gebhart/patrepeval huggingface dataset:
Freddies: DHT-Based Adaptive Query Processing via Federated Eddies (2003)

In response to the ever increasing scale, distribution, and complexity of data processing, database research in the past few years has focused on adaptive query processing. However, many of these solutions, although aimed at processing wide-area data, remain centralized solutions. In this paper, we present FREddies, an extension of the centralized Eddy operator for use in a P2P query processing system. FREddies operate within the framework of PIER, a DHT-based P2P query processor. FREddies optimize the query during runtime and require no global knowledge. We show that FREddies using rudimentary routing policies can perform competitively with a traditional static query optimization approach. Furthermore, we validate our simulation results in the real world environment of PlanetLab
Evaluation of Metal Oxide Thin-Film Electrolyte-Gated Field Effect Transistors for Glucose Monitoring in Small Volume of Body Analytes (2020)

Monitoringof chronic diseases such as diabetes without painful detection from blood enables people to improve their quality of life. Although various nanomaterials have remarkable characteristics that allow them to be used, the complexity of reliable fabrication is still challenging for their real applications. By using InGaZnO, simply deposited as thin-film structure, combined with electrolyte-gated field-effect transistors, highly sensitive sensing performance was demonstrated. The sensor characteristics were evaluated on the device level in various concentration of pH and glucose. It also exhibited good sensing capability in a high ionic solution over the screening effect with low interference among potential impediments for glucose. The sensing range and detection limit of device represent that sensing glucose in tear level could be practicable.
Solution Structure of Vanabin2, a Vanadium(IV)-Binding Protein from the Vanadium-Rich Ascidian Ascidia sydneiensis samea (2005)

Ascidians belonging to the suborder Phlebobranchia are known to accumulate high levels of a transition metal, vanadium, in their blood cells, called vanadocytes, although the mechanism for this biological phenomenon remains unclear. Recently, we identified vanadium(IV)-binding proteins, designated as Vanabins, from vanadium-accumulating ascidians. Here, we report the first 3D structure of Vanabin2 from an ascidian, Ascidia sydneiensis samea, in an aqueous solution. The structure revealed a novel bow-shaped conformation, with four alpha-helices connected by nine disulfide bonds. There are no structural homologues reported so far. The 15N heteronuclear single-quantum coherence (HSQC) perturbation experiments of Vanabin2 indicated that vanadyl cations, which are exclusively localized on the same face of the molecule, are coordinated by amine nitrogens derived from amino acid residues such as lysines, arginines, and histidines, as suggested by the electron paramagnetic resonance (EPR) results. The present NMR studies provide information that will contribute toward elucidating the mechanism of vanadium accumulation in ascidians.
Discrepancies and Error Evaluation Metrics for Machine Learning Interatomic Potentials (2023)

Machine learning interatomic potentials (MLPs) are a promising technique for atomic modeling. While high accuracy and small errors are widely reported for MLPs, an open concern is whether MLPs can accurately reproduce atomistic dynamics and related physical properties in their applications in molecular dynamics (MD) simulations. In this study, we examine the current state-of-the-art MLPs and uncover a number of discrepancies related to atom dynamics, defects, and rare events (REs), in their MD simulations compared to ab initio methods. Our findings reveal that low averaged errors by current MLP testing are insufficient, leading us to develop novel quantitative metrics that better indicate the accurate prediction of related properties by MLPs in MD simulations. The MLPs optimized by the RE-based evaluation metrics are demonstrated to have improved prediction in multiple properties. The identified errors, the developed evaluation metrics, and the proposed process of developing such metrics are general to MLPs, thus providing valuable guidance for future testing, development, and improvements of accurate, robust, and reliable MLPs for atomistic modeling.
Collecting Single-Phase Retrograde Gas Samples at Near-Dewpoint Reservoir Pressure in Carbonates Using a Pump-Out Formation Tester with an Oval Pad (2007)

Abstract Collecting representative, single-phase retrograde gas samples from heterogeneous fractured carbonate formations is challenging, especially for cases in which the reservoir pressure narrowly exceeds the dewpoint. Conventional wireline probe/packer assemblies are undesirable in this situation because their small diameter probes increase the pressure drawdown, compared to other available intake configurations. Furthermore, the likelihood of establishing hydraulic communication with an open fracture or vug is low with a ½-in. diameter probe, compared to setting straddle packers spanning a 1-m formation interval. The straddle packer intake geometry reduces the drawdown pressure required to establish flow, thus maintaining the flowing pressure above the dewpoint and preventing the onset of unwanted condensation. Inflatable straddle packers can be run with pump-out test tools, but they have temperature, pressure, and operational limitations. The new Oval Pad* design, an elongated oval-shaped probe/pad assembly, possesses many of the advantages of dual packers without their limitations. Like a straddle packer, the Oval Pad tool is effective when testing thinly laminated and tight formations as well as fractured or vuggy carbonates. The oval shape enables the pad to encompass a significant vertical length of the borehole while establishing a pressure seal with the formation. A retrograde gas reservoir is contained within the vuggy carbonates in the Jambi Merang area of South Sumatra. Here the reservoir pressure narrowly exceeds the dewpoint. Pressure must be maintained above the dewpoint during sampling operations to prevent unwanted phase separation. The RDT pump-out tester was fitted with Oval Pad and nitrogen-charged sample bottles to collect single-phase samples and to keep the phase intact until PVT properties can be analyzed in the laboratory. These samples were necessary to determine laboratory PVT properties and to define a production strategy. This paper presents the details and challenges of the successful collection of single-phase samples in this environment.
High strength and high electrical conductivity of UFG Al-2%Fe alloy achieved by high-pressure torsion and aging (2014)

In this study, Al-2%Fe samples extracted from a cast ingot in the shape of rings were processed by High-Pressure Torsion (HPT) at room temperature. Suitable specimens were extracted for evaluation of mechanical properties and electrical resistivity. High tensile strength of ~600 MPa was attained by HPT due to grain refinement down to an average grain size of ~130 nm and by subsequent aging accompanied by nano-sized (~10 nm) AhFe precipitates. The resulting conductivity (IACS%) was recovered from ~40% in the steady state after HPT to well above 50% in the peak-aged condition, which is in the range of current Al electrical alloys.
The contribution of deeper layers in slow sand filters to pathogens removal (2023)

Slow Sand Filtration is popular in drinking water treatment for the removal of a wide range of contaminants (e.g., particles, organic matter, and microorganisms). The Schmutzdecke in slow sand filters (SSFs) is known to be essential for pathogen removal, however, this layer is also responsible for increased head loss. Since the role of deeper layers in bacteria and virus removal is poorly understood, this research investigated the removal of E.coli WR1 and PhiX 174 at different depths of a full-scale SSF. Filter material from top (0-5 cm), middle (5-20 cm) and deep (20-35 cm) layers of an established filter was used in an innovative experimental set-up to differentiate physical-chemical and biological removal processes. In the analysis, we distinguished between removal by biological activity, biofilm and just sand. In addition, we modelled processes by a one-side kinetic model. The different layers contributed substantially to overall log removal of E.coli WR1 (1.4-1.7 log<sub>10</sub>) and PhiX 174 (0.4-0.6 log<sub>10</sub>). For E.coli WR1, biological activity caused major removal, followed by removal within biofilm and sand, whereas, removal of PhiX 174 mainly occurred within sand, followed by biofilm and biological activity. Narrow pore radii in the top layer obtained by micro-computed tomography scanner suggested enhanced retention of bacteria due to constrained transport. The retention rates of E.coli WR1 and PhiX 174 in top layer were four and five times higher than deeper layers, respectively (k<sub>ret</sub> 1.09 min<sup>-1</sup> vs 0.26 min<sup>-1</sup> for E.coli WR1 and k<sub>ret</sub> 0.32 min<sup>-1</sup> vs of 0.06 min<sup>-1</sup> for PhiX 174). While this higher rate was restricted to the Schmutzdecke alone (top 5 cm), the deeper layers extend to around 1 m in full-scale filters. Therefore, the contribution of deeper layers of established SSFs to the overall log removal of bacteria and viruses is much more substantial than the Schmutzdecke.
Superconducting magnet program for x ray lithography source at Brookhaven National Laboratory (1991)

DttRP.4:o develop a compact ekczon storage ring to be used as a X-Ray source for producing high density computer chips. The circumference of this machine is 8.5 meters, the machine lattice consists of four quadrupoles, two sexrupoles and a pair of air-core combined function 3.87 T&amp;amp;a superconducting dipoles. BNL is developing the superconducting dipoles in collaboration with its industrial partners GDSSD and GSED. This paper will describe the field characteristics and engineer-ing realization of these magaets and present the current status of the program. I. INTR0Dum0N Synchrotron based X-Ray Lithography is recognized as a promising method to pmduce large quantity of sub-a&amp;amp;ma size computer chips at an affordable cost. Brookhaven National Lbxatoty was funded in 1988 to develop a compact
Feasibility of single‐shot multi‐level multi‐angle diffusion tensor imaging of the human cervical spinal cord at 7T (2018)

Purpose Diffusion tensor imaging (DTI), which is frequently used to characterize microstructure impairments in many spinal cord diseases at clinical fields, may benefit from 7T investigations. Yet, it presents specific technical challenges, such as increased magnetic susceptibility‐induced image distortions. Methods Eight healthy volunteers were scanned at 7T using a prototype diffusion multi‐slice multi‐angle (MSMA) single‐shot spin‐echo echo planar imaging (EPI) sequence developed to explore the whole cervical spinal cord while limiting the partial volume effects related to the cord curvature. To mitigate the increased susceptibility‐induced distortions encountered at 7T, a reverse phase‐encoding strategy was also used. Images acquired from C1‐to‐C7 were registered to the AMU 40 template to automatically extract DTI metrics in gray matter/white matter regions of interest. Effects of inhomogeneities on the DTI metrics and repeatability of the measurements were also investigated. Lastly, a DTI acquisition with a 400‐µm in‐plane resolution was acquired on one volunteer to push forward 7T potentialities. Results The MSMA sequence allowed accessing to high‐resolution axial diffusion images sampling the whole cord within a single acquisition. DTI metrics were found in agreement with literature at lower field, stable along a 50–120% relative variation range, with a mean inter‐scan coefficient of variation of 8%. The two‐‐fold spatial‐resolution increase of the additional DTI acquisition enabled main white matter tracts visualization on a single‐subject basis. Conclusion Although C7‐level imaging needs some improvement, this preliminary study shows that transverse 7T DTI of the whole cervical spinal cord is feasible, laying the groundwork for improved multi‐parametric MR investigations and microstructure characterization of the spinal cord. Magn Reson Med 80:947–957, 2018. © 2018 International Society for Magnetic Resonance in Medicine.
<title>Design Techniques For WFOV High-Resolution Reflecting Optics</title> (1978)

1. Design techniques for all-reflecting optics from first-order layout through final design based on large optical design programs with interactive plotting are discussed. The design process is demonstrated for three different optical designs, each having a unique set of FOV, packaging, and resolution requirements.
Partial discharge characteristics in UHF-band of composite insulation system including various artificial defects in transformer (2008)

Experiments of partial discharge (PD) current pulse and phase resolved PD characteristics were performed using various artificial defects in oil/pressboard composite insulation system in oil-filled transformer. As artificial defects, we used barrier insulation model-in-oil, oil wedge model, air void model, floating electrode model, and oil gap model. As a result, it was found that the rise time, fall time, and pulse width of each PD current pulse differed depending on each model. Moreover, we confirmed the existence of PD-radiated electromagnetic wave with frequency UHF band for the defects. It was shown from these results that UHF method is applicable for detecting PD originating from the defects and identifying the defect types in oil-filled transformer.
Mixed two- and three-photon absorption in bulk rutile (TiO_2) around 800 nm (2012)

We observe mixed two- and three-photon absorption in bulk rutile (TiO2) around 800 nm using the open aperture Z-scan technique. We fit the data with an extended model that includes multiphoton absorption, beam quality, and ellipticity. The extracted two- and three-photon absorption coefficients are below 1 mm/GW and 2 mm3/GW2, respectively. We observe negligible two-photon absorption for 813-nm light polarized along the extraordinary axis. We measure the nonlinear index of refraction and obtain two-photon nonlinear figures of merit greater than 1.1 at 774 nm and greater than 12 at 813 nm. Similarly, we obtain three-photon figures of merit that allow operational intensities up to 0.57 GW/mm2. We conclude that rutile is a promising material for all-optical switching applications around 800 nm.
Crystallization and Vitrification Kinetics by Design: The Role of\n Chemical Bonding (2021)

Controlling a state of material between its crystalline and glassy phase has\nfostered many real-world applications. Nevertheless, design rules for\ncrystallization and vitrification kinetics still lack predictive power. Here,\nwe identify stoichiometry trends for these processes in phase change materials,\ni.e. along the GeTe-GeSe, GeTe-SnTe, and GeTe-Sb2Te3 pseudo-binary lines\nemploying a pump-probe laser setup and calorimetry. We discover a clear\nstoichiometry dependence of crystallization speed along a line connecting\nregions characterized by two fundamental bonding types, metallic and covalent\nbonding. Increasing covalency slows down crystallization by six orders of\nmagnitude and promotes vitrification. The stoichiometry dependence is\ncorrelated with material properties, such as the optical properties of the\ncrystalline phase and a bond indicator, the number of electrons shared between\nadjacent atoms. A quantum-chemical map explains these trends and provides a\nblueprint to design crystallization kinetics.\n
Six-Dimensional Correction of Intra-Fractional Prostate Motion with CyberKnife Stereotactic Body Radiation Therapy (2011)

Large fraction radiation therapy offers a shorter course of treatment and radiobiological advantages for prostate cancer treatment. The CyberKnife is an attractive technology for delivering large fraction doses based on the ability to deliver highly conformal radiation therapy to moving targets. In addition to intra-fractional translational motion (left-right, superior-inferior, and anterior-posterior), prostate rotation (pitch, roll, and yaw) can increase geographical miss risk. We describe our experience with six-dimensional (6D) intra-fraction prostate motion correction using CyberKnife stereotactic body radiation therapy (SBRT). Eighty-eight patients were treated by SBRT alone or with supplemental external radiation therapy. Trans-perineal placement of four gold fiducials within the prostate accommodated X-ray guided prostate localization and beam adjustment. Fiducial separation and non-overlapping positioning permitted the orthogonal imaging required for 6D tracking. Fiducial placement accuracy was assessed using the CyberKnife fiducial extraction algorithm. Acute toxicities were assessed using Common Toxicity Criteria v3. There were no Grade 3, or higher, complications and acute morbidity was minimal. Ninety-eight percent of patients completed treatment employing 6D prostate motion tracking with intra-fractional beam correction. Suboptimal fiducial placement limited treatment to 3D tracking in two patients. Our experience may guide others in performing 6D correction of prostate motion with CyberKnife SBRT.
Experiences in Implementing uHTS - Cutting Edge Technology Meets the Real World (2004)

Driven by growing corporate compound files, the demands of target biology, and attempts to cut cost, the number of solutions to HTS has spiralled. In quick succession new assay technologies and screening platforms are appearing on the market, with the promise of screening faster than ever in low volume high density formats whilst providing high quality data. Within this world of rapid change, Pfizer has applied cutting edge technology to HTS by introducing screening in 1 microl formats utilising single molecule detection technology. Instead of resource intensive in-house development, Pfizer entered into a collaboration with Evotec OAI / Evotec Technologies and introduced their Mark-II EVOscreen platform. In this article we will outline the benefits of the approach taken at Pfizer, Sandwich, and introduce the Mark-II EVOscreen platform, illustrating the potential but also possible pitfalls of HTS miniaturisation.
Screening Nylon-3 Polymers, a New Class of Cationic Amphiphiles, for siRNA Delivery (2014)

[Image: see text] Amphiphilic nucleic acid carriers have attracted strong interest. Three groups of nylon-3 copolymers (poly-β-peptides) possessing different cationic/hydrophobic content were evaluated as siRNA delivery agents in this study. Their ability to condense siRNA was determined in SYBR Gold assays. Their cytotoxicity was tested by MTT assays, their efficiency of delivering Alexa Fluor-488-labeled siRNA intracellularly in the presence and absence of uptake inhibitors was assessed by flow cytometry, and their transfection efficacies were studied by luciferase knockdown in a cell line stably expressing luciferase (H1299/Luc). Endosomal release was determined by confocal laser scanning microscopy and colocalization with lysotracker. All polymers efficiently condensed siRNA at nitrogen-to-phosphate (N/P) ratios of 5 or lower, as reflected in hydrodynamic diameters smaller than that at N/P 1. Although several formulations had negative zeta potentials at N/P 1, G2C and G2D polyplexes yielded >80% uptake in H1299/Luc cells, as determined by flow cytometry. Luciferase knockdown (20–65%) was observed after transfection with polyplexes made of the high molecular weight polymers that were the most hydrophobic. The ability of nylon-3 polymers to deliver siRNA intracellularly even at negative zeta potential implies that they mediate transport across cell membranes based on their amphiphilicity. The cellular uptake route was determined to strongly depend on the presence of cholesterol in the cell membrane. These polymers are, therefore, very promising for siRNA delivery at reduced surface charge and toxicity. Our study identified nylon-3 formulations at low N/P ratios for effective gene knockdown, indicating that nylon-3 polymers are a new, promising type of gene delivery agent.
Semi-Active Suspension Control on Bicycles: Anti-Dive during Road Excitation. (2019)

Suspension systems on bicycles have a tendency to severe brake-induced dive-in, caused by the small wheelbase in combination with a high center of gravity. Semi-active dampers allow the implementation of anti-dive functionality, preventing this behavior. Experimental analysis has shown that this yields significant advantages during brake control on level surfaces. In the presence of additional road excitation, however, a strong conflict arises. A specific test case is a bump occurring while braking, when the damping is set to the hardest value in order to mitigate dive-in. A simulative analysis illustrates that especially the dynamic wheel load is affected, which during braking is safety critical. By simulation and experimental implementation it is shown that using a simple semi-active control rule a decent trade-off can be found. Finally, the influence of the actuator response time is evaluated.
Eyedrops Containing SA9000 Prodrugs Result in Sustained Reductions in Intraocular Pressure in Rabbits (2009)

These data suggest that novel thiol donor adduction can improve the ocular bioavailability and tolerability of SA9000. SA9000-cysteine prodrugs may represent a new option for the topical treatment of glaucoma.
Allogeneic transplantation using CD34+ selected peripheral blood progenitor cells combined with non‐mobilized donor T cells for refractory severe aplastic anaemia (2017)

Allogeneic haematopoietic stem cell transplantation is curative for severe aplastic anaemia (SAA) unresponsive to immunosuppressive therapy. To reduce chronic graft-versus-host disease (GVHD), which occurs more frequently after peripheral blood stem cell (PBSC) transplantation compared to bone-marrow transplantation (BMT), and to prevent graft rejection, we developed a novel partial T-cell depleted transplant that infuses high numbers of granulocyte colony-stimulating factor-mobilized CD34<sup>+</sup> selected PBSCs combined with a BMT-equivalent dose of non-mobilized donor T-cells. Fifteen patients with refractory SAA received cyclophosphamide, anti-thymocyte globulin and fludarabine conditioning, and were transplanted with a median 8 × 10<sup>6</sup> CD34<sup>+</sup> cells/kg and 2 × 10<sup>7</sup> non-mobilized CD3<sup>+</sup> T-cells/kg from human leucocyte antigen-matched sibling donors. All achieved sustained engraftment with only two developing acute and two developing chronic GVHD. With a 3·5-year median follow-up, 86% of patients survived and were transfusion-independent. When compared to a retrospective cohort of 56 bone-marrow failure patients that received the identical transplant preparative regimen and GVHD prophylaxis with the exception that the allograft contained unmanipulated PBSCs, partial T-cell depleted transplant recipients had delayed donor T-cell chimerism and relative reduction of 75% in the incidence of acute grade II-IV GVHD (13% vs. 52%; P = 0·010) and of 82% in chronic GVHD (13% vs. 72%; P = 0·0004). In multivariate analysis, partial T-cell depleted transplants remained significantly associated with a reduced risk of GVHD. In conclusion, for patients with refractory SAA, this novel transplant strategy achieves excellent engraftment and survival when compared to unmanipulated PBSC transplants and dramatically reduces the incidence of both acute and chronic GVHD.