pinecone/core-2020-05-10-deduplication huggingface dataset:
A nucleotide-level coarse-grained model of RNA

We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use
Molecular imaging in atherosclerosis

Atherosclerosis is the major cause of cardiovascular disease, which still has the leading position in morbidity and mortality in the Western world. Many risk factors and pathobiological processes are acting together in the development of atherosclerosis. This leads to different remodelling stages (positive and negative) which are both associated with plaque physiology and clinical presentation. The different remodelling stages of atherosclerosis are explained with their clinical relevance. Recent advances in basic science have established that atherosclerosis is not only a lipid storage disease, but that also inflammation has a fundamental role in all stages of the disease. The molecular events leading to atherosclerosis will be extensively reviewed and described. Further on in this review different modalities and their role in the different stages of atherosclerosis will be discussed. Non-nuclear invasive imaging techniques (intravascular ultrasound, intravascular MRI, intracoronary angioscopy and intravascular optical coherence tomography) and non-nuclear non-invasive imaging techniques (ultrasound with Doppler flow, electron-bean computed tomography, coronary computed tomography angiography, MRI and coronary artery MR angiography) will be reviewed. After that we focus on nuclear imaging techniques for detecting atherosclerotic plaques, divided into three groups: atherosclerotic lesion components, inflammation and thrombosis. This emerging area of nuclear imaging techniques can provide measures of biological activity of atherosclerotic plaques, thereby improving the prediction of clinical events. As we will see in the future perspectives, at present, there is no special tracer that can be called the diagnostic tool to diagnose prospective stroke or infarction in patients. Nevertheless, we expect such a tracer to be developed in the next few years and maybe, theoretically, it could even be used for targeted therapy (in the form of a beta-emitter) to combat cardiovascular disease
North-directed Triassic nappes in Northeastern Vietnam (East Bac Bo)

International audienceA careful re-examination of the previous tectonic descriptions and the acquisition of new structural and kinematic data have been undertaken in northeastern Vietnam. The structure of the area consists of a system of slightly metamorphosed but ductilely deformed nappes, including recumbent folds, formed during the Triassic, prior to the unconformable deposition of the Upper Triassic terrigenous sediments. These results confirm the previous interpretation of " preyunnanaises nappes ", represented by Middle-Upper Paleozoic foliated limestone resting through a flat mylonitic contact over an intermediate " Song Mien unit " (Deprat, 1915), the latter made essentially of deformed Lower Triassic sedimentary and volcanic formations, which previously filled the Song Hien rift (Bourret, 1922). In the external part of the belt, the Triassic strata conformably overlie slightly deformed and unmetamorphosed Upper Paleozoic rocks, forming an autochthonous domain. Alternatively, the same Triassic succession can be seen resting tectonically through décollement zones, directly over the Middle Paleozoic marbles, to form a distinct but subsidiary allochthonous unit. Our data show that the Song Chay orthogneiss and its Lower Paleozoic sedimentary country rocks belong to the main nappe. They also demonstrate that this nappe was transported to the N-NE. A newly discovered ophiolitic mélange of supposed oceanic nature and Triassic age, lying along the Song Chay Fault, North of the Nui Con Voi, could hypothetically represent the rooted zone of the nappe. A Tertiary overprinting event, in particular accommodated by strike-slip movements, likely accounts for the present orocline of NE Vietnam
Hole escape processes detrimental to photoluminescence efficiency in a blue InGaN multiple-quantum-well diode under reverse bias conditions

Photoluminescence (PL) properties of a blue In0.3Ga0.7N multiple-quantum-well (MQW) diode with an additional n+-doped In0.18Ga0.82N electron reservoir layer (ERL) have been investigated at 20  K as a function of reverse bias under indirect barrier excitation. A PL intensity ratio of MQW/ERL is observed to be significantly quenched by increasing the reverse field due to electron-hole separation and carrier escape, in spite of observed blueshifts, when the excitation power is decreased by two orders of magnitude. The PL intensity reduction suggests that the hole escape process plays an important role for determination of the PL efficiency under the reverse bias
Cost effectiveness of a combination of instruments for global warming: a quantitative approach for Spain

Climate change is an important environmental problem and one whose economic implications are many and varied. This paper starts with the presumption that mitigation of greenhouse gases is a necessary policy that has to be designed in a cost effective way. It is well known that market instruments are the best option for cost effectiveness. But the discussion regarding which of the various market instruments should be used, how they may interact and what combinations of policies should be implemented is still open and very lively. In this paper we propose a combination of instruments: the marketable emission permits already in place in Europe for major economic sectors and a CO(2) tax for economic sectors not included in the emissions permit scheme. The study uses an applied general equilibrium model for the Spanish economy to compute the results obtained with the new mix of instruments proposed. As the combination of the market for emission permits and the CO(2) tax admits different possibilities that depend on how the mitigation is distributed among the economic sectors, we concentrate on four possibilities: cost-effective, equalitarian, proportional to emissions, and proportional to output distributions. Other alternatives to the CO(2) tax are also analysed (tax on energy, on oil and on electricity). Our findings suggest that careful, well designed policies are needed as any deviation imposes significant additional costs that increase more than proportionally to the level of emissions reduction targeted by the EU
Pharmacovigilance in hospice/palliative care. Net effect of haloperidol for delirium

Prescribing practice in hospice/palliative care is largely extrapolated from other areas of clinical practice, with few studies of net medication effects (benefits and harms) in hospice/palliative care to guide prescribing decisions. Hospice/palliative care patients differ in multiple ways from better studied participant groups, hence the applicability of studies in other participant groups is uncertain. Haloperidol, a butyrophenone derivative and dopamine antagonist, is commonly prescribed for nausea, vomiting, and delirium in hospice/palliative care. Its frequent use in delirium occurs despite little evidence of the effect of antipsychotics on the untreated course of delirium. The aim of this study was to examine the immediate and short-term clinical benefits and harms of haloperidol for delirium in hospice/palliative care patients. METHOD: A consecutive cohort of participants from 14 centers across four countries who had haloperidol commenced for delirium were recruited. Data were collected at three time points: baseline, 48 hours (clinical benefits), and day 10 (clinical harms). Investigators were also able to report clinical harms at any time up to 14 days after it was commenced. RESULTS: Of the 119 participants included, the average dose was 2.1?mg per 24 hours; 42 of 106 (35.2%) reported benefit at 48 hours. Harm was reported in 14 of 119 (12%) at 10 days, the most frequent being somnolence (n=11) and urinary retention (n=6). Seven participants had their medication ceased due to harms (2 for somnolence and 2 for rigidity). Approximately half (55/119) were still being treated with haloperidol after 10 days. CONCLUSION: Overall, 1 in 3 participants gained net clinical benefit at 10 days
A comprehensive review of hybrid forward osmosis systems: Performance, applications and future prospects

Forward osmosis (FO) has been increasingly studied in the past decade for its potential as an emerging low-energy water and wastewater treatment process. However, the term “low-energy” may only be suitable for those applications in where no further treatment of the draw solution (DS) is required either in the form of pretreatment or post-treatment to the FO process (e.g. where the diluted DS is the targeted final product which can be used directly or simply discarded). In most applications, FO has to be coupled with another separation process in a so-called hybrid FO system to either separate the DS from the final product water or to be used as an advanced pre-treatment process to conventional desalination technologies. The additional process increases the capital cost as well as the energy demand of the overall system which is one of the several challenges that hybrid FO systems need to overcome to compete with other separation technologies. Yet, there are some applications where hybrid FO systems can outperform conventional processes and this study aims to provide a comprehensive review on the current state of hybrid FO systems. The recent development and performance of hybrid FO systems in different applications have been reported. This review also highlights the future research directions for the current hybrid FO systems to achieve successful implementation
On the origin and application of the Bruggeman correlation for analysing transport phenomena in electrochemical systems

The widely used Bruggeman equations correlate tortuosity factors of porous media with their porosity. Finding diverse application from optics to bubble formation, it received considerable attention in fuel cell and battery research, recently. The ability to estimate tortuous mass transport resistance based on porosity alone is attractive, because direct access to the tortuosity factors is notoriously difficult. The correlation, however, has limitations, which are not widely appreciated owing to the limited accessibility of the original manuscript. We retrace Bruggeman's derivation, together with its initial assumptions, and comment on validity and limitations apparent from the original work to offer some guidance on its use
Failure locus of fiber-reinforced composites under transverse compression and out-of-plane shear

The failure locus a fiber-reinforced composite lamina, made up of 50 vol.% of carbon fibers embedded in an epoxy matrix, is computed under transverse compression and out-of-plane shear, a stress state whose experimental reproduction is highly complex. The mechanical response was obtained by the finite element method of a representative volume element of the lamina, which explicitly takes into account the fibers and the matrix in the lamina. The actual deformation and failure mechanisms experimentally observed in the matrix, fibers and interfaces were included in the simulations through the appropriate constitutive equations. Two sets of simulations were performed, assuming that the fiber/matrix interface was either strong or weak. The corresponding failure loci were compared with those given by three failure criteria for composites (Hashin, Puck and LaRC) which provide reasonable predictions in other multiaxial stress states. The estimations of the failure criteria were largely consistent with the numerical simulations in the composites with a strong interface but overestimated the composite strength when the interface was weak because the effect of interface decohesion (which becomes dominant) was not taken into account. These results point out the need to include interface fracture in the failure criteria for composites
Two-dimensional electrophoresis as a tool for structural and genetic studies of seed proteins from Poaceae and Fagaceae.

The application of two-dimensional electrophoretic procedures to structural and genetic studies of seed proteins from Poaceae (including the cultivated cereals) and Fagaceae is described. The following related problems have been considered: covalent and non-covalent association of protein subunits in multiple oligomeric structures; chromosomal locations of genes encoding seed proteins; quantitation of gene products in relation to gene expression and regulation; purification of protein components to study their homology relationships and in vitro activities; evolutionary and phylogenetic relationships; identification of genetic stocks. Isoelectric focusing, pore-gradient electrophoresis, electrophoresis at different pH's, are among the separation procedures used in the first dimension, whereas sodium dodecyl sulfate-polyacrylamide gel electrophoresis and starch-gel electrophoresis at acid pH have been the preferred second-dimensional methods. Dissociating conditions (sodium dodecyl sulfate, Nonidet P-40, or urea) and reducing conditions (2-mercaptoethanol) have been used when require
Biomaterials from beer manufacture waste for bone growth scaffolds

Agricultural wastes are a source of renewable raw materials (RRM), with structures that can be tailored for the use envisaged. Here, they have proved to be good replacement candidates for use as biomaterials for the growth of osteoblasts in bone replacement therapies. Their preparation is more cost effective than that of materials presently in use with the added bonus of converting a low-cost waste into a value-added product. Due to their origin these solids are ecomaterials. In this study, several techniques, including X-ray diffraction (XRD), chemical analysis, mercury intrusion porosimetry (MIP), scanning electron microscopy (SEM), and bioassays, were used to compare the biocompatibility and cell growth of scaffolds produced from beer bagasse, a waste material from beer production, with a control sample used in bone and dental regenerative processes
PV self-consumption optimization with storage and Active DSM for the residential sector

With the rising prices of the retail electricity and the decreasing cost of the PV technology, grid parity with commercial electricity will soon become a reality in Europe. This fact, together with less attractive PV feed-in-tariffs in the near future and incentives to promote self-consumption suggest, that new operation modes for the PV Distributed Generation should be explored; differently from the traditional approach which is only based on maximizing the exported electricity to the grid. The smart metering is experiencing a growth in Europe and the United States but the possibilities of its use are still uncertain, in our system we propose their use to manage the storage and to allow the user to know their electrical power and energy balances. The ADSM has many benefits studied previously but also it has important challenges, in this paper we can observe and ADSM implementation example where we propose a solution to these challenges. In this paper we study the effects of the Active Demand-Side Management (ADSM) and storage systems in the amount of consumed local electrical energy. It has been developed on a prototype of a self-sufficient solar house called “MagicBox” equipped with grid connection, PV generation, lead–acid batteries, controllable appliances and smart metering. We carried out simulations for long-time experiments (yearly studies) and real measures for short and mid-time experiments (daily and weekly studies). Results show the relationship between the electricity flows and the storage capacity, which is not linear and becomes an important design criterion
The relationship between soil geochemistry and the bioaccessibility of trace elements in playground soil

A total of 32 samples of surficial soil were collected from 16 playground areas in Madrid (Spain), in order to investigate the importance of the geochemistry of the soil on subsequent bioaccessibility of trace elements. The in vitro bioaccessibility of As, Co, Cr, Cu, Ni, Pb and Zn was evaluated by means of two extraction processes that simulate the gastric environment and one that reproduces a gastric + intestinal digestion sequence. The results of the in vitro bioaccessibility were compared against aqua regia extractions (“total” concentration), and it was found that total concentrations of As, Cu, Pb and Zn were double those of bioaccessible values, whilst that of Cr was ten times higher. Whereas the results of the gastric + intestinal extraction were affected by a high uncertainty, both gastric methods offered very similar and consistent results, with bioaccessibilities following the order: As = Cu = Pb = Zn > Co > Ni > Cr, and ranging from 63 to 7 %. Selected soil properties including pH, organic matter, Fe and CaCO3 content were determined to assess their influence on trace element bioaccessibility, and it was found that Cu, Pb and Zn were predominantly bound to organic matter and, to a lesser extent, Fe oxides. The former fraction was readily accessible in the gastric solution, whereas Fe oxides seemed to recapture negatively charged chloride complexes of these elements in the gastric solution, lowering their bioaccessibility. The homogeneous pH of the playground soils included in the study does not influence trace element bioaccessibility to any significant extent except for Cr, where the very low gastric accessibility seems to be related to the strongly pH-dependent formation of complexes with organic matter. The results for As, which have been previously described and discussed in detail in Mingot et al. (Chemosphere 84: 1386–1391, 2011), indicate a high gastric bioaccessibility for this element as a consequence of its strong association with calcium carbonate and the ease with which these bonds are broken in the gastric solution. The calculation of risk assessments are therefore dependant on the methodology used and the specific environment they address. This has impacts on management strategies formulated to ensure that the most vulnerable of society, children, can live and play without adverse consequences to their health
The structure and dynamics of the global network of inter-firm R&D partnerships 1989-2002

This paper examines the structure and dynamics of the global network of inter-firm research and development (R&D) partnerships using longitudinal data for 1989--2002. We contribute to a recent literature that has attributed patterns and changes in the network to major political and technological developments, but which has omitted the structure in the underlying firm population.  Two often made claims are that R&D collaboration is important in nowadays fierce competitive environment, but that the importance of international partnerships has declined over time.  We integrate data on firms and alliances and confront both hypotheses with our data and a novel set of methods, which enable to control for structure in the firm population.
Effect of Gender on the Pharmacokinetics of Eslicarbazepine Acetate (BIA 2-093), a New Voltage-gated Sodium Channel Blocker

Purpose. To determine the effect of gender on the pharmacokinetics of eslicarbazepine
acetate, a novel voltage-gated sodium channel blocker in the development for the treatment of
epilepsy and bipolar disorder.
Methods. Single-centre, open-label, parallel-group study in 12 female and 12 male healthy
subjects. The study consisted of a single-dose (600 mg) period and a multiple-dose (600 mg, oncedaily,
for 8 days) period, separated by 4 days.
Results. Eslicarbazepine acetate was rapidly and extensively metabolized to eslicarbazepine
(S-licarbazepine), the main active metabolite. Following a single-dose, arithmetic mean eslicarbazepine
maximum plasma concentrations (Cmax) and area under the plasma concentration-time
curve over 24 h (AUC0 24) and from 0 to infinity (AUC0 1) were, respectively, 9.3 mg/ml,
128.5 mg h/ml and 171.9 mg h/ml in male subjects and 10.1 mg/ml, 150.1 mg h/ml and 205.0 mg h/ml
in female subjects. At steady-state, Cmax, AUC0 24 and AUC0 1 were 15.5 mg/ml, 207.8 mg h/ml and
295.8 mg h/ml in male subjects, and 16.8 mg/ml, 214.5 mg h/ml and 295.2 mg h/ml in female subjects.
Steady-state plasma concentrations were attained at 4 to 5 days of administration in both groups.
Eslicarbazepine Cmax, AUC0 24 and AUC0 1 female:male geometric mean ratios (90%CI) were,
respectively, 1.09 (0.94; 1.24), 1.16 (1.00; 1.33) and 1.17 (0.99; 1.38) following single-dose, and 1.10
(0.97; 1.25), 1.04 (0.92; 1.17) and 1.01 (0.88; 1.16) at steady-state.
Conclusion. At steady-state, the pharmacokinetic profile of eslicarbazepine acetate was not
affected by gender
A simple model for viscous regularization of elasto-plastic constitutive laws with softening

An overlay-type rheological model is presented, which is used to introduce viscosity in inviscid elasto-plastic material laws with softening, in order to reduce the mesh-dependency of Finite Element solutions. This model is intended to be an alternative to the well-known visco-plastic formulations of Perzyna and Duvaut-Lions. A time integration algorithm for the visco-elastic model component is presented, being demonstrated in the paper, that it is unconditionally stable and oscillation-free. The algorithm is tested in a problem with slip driven softening (von Mises material) and in a problem with decohesion driven softening (Cam-Clay model). Figures showing the capability of the algorithm to regularize the solution are presented. Copyright © 2004 John Wiley & Sons, Ltd.http://dx.doi.org/10.1002/cnm.70
M&M's: Building Binary Software Components for Supporting Mobile-Agent Enabled Applications

Mobile Agents provide a new promising paradigm for developing distributed applications. Nevertheless, although the basic concept has been around for some years and many agent platforms are available both from the industry and research community, there are currently few examples where the technology has been deployed in the real world. One important reason for this is that using the current available agent frameworks it is quite difficult to develop applications without having to center them completely on the agents and on the agent infrastructure. In this paper, we present the M&M project, taking place at the University of Coimbra. In this project, we are developing an extensive component-based framework that enables ordinary applications to use mobile agents in a flexible and easy way. By using this approach, applications can be developed using current object-oriented approaches and become able of sending and receiving agents by the simple drag-and-drop of mobility components. The framework was implemented using the JavaBeans component model and provides integration with ActiveX, which allows applications to be written in a wide variety of programming languages. By using this framework, the development of applications that can make use of mobile regents is greatly simplified, which can contribute to a wider spreading of the mobile agent technology.http://dx.doi.org/10.1023/A:101340520176