gebhart/patrepeval huggingface dataset:
Functional hybrid nickel nanostructures as recyclable SERS substrates: detection of explosives and biowarfare agents (2012)

We present the synthesis of highly anisotropic nickel nanowires (NWs) and large area, free-standing carpets extending over cm(2) area by simple solution phase chemistry. The materials can be post-synthetically manipulated to produce hybrid tubes, wires, and carpets by galvanic exchange reactions with Au(3+), Ag(+), Pt(2+), and Pd(2+). All of these structures, especially the hybrid carpets and tubes, have been prepared in bulk and are surface enhanced Raman scattering (SERS) active substrates. Molecules of relevance such as dipicolinic acid (constituting 5-15% of the dry weight of bacterial spores of Bacillus anthracis), dinitrotoluene, hexahydro-1,3,5-triazine (RDX), and trinitrotoluene at nanomolar concentrations have been detected. An enhancement factor of ∼10(10) was observed for the Ni-Au nanocarpet. The reusability of the Ni-Au nanocarpet for SERS applications was tested 5 times without affecting the sensitivity. The reusability and sensitivity over large area have been demonstrated by Raman microscopy. Our method provides an easy and cost effective way to produce recyclable, large area, SERS active substrates with high sensitivity and reproducibility which can overcome the limitation of one-time use of traditional SERS substrates.
A hybrid method for modelling engine noise (2000)

Methods for modelling the radiated noise of automotive engines have become increasingly sophisticated over the past 30 years. However, the ever reducing development time demanded by vehicle manufacturers has meant that many of the current modelling methods fail to deliver results in time to be of assistance in such development. \nThis paper proposes a simple hybrid modelling approach that has significant speed advantages. The power of current techniques (e.g. Finite Element Methods) is still retained for relative predictions, but the all important absolute levels are determined using an empirically based parametric noise generation model.&lt;br/&gt;The emphasis of the paper is on the creation of this core parametric noise generation model although examples are given of how the more traditionally based peripheral or satellite models are incorporated.&lt;br/&gt;Results for a parametric model of a state of the art HSDI engine are presented and the relatively minor anomalies seen in these results are discussed.&lt;br/&gt;
Chitosan Derivatives Active against Multidrug-Resistant Bacteria and Pathogenic Fungi: In Vivo Evaluation as Topical Antimicrobials (2016)

The continuous rise of antimicrobial resistance and the dearth of new antibiotics in the clinical pipeline raise an urgent call for the development of potent antimicrobial agents. Cationic chitosan derivatives, N-(2-hydroxypropyl)-3-trimethylammonium chitosan chlorides (HTCC), have been widely studied as potent antibacterial agents. However, their systemic structure-activity relationship, activity toward drug-resistant bacteria and fungi, and mode of action are very rare. Moreover, toxicity and efficacy of these polymers under in vivo conditions are yet to be established. Herein, we investigated antibacterial and antifungal efficacies of the HTCC polymers against multidrug resistant bacteria including clinical isolates and pathogenic fungi, studied their mechanism of action, and evaluated cytotoxic and antimicrobial activities in vitro and in vivo. The polymers were found to be active against both bacteria and fungi (MIC = 125-250 μg/mL) and displayed rapid microbicidal kinetics, killing pathogens within 60-120 min. Moreover, the polymers were shown to target both bacterial and fungal cell membrane leading to membrane disruption and found to be effective in hindering bacterial resistance development. Importantly, very low toxicity toward human erythrocytes (HC<sub>50</sub> = >10000 μg/mL) and embryo kidney cells were observed for the cationic polymers in vitro. Further, no inflammation toward skin tissue was observed in vivo for the most active polymer even at 200 mg/kg when applied on the mice skin. In a murine model of superficial skin infection, the polymer showed significant reduction of methicillin-resistant Staphylococcus aureus (MRSA) burden (3.2 log MRSA reduction at 100 mg/kg) with no to minimal inflammation. Taken together, these selectively active polymers show promise to be used as potent antimicrobial agents in topical and other infections.
Osteoactivin Promotes Migration of Oral Squamous Cell Carcinomas (2015)

Nearly 50% of patients with oral squamous cell carcinoma (OSCC) die of metastases or locoregional recurrence. Metastasis is mediated by cancer cell adhesion, migration, and invasion. Osteoactivin (OA) overexpression plays a role in metastases in several malignancies. The aims were to determine how integrin interactions modulate OA-induced OSCC cell migration; and to investigate OA effects on cell survival and proliferation. We confirmed OA mRNA and protein overexpression in OSCC cell lines. We assessed OA's interactions with integrins using adhesion inhibition assays, fluorescent immunocytochemistry and co-immunoprecipitation. We investigated OA-mediated activation of mitogen-activated protein kinases (MAPKs) and cell survival. Integrin inhibition effects on OA-mediated cell migration were determined. We assessed effects of OA knock-down on cell migration and proliferation. OA is overexpressed in OSCC cell lines, and serves as a migration-promoting adhesion molecule. OA co-localized with integrin subunits, and co-immunoprecipitated with the subunits. Integrin blocking antibodies, especially those directed against the β1 subunit, inhibited cell adhesion (P = 0.03 for SCC15 cells). Adhesion to OA activated MAPKs in UMSCC14a cells and OA treatment promoted survival of SCC15 cells. Integrin-neutralizing antibodies enhanced cell migration with OA in the extracellular matrix. OA knock-down resulted in decreased proliferation of SCC15 and SCC25 cells, but did not inhibit cell migration. OA in the extracellular matrix promotes OSCC cell adhesion and migration, and may be a novel target in the prevention of HNSCC spread. J. Cell. Physiol. 231: 1761-1770, 2016. © 2015 Wiley Periodicals, Inc.
From Solution to Gas Phase: The Implications of Intramolecular Interactions on the Evaporative Dynamics of Substance P During Electrospray Ionization (2015)

Substance P (RPKPQQFFGLM-NH2) [M + 3H](3+) ions have been shown to occupy two distinct conformer states, a compact population of conformers that is formed by evaporation of hydrated ions, and an elongated population of conformers that is formed by collisional heating of the compact conformer. Molecular dynamics (MD) simulations and amino acid mutations revealed that the compact conformer is stabilized by intramolecular interactions between the localized charge-carrying sites, specifically the N-terminus, R(1), and K(3), with the side chains of glutamine and phenylalanine residues present in the peptide. Here, we employ amino acid mutations and cryogenic ion mobility-mass spectrometry (cryo-IM-MS) in an effort to understand how eliminating specific intramolecular interactions alters ion hydration, as well as the dehydration dynamics of substance P during the final stages of the electrospray process. The results clearly illustrate a direct link between the stabilizing effects of intramolecular self-solvation and the formation of substance P [M + 3H](3+) ions. Most notably, removal of these stabilizing interactions leads to a reduction in the abundances of [M + 3H](3+) ions induced by charge reduction reactions, i.e., loss of H(+)(H2O)n ions to form [M + 2H](2+) ions during the final stages of the electrospray process.
Diazirines as Potential Molecular Imaging Tags: Probing the Requirements for Efficient and Long‐Lived SABRE‐Induced Hyperpolarization (2017)

Diazirines are an attractive class of potential molecular tags for magnetic resonance imaging owing to their biocompatibility and ease of incorporation into a large variety of molecules. As recently reported, <sup>15</sup> N<sub>2</sub> -diazirine can be hyperpolarized by the SABRE-SHEATH method, sustaining both singlet and magnetization states, thus offering a path to long-lived polarization storage. Herein, we show the generality of this approach by illustrating that the diazirine tag alone is sufficient for achieving excellent signal enhancements with long-lasting polarization. Our investigations reveal the critical role of Lewis basic additives, including water, on achieving SABRE-promoted hyperpolarization. The application of this strategy to a <sup>15</sup> N<sub>2</sub> -diazirine-containing choline derivative demonstrates the potential of <sup>15</sup> N<sub>2</sub> -diazirines as molecular imaging tags for biomedical applications.
Carbon-oxygen surface formation enhances secondary electron yield in Cu, Ag and Au (2022)

First-principles calculations coupled with Monte Carlo simulations are used to probe the role of a surface CO monolayer formation on secondary electron emission (SEE) from Cu, Ag, and Au (110) materials. It is shown that formation of such a layer increases the secondary electron emission in all systems. Analysis of calculated total density of states (TDOS) in Cu, Ag, and Au, and partial density of states (PDOS) of C and O confirm the formation of a covalent type bonding between C and O atoms. It is shown that such a bond modifies the TDOS and extended it to lower energies, which is then responsible for an increase in the probability density of secondary electron generation. Furthermore, a reduction in inelastic mean free path is predicted for all systems. Our predicted results for the secondary electron yield (SEY) compare very favorably with experimental data in all three materials, and exhibit increases in SEY. This is seen to occur despite increases in the work function for Cu, Ag, and Au. The present analysis can be extended to other absorbates and gas atoms at the surface, and such analyses will be present elsewhere.
Space–Charge Profiles and Carrier Transport Properties in Dopant‐Free GaN‐Based p‐n Junction Formed by Distributed Polarization Doping (2022)

Herein, the operation of dopant‐free GaN‐based p‐n junctions formed by distributed polarization doping (DPD) is experimentally demonstrated and their space charge profiles and carrier transport properties are investigated. The device exhibits ideal space charge profiles explained by polarization effects and demonstrates the excellent controllability of DPD. In addition, it shows rectification and electroluminescence under forward‐biased conditions. The carrier transport properties could be explained by the conventional recombination/diffusion model used for impurity‐doped p‐n junctions. Repeatable breakdowns are also observed in all devices and the temperature‐dependent breakdown voltages reveal that the breakdowns are caused by avalanche multiplication, which is also the same as those reported in impurity‐doped GaN p‐n diodes. These results indicate that DPD is a promising doping technology for GaN‐based power devices overcoming any issues associated with conventional impurity doping.
Supplementary Figure 1 from SMAD4 Loss in Colorectal Cancer Patients Correlates with Recurrence, Loss of Immune Infiltrate, and Chemoresistance (2023)

&lt;p&gt;Kaplan-Meier graphs with number of subjects at risk comparing recurrence-free survival (RFS) by (a) TIL status, or (b) PLA status, with arrows indicating patients whose tumors were also SMAD4 loss.&lt;/p&gt;
Precision targeted therapy of ovarian cancer (2016)

The review is aimed at describing modern approaches to detection as well as precision and personalized treatment of ovarian cancer. Modern methods and future directions of nanotechnology-based targeted and personalized therapy are discussed.
Model-driven business performance management (2005)

In this paper, we present a model-driven approach to business performance management (BPM). BPM is a new frontier in IT-enabled enterprise that supports the monitoring and control of business operations. BPM solutions must be able to efficiently process business events, compute business metrics, detect business situations, and provide the real-time visibility of key performance indicators. In addition, system support is required for the rapid development of BPM solutions and the adaptation of the solutions to the dynamic business environment. We have adopted a meta-model, dubbed the observation meta-model, for capturing the business requirements for BPM, which frees solution developers from low-level programming concerns. We have also used a hybrid compilation-interpretation approach to map an observation model to the runtime executable. First, we extract and refactor the data aspect of the observation model to facilitate runtime access. Second, we compile the operational aspect of the model, such as logic for metric computation and situation detection, into Java code. Third, we develop a runtime engine that interprets the refactored model and dynamically loads the generated code, according to the meta-model. Our framework further enables the evolution and hot deployment of the observation model and provides the platform for several on-going customer engagement efforts
Plasticine (2017)

Reconfigurable architectures have gained popularity in recent years as they allow the design of energy-efficient accelerators. Fine-grain fabrics (e.g. FPGAs) have traditionally suffered from performance and power inefficiencies due to bit-level reconfigurable abstractions. Both fine-grain and coarse-grain architectures (e.g. CGRAs) traditionally require low level programming and suffer from long compilation times. We address both challenges with Plasticine, a new spatially reconfigurable architecture designed to efficiently execute applications composed of parallel patterns. Parallel patterns have emerged from recent research on parallel programming as powerful, high-level abstractions that can elegantly capture data locality, memory access patterns, and parallelism across a wide range of dense and sparse applications. We motivate Plasticine by first observing key application characteristics captured by parallel patterns that are amenable to hardware acceleration, such as hierarchical parallelism, data locality, memory access patterns, and control flow. Based on these observations, we architect Plasticine as a collection of Pattern Compute Units and Pattern Memory Units. Pattern Compute Units are multi-stage pipelines of reconfigurable SIMD functional units that can efficiently execute nested patterns. Data locality is exploited in Pattern Memory Units using banked scratchpad memories and configurable address decoders. Multiple on-chip address generators and scatter-gather engines make efficient use of DRAM bandwidth by supporting a large number of outstanding memory requests, memory coalescing, and burst mode for dense accesses. Plasticine has an area footprint of 113 mm2 in a 28nm process, and consumes a maximum power of 49 W at a 1 GHz clock. Using a cycle-accurate simulator, we demonstrate that Plasticine provides an improvement of up to 76.9x in performance-per-Watt over a conventional FPGA over a wide range of dense and sparse applications.
Segmentation Of Specular Highlights From Object Surfaces (1989)

A major hindrance to image segmentation tasks are the presence of specular highlights on object surfaces. Specular highlights appear on object surfaces where the specular component of reflection from illuminating light sources is so dominant that most detail of the object surface is obscured by a bright region of reflected light. Specular highlights are very common artifacts of most lighting environments and are not part of the intrinsic visible detail of an object surface. As a result, in addition to obscuring visible detail, specular highlight regions of an image can easily deceive image understanding algorithms into interpreting these regions as separate objects or regions on an object with high albedo. Recently, a couple of approaches to identifying specular highlight regions in images of object surfaces have produced some good results using color analysis. Unfortunately these methods work only for dielectric materials (e.g. plastic, rubber etc..) and require that the color of the object be different from the color of the light source. In this paper a technique is presented exploiting the polarization properties of reflected light to identify specular highlight regions. This technique works for both dielectric and metal surfaces regardless of the color of the illuminating light source, or the color detail on the object surface. In addition to separating out diffuse and specular components of reflection, the technique presented here also as a bonus can identify whether certain image regions correspond to a dielectric or metal object surface. Extensive experimentation will be presented for a variety of dielectric and metal surfaces, both polished and rough. Experimentation with coated surfaces using the technique presented here have not yet been studied.
Ambient effects on the laser durability of 157-nm optical coatings (2003)

We present results of the durability of antireflectance (AR) coatings under laser irradiation with emphasis on the interplay between coating materials and ambient. We find that introducing ppm-levels of water has a dramatic impact on the performance of certain coatings. In particular, no significant degradation of a coating was observed for up to 1MJ/cm<sup>2</sup> dose in the presence of ~20 ppm H<sub>2</sub>O, whereas linear transmission drop of several percent was observed when irradiating a coating of similar design in <0.1 ppm H<sub>2</sub>O but under 1.5 ppm O<sub>2</sub>. Cycling water concentration on and off leads a corresponding cycling of transmission of the coatings. Adding water vapor to the ambient has a much greater benefit to coating durability than adding corresponding amounts of gas phase oxygen. In a series of experiments involving the same coating stack with different degrees of porosity of the outer layer, moisture was found to have the greatest impact on the most porous coating.
The DragonBeam Framework (2016)

The sophistication of malicious adversaries is increasing every day and most defenses are often easily overcome by such attackers. Many existing defensive mechanisms often make differing assumptions about the underlying systems and use varied architectures to implement their solutions. This often leads to fragmentation among solutions and could even open up additional vulnerabilities in the system.
Reticulated vitreous carbon field emission cathodes for light source applications (2002)

Field emission cathodes, fabricated from reticulated vitreous carbon (RVC), have been used in cathodoluminescent light source applications. Electron emission has been evaluated at different current levels (10 to 500 /spl mu/A) for over 5000 hours in sealed glass devices.
Gene Knockout Reveals a Novel Gene Cluster for the Synthesis of a Class of Cell Wall Lipids Unique to Pathogenic Mycobacteria (1997)

Surface-exposed unusual lipids containing phthiocerol and phenolphthiocerol are found only in the cell wall of slow-growing pathogenic mycobacteria and are thought to play important roles in host-pathogen interaction. The enzymology and molecular genetics of biosynthesis of phthiocerol and phenolphthiocerol are unknown. We postulate the domain organization of a set of multifunctional enzymes and a cluster of genes (pps) that would encode these enzymes for the biosynthesis of phthiocerol and phenolphthiocerol. A cosmid containing the postulated pps gene cluster was identified by screening a genomic library of Mycobacterium bovis BCG with the postulated homologous domains from mycocerosic acid synthase and fatty acid synthase genes as probes. Homologous cosmids were also identified in the genomic libraries of Mycobacterium tuberculosis and Mycobacterium leprae. M. bovis BCG was transformed with a pps disruption construct, made from the BCG cosmid by introducing the hygromycin resistance gene as the positive-selectable marker and the sacB gene as the counter-selectable marker. Gene disruption by homologous recombination with double crossover was confirmed by polymerase chain reaction and Southern hybridization. Chromatographic analysis showed that the phenolphthiocerol derivative, mycoside B, and phthiocerol dimycocerosates were not produced by the gene knockout mutants. This result confirms the identity of the pps genes. With the identification of the pps gene clusters in both M. tuberculosis and M. leprae, it should be possible to test the postulated roles of these unique lipids in tuberculosis and leprosy.
Synthesis and Characterization of Star-Shaped Poly(ethylene-co-propylene) Polymers Bearing Terminal Self-Complementary Multiple Hydrogen-Bonding Sites (2006)

The polymerization of isoprene was initiated with 3-(tert-butyldimethylsilyloxy)-1-propyllithium (TBDMSPrLi), which contained a silyl-protected hydroxyl functionality. Living poly(isoprenyllithium) with controlled molecular weight and narrow molecular weight distribution coupled efficiently with divinylbenzene to form well-defined star-shaped polymers. Both linear and star-shaped polymers were subsequently hydrogenated to poly(ethylene-co-propylene) and deprotected quantitatively to yield terminal primary hydroxyl functionality. High conversions of hydroxyl functionality to the 2-ureido-4[1H]-pyrimidinone (UPy) quadruple hydrogen-bonding group were achieved using isocyanate coupling and subsequent reaction with 6-methylisocytosine. Nonfunctionalized and UPy-functionalized linear and star-shaped poly(ethylene-co-propylene)s were characterized using 1H NMR spectroscopy, dynamic mechanical analysis (DMA), differential scanning calorimetry (DSC), tensile testing, and melt rheology. The observed glass transition temperatures were independent of molecular architecture for the UPy-functionalized polymers and nonfunctionalized analogues using both DSC and DMA. Tensile testing revealed the UPy-functionalized star polymers (UPy-Star) exhibited a higher Young's modulus and lower percent elongation at failure compared to the UPy-telechelic polymers with Mn of 24 000 g/mol (UPy-24K-T) analogues. UPy-Star polymer exhibited a rubbery plateau region over a well-defined frequency range, and in contrast, the UPy-functionalized linear polymers were in the terminal flow regime, which suggested greater association for the star-shaped polymers. In addition, complex viscosity data revealed a non-Newtonian behavior for the star-shaped polymers in contrast to linear analogues, which is also consistent with a highly associated structure.
Defining and predicting radiographic knee osteoarthritis progression: a systematic review of findings from the osteoarthritis initiative (2022)

The cumulative evidence suggests that combinations of structural and clinical risk factors may be able to predict radiographic KOA progression, particularly in patients with accelerated progression. Clinically relevant and feasible prediction models and risk calculators may provide valuable decision-making support when caring for patients at risk of KOA progression, although standardization in modeling and variable identification does not yet exist.