gebhart/patrepeval huggingface dataset:
Toward detection of DNA‐bound proteins using solid‐state nanopores: Insights from computer simulations (2012)

Through all-atom molecular dynamics simulations, we explore the use of nanopores in thin synthetic membranes for detection and identification of DNA binding proteins. Reproducing the setup of a typical experiment, we simulate electric field driven transport of DNA-bound proteins through nanopores smaller in diameter than the proteins. As model systems, we use restriction enzymes EcoRI and BamHI specifically and nonspecifically bound to a fragment of dsDNA, and streptavidin and NeutrAvidin proteins bound to dsDNA and ssDNA via a biotin linker. Our simulations elucidate the molecular mechanics of nanopore-induced rupture of a protein-DNA complex, the effective force applied to the DNA-protein bond by the electrophoretic force in a nanopore, and the role of DNA-surface interactions in the rupture process. We evaluate the ability of the nanopore ionic current and the local electrostatic potential measured by an embedded electrode to report capture of DNA, capture of a DNA-bound protein, and rupture of the DNA-protein bond. We find that changes in the strain on dsDNA can reveal the rupture of a protein-DNA complex by altering both the nanopore ionic current and the potential of the embedded electrode. Based on the results of our simulations, we suggest a new method for detection of DNA binding proteins that utilizes peeling of a nicked double strand under the electrophoretic force in a nanopore.
A General Hardware-Oriented Method for Evaluation of Functions and Computations in a Digital Computer (1977)

A parallel computational method, amenable for efficient hardware-level implementation, is described. It provides a simple and fast algorithm for the evaluation of polynomials, certain rational functions and arithmetic expressions, solving a class of systems of linear equations, or performing the basic arithmetic operations in a fixed-point number representation system. The time required to perform the computation is of the order of m carry-free addition operations, m being the number of digits in the solution. In particular, the method is suitable for fast evaluation of mathematical functions in hardware.
Recognition of handwritten Chinese characters by modified Hough transform techniques (1989)

Chinese characters are mapped from the spatial domain into the parametric one for stroke extraction, and the dynamic programming matching (DP matching) algorithm is applied to recognize Chinese characters. This method overcomes not only the problem of noise sensitivity in the local feature approach, but also the problem of being time consuming in the global feature approach. Results are presented for two experiments conducted for a database called ETL8, which contains 881 Chinese characters and 160 variations for each one, to prove the usefulness of the MHT and DP matching methods. An actual recognition rate of 94.5% was obtained for 351 Chinese characters in the ETL8.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Toxicity of Protein Oligomers Is Rationalized by a Function Combining Size and Surface Hydrophobicity (2014)

The misfolding and aberrant assembly of peptides and proteins into fibrillar aggregates is the hallmark of many pathologies. Fibril formation is accompanied by oligomeric species thought to be the primary pathogenic agents in many of these diseases. With the aim of identifying the structural determinants responsible for the toxicity of misfolded oligomers, we created 12 oligomeric variants from the N-terminal domain of the E. coli HypF protein (HypF-N) by replacing one or more charged amino acid residues with neutral apolar residues and allowing the mutated proteins to aggregate under two sets of conditions. The resulting oligomeric species have different degrees of cytotoxicity when added to the extracellular medium of the cells, as assessed by the extent of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction, apoptosis, and influx of Ca2+ into the cells. The structural properties of the oligomeric variants were characterized by evaluating their surface hydrophobicity with 8-anilinonaphthalene-1-sulfonate (ANS) binding and by measuring their size by means of turbidimetry as well as light scattering. We find that increases in the surface hydrophobicity of the oligomers following mutation can promote the formation of larger assemblies and that the overall toxicity correlates with a combination of both surface hydrophobicity and size, with the most toxic oligomers having high hydrophobicity and small size. These results have allowed the relationships between these three parameters to be studied simultaneously and quantitatively, and have enabled the generation of an equation that is able to rationalize and even predict toxicity of the oligomers resulting from their surface hydrophobicity and size.
Utilization of Nucleoside Diphosphate Glucoses in Developing Cotton Fibers (1974)

The capacity for biosynthesis of hot alkali-insoluble products using uridine diphosphate (UDP)-glucose and guanosine diphosphate (GDP)-glucose as substrate has been studied in isolated cotton fibers harvested at various stages of development following anthesis. During the period of rapid elongation and primary wall synthesis (7-14 days postanthesis), incorporation of radioactivity from GDP-(14)C-glucose into hot alkali-insoluble product is high. This activity gradually declines and is not demonstrated in older fibers undergoing active deposition of secondary wall. With respect to all characteristics examined, the product from GDP-glucose resembles cellulose. Incorporation of UDP-(14)C-glucose into hot alkali-insoluble product was low in young fibers but increased to high levels in older fibers. This product was shown to be soluble in chloroform-methanol, and when chromatographed in lipid solvents it was separated into three components. Activity for the production of two of these three presumed glucolipids increased with increasing age of fibers.
Phase Controlled Scanning Force Microscope (1994)

A noncontact scanning force microscope employing a novel tip height control system using phase lock technology has been developed. An oscillator using a cantilever as a mechanical resonator is used as a voltage controlled oscillator in a phase locked loop, and its output signal is phase locked to a high-precision signal source. Its most remarkable feature is that this tip height control is unconditionally stable. Thus, it was possible to realize the desired system response by adjusting the loop parameters. Its efficiency was demonstrated by imaging the surface of a magneto-optical disk at the lowest tip height which was impossible to achieve with a conventional servo technology.
Tandem reduction/cyclization of o-nitrophenyl propargyl alcohols---A novel synthesis of 2- & 2,4-disubstituted quinolines and application to the synthesis of streptonigrin (2008)

The quinoline ring system is a common structural component of a wide variety of natural products with highly desirable biological activity, including antimalarial agents such as quinine, chloroquine and mefloquine, as well as antitumor agents such as dynemicin A, luotonin A, and camptothecin. The synthesis of the highly effective, yet prohibitively toxic, antitumor antibiotic streptonigrin is targeted in this research. A concise, convergent synthesis of this antitumor agent will pave the way for an expeditous survey of streptonigrin analogues that have similar pharmaceutical value with diminished toxicity. Our retrosynthetic plan required the development of new methodology to form the heterocyclic ring of quinoline, in a manner that would allow the utilization of palladium-catalyzed coupling of complex aryl triflates to form the tetracyclic structure of this highly functionalized natural product. A method has been developed to synthesize complex, substituted quinolines in a facile manner through the utilization of o-nitrophenyl propargyl alcohols. Through either direct lithium acetylide addition of available alkynes, or Sonogashira coupling to terminal propargyl alcohols, the assembly of complex internal propargyl alcohols has directly lead to 2-aryl-, 2-alkenyl- and 2-alkylquinolines via reductive cyclization under mildly acid conditions. This reductive cyclization takes advantage of the facile Meyer-Schuster rearrangement of resonance-stabilized o-anilinopropargyl alcohols to o-aminochalcones, which cyclize to quinoline in a one-pot procedure. This work has also examined the use of this reductive cyclization to form 2-pyridylquinolines, however such cyclization has repeatedly led to the 4-quinolone. The mechanism of such an anomalous cyclization has been studied. Although the mechanism has not been definitively identified, several potential pathways have been examined, with evidence favoring an acid-catalyzed, non-Meyer-Schuster rearrangement of the propargyl alcohol leading to cyclization and oxidative rearomatization to form the observed quinolone. Lastly, reductive cyclization has been applied to model systems for the ABC-ring system of the natural product streptonigrin. The synthesis of an appropriate A-ring precursor o-mononitrobenzaldehyde has been achieved, and elaborated to the final 6,8-dimethoxy-2-(2'-pyridyl)quinolone through reductive cyclization. A more intriguing A-ring precursor dinitrobenzaldehyde, with built-in functionality to produce streptonigrin's 7-amino group, was also targeted. Efforts toward its regioselective synthesis are also described.
Retrospective survey of Chikungunya disease in Réunion Island hospital staff (2007)

Réunion Island (Indian Ocean) has been suffering from its first known Chikungunya virus (CHIKV) epidemic since February 2005. To achieve a better understanding of the disease, a questionnaire was drawn up for hospital staff members and their household. CHIKV infected about one-third of the studied population, the proportion increasing with age and being higher in women. Presence of a garden was associated with CHIKV infection. The geographical distribution of cases was concordant with insect vector Aedes albopictus distribution. The main clinical signs were arthralgia and fever. The disease evolved towards full recovery in 34.4% of cases, a relapse in 55.6%, or a chronic form in 10%. Paracetamol was used as a painkiller in 95% of cases, sometimes associated with non-steroidal anti-inflammatory drugs, corticoids, or traditional herbal medicine. The survey provided valuable information on the factors that favour transmission, the clinical signs, the importance of relapses and the therapies used.
Far‐Ultraviolet Observations with the<i>Voyager</i>Ultraviolet Spectrometer: New Evidence for Interacting Winds in Symbiotic Systems (1997)

The interacting winds model has been used to explain many observational phenomena of symbiotic systems and planetary nebulae successfully. New observational results on seven symbiotic systems, obtained by the ultraviolet spectrometer (UVS) on board of spacecrafts Voyager 1 and Voyager 2, provide strong new evidence supporting the interacting winds model. Three of the systems observed by the Voyager UVS show strong O VI λ1035 and other far-ultraviolet (FUV) lines, including N V λ1240. A one-dimensional photoionization program, CLOUDY, is used to calculate the luminosities of FUV lines to compare with the observational results from the Voyager UVS. The calculations show that, based on a photoionization model, a thin dense shell is necessary to produce the observed lines. The density, radius, and thickness of the shell is consistent with that predicted by the interacting winds model. A model spectrum is produced that is well matched with the Voyager UVS spectrum. The calculations also explain why some of the symbiotic systems have O VI λ1035 but others do not, based on the interacting winds model.
Cytotoxic interactions of heat and an ether lipid analogue in human ovarian carcinoma cells. (1989)

Ether lipid (EL) analogues of platelet activating factor are known to have a cell membrane-mediated antitumor activity. Although previous studies demonstrated additive interactions with EL and conventional DNA-interacting chemotherapeutic agents, little is known about the interaction of EL with heat. In this study, the cytotoxic interaction of one EL analogue, ET-18-OMe, with heat was measured at two different temperatures, 42 and 44 degrees C, using BG-1 human ovarian carcinoma cells. When the number of colonies, greater than or equal to 40 microns in diameter, was counted as a function of incubation time, the rate of colony formation was suppressed by treatment with ET-18-OMe alone at doses greater than or equal to 2.0 microM or with heat alone. The combination of ET-18-OMe with heat inhibited the colony formation of the slowest growing fraction of the heated cells. The dose-response curve for BG-1 cells after continuous exposure to ET-18-OMe alone was exponential with a small shoulder (Dq = 0.25 microM). The T0 value (the time to reduce survival on the exponential portion of the curve by a factor of 1/e) of the 44 degrees C dose-response curve (30 min) was reduced to half (15 min) by the addition of 0.25 to 1.0 microM ET-18-OMe, but increased again to 24 min when heat was combined with ET-18-OMe concentrations greater than or equal to 2.0 microM. The thermotolerant tail seen in the dose-response curve after continuous heating at 42 degrees C was removed by adding as little as 0.25 microM ET-18-OMe. Isobologram analysis for the combined treatments with 44 degrees C heat and ET-18-OMe at surviving fractions of 0.5, 0.3, 0.1, and 0.01 showed that the treatments were supraadditive at low concentrations (less than 0.5 microM) of ET-18-OMe and additive at moderate concentrations (0.5 to 1.0 microM) of ET-18-OMe. Similarly, the interaction of ET-18-OMe with 42 degrees C heat at surviving fractions of 0.3 and 0.1 was supraadditive at low concentrations (less than 0.5 microM) of the ET-18-OMe and additive with moderate concentrations (0.5 to 1.5 microM) of ET-18-OMe. Because the greatest interaction of ET-18-OMe and heat occurred at clinically achievable doses of both agents, this combination of agents should be considered for use in clinical trials.
Frame content independent stripping for token rings (2002)

A frame content independent stripping (FCIS) algorithm for token rings is described that can be used by source-routing bridges due to its simplicity and the fact that the resulting size of the fragments remaining on the ring is very small. The FCIS algorithm counts the number of outstanding frames that a station has transmitted but not yet stripped from the ring and in addition places a global delimiter such as a void frame at the end of the transmission of the information frames. The station then stops stripping when either the count goes to zero or when the void frame or token is received by the station. The algorithm is simple to implement and does not place any topological restrictions on the network. It also allows for interoperation with stations which do not implement the FCIS algorithm. With the FCIS algorithm, frames are stripped at the earliest possible moment. It is shown that the combination of both the count and void is necessary for an FCIS algorithm by demonstrating that the inclusion of either just the void or the count could result in considerable overstripping of frames on the ring due to errors on the ring. The void frame adds a total of 28 bytes of overhead to every transmission opportunity at a participating station.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Modular flux transfer (2013)

The highest fidelity images to date of complex materials like cloth use extremely high-resolution volumetric models. However, rendering such complex volumetric media is expensive, with brute-force path tracing often the only viable solution. Fortunately, common volumetric materials (fabrics, finished wood, synthesized solid textures) are structured, with repeated patterns approximated by tiling a small number of exemplar blocks. In this paper, we introduce a precomputation-based rendering approach for such volumetric media with repeated structures based on a modular transfer formulation. We model each exemplar block as a voxel grid and precompute voxel-to-voxel, patch-to-patch, and patch-to-voxel flux transfer matrices. At render time, when blocks are tiled to produce a high-resolution volume, we accurately compute low-order scattering, with modular flux transfer used to approximate higher-order scattering. We achieve speedups of up to 12× over path tracing on extremely complex volumes, with minimal loss of quality. In addition, we demonstrate that our approach outperforms photon mapping on these materials.
A new generation high speed low loss IGBT module (2005)

By virtue of simulation and advanced process technologies the IGBT and the fast recovery diode chip structures have been modified to develop new generation low-loss power chips. These newly structured chips have been integrated into a moduler housing to form a 100A,600V dual type IGBT module that has exhibited superior characteristics, particularly in terms of reducing operational power loss over the conventional second generation counterpart. This paper will give details of this new generation IGBT module development and describe its characteristical superiority.
Die Bedeutung der Chemie für die Entwicklung von Hochleistungskeramiken (1987)

Abstract Hochleistungskeramiken haben aufgrund ihrer mechanischen, thermischen und chemischen Stabilität ein Eigenschaftsprofil, mit dem die Grenzen der heute verfügbaren Werkstoffklassen in vielen Bereichen überwunden werden können. Trotz dieser günstigen Ausgangssituation sind die weltweiten Anstrengungen zur Einführung dieser neuen Werkstoffgruppe sowohl in konventionelle Anwendungen als auch in neue Technologien nicht frei von Rückschlägen. Die Ursache dafür ist letztlich die große Sprödigkeit dieser Werkstoffe. Zwar haben die Konstrukteure nach Einführung der Bruchmechanik auf vielen Gebieten gelernt, mit spröden Werkstoffen umzugehen und deren Eigenschaften in extrem belasteten Bauteilen voll auszunutzen. Auch waren die Werkstoffwissenschaftler bei der Entwicklung von Keramiken mit hohen Festigkeits‐ und Bruchzähigkeitswerten erfolgreich. Trotzdem können Hochleistungskeramiken bisher nur begrenzt eingesetzt werden, da in vielen Fällen die Zuverlässigkeit der Bauteile beschränkt ist. Kleine und kleinste Fehler wie Mikroporen und ‐risse sowie jede chemische und physikalische Inhomogenität im Gefüge können wegen der hohen Sprödigkeit ein katastrophales Versagen der Bauteile bewirken. Da nun einerseits diese Fehler in der Regel von einer nicht hinreichenden Beherrschung der Prozeßabläufe herrühren und andererseits bei der Herstellung der Keramiken viele chemische Verfahrensschritte durchlaufen werden, ist von einer konsequenten Anwendung chemischer Denk‐und Vorgehensweisen ein wichtiger Beitrag zur Überwindung der Schwierigkeiten zu erhoffen.
Deconvolution Method for View Interpolation Using Multiple Images of Circular Camera Array (2006)

This paper deals with a view interpolation problem using multiple images captured with a circular camera array. A novel deconvolution method for reconstructing a virtual image at the center of the camera array is presented and discussed in a framework of image restoration in the frequency domain. The reconstruction filter does not depend on the scene structure; therefore the presented method requires no depth estimation. The simulation result using synthetic images shows that increasing the number of the cameras improves the quality of the virtual image.
Robust time-domain timing and frequency synchronization for OFDM systems (2009)

A robust and efficient technique for frame/symbol timing and carrier frequency synchronization in OFDM systems is presented. It uses a preamble consisting of only one training symbol with two identical parts to achieve reliable timing and frequency accuracy in the time-domain, over a wide frequency estimation range which can be up to half of the signal sampling frequency. Also, it has a low complexity which is adaptive to the degree of channel distortion. Computer simulations in the Rayleigh fading ISI channel show that the proposed method achieves superior performance to existing techniques in terms of timing and frequency accuracy. Also, its operation in the time-domain helps to achieve faster synchronization convergence.
Volumetry of Hippocampus and Amygdala with High-resolution MRI and Three-dimensional Analysis Software: Minimizing the Discrepancies between Laboratories (2000)

Within the medial temporal lobe, both the hippocampus and amygdala are frequently targeted by researchers and clinicians for volumetric analysis based on magnetic resonance imaging (MRI). However, different data acquisition techniques, analysis software and anatomical boundaries have in the past made it difficult to compare results of MRI studies from different laboratories. In order to reduce these differences, a segmentation protocol was established with 40 healthy normal control subjects recently scanned in our laboratory. Data acquisition was performed with a three-dimensional gradient echo technique, and scans were corrected for non-uniformity and registered into standard stereotaxic space prior to segmentation. Volumetric analysis was performed manually using three-dimensional software that allows simultaneous analysis of sagittal, coronal and horizontal images. Intra- and inter-rater coefficients yielded correlation coefficients comparable with other protocols. The hippocampal volume was larger in the right hemisphere (3324 versus 3208 mm(3)), while no interhemispheric differences for the amygdala (1154 versus 1160 mm(3)) could be observed. Most importantly, results from recent segmentation protocols for hippocampus and amygdala seem to approach each other with regard to mean volumes and interhemispheric differences. This indicates that the advances in scanning technique, volume preparation and segmentation protocols allow a more precise definition of medial temporal lobe structures with MRI, and that results for mean volumes for hippocampus and amygdala from different laboratories will eventually become comparable.
Liquid crystals in dynamic holography (review) (2011)

We review basic schemes and methods of recording of holographic gratings in liquid crystals, compositions, and devices on their basis. We consider various photochemical and electrooptical mechanisms of this recording, as well as some particular applications of dynamic holography in liquid crystals.