gebhart/patrepeval huggingface dataset:
Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase (2003)

Despite much work, many key aspects of the mechanism of the dihydrofolate reductase (DHFR) catalyzed reduction of dihydrofolate remain unresolved. In bacterial forms of DHFR both substrate and water access to the active site are controlled by the conformation of the mobile M20 loop. In vertebrate DHFRs only one conformation of the residues corresponding to the M20 loop has been observed. Access to the active site was proposed to be controlled by residue 31. MD simulations of chicken DHFR complexed with substrates and cofactor revealed a closing of the side chain of Tyr 31 over the active site on binding of dihydrofolate. This conformational change was dependent on the presence of glutamate on the para-aminobenzoylamide moiety of dihydrofolate. In its absence, the conformation remained open. Although water could enter the active site and hydrogen bond to N5 of dihydrofolate, indicating the feasibility of water as the proton donor, this was not controlled by the conformation of Tyr 31. The water accessibility of the active site was low for both conformations of Tyr 31. However, when hydride was transferred from NADPH to C6 of dihydrofolate before protonation, the average time during which water was found in hydrogen bonding distance to N5 of dihydrofolate in the active site increased almost fivefold. These results indicated that water can serve as the Broensted acid for the protonation of N5 of dihydrofolate during the DHFR catalyzed reduction.
A faster checkpointing and recovery algorithm with a hierarchical storage approach (2005)

Fault tolerance is an inevitable part of cluster operating system. In Score cluster system, it provides coordinated checkpointing, rollback recovery mechanism and watch-dog timer detector for fault tolerance. In the checkpointing algorithm in Score, disk write is the bottleneck. To eliminate disk write overhead, this paper proposes a new diskless checkpointing and rollback recovery algorithm. Since the proposed algorithm does not need to calculate parity and write the checkpointing data into disk, it is analyzed to be a faster checkpointing algorithm than the original one. Based on comparison, the recovery time of the proposed algorithm is also less. However, the cluster can not tolerant multiple transient failure using this diskless checkpointing algorithm. To compensate this drawback, a hierarchical storage strategy is adopted. An experimental result shows that this diskless algorithm with a hierarchical storage approach is fast and effective.
Joint optimization of sensing and radio resource allocation in collaborative femtocell networks (2012)

The goal of this work is to propose a joint optimization of sensing parameters and radio resource allocation useful for cognitive radio networks where the nodes cooperate to improve their local decision capabilities using a fully decentralized approach. The proposed optimization aims at maximizing the opportunistic throughput, taking into account decision errors, sensing time and time necessary to achieve a consensus over the sensed variables, under the constraint that the undue interference be limited.
Mesh and pyramid algorithms for iconic indexing (1992)

Parallel algorithms on meshes and pyramids for iconic indexing are presented. The algorithms are asymptotically superior to previously known parallel algorithms. Also presented are experimental results for these algorithms on the Connection Machine (CM-2).
Protein and mitochondrial content in the gastrocnemius predicts mortality rates in patients with peripheral arterial disease (2012)

Thompson, Jonathan Robert MD; Swanson, Stanley A. BA; Haynatzki, Gleb PhD; Casale, George P. PhD; Johanning, Jason M. MD, FACS; Papoutsi, Eva BA; Koutakis, Panagiotis MS; Miserlis, Dimitrios MD; Zhu, Zhen MD; Pipinos, Iraklis I. MD, PhD, FACS Author Information
Quantitative electron microscopy of InN–GaN alloys (2006)

Abstract The local element distribution in quantum wells largely affects physical properties of devices made from such materials. In the past, quantitative electron microscopy was developed to access the stoichiometry on an atomic scale as shown on the cover page of this issue's Editor's Choice [1] for the GaN/In x Ga 1– x N/GaN and the GaAs/Al x Ga 1– x As/GaAs system by the application of QUANTITEM and Chemical Imaging, respectively. In case of GaN/In x Ga 1– x N/GaN local strain mapping allows for extracting similar data and an unusual large indium fluctuation can be observed if compared with the aluminum distribution in GaAs/Al x Ga 1– x As/GaAs quantum well structures. However, radiation damage, sample preparation and microscope stability affect the data analyses and it is of essence to monitor and control such effects as outlined in the related paper. The first author Til Bartel is a PhD candidate in physics at the Technical University of Berlin, currently visiting LBNL in California to apply transmission electron microscopy to III‐nitride semiconductors. Christian Kisielowski is Staff Scientist and Principle Investigator at the National Center for Electron Microscopy (NCEM) and is responsible for the development and application of high resolution electron microscopy. The present special issue of physica status solidi (a) is a compilation of presentations from the recent symposium on Indium Nitride and Indium Rich Related Alloys at the E‐MRS 2005 Fall Meeting in Warsaw.
Sensory Desensitization Training for Successful Net Application and EEG/ERP Acquisition in Difficult to Test Children (2013)

This study examined the effectiveness of sensory desensitization training for 12 nonverbal children with autism to facilitate participation in an electrophysiological study assessing linguistic processing. Sensory desensitization was achieved for 10 of the 12 children and thus allowed collection of usable data in a passive linguistic paradigm. Application of such desensitization methods may be useful as a precursor to other assessment protocols for individuals who are difficult to test.
Evaluating Past And Improving Present And Future Measurements Of Black Carbon Particles In The Atmosphere (2007)

Soot produced from the combustion of fossil fuel is a public health concern. The strongly light-absorbing black carbon (BC) core of soot contributes to global warming and regional climate change. This research evaluates the accuracy of BC measurements and estimates trends in ambient BC concentrations and BC emission factors from diesel vehicles in California. The aethalometer is a widely used instrument for measuring BC concentrations. Laboratory and field measurements show that temporally resolved BC measurements are subject to error because the response of the aethalometer diminishes as its sampling filter becomes increasingly darkened with black particles. The magnitude of the error depends on the relative amounts of light-absorbing BC and light-scattering particles sampled. A retrospective analysis of ambient BC concentrations is performed, based on archived measurements of coefficient of haze (COH). It is shown that COH levels can be converted to BC concentrations. Estimated annual BC concentrations for the San Francisco Bay Area, where diesel vehicle are the dominant BC source, decreased by a factor of ~3 from the late 1960s to the early 2000s despite a factor of ~6 increase in diesel fuel consumption. Derived diesel BC emission factors (expressed as mass of BC emitted per mass of diesel fuel consumed) decreased from ~13 to &lt;1 g kg-1 over this period. The decreases in ambient concentrations and emission factors are attributed to pollutant abatement policies in California. Further evaluation of BC measurement methods and analysis of BC trends at other locations in California is recommended.
Phenotypic characteristics of cells derived from precursors of human melanoma. (1983)

Of 66 specimens from benign melanocytic nevi, including common acquired and congenital nevi, Spitz tumors (epithelioid cell nevi), and melanocytic nevi with dysplasia, 57 could be grown in tissue culture. The cultured cells were identified as melanocytes by the presence of premelanosomes and melanosomes. Cells from 28 of 32 nevus cultures grew in an anchorage-independent way in soft agar with a colony-forming efficiency between 0.001 and 1%. Clones derived from single cells and soft agar-selected colonies showed marked phenotypic heterogeneity, but all had a limited life span and did not undergo transformation in culture. These cells were nontumorigenic in nude mice. Cultured nevus cells expressed antigens present on melanoma but absent on normal fibroblasts and/or melanocytes as tested with monoclonal anti-melanoma antibodies. The anti-melanoma antibodies bound equally well to dysplastic, congenital, and common acquired nevi. Antigens are released by nevus cells similar to melanoma cells.
Chemical synthesis, molecular cloning and expression of gene coding for a Bowman-Birk-type proteinase inhibitor (1987)

A gene coding for a Bowman-Birk-type proteinase inhibitor was synthesized chemically, cloned and expressed in Escherichia coli as a fusion protein with a ß-galactosidase fragment. The corresponding mutant inhibitor, carrying a P1= Arg16 instead of Lys and an Ile27 instead of Met was obtained after cyanogen bromide cleavage, refolding and affinity chromatography on trypsin-Sepharose. Dissociation constants of complexes with trypsin of this mutant and wild-type Bowman-Birk inhibitor are identical within experimental error. This is explained by differential patterns of hydrogen bonds between side-chains of Arg or Lys in proteinase inhibitors and the primary specificity pocket of trypsin.
ChemInform Abstract: PHASE EQUILIBRIA AND VAPOR PRESSURES IN THE GA+P SYSTEM (1974)

Abstract Zusammensetzung und Dampfdrücke werden längs der Ga‐reichen Liquiduskurve im System Ga‐Perneut bestimmt.
Adaptive document discovery for vertical search engines (2011)

Vertical search engines attempt to aggregate all available online data for a specific vertical into a normalized and structured data model. There are two common strategies for aggregating data: 1) data feeds, and 2) web crawling. Data feeds use source-specific translation rules to collect structured data, but require the source to specifically expose the data. Web crawling collects data through the same interface that users view it, which requires additional work to identify and extract the relevant content from unstructured or semi-structured text. Generalizing these tasks across many websites is difficult because each website presents content in its own arbitrary way. This thesis proposes a strategy for identifying relevant content across many websites with improved accuracy. Many well known statistical document classification algorithms can distinguish between classes of documents with high accuracy. These algorithms fail when test data is significantly different than training data, as is often the case in the vertical search context. This thesis adaptively builds website-specific document classifiers to avoid common classification failure conditions. Training data is selected dynamically by exploiting common user interface patterns. The results obtained here demonstrate that using adaptive document classifiers improves accuracy with minimal performance costs.
DNA Hybridization in Thermoresponsive Polymer Nanoparticles (2010)

We achieve very high hybridization efficiencies by using a new method to immobilize DNA strands on the surface of thermoresponsive polymer nanoparticles. Hybridization efficiencies of about 70 % are obtained between the DNA immobilized in the particles and a complementary strand in solution, even at very low ionic strengths (1 mM). The polymer nanoparticles have a glassy poly(methylmethacrylate) (PMMA) core and a thermoresponsive shell of poly(N-isopropylacrylamide) (PNIPAM) containing positive charges. After a DNA strand labeled with a fluorescence probe is loaded onto the particles at room temperature, the temperature is increased above the volume phase transition temperature of the PNIPAM shell, TVPT approximately 28 degrees C. The collapse of the particle shell immobilizes the DNA while maintaining its availability for hybridization with a complementary strand. Förster resonance energy transfer (FRET) is used to detect the hybridization with a complementary DNA strand labeled with a FRET acceptor probe.
Software controlled mechanically reconfigurable antennas for cognitive radio (2013)

The ability of a communication protocol to dynamically sense and access the spectrum has increased the efficiency of communication systems. This dynamic communication scheme also known as cognitive radio is intelligent and able to learn and adapt to new environments and wireless communication channels. Cognitive radio has various requirements and depends vastly on the type of communication standard that is available. Thus cognitive radio is divided into two main categories: Spectrum interweave and spectrum underlay. In this work we only discuss antennas for spectrum interweave cognitive radio.
ΔV, BEV and Coefficient of Restitution Relationships as Applied to the Interpretation of Vehicle Crash Test Data (2001)

<div class="htmlview paragraph">Prior theoretical work relating barrier equivalent velocity (BEV) and change in vehicle velocity, ΔV, has either neglected restitution or mischaracterized its role. Based on fundamental structural dynamics principles, improved relationships between BEV, ΔV, coefficient of restitution, and vehicle mass and stiffness are formulated. These corrected relationships are then utilized in the assessment of four classes of vehicular impact testing: vehicle to vehicle (VTV), vehicle to infinitely massive rigid barrier (VRB), vehicle to infinitely massive compliant barrier (VCB) and vehicle to finite mass movable rigid barrier (VFMB).</div>
Values, Axial Currencies, and Computational Axiology: Digital Currencies Can Do More than Buy Stuff (2018)

Eleven to twelve thousand years ago, early humans lived in small communities with no discernible hierarchy. The "agrarian revolution" resulted in communities growing on such a scale that mechanisms of self-organization - e.g., for monitoring, keeping order, and ensuring a "satisfactory" allocation of resources - were no longer efficient or effective. However, the concurrent "cognitive" revolution resulted in the faculty of imagination, in particular, the imagination of rules, to solve such problems [1].
Insights into <i>Mycoplasma genitalium</i> metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein (2010)

Mycoplasma genitalium is one of the smallest organisms capable of self-replication and its sequence is considered a starting point for understanding the minimal genome required for life. MG289, a putative phosphonate substrate binding protein, is considered to be one of these essential genes. The crystal structure of MG289 has been solved at 1.95 Å resolution. The structurally identified thiamine binding region reveals possible mechanisms for ligand promiscuity. MG289 was determined to be an extracytoplasmic thiamine binding lipoprotein. Computational analysis, size exclusion chromatography, and small angle X-ray scattering indicates that MG289 homodimerizes in a concentration-dependant manner. Comparisons to the thiamine pyrophosphate binding homolog Cypl reveal insights into the metabolic differences between mycoplasmal species including identifying possible kinases for cofactor phosphorylation and describing the mechanism of thiamine transport into the cell. These results provide a baseline to build our understanding of the minimal metabolic requirements of a living organism.
Winning the game: brain processes in expert, young elite and amateur table tennis players (2014)

(1) compared with amateurs and young elite, expert table tennis players are characterized by enhanced cortical activation in the motor and fronto-parietal cortex during motor imagery in response to table tennis videos; (2) in elite athletes, world rank points are associated with stronger cortical activation. To this aim, electroencephalographic data were recorded in 14 expert, 15 amateur and 15 young elite right-handed table tennis players. All subjects watched videos of a serve and imagined themselves responding with a specific table tennis stroke. With reference to a baseline period, power decrease/increase of the sensorimotor rhythm (SMR) during the pretask- and task period indexed the cortical activation/deactivation (event-related desynchronization/synchronization, ERD/ERS). Regarding hypothesis (1), 8-10 Hz SMR ERD was stronger in elite athletes than in amateurs with an intermediate ERD in young elite athletes in the motor cortex. Regarding hypothesis (2), there was no correlation between ERD/ERS in the motor cortex and world rank points in elite experts, but a weaker ERD in the fronto-parietal cortex was associated with higher world rank points. These results suggest that motor skill in table tennis is associated with focused excitability of the motor cortex during reaction, movement planning and execution with high attentional demands. Among elite experts, less activation of the fronto-parietal attention network may be necessary to become a world champion.
Stability and Emulsion-Forming Ability of Water-Soluble Fish Myofibrillar Protein Prepared by Conjugation with Alginate Oligosaccharide (2003)

Carp myofibrillar protein (Mf) was conjugated with alginate oligosaccharide (AO) through the Maillard reaction under low relative humidity, and the functional properties of the Mf-AO conjugate were investigated under different NaCl concentrations and pH levels. Mf became highly solubilized at lower NaCl concentrations by conjugation with AO, with a slight loss of available lysine. The thermal stability of Mf was effectively improved by conjugation with AO. Heat treatment at 80 degrees C for 2 h had no effect on the solubility of the Mf-AO conjugate attached to 227 microg/mg of AO regardless of the NaCl concentration and pH. Furthermore, the Mf-AO conjugate showed excellent emulsion-forming ability regardless of NaCl concentration. The improved functionalities of Mf by conjugation with AO remained even at a nearly isoelectric point. These results indicate that conjugation with AO through the Maillard reaction is an effective way to prepare high-functional food material from fish muscle protein.
Differential effects of imatinib mesylate against uveal melanoma in vitro and in vivo (2008)

Uveal melanoma is refractory to chemotherapy. The receptor tyrosine kinase inhibitor, imatinib mesylate, has demonstrated antiproliferative effects against uveal melanoma cells in vitro. The effects of imatinib mesylate, alone and combined with the alklyating agent, temozolomide, were examined in vivo as well as in vitro. Proliferation and angiogenic factor production of human uveal melanoma cell lines in response to imatinib mesylate and temozolomide were examined in vitro. Tumor growth, angiogenic factor production, tumor interstitial fluid pressure, and stroma constituents in response to imatinib mesylate and temozolomide were examined in vivo in mice bearing human uveal melanoma xenografts. Imatinib mesylate in vitro antagonized the antiproliferative effects of temozolomide and increased the production of angiogenic factors. In contrast, pretreatment with imatinib mesylate in vivo could improve the antitumor activity of temozolomide. Imatinib mesylate in vivo decreased the production of angiogenic factors in the tumor stroma and tumor interstitial fluid pressure. These effects were transient. Increases in angiogenic factors, interstitial fluid pressure, and tumor infiltrating macrophages were observed with continued imatinib mesylate treatment in vivo. The antitumor effects of imatinib mesylate can vary in vivo when compared with in vitro. Imatinib mesylate can both positively and negatively modify host-tumor interactions in uveal melanoma.
Phylogenetic analysis of RNA editing: a primitive genetic phenomenon. (1994)

RNA editing by extensive uridine addition and deletion creates over 90% of the amino acid codons in the cytochrome-c oxidase subunit III (COIII) transcript in Trypanosoma brucei and Herpetomonas, whereas editing of the COIII transcripts in Leishmania tarentolae and Crithidia fasciculata generates only 6% of the amino acid codons and is limited to the 5' ends. Is extensive RNA editing a primitive or derived character? We constructed a phylogenetic tree based on nuclear small-subunit and mitochondrial large- and small-subunit ribosomal RNA sequences for nine species of kinetoplastid protozoa. Our results suggest that extensive editing is a primitive genetic phenomenon that has disappeared in recent evolutionary time and also that there have been multiple losses of the digenetic lifestyle by loss of the vertebrate host in parasite evolution.
La creación discursiva de etimologismos basada en aspectos socio-culturales (2011)

espanolEn el marco general de la motivacion del lenguaje existen procesos de regeneracion y creacion lexica en los que se manifiestan especialmente la relacion entre lenguaje y aspectos socio-culturales. Dirigiremos nuestra atencion hacia la creacion de etimologismos mediante procesos de etimologizacion, tradicional 'etimologia popular', en la que ha de darse una reinterpretacion significativa. El hablante, en un contexto discursivo determinado, establece conexiones semiotico-linguisticas y/o designativas para crear las nuevas unidades. En este trabajo pretendemos, mediante el analisis de un grupo de etimologismos, constatar la necesidad de tener en cuenta tales componentes socio-culturales a la hora de explicar el funcionamiento de los procesos de motivacion linguistica por etimologizacion que pueden repercutir en la configuracion del sistema linguistico. EnglishWhithin the general framework of the motivation of language there are processes of lexical creation and regeneration that highlight the relation between language and socio-cultural aspects. We will turn our attention to the formation of 'etymologisms' through 'etymologization' processes, traditionally known as 'folk etymology' where a necessary significant reinterpretation is given. The speaker, in a given discursive context, establishes semiotic-linguistic or designative connections to create new units. In this work we analyse a group of 'etymologisms' in order to determine the necessity of taking into account these socio-cultural components when explaining the operation of linguistic motivational 'etymologization' processes. These may affect the configuration of the linguistic system.
Reflection and Transmission of Radiation by Metal Films and the Influence of Nonabsorbing Backings* (1951)

A set of equations is presented for the reflection and transmission of normally incident radiation by absorbing (metal) films on nonabsorbing backings.Using these equations, the results of two different methods of calculation of the reflection and transmission coefficients of a thick nonabsorbing plate are shown to be practically identical, both with and without an absorbing (metal) film on one surface of the plate. One of these methods involves the addition of intensities of the multiple reflections from the two surfaces of the plate. The other method is a rigorous calculation involving solution of the boundary condition equations (amplitude addition) for small areas followed by intensity averaging over the whole plate.In order to calculate optical constants of a metal film on a thick nonabsorbing backing, the much simpler method of intensity addition of internal reflections in the backing may usually be applied.