gebhart/patrepeval huggingface dataset:
Scoring optimisation of unbound protein–protein docking including protein binding site predictions (2011)

The prediction of the structure of the protein-protein complex is of great importance to better understand molecular recognition processes. During systematic protein-protein docking, the surface of a protein molecule is scanned for putative binding sites of a partner protein. The possibility to include external data based on either experiments or bioinformatic predictions on putative binding sites during docking has been systematically explored. The external data were included during docking with a coarse-grained protein model and on the basis of force field weights to bias the docking search towards a predicted or known binding region. The approach was tested on a large set of protein partners in unbound conformations. The significant improvement of the docking performance was found if reliable data on the native binding sites were available. This was possible even if data for single key amino acids at a binding interface are included. In case of binding site predictions with limited accuracy, only modest improvement compared with unbiased docking was found. The optimisation of the protocol to bias the search towards predicted binding sites was found to further improve the docking performance resulting in approximately 40% acceptable solutions within the top 10 docking predictions compared with 22% in case of unbiased docking of unbound protein structures.
Dispersion of extensional waves in fluid-saturated porous cylinders at ultrasonic frequencies (1983)

Ultrasonic dispersion of extensional waves in fluid-saturated porous cylinders is studied by analyzing generalized Pochhammer equations derived using Biot’s theory. Cases with open-pore surface and closed-pore surface boundary conditions are considered. For both cases, the dispersion of the fast extensional wave does not differ much qualitatively from the dispersion expected for extensional waves in isotropic elastic cylinders. A slow extensional wave propagates in the case with a closed-pore surface but not in the case with an open-pore surface. The propagating slow wave has very weak dispersion and its speed is always lower than, but close to, the bulk slow wave speed.
Ionic polymer metal composites: II. Manufacturing techniques (2003)

This paper, the second in a series of four review papers to appear in this journal, presents a detailed description of various techniques and experimental procedures in manufacturing ionic polymer–metal composites (IPMCs) that, if fully developed, can be used as effective biomimetic sensors, actuators and artificial muscles as well as fully electroded with embedded electrodes for fuel cells. The performance of IPMCs manufactured by different manufacturing techniques are presented and compared. In particular, a number of issues such as force optimization using the Taguchi design of experiment technique, effects of different cations on electromechanical performance of IPMCs, electrode and particle size and distribution control, manufacturing cost minimization approaches, scaling and three-dimensional (3D) muscle production issues and heterogeneous composites by physical loading techniques are also reviewed and discussed.
Physiological roles of dietary glutamate signaling via gut–brain axis due to efficient digestion and absorption (2013)

Dietary glutamate (Glu) stimulates to evoke the umami taste, one of the five basic tastes, enhancing food palatability. But it is also the main gut energy source for the absorption and metabolism for each nutrient, thus, only a trace amount of Glu reaches the general circulation. Recently, we demonstrated a unique gut sensing system for free Glu (glutamate signaling). Glu is the only nutrient among amino acids, sugars and electrolytes that activates rat gastric vagal afferents from the luminal side specifically via metabotropic Glu receptors type 1 on mucosal cells releasing mucin and nitrite mono-oxide (NO), then NO stimulates serotonin (5HT) release at the enterochromaffin cell. Finally released 5HT stimulates 5HT3 receptor at the nerve end of the vagal afferent fiber. Functional magnetic resonance imaging (f-MRI, 4.7 T) analysis revealed that luminal sensing with 1 % (w/v) monosodium L-glutamate (MSG) in rat stomach activates both the medial preoptic area (body temperature controller) and the dorsomedial hypothalamus (basic metabolic regulator), resulting in diet-induced thermogenesis during mealing without changes of appetite for food. Interestingly, rats were forced to eat a high fat and high sugar diet with free access to 1 % (w/w) MSG and water in a choice paradigm and showed the strong preference for the MSG solution and subsequently, they displayed lower fat deposition, weight gain and blood leptin. On the other hand, these brain functional changes by the f-MRI signal after 60 mM MSG intubation into the stomach was abolished in the case of total vagotomized rats, suggesting that luminal glutamate signaling contributes to control digestion and thermogenesis without obesity.
Structurally Controlled Dynamics in Azobenzene-Based Supramolecular Self-Assemblies in Solid State (2016)

&lt;p&gt;Light-responsive supramolecular self-assemblies exhibit interplay between order and dynamics of the self-assembling motifs, through which the thermal isomerization rate of azobenzene chromophores can be tuned by orders of magnitude. By using supramolecular complexes of 4-(4-alkylphenylazo)phenols hydrogen-bonded to poly(4-vinylpyridine) as model systems, we demonstrate that the thermal isomerization rate of the hydroxyazobenzene derivatives increases 5700-fold when the material undergoes a transformation from a disordered, low-azobenzene-concentration state to a high-concentration state exhibiting lamellar, smectic-like self-assembly. Drastically smaller thermal isomerization rates are observed in disordered structures. This allows us to attribute the change to a combination of increased number density of the hydroxyazobenzenes inducing plasticization, and cooperativity created by the chromophore-chromophore interactions through self-assembled molecular order and alignment. Our results pinpoint the importance of molecular self-assembly and intermolecular interactions in modifying the dynamics in supramolecular complexes in a controlled manner. We foresee this to be important in light-controlled dynamic materials.&lt;/p&gt;
The Impact of Automatic Identification on Supply Chain Operations (2003)

Abstract Automated Identification (Auto ID) applications can provide corporate information systems with the identity of each physical item in the supply chain in an automated and timely manner. The real time availability of item identity allows other information, related to the item, to be drawn on in order to assess both the current state of the product and future actions required. In the context of supply chain operations, widespread introduction of such systems represents a major opportunity to overhaul and improve tracking and tracing systems, process control and inventory management. In the longer term, it is possible that Auto ID systems may enable a complete re‐engineering of the supply chain, by removing a number of the constraints that limit today's supply chain structures. In this paper, we review some key challenges in supply chain operations and introduce the main elements of an Auto ID system. Using a simple categorization of supply chain operations, areas for short term deployment of Auto ID are identified and opportunities for longer term re‐engineering of different sections of the supply chain are highlighted.
Migration of Cells From the Yolk Sac to Hematopoietic Tissues After In Utero Transplantation of Early and Mid Gestation Canine Fetuses (2011)

These studies demonstrated that cells injected into the yolk sacs of early gestation canine fetuses migrate to recipient hematopoietic tissues. Thus, yolk sac injection offers a safe and effective approach for engraftment of cells to fetal hematopoietic tissues.
The use of botulinum toxin in spastic infantile cerebral palsy (2009)

Cerebral palsy is not a specific disease but a group of clinical syndromes, caused by a non-progressive injury to the developing brain that results in a disorder of movement and posture that is permanent but not unchanging. It is the most common cause of physical disability affecting children in developed countries. The incidence is steady in most countries at approximately 2/1000 live births. The location, timing, and severity of the brain lesion are extremely variable, which results in many different clinical presentations. Despite the static nature of the brain injury, the majority of children with cerebral palsy develop progressive musculoskeletal problems such as spastic posturing and muscle contractures (Koman et al., 2004).
Boosting Antimicrobial Peptides by Hydrophobic Oligopeptide End Tags (2009)

A novel approach for boosting antimicrobial peptides through end tagging with hydrophobic oligopeptide stretches is demonstrated. Focusing on two peptides derived from kininogen, GKHKNKGKKNGKHNGWK (GKH17) and HKHGHGHGKHKNKGKKN (HKH17), tagging resulted in enhanced killing of Gram-positive Staphylococcus aureus, Gram-negative Escherichia coli, and fungal Candida albicans. Microbicidal potency increased with tag length, also in plasma, and was larger for Trp and Phe stretches than for aliphatic ones. The enhanced microbicidal effects correlated to a higher degree of bacterial wall rupture. Analogously, tagging promoted peptide binding to model phospholipid membranes and liposome rupture, particularly for anionic and cholesterol-void membranes. Tagged peptides displayed low toxicity, particularly in the presence of serum, and resisted degradation by human leukocyte elastase and by staphylococcal aureolysin and V8 proteinase. The biological relevance of these findings was demonstrated ex vivo and in vivo in porcine S. aureus skin infection models. The generality of end tagging for facile boosting of antimicrobial peptides without the need for post-synthesis modification was also demonstrated.
Ship ballasts in the Bay of Cadiz: Their use as pavements in the Cadiz Old City quarters during the 17th–19th century. Petrological and archaeometric approach (2018)

In recent centuries many of the old quarters of the city of Cádiz have been paved with rocks boulders of very different petrographic natures. The popular tradition supposes an imported origin to these materials, indicating that they were part of the ballast of the Spanish galleons that came from America. In recent years we have been carrying out two types of actions on these heritage materials, on the one hand: an archaeometric study based on the petrological, mineralogical and geochemical analysis of many of these rocks, trying to determine their petrographic, paleontological, textural, etc. features, that will allow to elaborate hypotheses about their possible areas of origin. On the other hand: an historical study based on the different archives of the city or other archives in the region, to obtain information about the maritime traffic to and from the city of Cádiz urbanism and its bay, over the last five centuries, as well as the use of these materials in the paving of the city and its houses. Besides the study of the pavements of the old town of Cádiz, which are also present in other cities of the Bay, such as San Fernando or Chiclana de la Frontera, accumulations of anthropic origin (saburra), are being sampled at different points of the Bay of Cádiz, where boats throw ballast throughout history. The data obtained is being compared with the analysis of geological samples from our litoteca, from different outcrops of the Gibraltar Strait region and the SW of the peninsula, as well as from the Atlantic coasts of western Europe, northern Africa, the Canary Islands and we pretend in the near future, of the American continent. Special attention will be given to those ports or areas of provisioning of ships in this historical period between the fifteenth and nineteenth centuries. Some of the rocks studied seem to have a local-regional origin, but a great majority of them undoubtedly have an exotic origin to this geographical area, so they would come from the ballast transported by the different ships that made commercial routes, especially along the Atlantic Ocean, or from warships or ships that participated in the different attacks and invasions of the city.
Development of a super long reach coupled tendon-driven manipulator “Super Dragon” (2019)

The decommissioning of the Fukushima Daiichi Nuclear Power Plants is a national urgent problem in Japan. The distribution and characteristics of the fuel debris inside the nuclear reactor must be investigated to safely retrieve them. This study describes a 10 m-long articulated manipulator for investigation inside the primary container vessel. We employed a coupled tendon-driven mechanism and a gravity compensation mechanism using synthetic fiber ropes to design a lightweight and slender articulated manipulator. After discussing the basic principle and control algorithm, we focus on the detailed mechanical design of a prototype model. We confirmed its feasibility through basic motion experiments.
A Nonlinear Phenomenon on Self-Oscillating Current Controllers: The Indirect Synchronization (2009)

In this paper, a particular phenomenon called <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">indirect synchronization</i> is investigated on self-oscillating current controllers. This phenomenon appears in <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">medium frequencies</i> , when the reference signal frequency tends to the switching frequency. In a previous work, it has been shown that the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">indirect synchronization</i> causes discontinuities on the frequential response of the system, making the various linear or continuous models inefficient. For high-accuracy applications, such as active filtering or high-precision power supply, these discontinuities are a real problem. Thus, it seems important to offer an analytical description of this phenomenon. In this paper, an analytical model of the indirect synchronization phenomenon is proposed and checked by simulation and experimental results.
Preparation and Evaluation of Liquid-Crystal Formulations with Skin-permeation-enhancing Abilities for Entrapped Drugs (2011)

The usefulness of liquid crystals (LC) in topical formulations for application to skin was evaluated by measuring the in vitro permeation profile of a model compound, calcein, entrapped in a LC formulation, through excised hairless rat skin and a three-dimensional cultured human-skin model; the viability was determined using the MTT assay. Two physically stable LCs were prepared from a mixture of mono-, di-, and tri-esters 1, and monoesters 2, composed of erythritol and phytanylacetic acid. Cryo-transmission electron microscopy (cryo-TEM), electron diffraction patterns, and small-angle X-ray diffraction (SAXS) observations of the LC nanodispersions showed that the structures of the LCs were reverse hexagonal (LC-A) and cubic (LC-B). The skin-permeation properties of calcein were enhanced by entrapping in the LCs as a result of the increase in calcein partition from the LC dispersion solution into the skin; the properties were analyzed using a skin-permeation-time profile. Drug partitioning could also be modified by the LC structure. No skin damage was caused by the LC formulation in these experiments.The present study suggests that LC dispersions are potential additives in topical drug formulations and cosmetic formulations.
ChemInform Abstract: Synthesis of Cyclic Imines via Ethylenetetramethyldisilyl‐Protected . omega.‐Amino Imines. Application to the Synthesis of Alkaloids. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Activated Carbons Chemically Modified by Concentrated H2SO4 for the Adsorption of the Pollutants from Wastewater and the Dibenzothiophene from Fuel Oils (2003)

The surface properties, porosities, and adsorption capacities of activated carbons (AC) are modified by the oxidation treatment using concentrated H2SO4 at temperatures 150−270 °C. The modified AC was characterized by N2 adsorption, base titration, FTIR, and the adsorption of iodine, chlorophenol, methylene blue, and dibenzothiophene. The treatment of AC with concentrated H2SO4 at 250 °C greatly increases the mesoporous volume from 0.243 mL/g to 0.452 mL/g, specific surface areas from 393 m2/g to 745 m2/g, and acidic surface oxygen complexes from 0.071 meq/g to 1.986 meq/g as compared with the unmodified AC. The base titration results indicate that the amount of acidic surface oxygen groups on the modified AC increases with increasing the treatment temperatures and carboxyls and phenols are the most abundant carbon−oxygen functional groups. The carboxyl groups, COO- species, and hydroxyl groups are detected mainly for the sample treated at 250 °C. The mesoporous properties of the AC modified by concentrated H2SO4 were further tested by the adsorption of methylene blue and dibenzothiophene. The AC modified by concentrated H2SO4 at 250 °C has much higher adsorption capacities for large molecules (e.g., methylene blue and dibenzothiophene) than the unmodified AC but less adsorption capacities for small molecules (e.g., iodine). The adsorption results from aqueous solutions have been interpreted using Freundlich adsorption models.
6-Substituted benzimidazoles as new nonpeptide angiotensin II receptor antagonists: synthesis, biological activity, and structure-activity relationships (1993)

Starting from the recently reported nonpeptidic angiotensin II (AII) receptor antagonists DuP753 (1) and Exp 7711 (2), we have designed and investigated novel substituted benzimidazoles. Systemic variation of several substituents at the benzimidazole ring positions 4-7 led to the finding that substitution in position 6 with acylamino groups results in highly active AII antagonists. Compounds with 6-membered lactam or sultam substituents in position 6 of benzimidazole showed receptor activities in the low nanomolar range but were only weakly active when given orally to rats. In contrast, analogous substitution of the benzimidazole moiety with basic heterocycles resulted in potent AII antagonists which were also well absorbed after oral application. The most active compound of this series, 33 (BIBR 277), was selected as a candidate for clinical development. On the basis of molecular modeling studies a binding model of this new class of AII antagonists to the AT1 receptor is proposed.
Physically-Based Simulations of the Cyclic Behavior of FCC Polycrystals (2014)

Two homogeneization approaches are used in order predict the cyclic elastic-plastic behaviour of 316L(N) polycrystals, either
[RelE toxin protein of Mycobacterium tuberculosis induces growth inhibition of lung cancer A-549 cell]. (2008)

The RelE toxin protein of mycobacterium tuberculosis has growth inhibition and apoptotic effect on lung cancer A-549 cell.
A 170 mW 10 b 50 Msample/s CMOS ADC in 1 mm/sup 2/ (2005)

This 10 b AD-converter at a sample rate of 5O MSample/s, embedded in 50mm/sup 2/ of digital circuitry, shows 8.7 effective bits. A straight flash-architecture would need 1023 accurate fast comparators. With a 2 V input range, a comparator offset voltage of no more than 1 mV can be tolerated. Taking into account that the 1 mV is a 3-6 sigma value, leads to a large chip. If, however, the signals to the comparator are amplified before the critical decision, simple small comparators would suffice. To cope with the dynamic offset caused by the clocking and latch action of the comparator itself, the architecture must tolerate comparator offsets of up to 60-80 mV. Hence, a gain of at least 30 is necessary. A single amplifier however, could not handle this, as the input range of 2 V would be amplified to 60 V. The approach here is to use a distributed amplifier.
Paracrine Signaling Through MYCN Enhances Tumor-Vascular Interactions in Neuroblastoma (2012)

Neuroblastoma, a tumor of peripheral neural crest origin, numbers among the most common childhood cancers. Both amplification of the proto-oncogene MYCN and increased neoangiogenesis mark high-risk disease. Because angiogenesis is regulated by phosphatidylinositol 3-kinase (PI3K), we tested a clinical PI3K inhibitor, NVP-BEZ235, in MYCN-dependent neuroblastoma. NVP-BEZ235 decreased angiogenesis and improved survival in both primary human (highly pretreated recurrent MYCN-amplified orthotopic xenograft) and transgenic mouse models for MYCN-driven neuroblastoma. Using both gain- and loss-of-function approaches, we demonstrated that the antiangiogenic efficacy of NVP-BEZ235 depended critically on MYCN in vitro and in vivo. Thus, clinical PI3K/mammalian target of rapamycin inhibitors drove degradation of MYCN in tumor cells, with secondary paracrine blockade of angiogenesis. Our data demonstrated significantly improved survival in treated animals and suggest that NVP-BEZ235 should be tested in children with high-risk, MYCN-amplified neuroblastoma.
La catedral de Coria (Cáceres): estudio histórico-artístico (2016)

La tesis titulada La Catedral de Coria: estudio historico artistico descubre nueva informacion sobre el origen del templo cauriense que esta relacionada con su antiguedad y su transformacion a partir de finales del siglo XV, desarrollada durante 77 anos. En ella se demuestra que sus rejas principales, del coro y del altar mayor, fueron forjadas por Urson Tesem. Tambien Rodrigo de Vidana levanto, apoyando sobre su pasado visigodo, un balcon abierto (que posiblemente tuviera como modelo los balcones de solana del norte de la peninsula Iberica) y esculpio, junto con el taller local, los relieves historicos. El proyecto de la catedral renovada, que conserva sus hastiales y edificios antiguos, lo diseno Enrique Egas; otros maestros como Martin de Solorzano, Bartolome de Pelayos, Sebastian de Lasarte o Michel de Villarreal con sus equipos de canteros lo llevaron a cabo. El maestro Juan de Alava amplio con capillas laterales la planta de salon disenada por Egas en el flanco sur, trabajos que fueron llevados a cabo por Esteban de Lizcano, Pedro de Ibarra y el taller local de Coria.
Assessment and Simulation of the Responsive Demand Potential in End-User Facilities: Application to a University Customer (2004)

Many problems have appeared with the practical implementation of restructured electrical business in the U.S. and European Union such as lack of generation, network constraints, etc. A good example of these problems is the scarce participation of the demand in the electricity markets - energy, reserve, and other ancillary services - problems that could be solved through new demand responsive programs, aimed to replace the traditional demand side management programs into voluntary demand participation programs. A methodology for the generation of demand side bids and offers in large customer facilities and a real application to a university customer is presented in this paper. The methodology is based on the knowledge of the physical processes involved in the electricity consumption and on the flexibility of the required supply. The result of the methodology proposed is a set of demand packages that can be used to participate in different electricity markets, whose possibilities - in the market arena - will be explored in a consequent paper.