gebhart/patrepeval huggingface dataset:
Reawakening Retrocyclins: Ancestral Human Defensins Active Against HIV-1 (2009)

Human alpha and beta defensins contribute substantially to innate immune defenses against microbial and viral infections. Certain nonhuman primates also produce theta-defensins-18 residue cyclic peptides that act as HIV-1 entry inhibitors. Multiple human theta-defensin genes exist, but they harbor a premature termination codon that blocks translation. Consequently, the theta-defensins (retrocyclins) encoded within the human genome are not expressed as peptides. In vivo production of theta-defensins in rhesus macaques involves the post-translational ligation of two nonapeptides, each derived from a 12-residue "demidefensin" precursor. Neither the mechanism of this unique process nor its existence in human cells is known. To ascertain if human cells retained the ability to process demidefensins, we transfected human promyelocytic cells with plasmids containing repaired retrocyclin-like genes. The expected peptides were isolated, their sequences were verified by mass spectrometric analyses, and their anti-HIV-1 activity was confirmed in vitro. Our study reveals for the first time, to our knowledge, that human cells have the ability to make cyclic theta-defensins. Given this evidence that human cells could make theta-defensins, we attempted to restore endogenous expression of retrocyclin peptides. Since human theta-defensin genes are transcribed, we used aminoglycosides to read-through the premature termination codon found in the mRNA transcripts. This treatment induced the production of intact, bioactive retrocyclin-1 peptide by human epithelial cells and cervicovaginal tissues. The ability to reawaken retrocyclin genes from their 7 million years of slumber using aminoglycosides could provide a novel way to secure enhanced resistance to HIV-1 infection.
Power Line Communications (2010)

List of Contributors. Preface. List of Acronyms. 1 Introduction (The Editors). References. 2 Channel Characterization (P. Amirshahi, F. Canete, K. Dostert, S. Galli, M. Katayama and M. Kavehrad). 2.1 Introduction. 2.2 Channel Modeling Fundamentals. 2.3 Models for Outdoor Channels: LV Case. 2.4 Models for Outdoor Channels: MV Case. 2.5 Models for Indoor Channels. 2.6 Noise and Disturbances. 2.7 MeasuringTechniques. 2.8 PLC Channel EmulationTools. 2.9 Reference Channels for Access Domain. 3 Electromagnetic Compatibility (H. Hirsch and M. Koch). 3.1 Introduction. 3.2 Parameters for EMC Considerations. 3.3 Electromagnetic Emission. 3.4 Electromagnetic Susceptibility. 3.5 EMC Coordination. 3.6 EMC Regulationin Europe. 3.7 Final Remarks. 4 Coupling (P. A. Janse van Rensburg). 4.1 Introduction. 4.2 Filtering Basics. 4.3 Transformer-Capacitor Coupler Design. 4.4 Impedance Adaptation Concepts. 4.5 Experimental Verification. 4.6 Further Possibilities. 5 Digital Transmission Techniques (M. Ardakani, G. Colavolpe, K. Dostert, H. C. Ferreira, D. Fertonani, T. G. Swart, A. M. Tonello, D. Umehara and A. J. H. Vinck). 5.1 Introduction. 5.2 Modulation and Coding for Narrowband PLC Systems. 5.3 Modulation and Coding for Broadband PLC Systems. 5.4 Conclusion. 6 Protocols for PLC Systems (G. Bumiller, H. Hrasnica, L. Lampe, M. Lobashov and T. Stockhammer). 6.1 Introduction. 6.2 Broadband PLC Media Access Control Layer. 6.3 Protocols for PLC Supporting Energy Management Systems. 6.4 Internet Protocol Television Over PLC. 7 Industrial and International Standards on PLC-based Networking Technologies (Galli, M. Koch, H. A. Latchman, S. Lee and V. Oksman). 7.1 Introduction. 7.2 PLC Standardization by Industrial Alliances. 7.3 International Standards on PLC-Networking Technology. 7.4 ETSI and CENELEC Standards. 7.5 International EMC Product Standardization. 8 Systems and Implementations (I. Berganza Valmala, G. Bumiller, H. A. Latchman, M. V. Ribeiro, A. Sendin Escalona, E. R. Wade and L. W. Yonge). 8.1 Introduction. 8.2 PLC Smart Grid Systems. 8.3 PLC Broadband Access Systems. 8.4 Multimedia PLC Systems. 8.5 DC-PLC Systems. 8.6 PLC in Emerging Countries. 9 Conclusions (The Editors). Index.
The TRANSFAC system on gene expression regulation (2001)

The TRANSFAC database on transcription factors and their DNA-binding sites and profiles (http://www.gene-regulation.de/) has been quantitatively extended and supplemented by a number of modules. These modules give information about pathologically relevant mutations in regulatory regions and transcription factor genes (PathoDB), scaffold/matrix attached regions (S/MARt DB), signal transduction (TRANSPATH) and gene expression sources (CYTOMER). Altogether, these distinct database modules constitute the TRANSFAC system. They are accompanied by a number of program routines for identifying potential transcription factor binding sites or for localizing individual components in the regulatory network of a cell.
Efficacy and safety of a testosterone patch for the treatment of hypoactive sexual desire disorder in surgically menopausal women (2006)

In Brief Objective: Evaluation of the use of testosterone therapy for hypoactive sexual desire disorder (HSDD) after oophorectomy has mostly involved women treated with oral estrogen preparations. We investigated the efficacy and safety of a testosterone patch in surgically menopausal women receiving concurrent transdermal estrogen. Design: Women with HSDD after oophorectomy, for whom this was a concern, who were using transdermal estrogen, were recruited to a 24-week, randomized, double-blind, placebo-controlled trial in Europe and Australia. Patients were randomly allocated to placebo (n = 40) or testosterone 300 μg/day (n = 37) treatment. Primary endpoints were changes in sexual desire measured by the sexual desire domain of the Profile of Female Sexual Function and the frequency of satisfying sexual activity at 24 weeks. Results: Sixty-one women (79%) completed the trial. All subjects who received at least one application of study medication were included in analysis. The testosterone-treated group experienced a significantly greater change from baseline in the domain sexual desire score compared with placebo (change from baseline, 16.43 versus 5.98; P = 0.02). The domain scores for arousal, orgasm, decreased sexual concerns, responsiveness, and self-image as well as decreased distress were also significantly greater with testosterone therapy than placebo. The frequency of satisfactory sexual events increased but was not statistically different between treatment groups (P = 0.06) Adverse events occurred with similar frequency in both groups, and no serious risks of therapy were observed Conclusions: In this study, transdermal testosterone therapy via a skin patch improved sexual desire and other sexual function domains. It was well tolerated in these oophorectomized women with HSDD receiving concomitant transdermal estrogen. Published studies of testosterone therapy for surgically menopausal women have mostly involved concurrent oral estrogen therapy. In this trial, oophorectomized women with low sexual desire using transdermal estradiol therapy were treated with transdermal testosterone therapy or placebo. Testosterone therapy significantly improved sexual desire and other sexual function domains versus placebo and was well tolerated.
Underwater Ambient Noise. Proceedings of a Conference Held at SACLANTCEN on 11-14 May 1982. Volume 2. Unclassified Papers. Part 1 (1982)

Abstract : Contents: BACKGROUND--Role of propagation in ambient noise; MECHANISMS--Acoustic source characteristics of merchant ships; Flow-noise interference in measurements of infrasonic ambient noise; LOW-FREQUENCY PHENOMENA--Low-frequency seismic and hydroacoustic noise measurements in a fjord; Seismic and hydroacoustic sensing of infrasonic noise in coastal waters; MEASUREMENTS AND MEASUREMENT TECHNIQUES--Le programme Ulysse; Arctic ambient noise statistical measurement results and their implications to sonar performance improvements; Acoustic ambient noise in the Barents Sea; Depth dependence of directionality of ambient noise in the North Pacific: experimental data and equipment design; Ambient noise levels in the northeast Pacific ocean as measured by aircraft-dropped sonobuoys; PROCESSING TECHNIQUES--A real-time system for towed-array calibration and performance analysis, or how to get 50 dB sidelobes from a towed array; Notes on the interpretation of ambient noise statistics.
The Isopaque–Ficoll Method Re‐evaluated: Selective Loss of Autologous Rosette‐forming Lymphocytes during Isolation of Mononuclear Cells from Human Peripheral Blood (1980)

A subpopulation of lymphocytes is defined, which--under conditions used for isolating mononuclear cells from peripheral blood by the Isopaque-Ficoll gradient--is lost to the erythrocyte pellet because of rosette formation with the autologous erythrocytes in the gradient. Reapplication of the resuspended erythrocyte pellet on a new gradient with higher density could, however, recover the subpopulation. Lymphocyte surface marker analysis on such cells showed that they were enriched in T cells (judged by rosette formation with sheep erythrocytes) and in autorosette-forming cells. The importance of these findings is discussed in relation to the wide use of the Isopaque-Ficoll method.
Novel RNA Synthesis Method Using 5‘-O-Silyl-2‘-O-orthoester Protecting Groups (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNovel RNA Synthesis Method Using 5'-O-Silyl-2'-O-orthoester Protecting GroupsStephen A. Scaringe, Francine E. Wincott, and Marvin H. CaruthersView Author Information Dharmacon Research, Inc., Boulder, Colorado 80301 Ribozyme Pharmaceuticals, Inc., Boulder, Colorado 80301 University of Colorado, Boulder, Colorado 80309 Cite this: J. Am. Chem. Soc. 1998, 120, 45, 11820–11821Publication Date (Web):November 3, 1998Publication History Received5 March 1998Published online3 November 1998Published inissue 1 November 1998https://pubs.acs.org/doi/10.1021/ja980730vhttps://doi.org/10.1021/ja980730vrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views2594Altmetric-Citations204LEARN 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 SUBJECTS:Biopolymers,Genetics,High-performance liquid chromatography,Protective groups,Quality management Get e-Alerts
Error-Transparent Quantum Gates for Small Logical Qubit Architectures (2018)

One of the largest obstacles to building a quantum computer is gate error, where the physical evolution of the state of a qubit or group of qubits during a gate operation does not match the intended unitary transformation. Gate error stems from a combination of control errors and random single qubit errors from interaction with the environment. While great strides have been made in mitigating control errors, intrinsic qubit error remains a serious problem that limits gate fidelity in modern qubit architectures. Simultaneously, recent developments of small error-corrected logical qubit devices promise significant increases in logical state lifetime, but translating those improvements into increases in gate fidelity is a complex challenge. In this Letter, we construct protocols for gates on and between small logical qubit devices which inherit the parent device's tolerance to single qubit errors which occur at any time before or during the gate. We consider two such devices, a passive implementation of the three-qubit bit flip code, and the author's own [E. Kapit, Phys. Rev. Lett. 116, 150501 (2016)PRLTAO0031-900710.1103/PhysRevLett.116.150501] very small logical qubit (VSLQ) design, and propose error-tolerant gate sets for both. The effective logical gate error rate in these models displays superlinear error reduction with linear increases in single qubit lifetime, proving that passive error correction is capable of increasing gate fidelity. Using a standard phenomenological noise model for superconducting qubits, we demonstrate a realistic, universal one- and two-qubit gate set for the VSLQ, with error rates an order of magnitude lower than those for same-duration operations on single qubits or pairs of qubits. These developments further suggest that incorporating small logical qubits into a measurement based code could substantially improve code performance.
Remission in depression: definition and initial treatment approaches (2006)

Although remission is recognized as the optimal outcome of treatment for depression, remission lacks a universally accepted definition. This is partly due to the lack of objective biologic markers or tests that confirm a response to treatment and no well-defined end points of treatment. Significant symptoms may still exist even though patients may have a full response as measured by currently available standardized psychiatric rating scales. In addition, many patients may experience marked improvement in depressive symptoms but still have impaired psychosocial and work function. Wellness should be determined by evaluating a combination of three key domains: symptoms, functional status and pathophysiologic changes. In choosing an initial medication for depression, physicians are often guided by a mix of evidence-based medicine and unvalidated or even inaccurate clinical lore. In general, most available agents have comparable effectiveness; however, the subtype of depression and age of the patient should be considered.
ATP-dependent bile-salt transport in canalicular rat liver plasma-membrane vesicles (1992)

The present study identifies and characterizes a novel ATP-dependent bile-salt transport system in isolated canalicular rat liver plasma-membrane (cLPM) vesicles. ATP (1-5 mM) stimulated taurocholate uptake into cLPM vesicles between 6- and 8-fold above equilibrium uptake values (overshoot) and above values for incubations in the absence of ATP. The ATP-dependent portion of taurocholate uptake was 2-fold higher in the presence of equilibrated KNO3 as compared with potassium gluconate, indicating that the stimulatory effect of ATP was not due to the generation of an intravesicular positive membrane potential. Saturation kinetics revealed a very high affinity (Km approximately 2.1 microM) of the system for taurocholate. The system could only minimally be stimulated by nucleotides other than ATP. Furthermore, it was preferentially inhibited by conjugated univalent bile salts. Further strong inhibitory effects were observed with valinomycin, oligomycin, 4,4'-di-isothiocyano-2,2'-stilbene disulphonate, sulphobromophthalein, leukotriene C4 and N-ethylmaleimide, whereas nigericin, vanadate, GSH, GSSG and daunomycin exerted only weak inhibitory effects or none at all. These results indicate the presence of a high-affinity primary ATP-dependent bile-salt transport system in cLPM vesicles. This transport system might be regulated in vivo by the number of carriers present at the perspective transport site(s), which, in addition to the canalicular membrane, might also include pericanalicular membrane vesicles.
Improving Accuracy of the Kalman Filter Algorithm in Dynamic Conditions Using ANN-Based Learning Module (2019)

Prediction algorithms enable computers to learn from historical data in order to make accurate decisions about an uncertain future to maximize expected benefit or avoid potential loss. Conventional prediction algorithms are usually based on a trained model, which is learned from historical data. However, the problem with such prediction algorithms is their inability to adapt to dynamic scenarios and changing conditions. This paper presents a novel learning to prediction model to improve the performance of prediction algorithms under dynamic conditions. In the proposed model, a learning module is attached to the prediction algorithm, which acts as a supervisor to monitor and improve the performance of the prediction algorithm continuously by analyzing its output and considering external factors that may have an influence on its performance. To evaluate the effectiveness of the proposed learning to prediction model, we have developed the artificial neural network (ANN)-based learning module to improve the prediction accuracy of the Kalman filter algorithm as a case study. For experimental analysis, we consider a scenario where the Kalman filter algorithm is used to predict actual temperature from noisy sensor readings. the Kalman filter algorithm uses fixed process error covariance R, which is not suitable for dynamic situations where the error in sensor readings varies due to some external factors. In this study, we assume variable error in temperature sensor readings due to the changing humidity level. We have developed a learning module based on ANN to estimate the amount of error in current readings and to update R in the Kalman filter accordingly. Through experiments, we observed that the Kalman filter with the learning module performed better (4.41%–11.19%) than the conventional Kalman filter algorithm in terms of the root mean squared error metric.
Watch What You Just Said: Image Captioning with Text-Conditional Attention (2016)

Attention mechanisms have attracted considerable interest in image captioning due to its powerful performance. However, existing methods use only visual content as attention and whether textual context can improve attention in image captioning remains unsolved. To explore this problem, we propose a novel attention mechanism, called \textit{text-conditional attention}, which allows the caption generator to focus on certain image features given previously generated text. To obtain text-related image features for our attention model, we adopt the guiding Long Short-Term Memory (gLSTM) captioning architecture with CNN fine-tuning. Our proposed method allows joint learning of the image embedding, text embedding, text-conditional attention and language model with one network architecture in an end-to-end manner. We perform extensive experiments on the MS-COCO dataset. The experimental results show that our method outperforms state-of-the-art captioning methods on various quantitative metrics as well as in human evaluation, which supports the use of our text-conditional attention in image captioning.
Effects of Resveratrol on the Recovery of Muscle Mass Following Disuse in the Plantaris Muscle of Aged Rats (2013)

Aging is associated with poor skeletal muscle regenerative ability following extended periods of hospitalization and other forms of muscular disuse. Resveratrol (3,5,4'-trihydroxystilbene) is a natural phytoalexin which has been shown in skeletal muscle to improve oxidative stress levels in muscles of aged rats. As muscle disuse and reloading after disuse increases oxidative stress, we hypothesized that resveratrol supplementation would improve muscle regeneration after disuse. A total of thirty-six male Fisher 344 × Brown Norway rats (32 mo.) were treated with either a water vehicle or resveratrol via oral gavage. The animals received hindlimb suspension for 14 days. Thereafter, they were either sacrificed or allowed an additional 14 day period of cage ambulation during reloading. A total of six rats from the vehicle and the resveratrol treated groups were used for the hindlimb suspension and recovery protocols. Furthermore, two groups of 6 vehicle treated animals maintained normal ambulation throughout the experiment, and were used as control animals for the hindlimb suspension and reloading groups. The data show that resveratrol supplementation was unable to attenuate the decreases in plantaris muscle wet weight during hindlimb suspension but it improved muscle mass during reloading after hindlimb suspension. Although resveratrol did not prevent fiber atrophy during the period of disuse, it increased the fiber cross sectional area of type IIA and IIB fibers in response to reloading after hindlimb suspension. There was a modest enhancement of myogenic precursor cell proliferation in resveratrol-treated muscles after reloading, but this failed to reach statistical significance. The resveratrol-associated improvement in type II fiber size and muscle mass recovery after disuse may have been due to decreases in the abundance of pro-apoptotic proteins Bax, cleaved caspase 3 and cleaved caspase 9 in reloaded muscles. Resveratrol appears to have modest therapeutic benefits for improving muscle mass after disuse in aging.
Routing and wavelength assignment in all-optical networks (1995)

Considers routing connections in a reconfigurable optical network using WDM. Each connection between a pair of nodes in the network is assigned a path through the network and a wavelength on that path, such that connections whose paths share a common link in the network are assigned different wavelengths. The authors derive an upper bound on the carried traffic of connections (or equivalently, a lower bound on the blocking probability) for any routing and wavelength assignment (RWA) algorithm in such a network. The bound scales with the number of wavelengths and is achieved asymptotically (when a large number of wavelengths is available) by a fixed RWA algorithm. The bound can be used as a metric against which the performance of different RWA algorithms can be compared for networks of moderate size. The authors illustrate this by comparing the performance of a simple shortest-path RWA (SP-RWA) algorithm via simulation relative to the bound. They also derive a similar bound for optical networks using dynamic wavelength converters, which are equivalent to circuit-switched telephone networks, and compare the two cases. Finally, they quantify the amount of wavelength reuse achievable in large networks using the SP-RWA via simulation as a function of the number of wavelengths, number of edges, and number of nodes for randomly constructed networks as well as de Bruijn networks. They also quantify the difference in wavelength reuse between two different optical node architectures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Near Shannon limit performance of low density paritycheck codes (1997)

The authors report the empirical performance of Gallager&apos;s low density parity check codes on Gaussian channels. They show that performance substantially better than that of standard convolutional and concatenated codes can be achieved; indeed the performance is almost as close to the Shannon limit as that of turbo codes.