gebhart/patrepeval huggingface dataset:
New 3D-Culture Approaches to Study Interactions of Bone Marrow Adipocytes with Metastatic Prostate Cancer Cells (2016)

Adipocytes are a major component of the bone marrow that can critically affect metastatic progression in bone. Understanding how the marrow fat cells influence growth, behavior, and survival of tumor cells requires utilization of in vitro cell systems that can closely mimic the physiological microenvironment. Herein, we present two new three-dimensional (3D) culture approaches to study adipocyte-tumor cell interactions in vitro. The first is a transwell-based system composed of the marrow-derived adipocytes in 3D collagen I gels and reconstituted basement membrane-overlayed prostate tumor cell spheroids. Tumor cells cultured under these 3D conditions are continuously exposed to adipocyte-derived factors, and their response can be evaluated by morphological and immunohistochemical analyses. We show via immunofluorescence analysis of metabolism-associated proteins that under 3D conditions tumor cells have significantly different metabolic response to adipocytes than tumor cells grown in 2D culture. We also demonstrate that this model allows for incorporation of other cell types, such as bone marrow macrophages, and utilization of dye-quenched collagen substrates for examination of proteolysis-driven responses to adipocyte- and macrophage-derived factors. Our second 3D culture system is designed to study tumor cell invasion toward the adipocytes and the consequent interaction between the two cell types. In this model, marrow adipocytes are separated from the fluorescently labeled tumor cells by a layer of collagen I. At designated time points, adipocytes are stained with BODIPY and confocal z-stacks are taken through the depth of the entire culture to determine the distance traveled between the two cell types over time. We demonstrate that this system can be utilized to study effects of candidate factors on tumor invasion toward the adipocytes. We also show that immunohistochemical analyses can be performed to evaluate the impact of direct interaction of prostate tumor cells with adipocytes. Our models underline the importance of using the appropriate culture conditions to mimic physiological interactions between marrow adipocytes and metastatic tumor cells. These systems have a potential to be utilized for analyses of various factors that may be regulated by the adipocytes in bone. Their application likely extends beyond metastatic prostate cancer to other tumors that colonize the bone marrow microenvironment.
High efficiency (1.2 mW/mA) top-surface-emitting GaAs quantum well lasers (1990)

Highly efficient (1.2 mW/mA, >70% CW differential quantum efficiency), top-surface-emitting, vertical cavity lasers are achieved at room temperature. Buried damage layers by proton implantation are used for efficient current funnelling. The CW threshold currents are 3.5–8.0 mA, at 3.7–4.2 V bias, for 10.30 μm diameter lasers. The lasing wavelengths are 845–848 nm.
Wheat Germ Agglutinin Functionalized Complexation Hydrogels for Oral Insulin Delivery (2008)

Insulin was loaded into hydrogel microparticles after two hours with loading efficiencies greater than 70% for both poly(methacrylic acid-grafted-ethylene glycol) (P(MAA-g-EG)) and poly(methacrylic acid-grafted-ethylene glycol) functionalized with wheat germ agglutinin (P(MAA-g-EG) WGA). The pH-responsive release results demonstrated that the pH shift from the stomach to the small intestine can be used as a physiologic trigger to release insulin from P(MAA-g-EG) and P(MAA-g-EG) WGA microparticles, thus limiting release of insulin into the acidic environment of the stomach. Microplates were successfully treated with PGM to create a surface that allowed for specific binding between mucins and lectins. The 1% PGM treatment followed by a 2 h BSA blocking step gave the most consistent results when incubated with F-WGA. In addition, the PGM-treated microplates were shown to create specific interactions between F-WGA and the PGM by use of a competitive carbohydrate. The 1% PGM treated microplates were also used to show that adhesion was improved in the P(MAA-g-EG) WGA microparticles over the P(MAA-g-EG) microparticles. The interaction between the PGM-treated microplate and P(MAA-g-EG) WGA was again shown to be specific by adding a competitive carbohydrate, while the interaction between P(MAA-g-EG) and the PGM-treated microplate was nonspecific. Cellular monolayers were used as another method for demonstrating that the functionalized microparticles increase adhesion over the nonfunctionalized microparticles. This work has focused on improving the mucoadhesive nature of P(MAA-g-EG) by functionalizing these hydrogel carriers with wheat germ agglutinin (WGA) to create a specific mucosal interaction and then evaluating the potential of these carriers as oral insulin delivery systems by in vitro methods. From these studies, it is concluded that the addition of the WGA on the microparticles produces a specific adhesion to carbohydrate-containing surfaces and that P(MAA-g-EG) WGA shows great promise as an oral insulin delivery system.
Erratum: "Magnetotransport properties and spin-torque effects in current perpendicular to the plane spine valves with Co–Fe–Al magnetic layers” [J. Appl. Phys. 101, 093905 (2007)] (2007)

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Phagocytosing neutrophils produce and release high amounts of the neutrophil-activating peptide 1/interleukin 8. (1991)

After phagocytosis of yeast opsonized with IgG, neutrophil leukocytes (polymorphonuclear leukocytes [PMN]) expressed high levels of neutrophil-activating peptide 1/interleukin 8 (NAP-1/IL-8) mRNA, which peaked after 3-5 h and were still elevated after 18 h. A similar but quantitatively less prominent effect was obtained with lipopolysaccharide (LPS). After phagocytosis, but not after exposure to LPS, the PMN progressively released considerable amounts of NAP-1/IL-8 into the culture medium (18.6-50 ng/ml in 18 h). The peptide released was biologically active, as indicated by the transient elevation of cytosolic-free calcium in PMN exposed to aliquots of the culture supernatants, and desensitization by prestimulation of the cells with recombinant NAP-1/IL-8. By producing NAP-1/IL-8 at sites where they phagocytose invading microorganisms, PMN could enhance the recruitment of new defense cells.
A HIGH-VOLUME SMALL CUTPOINT VIRTUAL IMPACTOR FOR SEPARATION OF ATMOSPHERIC PARTICULATE FROM GASEOUS POLLUTANTS (1994)

ABSTRACT This paper discusses the development of an alternative technology to sample separately the gas and particulate phases of atmospheric pollutants. The key feature of this technique is the utilization of a slit nozzle virtual impactor with a small 50% cutpoint (0.1 µm) to sample atmospheric pollutants at high flow rates (225 LPM). In contrast to the diffusion denuder/filter pack and impactor/filter pack techniques, which collect gas and particulate phases sequentially, the two phases are separated in a virtual impactor and collected independently, to eliminate sampling artifacts. The virtual impactor has been characterized in laboratory studies using fluorescent monodisperse aerosols, and in field studies by comparing its performance to the performance of a collocated dichotomous sampler. The results indicate that the minor flow (consisting of particles in the range 0.1 < dp < 2.5 µ m) flow of the virtual impactor contained on the average 80% of the total ambient fine mass. In addition, particle losses range from 5 to 15%, and tend to slightly increase with particle size.
Molecular Characterization of the <i>Salmonella enterica</i> Serovar Typhi Vi-Typing Bacteriophage E1 (2008)

Some bacteriophages target potentially pathogenic bacteria by exploiting surface-associated virulence factors as receptors. For example, phage have been identified that exhibit specificity for Vi capsule producing Salmonella enterica serovar Typhi. Here we have characterized the Vi-associated E1-typing bacteriophage using a number of molecular approaches. The absolute requirement for Vi capsule expression for infectivity was demonstrated using different Vi-negative S. enterica derivatives. The phage particles were shown to have an icosahedral head and a long noncontractile tail structure. The genome is 45,362 bp in length with defined capsid and tail regions that exhibit significant homology to the S. enterica transducing phage ES18. Mass spectrometry was used to confirm the presence of a number of hypothetical proteins in the Vi phage E1 particle and demonstrate that a number of phage proteins are modified posttranslationally. The genome of the Vi phage E1 is significantly related to other bacteriophages belonging to the same serovar Typhi phage-typing set, and we demonstrate a role for phage DNA modification in determining host specificity.
Dominance of Broken Bonds and Unpaired Nonbonding π-Electrons in the Band Gap Expansion and Edge States Generation in Graphene Nanoribbons (2008)

Incorporating the bond-order-length-strength (BOLS) correlation theory [Sun, C. Q. Prog. Solid State Chem. 2007, 35, 1] to density functional theory calculations and experimental observations has led to consistent insight into the electronic behavior of graphene nanoribbons (GNRs) from the perspective of bond formation, dissociation and relaxation and the associated dynamics and energetics of charge densification, localization, and polarization. The consistency between the BOLS predictions and the observed coordination dependence of bond contraction and the associated thermal instability, mechanical strength, and band structure variation in various situations evidence the significance of the broken bond that induces local strain and quantum trapping. The inconsistency between the theoretically and experimentally observed band gap expansions in GNRs indicates particularly the impact of the unpaired nonbonding (called π-bond) electrons and the adsorbate-induced inhomogeneous repulsion along the edges. A perturbation to the Hamiltonian by the local strain and edge trapping dictates intrinsically the band structure yet the presence and polarization of the nonbonding states by the nearby densely trapped bonding electrons and the adsorbate-induced inhomogeneous repulsion along the edges dominate the observed edge states.
Early immune recovery after autologous transplantation in non-Hodgkin lymphoma patients: predictive factors and clinical significance (2016)

Limited data is available about the factors affecting early immune recovery or its clinical significance after autologous stem cell transplantation (auto-SCT). We prospectively analyzed factors affecting early immune recovery and outcome among 72 non-Hodgkin lymphoma (NHL) patients. Absolute lymphocyte count 15 d after auto-SCT (ALC-15) ≥ 0.5 × 10(9)/L was associated with the use of plerixafor (p = 0.004), the number of CD34(+) cells (p = 0.015), and CD34(+) CD38(-) cells (p = 0.005) in the grafts. ALC-15 ≥ 0.5 × 10(9)/L was associated with improved overall survival (p = 0.021). In patients with aggressive histology, ALC-15 ≥ 0.5 × 10(9)/L was beneficial in regard to both progression-free survival (p = 0.015) and overall survival (p = 0.002). Early immune recovery seems to be important in transplanted patients with NHL and, therefore, an easy and affordable method for disease-related risk analysis. Patients with aggressive histology and slow immune recovery may need additional post-transplant treatment.
Delay-constrained energy-efficient wireless packet scheduling with QoS guarantees (2005)

This paper considers packet scheduling with delay constraint that minimizes the average transmission energy expenditure in a wireless environment. There were recent studies that modeled transmission rate as a linear combination of input packet arrivals in the derivation of optimal scheduling policies for independent input arrivals. In this paper, we extend the scheduling policies in two aspects. We first consider the impact of input time-correlation and derive an optimal scheduling policy for energy minimization. It is observed that existing energy optimized scheduling policies save energy by transmitting packets slowly. They may result in unexpected deadline misses. We establish a relationship between the maximum reliable transmission rate and a QoS constraint, characterized by a deadline miss rate. The relationship facilitates the trade-off study of power consumption and delay constraint. Simulation results verify the relationship and show the superiority of the scheduler in comparison with the existing approaches.
Ice Forces on Conival Structures (1979)

ABSTRACT In some Arctic- offshore areas, the principal design loads for a fixed offshore structure will be those associated with the impingement of relatively uniform sheets of ice. There are many uncertainties and approximations associated with analytical treatments of this complex phenomenon. Since 1970 Chevron Oil Field Research Company has been operating an experimental ice force model tank to investigate ice forces on various model structures due to uniform ice sheets with various characteristics. This paper describes this facility and the procedures used in it to carry out determinations of ice forces on conical structures. Also described are the utilization of an-appropriately weakened model ice, and the determination of its mechanical properties. Included are descriptions of experiments conducted on 45° and 60° model cones, as well as experiments on a multiangle conical structure. This latter structure consists of two cones, with the lower cone having a shallower slope angle than the upper. Qualitative aspects of the ice sheet properties and of the horizontal and vertical force time histories for these experiments are also included. A principal conclusion is that small-scale modeling of ice-structure interaction can be carried out on a routine basis. INTRODUCTION In considering the problem of determining the forces that may be exerted on an offshore platform by impinging ice, it is important to note that the nature and properties of the ice features that the platform may encounter and the geometry of the platform are some of the principal factors that affect the magnitude of the forces. These same factors also influence the approaches that may be taken to evaluate the magnitude of the forces. For example, model testing with full strength ice may be appropriate for evaluating ice forces on cylindrical structures wherein the mode of ice failure is crushing. The same type of testing will generally not be appropriate, however, for evaluating ice forces on conical structures. Development of offshore structures for near shore areas o£ the Beaufort Sea provided the primary motivation for the work described herein; however, the methodology presented is also applicable to designs for other ice-infested areas. Model ice force experiments conducted in the Chevron ice force test facility, and discussed below, were aimed at investigating ice forces imposed by uniform ice sheets impinging on conical structures. Descriptions of the test procedures, model ice properties, ice test features, and data analysis procedures are included in the discussion. In addition, observations based on tests of single-angle and multiangle model cones are presented. CONTROLLING FACTORS Ice Features The sea ice occurring in the Arctic off the north coast of Alaska may generally be divided into three distinct zones or regions, namely (1) a fast ice zone, (2) a seasonal pack ice zone, and (3) a polar pack zone. The land fast ice zone consists of seasonal ice that extends from shore to roughly the 20-meter bathymetric contour. The seasonal pack ice zone extends roughly from the fast ice zone to the edge of the continental shelf.
High Pressure Interpass Rolling of Wire + Arc Additively Manufactured Titanium Components (2014)

Wire + Arc Additively Manufactured components contain significant residual stresses that manifest in distortion. Each layer of an additively manufactured wall was rolled with the aim of reducing the residual stress. Neutron diffraction and contour method measurements show that the residual stresses were reduced particularly at the boundary with the substrate. The process also reduced distortion, and refined the microstructure which may facilitate implementation on aerospace components.
An Assessment of Critical Dimension Small Angle X-ray Scattering Metrology for Advanced Semiconductor Manufacturing (2015)

Simultaneous migration of planar transistors to FinFET architectures, the introduction of a plurality of materials to ensure suitable electrical characteristics, and the establishment of reliable multiple patterning lithography schemes to pattern sub-10 nm feature sizes imposes formidable challenges to current in-line dimensional metrologies. Because the shape of a FinFET channel cross-section immediately influences the electrical characteristics, the evaluation of 3D device structures requires measurement of parameters beyond traditional critical dimension (CD), including their sidewall angles, top corner rounding and footing, roughness, recesses and undercuts at single nanometer dimensions; thus, metrologies require sub-nm and approaching atomic level measurement uncertainty. Synchrotron critical dimension small angle X-ray scattering (CD-SAXS) has unique capabilities to non-destructively monitor the cross-section shape of surface structures with single nanometer uncertainty and can perform overlay metrology to sub-nm uncertainty. In this dissertation, we perform a systematic experimental investigation using CD-SAXS metrology on a hierarchy of semiconductor 3D device architectures including, high-aspect-ratio contact holes, H2 annealed Si fins, and a series of grating type samples at multiple points along a FinFET fabrication process increasing in structural intricacy and ending with fully fabricated FinFET. Comparative studies between CD-SAXS metrology and other relevant semiconductor dimensional metrologies, particularly CDSEM, CD-AFM and TEM are used to determine physical limits of CD-SAXS approach for advanced semiconductor samples. CD-SAXS experimental tradeoffs, advice for model-dependent analysis and thoughts on the compatibility with a semiconductor manufacturing environment are discussed.
Discovery of 2‐Aminothiazole‐4‐carboxamides, a Novel Class of Muscarinic M<sub>3</sub> Selective Antagonists, Through Solution‐Phase Parallel Synthesis. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
EXCES: External caching in energy saving storage systems (2008)

Power consumption within the disk-based storage subsystem forms a substantial portion of the overall energy footprint in commodity systems. Researchers have proposed external caching on a persistent, low-power storage device, which we term external caching device (ECD), to minimize disk activity and conserve energy. While recent simulation-based studies have argued in favor of this approach, the lack of an actual system implementation has precluded answering several key questions about external caching systems. We present the design and implementation of EXCES, an external caching system that employs prefetching, caching, and buffering of disk data for reducing disk activity. EXCES addresses important questions related to external caching, including the estimation of future data popularity, I/O indirection, continuous reconfiguration of the ECD contents, and data consistency. We evaluated EXCES with both micro- and macro- benchmarks that address idle, I/O intensive, and real-world workloads. Overall system energy savings was found to lie in the modest 2–14% range, depending on the workload, in somewhat of a contrast to the higher values predicted by earlier studies. Furthermore, while the CPU and memory overheads of EXCES were well within acceptable limits, we found that flash-based external caching can substantially degrade I/O performance. We believe that external caching systems hold promise. Further improvements in ECD technology, both in terms of their power consumption and performance characteristics can help realize the full potential of such systems.
Two alternative models concerning the perialveolar microcirculation in mammalian lungs (2005)

Despite the fact that the concept of sheet-flow in the pulmonary microcirculation of mammals was introduced more than three decades ago, the capillary circulatory model still prevails in the physiological literature. Since cardiac output is identical in the systemic and in pulmonary circulations, it is noteworthy that in the former, the resulting arterial pressure is five times higher than that of the latter, which means that the corresponding microcirculations must be radically different. The present study addresses this problem from both morphological and physiological perspectives.
Rapid, Point-of-Care Extraction of Human Immunodeficiency Virus Type 1 Proviral DNA from Whole Blood for Detection by Real-Time PCR (2009)

PCR detection of human immunodeficiency virus type 1 (HIV-1) proviral DNA is the method recommended for use for the diagnosis of HIV-1 infection in infants in limited-resource settings. Currently, testing must be performed in central laboratories, which are usually located some distance from health care facilities. While the collection and transportation of samples, such as dried blood spots, has improved test accessibility, the results are often not returned for several weeks. To enable PCR to be performed at the point of care while the mothers wait, we have developed a vertical filtration method that uses a separation membrane and an absorbent pad to extract cellular DNA from whole blood in less than 2 min. Cells are trapped in the separation membrane as the specimen is collected, and then a lysis buffer is added. The membrane retains the DNA, while the buffer washes away PCR inhibitors, which get wicked into the absorbent blotter pad. The membrane containing the entrapped DNA is then added to the PCR mixture without further purification. The method demonstrates a high degree of reproducibility and analytical sensitivity and allows the quantification of as few as 20 copies of HIV-1 proviral DNA from 100 microl of blood. In a blinded study with 182 longitudinal samples from infants (ages, 0 to 72 weeks) obtained from the Women and Infants Transmission Study, our assay demonstrated a sensitivity of 99% and a specificity of 100%.
An adaptive divide-and-predict coding for intra-frame of H.264/AVC (2009)

A new intra-frame coding scheme is proposed for progressive video sequences in H.264/AVC. In the proposed method, every other pixel is sampled either in a horizontal or vertical direction without any anti-aliasing filtering, and two sub-frames of the even-pixel and odd-pixel are then generated. The even-pixel and odd-pixel sub-frames are coded by the intra-and inter-frame coding methods, respectively. Our proposed method can be expanded into a multi-level case in which the even-pixel sub-frame is again subdivided into an even-pixel sub-frame and an odd-pixel sub-frame, and so on to further improve the coding efficiency. The experimental results show that our proposed method reduces the bitrate by approximately 8.25% more than the conventional intra-frame coding in H.264/AVC.
Natural Convection over Heated L-corner (2006)

Experimental investigations have been carried out on natural convective flows over a heated L-corner in which the vertical plate was shorter than the horizontal plate. Special interest was paid to the fluid flow and heat transfer around the vertical plate. The height of vertical plates, H, were varied as H=10-150mm. The width of horizontal plate was 350mm constant. The test fluid was water. The flow fields and the surface temperatures were visualized with fluorescent dye and liquid crystal thermometry, respectively. The local heat transfer coefficients of the vertical plate were also measured. The result shows that the recirculating flow appears irregularly around the vertical plate when H is less than 30mm. It is also found that the local heat transfer coefficients show a maximum at H/2 when the recirculating flow appears around the vertical plate.