gebhart/patrepeval huggingface dataset:
Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning (2020)

Accompanied with an increase of revealed biomolecular structures owing to advancements in structural biology, the molecular dynamics (MD) approach, especially coarse-grained (CG) MD suitable for macromolecules, is becoming increasingly important for elucidating their dynamics and behavior. In fact, CG-MD simulation has succeeded in qualitatively reproducing numerous biological processes for various biomolecules such as conformational changes and protein folding with reasonable calculation costs. However, CG-MD simulations strongly depend on various parameters, and selecting an appropriate parameter set is necessary to reproduce a particular biological process. Because exhaustive examination of all candidate parameters is inefficient, it is important to identify successful parameters. Furthermore, the successful region, in which the desired process is reproducible, is essential for describing the detailed mechanics of functional processes and environmental sensitivity and robustness. We propose an efficient search method for identifying the successful region by using two machine learning techniques, Bayesian optimization and active learning. We evaluated its performance using F1-ATPase, a biological rotary motor, with CG-MD simulations. We successfully identified the successful region with lower computational costs (12.3% in the best case) without sacrificing accuracy compared to exhaustive search. This method can accelerate not only parameter search but also biological discussion of the detailed mechanics of functional processes and environmental sensitivity based on MD simulation studies.
Deep Dynamic Time Warping: End-to-End Local Representation Learning for Online Signature Verification (2019)

Siamese networks have been shown to be successful in learning deep representations for multivariate time series verification. However, most related studies optimize a global distance objective and suffer from a low discriminative power due to the loss of temporal information. To address this issue, we propose an end-to-end, neural network-based framework for learning local representations of time series, and demonstrate its effectiveness for online signature verification. This framework optimizes a Siamese network with a local embedding loss, and learns a feature space that preserves the temporal location-wise distances between time series. To achieve invariance to non-linear temporal distortion, we propose building a dynamic time warping block on top of the Siamese network, which will greatly improve the accuracy for local correspondences across intra-personal variability. Validation with respect to online signature verification demonstrates the advantage of our framework over existing techniques that use either handcrafted or learned feature representations.
Modeling percolation in high-aspect-ratio fiber systems. I. Soft-core versus hard-core models (2007)

Numerical and analytical studies of the onset of percolation in high-aspect-ratio fiber fiber systems such as nanotube reinforced polymers available in the literature have consistently modeled fibers as penetrable, straight, capped cylinders, also referred to as spherocylinders. In reality, however, fibers of very high-aspect ratio embedded in a polymer do not come into direct physical contact with each other, let alone exhibit any degree of penetrability. Further, embedded fibers of very high-aspect ratio are often actually wavy, rather than straight. In this two-part paper we address these critical differences between known physical systems, and the presently used spherocylinder percolation model. In Paper I we evaluate the effect of allowing penetration of the model fibers on simulation results by comparing the soft-core and the hard-core approaches to modeling percolation onset. We use Monte Carlo simulations to investigate the relationship between percolation threshold and excluded volume for both modeling approaches. Our results show that the generally accepted inverse proportionality between percolation threshold and excluded volume holds for both models. We further demonstrate that the error introduced by allowing the fibers to intersect is non-negligible, and is a function of both aspect ratio and tunneling distance. Thus while the results of both the soft-core model and hard-core assumptions can be matched to select experimental results, the hard-core model is more appropriate for modeling percolation in nanotubes-reinforced composites. The hard-core model can also potentially be used as a tool in calculating the tunneling distance in composite materials, given the fiber morphology and experimentally derived electrical percolation threshold. In Paper II we investigate the effect of the waviness of the fibers on the onset of percolation in fiber reinforced composites.
<title>Controlling diode laser bar temperature by micro channel liquid cooling</title> (1999)

In this paper investigations of temperature control of micro channel cooled high power diode lasers are presented. After a short motivation the theoretical background of a complete liquid cooling system is introduced and the simulation results are compared to the behavior of a real-world system. Because of the nonlinear dependence of the thermal resistance on the water flux modern control algorithms are required to achieve a sufficient control quality and robustness. Their design and characterization are presented as well. Based on the results of diode laser temperature control the potentials to realize a highly efficient wavelength control are discussed. To support future system integration and to realize the controller with minimal hardware expenditure an application specific integrated circuit (ASIC) was developed.
Modeling service engagements in dynamic organizations: multiagent model and architecture for policy-based governance (2008)

Service engagements arise commonly in business and scientific computing. A service engagement is characterized by autonomous parties coming together in a contractual arrangement to share resources or carry out tasks for one another. The autonomy of the participants is key, meaning that there is no unique locus for policy application. Yet, autonomy is not properly treated by current approaches for designing service engagements, which typically take the perspective of one of the participants. 
We provide an agent-based conceptual model for specifying service engagements as arising within dynamic service organizations or Orgs. The atoms of a service engagement are formalized as commitments among the participants, to be created and manipulated as the engagement progresses. An Org scopes the commitments formed in an engagement. 
Orgs and their members are modeled as agents. A service contract provides a natural arms-length abstraction for modeling service engagements and is formalized as comprising a set of commitments among the contracting agents. An institution is a kind of an Org that acts as a social and legal context, within which Orgs arise modeling different service engagements. We provide a policy-based architecture for the governance of service engagements. 
We propose innovations in policy-based architecture to model and govern complex Orgs. Traditional policy-based frameworks emphasize reactive behaviors wherein an external request causes a policy engine to compute a response. However, business service settings require richer policies and call for proactive behaviors. A business must not only respond to explicit requests, but also monitor its environment, collate events, and potentially act in anticipation of events in order to ensure that its policies are satisfied. 
The core of this research is an approach to formalize service engagements based on commitments and to study their dynamics in the presence of policies specified by each of the participants. We describe a methodology for service engagement design using a set of design patterns that capture commonly occurring elements of service engagements. We have implemented MAVOS, a prototype of a policy-based multiagent system to model Orgs that demonstrates and evaluates our approach on realistic scenarios involving Orgs.
Percutaneous ablation in the kidney (2012)

Percutaneous ablation in the kidney is now performed as a standard therapeutic nephron-sparing option in patients who are poor candidates for resection. Its increasing use has been largely prompted by the rising incidental detection of renal cell carcinomas with cross-sectional imaging and the need to preserve renal function in patients with comorbid conditions, multiple renal cell carcinomas, and/or heritable renal cancer syndromes. Clinical studies to date indicate that radiofrequency ablation and cryoablation are effective therapies with acceptable short- to intermediate-term outcomes and with a low risk in the appropriate setting, with attention to pre-, peri-, and postprocedural detail. The results following percutaneous radiofrequency ablation and cryoablation in the treatment of renal cell carcinoma are reviewed in this article, including those of several larger scale studies of ablation of T1a tumors. Clinical and technical considerations unique to ablation in the kidney are presented, and potential complications are discussed.
Combined UV-Vis-absorbance and Reflectance Spectroscopy Study of Dye Transfer Kinetics in Aqueous Mixtures of Surfactants (2017)

We report an analytical approach to study the kinetics of desorption and exhaustion of a hydrophobic dye in a multicomponent washing model environment. The process of dye transfer between an acceptor textile (white polyamide), detergent micelles and a donor textile (red polyester) was quantified by a combination of colorimetric analyses. UV-Vis absorbance and UV- reflectance spectroscopy were used to follow the concentration of the solubilised dye in the micelles and the amount of dyer transferred to the acceptor textile, respectively, as a function of time. Up to ≃ 10 min of the washing process, the released dye is predominantly solubilised in surfactant micelles. At later times, the adsorption of the dye on the hydrophobic surface of the acceptor textile is energetically favoured. The shift of the desorption equilibrium in the presence of the acceptor textile results in ≃ 30% increase in the release of the dye. The reported methodology provides insight into the competition between solubilisation of hydrophobic molecules by amphiphiles and dye adsorption on solid substrates, important for designing novel concepts of dye transfer inhibition.
Discovery and characterization of an L‐kynurenine responsive transcriptional regulator of the oxidative tryptophan degradation pathway in Burkholderia xenovorans (2012)

To uncover the transcriptional regulation of oxidative tryptophan degradation, comparative genomics were used which focused on the operon containing the genes kynA, kynU and kynB . In β and γ‐proteobacteria, including Burkholderia, Ralstonia, Collimonas , Cupriavidus and Pseudomonas species, there is a conserved asnC/lrp family transcriptional regulator (TR) gene located upstream of the operon on the opposite strand. In Burkholderia xenovorans the TR is Bxe_A0736 and we designate it as kynR . Using DNAse footprinting with fluorescence capillary electrophoresis, we determined that the KynR protein binds a set of four degenerate, palindromic sequences within the intergenic region from 35 bp upstream of kynB to over the start site of kynR . The optimal consensus sequence is ATATTCCGAATAT. KynR binds L‐kynurenine with greater affinity than any other amino acid or tryptophan degradation product and does so with a dissociation constant of 67 ± 14 μM, as determined by frontal affinity chromatography with ESI‐MS detection (FAC‐MS). Using fluorescence anisotropy, we determined that L‐kynurenine increases the affinity of KynR for a 39 bp section of the regulatory site from 145 +/− 2 nM to 97 +/− 1 nM. We propose that KynR promotes the transcription of kynA , kynU and kynB in the presence of L‐kynurenine while inhibiting the transcription of its own gene, kynR . This research was funded by the DOE/LANL LDRD program.
Front-to-Rear Crashes Involving Two Vehicles With Severe Driver Injury (2012)

In front-to-rear crashes with two vehicles, typically one driver was severely injured, not both. The risk of severe injury was not significantly different for drivers in the front or rear impacts. The risk was higher in rear impacts due to intrusion into the driver's seating area that supported or pushed the driver's seat forward. The risk for drivers in frontal crashes was also often related to intrusion due to offset loading and occupant compartment deformation.
Immunohistochemical detection of MUC5AC and MUC5B mucins in ferrets (2023)

MUC5AC and MUC5B mucins were detected most commonly in large airways and least in small airways, consistent with reported goblet cell density in airway surface epithelia. We evaluated whether staining method affected the detection of goblet cell mucins in serial sections of bronchial surface epithelia. Significant differences between stains were not observed suggesting common co-expression MUC5AC and MUC5B proteins in goblet cells of airway surface epithelia. Gallbladder and stomach tissues are reported to have differential mucin enrichment, so we tested these tissues in wildtype ferrets. Stomach tissues were enriched in MUC5AC and gallbladder tissues enriched in MUC5B, mucin enrichment similar to human tissues. Mucin immunostaining techniques were further qualified for specificity using lung tissue from recently generated MUC5AC<sup>-/-</sup> and MUC5B<sup>-/-</sup> ferrets. Qualified techniques for MUC5AC and MUC5B immunohistochemistry will be useful tools for mucin tissue studies in CF and other ferret models.
Characterization of two newly established human cell lines from patients with large-cell anaplastic lung carcinoma (1982)

Two permanent cell lines, designated LU-65 and SK-Luci-6, were established from large-cell anaplastic lung cancers of two patients. Both cell lines grew as solid tumors in nude mice. The histologic pattern of the tumors in the nude mouse resembled that of the primary lung cancers in that the xeno-transplanted tissues showed no distinctive features indicative of cell type, a finding consistent with origin from a large-cell anaplastic lung cancer. Cells from both lines formed clones in semisolid agar. Flow cytometric analysis of SK-Luci-6 showed a hypertriploid stemline with a very high RNA-index. Line LU-65 had a hyperdiploid stemline evolving into a hypertriploid stemline with a high RNA-index. Chromosome analysis showed aneuploidy with abnormalities and marker chromosomes in both tumor cell lines. The isoenzyme pattern of LU-65 and Sk-Luci-6 indicated that they were of human origin and distinct from HeLa cells or another common contaminating line. Both cell lines released biologically active agents that could have caused the neutrophilia and hypercalcemia seen in the patients.
Influence of the method of preparation of ultrastable Y zeolites on extraframework aluminium and the activity and selectivity during the cracking of gas oil (1987)

Caracterisation par spectrometrie IR de zeolites HY ultrastables ayant un rapport Si/Al de 8, desaluminees par Fe 6 Si(NH 4 ) 2 ou par de la vapeur. Influence de leur mode de preparation sur leurs activite et selectivite lors du craquage de gas oil
Why We Don't Know How Many Colors There Are (2012)

There have been many attempts to answer the question of how many distinct colors there are, with widely varying answers. Here we present an analysis of what it would take to arrive at a reliable answer and show how currently available models fail to make predictions under the wide range of conditions that needs to be considered. Gamut volumes are reported for a number of light sources and viewing modes and the conclusion is drawn that the only reliable data we have comes from psychophysical work. The color gamut of the LUTCHI data in CIECAM02 is therefore shown as an alternative to the gamut of all possible colors.
Principles of Writing Construction Specifications and Special Provisions (2018)

This presentation will assist project managers and designers in preparing the necessary information required for Department contracts involving Standard Specifications and Special Provisions. Attendees will see examples of both the right and wrong ways to present a Unique Special Provision, things to avoid, and questions to ask to adhere to legal, moral, and ethical construction standards.
A Practical Petrophysical Approach for Brittleness Prediction from Porosity and Sonic Logging in Shale Reservoirs (2014)

Abstract Brittleness has been used as one of the important descriptors for the characterization of unconventional shale reservoirs. The degree of brittleness in shale reservoirs is determined upon the basis of its mineralogical composition, which can be obtained from mineralogical logging tools (such as ECS™, FLeX™, GEM™, Litho Scanner™), or XRD tests in the laboratory. Generally, measurements of mineralogical brittleness are obtained from physical sources and lead to relatively reliable interpretation results. However, mineralogical logging is expensive and not commonly available in the shale play. Alternatively, brittleness can also be calculated from dynamic Young's modulus and Poisson's ratio, but the absence of shear slowness in some wells restricts its wide application. Internal friction angle based brittleness can give similar interpretation results as the preceding two methods, but its accuracy depends highly on the quality of correlations. It is observed that the curves of the three different brittlenesses demonstrate similar shapes. Therefore, we have attempted to build correlations between mineralogical brittleness and porosity or sonic compressional slowness for typical shale plays (Woodford, Barnett, and Eagle Ford shale), and have proven their validity with the data obtained from wells not included in the development of correlations. Applications of these findings include: (1) enabling the possibility of evaluating brittleness in plays lacking mineralogical and shear sonic loggings, thus reducing the quantity of laboratory testing, (2) inspiring operators to develop in-house correlations of brittleness for shale gas plays, and (3) investigating similar correlations in emerging unconventional oil plays, such as Granite Wash.
Pharmacological Characterization of the Autonomous Innervation of the Guinea Pig Tracheobronchial Smooth Muscle (1981)

From the trachea, main bronchi and hilus bronchi of guinea pigs, preparations were isolated for registration of mechanical tension on electrical field stimulation and drugs. The trachea contracted on short trains of electrical stimulation. Usually these contractions were followed by a relaxant response. The contractions were abolished while the relaxations were potentiated by atropine. In the main bronchi field stimulation induced a contractile response which was abolished by atropine. In the latter preparation relaxant responses were never observed, even not after atropine. In the trachea and main bronchi neither the alpha 1 blocker prazosin nor the alpha2 blocker yohimbine affected the contractile or relaxant responses when used in alpha-blocking concentrations. The relaxant response in trachea was neither affected by the "P1 blocker" theophylline nor by the "P2 blocker" quinidine but it was partially inhibited by guanethidine or beta-blocking agents. The hilus bronchi contracted on field stimulation as well as histamine. The contractile response on electrical stimulation was only slightly inhibited by atropine or guanethidine. In all three preparations responses on field stimulation were abolished by tetrodotoxin. It is suggested that in both trachea and main bronchi excitatory cholinergic innervation is present. Further, the trachea but not the main bronchi is innervated by both adrenergic and nonadrenergic inhibitory nerves. The hilus bronchi contains a non-adrenergic non-cholinergic excitatory nervous system.
Staphylococcus epidermidis polysaccharide intercellular adhesin activates complement (2011)

Staphylococcus epidermidis is a frequent cause of nosocomial infections. The central virulence factor of S. epidermidis is biofilm formation. Polysaccharide intercellular adhesin (PIA) constitutes the major biofilm matrix-component. PIA and biofilm have been implicated in S. epidermidis evasion of host immune defence. We examined the effects of S. epidermidis PIA on the inflammatory response with focus on complement activation. We used a human whole-blood ex vivo model of infection and compared the effects of a PIA-positive S. epidermidis strain (SE1457) and its PIA-negative isogenic mutant (M10). The independent effect of purified PIA on complement activation was investigated. In glucose-rich media, the mutant formed a proteinacious DNA-rich biofilm, whereas SE1457 formed a thick PIA-biofilm. In biofilm growth, SE1457 induced a stronger activation of the complement system compared with M10. We verified that purified PIA was independently responsible for a strong activation of the complement system. In contrast, M10 induced higher granulocyte activation by expression of CD11b and higher secretion of cytokines. We conclude that PIA has potent pro-inflammatory properties by activating the complement system. However, in a complex balance of the immune response, the decreased activation of granulocytes and cytokines by a PIA biofilm may limit host eradication of S. epidermidis.
Fabrication of regular silicon microstructures by photo‐electrochemical etching of silicon (2005)

In this paper photo-electrochemical etching of silicon in HF-based solutions is employed as a versatile technique for fabrication of original silicon microstructures, alternative to commonly used methods. Photo-electrochemical etching, a well known technique for regular macropore formation, has been exploited to produce a multitude of different regular silicon microstructures (microtubes, microtips, microchannels, microspirals, micropillars, microwalls, etc.). This micromachining technique is here detailed and some applications are reported. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Automatic PMD Compensation over Transoceanic Distance with Time Varying SOP, PSP, and PMD (2008)

Automatic receiver PMD compensation was successfully demonstrated with 40Gb/s RZ- DPSK signals using a circulating loop transmission line. The long-term Q-factor histogram was significantly improved. PMD compensation was not as effective for the APol RZ-DPSK format.
Binding BIKE errors to a key pair. (2021)

The KEM BIKE is a Round-3 alternative finalist in the NIST Post-Quantum Cryptography project. It uses the FO\(^{\not \bot }\) transformation so that an instantiation with a decoder that has a DFR of \(2^{-128}\) will make it IND-CCA secure. The current BIKE design does not bind the randomness of the ciphertexts (i.e., the error vectors) to a specific public key. We propose to change this design, although currently, there is no attack that leverages this property. This modification can be considered if BIKE is eventually standardized.