gebhart/patrepeval huggingface dataset:
Compensation-aware data types in RDBMS (2009)

In a traditional database system, the transaction management protocols and mechanisms are constrained by the fundamental properties of atomicity, consistency, isolation, and durability (ACID). A transaction management system with strict ACID properties typically employs read and write locks, held for the duration of the transaction, to protect its uncommitted data from being seen and modified by some other transaction. While this approach is effective for applications involving short execution times and relatively small number of concurrent operations, it is too restrictive for applications that involve reactive, long-lived, and complex transactions. The common denominator of such applications is the need for transactions to read and possibly modify uncommitted data values [1] and for the database system to still retain the ability to abort a transaction and the ability to recover from failures. This paper proposes a Business Transaction framework that allows long lasting, discontinuous, and resumable transactions to perform shared updates to common data by holding semantic locks on the modified rows. Under this framework, basic SQL data types are made compensation-aware by associating domain-specific shared update semantics with them. These semantics ensure that each data modification operation is compatible with other uncommitted activity on the same data and that the operation can be undone, if needed, without resorting to cascading aborts. This paper describes the key concepts and presents our approach for supporting shared updates in Oracle RDBMS.
An<i>in vitro</i>model of mesenchymal stem cell targeting using magnetic particle labelling (2012)

The specific targeting of cells to sites of tissue damage in vivo is a major challenge precluding the success of stem cell-based therapies. Magnetic particle-based targeting may provide a solution. Our aim was to provide a model system to study the trapping and potential targeting of human mesenchymal stem cells (MSCs) during in vitro fluid flow, which ultimately will inform cell targeting in vivo. In this system magnet arrays were used to trap superparamagnetic iron oxide particle-doped MSCs. The in vitro experiments demonstrated successful cell trapping, where the volume of cells trapped increased with magnetic particle concentration and decreased with increasing flow rate. Analysis of gene expression revealed significant increases in COL1A2 and SOX9. Using principles established in vitro, a proof-of-concept in vivo experiment demonstrated that magnetic particle-doped, luciferase-expressing MSCs were trapped by an implanted magnet in a subcutaneous wound model in nude mice. Our results demonstrate the effectiveness of using an in vitro model for testing superparamagnetic iron oxide particles to develop successful MSC targeting strategies during fluid flow, which ultimately can be translated to in vivo targeted delivery of cells via the circulation in a variety of tissue-repair models.
Image Sensing Technology. High-Performance Nondestructive Bulk Charge Detection for CCD Image Sensors. (2001)

This paper describes the theoretical operation and measured characteristics of a charge detection amplifier, which detects charge that moves in the bulk of a silicon CCD channel. The charge detection is nondestructive and, therefore, free of kTC noise. The detector is very high speed and low-noise operation make it suitable for high-resolution CCD image sensors. A simple gradual channel transistor approximation was used to derive a first-order device model, which was then used to predict the charge-conversion sensitivity, linearity, and noise. The derived theoretical results were compared with detailed measurements, which included the measured conversion gain, linearity, reset feed through, noise, and hot-carrier effects. The analysis and measurements demonstrated that this bulk charge detection (BCD) is superior to today's state-of-the-art floating-diffusion charge-detection amplifiers in high-speed applications.
A novel switch architecture for high-performance computing and signal processing networks (2004)

This work describes low-latency switch architecture for high performance packet-switched networks. The switch architecture is a combination of input buffers capable of avoiding head-of-line blocking and an internal switch interconnect capable of allowing different input ports to access a single output port simultaneously. The switch was designed for the RapidIO protocol, but provides improved performance in other switched fabrics as well. OPNET Modeler was used to develop models of the proposed switch architecture and to evaluate the performance of the switch for three different network topologies. Models of two standard switch architectures were also developed and simulated for comparison.
Modeling complicated rheological behaviors in encapsulating shells of lipid-coated microbubbles accounting for nonlinear changes of both shell viscosity and elasticity (2013)

It has been accepted that the dynamic responses of ultrasound contrast agent (UCA) microbubbles will be significantly affected by the encapsulating shell properties (e.g., shell elasticity and viscosity). In this work, a new model is proposed to describe the complicated rheological behaviors in an encapsulating shell of UCA microbubbles by applying the nonlinear 'Cross law' to the shell viscous term in the Marmottant model. The proposed new model was verified by fitting the dynamic responses of UCAs measured with either a high-speed optical imaging system or a light scattering system. The comparison results between the measured radius-time curves and the numerical simulations demonstrate that the 'compression-only' behavior of UCAs can be successfully simulated with the new model. Then, the shell elastic and viscous coefficients of SonoVue microbubbles were evaluated based on the new model simulations, and compared to the results obtained from some existing UCA models. The results confirm the capability of the current model for reducing the dependence of bubble shell parameters on the initial bubble radius, which indicates that the current model might be more comprehensive to describe the complex rheological nature (e.g., 'shear-thinning' and 'strain-softening') in encapsulating shells of UCA microbubbles by taking into account the nonlinear changes of both shell elasticity and shell viscosity.
A Framework of Cognitive Situation Modeling and Recognition (2006)

This paper scopes the issues of situation management in dynamic systems, defines the basic concepts, and identifies several key enabling technologies. Particular focus of the paper is given to situation modeling. The paper reviews the major aspects of situation modeling and discusses associated technologies, including situation calculus, situation semantics, situation control, situation awareness and others. In more detail, we present an approach to situation modeling and management which is based on combining multi-agent systems and event correlation
Efficacy of Bacteriophage Therapy on Horizontal Transmission of Salmonella Gallinarum on Commercial Layer Chickens (2011)

A Salmonella Gallinarum (SG)-specific bacteriophage isolated from sewage effluent was used to prevent horizontal transmission of SG in commercial layer chickens. Six-week-old chickens, each challenged with 5 x 10(8) colony-forming units of SG, cohabited with contact chickens treated with 10(6) plaque-forming units/kg of bacteriophage, prepared in feed additives, for 7 days before, and 21 days after challenge with SG. Mortality was observed for 3 wk after challenge and SG was periodically reisolated from the liver, spleen, and cecum of chickens. SG re-isolation from organs was decreased and a significant (P < 0.05) reduction in mortality was observed in contact chickens treated with the bacteriophage, as compared to untreated contact chickens, indicating that bacteriophage administration in feed additives significantly prevented the horizontal transmission of SG. These results provide important insights into prevention and control strategies against SG infection and suggest that the use of bacteriophages may be a novel, safe, and effectively plausible alternative to antibiotics for the prevention of SG infection in poultry.
Understanding the Impact of Diverse Streaming Workloads on End-User Quality of Service (2006)

Streaming media has experienced explosive growth over the last few years and will continue to increase in popularity as individual users can easily produce digital images and video. Large scale streaming will require network operators to deploy and manage a larger number of streaming servers within their networks. In order to determine the number of servers needed, and to design the appropriate management policies for a particular workload, administrators will need to understand the performance characteristics of those servers, how to measure performance, and how different workloads can affect performance. In this paper we make the case for a more complete measurement methodology by showing that streaming server performance can vary substantially based on the type of streaming workload, and, as a result, affect the end-user quality of service.
From Flexible and Stretchable Meta-Atom to Metamaterial: A Wearable Microwave Meta-Skin with Tunable Frequency Selective and Cloaking Effects (2016)

This paper reports a flexible and stretchable metamaterial-based "skin" or meta-skin with tunable frequency selective and cloaking effects in microwave frequency regime. The meta-skin is composed of an array of liquid metallic split ring resonators (SRRs) embedded in a stretchable elastomer. When stretched, the meta-skin performs as a tunable frequency selective surface with a wide resonance frequency tuning range. When wrapped around a curved dielectric material, the meta-skin functions as a flexible "cloaking" surface to significantly suppress scattering from the surface of the dielectric material along different directions. We studied frequency responses of multilayer meta-skins to stretching in a planar direction and to changing the spacing between neighboring layers in vertical direction. We also investigated scattering suppression effect of the meta-skin coated on a finite-length dielectric rod in free space. This meta-skin technology will benefit many electromagnetic applications, such as frequency tuning, shielding, and scattering suppression.
Controversies in neurosurgery: Irreducible basilar invagination and atlanto-axial dislocation: A trans-oral procedure may be avoided in a majority, but still may be required in some cases (2014)

Basilar invagination (BI) and atlanto-axial dislocation (AAD) are mostly irreducible in nature and are quite complex pathologies to manage. Traditionally they required a trans-oral excision of odontoid process followed by a posterior instrumented fusion. This has been challenged recently, where a single staged posterior only procedure addresses both reduction and decompression in the same sitting. This evidence was based on earlier publication and also on the author’s own experience, where he described a new technique (distraction, compression, extension and reduction), which performed for the 1<sup>st</sup> time a 2-axis movement in the cranio-vertebral junction (CVJ) allowing effective reduction of both AAD and BI. This technique has now become a standard in the author’s armentorium for management of CVJ anomalies and allowed a single stage posterior only surgery for 95% of these pathologies managed by him. Although this technique could address a majority of cases of developmental BI and AAD, it becomes important to understand that a trans-oral excision of dens followed by a posterior instrumented fusion will still be required in some cases. These include certain cases of clival segmentation anomalies, very severe BI, infective pathologies like tuberculosis with circumferential compression and bony destruction and tumors. The following review article is based on the author’s personal experience of over 500 cases and discusses the advantages and limitations of single staged surgery and the indications of trans-oral surgery in this rapidly evolving field.
Grape-Derived Polyphenolics Prevent A  Oligomerization and Attenuate Cognitive Deterioration in a Mouse Model of Alzheimer's Disease (2008)

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive impairments in memory and cognition. Extracellular accumulation of soluble high-molecular-weight (HMW) Abeta oligomers has been proposed to be largely responsible for AD dementia and memory deficits in the Tg2576 mice, a model of AD. In this study, we found that a naturally derived grape seed polyphenolic extract can significantly inhibit amyloid beta-protein aggregation into high-molecular-weight oligomers in vitro. When orally administered to Tg2576 mice, this polyphenolic preparation significantly attenuates AD-type cognitive deterioration coincidentally with reduced HMW soluble oligomeric Abeta in the brain. Our study suggests that grape seed-derived polyphenolics may be useful agents to prevent or treat AD.
Discovery of Mcl-1 inhibitors from integrated high throughput and virtual screening (2018)

Protein-protein interactions (PPIs) represent important and promising therapeutic targets that are associated with the regulation of various molecular pathways, particularly in cancer. Although they were once considered "undruggable," the recent advances in screening strategies, structure-based design, and elucidating the nature of hot spots on PPI interfaces, have led to the discovery and development of successful small-molecule inhibitors. In this report, we are describing an integrated high-throughput and computational screening approach to enable the discovery of small-molecule PPI inhibitors of the anti-apoptotic protein, Mcl-1. Applying this strategy, followed by biochemical, biophysical, and biological characterization, nineteen new chemical scaffolds were discovered and validated as Mcl-1 inhibitors. A novel series of Mcl-1 inhibitors was designed and synthesized based on the identified difuryl-triazine core scaffold and structure-activity studies were undertaken to improve the binding affinity to Mcl-1. Compounds with improved in vitro binding potency demonstrated on-target activity in cell-based studies. The obtained results demonstrate that structure-based analysis complements the experimental high-throughput screening in identifying novel PPI inhibitor scaffolds and guides follow-up medicinal chemistry efforts. Furthermore, our work provides an example that can be applied to the analysis of available screening data against numerous targets in the PubChem BioAssay Database, leading to the identification of promising lead compounds, fuelling drug discovery pipelines.
8,9-Dihydroxy-2,3,7,11b-tetrahydro-1<i>H</i>-naph[1,2,3-<i>de</i>]isoquinoline:  A Potent Full Dopamine D<sub>1</sub> Agonist Containing a Rigid β-Phenyldopamine Pharmacophore (1996)

The present work reports the synthesis and preliminary pharmacological characterization of 8,9-dihydroxy-2,3,7,11b-tetrahydro-1H-naph[1,2,3-de] isoquinoline (4, dinapsoline). This molecule was designed to conserve the essential elements contained in our D1 agonist pharmacophore model (i.e., position and orientation of the nitrogen, hydroxyls, and phenyl rings). It involved taking the backbone of dihydrexidine [3; (+/-)-trans-10, 11-dihydroxy-5,6,6a,7,8,12b-hexahydrobenzo[a] phenanthridine], the first high-affinity full D1 agonist, and tethering the two phenyl rings of dihydrexidine through a methylene bridge and removing the C(7)-C(8) ethano bridge. Preliminary molecular modeling studies demonstrated that these modifications conserved the essential elements of the hypothesized pharmacopore. Dinapsoline 4 had almost identical affinity (KI = 5.9 nM) to 3 at rat striatal D1 receptors and had a shallow competition curve (nH = 0.66) that suggested agonist properties. Consistent with this, in both rat striatum and C-6-mD1 cells, dinapsoline 4 was a full agonist with an EC50 of ca. 30 nM in stimulating synthesis of cAMP via D1 receptors. The design and synthesis of dinapsoline 4 provide a powerful test of the model of the D1 pharmacophore we have developed and provide another chemical series that can be useful probes for the study of D1 receptors. An interesting property of 3 is that it also has relatively high D2 affinity (K0.5 = 50 nM) despite having an accessory phenyl ring usually though to convey D1 selectivity. Dinapsoline 4 was found to have even higher affinity for the D2 receptor (K0.5 = 31 nM) than 3. Because of the high affinity of 4 for D2 receptors, it and its analogs can be powerful tools for exploring the mechanisms of "functional selectivity" (i.e., that 3 is an agonist at some D2 receptors, but an antagonist at others). Together, these data suggest that 4 and its derivatives may be powerful tools in the study of dopamine receptor function and also have potential clinical utility in Parkinson's disease and other conditions where perturbation of dopamine receptors is useful.
Application of Millimeter-Wave Radiometry for Remote Chemical Detection (2008)

Passive millimeter-wave systems have been used in the past to remotely map solid targets and to measure low-pressure spectral lines of stratospheric and interstellar gases; however, its application to pressure-broadened spectral line detection of industrial emissions is new. We developed a radiative transfer model to determine feasibility and system requirements for passive millimeter-wave spectral detection of terrestrial gases. We designed and built a Dicke-switched multispectral radiometer in the 146-154-GHz band to detect nitric oxide (NO), a prototypical gas of nuclear fuel processing operations. We first tested the spectral detection capability of the radiometer in the laboratory using a gas cell and then field tested it at the Nevada test site at a distance of 600 m from a stack that released hot plumes of NO and air. With features such as Dicke-switched integration, frequent online calibration, and spectral baseline subtraction, we demonstrated the feasibility of remote detection of terrestrial gases by a ground-based radiometer.
Chalcogenide-mold interactions during precision glass molding (PGM) of GeAsSe glasses (2013)

Five chalcogenide glasses in the GeAsSe ternary glass system were melted, fabricated into flats, and molded between planar, uncoated, binderless WC molds using a laboratory-scale precision glass molding machine. The five glasses originate at the binary arsenic triselenide (As<sub>40</sub>Se<sub>60</sub>) and are modified by replacing As with Se in 5 mol% increments, or by locking the As:Se ratio and adding Ge, also in 5 mol% increments. The glasses are separated into two groups, one for the Ge-free compositions and the other for the Ge-containing compositions. This effort analyzes the differences between the Ge-containing and the Ge-free glasses on the post-molded glass and mold surface behavior, as well as the mold lifetime. Fabrication features, such as scratch and/or dig marks were present on the glass and mold surfaces prior to the PGM process. White light interferometry analysis of the surfaces shows an overall reduction in the RMS roughness of the glass after molding, and an increase of the roughness of the molds, after 15 molding cycles. After molding, the quantity of observable defects, primarily deposits and dig marks are increased for both the glass and mold surfaces. Deposits found on the WC molds and glasses were analyzed using Electron Dispersive X-ray Spectroscopy (EDS) and showed no evidence of being due to material transfer between the WC molds and the glass constituents. In general the main observable difference in the analysis of the two post molded sets, despite the changes in chemistry, is the quantity of molding induced defects near the edge of the GeAsSe samples.
RON: Reverse Connection with Objectness Prior Networks for Object Detection (2017)

We present RON, an efficient and effective framework for generic object detection. Our motivation is to smartly associate the best of the region-based (e.g., Faster R-CNN) and region-free (e.g., SSD) methodologies. Under fully convolutional architecture, RON mainly focuses on two fundamental problems: (a) multi-scale object localization and (b) negative sample mining. To address (a), we design the reverse connection, which enables the network to detect objects on multi-levels of CNNs. To deal with (b), we propose the objectness prior to significantly reduce the searching space of objects. We optimize the reverse connection, objectness prior and object detector jointly by a multi-task loss function, thus RON can directly predict final detection results from all locations of various feature maps. Extensive experiments on the challenging PASCAL VOC 2007, PASCAL VOC 2012 and MS COCO benchmarks demonstrate the competitive performance of RON. Specifically, with VGG-16 and low resolution 384×384 input size, the network gets 81.3% mAP on PASCAL VOC 2007, 80.7% mAP on PASCAL VOC 2012 datasets. Its superiority increases when datasets become larger and more difficult, as demonstrated by the results on the MS COCO dataset. With 1.5G GPU memory at test phase, the speed of the network is 15 FPS, 3 times faster than the Faster R-CNN counterpart. Code will be made publicly available.
Spreading depression in continuous electroencephalography of brain trauma (2014)

Leão's spreading depression can be observed in clinically standard, continuous scalp EEG, and underlying depolarizations can spread widely across the injured cerebral hemisphere. These results open the possibility of monitoring noninvasively a neuronal pathophysiological mechanism in a wide range of disorders including ischemic stroke, subarachnoid hemorrhage, and brain trauma, and suggest a novel application for continuous EEG.
An island-style-routing compatible fault-tolerant FPGA architecture with self-repairing capabilities (2012)

In this work, we have developed a fault-tolerant architecture which is compatible with existing island-style routing network. Due to this compatibility, the proposed architecture can not only be implemented easily in the existing FPGA devices but a new fault-tolerant FPGA device can also be fabricated without refining the existing routing architecture. A generic fault-tolerant Computation Cell is developed which along with its self-checking circuitry also consists of an internal router to route un-faulty function out of the cell. The proposed fault-tolerant FPGA architecture is comprised of Computation Tiles each of which consists of computation cells which are able to heal themselves from transient errors. Computation Tile also contains stem cells which help computation cells to recover from permanent errors all at once. This architecture is centrally controlled by an on-chip fault-tolerant core whose main responsibility is to define the healing priority when an error occurs in more than one of the computation tile at the same time. It also communicates with the external PC software which identifies the faulty tile and reconfigures it through dynamic partial reconfiguration. The robust operation of a proposed architecture is implemented and verified on XILINX Virtex-5 FPGA device. From our proposed fault-tolerant scheme of utilizing the existing routing strategies together with partial reconfiguration of stem cells we achieved a number of benefits, including a fast fault recovery and avoidance of using complicated routing strategies, as compared to recently developed fault-tolerant FPGA architectures.