gebhart/patrepeval huggingface dataset:
Effects of Mutations in the G Tract of the Human Immunodeficiency Virus Type 1 Polypurine Tract on Virus Replication and RNase H Cleavage (2004)

The RNase H cleavages that generate and remove the polypurine tract (PPT) primer during retroviral reverse transcription must be specific in order to create a linear viral DNA that is suitable for integration. Lentiviruses contain a highly conserved sequence consisting of six guanine residues at the 3' end of the PPT (hereafter referred to as the G tract). We introduced mutations into the G tract of a human immunodeficiency virus type 1-based vector and determined the effects on the virus titer and RNase H cleavage specificity. Most mutations in the G tract had little or no effect on the virus titer. Mutations at the second and fifth positions of the G tract increased the proportion of two-long-terminal-repeat (2-LTR) circle junctions with one or two nucleotide insertions. The second and fifth positions of the G tract make specific contacts with amino acids in the RNase H domain that are important for RNase H cleavage specificity. These complementary data define protein-nucleic acid interactions that help control the specificity of RNase H cleavage. When the G-tract mutants were analyzed in a viral background that was deficient in integrase, in most cases the proportion of consensus 2-LTR circle junctions increased. However, in the case of a mutant with Ts at the second and fifth positions of the G tract, the proportion of 2-LTR circle junctions containing the one-nucleotide insertion increased, suggesting that linear viral DNAs containing an extra base are substrates for integration. This result is consistent with the idea that the 3' end-processing reactions of retroviral integrases may help to generate defined ends from a heterogenous population of linear viral DNAs.
Modeling of gain dynamics in erbium-doped fiber amplifiers (2002)

In summary, we have obtained a model of the time dependent gain of an Er-doped fiber amplifier (EDFA). Only one ordinary differential equation need be solved, which is much simpler than previous time dependent models which require solution of coupled partial differential equations. This model agrees with experimental data and can be very useful in the study of power transients in amplified optical networks.
Distinct hydrogen peroxide-induced constriction in multiple mouse arteries: potential influence of vascular polarization. (2008)

It is a matter of controversy whether the reactive oxygen species hydrogen peroxide (H(2)O(2)) contributes to tone in the vasculature as a vasodilator or vasoconstricting factor. To address this, we hypothesized that H(2)O(2) can constrict quiescent, non-preconstricted blood vessels, but that the contractile response may be different across various vessel beds. As this variable response may be related to the quiescent state of polarization, we further tested whether partial KCl depolarization would unmask or potentiate H(2)O(2)-induced constriction. We harvested thoracic and abdominal aorta, the carotid and superior mesenteric artery from mice and placed them in myograph systems to measure contractile responses. Under quiescent conditions without pre-contraction, we found that H(2)O(2)-contracted abdominal aorta with a peak of 21 +/- 4.9% of the reference constriction to 100 mMKCl (p < 0.05), the thoracic aorta contracted by 9.1 +/- 3.6% (p < 0.05), the carotid artery contracted by 5.1 +/- 1.9% (p < 0.05), but there was no contraction in the mesenteric artery at any concentration of H(2)O(2) tested in the quiescent state. If the quiescent vessels were then partially depolarized using 30 or 100 mMKCl, we found a significant potentiation of the contractile response to H(2)O(2) of 3-7 fold in each of the abdominal, thoracic and carotid vessels, and an unmasking of a significant (71 +/- 6.9%, p < 0.05) contractile response to H(2)O(2) in the mesenteric artery. Thus, we found large variations in the ability of H(2)O(2) to constrict these quiescent arteries, but partial KCl depolarization either significantly exaggerated the H(2)O(2)-induced constriction, or in the otherwise refractory mesenteric, revealed an H(2)O(2)-provoked vasoconstriction. Thus, H(2)O(2) is a vasoconstrictor in quiescent or partially depolarized vessels. We conclude that H(2)O(2) elicits distinct constrictor effects across different vascular beds, and this may be due to their underlying state of polarization.
Molecular Mechanisms Involved in the Angiotensin-(1-7)/Mas Signaling Pathway in Cardiomyocytes (2008)

Recently there has been growing evidence suggesting that beneficial effects of angiotensin-(1-7) [Ang-(1-7)] in the heart are mediated by its receptor Mas. However, the signaling pathways involved in these effects in cardiomyocytes are unknown. Here, we investigated the involvement of the Ang-(1-7)/Mas axis in NO generation and Ca(2+) handling in adult ventricular myocytes using a combination of molecular biology, intracellular Ca(2+) imaging, and confocal microscopy. Acute Ang-(1-7) treatment (10 nmol/L) leads to NO production and activates endothelial NO synthase and Akt in cardiomyocytes. Ang-(1-7)-dependent NO raise was abolished by pretreatment with A-779 (1 micromol/L). To confirm that Ang-(1-7) action is mediated by Mas, we used cardiomyocytes isolated from Mas-deficient mice. In Mas-deficient cardiomyocytes, Ang-(1-7) failed to increase NO levels. Moreover, Mas-ablation was accompanied by significant alterations in the proteins involved in the regulation of endothelial NO synthase activity, indicating that endothelial NO synthase and its binding partners are important effectors of the Mas-mediated pathway in cardiomyocytes. We then investigated the role of the Ang-(1-7)/Mas axis on Ca(2+) signaling. Cardiomyocytes treated with 10 nmol/L of Ang-(1-7) did not show changes in Ca(2+)-transient parameters such as peak Ca(2+) transients and kinetics of decay. Nevertheless, cardiomyocytes from Mas-deficient mice presented reduced peak and slower [Ca(2+)](i) transients when compared with wild-type cardiomyocytes. Lower Ca(2+) ATPase of the sarcoplasmic reticulum expression levels accompanied the reduced Ca(2+) transient in Mas-deficient cardiomyocytes. Therefore, chronic Mas-deficiency leads to impaired Ca(2+) handling in cardiomyocytes. Collectively, these observations reveal a key role for the Ang-(1-7)/Mas axis as a modulator of cardiomyocyte function.
Combining Hybrid Input-Output Automaton and Game Theory for Security Modeling of Cyber-Physical Systems (2020)

We consider a security setting in which the Cyber-Physical System (CPS) is composed of subnetworks where each subnetwork is under ownership of one defender. Such CPS can be represented by an attack graph where the defenders are required to invest (subject to a budget constraint) on the graph's edges in order to protect their critical assets (where each defender's critical asset has a certain value to the defender if compromised). We model such CPS using Hybrid Input-Output Automaton (HIOA) where each subnetwork is represented by a HIOA module. We first establish the building blocks needed in our setting. We then present our model that characterizes the continuous time evolution of the investments and discrete transitions between different states (where each state represents different condition and/or perturbation) within the system. Finally, we provide a real-world CPS example to validate our modeling.
Low-temperature deposition of silicon dioxide films from electron cyclotron resonant microwave plasmas (1989)

Silicon dioxide films were deposited on crystalline silicon substrates by electron cyclotron resonant (ECR) microwave plasma-enhanced chemical vapor deposition (PECVD). Films were grown on Si〈100〉 substrates at temperatures of 140–600 °C, flow rates of 0.5–10 sccm SiH4, 10–30 sccm O2, and at a pressure of 10−3 Torr. Infrared absorption spectroscopy of the samples indicated no detectable SiH, OH, or SiOH groups. Neither an afterglow chemistry nor He dilution was required to eliminate H impurities as was previously reported for silicon oxide films deposited from rf plasmas. This suggests that significant differences exist between rf and ECR microwave plasma chemistries. We have found that the stoichiometry and index of refraction was not sensitive to oxidant ratio for a wide range of conditions in contrast to other studies. Stoichiometric SiO2 films, with good physical properties, were grown for a much wider range of oxidant ratios relative to those which are characteristic of the rf PECVD technique. In addition, films grown under optimal conditions had infrared absorption spectra nearly identical to those of thermally grown oxides and index of refraction of 1.456, as measured by ellipsometry. We concluded that by using an ECR microwave plasma, SiO2 films with optical and bonding properties comparable to oxides thermally grown at 1000 °C in dry oxygen can be deposited at a low temperature (350 °C) and a low pressure (10−3 Torr) in a O2/SiH4 reactant gas mixture without the need for a carrier gas.
Left Cardiac Sympathetic Denervation Monotherapy in Patients With Congenital Long QT Syndrome (2020)

LCSD may be a safe and effective stand-alone therapy for select patients who do not tolerate beta-blockers. However, LCSD is not curative and patient selection will be critical when potentially considering LCSD as monotherapy.
Donor−Acceptor‐Functionalized Subphthalocyanines for Dye‐Sensitized Solar Cells (2018)

Abstract Boron subphthalocyanines (SubPcs) are attractive as light harvesting materials in photovoltaic devices. Here we present the synthesis, optical and electrochemical properties, and device performances of a series of donor−acceptor‐functionalized SubPc derivatives incorporating a carboxylic acid for anchoring onto TiO 2 . Liquid‐ and solid‐state dye‐sensitized solar cells (DSCs) were prepared from three compounds, and a triad system consisting of two aniline donor moieties and a benzothiadiazole acceptor moiety was found to exhibit the highest power conversion efficiency (PCE) in the series (PCE=1.54 %; solid‐state device). The compounds were prepared by stepwise acetylenic coupling reactions. In addition, we present the synthesis and optical properties of a SubPc derivative incorporating three anilino‐substituted 1,1,4,4‐tetracyanobutadiene units, prepared by the [2+2] cycloaddition between three ethynyl units at the SubPc periphery and three tetracyanoethylene molecules followed by electrocyclic ring‐opening reactions.
Muller Cell Reactivity and Photoreceptor Cell Death Are Reduced after Experimental Retinal Detachment Using an Inhibitor of the Akt/mTOR Pathway (2009)

Palomid 529 is an effective suppressor of Müller cell proliferation, glial scar formation, and photoreceptor cell death in a rabbit model of RD. This suggests that inhibiting the Akt/mTOR signal transduction pathway may be an effective strategy to decrease proliferation and photoreceptor cell death induced by detachment and perhaps represents a novel therapy for related human diseases such as proliferative vitreoretinopathy.
A Machine Learning Framework for Physics-Based Multi-Fidelity Modeling and Health Monitoring for a Composite Wing (2022)

Abstract Computational mechanics is a useful tool in the structural health monitoring community for accurately predicting the mechanical performance of various components. However, high-fidelity models simulated through the finite element analysis (FEA) necessitate a large amount of computing power. This paper presents a new approach to develop a multi-fidelity model using artificial neural networks for health monitoring purposes. The proposed framework provides significant savings in computational time compared to a model trained only using high-fidelity data, while maintaining an acceptable level of accuracy. The analysis is conducted using two finite element models, of different fidelity, of an unmanned aerial vehicle (UAV) wing, with damage modeled at six locations, and varying severity. The damage is modeled by changing the stiffness properties of the materials at these locations. The algorithm developed aims at minimizing the number of high-fidelity data points for correcting the outputs of the low-fidelity model. It was observed that the low-fidelity model requires 8 high-fidelity data points to meet the desired error tolerance. This corrected low-fidelity model is then used for locating and quantifying the damage given the strains and frequency by expanding the previously trained network to output damage diagnosis results. The model with applied correction is able to locate the damage with an accuracy of ∼ 94% and quantify the damage with an accuracy of 93%. The performance of the corrected low-fidelity model is compared with a network trained only with high-fidelity datasets and it was observed that the corrected model requires 54% fewer data points as compared to the high-fidelity trained network.
Phase I study of high-dose busulfan, melphalan and thiotepa with autologous stem cell support in patients with refractory malignancies. (1994)

The purpose of this study was to determine the maximal tolerated dose of thiotepa administered with busulfan 12 mg/kg and melphalan 100 mg/m2 followed by autologous stem cell transplantation in patients with refractory malignancies. Twenty-eight patients with refractory malignancies received high-dose busulfan 12 mg/kg, melphalan 100 mg/m2 and escalating doses of thiotepa 450-550 mg/m2 followed by infusion of cryopreserved autologous peripheral blood stem cells (n = 26) or marrow (n = 2). The maximum tolerated dose was determined to be busulfan 12 mg/kg, melphalan 100 mg/m2 and thiotepa 500 mg/m2. Two of three patients receiving thiotepa 550 mg/m2 experienced grade 3 colitis. Twenty patients were enrolled at the maximum tolerated dose and the incidence of grade 3-4 regimen-related toxicity and mortality was 10% and 5%, respectively. Ninety-five per cent of patients experienced grade 1-2 mucositis, 50% grade 1-2 gastrointestinal toxicity, 35% grade I hepatic toxicity and 20% experienced grade 1-2 skin toxicity. The median time to achieve a granulocyte count of 0.5 x 10(9)/I was 10 days (range 8-20 days) and platelet transfusion independence was 10 days (range 1-26 days). Five of ten patients with stage 4 refractory breast cancer achieved a complete and two a partial remission with a complete response rate of 50% and a overall response rate of 70%. In conclusion, busulfan, melphalan and thiotepa can be administered in high doses with tolerable mucositis as the major side-effect. This combination has significant activity in patients with breast cancer, and phase II studies in patients with breast cancer and other chemotherapy sensitive malignancies are warranted.
Correction: Au@UiO-66: a base free oxidation catalyst (2015)

Correction for ‘Au@UiO-66: a base free oxidation catalyst’ by K. Leus <italic>et al.</italic>, <italic>RSC Adv.</italic>, 2015, <bold>5</bold>, 22334–22342.
The interaction between renin-angiotensin system and sympathetic nervous system in the peripheral vasculature of normal Sprague-Dawley rats (2011)

To evaluate possible interactions between the renin-angiotensin system (RAS) and the sympathetic nervous system (SNS) in the systemic circulation upon the intravenous administration of angiotensin II and a set of adrenergic agonists in normal Sprague-Dawley (SD) rats. Rats were treated with carvedilol, a non-selective \beta- and selective \alpha_1-adrenoceptor blocker, in a dose of (5 mg/kg) orally for 7 days, and on day 8, the animals were pentobarbitone-anaesthetized and prepared for systemic hemodynamic study. Dose-response relationships in terms of elevation in the magnitude of the mean arterial blood pressure in response to intravenous injection of noradrenaline (NA), phenylephrine (PE), methoxamine (ME), and angiotensin II (Ang II) were determined. Data, mean ± S.E.M., were subjected to ANOVA with significance at P < 0.05. Carvedilol blunted the peripheral vascular response to NA, PE, ME, and Ang II (all P < 0.05). It is concluded that peripheral vasoconstriction induced by Ang II is contributed to by adrenergic action. Furthermore, there is a cross-talk relationship between RAS and SNS in determining the responsiveness of the peripheral vasculature to adrenergic agonists and angiotensin II in normal rats.
Electrophysiology and Hemodynamics of Open Chest Resuscitation from Cardiac Arrest in a Swine (2008)

Our laboratory employs a swine model of prolonged ventricular fibrillation (VF). This model simulates out-of-hospital cardiac arrest and resuscitation coupled with a realistic emergency medical services response time. To demonstrate some of the key phenomena that we observe during cardiac arrest, we filmed a complete procedure from induction of arrest to return of spontaneous circulation. We then paired the video footage with real-time data traces, including electrocardiogram (ECG) and arterial, venous, and coronary perfusion pressures. A quantitative measure of VF ECG waveform organization, the scaling exponent, was calculated from the ECG trace and also paired with the video footage (available as supporting information in the online version of this paper). A 25-kg female swine was sedated, anesthetized, intubated, and paralyzed. Pressure transducers were placed in the right atrium and aorta via femoral cutdown. Cardiac rhythm was monitored with Lead II ECG. Coronary perfusion pressure was calculated as the difference between aortic and right atrial pressures. All pressure and ECG data were recorded with an electronic data recording system. The chest was opened (Figure 1), and the pericardium was removed. Cardiac arrest was induced with a 3-second, 100-mA shock to the chest. The animal remained in untreated VF for 8 minutes, followed by manual compressions, advanced cardiac life support (ACLS) drug administration, and defibrillation. Exposed heart oriented with apex on the left, paired with ECG and scaling exponent (lower right of ECG). During untreated cardiac arrest, a clear relationship between the fibrillating activity of the myocardium and the organization of the ECG waveform was apparent over the course of 8 minutes. During the resuscitation phase, the administration of manual compressions and ACLS drugs resulted in a substantial increase in coronary perfusion pressure over time and subsequent increases in myocardial activity and ECG organization. Video Clip S1. Electrophysiology and hemodynamics of open chest resuscitation from cardiac arrest. Please note: Wiley Periodicals Inc. are not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Correction: The potential of paper-based diagnostics to meet the ASSURED criteria (2018)

[This corrects the article DOI: 10.1039/C8RA06132G.].
Dynamic Positioning System as Dynamic Energy Storage on Diesel-Electric Ships (2014)

A dynamic positioning (DP) system on a diesel-electric ship applies electric power to keep the positioning and heading of the ship subject to dynamic disturbances due to the winds, waves and other external forces using electric thrusters. Vice versa, position and heading errors can be allowed in order to implement energy storage in the kinetic and potential energy of the ship motion using the DP control system to convert between mechanical and electrical power. New simple formulas are derived in order to relate the dynamic energy storage capacity to the maximum allowed ship position deviation, as a function of the frequency of the requested dynamic energy storage. The benefits of DP dynamic energy storage are found to be reduced diesel-generator maintenance need, reduced fuel consumption and emissions, reduced risk for blackout, and increased operational flexibility allowing power-consuming operations such as drilling and lifting to be safely prioritized over DP for short periods of time.
Performance and implications of semantic indexing in a distributed environment (1999)

A research prototype is presented for semantic indexing and retrieval in Information Retrieval. The prototype is motivated by a desire to provide a more efficient and effective information retrieval system compared to the current state of the art. An overview of the Interspace architecture layers is discussed. An object model supporting semantic operations is developed. The model contains a rich set of classes and relationships of the data for the semantic indexing module. The basis of our semantic indexing is done by the creation of concept space. A concept space is an index of a collection that uses document statistics to capture the relationships between concepts. It is useful for boosting text search, by term suggestion of alternative terms semantically related to query terms. Over the years, we have developed generic technology for concept spaces computation on large collections across many subjects. Recent computations on discipline-scale collections have been made on high-end supercomputers. This paper describes our implementation and implications of the computation in a distributed computing environment. Experimental results using different collection sizes and number of processes are presented to show the feasibility of this approach. We also show that laboratory and community collections are already easily computable using a group of PCs in a lab via a message-passing model. We conclude that PC clusters will shortly be able to compute semantic indexes for any real collections.
Supplementary Figure S1 from Biomarker Associations with Efficacy of Abiraterone Acetate and Exemestane in Postmenopausal Patients with Estrogen Receptor–Positive Metastatic Breast Cancer (2023)

&lt;p&gt;Supplementary Figure S1. Comparison of associations of the negative expression of androgen receptor (AR) (&lt; 10%) with progression-free survival (PFS).&lt;/p&gt;
Experimental study of molecular entanglement in polymer networks (1994)

Abstract Elastomeric molecular networks have been prepared by endlinking polydimethyl siloxane molecules having functional chain ends, both in the presence of an unreactive polymeric diluent and in the undiluted state. Values of tensile (Young) modulus were found to be in good agreement with the simple molecular theory of rubberlike elasticity for networks prepared in a highly diluted state. For concentrated systems the modulus was anomalously high, however. The discrepancy can be attributed to chain entanglements. A second interpenetrating network was introduced into networks formed in the diluted state by replacing the diluent polymer by reactive polymer, which was then gelled in situ. The modulus of these combined networks was much higher than the sum of the moduli of the constituent networks, implying a large contribution from molecular entanglements. © 1994 John Wiley &amp; Sons, Inc.
Continuous wave terahertz wave spectrometer based on diode laser pumping: Potential applications in high resolution spectroscopy (2009)

We constructed a high resolution terahertz (THz) spectroscopic system with an automatic scanning control using a continuous wave (cw) THz wave generator based on difference frequency generation method by excitation of phonon-polariton mode in GaP. The pump and signals lasers were compact, tunable external cavity laser, and distributed feedback (DFB) lasers, respectively. The generated THz waves were tuned automatically by changing the temperature of the DFB laser using a system control. We present the water vapor transmission characteristics of the THz wave and also absorption spectrum of a white polyethylene in the frequency range of 1.97-2.45 THz. The spectroscopic measurements performed at an output power level of 2 nW, which was obtained with a 15-mm-long GaP crystal at 2 THz. The advantage of this cw THz spectrometer is wide frequency tuning range (0.7-4.42 THz) with an estimated linewidth of full width at quarter maximum <8 MHz and this system has a potential application in high resolution spectroscopy.