gebhart/patrepeval huggingface dataset:
Increased expression of p53 protein in human leukemia cells. (1986)

We examined synthesis of the cellular phosphoprotein p53 in fresh bone marrow or peripheral blood cells from normal donors and from patients with leukemia, preleukemia, or other hematopoietic disorders. Lysates of cells labeled with [35S]methionine were immunoprecipitated with monoclonal antibodies to p53, and the immunoprecipitates were analyzed by NaDodSO4/polyacrylamide gel electrophoresis and autoradiography. Bone marrow or peripheral blood cells from 8 of 33 patients with hematopoietic disorders showed increased p53, seven of the eight occurring in cells of patients with preleukemia or acute myelogenous leukemia. Increased p53 synthesis was not associated with p53 gene amplification, as shown by Southern blot analysis. Synthesis of p53 was not increased in any of nine normal human bone marrow samples or eight normal human peripheral blood granulocyte, macrophage, and lymphocyte samples. The hematopoietic cells of patients in remission or with chronic forms of leukemia did not generally synthesize elevated levels of p53. In addition, we found negligible p53 mRNA and protein expression in a variety of human myeloid leukemia lines blocked at different stages of differentiation. Southern blot analysis showed that, except for the HL-60 cells, the p53 gene of the myeloid cell lines was intact. In view of recent evidence implicating p53 in transformation of cultured cells, our results using fresh leukemia cells suggest that p53 may contribute to the phenotype of certain leukemias in vivo.
Tuning the Case-Dependent Parameters of Relaxation Zones for Flow Simulations With Strongly Reflecting Bodies in Free-Surface Waves (2018)

In finite-volume-based flow simulations with free-surface waves, wave reflections at the domain boundaries must be minimized. This can be achieved by introducing source terms in the governing equations, for which two different approaches are widely used, namely 'forcing zones' and 'relaxation zones'. Both approaches have case-dependent parameters, which must be tuned to the waves to obtain reliable results. For forcing zones, a theory to predict reflection coefficients was proposed by Peri\'c and Abdel-Maksoud (2018); its use for tuning forcing zone parameters was demonstrated via comparison to flow simulation results for regular, long-crested waves in deep-water. This paper extends their theory to apply to relaxation zones, which blend two solutions by fading from one to the other. The theory predictions are validated via flow simulations using two different codes, Siemens STAR-CCM+ and the foam-extend Naval Hydro Pack. The validation is performed via parameter studies for different blending functions, zone thicknesses and source term magnitudes. Simulations are run for long-crested waves under shallow-water and deep-water conditions in 2D and for deep-water conditions in 3D with an additional strongly reflecting body within the domain. The results show that the theory satisfactorily predicts the optimum relaxation zone parameters. Recommendations for engineering practice are provided.
Streamlining the REDCap training and user account creation process (2015)

Summary: A description of the online training creation and implementation and how it is tied to streamlining the account creation process for REDCap.
Large-scale, computer-aided thermal design of power GaAs integrated devices and circuits (2005)

A three-dimensional large-scale thermal simulation tool is applied to the design of power III-V devices and integrated circuits (ICs). After a short description of the modelling approach, which allows for non-linear multilayered and thinned substrates, via holes, and heat conduction through surface metallizations, simulation examples are discussed concerning GEC-Marconi power MESFETs with improved heat sinking and power ICs.
Analysis of level A <i>in vitro–in vivo</i> correlations for an extended‐release formulation with limited bioavailability (2012)

A two-stage, numerical deconvolution approach was employed to develop level A in vitro-in vivo correlations using data for three formulations of an extended-release oral dosage form. The in vitro dissolution data for all formulations exhibited near-complete dissolution within the time frame of the test. The pharmacokinetic concentration-time profiles for 16 subjects in a cross-over study demonstrated notably limited bioavailability for the slowest formulation. These data were used as the basis for the IVIVC model development. Two models were identified that satisfied the nominal requirements for a conclusive internal predictability of the IVIVC, provided that all three formulations were used as internal datasets. These were a simple linear model with absorption cut-off and a piecewise-linear variable absorption scale model. A subsequent cross-validation of the models' robustness indicated that neither model predicted satisfactorily the pharmacokinetic characteristics of all formulations in a conclusive manner. The piecewise-linear variable absorption scale model provided the most accurate results, particularly with respect to the prediction of the slowest formulation's pharmacokinetic metrics. But this latter model also involved additional free parameters compared with the simple linear model with absorption cut-off. It is argued that more complex IVIVC models with extra parameterization require comprehensive validation to ascertain the accuracy and robustness of the model. In order to achieve this, it is necessary to ensure a complete suite of supporting datasets for internal and external validation, irrespective of the mathematical approach used subsequently to develop the IVIVC.
New Insights into Quinine–DNA Binding Using Raman Spectroscopy and Molecular Dynamics Simulations (2018)

Quinine's ability to bind DNA and potentially inhibit transcription and translation has been examined as a mode of action for its antimalarial activity. UV absorption and fluorescence-based studies have lacked the chemical specificity to develop an unambiguous molecular-level picture of the binding interaction. To address this, we use Raman spectroscopy and molecular dynamics (MD) to investigate quinine-DNA interactions. We demonstrate that quinine's strongest Raman band in the fingerprint region, which derives from a symmetric stretching mode of the quinoline ring, is highly sensitive to the local chemical environment and pH. The frequency shifts observed for this mode in solvents of varying polarity can be explained in terms of the Stark effect using a simple Onsager solvation model, indicating that the vibration reports on the local electrostatic environment. However, specific chemical interactions between the quinoline ring and its environment, such as hydrogen bonding and π-stacking, perturb the frequency of this mode in a more complicated but predictable manner. We use this vibration as a spectroscopic probe to investigate the binding interaction between quinine and DNA. We find that, when the quinoline ring is protonated, quinine weakly intercalates into DNA by forming π-stacking interactions with the base pairs. The Raman spectra indicate that quinine can intercalate into DNA with a ratio reaching up to roughly one molecule per 25 base pairs. Our results are confirmed by MD simulations, which also show that the quinoline ring adopts a t-shaped π-stacking geometry with the DNA base pairs, whereas the quinuclidine head group weakly interacts with the phosphate backbone in the minor groove. We expect that the spectral correlations determined here will enable future studies to probe quinine's antimalarial activities, such as disrupting hemozoin biocrystallization, which is hypothesized to be, among other things, one of its primary modes of action against Plasmodium parasites.
Exploiting Atomic Nature of the Interface for Controlling Mode Coupling in Microresonators (2022)

We show the ability to control the degree of mode coupling in high quality factor silicon nitride (Si3N4) microresonators by controlling the atomic nature of the resonators interface.
Dynamic task mapping onto multi-core architectures through stream rewriting (2013)

Task graphs provide an efficient model of computation for specification, analysis, and implementation of concurrent applications. In this paper, we present a novel approach for mapping the class of series-parallel task graphs onto multi-core architectures based on pattern matching. Both the topology of the graph and the state of the tasks are encoded as a stream of tokens, which is iteratively rewritten at multiple positions in parallel. Hence, our technique is most useful for compute-intensive applications that must adapt to frequently varying and unpredictable workload at runtime. Several complex examples have been evaluated on a multi-core architecture and the experimental results show the effectiveness of our approach.
Demonstration of Independent Turbulence Mitigation of Two 100-Gbit/s QPSK Orbital-Angular-Momentum Multiplexed Beams using Wavefront Shaping and Controlled Scattering (2019)

We experimentally demonstrate using wavefront shaping and controlled scattering to mitigate different-strength turbulence effects (D/r 0 = 2.4,6.0) in a 200-Gbit/s orbital angular momentum (OAM)-multiplexed link.
2P1-B03 Whole-body Climbing Motion Generation based on Body Retention Load Index and Decoupling of Physical/Geometrical Posture State Search(Humanoid) (2013)

Climbing motion with hands and feet must be considered from the standpoints of torque, friction, balance, collision, and geometory. Massive search of constraint's space is needed. In this paper, forcusing on the necessity of the mechanical optimization for climbing higher objects, the body retention load index (BRLI) which considers mechanical constrains like friction, balance and torque is introduced, and based on that, it becomes possible to decide where hands and feet to be placed and what kinds of poses are better. We confirm effectiveness of our proposed method through simulation results and finally show the experiments in which a HRP-2 robot climbed a ladder and a car.
Nanosilicate-hydrogel microspheres formed by aqueous two-phase separation for sustained release of small molecules (2023)

Introduction: Hydrogel microspheres are an attractive option for drug delivery applications due to their ease of injection and potential for tunable controlled delivery. However, their utility is limited due to high initial burst release and rapid overall release, which is especially pronounced for small molecules or small size microspheres. We and others have shown that the addition of two-dimensional nanosilicate (NS) particles to hydrogels can significantly prolong release kinetics from hydrogels while minimizing burst release. Materials and Methods: Here we explored whether NS could modulate release kinetics of small molecules from small size injectable microspheres. Polyethylene glycol (PEG)-based hydrogel microspheres were fabricated via polymer/salt aqueous two-phase separation (ATPS), which is facile, high yield, and scalable, without the need for organic solvents or oils. Results and Discussion: Importantly, NS and acridine orange (AO), a model cationic small molecule, were shown to phase separate into the PEG-rich phase, allowing for successful encapsulation within hydrogel microspheres. The fabricated microspheres were stable, similar in size to red blood cells, and easily injectable. The effect of various fabrication parameters, including the addition of NS and AO, on microsphere size and polydispersity were explored. Release of AO was significantly slowed from PEG-NS microspheres compared to PEG-only microspheres and correlated with NS concentration. Two additional small molecules, the chemotherapeutic doxorubicin (positive charge), and the model small molecule Brilliant Blue FCF (negative charge), were shown to exhibit prolonged release, underscoring the broad utility of the system. The dependence of release kinetics on encapsulated NS concentration allows for tunable and prolonged release of small molecules from an injectable hydrogel delivery device.
Satellite-Linked Remote Physiologic Monitoring During Simulated Rural Ground Ambulance and Rotor Wing Transports (2023)

Telemedicine and remote monitoring are rapidly gaining momentum in health care, including in-home and postdischarge monitoring. However, remote monitoring for telemedicine teams and receiving medical centers is yet to reach emergency medical services. When transporting a critically ill patient, continuous vital sign monitoring may be helpful to enhance receiving center collaboration and change care delivery before arrival when necessary. Our primary objective was to demonstrate successful transmission and reception of real-time physiologic summary data to a hospital base station during ambulance transport using a low-energy Bluetooth wireless wearable device linked to iridium satellite communications. We completed our proof-of-concept study on 2 simulated ground ambulance transports and 1 helicopter flight in rural areas surrounding Rochester, Minnesota. Each simulated transport used Mayo Clinic-developed wearable devices paired one-to-one with a physiologic communication kit. Electrocardiographic and photoplethysmographic waveforms were processed on the wearables every 5 minutes, with vital sign data generated and transmitted to an iridium satellite and relayed to a base station network-protected computer and mobile application with real-time display of summary and location. Data and geolocation were tracked in real time with a mobile application during the simulated transport, and summary data packets were saved on Mayo Clinic servers. During the 3 simulated rural transports, all (n=7; 100%) wearables successfully captured, recorded, and transmitted raw waveform physiologic signals. All devices transmitted successfully via the iridium satellite to the base station network-protected computer and mobile application. In all, 106 (69%) of 154 transmissions were successfully processed. Our project demonstrated successful remote monitoring of physiologic vital signs during transport in rural, low-cellular signal areas. The use of live remote monitoring should be explored to understand its utility in practice and outcomes.
Sultanate of Oman Giant Fractured Carbonate Field, Fracture Model Impact on Understanding Field Connectivity from Seismic to Flow (2022)

Abstract The paper presents an integrated reservoir modeling (IRM) of a giant complex fractured carbonate reservoir to get insights about the reservoir's displacement process. Historically the field has undergone many recovery mechanisms, nowadays two still remains: Gas-Oil Gravity Drainage (GOGD) and waterflood. A major change in understanding the vertical connectivity of the different reservoir units henders the future development options. A decision-based approach was followed to select an economically feasible field development option. Selection of economically feasible development option need; field performance review, full frame structure and geological model is built, ideal conceptual sector models sliced from the full frame structural model and numerical dynamic simulation is carried out with different development options (water injection (WI), gas oil gravity drainage (GOGD) and mixture of WI and GOGD). Understanding the fluid flow behavior in fractured carbonate reservoirs is complex and challenging. The complexity directly linked to the understanding of the fracture hierarchy and connectivity. The field development plan at the time of analyzing the field data was water injection with very good recovery factor that cannot be explained by the injected water pore volume. Applying the integrated reservoir modeling (IRM) procedures, full filed performance review is carried out, update of subsurface models with different fracture model realizations and run numerical dynamic simulations over idealized conceptual models with different development options. Full filed history match is carried out on the selected development option. Front Loading and data analysis is key for successful modeling strategy, the main uncertainty is the fracture distribution, better understanding of the reservoir units cross flow, understand the effect of different development options on recovery factor in significantly short time and create reasonable scenarios of subsurface. Well performance showed some effects of water injection. Gas oil gravity is the dominant recovery process. Gas recirculation of shallow wells have negative effects on the GOGD process. Adding water injectors with continuous gas injection has negative effects on the recovery factor. The fracture hierarchy is key to understand the subsurface. All the studied reservoir units are in communication via fracture corridors. The main recovery mechanism is gas oil gravity drainage (GOGD). WI may have local effects but as development concept it will not add value. Well location relative to fracture corridors is critical to achieve better history match. Water injection has negative effect on field recovery and operationally (WRFM). Filed operation optimization (optimize gas injection) can result in maintain the same rate with lower CPEX and OPEX (Capital spending efficiency). This paper presents significant importance understanding the integration and clear vision of the modeling strategy that saves effort and money.
Fundamental Analysis of a Linear Type Trochoidal Gear (3rd Report) (2004)

To realize a positioning with high accuracy for straight-corner slide system, the internal gear type trochoidal corner curve rack system has been developed. This system consists of a straight trochoidal rack, a corner curve rack with internal gear type trochoidal cam tooth, a roller pinion and a linear-corner slide system. Also the tooth profile is generated using trochoidal curve loci. In this report, the motion principle is analyzed using the polar complex vectors analysis which is similar to the linear motion type cam rack. And to eliminate a backlash on the connecting section of a straight rack and a corner rack, the conditions to modify the teeth profile are shown. It is proved that a reduction ratio and a tooth height are limited to keep the non-backlash meshing for the straight-corner slide system. Also the combination of each profile shifting coefficient of the straight rack and the corner curve rack is limited.
Universal Method for Separating Spin Pumping from Spin Rectification Voltage of Ferromagnetic Resonance (2013)

We develop a method for universally resolving the important issue of separating spin pumping from spin rectification signals in bilayer spintronics devices. This method is based on the characteristic distinction of spin pumping and spin rectification, as revealed in their different angular and field symmetries. It applies generally for analyzing charge voltages in bilayers induced by the ferromagnetic resonance (FMR), independent of FMR line shape. Hence, it solves the outstanding problem that device-specific microwave properties restrict the universal quantification of the spin Hall angle in bilayer devices via FMR experiments. Furthermore, it paves the way for directly measuring the nonlinear evolution of spin current generated by spin pumping. The spin Hall angle in a Py/Pt bilayer is thereby directly measured as 0.021±0.015 up to a large precession cone angle of about 20°.
Liv(e)-ing on the Edge: User-Uploaded Live Streams Driven by "First-Mile" Edge Decisions (2019)

As users equipped with high-resolution cameras spontaneously capture and live-stream videos to interested parties through distributors like Twitch or Facebook Live, a new style of video delivery is emerging: user-upload streaming. Unlike video-on-demand and traditional live-streaming in which video is stored by professional content providers and distributed using standard CDN techniques, in user-upload streaming, the video is generated and uploaded on-the-fly by heterogeneous clients with restricted bandwidth and long latencies to the distributor. Hence, it is crucial to factor in client-side "first-mile" factors when making edge decisions. In this paper, we present a systematic design of a video delivery architecture for user-upload streaming, which focuses on the upload server and upload bitrate as the important "first-mile" edge factors that influence downstream delivery and quality-of-experience for viewers. We present a polynomial-time algorithm to minimize the end-to-end latency and maximize the video rate for all users for the scenario where the upload and download server are the same. Further, we present efficient heuristics for the general (NP-complete) version where the upload streams are routed through the distributor's overlay network. Finally, we validate the efficacy of our algorithms through extensive trace-based simulations based on real-world data sets.
Direct Measurements of Polymer Brush Conformation Using Small-Angle Neutron Scattering (SANS) from Highly Grafted Iron Oxide Nanoparticles in Homopolymer Melts (2013)

Small-angle neutron scattering (SANS) is a sensitive technique that is able to probe the structure of polymer-grafted nanoparticles and free polymer chains. Here, we combine SANS measurements with self-consistent field theory (SCFT) calculations to study the structure of deuterated poly(methyl methacrylate) (dPMMA) nanocomposites containing PMMA-grafted Fe3O4 nanospheres, with a specific emphasis on the conformation of the PMMA brush chains. We present a new, detailed SANS model which is able to account for the excluded volume of the grafted polymer chains, and compare the experimentally measured brush chain conformations to predictions from SCFT calculations for a polymer-grafted nanosphere, and previous studies by others. The results of the SANS measurements are in qualitative agreement with SCFT calculations and in excellent quantitative agreement with previous studies that indirectly assessed the structure of the polymer chains by measuring the hydrodynamic radius of the nanoparticles. Unlike previous methods, however, SANS provides direct measurements of the polymer brush conformation.
HLA in health and disease (2000)

Introduction to the HLA System: P. Travers, Structure of Class I and II Molecules. C.M. Milner, R.D. Campbell and J. Trowsdale, Molecular Genetics of the Human MHC. R.J. Baker and A.N. Warrens, The Biology of MHC Molecules. C. AuPeh, A.W. Purcell, and J. McCluskey, The Function of MHC Molecules: Antigen Presentation. T.J. Vyse and B. Morley, The Analysis of Genetic Susceptibility. A. Warrens, Appendix. A. Warrens and R. Lechler, Mechanisms of HLA and Disease Associations. Disease Associations: G.T. Nepom, HLA-Associations with Rheumatoid Arthritis. P. Bowness, HLA and the Spondylarthopathies. R. Phelps and A. Rees, The HLA Complex in Renal Disease. J. Hillert and A. Fogdell-Hahn, HLA Associations in Neurological Diseases. G.T. Nepom, Type 1 Diabetes (IDDM). A.P. Weetman, Endocrinology. L.M. Sollid, A. Spurkland, and E. Thorsby, HLA Associations in Gastrointestinal Diseases. J.S. Pulido and J.W. Steilein, HLA and the Eye. P.A. Glynne and N.M. Price, HLA and Infectious Diseases. M.C. Pickering, M. Perraudeau, and M. Walport, The Systemic Vasculitides, Systemic Lupus Erythematosus, and Sjogren's Syndrome. A. Friedman, Association of the HLA System with Dermatological Diseases. R. Baker and G. Opelz, HLA and Transplantation: Alloimmune Response and the Role of HLA Matching in Clinical Transplantation. P. Wright, V. Nimgaonkar, R. Ganguli, and R. Murray, Psychiatric Disease. Definition of HLA Polymorphism: J.J. van Rood, The History of the Discovery of HLA. P. Dyer, S. Martin, and R. Stanford, Serological Methods in HLA Typing. P. Mason and R. Lechler, Cellular Methods in Testing Histocompatibility. H. Erlich, PCR-Based Methods in HLA Typing. J. Bodmer, W.F. Bodmer, and S. Marsh, HLA Nomenclature: The Name of the Rose. R. Bontrop and J. Kaufman, Evolution of HLA Polymorphisms.