gebhart/patrepeval huggingface dataset:
Novel flexible Parylene neural probe with 3D sheath structure for enhancing tissue integration (2012)

A Parylene C neural probe with a three dimensional sheath structure was designed, fabricated, and characterized. Multiple platinum (Pt) electrodes for recording neural signals were fabricated on both inner and outer surfaces of the sheath structure. Thermoforming of Parylene was used to create the three dimensional sheath structures from flat surface micromachined microchannels using solid microwires as molds. Benchtop electrochemical characterization was performed on the thin film Pt electrodes using cyclic voltammetry and electrochemical impedance spectroscopy and showed that electrodes possessed low impedances suitable for neuronal recordings. A procedure for implantation of the neural probe was developed and successfully demonstrated in vitro into an agarose brain tissue model. The electrode-lined sheath will be decorated with eluting neurotrophic factors to promote in vivo neural tissue ingrowth post-implantation. These features will enhance tissue integration and improve recording quality towards realizing reliable chronic neural interfaces.
Solid‐state NMR investigations of interaction contributions that determine the alignment of helical polypeptides in biological membranes (2001)

Helical peptides reconstituted into oriented phospholipid bilayers were studied by proton-decoupled 15N solid-state NMR spectroscopy. Whereas hydrophobic channel peptides, such as the N-terminal region of Vpu of HIV-1, adopt transmembrane orientations, amphipathic peptide antibiotics are oriented parallel to the bilayer surface. The interaction contributions that determine the alignment of helical peptides in lipid membranes were analysed using model sequences, and peptides that change their topology in a pH-dependent manner have been designed. The energy contributions of histidines, lysines, leucines and alanines as well as the alignment of peptides and phospholipids under conditions of hydrophobic mismatch have been investigated in considerable detail.
Resilient Distributed Datasets (2016)

Today, a myriad data sources, from the Internet to business operations to scientific instruments, produce large and valuable data streams. However, the processing capabilities of single machines have not kept up with the size of data. As a result, organizations increasingly need to scale out these computations to clusters of hundreds of machines. At the same time, the speed and sophistication required of data processing have grown. In addition to simple queries, complex algorithms like machine learning and graph analysis are becoming common. And in addition to batch processing, streaming analysis of real-time data is required to let organizations take timely action. Future computing platforms will need to not only scale out traditional workloads, but support these new applications too. This book, a revised version of the 2014 ACM Dissertation Award winning dissertation, proposes an architecture for cluster computing systems that can tackle emerging data processing workloads at scale. Whereas early cluster computing systems, like MapReduce, handled batch processing, our architecture also enables streaming and interactive queries, while keeping MapReduce's scalability and fault tolerance. And whereas most deployed systems only support simple one-pass computations (e.g., SQL queries), ours also extends to the multi-pass algorithms required for complex analytics like machine learning. Finally, unlike the specialized systems proposed for some of these workloads, our architecture allows these computations to be combined, enabling rich new applications that intermix, for example, streaming and batch processing. We achieve these results through a simple extension to MapReduce that adds primitives for data sharing, called Resilient Distributed Datasets (RDDs). We show that this is enough to capture a wide range of workloads. We implement RDDs in the open source Spark system, which we evaluate using synthetic and real workloads. Spark matches or exceeds the performance of specialized systems in many domains, while offering stronger fault tolerance properties and allowing these workloads to be combined. Finally, we examine the generality of RDDs from both a theoretical modeling perspective and a systems perspective. This version of the dissertation makes corrections throughout the text and adds a new section on the evolution of Apache Spark in industry since 2014. In addition, editing, formatting, drawing of illustrations, and links for the references have been added.
Aging and rheology in soft materials (2000)

We study theoretically the role of ageing in the rheology of soft materials. We define several generalized rheological response functions suited to ageing samples (in which time translation invariance is lost). These are then used to study ageing effects within a simple scalar model (the “soft glassy rheology” or SGR model) whose constitutive equations relate shear stress to shear strain among a set of elastic elements, with distributed yield thresholds, undergoing activated dynamics governed by a “noise temperature”, x. (Between yields, each element follows affinely the applied shear.) For 1 &lt; x &lt; 2 there is a power-law fluid regime in which transients occur, but no ageing. For x &lt; 1, the model has a macroscopic yield stress. So long as this yield stress is not exceeded, ageing occurs, with a sample’s apparent relaxation time being of order its own age. The (age-dependent) linear viscoelastic loss modulus G ′ ′ (ω, t) rises as frequency is lowered, but falls with age t, so as to always remain less than G ′ (ω, t) (which is nearly constant). Significant ageing is also predicted for the stress overshoot in nonlinear shear startup and for the creep compliance. Though obviously oversimplified, the SGR model may provide a valuable paradigm for the experimental and theoretical study of rheological ageing phenomena in soft solids. 1
Optimum Linear Joint Transmit-Receive Processing for MIMO Channels with QoS Constraints (2004)

This paper considers vector communications through multiple-input multiple-output (MIMO) channels with a set of quality of service (QoS) requirements for the simultaneously established substreams. Linear transmit-receive processing (also termed linear precoder at the transmitter and linear equalizer at the receiver) is designed to satisfy the QoS constraints with minimum transmitted power (the exact conditions under which the problem becomes unfeasible are given). Although the original problem is a complicated nonconvex problem with matrix-valued variables, with the aid of majorization theory, we reformulate it as a simple convex optimization problem with scalar variables. We then propose a practical and efficient multilevel water-filling algorithm to optimally solve the problem for the general case of different QoS requirements. The optimal transmit-receive processing is shown to diagonalize the channel matrix only after a very specific prerotation of the data symbols. For situations in which the resulting transmit power is too large, we give the precise way to relax the QoS constraints in order to reduce the required power based on a perturbation analysis. We also propose a robust design under channel estimation errors that has an important interest for practical systems. Numerical results from simulations are given to support the mathematical development of the problem.
Denaturing Gradient Gel Electrophoresis Analysis of the 16S rRNA Gene V1 Region To Monitor Dynamic Changes in the Bacterial Population during Fermentation of Italian Sausages (2001)

In this study, a PCR-denaturing gradient gel electrophoresis (DGGE) protocol was used to monitor the dynamic changes in the microbial population during ripening of natural fermented sausages. The method was first optimized by using control strains from international collections, and a natural sausage fermentation was studied by PCR-DGGE and traditional methods. Total microbial DNA and RNA were extracted directly from the sausages and subjected to PCR and reverse transcription-PCR, and the amplicons obtained were analyzed by DGGE. Lactic acid bacteria (LAB) were present together with other organisms, mainly members of the family Micrococcaceae and meat contaminants, such as Brochothrix thermosphacta and Enterococcus sp., during the first 3 days of fermentation. After 3 days, LAB represented the main population, which was responsible for the acidification and proteolysis that determined the characteristic organoleptic profile of the Friuli Venezia Giulia fermented sausages. The PCR-DGGE protocol for studying sausage fermentation proved to be a good tool for monitoring the process in real time, and it makes technological adjustments possible when they are required.
The History of Drug Research: From Hansch to the Present (1992)

Abstract The introduction by Hansch of the QSAR concept in the design of bioactive molecules opened new perspectives in organic chemistry. In the present contribution we will briefly review a number of factors contributing to the development of modern medicinal chemistry, particularly focussing on the increasing role of computers.
Metal‐Free Photocatalytic Graphitic Carbon Nitride on p‐Type Chalcopyrite as a Composite Photocathode for Light‐Induced Hydrogen Evolution (2012)

Recently, it has been shown that an abundant material, polymeric carbon nitride, can produce hydrogen from water under visible-light irradiation in the presence of a sacrificial donor. We present herein the preparation and characterization of graphitic carbon nitride (g-C(3)N(4)) films on p-type semiconducting CuGaSe(2) chalcopyrite thin-film substrates by thermal condensation of a dicyandiamide precursor under inert-gas conditions. Structural and surface morphological studies of the carbon nitride films suggest a high porosity of g-C(3)N(4) thin films consisting of a network of nanocrystallites. Photoelectrochemical investigations show light-induced hydrogen evolution upon cathodic polarization for a wide range of proton concentrations in the aqueous electrolyte. Additionally, synchrotron radiation-based photoelectron spectroscopy has been applied to study the surface/near-surface chemical composition of the utilized g-C(3)N(4) film photocathodes. For the first time, it has been shown that g-C(3)N(4) films coated on p-type CuGaSe(2) thin films can be successfully applied as new photoelectrochemical composite photocathodes for light-induced hydrogen evolution.
Evaluation of a Structural Model of <i>Pseudomonas aeruginosa</i> Outer Membrane Protein OprM, an Efflux Component Involved in Intrinsic Antibiotic Resistance (2001)

The outer membrane protein OprM of Pseudomonas aeruginosa is involved in intrinsic and mutational multiple-antibiotic resistance as part of two resistance-nodulation-division efflux systems. The crystal structure of TolC, a homologous protein in Escherichia coli, was recently published (V. Koronakis, A. Sharff, E. Koronakis, B. Luisl, and C. Hughes, Nature 405:914-919, 2000), demonstrating a distinctive architecture comprising outer membrane beta-barrel and periplasmic helical-barrel structures, which assemble differently from the common beta-barrel-only conformation of porins. Based on their sequence similarity, a similar content of alpha-helical and beta-sheet structure determined by circular dichroism spectroscopy, and our observation that OprM, like TolC, reconstitutes channels in planar bilayer membranes, OprM and TolC were considered to be structurally homologous, and a model of OprM was constructed by threading its sequence to the TolC crystal structure. Residues thought to be important for the TolC structure were conserved in space in this OprM model. Analyses of deletion mutants and previously isolated insertion mutants of OprM in the context of this model allowed us to propose roles for different protein domains. Our data indicate that the helical barrel of the protein is critical for both the function and the integrity of the protein, while a C-terminal domain localized around the equatorial plane of this helical barrel is dispensable. Extracellular loops appear to play a lesser role in substrate specificity for this efflux protein compared to classical porins, and there appears to be a correlation between the change in antimicrobial activity for OprM mutants and the pore size. Our model and channel formation studies support the "iris" mechanism of action for TolC and permit us now to form more focused hypotheses about the functional domains of OprM and its related family of efflux proteins.
Rh-Catalyzed Arylation and Alkenylation of C<sub>60</sub> Using Organoboron Compounds (2007)

A new organoboron-based arylation and alkenylation of C60 catalyzed by a rhodium complex was developed. A treatment of C60 with an organoboron compound in the presence of a catalytic amount of [Rh(cod)(CH3CN)2]BF4 in H2O/1,2-Cl2C6H4 furnished a functionalized fullerene (R−C60−H) with good to excellent selectivity. Aryl, heteroaryl, and alkenyl groups can be installed by the reactions using the corresponding boronic acids, pinacol esters, and potassium trifluoroborates.
Interethnic Relations between ESL Students (2006)

This study is part of a larger investigation into Japanese students' use of English and friendship buildup inside and outside Canadian English as a second language (ESL) institutes. Both qualitative and quantitative data were garnered primarily from formal in-depth interviews with nine Japanese students and questionnaire surveys with 216 students. Based on the data, the present study explores Japanese students' friendship with Korean students, large numbers of whom are enrolled in ESL schools in English-speaking countries. The study provides evidence of the frequent opportunities for members of these two groups to communicate with each other, which sometimes leads to Japanese students' overgeneralised positive perceptions of Koreans as a whole. Also documented are the varying impacts of Korean students' references to Japan's war-time invasion of Korea upon Japanese students, ranging from appreciation of this new knowledge to the development of negative perceptions of Korean students. Furthermore, the study reveals that the combination of quantity and quality contact can cause the formation and consolidation of bonding between Japanese and Korean students, which then opens up a historically sensitive dialogue without jeopardising their long-term relationship.
Methodology for estimating regional and global trends of child malnutrition (2004)

Linear mixed-effect models made best use of all available information. Trends are uneven across regions, with some showing a need for more concerted and efficient interventions to meet the MDG of reducing levels of child malnutrition by half between 1990 and 2015.
Review: Gp-340/DMBT1 in mucosal innate immunity (2010)

Deleted in Malignant Brain Tumour 1 (DMBT1) is a gene that encodes alternatively spliced proteins involved in mucosal innate immunity. It also encodes a glycoprotein with a molecular mass of 340 kDa, and is referred to as gp-340 (DMBT1(gp340)) and salivary agglutinin (DMBT1(SAG)). DMBT1(gp340) is secreted into broncho-alveolar surface lining fluid whereas DMBT(SAG) is present in the saliva. The two molecules were shown to be identical and both interact with and agglutinate several Gram-negative and Gram-positive bacteria including Streptococcus mutans, a bacterium responsible for caries in the oral cavity. DMBT1(gp340) interacts with surfactant proteins A and D (SP-D). DMBT1(gp340) and SP-D can individually and together interact and agglutinate influenza A virus. DMBT1(gp340) also binds to HIV-1 and facilitates transcytosis of the virus into epithelial cells. DMBT1 binds to a variety of other host proteins, including serum and secretory IgA, C1q, lactoferrin, MUC5B and trefoil factor 2 (TFF2), all molecules with involvement in innate immunity and/or wound-healing processes. Recent generation of Dmbt1-deficient mice has provided the research field of DMBT1 with a model that allows research to progress from in vitro studies to in vivo functional studies of the multifunctional proteins encoded by the DMBT1 gene.
Multiple System Organ Failure (1980)

Multiple system organ failure (MSOF) remains a principal cause of death after major operative procedures and/or severe trauma. We studied multiple parameters in 553 consecutive emergency surgical patients to determine the incidence of MSOF, the predisposing factors to MSOF, and the sequelae of MSOF. Thirty-eight patients had MSOF; mortality was 74% for these patients. Evaluation of multiple factors demonstrated that (1) MSOF is primarily due to infection, (2) the temporal sequence of organ failure is lung, liver, gastric mucosa, and kidney, and (3) MSOF is the most common fatal expression of uncontrolled infection.
Scene Classification by Fuzzy Local Moments (1998)

The identification of images irrespective of their location, size and orientation is one of the important tasks in pattern analysis. The use of global moment features has been one of the most popular techniques for this purpose. We present a simple and effective method for gray-level image representation and identification which utilizes fuzzy radial moments of image segments (local moments) as features as opposed to global features. A multilayer perceptron neural network is employed for classification. Fuzzy entropy measure is applied to optimize the parameters of the membership function. The technique does not require translation, scaling or rotation of the image. Furthermore, it is suitable for parallel implementation which is an advantage for real-time applications. The classification capability and robustness of the technique are demonstrated by experiments on scaled, rotated and noisy gray-level images of uppercase and lowercase characters and digits of English alphabet, as well as the images of a set of tools. The proposed approach can handle rotation, scale and translation invariance, noise and fuzziness simultaneously.
The Prudential Regulation of Financial Institutions: Why Regulatory Responses to the Crisis Might Not Prove Sufficient (2017)

It is now six years since a devastating financial and economic crisis rocked the global economy. Supported strongly by the G20 process, international regulators led by the Financial Stability Board have been working hard ever since to develop new regulatory standards designed to prevent a recurrence of these events. These international standards are intended to provide guidance for the drawing up of national legislation and regulation, and have already had a pervasive influence around the world. This paper surveys recent international developments concerning the prudential regulation of financial institutions: banks, the shadow banking system and insurance companies. It concludes that, while substantial progress has been made, the global economy nevertheless remains vulnerable to possible future financial instability. This possibility reflects three sets of concerns. First, measures taken to manage the crisis to date have actually made the prevention of future crises more difficult. Second, the continuing active debate over virtually every aspect of the new regulatory guidelines indicates that the analytical foundations of what is being proposed remain highly contestable. Third, implementation of the new proposals could suffer from different practices across regions. Looking forward, the financial sector will undoubtedly continue to innovate in response to competitive pressures and in an attempt to circumvent whatever regulations do come into effect. If we view the financial sector as a complex adaptive system, continuous innovation would only be expected. This perspective also provides a number of insights as to how regulators should respond in turn. Not least, it suggests that attempts to reduce complexity would not be misguided and that complex behaviour need not necessarily be accompanied by still more complex regulation. Removing impediments to more effective self discipline and market discipline in the financial sector would also seem recommended.
Endothelial and Epithelial Cell Adhesion Molecules (1991)

This review will discuss a number of specific cell adhesion molecules present on the surface of endothelial and epithelial cells in the lung. Molecules such as integrins, proteoglycans, and the hyaluronic acid receptor, CD44, are found on the abluminal or basement membrane side of the cell and function as cell-substratum receptors. Cadherins, integrins, and platelet-endothelial cell adhesion molecule-1 (PECAM-1) are present at the cell-cell borders of adjacent endothelial and/or epithelial cells and function to initiate or maintain cell-cell adhesion. Finally, a number of inducible cell adhesion molecules such as endothelial-leukocyte adhesion molecule-1 (ELAM-1), granule-associated membrane protein 140 (GMP140), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1) are expressed on the luminal surfaces of these cells during inflammation and function as cell-cell adhesion molecules important in white blood cell, platelet, or tumor cell adhesion. These adhesion molecules likely play important roles in maintaining the normal structure and function of the lung, as well as participating in pulmonary processes such as inflammation, wound healing, and the development and spread of malignant disease.
Standardization of cattle karyotype nomenclature: Report of the committee for the standardization of the cattle karyotype (1996)

The purpose of this paper is to publish a table which correlates the previous nomenclature with marker genes mapped on cattle chromosomes. This table also presents the human correspondences and the chromosome measurements expressed as relative lengths.
Label-free reflectance hyperspectral imaging for tumor margin assessment: a pilot study on surgical specimens of cancer patients (2017)

A label-free, hyperspectral imaging (HSI) approach has been proposed for tumor margin assessment. HSI data, i.e., hypercube (x,y,λ), consist of a series of high-resolution images of the same field of view that are acquired at different wavelengths. Every pixel on an HSI image has an optical spectrum. In this pilot clinical study, a pipeline of a machine-learning-based quantification method for HSI data was implemented and evaluated in patient specimens. Spectral features from HSI data were used for the classification of cancer and normal tissue. Surgical tissue specimens were collected from 16 human patients who underwent head and neck (H&N) cancer surgery. HSI, autofluorescence images, and fluorescence images with 2-deoxy-2-[(7-nitro-2,1,3-benzoxadiazol-4-yl)amino]-D-glucose (2-NBDG) and proflavine were acquired from each specimen. Digitized histologic slides were examined by an H&N pathologist. The HSI and classification method were able to distinguish between cancer and normal tissue from the oral cavity with an average accuracy of 90%±8%, sensitivity of 89%±9%, and specificity of 91%±6%. For tissue specimens from the thyroid, the method achieved an average accuracy of 94%±6%, sensitivity of 94%±6%, and specificity of 95%±6%. HSI outperformed autofluorescence imaging or fluorescence imaging with vital dye (2-NBDG or proflavine). This study demonstrated the feasibility of label-free, HSI for tumor margin assessment in surgical tissue specimens of H&N cancer patients. Further development of the HSI technology is warranted for its application in image-guided surgery.