gebhart/patrepeval huggingface dataset:
Fabrication and characterization of a microsystem for a micro-scale heat transfer study (1999)

A micro-system consisting of micro-channels with integrated temperature sensors was successfully designed and fabricated for the study of the heat-transfer properties of fluid flow in micro-domains. Surface micro-machining technology was used to construct the micro-channels with dimensions of about 40 m 1.4 m 4000 m. Polysilicon thermistors, 4 m 4 m 0.4 m in size were suspended across the channels and directly exposed to the fluid for local temperature measurements. The micro-channels and the micro-sensors were calibrated and the micro-system was characterized. The integrated micro-system performance was theoretically analysed to provide a framework for the interpretation of the experimental data, and the various heat-transfer mechanisms are subsequently discussed.
High-accuracy measurement of 240-m distance in an optical tunnel by use of a compact femtosecond laser (2000)

A high-accuracy optical distance meter with a mode-locked femtosecond laser is proposed for distance measurements in a 310-m-long optical tunnel. We measured the phase shift of the optical beat component between longitudinal modes of a mode-locked laser. A high resolution of 50 microm at 240-m distance was obtained without cyclic error correction. The group refractive index of air is automatically extracted to an accuracy of 6 parts per million (ppm) by two-color measurement with the pulses of fundamental and second-harmonic wavelengths. Finally, an absolute mechanical distance of 240 m was obtained to within 8-ppm accuracy by use of a series of beat frequencies with the advantage of a wide range of intermode frequency, together with the results of the two-color measurement.
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints (2003)

Hybrid energy methods such as QM/MM and ONIOM, that combine different levels of theory into one calculation, have been very successful in describing large systems. Geometry optimization methods can take advantage of the partitioning of these calculations into a region treated at a quantum mechanical (QM) level of theory and the larger, remaining region treated by an inexpensive method such as molecular mechanics (MM). A series of microiterations can be employed to fully optimize the MM region for each optimization step in the QM region. Cartesian coordinates are used for the MM region and are chosen so that the internal coordinates of the QM region remain constant during the microiterations. The coordinates of the MM region are augmented to permit rigid body translation and rotation of the QM region. This is essential if any atoms in the MM region are constrained, but it also improves the efficiency of unconstrained optimizations. Because of the microiterations, special care is needed for the optimization step in the QM region so that the system remains in the same local valley during the course of the optimization. The optimization methodology with microiterations, constraints, and step-size control are illustrated by calculations on bacteriorhodopsin and other systems.
Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening (2012)

The diphtheria toxin-like ADP-ribosyltransferases (ARTDs) are an enzyme family that catalyzes the transfer of ADP-ribose units onto substrate proteins by using nicotinamide adenine dinucleotide (NAD(+)) as a cosubstrate. They have a documented role in chromatin remodelling and DNA repair, and inhibitors of ARTD1 and 2 (PARP1 and 2) are currently in clinical trials for the treatment of cancer. The detailed function of most other ARTDs is still unknown. By using virtual screening, we identified small ligands of ARTD7 (PARP15/BAL3) and ARTD8 (PARP14/BAL2). Thermal-shift assays confirmed that 16 compounds, belonging to eight structural classes, bound to ARTD7/ARTD8. Affinity measurements with isothermal titration calorimetry for two isomers of the most promising hit compound confirmed binding in the low micromolar range to ARTD8. Crystal structures showed anchoring of the hits in the nicotinamide pocket. These results form a starting point in the development of chemical tools for the study of the role and function of ARTD7 and ARTD8.
Phosphoramidate End Labeling of Inorganic Polyphosphates: Facile Manipulation of Polyphosphate for Investigating and Modulating Its Biological Activities (2010)

Polyphosphates, linear polymers of inorganic phosphates linked by phosphoanhydride bonds, are widely present among organisms and play diverse roles in biology, including functioning as potent natural modulators of the human blood clotting system. However, studies of protein-polyphosphate interactions are hampered by a dearth of methods for derivatizing polyphosphate or immobilizing it onto solid supports. We now report that EDAC (1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide) efficiently promotes the covalent attachment of a variety of primary amine-containing labels and probes to the terminal phosphates of polyphosphates via stable phosphoramidate linkages. Using (31)P NMR, we confirmed that EDAC-mediated reactions between primary amines and polyphosphate result in phosphoramidate linkages with the terminal phosphate groups. We show that polyphosphate can be biotinylated, labeled with fluorophores, and immobilized onto solid supports, that immobilized polyphosphate can be readily used to quantify protein binding affinities, that covalently derivatized or immobilized polyphosphate retains its ability to trigger blood clotting, and that derivatizing the ends of polyphosphate with spermidine protects it from exopolyphosphatase degradation. Our findings open up essentially the entire armamentarium of protein chemistry to modifying polyphosphate, which should greatly facilitate studies of its biological roles.
Hemingway: Modeling Distributed Optimization Algorithms (2017)

Distributed optimization algorithms are widely used in many industrial machine learning applications. However choosing the appropriate algorithm and cluster size is often difficult for users as the performance and convergence rate of optimization algorithms vary with the size of the cluster. In this paper we make the case for an ML-optimizer that can select the appropriate algorithm and cluster size to use for a given problem. To do this we propose building two models: one that captures the system level characteristics of how computation, communication change as we increase cluster sizes and another that captures how convergence rates change with cluster sizes. We present preliminary results from our prototype implementation called Hemingway and discuss some of the challenges involved in developing such a system.
Cationic Peptides: Distribution and Mechanisms of Resistance (2002)

Cationic antimicrobial peptides are observed throughout nature. In mammals they are observed both at epithelial surfaces and within the granules of phagocytic cells. They are an important component of innate defences, since in addition to their ability to kill microorganisms, they are able to modulate inflammatory responses. With respect to their ability to kill bacteria, it is very difficult to isolate resistant mutants. However there are a few known mechanisms of intrinsic resistance, including PhoPQ-dependent and other alterations in lipopolysaccharide structure that influence self promoted uptake, and protease-mediated resistance.
In situ observation of the tip shape of AuGe liquid alloy ion sources using a high voltage transmission electron microscope (1996)

A AuGe liquid alloy ion source was observed in situ under various operating conditions in a 1 MeV transmission electron microscope. The formation of a field-stabilized liquid cone, the change in the cone shape as a function of ion emission current, spatial shifts of the liquid cone, and microdroplet emission were investigated. Below the onset voltage the shape of the tip covered with liquid AuGe alloy is spherical. At the onset voltage a Taylor cone is formed. At ion emission currents Ie larger than 4 μA a jetlike protrusion at the Taylor cone vertex can definitively be seen. At lower emission currents possible jet formation cannot be identified unambiguously. The cone half-angle α decreases linearly with the ion emission current, while the jet length and the jet diameter increase linearly with Ie. Emission of microdroplets was observed from the surroundings of the Taylor cone region. Microdroplets with a radius between 80 and 2300 nm are emitted in time intervals of about 0.1 s and more.
Bovine papillomavirus type 1 3' early region transformation and plasmid maintenance functions (1986)

We examined bovine papillomavirus type 1 (BPV-1) DNAs mutated in the E2 open reading frame (ORF) to determine their ability (i) to transform C127 cells and (ii) to remain extrachromosomal in transfected cells. Results obtained with deletion mutants and insertion mutants containing a linker with translational termination codons in all possible reading frames indicated that an E2 ORF gene product(s) is necessary for efficient transformation, as well as viral plasmid replication and maintenance in the context of the full BPV-1 genome. Complementation assays in which mutant BPV-1 DNAs were transfected into cell lines expressing some viral functions from integrated BPV-1 cDNAs demonstrated that the E2 ORF product, when provided in trans, could allow BPV-1 E2 mutants to remain extrachromosomal. The E2 function could also augment transformation of some, but not all, BPV-1 E2 mutants, allowing identification of another region of BPV-1 involved in cellular transformation. It is likely that the role of the BPV-1 E2 product(s) in transformation and plasmid maintenance is indirect. A BPV-1 mutant altered in the E5 ORF is transformation defective and unable to replicate as a stable plasmid in C127 cells.
Design Criteria for Engineering Inorganic Material- Specific Peptides (2005)

Development of a fundamental understanding of how peptides specifically interact with inorganic material surfaces is crucial to furthering many applications in the field of nanobiotechnology. Herein, we report systematic study of peptide sequence-activity relationships for binding to II-VI semiconductors (CdS, CdSe, ZnS, ZnSe) and Au using a yeast surface display system, and we define criteria for tuning peptide affinity and specificity for these material surfaces. First, homohexapeptides of the 20 naturally occurring amino acids were engineered, expressed on yeast surface, and assayed for the ability to bind each material surface in order to define functional groups sufficient for binding. Histidine (H6) was able to mediate binding of yeast to the five materials studied, while tryptophan (W6), cysteine (C6), and methionine (M6) exhibited different levels of binding to single-crystalline ZnS and ZnSe and polycrystalline Au surfaces. The ability of neighboring amino acids to up- and down-modulate histidine binding was then evaluated by use of interdigitated peptides (XHXHXHX). While the 20 amino acids exhibited a unique fingerprint of modulation for each material, some general trends emerged. With neutral defined by alanine, up-modulation occurred with glycine, basic amino acids, and the previously defined binding amino acids histidine, tryptophan, cysteine, and methionine, and down-modulation generally occurred with acidic, polar, and hydrophobic residues. We conclude that certain amino acids directly bind the material surface while neighboring amino acids locally modulate the binding environment for the materials we studied. Therefore, by the specific placement of up- and down-modulating amino acids, material specificity can be controlled. Finally, by employing the compositional and spatial criteria developed herein, it was possible to predictively design peptide sequences with material specificity, including a multimaterial binder, a Au-specific binder, and a ZnS-specific binder, that were verified as such in the context of yeast display.
Frequency of infection in patients with rheumatoid arthritis compared with controls: A population‐based study (2002)

In this study, patients with RA were at increased risk of developing infections compared with non-RA subjects. This may be due to immunomodulatory effects of RA, or to agents with immunosuppressive effects used in its treatment.
HindIII and Sst I restriction sites mapped on rabbit poxvirus and vaccinia virus DNA (1977)

The DNAs of two closely related orthopoxviruses, rabbit poxvirus (RPV) and vaccinia virus (VV), were mapped by overlapping-fragment analysis using restriction endonucleases HindIII and Sst I. The exact arrangement of these fragments was accomplished by total digestion of isolated partial restriction products and by end-fragment determination. RPV and VV DNAs showed identical restriction patterns in an internal region comprising approximately 60% of the genome. The size, by electrophoretical analysis of the RPV DNA, was 118 X 10(6) daltons, some 6 X 10(6) daltons less than VV DNA. The two opposite terminal restriction fragments of RPV DNA cross-hybridized to each other.
Analysis of Preload-Dependent Reversible Mechanical Interlocking Using Beetle-Inspired Wing Locking Device (2011)

We report an analysis of preload-dependent reversible interlocking between regularly arrayed, high aspect ratio (AR) polymer micro- and nanofibers. Such a reversible interlocking is inspired from the wing-locking device of a beetle where densely populated microhairs (termed microtrichia) on the cuticular surface form numerous hair-to-hair contacts to maximize lateral shear adhesion. To mimic this, we fabricate various high AR, vertical micro- and nanopillars on a flexible substrate and investigate the shear locking force with different preloads (0.1-10 N/cm(2)). A simple theoretical model is developed based on the competition between van der Waals (VdW) attraction and deflection forces of pillars, which can explain the preload-dependent maximum deflection, tilting angle, and total shear adhesion force.
The nature of arousal in sleep (2004)

The role of arousals in sleep is gaining interest among both basic researchers and clinicians. In the last 20 years increasing evidence shows that arousals are deeply involved in the pathophysiology of sleep disorders. The nature of arousals in sleep is still a matter of debate. According to the conceptual framework of the American Sleep Disorders Association criteria, arousals are a marker of sleep disruption representing a detrimental and harmful feature for sleep. In contrast, our view indicates arousals as elements weaved into the texture of sleep taking part in the regulation of the sleep process. In addition, the concept of micro-arousal (MA) has been extended, incorporating, besides the classical low-voltage fast-rhythm electroencephalographic (EEG) arousals, high-amplitude EEG bursts, be they like delta-like or K-complexes, which reflects a special kind of arousal process, mobilizing parallely antiarousal swings. In physiologic conditions, the slow and fast MA are not randomly scattered but appear structurally distributed within sleep representing state-specific arousal responses. MA preceded by slow waves occurs more frequently across the descending part of sleep cycles and in the first cycles, while the traditional fast type of arousals across the ascending slope of cycles prevails during the last third of sleep. The uniform arousal characteristics of these two types of MAs is supported by the finding that different MAs are associated with an increasing magnitude of vegetative activation ranging hierarchically from the weaker slow EEG types (coupled with mild autonomic activation) to the stronger rapid EEG types (coupled with a vigorous autonomic activation). Finally, it has been ascertained that MA are not isolated events but are basically endowed with a periodic nature expressed in non-rapid eye movement (NREM) sleep by the cyclic alternating pattern (CAP). Understanding the role of arousals and CAP and the relationship between physiologic and pathologic MA can shed light on the adaptive properties of the sleeping brain and provide insight into the pathomechanisms of sleep disturbances. Functional significance of arousal in sleep, and particularly in NREM sleep, is to ensure the reversibility of sleep, without which it would be identical to coma. Arousals may connect the sleeper with the surrounding world maintaining the selection of relevant incoming information and adapting the organism to the dangers and demands of the outer world. In this dynamic perspective, ongoing phasic events carry on the one hand arousal influences and on the other elements of information processing. The other function of arousals is tailoring the more or less stereotyped endogenously determined sleep process driven by chemical influences according to internal and external demands. In this perspective, arousals shape the individual course of night sleep as a variation of the sleep program.
Neuroinflammatory processes in Parkinson's disease (2003)

Parkinson's disease (PD) is a movement disorder characterized by the progressive degeneration of dopaminergic neurons in the midbrain. To date, its cause remains unknown and the mechanism of nerve cell death uncertain. Apart from the massive loss of dopaminergic neurons, PD brains also show a conspicuous glial reaction together with signs of a neuroinflammatory reaction manifested by elevated cytokine levels and upregulation of inflammatory-associated factors such as cyclooxygenase-2 and inducible nitric oxide synthase. Mounting evidence also suggests a possible deleterious effect of these neuroinflammatory processes in experimental models of the disease. We propose that, in PD, neuroinflammation plays a role in the cascade of events leading to nerve cell death, thus propagating the neurodegenerative process. In this review, we summarize and discuss the latest findings regarding neuroinflammatory aspects in PD.
Inductive and Inhibitory Effects of Light on Cell Division in Chattonella antiqua (1985)

The cell division of a red tide flagellate, Chattonella antiqua, was synchronously induced under light and dark regimes of 10L14D (a light period, L, for 10 h followed by a dark period, D, for 14 h), 12L12D and l4L10D. In all regimes cell number began to increase ca. 14 h after the onset of L and almost doubled during one LD cycle. When the light-off timing of the last L was changed or the whole L was shifted, cells that had been synchronized under 12L12D invariably began to divide ca. 14 h after the onset of L. This shows that the timing of cell division was determined by the time of the onset of L. When cells were continuously exposed to light after a cell division, the subsequent cell division was inhibited. This effect was limited to cells that had been synchronized under short-day conditions. Thus it can be concluded that light has both inductive and inhibitory effects on cell division in this alga, the latter effect depending upon the previously given light and dark regimes.
Decoding compression with reversible embedded wavelets (CREW) codestreams (1998)

The <i>Journal of Electronic Imaging</i> (JEI), copublished bimonthly with the Society for Imaging Science and Technology, publishes peer-reviewed papers that cover research and applications in all areas of electronic imaging science and technology.
DNA Replication Fidelity (2000)

DNA replication fidelity is a key determinant of genome stability and is central to the evolution of species and to the origins of human diseases. Here we review our current understanding of replication fidelity, with emphasis on structural and biochemical studies of DNA polymerases that provide new insights into the importance of hydrogen bonding, base pair geometry, and substrate-induced conformational changes to fidelity. These studies also reveal polymerase interactions with the DNA minor groove at and upstream of the active site that influence nucleotide selectivity, the efficiency of exonucleolytic proofreading, and the rate of forming errors via strand misalignments. We highlight common features that are relevant to the fidelity of any DNA synthesis reaction, and consider why fidelity varies depending on the enzymes, the error, and the local sequence environment.
Contributions to somatic and germline lineages of chicken blastodermal cells maintained in culture (1996)

Chicken blastodermal cells were cultured for 48 hr as explanted intact embryos, as dispersed cells in a monolayer, or with a confluent layer of mouse fibroblasts. The cells were then dispersed and injected into stage X (E-G&K) recipient embryos that were exposed to 600 rads of irradiation from a 60Co source. Regardless of the conditions in which the cells were cultured, chimeras with contributions to both somatic tissues and the germline were observed. When blastodermal cells were co-cultured with mouse embryonic fibroblasts, significantly more somatic chimeras were observed and the proportion of feather follicles derived from donor cells was increased relative to that observed following the injection of cells derived from explanted embryos or monolayer cultures. Culture of blastodermal cells in any of the systems, however, yielded fewer chimeras that exhibited reduced contributions to somatic tissues in comparison to the frequency and extent of somatic chimerism observed following injection of freshly prepared cells. Contributions to the germline were observed at an equal frequency regardless of the conditions of culture, but were significantly reduced in comparison to the frequency and rate of germline transmission following injection of cells obtained directly from stage X (E-G&K) embryos. These data demonstrate that some cells retain the ability to contribute to germline and somatic tissues after 48 hr in culture and that the ability to contribute to the somatic and germline lineages is not retained equally.
SIRT2 deacetylates FOXO3a in response to oxidative stress and caloric restriction (2007)

The sirtuin family of nicotinamide adenine dinucleotide-dependent (NAD) deacetylases plays an important role in aging and metabolic regulation. In yeast, the Sir2 gene and its homolog Hst2 independently mediate the action of caloric restriction on lifespan extension. The mammalian Sir2 ortholog, SIRT1, is up-regulated by caloric restriction and deacetylates a variety of substrates, including histones and the forkhead box O (FOXO) transcription factors. The mammalian ortholog of Hst2, SIRT2, was shown to co-localize with microtubules and functions as alpha-tubulin deacetylase. During G2/M phase, SIRT2 proteins enter nuclei and deacetylate histones. We report here that the expression of SIRT2 is elevated in the white adipose tissue and kidney of caloric-restricted mice. Oxidative stress, such as hydrogen peroxide treatment, also increases SIRT2 expression in cells. We have demonstrated that SIRT2 binds to FOXO3a and reduces its acetylation level. SIRT2 hence increases FOXO DNA binding and elevates the expression of FOXO target genes, p27(Kip1), manganese superoxide dismutase and Bim. As a consequence, SIRT2 decreases cellular levels of reactive oxygen species. Furthermore, as Bim is a pro-apoptotic factor, SIRT2 promotes cell death when cells are under severe stress. Therefore, mammalian SIRT2 responds to caloric restriction and oxidative stress to deacetylate FOXO transcription factors.