gebhart/patrepeval huggingface dataset:
Vacancy Coalescence during Oxidation of Iron Nanoparticles (2007)

In the present work, we analyze the geometry and composition of the nanostructures obtained from the oxidation of iron nanoparticles. The initial oxidation of iron takes place by outward diffusion of cations through the growing oxide shell. This net material flow is balanced by an opposite flow of vacancies, which coalesce at the metal/oxide interface. Thus, the partial oxidation of colloidal iron nanoparticles leads to the formation of core−void−shell nanostructures. Furthermore, the complete oxidation of iron nanoparticles in the 3−8 nm size range leads to the formation of hollow iron oxide nanoparticles. We analyze the size and temperature range in which vacancy coalescence during oxidation of amine-stabilized iron nanoparticles takes place. Maghemite is the crystallographic structure obtained from the complete oxidation of iron nanoparticles under our synthetic conditions.
Branched aliphatic alkanes with quaternary substituted carbon atoms in modern and ancient geologic samples (2003)

A pseudohomologous series of branched aliphatic alkanes with a quaternary substituted carbon atom (BAQCs, specifically 2,2-dimethylalkanes and 3,3- and 5,5-diethylalkanes) were identified in warm (65 degrees C) deep-sea hydrothermal waters and Late Cretaceous black shales. 5,5-Diethylalkanes were also observed in modern and Holocene marine shelf sediments and in shales spanning the last 800 million years of the geological record. The carbon number distribution of BAQCs indicates a biological origin. These compounds were observed but not identified in previous studies of 2.0 billion- to 2.2 billion-year-old metasediments and were commonly misidentified in other sediment samples, indicating that BAQCs are widespread in the geological record. The source organisms of BAQCs are unknown, but their paleobiogeographic distribution suggests that they have an affinity for sulfides and might be nonphotosynthetic sulfide oxidizers.
Forming Antifouling Organic Multilayers on Porous Silicon Rugate Filters Towards In Vivo/Ex Vivo Biophotonic Devices (2007)

Abstract We describe the development and optimization of porous silicon photonic crystal surface chemistry towards implantable optical devices. Porous silicon rugate filters were prepared to obtain a narrow linewidth reflectivity peak in the near‐infrared (700–1000 nm) with low background reflectivity elsewhere. The morphology of the mesoporous structures (pore diameter < 50 nm) was such that only small proteins could infiltrate the pores whereas larger proteins were excluded. To provide stability in biological media, we established an approach to build organic multilayers containing hexa(ethylene oxide) moieties in porous silicon. The optical changes associated with organic derivatization were monitored concurrently with FTIR characterization. Furthermore, the antifouling capability of our chemical strategy is assessed and the penetration of different sized proteins into the structure was determined. The structural stability in biological environments was evaluated by incubation in human blood plasma over time while monitoring the optical signature of the photonic crystal.
Low Temperature Silver Sinter Processes on ENIG Surfaces (2016)

The demand for compact and highly integrated power electronic devices is growing continuously. However, the increase in power density leads to higher operation temperatures of the power modules causing premature device failures. One of the major failure sources is the standard SAC solder to attach the die. Novel low temperature silver sinter die attachment materials are much more reliable. Most commercially available sinter materials have to be applied on noble surfaces like gold or silver. Therefore, the chip is metalized with silver and the DCB is coated by a layer of electroless nickel and immersion gold (ENIG). However, the sinter process quality on the ENIG layer is not always constant. Shear tests on various ENIG layers have been conducted exposing quality variations covering a range from 5 N/mm(exp 2) to more than 90 N/mm(exp 2). Wet chemical analysis as well as FIB-SEM and XPS-investigations have been performed to identify the root cause. We observed that test specimens showing lower shear values exhibit a higher copper and nickel concentration on the surface. These non-noble metals influence the formation of the intermetallic phase of the sinter layer and the substrate. Consequently, the mechanical stability and thermal resilience is reduced.
Correlation of mammographic breast density with Ki-67 expression in benign breast epithelial cells obtained by random periareolar fine needle aspiration of high risk women (2006)

1011 >Background: Known risk factors for breast cancer development include elements incorporated into the Gail risk model, mammographic breast density and cytologic atypia detected by Random Periareolar Fine Needle Aspiration (RPFNA). Ki-67 expression is a possible risk biomarker and is currently being used as a response biomarker in chemoprevention trials. We have previously shown that Ki-67 expression is higher in RPFNA specimens of benign breast cells exhibiting cytologic atypia. It is not known whether there is a correlation between mammographic density and Ki-67 expression in benign breast ductal cells obtained by RPFNA. Methods: 344 women at high risk of developing breast cancer (based on personal or family history) seen at The University of Kansas Medical Center high risk breast clinic, who underwent RPFNA with cytomorphology and Ki-67 assessment, plus a mammogram were included in the study. Mammographic breast density was assessed using the Cumulus program. Categorical variables were analyzed by Chi-square test and continuous variables were analyzed by non-parametric test and linear regression. Results: 40% of women were premenopausal, 7% perimenopausal and 53% were postmenopausal. Median age was 49 years, median 5 year Gail Risk was 2.2%, and median Ki-67 was 1.9%. Median mammographic breast density was 37%. Ki-67 expression increased with cytologic abnormality and number of cells collected, but was unrelated to Gail risk (as observed previously). Breast density was higher in pre-menopausal women (p=0.001), those with lower BMI (p< 0.001), and lower 5-year Gail risk (p=0.012); Breast density showed no correlation with Ki-67 expression or cytomorphology. Conclusion: Given the lack of correlation of mammographic breast density with either cytomorphology or Ki-67 expression in RPFNA specimens, mammographic density and Ki-67 expression should be considered as potentially complementary response biomarkers for breast cancer chemoprevention trials. No significant financial relationships to disclose.
<title>Use of graphics hardware to accelerate algebraic reconstruction methods</title> (1999)

The Algebraic Reconstruction Technique (ART) reconstructs a 2D or 3D object from its projections. It has, in certain scenarios, many advantages over the more popular Filtered Backprojection approaches and has also recently been shown to perform well for 3D cone-beam reconstruction. However, so far, ART's slow speed has prohibited its routine use in clinical applications. Currently, a software implementation requires several hours for a 3D reconstruction, even on modest reconstruction grid sizes. Although one solution to combat these problems would be the time-consuming design of expensive custom accelerator boards, we would rather like to resort to existing and widely available hardware for our purposes. In this sense, we find that ART's main operations, i.e., volume projections and image backprojections, can be performed very rapidly on standard 2D texture mapping hardware, resident in many graphics workstations and PC graphics boards. In this paper, we discuss the use of this hardware in two volume decomposition modes: voxel and slice. Although we find that the speedups obtained in the voxel mode are respectable, the speedups obtained in the slice-mode are tremendous. Here, a quality cone-beam reconstruction on a 128<SUP>3</SUP> grid can be obtained in less than 2 minutes, which corresponds to a speedup of over 70. Since our rapid ART reconstruction algorithm can be run on the same workstations that are typically used for the viewing of clinical datasets, it is immediately available for routine parallel- and cone-beam CT.
Validation of Conductance Catheter System for Quantification of Murine Pressure-Volume Loops (2001)

The purpose of this study was to define the validation methods and outcomes of a conductance catheter system specifically for in vivo murine cardiac hemodynamic analysis. To express the relationship between conductance and blood volumes, we used an in vitro model to derive a volume-conductance line. The volume-conductance line was used to compute raw volume from the modified conductance signals. The parallel volume was calibrated with hypertonic (15%) saline injected from extrajugular vein. The ventricular volume was computed by raw volume minus parallel volume. The accuracy of conductance volumetric measurements was validated with a static in situ infusion of calibrated volumes of whole blood injected into arrested left ventricles. In vivo dynamic measurements were performed with 24 C57B1/6 mice, 6 months old; for comparison of established values. The in situ model showed that after calibration, the experimental coefficient, alpha, was equal to 1 and the measured volume by conductance catheter was equal to the true volume of the left ventricle (y = 0.982x + 0.513, p < .0001). For the in vivo models, the end-diastolic volumes and the stroke volumes and cardiac output determined with the conductance catheter system were 17.3 +/- 1.0 microL, 10.6 +/- 0.9 microL, and 6.0 +/- 0.5 mL/min, respectively. We validated the relationship between measured volume by conductance catheter and the true volume and demonstrated the accuracy of the volume-conductance line for conversion of conductance to volume.
Synchronization in Packet Networks: Timing Metrics and Monitoring (2008)

Abstract : Packet Delay Variation (PDV) is a major impediment to transferring timing from a source (Master/Server) to destination (Slave/Client) over a packet-switched network. PDV directly affects frequency alignment (synchronization) and asymmetry of PDV impacts time alignment (phase). There is considerable interest in the industry to establish a relationship between PDV and the ability to recover time/phase/frequency via a packet-based method (e.g., PTP, NTP). Recent developments in PDV analysis have indicated that it is feasible to build accurate models of network behavior under varying conditions of load, number of switches, forwarding algorithms, QoS implementation, and so on. It has also been shown that no single metric (e.g., TDEV, minTDEV) is sufficient to characterize PDV and that a suite of metrics is necessary. Study of PDV also develops intuition and permits heuristic approaches to be devised that use nonlinear processing to filtering of the PDV, greatly enhancing the performance of clock recovery compared to linear PLL methods. In this presentation, Brilliant will provide experimental results and demonstrate that: (1) Practice does indeed have relationship to theory. Proper measurements are indeed consistent, repeatable, and significantly predictable; (2) Proper heuristics and multiple metrics provide high-quality clock recovery and knowledge of the transport layer (e.g., GigE, xDSL) can be applied to improve performance.
Oligomerized tumor necrosis factor‐related apoptosis inducing ligand strongly induces cell death in myeloma cells, but also activates proinflammatory signaling pathways (2009)

The oligomerization status of soluble tumor necrosis factor-related apoptosis inducing ligand (TRAIL) trimers has an overwhelming impact on cell death induction in a cell-type dependent fashion. Thus, we evaluated the ability of single and oligomerized TRAIL trimers to induce cell death in human myeloma cells. In all myeloma cell lines analyzed, oligomerized TRAIL trimers induced caspase activation and complete cell death, whereas non-oligomerized TRAIL trimers showed no or only a modest effect. Caspase activation induced by oligomerized TRAIL was blocked in all cell lines by the pan-caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone (z-VAD-fmk). Cell death induction was largely blocked in two cell lines by z-VAD-fmk, but was only marginally attenuated in three other cell lines, indicating that TRAIL induces caspase-dependent and caspase-independent cell death in myeloma cells. Preceding cell death, TRAIL activated nuclear factor kappaB, c-Jun N-terminal kinase, p38 and p42/44. Although TRAIL-induced stimulation of c-Jun N-terminal kinase and p38 was caspase-dependent in a cell type-specific fashion, activation of nuclear factor kappaB and p42/44 was caspase-independent in all cases. In accordance with activation of the nuclear factor kappaB pathway, we observed transcriptional up-regulation of several well established nuclear factor kappaB target genes. Furthermore, we found that TRAIL activates proinflammatory pathways in approximately 50% of primary myeloma samples. Taken together, our data suggest (a) that oligomerized TRAIL variants are necessary to ensure maximal cell death induction in myeloma cells and (b) TRAIL should be used in combination with anti-inflammatory drugs for treatment of myeloma to avoid and/or minimize any potential side-effects arising from the proinflammatory properties of the molecule.
The Antiangiogenic Activity of rPAI-1 <sub>23</sub> Inhibits Vasa Vasorum and Growth of Atherosclerotic Plaque (2009)

Plaque vascularity has been implicated in its growth and stability. However, there is a paucity of information regarding the origin of plaque vasculature and the role of vasa vasorum in plaque growth. To inhibit growth of vasa vasorum in atherogenic mice and assess its effect on plaque growth, we used a truncated plasminogen activator inhibitor (PAI)-1 protein, rPAI-1(23), that has significant antiangiogenic activity. Female LDLR(-/-)ApoB-48-deficient mice fed Paigen's diet without cholate for 20 weeks received rPAI-1(23) treatment (n=21) for the last 6 weeks. Plaque size and vasa vasorum density were compared to 2 controls: mice fed Paigen's diet and treated with saline for the last 6 weeks (n=16) and mice fed Paigen's diet until the onset of treatment (n=14). The rPAI-1(23) treatment significantly reduced plaque area and plaque cholesterol in the descending aorta and plaque area in the innominate artery. Measurements of reconstructed confocal microscopy images of vasa vasorum demonstrate that rPAI-1(23) treatment decreased vasa vasorum area and length, which was supported by microCT images. Confocal images provide evidence for vascularized plaque in the saline-treated group but not in rPAI-1(23)-treated mice. The increased vessel density in saline-treated mice is attributable, in part, to upregulated fibroblast growth factor-2 expression, which is inhibited by rPAI-1(23). In conclusion, rPAI-1(23) inhibits growth of vasa vasorum, as well as vessels within the adjacent plaque and vessel wall, through inhibition of fibroblast growth factor-2, leading to reduced plaque growth in atherogenic female LDLR(-/-)ApoB-48-deficient mice.
Complex roles of the CXCR3 chemokines in immune-mediated neurological disease (96.1) (2007)

Abstract The chemokine receptor CXCR3 binds CXCL9, CXCL10 and CXCL11 and promotes the trafficking of activated T-cells. Although these chemokines are highly elevated in the CNS in MS and the animal model, experimental autoimmune encephalomyelitis (EAE), their role is unknown. Here we show that while IFN-γ is the principal mediator of CXCR3 ligand gene expression in the CNS in EAE, the cellular localization of the individual chemokine genes is divergent suggesting functional specialisation of the CXCR3 ligand chemokines. Transgenic mice (GF-) were generated with astrocyte-production of CXCL9, CXCL10 or CXCL11. These mice do not develop neurological disease. In GF-CXCL10 and -CXCL11 mice, modest non-reactive leukocytic infiltrates were seen in the CNS. Thus, these chemokines when produced chronically are a poor stimulus for the CNS recruitment and activation of T-cells. The role of CXCR3 signaling in MOG-induced EAE was examined in CXCR3 KO mice and in GF-CXCL9, -CXCL10 or -CXCL11 mice. CXCR3 KO, GF-CXCL9 and -CXCL11 mice had more severe EAE with widely disseminated demyelinating lesions throughout the CNS. In CXCR3 KO mice with EAE the number of suppressor Treg cells in the brain was reduced. Thus, in EAE, CXCR3 chemokine ligands: have non-redundant functions, are not involved in the initial recruitment of effector T-cells to the CNS, and retain T-cells to the perivascular space and foster Treg cell interactions thereby limiting lesion spread and tissue destruction. Support: NIH NS044905.
Challenges in Future Avionic Systems on Multi-Core Platforms (2014)

Modern avionic system development is undergoing a major transition, from federated systems to Integrated Modular Avionics (IMA) where several applications with mixed criticality will reside on the same platform. Moreover, there is a departure from today's single core computing, and we need to address the problem of how to guarantee determinism (in time and space) for application tasks running on multiple cores and interacting through shared memory. This paper summarizes the main challenges and briefly describes some active directions in research regarding temporal partitioning. It also outlines the forthcoming research that we will pursue for quantifying time bounds on memory access related interference, to ensure determinism and comply with certification requirements.
VISUALIZATION OF A DOCUMENT COLLECTION WITH IMPLICIT AND EXPLICIT LINKS: The Vibe System (1993)

We study a document collection based on the implicit associations among the documents and on the explicit links, such as hypertext links, citations or author names, that exist among the documents. The paper presents a visualization method that gives an overview of a document collection, where both implicit and explicit links are shown. Both hypertext and nonhypertext document collections may be visualized. The technique presented shows promise in providing a tool for presenting a holistic view of a document collection.
Hepatocyte Growth Factor Regulates the miR-206-HDAC4 Cascade to Control Neurogenic Muscle Atrophy following Surgical Denervation in Mice (2018)

Hepatocyte growth factor (HGF) has been well characterized for its roles in the migration of muscle progenitors during embryogenesis and the differentiation of muscle stem cells, but its function in adult neurogenic muscle atrophic conditions is poorly understood. Here we investigated whether HGF/c-met signaling has any effects on muscle-atrophic conditions. It was found that HGF expression was upregulated in skeletal muscle tissue following surgical denervation and in hSOD1-G93A transgenic mice showing severe muscle loss. Pharmacological inhibition of the c-met receptor decreased the expression level of pri-miR-206, enhanced that of HDAC4 and atrogenes, and resulted in increased muscle atrophy. In C2C12 cells, HGF inhibited phosphorylation of Smad3 and relieved TGF-β-mediated suppression of miR-206 expression via JNK. When extra HGF was exogenously provided through intramuscular injection of plasmid DNA expressing HGF, the extent of muscle atrophy was reduced, and the levels of all affected biochemical markers were changed accordingly, including those of primary and mature miR-206, HDAC4, and various atrogenes. Taken together, our finding suggested that HGF might play an important role in regard to neurogenic muscle atrophy and that HGF might be used as a platform to develop therapeutic agents for neuromuscular disorders.
Identification of a cellular ligand for the natural cytotoxicity receptor NKp44 (2013)

With an array of activating and inhibitory receptors, natural killer (NK) cells are involved in the eradication of infected, transformed, and tumor cells. NKp44 is a member of the natural cytotoxicity receptor family, which is exclusively expressed on activated NK cells. Here, we identify natural cytotoxicity receptor NKp44 (NKp44L), a novel isoform of the mixed-lineage leukemia-5 protein, as a cellular ligand for NKp44. Unlike the other MLL family members, NKp44L is excluded from the nucleus, but expressed at the cell-surface level; its subcellular localization is being associated with the presence of a specific C-terminal motif. Strikingly, NKp44L has not been detected on circulating cells isolated from healthy individuals, but it is expressed on a large panel of the tumor and transformed cells. The sharply decreased NK lysis activity induced by anti-NKp44L antibodies directly demonstrates the role of NKp44L in cytotoxicity. Taken together, these results show that NKp44L could be critical for NK cell-mediated innate immunity. The identification and cellular distribution of NKp44L highlight the role of this self-molecule as a danger signal to alert the NK cell network.
Streaming First Story Detection with application to Twitter (2010)

With the recent rise in popularity and size of social media, there is a growing need for systems that can extract useful information from this amount of data. We address the problem of detecting new events from a stream of Twitter posts. To make event detection feasible on web-scale corpora, we present an algorithm based on locality-sensitive hashing which is able overcome the limitations of traditional approaches, while maintaining competitive results. In particular, a comparison with a stateof-the-art system on the first story detection task shows that we achieve over an order of magnitude speedup in processing time, while retaining comparable performance. Event detection experiments on a collection of 160 million Twitter posts show that celebrity deaths are the fastest spreading news on Twitter. 1
ChemInform Abstract: Synthesis of Functionalized Trienes and Regioselective Formation of Medium‐Ring Lactones Through Intramolecular Diels‐Alder Reaction. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Magnetic Resonance Imaging: Physical Principles and Sequence Design (1999)

Magnetic Resonance Imaging: A Preview. Classical of a Single Nucleus to a Magnetic Field. Rotating Reference Frames and Resonance. Magnetization, Relaxation and the Bloch Equation. The Quantum Mechanical Basis of Precession and Excitation. The Quantum Mechanical Basis of Thermal Equilibrium and Longitudinal Relaxation. Signal Detection Concepts. Introductory Signal Acquisition Methods: Free Induction Decay, Spin Echoes, Inversion Recovery and Spectroscopy. One-Dimensional Fourier Imaging, k-Space and Gradient Echoes. Multi-Dimensional Fourier Imaging and Slice Excitation. The Continuous and Discrete Fourier Transforms. Sampling and Aliasing in Image Reconstruction. Filtering and Resolution in Fourier Transform Image Reconstruction. Projection Reconstruction of Images. Signal, Contrast and Noise. A Closer Look at Radiofrequency Pulses. Water/Fat Separation Techniques. Fast Imaging in the Steady State. Segmented k-Space and Echo Planar Imaging. Magnetic Field Inhomogeneity Effects and T-2 Dephasing. Random Walks, Relaxation and Diffusion. Spin Density, T-1 and T-2 Quantification Methods in MR Imaging. Motion Artifacts and Flow Compensation. MR Angiography and Flow Quantification. Magnetic Properties of Tissues: Theory and Measurement. Sequence Design, Artifacts and Nomenclature. Introduction to MRI Coils and Magnets. Appendices. Index.