gebhart/patrepeval huggingface dataset:
Dynamic workflow composition using Markov decision processes (2004)

The advent of Web services has made automated workflow composition relevant to Web based applications. One technique, that has received some attention, for automatically composing workflows is AI-based classical planning. However, classical planning suffers from the paradox of first assuming deterministic behavior of Web services, then requiring the additional overhead of execution monitoring to recover from unexpected behavior of services. To address these concerns, we propose using Markov decision processes (MDPs), to model workflow composition. Our method models both, the inherent stochastic nature of Web services, and the dynamic nature of the environment. The resulting workflows are robust to nondeterministic behaviors of Web services and adaptive to a changing environment. Using an example scenario, we demonstrate our method and provide empirical results in its support.
Supplementary Figure 1 from Loss of Neural Cell Adhesion Molecule Induces Tumor Metastasis by Up-regulating Lymphangiogenesis (2023)

Supplementary Figure 1 from Loss of Neural Cell Adhesion Molecule Induces Tumor Metastasis by Up-regulating Lymphangiogenesis
A quadrature data-dependent DEM algorithm to improve image rejection of a complex ΣΔ modulator (2001)

A dynamic element matching (DEM) algorithm is presented that is controlled by the quadrature output data of a complex sigma-delta modulator. This DEM technique is used to correct the gain and phase errors between the circuits in the in-phase and quadrature-phase feedback paths of the modulator. The key feature of this DEM technique is that it does not cause leakage of high-frequency quantization noise in the signal band, as encounters with the periodic or pseudorandom DEM techniques. No test signal is required to measure the gain and phase errors, and as the DEM circuit is operating continuously, it compensates for changes in, e.g., temperature and supply voltage. A 0.35-/spl mu/m CMOS prototype chip has been designed to test the DEM circuit. A batch of 38 measured samples shows a typical mismatch-independent image rejection ratio of 63 dB with DEM.
Vehicle Lateral Control Under Fault in Front and/or Rear Sensors: Final Report (2004)

This report presents the research results of Task Order 4204(TO4204), "Vehicle Lateral Control under Fault in Front and/or Rear Sensors". This project is a continuing effort of the Partners for Advanced Transit and Highways (PATH) on the research of passenger vehicles for Automated Highway Systems (AHS).
Control Theory: a Foundational Technique for Self Managing Databases (2007)

Control theory is a well established discipline that has emerged from aeronautical, electrical, and mechanical engineering to provide a formal approach to building robust systems. While similar robustness concerns exist in database management systems, control theory is rarely used due to the lack of canonical control models and a dearth of control theory expertise among database researchers. We discuss our experience with using control theory to build self managing databases, showing experimental results, discussing pitfalls and limitations, and contrasting formal models against with feedback loops. While our experience indicates that control theory is a good paradigm for database self management, control theory should be used Judiciously since its techniques are not suited to all problems in database administration.
Molecular Features Underlying Selectivity in Chicken Bitter Taste Receptors (2018)

Chickens sense the bitter taste of structurally different molecules with merely three bitter taste receptors (<i>Gallus gallus</i> taste 2 receptors, ggTas2rs), representing a minimal case of bitter perception. Some bitter compounds like quinine, diphenidol and chlorpheniramine, activate all three ggTas2rs, while others selectively activate one or two of the receptors. We focus on bitter compounds with different selectivity profiles toward the three receptors, to shed light on the molecular recognition complexity in bitter taste. Using homology modeling and induced-fit docking simulations, we investigated the binding modes of ggTas2r agonists. Interestingly, promiscuous compounds are predicted to establish polar interactions with position 6.51 and hydrophobic interactions with positions 3.32 and 5.42 in all ggTas2rs; whereas certain residues are responsible for receptor selectivity. Lys<sup>3.29</sup> and Asn<sup>3.36</sup> are suggested as ggTas2r1-specificity-conferring residues; Gln<sup>6.55</sup> as ggTas2r2-specificity-conferring residue; Ser<sup>5.38</sup> and Gln<sup>7.42</sup> as ggTas2r7-specificity conferring residues. The selectivity profile of quinine analogs, quinidine, epiquinidine and ethylhydrocupreine, was then characterized by combining calcium-imaging experiments and <i>in silico</i> approaches. ggTas2r models were used to virtually screen BitterDB compounds. ~50% of compounds known to be bitter to human are likely to be bitter to chicken, with 25, 20, 37% predicted to be ggTas2r1, ggTas2r2, ggTas2r7 agonists, respectively. Predicted ggTas2rs agonists can be tested with <i>in vitro</i> and <i>in vivo</i> experiments, contributing to our understanding of bitter taste in chicken and, consequently, to the improvement of chicken feed.
Immunomagnetic Diffractometry for Detection of Diagnostic Serum Markers (2007)

We describe an integrated approach for detection of diagnostic markers using in situ assembled optical diffraction gratings in combination with immunomagnetic capture. Folate receptor (FR), a serum protein indicative of various cancers, was chosen as a model system to demonstrate the potential of the method. Magnetic beads coupled to FR antibody were used to capture FR from serum. The FR-bound magnetic beads self-assembled onto microcontact-printed folate-coupled BSA (F-BSA) patterns to form diffraction gratings which served to detect FR by measuring the diffraction intensities caused by laser illumination. The FR-containing beads, upon binding to the F-BSA surface, served as intrinsic signal enhancement agents, circumventing the need for additional enzymatic signal amplification or fluorescent labeling steps. With this approach, a detection sensitivity of 700 fM (20 pg/mL) was achieved. The potential use of this approach in clinical diagnostics was demonstrated by measuring FR concentration in blood samples obtained from cancer patients.
Two-photon-induced polymerization in a laser gain medium for optical microstructure (2003)

We have fabricated a polymeric solid-state microcavity in the laser gain media by a two-photon-induced polymerization technique. The photopolymerization resin contains conventional laser dye and dendrimer. A dendrimer can encapsulate the laser dye, and therefore increase its concentration up to 4 wt % with limited energy transfer during the photopolymerization process. The microcavity consisted of &amp;lt;0.4 μm linewidth polymerized strips arranged in layer-by-layer structure. The periodic variation in the refractive index gave rise to Bragg reflection. A laser emission was measured in the microcavity under optical excitation. The spectral linewidth was about 0.15 nm above the lasing threshold. The laser emission is attributed both to the distributed Bragg reflection and to the high gain of a polymeric medium containing laser dye with a high concentration.
Multi-section quantum dot superluminescent diodes for spectral shape engineering (2009)

The design and operating parameters of a novel multi-contact quantum dot superluminescent diode incorporating a number of features which inhibit lasing are described and compared with that of a single-contact device. Such devices allow the independent tuning of emission power and spectral shape; hence the penetration depth and resolution in optical coherence tomography are decoupled. The emission spectrum of a device utilising chirped quantum dots is shown to be tuned to produce a broadband single Gaussian emission, centred at the required wavelength of 1050 nm, at higher output powers than a single-contact device.
Molecular epidemiology of H5N1 avian influenza (2009)

The highly pathogenic Asian H5N1 influenza virus that was first detected in Guangdong in the People's Republic of China (China) in 1996 is unique in having spread to humans and other mammalian species. To date, this virus has not consistently transmitted between any mammalian species but the continued spread and evolution of these viruses in domestic poultry across Eurasia presents a continuing pandemic threat. These viruses have caused devastation in domestic poultry and have killed over 60% of infected humans. The H5N1 viruses are unique in having evolved into multiple clades and subclades by reassortment with other influenza viruses in the epicentre of southern China, and accumulation of point mutations has resulted in antigenic differences between the clades. Three waves of spread have occurred, wave one to East Asia and Southeast Asia, wave two through Qinghai Lake, China, to Europe, India and Africa, and wave three to Southeast Asia again. This paper deals with the molecular epidemiology of the evolution of the multiplicity of H5N1 clades. The continuing evolution of these H5N1 viruses and the possible establishment of secondary epicentres in Indonesia, Egypt and Nigeria present a continuing threat to poultry and people globally.
Computer-aided optimization of DC/DC converters for automotive applications (2002)

This paper investigates computer-aided optimization of DC/DC converters, with a focus on converters for dual-voltage automotive electrical systems. A new CAD optimization approach based on Monte Carlo search methods is introduced which allows the design space to be rapidly explored in an automated fashion and the most optimal designs and design approaches to be identified. The optimization approach also allows the effects of variations in design specifications on the cost, weight, and volume of an optimized converter to be readily determined.
Self-Nanoemulsifying Drug Delivery System Loaded with Psiadia punctulata Major Metabolites for Hypertensive Emergencies: Effect on Hemodynamics and Cardiac Conductance (2021)

Vasodilators are an important class of antihypertensive agents. However, they have limited clinical use due to the reflex tachycardia associated with their use which masks most of its antihypertensive effect and raises cardiac risk. Chemical investigation of <i>Psiadia punctulata</i> afforded five major methoxylated flavonoids (<b>1-5</b>) three of which (<b>1</b>, <b>4</b>, and <b>5</b>) showed vasodilator activity. Linoleic acid-based self-nanoemulsifying drug delivery system (SNEDDS) was utilized to develop intravenous (IV) formulations that contain compounds <b>1</b>, <b>4</b>, or <b>5</b>. The antihypertensive effect of the prepared SNEDDS formulations, loaded with each of the vasodilator compounds, was tested in the angiotensin-induced rat model of hypertension. Rats were subjected to real-time recording of blood hemodynamics and surface Electrocardiogram (ECG) while the pharmaceutical formulations were individually slowly injected in cumulative doses. Among the tested formulations, only that contains umuhengerin (<b>1</b>) and 5,3'-dihydroxy-6,7,4',5'-tetramethoxyflavone (<b>5</b>) showed potent antihypertensive effects. Low IV doses, from the prepared SNEDDS, containing either compound <b>1</b> or <b>5</b> showed a marked reduction in the elevated systolic blood pressure by 10 mmHg at 12 μg/kg and by more than 20 mmHg at 36 μg/kg. The developed SNEDDS formulation containing either compound <b>1</b> or <b>5</b> significantly reduced the elevated diastolic, pulse pressure, dicrotic notch pressure, and the systolic-dicrotic notch pressure difference. Moreover, both formulations decreased the ejection duration and increased the non-ejection duration while they did not affect the time to peak. Both formulations did not affect the AV conduction as appear from the lack of effect on <i>p</i> duration and PR intervals. Similarly, they did not affect the ventricular repolarization as no effect on QTc or JT interval. Both formulations decreased the R wave amplitude but increased the T wave amplitude. In conclusion, the careful selection of linoleic acid for the development of SNEDDS formulation rescues the vasodilating effect of <i>P. punctulata</i> compounds from being masked by the reflex tachycardia that is commonly associated with the decrease in peripheral resistance by most vasodilators. The prepared SNEDDS formulation could be suggested as an effective medication in the treatment of hypertensive emergencies, after clinical evaluation.
The Contractile Effect of Tachykinins on Human Prostatic Urethra: Involvement of NK-2 Receptors (1990)

The contractile response to natural tachykinins [substance P (SP), neurokinin A (NKA), arginin-neurokinin B (ArgNKB)] and to synthetic peptide [Pro9]SP sulfone, [beta Ala8]NKA(4-10) and [MePhe7]NKB, were investigated in the isolated smooth muscle from the human prostatic urethra. Natural tachykinins evoked concentration-related responses with the following order of potency: NKA----NKB--------SP. Among selective agonists [beta Ala8]NKA(4-10) produced concentration-related contractions, while [Pro9]SP sulfone and [MePhe7]NKB were inactive. These data indicate the presence of NK-2 receptors in the smooth muscle of the human prostatic urethra.
Supplementary Tables 1-3 and Supplementary Figures 1-4 from Genomic Profiling of Metastatic Uveal Melanoma and Clinical Results of a Phase I Study of the Protein Kinase C Inhibitor AEB071 (2023)

&lt;p&gt;Supplementary Table 1 shows the adverse events suspected to be study drug-related. Supplementary Table 2 shows the sequencing data availability by treatment group. Supplementary Table 3 shows the observed correlations between selected mutations/alterations. Supplementary Figure 1 shows the time on study for each patient. Supplementary Figure 2 shows the gene alterations ordered by chromosome and PFS. Supplementary Figure 3 shows gene alterations ordered by chromosome and percentage change from baseline. Supplementary Figure 4 shows Kaplan-Meier plot of PFS for patients with or without a GNAQ mutation.&lt;/p&gt;
Simulating large-scale airborne networks with ns-3 (2015)

Large-scale airborne networks, which connect airborne nodes with high-bandwidth communication links are being actively pursued commercially. We propose utilizing thousands of operational passenger and cargo aircraft as the principal components of an airborne network which could provide high-speed Internet to passengers on-board and on the ground. To simulate such a network we have augmented the ns-3 network simulator with a model for ingesting and processing aircraft position information, a steerable directional antenna model, a wireless point-to-point channel and associated net devices, and a distributed topology control application to manage the topology of the mesh network. We describe our implementation of these models and some tools for visualizing airborne networks. Using a simulation of a large airborne network, covering the United States, we perform experiments to evaluate the effectiveness of using the Optimized Link State Routing Protocol (OLSR) to route network traffic. Our simulations lead us to conclude that OLSR is likely not a good fit for our envisioned network.
Optimization of Current Excitation for Identification of Battery Electrochemical Parameters based on Analytic Sensitivity Expression (2020)

The quality of data plays an important role in determining the accuracy of battery parameter identification/estimation, and hence data optimization for estimation has received increasing attention lately. The main idea is to design input excitation that is most sensitive to the target parameter(s) under estimation. However, most existing studies are hampered by the complexity of sensitivity computation/optimization, and need to impose heuristic patterns on the input to facilitate the optimization. Consequently, they are not capable of finding the ultimate optimal input pattern, and explaining the underlying mechanism. This is especially the case for the parameters of the first-principle electrochemical battery model. This paper aims at performing direct optimization of input excitation with no imposed pattern to find the ultimate optimal profile for estimating battery electrochemical parameters. The practice is enabled by the analytic expressions of sensitivity derived in our previous work. Based on the optimization results, we will explore the features/patterns of optimal profiles for different parameters by correlating to the analytic sensitivity expressions.
Ultrastructural analysis of ribosomal gene transcription in vitro. (1980)

Xenopus laevis oocyte nuclei were manually isolated and incubated in vitro to synthesize RNA. Aliquots were removed before and during the reaction and prepared for electron microscopy, in order to observe the amplified ribosomal RNA (rRNA) genes. Before in vitro incubation the rRNA transcription units are covered with close-packed RNA polymerase molecules and attached rRNP fibers, which are interpreted to have initiated in vivo. With incubation, these close-packed transcription complexes move down the gene at a rate of 2.2 nucleotides per s. Behind this close-packed region we see RNA polymerase x nascent chain complexes at about one-fifth the in vivo frequency. These are interpreted to be in vitro initiation events. After 45 min of incubation, when most of the in vivo-initiated transcripts have terminated transcription, the in vitro-initiated transcripts define the same length transcription unit seen prior to incubation. These observations are consistent with correct in vitro initiation and termination by RNA polymerases on the endogenous amplified ribosomal DNA of Xenopus laevis.
Multi-Functional Reconfigurable Intelligent Surface (2023)

In this paper, we propose a new multi-functional reconfigurable intelligent surface (MF-RIS) architecture. Different from conventional RIS that only reflects signals, MF-RIS supports multiple functionalities on one surface, including reflection, transmission, amplification, and energy harvesting. As such, MF-RIS is capable of overcoming the double-fading attenuation and achieving full-space coverage by harvesting energy from the base station (BS). The physical implementation and the signal model of MF-RIS are introduced from the perspective of wireless communications. Then, we formulate a sum rate (SR) maximization problem in an MF-RIS-aided non-orthogonal multiple access network. By jointly optimizing the transmit strategy of the BS and the coefficient of the MF-RIS, we design an iterative algorithm to solve the formulated non-convex problem efficiently. Simulation results show that: i) MF-RIS provides up to 98.8% higher SR gain than self-sustainable RIS. ii) There exists a non-trivial trade-off between throughput improvement and self-sustainability, due to the limited number of RIS elements.
Exploiting interfacial water properties for desalination and purification applications. (2008)

A molecular-scale interpretation of interfacial processes is often downplayed in the analysis of traditional water treatment methods. However, such an approach is critical for the development of enhanced performance in traditional desalination and water treatments. Water confined between surfaces, within channels, or in pores is ubiquitous in technology and nature. Its physical and chemical properties in such environments are unpredictably different from bulk water. As a result, advances in water desalination and purification methods may be accomplished through an improved analysis of water behavior in these challenging environments using state-of-the-art microscopy, spectroscopy, experimental, and computational methods.
Combinatorial Techniques to Efficiently Investigate and Optimize Organic Thin Film Processing and Properties (2013)

In this article we present several developed and improved combinatorial techniques to optimize processing conditions and material properties of organic thin films. The combinatorial approach allows investigations of multi-variable dependencies and is the perfect tool to investigate organic thin films regarding their high performance purposes. In this context we develop and establish the reliable preparation of gradients of material composition, temperature, exposure, and immersion time. Furthermore we demonstrate the smart application of combinations of composition and processing gradients to create combinatorial libraries. First a binary combinatorial library is created by applying two gradients perpendicular to each other. A third gradient is carried out in very small areas and arranged matrix-like over the entire binary combinatorial library resulting in a ternary combinatorial library. Ternary combinatorial libraries allow identifying precise trends for the optimization of multi-variable dependent processes which is demonstrated on the lithographic patterning process. Here we verify conclusively the strong interaction and thus the interdependency of variables in the preparation and properties of complex organic thin film systems. The established gradient preparation techniques are not limited to lithographic patterning. It is possible to utilize and transfer the reported combinatorial techniques to other multi-variable dependent processes and to investigate and optimize thin film layers and devices for optical, electro-optical, and electronic applications.
Both ATP Sites of Human P-Glycoprotein Are Essential but Not Symmetric (1999)

Human P-glycoprotein (P-gp) is a cell surface drug efflux pump that contains two nucleotide binding domains (NBDs). Mutations were made in each of the Walker B consensus motifs of the NBDs at positions D555N and D1200N, thought to be involved in Mg(2+) binding. Although the mutant and wild-type P-gps were expressed equivalently at the cell surface and bound the drug analogue [(125)I]iodoarylazidoprazosin ([(125)I]IAAP) comparably, neither of the mutant proteins was able to transport fluorescent substrates nor had detectable basal nor drug-stimulated ATPase activities. The wild-type and D1200N P-gps were labeled comparably with [alpha-(32)P]-8-azido-ATP at a subsaturating concentration of 2.5 microM, whereas labeling of the D555N mutant was severely impaired. Mild trypsin digestion, to cleave the protein into two halves, demonstrated that the N-half of the wild-type and D1200N proteins was labeled preferentially with [alpha-(32)P]-8-azido-ATP. [alpha-(32)P]-8-Azido-ATP labeling at 4 degrees C was inhibited in a concentration-dependent manner by ATP with half-maximal inhibition at approximately 10-20 microM for the P-gp-D1200N mutant and wild-type P-gp. A chimeric protein containing two N-half NBDs was found to be functional for transport and was also asymmetric with respect to [alpha-(32)P]-8-azido-ATP labeling, suggesting that the context of the ATP site rather than its exact sequence is an important determinant for ATP binding. By use of [alpha-(32)P]-8-azido-ATP and vanadate trapping, it was determined that the C-half of wild-type P-gp was labeled preferentially under hydrolysis conditions; however, the N-half was still capable of being labeled with [alpha-(32)P]-8-azido-ATP. Neither mutant was labeled under vanadate trapping conditions, indicating loss of ATP hydrolysis activity in the mutants. In confirmation of the lack of ATP hydrolysis, no inhibition of [(125)I]IAAP labeling was observed in the mutants in the presence of vanadate. Taken together, these data suggest that the two NBDs are asymmetric and intimately linked and that a conformational change in the protein may occur upon ATP hydrolysis. Furthermore, these data are consistent with a model in which binding of ATP to one site affects ATP hydrolysis at the second site.