during a text reading task. We present overall measures for the central tendency and variability of feature values, and we quantify the test-retest reliability of features using either the Intraclass Correlation Coefficient (for normally distributed and normalized features) or Kendall's coefficient of concordance (for non-normally distributed features). Finally, for the case of normally distributed and normalized features we additionally perform factor analysis and provide interpretations of the resulting factors. The presented methods and analysis can provide a valuable tool for researchers in various fields that explore eye movements, such as in behavioral studies, attention and cognition research, medical research, biometric recognition, and humancomputer interaction.
Inhibition of Factor Xa in Prothrombinase Is Enhanced by Covalent Linkage of Antithrombin to Heparin. (2006)

Abstract The rate of prothrombin to thrombin conversion by factor Xa (Xa) is enhanced when Xa is incorporated into the surface-bound prothrombinase complex. However, in comparison to the free state, Xa within the prothrombinase complex is afforded protection from antithrombin + heparin (AT+H) inactivation. We have shown that, unlike AT+H, a covalent conjugate of AT and H (ATH) can neutralize fibrin-bound thrombin. In this study, AT+H and ATH were compared in their reaction with Xa +/− prothrombinase complex. Mixtures of CaCl2, phospholipid vesicles, factor Va (Va) and prothrombin in TSP buffer, were combined with Xa. Following addition of either AT+H or ATH, time samples were neutralized with Na2EDTA + polybrene + substrate (S-2222) and residual Xa activity measured. Second order rate constants (k2) were calculated from plots of activity versus time. Results were compared to corresponding experiments with Xa alone. AT+H inactivation of Xa in prothrombinase occurred at a k2 (x 107 M−1min−1) of 2.34 +/− 0.09. In contrast, neutralization of free Xa by AT+H was significantly faster (k2 = 8.34 +/− 0.18, p = 0.03). Reaction with ATH showed no significant rate difference for Xa inhibition in either the complexed or free states (18.5 +/− 3.3 and 16.3 +/− 3.7, respectively). Intriguingly, the rates achieved for ATH inhibition of complexed and free Xa were significantly greater than that for AT+H with free Xa (p=0.03 and p=0.02, respectively). We conclude that covalent complexes of AT and H do not encounter resistance in the inhibition of Xa in prothrombinase, as seen for non-covalent AT+H mixtures. Thus, it is possible for ATH to effectively inhibit the propagation phase of thrombin generation and thus dampen thrombin production via neutralization of Xa in prothrombinase.
Accumulation-based congestion control (2005)

This paper generalizes the TCP Vegas congestion avoidance mechanism and uses accumulation , buffered packets of a flow inside network routers, as a congestion measure based on which a family of congestion control schemes can be derived. We call this model Accumulation-based Congestion Control (ACC), which fits into the nonlinear optimization framework proposed by Kelly. The ACC model serves as a reference for packet-switching network implementations. We show that TCP Vegas is one possible scheme under this model. It is well known that Vegas suffers from round trip propagation delay estimation error and reverse path congestion. We therefore design a new Monaco scheme that solves these problems by employing an out-of-band, receiver-based accumulation estimator, with the support of two FIFO priority queues from the (congested) routers. Comparisons between these two schemes demonstrate that Monaco does not suffer from the problems mentioned above and achieves better performance than Vegas. We use ns-2 simulations and Linux implementation experiments to show that the static and dynamic performance of Monaco matches the theoretic results. One key issue regarding the ACC model in general, i.e., the scalability of bottleneck buffer requirement, and a solution using a virtual queueing algorithm are discussed and evaluated.
Synthesis and Inpainting-Based MR-CT Registration for Image-Guided Thermal Ablation of Liver Tumors (2019)

Thermal ablation is a minimally invasive procedure for treat-ing small or unresectable tumors. Although CT is widely used for guiding ablation procedures, the contrast of tumors against surrounding normal tissues in CT images is often poor, aggravating the difficulty in accurate thermal ablation. In this paper, we propose a fast MR-CT image registration method to overlay a pre-procedural MR (pMR) image onto an intra-procedural CT (iCT) image for guiding the thermal ablation of liver tumors. By first using a Cycle-GAN model with mutual information constraint to generate synthesized CT (sCT) image from the cor-responding pMR, pre-procedural MR-CT image registration is carried out through traditional mono-modality CT-CT image registration. At the intra-procedural stage, a partial-convolution-based network is first used to inpaint the probe and its artifacts in the iCT image. Then, an unsupervised registration network is used to efficiently align the pre-procedural CT (pCT) with the inpainted iCT (inpCT) image. The final transformation from pMR to iCT is obtained by combining the two estimated transformations,i.e., (1) from the pMR image space to the pCT image space (through sCT) and (2) from the pCT image space to the iCT image space (through inpCT). Experimental results confirm that the proposed method achieves high registration accuracy with a very fast computational speed.
InGaN/GaN/AlGaN-Based Laser Diodes Grown on GaN Substrates with a Fundamental Transverse Mode (1998)

An InGaN multiquantum-well (MQW)-structure laser diode (LD) was grown on an epitaxially laterally overgrown GaN on sapphire. The lowest threshold current densities between 1.2 and 2.8 kA/cm 2 were obtained when the number of InGaN well layers was two. The InGaN MQW LD was grown on a free-standing GaN substrate that was obtained by removing the sapphire substrate. The LDs with cleaved mirror facets showed an output power as high as 30 mW under room-temperature continuous-wave (CW) operation. The stable fundamental transverse mode was observed by reducing the ridge width to a value as small as 2 µm. The lifetime of the LDs at a constant output power of 5 mW was about 160 h under CW operation at an ambient temperature of 50°C, due to a high threshold current density of 6 kA/cm 2 .
Iminophosphoranes from the reaction of ylides with nitriles (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIminophosphoranes from the reaction of ylides with nitrilesEngelbert CiganekCite this: J. Org. Chem. 1970, 35, 11, 3631–3636Publication Date (Print):November 1, 1970Publication History Published online1 May 2002Published inissue 1 November 1970https://pubs.acs.org/doi/10.1021/jo00836a009https://doi.org/10.1021/jo00836a009research-articleACS PublicationsRequest reuse permissionsArticle Views326Altmetric-Citations53LEARN 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
Coded Fourier Transform (2017)

We consider the problem of computing the Fourier transform of high-dimensional vectors, distributedly over a cluster of machines consisting of a master node and multiple worker nodes, where the worker nodes can only store and process a fraction of the inputs. We show that by exploiting the algebraic structure of the Fourier transform operation and leveraging concepts from coding theory, one can efficiently deal with the straggler effects. In particular, we propose a computation strategy, named as coded FFT, which achieves the optimal recovery threshold, defined as the minimum number of workers that the master node needs to wait for in order to compute the output. This is the first code that achieves the optimum robustness in terms of tolerating stragglers or failures for computing Fourier transforms. Furthermore, the reconstruction process for coded FFT can be mapped to MDS decoding, which can be solved efficiently. Moreover, we extend coded FFT to settings including computing general $n$-dimensional Fourier transforms, and provide the optimal computing strategy for those settings.
DAS: Dynamic Adaptive Scheduling for Energy-Efficient Heterogeneous SoCs (2021)

Domain-specific systems-on-chip (DSSoCs) aim at bridging the gap between application-specific integrated circuits (ASICs) and general-purpose processors. Traditional operating system (OS) schedulers can undermine the potential of DSSoCs since their execution times can be orders of magnitude larger than the execution time of the task itself. To address this problem, we propose a dynamic adaptive scheduling (DAS) framework that combines the benefits of a fast (low-overhead) scheduler and a slow (sophisticated, high-performance but high-overhead) scheduler. Experiments with five real-world streaming applications show that DAS consistently outperforms both the fast and slow schedulers. For 40 different workloads, DAS achieves <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.29\times $ </tex-math></inline-formula> speedup and 45% lower EDP than the sophisticated scheduler at low data rates and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.28\times $ </tex-math></inline-formula> speedup and 37% lower EDP than the fast scheduler when the workload intensifies.
Hold and Sign: A Novel Behavioral Biometrics for Smartphone User Authentication (2016)

The search for new authentication methods to replace passwords for modern mobile devices such as smartphones and tablets has attracted a substantial amount of research in recent years. As a result, several new behavioral biometric schemes have been proposed. Most of these schemes, however, are uni-modal. This paper presents a new, bi-modal behavioral biometric solution for user authentication. The proposed mechanism takes into account micro-movements of a phone and movements of the user's finger during writing or signing on the touchscreen. More specifically, it profiles a user based on how he holds the phone and based on the characteristics of the points being pressed on the touchscreen, and not the produced signature image. We have implemented and evaluated our scheme on commercially available smartphones. Using Multilayer Perceptron (MLP) 1-class verifier, we achieved approx. 95% True Acceptance Rate (TAR) with 3.1% False Acceptance Rate (FAR) on a dataset of 30 volunteers. Preliminary results on usability show a positive opinion about our system.
Development of Baboon Preimplantation Embryos to Post-Implantation Stages In Vitro1 (1982)

Preimplantation baboon embryos were recovered nonsurgically and cultured in vitro to postimplantation stages. Most embryos (61/69) were cultured in CMRL-1066 medium supplemented with glutamine (1 mM), pyruvate (0.37 mM) and antibiotics; plus 20% heat-inactivated human cord serum (1-ICS) or fetal calf serum (FCS). Embryos were cultured in microtiter plate wells containing approximately 250 zl of medium in a gas atmosphere of 5% 02, depending upon the stage of development at recovery: and up to a 7-to 8-fold increase in size was achieved. These post-attachment embryos correspond in size and morphological appearance to 11-to 12-day (Stage Vc-VI) human and rhesus monkey embryos after fixation.
Display Considerations For Intravascular Ultrasonic Imaging (1989)

A display has been developed for intravascular ultrasonic imaging. Design of this display has a primary goal of providing guidance information for therapeutic interventions such as balloons, lasers, and atherectomy devices. Design considerations include catheter configuration, anatomy, acoustic properties of normal and diseased tissue, catheterization laboratory and operating room environment, acoustic and electrical safety, acoustic data sampling issues, and logistical support such as image measurement, storage and retrieval. Intravascular imaging is in an early stage of development so design flexibility and expandability are very important. The display which has been developed is capable of acquisition and display of grey scale images at rates varying from static B-scans to 30 frames per second. It stores images in a 640 X 480 X 8 bit format and is capable of black and white as well as color display in multiplevideo formats. The design is based on the industry standard PC-AT architecture and consists of two AT style circuit cards, one for high speed sampling and the other for scan conversion, graphics and video generation.
Protective Effects of AICAriboside in the Globally Ischemic Isolated Cat Heart (1985)

The effects of a purine precursor, AICAriboside (5-aminoimidazole-4-carboxamide riboside), on postischemic recovery of myocardial function and adenine nucleotides have been studied in the isolated blood-perfused cat heart. The isolated hearts received either AICAriboside or saline prior to 60 min of global ischemia and during 60 min of subsequent reperfusion. After 60 min of global ischemia and reperfusion, left ventricular function of the AICAriboside-treated hearts approached preischemic values, whereas contractile function of the saline-treated hearts remained depressed. At 60 min postischemia, recovery of left ventricular developed pressure (LVDP) was 62 +/- 10% for the saline-treated hearts as compared to 93 +/- 8% for the AICAriboside-treated hearts. Left ventricular compliance of the saline-treated hearts was decreased slightly at 60 min postischemia. In contrast, left ventricular compliance was increased in the isolated hearts which received AICAriboside. Myocardial ATP concentrations were decreased significantly at 60 min postischemia in both the saline-treated hearts and in the AICAriboside-treated hearts relative to nonischemic hearts. Similarly, total adenine nucleotides (TAN = ATP + ADP + AMP) were decreased significantly in both the saline-treated hearts and AICAriboside-treated hearts relative to nonischemic hearts. The present study demonstrates that AICAriboside protected globally ischemic hearts from the mechanical dysfunction associated with an ischemic insult but did not restore ATP or the total adenine nucleotide pool of the postischemic myocardium.
Expert Chording Text Entry on the Twiddler One-Handed Keyboard (2004)

Previously we demonstrated that after 400 minutes of practice, ten novices averaged over 26 words per minute (wpm) for text entry on the Twiddler one-handed chording keyboard, outperforming the multitap mobile text entry standard. We present a study that examines expert chording performance. Our five participants achieved an average rate of 47 wpm after approximately 25 hours of practice in varying conditions. One subject achieved a rate of 67 wpm, equivalent to the typing rate of the last author who has been a Twiddler user for ten years. We analyze the effects of learning on various aspects of chording, provide evidence that lack of visual feedback does not hinder expert typing speed and examine the potential use of multicharacter chords (MCCs) to increase text entry speed.
Fibronectin Binding Is Required for Acquisition of Mesenchymal/Endothelial Differentiation Potential in Human Circulating Monocytes (2012)

We previously reported monocyte-derived multipotential cells (MOMCs), which include progenitors capable of differentiating into a variety of mesenchymal cells and endothelial cells. In vitro generation of MOMCs from circulating CD14(+) monocytes requires their binding to extracellular matrix (ECM) protein and exposure to soluble factor(s) derived from circulating CD14(-) cells. Here, we investigated the molecular factors involved in MOMC generation by examining the binding of monocytes to ECM proteins. We found that MOMCs were obtained on the fibronectin, but not on type I collagen, laminin, or poly-L-lysine. MOMC generation was followed by changes in the expression profiles of transcription factors and was completely inhibited by either anti-α(5) integrin antibody or a synthetic peptide that competed with the RGD domain for the β(1)-integrin binding site. These results indicate that acquisition of the multidifferentiation potential by circulating monocytes depends on their binding to the RGD domain of fibronectin via cell-surface α(5)β(1) integrin.
Optimization of Natural Convection Field Using Adjoint Numerical Analysis (2004)

This paper presents an adjoint numerical analysis in natural convection heat transfer problems. To improve an objective function that indicates heat transfer characteristics such as temperature distribution or total heat transfer, we introduced adjoint variables into governing equations and applied the variational method. As a result, we obtain functional derivative of the objective function with respect to thermal boundary conditions. Using this functional derivative in the gradient-based method, we can decide distributed thermal boundary condition efficiently to improve or optimize the objective function.
Specificity of IgM and IgM Antibodies after Challenge with Antigenically Related Togaviruses (1974)

Abstract Rabbits were immunized with a group A or a group B togavirus and challenged 6 weeks later with a related togavirus from a different subgroup. IgG antibodies in antisera cross-reacted broadly at all times in hemagglutination-inhibition tests with group B viruses whereas within group A they were specific for the primary virus until challenge after which they reacted with both primary and challenge viruses. In contrast, IgM antibodies were clearly specific within both groups for the most recent immunizing virus; however, IgM memory was expressed when the challenge and primary viruses belonged to the same antigenic subgroup. The antigenic composition of both groups of togaviruses is discussed in relation to their envelope proteins, and hypotheses are proposed to account for the antibody specificities of the observed immunoglobulin responses.
Radiotherapy with 16 Gy may fail to eradicate testicular intraepithelial neoplasia: preliminary communication of a dose-reduction trial of the German Testicular Cancer Study Group (2003)

Low-dose radiotherapy to the testis is effective in eradicating testicular intraepithelial neoplasia (TIN, carcinoma in situ of the testis) at the risk of androgenic deficiency. The present trial was designed to define the lowest dose effective to control TIN assuming a dose-response relation of radiation-induced endocrinological damage. Patients with TIN in a solitary testicle or with bilateral TIN were treated with 18 Gy (14 patients) and 16 Gy (26 patients) (5 x 2 Gy per week). Biopsies to ascertain clearance of TIN were performed after 6 and 24 months. The median time of follow-up is 20.5 months. There were three adverse events. In one patient, relapse of TIN along with microinvasive seminoma was observed 2 years after 16 Gy irradiation. In two other patients, persistent spermatogonia were observed with the 16 and 18 Gy regimen after 6 and 24 months, respectively. All other post-treatment biopsies showed the Sertoli cell-only pattern. These results confirm that TIN is a radiosensitive lesion efficiently controlled in most cases with doses below 20 Gy. However, sporadic failures may occur. A dose of 16 Gy is probably unsafe and should no longer be used. Future investigations should not only focus on total dosage of irradiation but also on fractionation schedules.