gebhart/patrepeval huggingface dataset:
IAD of oxide coatings at low temperature: a comparison of processes based on different ion sources (1997)

A comparative study of different ion and plasma assisted physical vapor deposition processes at low temperature is reported. To work out a clear comparison of the different processes, the object of the study are single layers of different metal oxides like Ta<SUB>2</SUB>O<SUB>5</SUB>, TiO<SUB>2</SUB>, SiO<SUB>2</SUB> and mixed oxides like H4 (Merck) deposited on glass and silicon substrates. Three different types of ion- (or plasma-respectively) sources are used: the cold cathode ion source from Denton (CC 104), the end hall ion source Mark II from CSC and the advanced plasma source from Leybold. Each of these processes is run under conditions concerning process parameters like bias, ion current, ion energy, beam characteristics and gas flow, which were understood to be optimized also to maintain long-term stability as realistic production conditions. The resulting metal oxide single layers are characterized by their optical properties, dispersion curves for NUV and VIS as well as absorption and scatter at discrete wavelengths. Also discussed are mechanical properties like hardness and adherence. A test method is presented which clearly shows the superior behavior of the IAD coatings.
Coding of natural audio in MPEG-4 (2002)

MPEG-4 standardizes natural audio coding at bit rates ranging from 2 kbit/s, suitable for intelligible speech coding, to 64 kbit/s per channel, suitable for high-quality audio coding. Within this range, three categories of coding are defined: parametric coding, code excited linear predictive coding (CELP) and time/frequency (T/F) coding. The unique contribution of MPEG-4 audio is that not only does it scale across a wide range of bit rates, but it also scales across a broad set of other parameters, such as sampling rate, bandwidth, voice pitch and complexity. This paper presents an overview of the MPEG-4 natural audio coding framework and each of its component coding techniques.
Quantitative Structure-Activity Relationship Study of Histone Deacetylase Inhibitors (2004)

Histone deacetylases (HDACs) play a critical role in gene transcription and have become a novel target for the discovery of drugs against cancer and other diseases. During the past several years there have been extensive efforts in the identification and optimization of histone deacetylase inhibitors (HDACIs) as novel anticancer drugs. Here we report a comprehensive quantitative structure-activity relationship (QSAR) study of HDACIs in the hope of identifying the structural determinants for anticancer activity. We have identified, collected, and verified the structural and biological activity data for 124 compounds from various literature sources and performed an extensive QSAR study on this comprehensive data set by using various QSAR and classification methods. A highly predictive QSAR model with R(2) of 0.76 and leave-one-out cross-validated R(2) of 0.73 was obtained. The overall rate of cross-validated correct prediction of the classification model is around 92%. The QSAR and classification models provided direct guidance to our internal programs of identifying and optimizing HDAC inhibitors. Limitations of the models were also discussed.
The therapeutic potential of hydrogen sulfide: separating hype from hope (2011)

Hydrogen sulfide (H(2)S) has become the hot new signaling molecule that seemingly affects all organ systems and biological processes in which it has been investigated. It has also been shown to have both proinflammatory and anti-inflammatory actions and proapoptotic and anti-apoptotic effects and has even been reported to induce a hypometabolic state (suspended animation) in a few vertebrates. The exuberance over potential clinical applications of natural and synthetic H(2)S-"donating" compounds is understandable and a number of these function-targeted drugs have been developed and show clinical promise. However, the concentration of H(2)S in tissues and blood, as well as the intrinsic factors that affect these levels, has not been resolved, and it is imperative to address these points to distinguish between the physiological, pharmacological, and toxicological effects of this molecule. This review will provide an overview of H(2)S metabolism, a summary of many of its reported "physiological" actions, and it will discuss the recent development of a number of H(2)S-donating drugs that show clinical potential. It will also examine some of the misconceptions of H(2)S chemistry that have appeared in the literature and attempt to realign the definition of "physiological" H(2)S concentrations upon which much of this exuberance has been established.
Performance Enhancement by Using Switch-Beam Smart Antenna in 802.11a WLAN System (2005)

An IEEE 802.11a WLAN system physical layer use coded orthogonal frequency division multiplexing (COFDM) to combat frequency selective fading channel. The WLAN system with omni antenna suffers excess delay spread and inter-symbol interference in indoor radio propagation channel. The impact of frequency selective fading channel on WLAN performance is evaluated. Wireless communication usually utilizes smart antenna to enhance performance. This paper presents Monte Carlo simulation based on the IEEE 802.11a physical layer specification and utilizes switch-beam smart antenna operation at the access point (AP) to enhance WLAN performance. The paper analyzes the performance of using omni and switch-beam antenna in a real office indoor environment. Compared with using omni antenna, the simulation results show that utilizing switch-beam antenna in AP the BER performance improve about 2 dB in light-of-sight (LOS) case, and 6 dB in non-light-of-sight (NLOS) case.
Where do people draw lines? (2008)

This paper presents the results of a study in which artists made line drawings intended to convey specific 3D shapes. The study was designed so that drawings could be registered with rendered images of 3D models, supporting an analysis of how well the locations of the artists' lines correlate with other artists', with current computer graphics line definitions, and with the underlying differential properties of the 3D surface. Lines drawn by artists in this study largely overlapped one another (75% are within 1mm of another line), particularly along the occluding contours of the object. Most lines that do not overlap contours overlap large gradients of the image intensity, and correlate strongly with predictions made by recent line drawing algorithms in computer graphics. 14% were not well described by any of the local properties considered in this study. The result of our work is a publicly available data set of aligned drawings, an analysis of where lines appear in that data set based on local properties of 3D models, and algorithms to predict where artists will draw lines for new scenes.
Mesoscopic Conductors and Correlations in Laser Speckle Patterns (1991)

Submicrometer disordered metallic systems at low temperatures display interesting conductance fluctuation effects, owing to the interference of coherent electron wave transmission through the system. This quantum interference phenomenon also gives rise to the striking experimental observation that the 1/f noise power (where f is frequency) in disordered conductors increases as the temperature is decreased, contrary to common intuition. The theoretical techniques developed for this problem can be applied to the transmission of light through a random medium, and this yields novel predictions for the correlations in the laser speckle patterns and the possibility of studying the positions and motions of scatterers in a medium which multiply scatter the probing light.
4‐(Azolylphenyl)‐phthalazin‐1‐amines: Novel Inhibitors of VEGF Receptors I and II (2006)

Novel potent derivatives of phthalazine are described as ATP-competitive inhibitors of vascular endothelial growth factor receptors I and II (VEGFR-1/2). A number of compounds display VEGFR-2 inhibitory activity reaching that of Vatalanib 3 (IC50 < 100 nm) in an HTRF enzymatic assay. Several derivatives also show good potential for the development as VEGFR-2 specific inhibitors showing 15-20-fold selectivity over VEGFR-1.
Deadlock-free adaptive routing in multicomputer networks using virtual channels (1993)

The use of adaptive routing in a multicomputer interconnection network improves network performance by using all available paths and provides fault tolerance by allowing messages to be routed around failed channels and nodes. Two deadlock-free adaptive routing algorithms are described. Both algorithms allocate virtual channels using a count of the number of dimension reversals a packet has performed to eliminate cycles in resource dependency graphs. The static algorithm eliminates cycles in the network channel dependency graph. The dynamic algorithm improves virtual channel utilization by permitting dependency cycles and instead eliminating cycles in the packet wait-for graph. It is proved that these algorithms are deadlock-free. Experimental measurements of their performance are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Self‐association of EPEC intimin mediated by the β‐barrel‐containing anchor domain: a role in clustering of the Tir receptor (2003)

Outer membrane intimin directs attachment of enteropathogenic Escherichia coli (EPEC) via its Tir receptor in mammalian target cell membranes. Phosphorylation of Tir triggers local actin polymerization and the formation of 'pedestal-like' pseudopods. We demonstrate that the intimin protein contains three domains, a flexible N-terminus (residues 40-188), a central membrane-integrated beta-barrel (189-549), and a tightly folded Tir-binding domain (550-939). Intimin was shown by electron microscopy to form ring-like structures with an approximately 7 nm external diameter and an electron dense core, and to form channels of 50picoSiemens conductance in planar lipid bilayers. Gel filtration, multiangle light scattering and cross-linking showed that this central beta-barrel membrane-anchoring domain directs intimin dimerization. Isothermal titration calorimetry revealed a high affinity, single-binding site interaction of 2 : 1 stoichiometry between dimeric intimin and Tir, and modelling suggests that this interaction determines a reticular array-like superstructure underlying receptor clustering. In support of this model, actin rearrangement induced in Tir-primed cultured cells by intimin-containing proteoliposomes was dependent on the concentration of both intimin and Tir, and co-localized with clustered phosphorylated Tir.
Intraarterial Injection of Muscle-Derived Cd34+Sca-1+ Stem Cells Restores Dystrophin in mdx Mice (2001)

Duchenne muscular dystrophy is a lethal recessive disease characterized by widespread muscle damage throughout the body. This increases the difficulty of cell or gene therapy based on direct injections into muscles. One way to circumvent this obstacle would be to use circulating cells capable of homing to the sites of lesions. Here, we showed that stem cell antigen 1 (Sca-1), CD34 double-positive cells purified from the muscle tissues of newborn mice are multipotent in vitro and can undergo both myogenic and multimyeloid differentiation. These muscle-derived stem cells were isolated from newborn mice expressing the LacZ gene under the control of the muscle-specific desmin or troponin I promoter and injected into arterial circulation of the hindlimb of mdx mice. The ability of these cells to interact and firmly adhere to endothelium in mdx muscles microcirculation was demonstrated by intravital microscopy after an intraarterial injection. Donor Sca-1, CD34 muscle-derived stem cells were able to migrate from the circulation into host muscle tissues. Histochemical analysis showed colocalization of LacZ and dystrophin expression in all muscles of the injected hindlimb in all of five out of five 8-wk-old treated mdx mice. Their participation in the formation of muscle fibers was significantly increased by muscle damage done 48 h after their intraarterial injection, as indicated by the presence of 12% beta-galactosidase-positive fibers in muscle cross sections. Normal dystrophin transcripts detected enzymes in the muscles of the hind limb injected intraarterially by the mdx reverse transcription polymerase chain reaction method, which differentiates between normal and mdx message. Our results showed that the muscle-derived stem cells first attach to the capillaries of the muscles and then participate in regeneration after muscle damage.
Evidence for beneficial effect of recombinant interleukin-2 in HIV-associated B lymphoma (1991)

Mazza, P.; Bocchia, M.; Tura, S.; Tumietto, F.*; Costigliola, P.*; Coronado, O.*; Ricchi, E.*; Chlodo, F.* Author Information
Protein Data Bank Deposits (1998)

Since the Protein Data Bank (PDB) inaugurated the “Layered Release Protocol” on 9 July 1998 (F. E. Bloom, “Policy Change,” Science 's Compass, 10 July, p. [175][1]) ([www.pdb.bnl.gov/][2] and [www2.ebi.ac.uk/pdb][3]), results have exceeded our highest expectations. Specifically, since July we have received 931 new entries, of which 813 were submitted by means of our latest data deposition software (AutoDep 2.1), which allows for “release on publication.” For less than 22% of these, “on-hold” is requested, and the rest have been either immediately released or held until publication (see [table][4] below for details). This is in sharp contrast to the situation just a year ago, when more than 75% of new entries were requested to be put “on-hold” for 1 year.

View this table:

This is an enormous tribute to the journals that have set the new policy requiring “Release on Publication,” as well as to the PDB, which instituted the “Layered Release Protocol,” making it possible to access data concurrently with publication.

It is clear that there has been a profound change in the attitude of the vast majority of experimental crystallographers and nuclear magnetic resonance spectroscopists toward releasing their data either immediately or at the time of publication. This is an exciting development for structural biology that will have a positive impact on other scientific disciplines, industrial research, and education.

 [1]: /lookup/doi/10.1126/science.281.5374.175c
 [2]: http://www.pdb.bnl.gov/
 [3]: http://www2.ebi.ac.uk/pdb
 [4]: #T1
View-dependent geometry (1999)

When constructing 3D geometry for use in cel animation, the reference drawings of the object or character often contain various view-specific distortions, which cannot be captured with conventional 3D models. In this work we present a technique called View-Dependent Geometry, wherein a 3D model changes shape based on the direction it is viewed from. A view-dependent model consists of a base model, a set of key deformations (deformed versions of the base model), and a set of corresponding key viewpoints (which relate each 2D reference drawing to the 3D base model). Given an arbitrary viewpoint, our method interpolates the key deformations to generate a 3D model that is specific to the new viewpoint, thereby capturing the viewdependent distortions of the reference drawings.
Mediator kinase module and human tumorigenesis (2015)

Mediator is a conserved multi-subunit signal processor through which regulatory informatiosn conveyed by gene-specific transcription factors is transduced to RNA Polymerase II (Pol II). In humans, MED13, MED12, CDK8 and Cyclin C (CycC) comprise a four-subunit "kinase" module that exists in variable association with a 26-subunit Mediator core. Genetic and biochemical studies have established the Mediator kinase module as a major ingress of developmental and oncogenic signaling through Mediator, and much of its function in signal-dependent gene regulation derives from its resident CDK8 kinase activity. For example, CDK8-targeted substrate phosphorylation impacts transcription factor half-life, Pol II activity and chromatin chemistry and functional status. Recent structural and biochemical studies have revealed a precise network of physical and functional subunit interactions required for proper kinase module activity. Accordingly, pathologic change in this activity through altered expression or mutation of constituent kinase module subunits can have profound consequences for altered signaling and tumor formation. Herein, we review the structural organization, biological function and oncogenic potential of the Mediator kinase module. We focus principally on tumor-associated alterations in kinase module subunits for which mechanistic relationships as opposed to strictly correlative associations are established. These considerations point to an emerging picture of the Mediator kinase module as an oncogenic unit, one in which pathogenic activation/deactivation through component change drives tumor formation through perturbation of signal-dependent gene regulation. It follows that therapeutic strategies to combat CDK8-driven tumors will involve targeted modulation of CDK8 activity or pharmacologic manipulation of dysregulated CDK8-dependent signaling pathways.
High Epitope Expression Levels Increase Competition between T Cells (2006)

Both theoretical predictions and experimental findings suggest that T cell populations can compete with each other. There is some debate on whether T cells compete for aspecific stimuli, such as access to the surface on antigen-presenting cells (APCs) or for specific stimuli, such as their cognate epitope ligand. We have developed an individual-based computer simulation model to study T cell competition. Our model shows that the expression level of foreign epitopes per APC determines whether T cell competition is mainly for specific or aspecific stimuli. Under low epitope expression, competition is mainly for the specific epitope stimuli, and, hence, different epitope-specific T cell populations coexist readily. However, if epitope expression levels are high, aspecific competition becomes more important. Such between-specificity competition can lead to competitive exclusion between different epitope-specific T cell populations. Our model allows us to delineate the circumstances that facilitate coexistence of T cells of different epitope specificity. Understanding mechanisms of T cell coexistence has important practical implications for immune therapies that require a broad immune response.
Binder-Free and Carbon-Free Nanoparticle Batteries: A Method for Nanoparticle Electrodes without Polymeric Binders or Carbon Black (2012)

In this work, we have developed a new fabrication method for nanoparticle (NP) assemblies for Li-ion battery electrodes that require no additional support or conductive materials such as polymeric binders or carbon black. By eliminating these additives, we are able to improve the battery capacity/weight ratio. The NP film is formed by using electrophoretic deposition (EPD) of colloidally synthesized, monodisperse cobalt NPs that are transformed through the nanoscale Kirkendall effect into hollow Co(3)O(4). EPD forms a network of NPs that are mechanically very robust and electrically connected, enabling them to act as the Li-ion battery anode. The morphology change through cycles indicates stable 5-10 nm NPs form after the first lithiation remained throughout the cycling process. This NP-film battery made without binders and conductive additives shows high gravimetric (>830 mAh/g) and volumetric capacities (>2100 mAh/cm(3)) even after 50 cycles. Because similar films made from drop-casting do not perform well under equal conditions, EPD is seen as the critical step to create good contacts between the particles and electrodes resulting in this significant improvement in battery electrode assembly. This is a promising system for colloidal nanoparticles and a template for investigating the mechanism of lithiation and delithiation of NPs.
Gene expression in rainbow trout (Oncorhynchus mykiss) following intramuscular injection of DNA. (1996)

Expression of the firefly luciferase gene under the control of viral or fish promoters was observed in fish tissue after direct DNA injection of plasmid DNA. Plasmid DNA containing the firefly luciferase gene was injected into the skeletal muscle of rainbow trout (Oncorhynchus mykiss), and levels of luciferase activity were found to be dependent on the controlling promoter and the amount of injected DNA. Plasmids using the cytomegalovirus immediate early promoter (CMV-IEP) consistently produced the highest levels of luciferase activity. Maximal activity was observed five to seven days postinjection with 50 micrograms of DNA. This activity persisted in the tissues for as long as 115 days postinjection. When the DNA was examined up to two months postinjection, the predominant form was unreplicated, unintegrated DNA in linear and relaxed circular conformation. Expression of injected DNA was found predominantly within muscle cells along the injection path and in scattered muscle cells anterior to the injection site.
Ion homeostasis, channels, and transporters: an update on cellular mechanisms (2004)

The steady-state maintenance of highly asymmetric concentrations of the major inorganic cations and anions is a major function of both plasma membranes and the membranes of intracellular organelles. Homeostatic regulation of these ionic gradients is critical for most functions. Due to their charge, the movements of ions across biological membranes necessarily involves facilitation by intrinsic membrane transport proteins. The functional characterization and categorization of membrane transport proteins was a major focus of cell physiological research from the 1950s through the 1980s. On the basis of these functional analyses, ion transport proteins were broadly divided into two classes: channels and carrier-type transporters (which include exchangers, cotransporters, and ATP-driven ion pumps). Beginning in the mid-1980s, these functional analyses of ion transport and homeostasis were complemented by the cloning of genes encoding many ion channels and transporter proteins. Comparison of the predicted primary amino acid sequences and structures of functionally similar ion transport proteins facilitated their grouping within families and superfamilies of structurally related membrane proteins. Postgenomics research in ion transport biology increasingly involves two powerful approaches. One involves elucidation of the molecular structures, at the atomic level in some cases, of model ion transport proteins. The second uses the tools of cell biology to explore the cell-specific function or subcellular localization of ion transport proteins. This review will describe how these approaches have provided new, and sometimes surprising, insights regarding four major questions in current ion transporter research. 1) What are the fundamental differences between ion channels and ion transporters? 2) How does the interaction of an ion transport protein with so-called adapter proteins affect its subcellular localization or regulation by various intracellular signal transduction pathways? 3) How does the specific lipid composition of the local membrane microenvironment modulate the function of an ion transport protein? 4) How can the basic functional properties of a ubiquitously expressed ion transport protein vary depending on the cell type in which it is expressed?