gebhart/patrepeval huggingface dataset:
Programming Protein Polymerization with DNA (2018)

A strategy that utilizes DNA for controlling the association pathway of proteins is described. This strategy uses sequence-specific DNA interactions to program energy barriers for polymerization, allowing for either step-growth or chain-growth pathways to be accessed. Two sets of mutant green fluorescent protein (mGFP)-DNA monomers with single DNA modifications have been synthesized and characterized. Depending on the deliberately controlled sequence and conformation of the appended DNA, these monomers can be polymerized through either a step-growth or chain-growth pathway. Cryo-electron microscopy with Volta phase plate technology enables the visualization of the distribution of the oligomer and polymer products, and even the small mGFP-DNA monomers. Whereas cyclic and linear polymer distributions were observed for the step-growth DNA design, in the case of the chain-growth system linear chains exclusively were observed, and a dependence of the chain length on the concentration of the initiator strand was noted. Importantly, the chain-growth system possesses a living character whereby chains can be extended with the addition of fresh monomer. This work represents an important and early example of mechanistic control over protein assembly, thereby establishing a robust methodology for synthesizing oligomeric and polymeric protein-based materials with exceptional control over architecture.
Effect of ibopamine on diuresis and arterial blood pressure in anesthetized rats and its interactions with dopaminergic and alpha- and beta-adrenergic antagonists. (1986)

The present paper reports a study of the effect of ibopamine (SB-7505), the 3,4-diisobutyryl ester of N-methyldopamine (epinine), on diuresis and blood pressure in anesthetized rats. The results obtained demonstrate that ibopamine, administered orally at doses of 12.5 to 200 mg/kg, caused a dose-dependent diuresis. The increase in blood pressure was moderate and of short duration. The diuretic effect of ibopamine was antagonized by d-sulpiride, haloperidol, bulbocapnine and phenoxybenzamine, but not by l-sulpiride and l-propranolol. The increase in blood pressure was antagonized by phenoxybenzamine only. The diuretic effect of ibopamine in rats reflects agonist activity at dopamine receptors and, in part, alpha-adrenoceptors and is independent of beta-adrenoceptors.
[Relationship between the decrease in urinary sex-dependent low molecular weight proteins by morphine and hormonal parameters in male rats]. (1983)

The relationship between the decrease in urinary sex-dependent low molecular weight proteins (LMWP), which exist only in the male rat, and the serum levels of some hormones were examined in this study. Castration of male rats reduced the urinary excretion of LMWP by about 50%. Replacement therapy with testosterone increased the urinary LMWP excretion. Adrenalectomy did not affect the urinary excretion of LMWP. In the adrenalectomized rat, however, corticosterone increased LMWP excretion. Therefore, it is considered that testosterone and corticosterone play a part in the urinary excretion of LMWP under physiological conditions and that the effect of testosterone is more specific than that of corticosterone. Serum concentration of testosterone and corticosterone tended to increase in comparison with the control on the 7th day after chronic treatment with morphine (0.5 mg/g food), when the urinary excretion of LMWP was significantly decreased. Furthermore, after rats were chronically administered morphine following castration or adrenalectomy, the urinary LMWP excretion was markedly decreased in the same way as found in intact animals. On the other hand, the serum thyroxine level of rats treated with morphine for 7 days was significantly lower than that of the control. Thyroxine increased dose-dependently the decreased urinary excretion of LMWP induced by morphine administration. These findings suggest that the decrease in urinary excretion of LMWP after chronic treatment with morphine may be caused by the change of serum thyroxine level via the action of morphine on the endocrine functions.
Multichannel Wavelength Multicasting for QAM Signals Free of Pump-Phase-Noise using Flexible Coherent Multi-Carrier Pump (2015)

We propose and demonstrate pump-phase-noise-free 2-to-7 multichannel wavelength multicasting for QAM signals using flexible coherent multi-carrier pump. &lt;0.4dB penalty is obtained after multicasting with the proposed scheme even using 3-MHz-linewidth DFB laser as pump source.
Do Low Rate DoS Attacks Affect QoS Sensitive VoIP Traffic? (2006)

The low rate TCP DoS (Shrew) and the reduction of quality (RoQ) attacks have been proved to be detrimental to the TCP traffic in the Internet. In this paper, we investigate the effect of these attacks on the QoS sensitive real time UDP traffic like VoIP. The stealthy RoQ attacks in particular are hard to detect as its periodicity is not well defined as compared to the shrew attack, and they can be launched even with the destination IP address spoofed! The attack potency formula is tailored for our work to observe the detrimental effect of the attack on the VoIP traffic. We study the effect of the attack flow on three QoS parameters of a VoIP flow, namely, the delay, the jitter, and the packet loss. We have performed extensive ns2 simulations under realistic scenarios to validate the effect of these attacks on the real time UDP traffic. Our results indicate that both these attacks are capable of driving a VoIP call from good to acceptable quality, i.e., reduction of quality, and from acceptable quality to complete denial of service. We believe that it is critical to investigate the characteristics of any attack in order to develop sound mitigation mechanisms; this work highlights one such characteristic of the low rate DoS attack.
333: Pathologic Findings at Cystectomy for Bladder Cancer: Lack of Stage Migration Over Time (2004)

You have accessJournal of UrologyDiscussed Poster, Sunday, May 9, 2004, 8:00 am - 12:00 pm1 Apr 2004333: Pathologic Findings at Cystectomy for Bladder Cancer: Lack of Stage Migration Over Time Adam W. Levinson, Joshua D. Sclar, Kate H. Kraft, Kevin P. Asher, Aaron E. Katz, Michael Wechsler, Erik T. Goluboff, Mitchell C. Benson, Carl A. Olsson, and James M. McKiernan Adam W. LevinsonAdam W. Levinson More articles by this author , Joshua D. SclarJoshua D. Sclar More articles by this author , Kate H. KraftKate H. Kraft More articles by this author , Kevin P. AsherKevin P. Asher More articles by this author , Aaron E. KatzAaron E. Katz More articles by this author , Michael WechslerMichael Wechsler More articles by this author , Erik T. GoluboffErik T. Goluboff More articles by this author , Mitchell C. BensonMitchell C. Benson More articles by this author , Carl A. OlssonCarl A. Olsson More articles by this author , and James M. McKiernanJames M. McKiernan More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)37595-5AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "333: Pathologic Findings at Cystectomy for Bladder Cancer: Lack of Stage Migration Over Time." The Journal of Urology, 171(4S), pp. 87–88 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 171Issue 4SApril 2004Page: 87-88 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Adam W. Levinson More articles by this author Joshua D. Sclar More articles by this author Kate H. Kraft More articles by this author Kevin P. Asher More articles by this author Aaron E. Katz More articles by this author Michael Wechsler More articles by this author Erik T. Goluboff More articles by this author Mitchell C. Benson More articles by this author Carl A. Olsson More articles by this author James M. McKiernan More articles by this author Expand All Advertisement PDF downloadLoading ...
A Method for Extracting Faces and Irises for Facial Caricaturing. (1997)

As the first step for developing the system that generates facial caricatures automatically, we developed a method of extracting the facial region and the irises. The facial region is extracted by a thresholding procedure in which the threshold is selected based on the degree of the coincidence between the outermost edges and the region boundary. Then, another type of thresholding is performed in the facial region, and the boundary of the binary image is detected. Next, using a Hough transform, a number of small circles are detected as candidates for the irises. On the basis of the geometrical relation between the left and right irises, a pair of circles are finally selected as irises. We experimented with 30 face images. The facial regions were successfully extracted for all of images and irises were successfully recognized for 29 images. It was found that the unsuccessful case could be recovered by a verification process.
Quantitative-Proteomic Comparison of Alpha and Beta Cells to Uncover Novel Targets for Lineage Reprogramming (2014)

Type-1 diabetes (T1D) is an autoimmune disease in which insulin-secreting pancreatic beta cells are destroyed by the immune system. An emerging strategy to regenerate beta-cell mass is through transdifferentiation of pancreatic alpha cells to beta cells. We previously reported two small molecules, BRD7389 and GW8510, that induce insulin expression in a mouse alpha cell line and provide a glimpse into potential intermediate cell states in beta-cell reprogramming from alpha cells. These small-molecule studies suggested that inhibition of kinases in particular may induce the expression of several beta-cell markers in alpha cells. To identify potential lineage reprogramming protein targets, we compared the transcriptome, proteome, and phosphoproteome of alpha cells, beta cells, and compound-treated alpha cells. Our phosphoproteomic analysis indicated that two kinases, BRSK1 and CAMKK2, exhibit decreased phosphorylation in beta cells compared to alpha cells, and in compound-treated alpha cells compared to DMSO-treated alpha cells. Knock-down of these kinases in alpha cells resulted in expression of key beta-cell markers. These results provide evidence that perturbation of the kinome may be important for lineage reprogramming of alpha cells to beta cells.
Purification and first characterization of the secreted and cellular 52-kDa proteins regulated by estrogens in human-breast cancer cells (1986)

An estrogen-regulated 52-kDa glycoprotein secreted by MCF7 breast cancer cells was first purified from serum-free conditioned medium by concanavalin-A--Sepharose (ConA--Sepharose). The 13% pure protein was then used to obtain monoclonal antibodies to the 52-kDa protein [Garcia et al. (1985) Cancer Res. 45, 709-716]. Using ConA--Sepharose and monoclonal antibody affinity chromatographies, the secreted 52-kDa protein was finally purified to homogeneity as verified by silver staining of sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) and one single N-terminal amino acid. The purification factor was approximately 1400 and the yield 40%. The same two-step procedure, applied to MCF7 cell extracts, yielded four immunologically related proteins of 52 kDa, 48 kDa, 34 kDa and 17 kDa, which were purified 1250-fold with a yield of 30%. These components were further separated by high-performance liquid chromatography gel filtration under denaturing conditions. The final products were homogeneous on the basis of silver-stained SDS-PAGE and gel filtration. However, isoelectrofocusing showed that the pI of the secreted 52-kDa protein and the cellular 34-kDa protein varied from 5.5 to 6.5. Amino acid analysis of the secreted and the related cellular 34-kDa protein is given. Western immunoblotting, pulse chase studies and post-translational studies indicate that the 52-kDa protein is the precursors of a lysosomal enzyme which is partially secreted and partially processed into smaller cellular forms.
Accurate resolution of the electron-phonon coupling maps of molecular semiconductors: towards high performing electronics through engineered reduced dynamic disorder (2018)

info:eu-repo/semantics/nonPublished
Geomechanics of Organic Matters Contained in Shales: A Molecular-Level Investigation (2022)

Petrophysical and mechanical properties of kerogen are difficult to obtain through conventional techniques due to length scale limitations. Characterization of kerogen requires the isolation of organic materials from the rock matrix, which is associated with a high probability of mechanical damage or chemical alteration of the properties. Alternatively, computational modeling and molecular representation of kerogens can be used to simulate the outcomes of the experimental work. Volumetric and thermodynamics modeling of kerogens has provided the means for recreating nanoscale structures virtually. This research implements existing three-dimensional (3D) kerogen macromolecules to form kerogen structures that can be analyzed for the mechanical behavior of type II organic matters, mainly found in shales, at different maturity levels. Additionally, the underlying factors that could control the mechanical behavior, such as the density and porosity, were investigated. The results are compared against those reported following a similar methodology or other advanced fine-scale experimental work. The results revealed an elastomer-like mechanical behavior of kerogen with comparable elastic moduli regardless of maturity level. Moreover, the mechanical behavior of kerogen was sensitive to the type of fluid contained within the structure. Such observations can help shed more light on the macroscopic mechanical properties of shales, especially for formations with high organic contents.
High-throughput screening of perovskite alloys for piezoelectric performance and thermodynamic stability (2014)

We screen a large chemical space of perovskite alloys for systems with optimal properties to accommodate a morphotropic phase boundary (MPB) in their composition-temperature phase diagram, a crucial feature for high piezoelectric performance. We start from alloy end points previously identified in a high-throughput computational search. An interpolation scheme is used to estimate the relative energies between different perovskite distortions for alloy compositions with a minimum of computational effort. Suggested alloys are further screened for thermodynamic stability. The screening identifies alloy systems already known to host an MPB and suggests a few others that may be promising candidates for future experiments. Our method of investigation may be extended to other perovskite systems, e.g., (oxy-)nitrides, and provides a useful methodology for any application of high-throughput screening of isovalent alloy systems.
Suppl. Figure S3 from ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma (2023)

&lt;p&gt;S3: Correlation between MEKi responsiveness and sensitivity to nNeocuproine&lt;/p&gt;
ChemInform Abstract: Xanthenes: Fluorone Derivatives. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Removal of sperm tail using trypsin and pre-activation of oocyte facilitates intracytoplasmic sperm injection in mice and rats (2022)

We examined various methods to enhance the accessibility of intracytoplasmic sperm injection (ICSI) technology to more users by making the technique easier, more efficient, and practical. First, the methods for artificially removing the mouse sperm tail were evaluated. Trypsin treatment was found to efficiently remove the sperm tails. The resultant sperm cells had a lower oocyte activation capacity; however, the use of activated oocytes resulted in the same fecundity as that of fresh, untreated sperm. Pre-activated oocytes were more resistant to physical damage, showed higher survival rates, and required less time per injection. Testing this method in rats yielded similar results, although the oocyte activation method was different. Remarkably, this method resulted in higher birth rates of rat progeny than with conventional methods of rat ICSI. Our method thereby streamlines mouse and rat ICSI, making it more accessible to laboratories across many disciplines.
(Invited) Graphene-Derived Materials for Electrochemical Energy Storage: An Overview (2013)

Abstract not Available.
Efficiency-constrained particle swarm optimization of a modified bernstein polynomial for conformal array excitation amplitude synthesis (2005)

As various enabling technologies advance, conformal phased arrays are finding more numerous applications. Because a conformal array is curved, new far field pattern behaviors emerge and many of the traditional linear and planar phased array synthesis methods are not valid. This paper starts by reviewing the equations for the far field of a curved phased array, and provides a generalized definition of aperture efficiency appropriate for conformal arrays. A modified Bernstein polynomial, defined with just five parameters, is introduced which provides a flexible method to specify a variety of smooth unimodal amplitude distributions that are shown to give good sidelobe levels and aperture efficiencies. By using particle swarm optimization of the modified Bernstein polynomial parameters constrained to provide a specified aperture efficiency, a family of aperture distributions and corresponding far field patterns is produced that allows aperture efficiency to be traded for sidelobe level.
Role of band 3 in regulating metabolic flux of red blood cells (2009)

Deoxygenation elevates glycolytic flux and lowers pentose phosphate pathway (PPP) activity in mammalian erythrocytes. The membrane anion transport protein (band 3 or AE1) is thought to facilitate this process by binding glycolytic enzymes (GEs) and inhibiting their activity in an oxygen-dependent manner. However, this regulatory mechanism has not been demonstrated under physiological conditions. In this study, we introduce a (1)H-(13)C NMR technique for measuring metabolic fluxes in intact cells. The role of band 3 in mediating the oxygenated/deoxygenated metabolic transition was examined by treating cells with pervanadate, a reagent that prevents the GE-band 3 complex from forming. We report that pervanadate suppresses oxygen-dependent changes in glycolytic and PPP fluxes. Moreover, these metabolic alterations were not attributable to modulation of bisphosphoglycerate mutase, direct inhibition of GEs by pervanadate, or oxidation, which are the major side effects of pervanadate treatment. These data provide direct evidence supporting the role of band 3 in mediating oxygen-regulated metabolic transitions.
Effect of overhearing transmissions on energy efficiency in dense sensor networks (2004)

Energy efficiency is an important design criterion for the development of sensor networking protocols involving data dissemination and gathering. In-network processing of sensor data, aggregation, transmission power control in radios, and periodic cycling of node wake-up schedules are some techniques that have been roposed in the sensor networking literature for achieving energy efficiency. Owing to the broadcast nature of the wireless channel many nodes in the vicinity of a sender node may overhear its packet transmissions even if they are not the intended reci ients of these transmissions. Reception of these transmissions can result in unnecessary expenditure of battery energy of the recipients. In this paper,we investigate the impact of overhearing transmissions on total energy costs during data gathering and dissemination and attempt to minimize them systematically.We model the minimum energy data gathering problem as a directed minimum energy spanning tree problem where the energy cost of each edge in the wireless connectivity graph is augmented by the overhearing cost of the corresponding transmission. We observe that in dense sensor networks, overhearing costs constitute a significant fraction of the total energy cost and that computing the minimum spanning tree on the augmented cost metric results in energy savings, especially in networks with non-uniform s atial node distribution. We also study the impact of this new metric on the well known energy-efficient dissemination (also called broadcasting) algorithms for multihop wireless networks.We show via simulation that through this augmented cost metric, gains in energy efficiency of 10%or more are ossible without additional hardware and minimal additional complexity.
Imaging functional anatomy in the brain of mouse models of human disease (2012)

Defects in axonal transport have been implicated in a number of neurodegenerative diseases, from the poly‐Q diseases like Huntingtonˈs disease, to Alzheimerˈs disease. The temporal sequence by which a pathological process unfolds is often unknown because our detection system relies on fixed tissue. Magnetic resonance imaging (MRI), a non‐destructive imaging modality, allows longitudinal studies inside opaque structures in live animals. We use manganese‐enhanced MRI (MEMRI) to witness axonal transport within the living brain of animal models of Alzheimerˈs disease. Mn2+ enters neurons and is transported by endogenous axonal transport. Thus MEMRI allows us for the first time to measure transport dynamics in the living brain. We find that in mice deleted for amyloid precursor protein (APP), a cargo‐receptor for transport whose product is the main component of senile plaques, transport of Mn2+ is decreased in the optic nerve and in the important memory circuit from hippocampus to forebrain. Older mice over‐expressing mutant APP also display decreased transport, demonstrating a bimodal effect of APP on transport dynamics. Using statistical parametric mapping of genotypic cohorts, sensitive quantitative measurements of transport are possible. Structural MRI also reveals volumetric changes over time. We conclude that MEMRI reveals pathological progression of disease processes in the living brain.
Distinguishing a planetary transit from false positives: a Transformer-based classification for planetary transit signals (2023)

ABSTRACT Current space-based missions, such as the Transiting Exoplanet Survey Satellite (TESS), provide a large database of light curves that must be analysed efficiently and systematically. In recent years, deep learning (DL) methods, particularly convolutional neural networks (CNN), have been used to classify transit signals of candidate exoplanets automatically. However, CNNs have some drawbacks; for example, they require many layers to capture dependencies on sequential data, such as light curves, making the network so large that it eventually becomes impractical. The self-attention mechanism is a DL technique that attempts to mimic the action of selectively focusing on some relevant things while ignoring others. Models, such as the Transformer architecture, were recently proposed for sequential data with successful results. Based on these successful models, we present a new architecture for the automatic classification of transit signals. Our proposed architecture is designed to capture the most significant features of a transit signal and stellar parameters through the self-attention mechanism. In addition to model prediction, we take advantage of attention map inspection, obtaining a more interpretable DL approach. Thus, we can identify the relevance of each element to differentiate a transit signal from false positives, simplifying the manual examination of candidates. We show that our architecture achieves competitive results concerning the CNNs applied for recognizing exoplanetary transit signals in data from the TESS telescope. Based on these results, we demonstrate that applying this state-of-the-art DL model to light curves can be a powerful technique for transit signal detection while offering a level of interpretability.