gebhart/patrepeval huggingface dataset:
Regulation of the beta-adrenergic receptor-adenylate cyclase complex of 3T3-L1 fibroblasts by sodium butyrate (1986)

Mouse 3T3-L1 fibroblasts contain beta-adrenergic receptors (BAR), predominantly of the B/sub 1/ subtype. Incubation of these cells with 2-10 mM sodium butyrate (SB) for 24-48 hr results in a switch in the BAR subtype from B/sub 1/ to B/sub 2/ and promotes a 1.5 to 2.5 fold increase in total BAR number. Other short chain acids were not as effective as SB in promoting changes in BAR. BAR were assayed in membranes prepared from the 3T3-L1 cells using the radiolabeled antagonist (/sup 125/I)-cyanopindolol and the B/sub 2/ selective antagonist ICI 118.551. BAR subtype switch was confirmed functionally by measuring cellular cAMP accumulation in response to agonists. The structure and amount of the alpha subunits of the guanine nucleotide regulatory proteins N/sub s/ and N/sub i/ were determined by ADP-ribosylation using /sup 32/P-NAD and either cholera toxin or pertussis toxin for labeling of the respective subunits. Preincubation of cells with 5 mM SB for 48 hr resulted in a 2-3 fold increase in the labeling of the alpha subunits of both N/sub s/ and N/sub i/. A protein of M/sub r/ = 44,000 showed enhanced labeling by cholera toxin following SB treatment of the cells. These data indicate SB concomitantly regulatesmore » expression of BAR subtype and components of the adenylate cyclase in 3T3-L1 cells.« less
In Situ Incorporation of Praziquantel in Polymer Microparticles through Suspension Polymerization for Treatment of Schistosomiasis (2018)

Abstract Schistosomiasis is one of the major public health problems worldwide. Even though this is a common illness among preschool children in poor countries, treatment is carried out mainly through the administration of praziquantel tablets, which has some disadvantages, such as the strong bitter taste. As an alternative to overcome this problem, the development of new encapsulated praziquantel formulations is demanded. For this reason, suspension polymerizations are carried out for the in situ encapsulation of praziquantel into polymer microparticles, using methyl methacrylate (MMA) and cationic compounds (diethylaminoethyl methacrylate, DEAEMA, and dimethylaminoethyl methacrylate, DMAEMA) as comonomers. This technique allows for the preparation of polymer microparticles with high encapsulation efficiencies (&gt;90%) with characteristic sizes ranging from 0.5 to 1500 µm. Drug release profiles show that praziquantel is released from poly(methyl methacrylate) microparticles slowly due to the existence of strong diffusional resistance. On the other hand, the addition of cationic comonomers renders polymer particles sensitive to pH variations, allowing for faster release of praziquantel in acidic environments, as found in the stomach.
A personalized search engine based on Web‐snippet hierarchical clustering (2007)

Abstract We propose a (meta‐)search engine, called SnakeT (SNippet Aggregation for Knowledge ExtracTion), which queries more than 18 commodity search engines and offers two complementary views on their returned results. One is the classical flat‐ranked list, the other consists of a hierarchical organization of these results into folders created on‐the‐fly at query time and labeled with intelligible sentences that capture the themes of the results contained in them. Users can browse this hierarchy with various goals: knowledge extraction, query refinement and personalization of search results. In this novel form of personalization, the user is requested to interact with the hierarchy by selecting the folders whose labels (themes) best fit her query needs. SnakeT then personalizes on‐the‐fly the original ranked list by filtering out those results that do not belong to the selected folders. Consequently, this form of personalization is carried out by the users themselves and thus results fully adaptive, privacy preserving, scalable and non‐intrusive for the underlying search engines. We have extensively tested SnakeT and compared it against the best available Web‐snippet clustering engines. SnakeT is efficient and effective, and shows that a mutual reinforcement relationship between ranking and Web‐snippet clustering does exist. In fact, the better the ranking of the underlying search engines, the more relevant the results from which SnakeT distills the hierarchy of labeled folders, and hence the more useful this hierarchy is to the user. Vice versa , the more intelligible the folder hierarchy, the more effective the personalization offered by SnakeT on the ranking of the query results. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Chromogenic In Situ Hybridization (2009)

Our purposes were to perform a robust assessment of a new HER2 chromogenic in situ hybridization test and report on concordance of silver in situ hybridization (SISH) data with fluorescence in situ hybridization (FISH) data and on intraobserver and interlaboratory scoring consistency. HER2 results were scored from 45 breast cancers in 7 laboratories using the Ventana (Tucson, AZ) INFORM HER-2 SISH assay and in 1 central laboratory using a standard FISH assay. Overall, 94.8% of cases were successfully analyzed by SISH across the 6 participating laboratories that reported data. Concordance for diagnosis of HER2 amplification by SISH compared with FISH was high (96.0% overall). Intraobserver variability (8.0%) and intersite variability (12.66%) of absolute HER2/chromosome 17 ratios appear to be tightly controlled across all 6 participating laboratories. The Ventana INFORM HER-2 SISH assay is robust and reproducible, shows good concordance with a standard FISH assay, and complies with requirements in national guidelines for performance of diagnostic tests.
The Cilkprof Scalability Profiler (2015)

Cilkprof is a scalability profiler for multithreaded Cilk computations. Unlike its predecessor Cilkview, which analyzes only the whole-program scalability of a Cilk computation, Cilkprof collects work (serial running time) and span (critical-path length) data for each call site in the computation to assess how much each call site contributes to the overall work and span. Profiling work and span in this way enables a programmer to quickly diagnose scalability bottlenecks in a Cilk program. Despite the detail and quantity of information required to collect these measurements, Cilkprof runs with only constant asymptotic slowdown over the serial running time of the parallel computation. As an example of Cilkprof's usefulness, we used Cilkprof to diagnose a scalability bottleneck in an 1800-line parallel breadth-first search (PBFS) code. By examining Cilkprof's output in tandem with the source code, we were able to zero in on a call site within the PBFS routine that imposed a scalability bottleneck. A minor code modification then improved the parallelism of PBFS by a factor of 5. Using Cilkprof, it took us less than two hours to find and fix a scalability bug which had, until then, eluded us for months. This paper describes the Cilkprof algorithm and proves theoretically using an amortization argument that Cilkprof incurs only constant overhead compared with the application's native serial running time. Cilkprof was implemented by compiler instrumentation, that is, by modifying the LLVM compiler to insert instrumentation into user programs. On a suite of 16 application benchmarks, Cilkprof incurs a geometric-mean multiplicative overhead of only 1.9 and a maximum multiplicative overhead of only 7.4 compared with running the benchmarks without instrumentation.
Single view reflectance capture using multiplexed scattering and time-of-flight imaging (2011)

This paper introduces the concept of time-of-flight reflectance estimation, and demonstrates a new technique that allows a camera to rapidly acquire reflectance properties of objects from a single view-point, over relatively long distances and without encircling equipment. We measure material properties by indirectly illuminating an object by a laser source, and observing its reflected light indirectly using a time-of-flight camera. The configuration collectively acquires dense angular, but low spatial sampling, within a limited solid angle range - all from a single viewpoint. Our ultra-fast imaging approach captures space-time "streak images" that can separate out different bounces of light based on path length. Entanglements arise in the streak images mixing signals from multiple paths if they have the same total path length. We show how reflectances can be recovered by solving for a linear system of equations and assuming parametric material models; fitting to lower dimensional reflectance models enables us to disentangle measurements.
Fault-Tolerant Parallel Applications with Dynamic Parallel Schedules (2005)

Commodity computer clusters are often composed of hundreds of computing nodes. These generally off-the-shelf systems are not designed for high reliability. Node failures therefore drive the MTBF of such clusters to unacceptable levels. The software frameworks used for running parallel applications need to be fault-tolerant in order to ensure continued execution despite node failures. We propose an extension to the flow graph based Dynamic Parallel Schedules (DPS) development framework that allows non-trivial parallel applications to pursue their execution despite node failures. The proposed fault-tolerance mechanism relies on a set of backup threads located in the volatile storage of alternate nodes. These backup threads are kept up to date by duplication of the transmitted data objects and periodical checkpointing of thread states. In case of a failure, the current state of the threads that were on the failed node is reconstructed on the backup threads by re-executing operations. The corresponding valid re-execution order is automatically deduced from the data flow graph of the DPS application. Multiple simultaneous failures can be tolerated, provided that for each thread either the active thread or its corresponding backup thread survives. For threads that do not store a local state, an optimized mechanism eliminates the need for duplicate data object transmissions. The overhead induced by the fault tolerance mechanism consists mainly of duplicate data object transmissions that can, for compute bound applications, be carried out in parallel with ongoing computations. The increase in execution time due to fault tolerance therefore remains relatively low. It depends on the communication to computation ratio and on the parallel programs efficiency.
Artificial Intelligence, Machine Learning, and Cardiovascular Disease (2020)

Artificial intelligence (AI)-based applications have found widespread applications in many fields of science, technology, and medicine. The use of enhanced computing power of machines in clinical medicine and diagnostics has been under exploration since the 1960s. More recently, with the advent of advances in computing, algorithms enabling machine learning, especially deep learning networks that mimic the human brain in function, there has been renewed interest to use them in clinical medicine. In cardiovascular medicine, AI-based systems have found new applications in cardiovascular imaging, cardiovascular risk prediction, and newer drug targets. This article aims to describe different AI applications including machine learning and deep learning and their applications in cardiovascular medicine. AI-based applications have enhanced our understanding of different phenotypes of heart failure and congenital heart disease. These applications have led to newer treatment strategies for different types of cardiovascular diseases, newer approach to cardiovascular drug therapy and postmarketing survey of prescription drugs. However, there are several challenges in the clinical use of AI-based applications and interpretation of the results including data privacy, poorly selected/outdated data, selection bias, and unintentional continuance of historical biases/stereotypes in the data which can lead to erroneous conclusions. Still, AI is a transformative technology and has immense potential in health care.
Role of fluids on ultrasonic attenuation in porous materials (1990)

Measurements of P- and S-wave attenuation in saturated alundum and Berea sandstone were made under confinement with various pore fluids: water (1 cP, 72 mJ/m2), n-decane (0.92 cP, 28 mJ/m2), glycerol (1490 cP, 64 mJ/m2), and silicone oil (913 cP, 21 mJ/m2). The results for alundum indicate that attenuation for both P and S waves is controlled by viscosity: Qglycerol−1 &amp;gt; Qoil−1 &amp;gt; Qwater−1 &amp;gt; Qdecane−1. Attenuation in alundum is qualitatively consistent with Biot dissipation and is much less sensitive to confinement, presumably because it is composed of well-sintered contacts. P- and S-wave attenuation in Berea sandstone is not purely viscosity dependent: Qwater−1 &amp;gt; Qglycerol−1 &amp;gt; Qdecane−1 &amp;gt; Qoil−1. Glycerol at 25 °C has the same viscosity as silicone oil but results in P- and S-wave amplitudes that are 55% and 30%, respectively, smaller than those for silicone oil. This result is not consistent with Biot dissipation but may be explained by differences in surface tension or hydrogen bonding at the contacts between grains. [Work supported by Dept. of Energy.]
Co-operative scheduling for balancing throughput gains and fairness in cell-edge enhancement schemes for wireless networks (2013)

Multi-point reception techniques for enhancing cell-edge throughput are currently under standardization in cellular wireless standards as Single Frequency Dual Cell (SFDC) [1] in 3GPP and as Single Carrier Multi Link(SCML) [2] in 3GPP2. Unlike soft-handover operation, User Equipment(UEs) at cell-edge (handover zone) can independently request data from adjacent cells in multi point operation. Although the cell-edge UEs are benefited, there is a trade-off with fairness towards the in-cell UEs that get served only by a single serving cell, and the overall cell throughput and this paper proposes a joint scheduling algorithm to address this trade-off. To support practical implementation of such a scheme in current multi-vendor wireless networks, the cells participating in multi-point operation need to share throughput feedback via standards based mechanisms. Numerical results through computer simulation based on system parameters conforming to 3GPP2 evaluation methodology is presented. The results show that the proposed scheme can provide higher throughput for cell-edge users while maintaining the fairness towards other users in the system.
An experimental apparatus for measuring underwater acoustic scattering from structurally complex finite cylinders (1994)

Theoretical predictions of the scattering from submerged circular cylinders benefit from the simplicities inherent in the assumption of infinite length. Consequently, experimental verification of these predictions typically involves cylinders with high length to diameter ratios in order to approximate this assumption. However, there are obvious advantages in dealing with shorter targets. This paper describes an experimental apparatus for measuring the scattering from circular cylinders with length to diameter ratios of one. By minimizing the scattering from the endcaps and minimizing the extent to which the endcaps restrict the motion of the shell, the cylinder can be made to have scattering characteristics (in the plane perpendicular to its axis) similar to that of an infinitely long cylinder. Because larger diameters can be accommodated, a wide range of structural details can be more easily studied. Experimental results are presented for this shells, thin shells with ring supports, and ring supported thin shells with compliant outer layers. The experimental data are compared with numerical results from two- and three-dimensional computer models. [Work supported by ONR.]
Distributed Orchestration in Cloud Data Centers (2019)

Orchestration systems in cloud platforms are responsible for creating, managing and assigning the computational and network bandwidth resources to the requesting services. Conventional orchestration approaches in data centers are based on centralized solutions where they are a single point of failure, and a potential performance bottleneck. In this paper, using the notions of Markov approximation method and auction theory, we propose a fully distributed resource management scheme for data centers. The proposed solution takes into account the operational and economic constraints of the services and the servers in the data center and maximizes a global system utility function in a fully distributed manner. Simulation results show the effectiveness of the proposed solution in terms of speed of convergence, accuracy and resource utilization for applicability in next generation cloud systems.
A computationally efficient method for quantum transport simulation of Double-Gate MOSFETs (2009)

Quantum effects play an important role in determining the Double-Gate (DG) MOSFETs characteristics. The Non-Equilibrium Green's Function (NEGF) formalism provides a rigorous description of quantum transport in nanoscale devices. The traditional NEGF is heavy in computations and not suitable for 3D or even 2D device simulation. In this article, we propose a method that reduces the simulation time dramatically without loss of accuracy. The proposed method is used to simulate a 5 nm channel length DG MOSFET. The simulation time is reduced from 72 minutes to 11 minutes per bias point on a home PC: Intel® Pentium 4 CPU 2.4GHz, 768 MB RAM.
A comparison of three commercial platforms for urinary NGAL in critically ill adults (2015)

All three methods for uNGAL showed acceptable performance for the tested parameters and are comparable with each other at clinically relevant cutoffs. However, Architect yields lower results than the other two methods, with a bias more pronounced at higher uNGAL concentrations, suggesting additional standardization efforts will likely be necessary to better harmonize the uNGAL methods at various clinically relevant cutoffs.
PSMB11 Orchestrates the Development of CD4 and CD8 Thymocytes via Regulation of Gene Expression in Cortical Thymic Epithelial Cells (2018)

Abstract T cell development depends on sequential interactions of thymocytes with cortical thymic epithelial cells (cTECs) and medullary thymic epithelial cells. PSMB11 is a catalytic proteasomal subunit present exclusively in cTECs. Because proteasomes regulate transcriptional activity, we asked whether PSMB11 might affect gene expression in cTECs. We report that PSMB11 regulates the expression of 850 cTEC genes that modulate lymphostromal interactions primarily via the WNT signaling pathway. cTECs from Psmb11−/− mice 1) acquire features of medullary thymic epithelial cells and 2) retain CD8 thymocytes in the thymic cortex, thereby impairing phase 2 of positive selection, 3) perturbing CD8 T cell development, and 4) causing dramatic oxidative stress leading to apoptosis of CD8 thymocytes. Deletion of Psmb11 also causes major oxidative stress in CD4 thymocytes. However, CD4 thymocytes do not undergo apoptosis because, unlike CD8 thymocytes, they upregulate expression of chaperones and inhibitors of apoptosis. We conclude that PSMB11 has pervasive effects on both CD4 and CD8 thymocytes via regulation of gene expression in cTECs.
Nucleoside triphosphate pentose ring impact on CFTR gating and hydrolysis (2002)

Alterations in the pentose ring of ATP have a major impact on cystic fibrosis transmembrane conductance regulator (CFTR) function. Both 2'- and 3'-deoxy-ATP (dATP) accelerate ion channel openings and stabilize open channel structure better than ATP. Purified wild-type CFTR hydrolyzes dATP. The apparent first-order rate constants for hydrolysis at low substrate concentration are the same for dATP and ATP. This suggests that product release and/or relaxation of the enzyme structure to the initial ligand free state is the rate-limiting step in the CFTR hydrolytic cycle. Circumvention of the normal requirement for protein kinase A phosphorylation of the R-domain for channel activation implies that the impact of the deoxyribonucleotide interaction with the nucleotide binding domains is transmitted to the channel-forming elements of the protein more readily than that of the ribonucleotide.
Leveraging an Open Science Drug Discovery Model to Develop CNS-Penetrant ALK2 Inhibitors for the Treatment of Diffuse Intrinsic Pontine Glioma (2020)

There are currently no effective chemotherapeutic drugs approved for the treatment of diffuse intrinsic pontine glioma (DIPG), an aggressive pediatric cancer resident in the pons region of the brainstem. Radiation therapy is beneficial but not curative, with the condition being uniformly fatal. Analysis of the genomic landscape surrounding DIPG has revealed that activin receptor-like kinase-2 (ALK2) constitutes a potential target for therapeutic intervention given its dysregulation in the disease. We adopted an open science approach to develop a series of potent, selective, orally bioavailable, and brain-penetrant ALK2 inhibitors based on the lead compound LDN-214117. Modest structural changes to the C-3, C-4, and C-5 position substituents of the core pyridine ring afforded compounds M4K2009, M4K2117, and M4K2163, each with a superior potency, selectivity, and/or blood–brain barrier (BBB) penetration profile. Robust in vivo pharmacokinetic (PK) properties and tolerability mark these inhibitors as advanced preclinical compounds suitable for further development and evaluation in orthotopic models of DIPG.
Downregulation of Metabolic Activity Increases Cell Survival Under Hypoxic Conditions: Potential Applications for Tissue Engineering (2014)

A major challenge to the success of cell-based implants for tissue regeneration is an insufficient supply of oxygen before host vasculature is integrated into the implants, resulting in premature cell death and dysfunction. Whereas increasing oxygenation to the implants has been a major focus in the field, our strategy is aimed at lowering oxygen consumption by downregulating cellular metabolism of cell-based implants. Adenosine, which is a purine nucleoside that functions as an energy transferring molecule, has been reported to increase under hypoxia, resulting in reducing the adenosine triphosphate (ATP) demands of the Na(+)/K(+) ATPase. In the present study, we investigated whether adenosine could be used to downregulate cellular metabolism to achieve prolonged survival under hypoxic conditions. Murine myoblasts (C2C12) lacking a self-survival mechanism were treated with adenosine under 0.1% hypoxic stress. The cells, cultured in the presence of 5 mM adenosine, maintained their viability under hypoxia, and regained their normal growth and function of forming myotubes when transferred to normoxic conditions at day 11 without further supply of adenosine, whereas nontreated cells failed to survive. An increase in adenosine concentrations shortened the onset of reproliferation after transfer to normoxic conditions. This increase correlated with an increase in metabolic downregulation during the early phase of hypoxia. A higher intracellular ATP level was observed in adenosine-treated cells throughout the duration of hypoxia. This strategy of increasing cell survival under hypoxic conditions through downregulating cellular metabolism may be utilized for cell-based tissue regeneration applications as well as protecting tissues against hypoxic injuries.
Late Infection After Spinal Fusion for Adolescent Idiopathic Scoliosis: Implant Exchange Versus Removal (2023)

Level III.
Association of Family History of Cancer with Clinical and Pathological Outcomes for Prostate Cancer Patients on Active Surveillance (2022)

While FHP was associated with an increased risk of progression on AS, wide confidence intervals render this outcome of unclear clinical significance. FHC was not associated with risk of progression on AS. In the absence of known genetically defined hereditary cancer syndrome, we suggest FHP and/or FHC should not be used as a sole trigger to preclude patients from enrolling on AS.