pinecone/core-2020-05-10-deduplication huggingface dataset:
Antibody-specific model of amino acid substitution for immunological inferences from alignments of antibody sequences

Antibodies are glycoproteins produced by the immune system as a dynamically adaptive line of defense against invading pathogens. Very elegant and specific mutational mechanisms allow B lymphocytes to produce a large and diversified repertoire of antibodies, which is modified and enhanced throughout all adulthood. One of these mechanisms is somatic hypermutation, which stochastically mutates nucleotides in the antibody genes, forming new sequences with different properties and, eventually, higher affinity and selectivity to the pathogenic target. Since somatic hypermutation involves fast mutation of antibody sequences, this process can be described using a Markov substitution model of molecular evolution. Here, using large sets of antibody sequences from mice and humans, we infer an empirical amino acid substitution model AB, which is specific to antibody sequences. Compared to existing general amino acid models, we show that the AB model provides significantly better description for the somatic evolution of mice and human antibody sequences, as demonstrated on large next generation sequencing (NGS) antibody data. General amino acid models are reflective of conservation at the protein level due to functional constraints, with most frequent amino acids exchanges taking place between residues with the same or similar physicochemical properties. In contrast, within the variable part of antibody sequences we observed an elevated frequency of exchanges between amino acids with distinct physicochemical properties. This is indicative of a sui generis mutational mechanism, specific to antibody somatic hypermutation. We illustrate this property of antibody sequences by a comparative analysis of the network modularity implied by the AB model and general amino acid substitution models.
	We recommend using the new model for computational studies of antibody sequence maturation, including inference of alignments and phylogenetic trees describing antibody somatic hypermutation in large NGS data sets. The AB model is implemented in the open-source software CodonPhyML (http://sourceforge.net/projects/codonphyml) and can be downloaded and supplied by the user to ProGraphMSA (http://sourceforge.net/projects/prographmsa) or other alignment and phylogeny reconstruction programs that allow for user-defined substitution models
Greening agri-food value chains in emerging economies

This book provides insight into the implementation of Life Cycle approaches along the entire business value chain, supporting environmental, social and economic sustainability related to the development of industrial technologies, products, services and policies; and the development and management of smart agricultural systems, smart mobility systems, urban infrastructures and energy for the built environment. The book is based on papers presented at the 8th International Life Cycle Management Conference that took place from September 3-6, 2017 in Luxembourg, and which was organized by the Luxembourg Institute of Science and Technology (LIST) and the University of Luxembourg in the framework of the LCM Conference Series
Planning and the control of action

Planning has been found to have a powerful effect on human actions (e.g., Gollwitzer & Sheeran, 2006 ). But how do people plan? In this chapter we first introduce implementation intentions (e.g., Gollwitzer, 1999 ) as an efficient way of planning. Implementation intentions refer to specific plans in which individuals and groups can specify when, where, and how they intend to act using an if-then format (e.g., “If I come home from work on Fridays, then I will immediately put on my jogging shoes and go for a 30-minute run!”). After we examine how they support goal pursuit, we differentiate between spontaneous and strategic planning—two ways in which if–then plans can be made on the basis of goal-related knowledge. With respect to spontaneous planning, we highlight the importance of the accessibility of goal-related knowledge. We introduce goal systems theory (Kruglanski, Shah, Fishbach, Friedman, Chun, & Sleeth-Keppler, 2002 ) as a conceptual framework because it addresses the question of how goals can increase the accessibility of knowledge about when, where, and how to pursue the goal. To illustrate how the accessibility of goal-related knowledge facilitates goal attainment, we discuss a set of recent studies. They show that individuals spontaneously grasp goal-relevant information in the form of implementation intentions (Marquardt, Tröger, Wieber, & Gollwitzer, 2016 ; see also Marquardt, 2011 ) even if it is incidentally provided in their environment and that they use this knowledge to improve their goal attainment without being prompted to do so
Establishing criteria for human mesenchymal stem cell potency

This study sought to identify critical determinants of mesenchymal stem cell (MSC) potency using in vitro and in vivo attributes of cells isolated from the bone marrow of age‐ and sex‐matched donors. Adherence to plastic was not indicative of potency, yet capacity for long‐term expansion in vitro varied considerably between donors, allowing the grouping of MSCs from the donors into either those with high‐growth capacity or low‐growth capacity. Using this grouping strategy, high‐growth capacity MSCs were smaller in size, had greater colony‐forming efficiency, and had longer telomeres. Cell‐surface biomarker analysis revealed that the International Society for Cellular Therapy (ISCT) criteria did not distinguish between high‐growth capacity and low‐growth capacity MSCs, whereas STRO‐1 and platelet‐derived growth factor receptor alpha were preferentially expressed on high‐growth capacity MSCs. These cells also had the highest mean expression of the mRNA transcripts TWIST‐1 and DERMO‐1. Irrespective of these differences, both groups of donor MSCs produced similar levels of key growth factors and cytokines involved in tissue regeneration and were capable of multilineage differentiation. However, high‐growth capacity MSCs produced approximately double the volume of mineralized tissue compared to low‐growth capacity MSCs when assessed for ectopic bone‐forming ability. The additional phenotypic criteria presented in this study when combined with the existing ISCT minimum criteria and working proposal will permit an improved assessment of MSC potency and provide a basis for establishing the quality of MSCs prior to their therapeutic application. Stem Cells 2015;33:1878–189
Self-correcting quantum computers

Is the notion of a quantum computer (QC) resilient to thermal noise unphysical? We address this question from a constructive perspective and show that local quantum Hamiltonian models provide self-correcting QCs. To this end, we first give a sufficient condition on the connectedness of excitations for a stabilizer code model to be a self-correcting quantum memory. We then study the two main examples of topological stabilizer codes in arbitrary dimensions and establish their self-correcting capabilities. Also, we address the transversality properties of topological color codes, showing that six-dimensional color codes provide a self-correcting model that allows the transversal and local implementation of a universal set of operations in seven spatial dimensions. Finally, we give a procedure for initializing such quantum memories at finite temperature
Active deformation in old oceanic lithosphere and significance for earthquake hazard: Seismic imaging of the Coral Patch Ridge area and neighboring abyssal plains (SW Iberian Margin)

Recently acquired high-resolution multichannel seismic profiles together with bathymetric and sub-bottom profiler data from the external part of the Gulf of Cadiz (Iberia-Africa plate boundary) reveal active deformation involving old (Mesozoic) oceanic lithosphere. This area is located 180 km offshore the SW Iberian Peninsula and embraces the prominent NE-SW trending Coral Patch Ridge, and part of the surrounding deep Horseshoe and Seine abyssal plains. E-W trending dextral strike-slip faults showing surface deformation of flower-like structures predominate in the Horseshoe Abyssal Plain, whereas NE-SW trending compressive structures prevail in the Coral Patch Ridge and Seine Hills. Although the Coral Patch Ridge region is characterized by subdued seismic activity, the area is not free from seismic hazard. Most of the newly mapped faults correspond to active blind thrusts and strike-slip faults that are able to generate large magnitude earthquakes (Mw 7.2-8.4). This may represent a significant earthquake and tsunami hazard that has been overlooked so far
Influence of texture on the recrystallization mechanisms in an AZ31 Mg sheet alloy at dynamic rates

An AZ31 rolled sheet alloy has been tested at dynamic strain rates View the MathML source at 250 °C up to various intermediate strains before failure in order to investigate the predominant deformation and restoration mechanisms. In particular, tests have been carried out in compression along the rolling direction (RD), in tension along the RD and in compression along the normal direction (ND). It has been found that dynamic recrystallization (DRX) takes place despite the limited diffusion taking place under the high strain rates investigated. The DRX mechanisms and kinetics depend on the operative deformation mechanisms and thus vary for different loading modes (tension, compression) as well as for different relative orientations between the loading axis and the c-axes of the grains. In particular, DRX is enhanced by the operation of 〈c + a〉 slip, since cross-slip and climb take place more readily than for other slip systems, and thus the formation of high angle boundaries is easier. DRX is also clearly promoted by twinning
Trends in adult stature of peoples who inhabited the modern Portuguese territory from the Mesolithic to the late 20th century

This study documents long-term changes in stature from the Mesolithic to the late 20th century in the territory of modern Portugal. Data utilised originated from published sources and from a sample of the Lisbon identified skeletal collection, where long bone lengths were collected. Mean long bone lengths were obtained from 20 population samples and compiled into nine periods. Pooled long bone lengths for each period were then converted to stature estimates. Results show three major trends: (1) a slow increase in stature from prehistory to the Middle Ages; (2) a negative trend from the Middle Ages to the late 19th century; and (3) a very rapid increase in mean stature during the second half of the 20th century. The political and territorial stability of the Kingdom of Portugal may have contributed to the greater heights of the medieval Portuguese, compared with the Roman and Modern periods. The negative secular trend was rooted in poor and unsanitary living conditions and the spread of infectious disease, brought about by increased population growth and urbanisation. Although the end of the Middle Ages coincided with the age of discoveries, the population may not have benefited from the overall prosperity of this period. The 20th century witnessed minor and slow changes in the health status of the Portuguese, but it was not until major improvements in social and economic conditions that were initiated in the 1960s, and further progress in the 1970s, that the Portuguese grew taller than ever before. Since the Middle Ages other European countries have experienced similar oscillations, but showed an earlier recovery in stature after the industrial period. Copyright © 2008 John Wiley & Sons, Ltd.http://dx.doi.org/10.1002/oa.99
Approximate Query Answering Using Data Warehouse Striping

This paper presents and evaluates a simple but very effective method to implement large data warehouses on an arbitrary number of computers, achieving very high query execution performance and scalability. The data is distributed and processed in a potentially large number of autonomous computers using our technique called data warehouse striping (DWS). The major problem of DWS technique is that it would require a very expensive cluster of computers with fault tolerant capabilities to prevent a fault in a single computer to stop the whole system. In this paper, we propose a radically different approach to deal with the problem of the unavailability of one or more computers in the cluster, allowing the use of DWS with a very large number of inexpensive computers. The proposed approach is based on approximate query answering techniques that make it possible to deliver an approximate answer to the user even when one or more computers in the cluster are not available. The evaluation presented in the paper shows both analytically and experimentally that the approximate results obtained this way have a very small error that can be negligible in most of the cases.http://dx.doi.org/10.1023/A:101655130928
Applicability of ecological evaluation tools in estuarine ecosystems: the case of the lower Mondego estuary (Portugal)

Abstract  In accordance with the Water Framework Directive guidelines (WFD, 2000, European Communities Official Journal L327 2000/60/EC), classification schemes and ecological evaluation tools (based on benthic invertebrate fauna data sets from 1990 to 2002) were applied in the lower Mondego estuary. Two distinct scenarios could be tested due to the implementation of mitigation practices in 1999, following a long eutrophication process, which started by the early 1980s. Some discrepancies in the results were found by the application of the different indices. The AMBI index (accounting for taxonomic composition) and the ABC method (accounting for abundance and biomass k-dominance patterns) classifications often disagreed with those based on species diversity (Margalef and Shannon-Wiener). The ambiguous results made the classification a complex task to achieve, contrary to the Directive’s objective of maintaining it simple and clear. Our results suggest the necessity of adjusting some of the indices and their ranges to estuarine characteristics, namely to account the typical dominance and abundance of some particular species. These aspects are not taken into consideration by some of the indices proposed, which are more adapted to typical marine conditions. Based on our results, these widely applied indices might still improve their efficiency in estuarine systems allowing their use in the resembling types already established within the new Directive agenda.http://dx.doi.org/10.1007/s10750-007-0697-
The quantale of Galois connections

Galois connections were originally expressed in a contravariant form with transformations that reverse (rather than preserve) order. Nowadays its covariant form (as residuated maps) is more often used since it is more convenient; namely compositions of residuated maps are handled more easily. In this paper we show that this is not a serious disadvantage of the contravariant form (at least in the natural context for uniform structures, where we need it), by introducing an operation of composition in the complete lattice Gal( L, L) of all (contravariant) Galois connections in a complete lattice L, that allows us to work with Galois connections in the same way as one usually works with residuated maps. This operation endows Gal( L, L) with a structure of quantale whenever L is a locale, allowing the description of uniform structures in terms of Galois connections.http://dx.doi.org/10.1007/s00012-004-1901-
One-pot catalytic hydrolysis/hydrogenation of cellobiose into hexitols over Ru/Al-MCM-48

The simultaneous catalytic hydrolysis and hydrogenation of cellobiose, as a model constituent of biomass has been studied over Ru/Al-MCM-48. The catalyst, presenting both acidic and hydrogenating functions has been synthesized and characterized by means of N2 adsorption-desorption, SAXS, H2-TPR, XRD, TEM and NH3-TPD. A kinetic model is proposed, and possible reaction pathways and key intermediate compounds of conversion of cellobiose to hexitols are discussed. In the kinetic study the effects of pressure, temperature and time on the onepot reaction were evaluated. A maximum yield around 91% of hexitols was achieved at 180 °C, 5 MPa of H2 and 7 min, where sorbitol was the main compound in the final product with 82% yield. Cellobitol was the main reaction intermediate. Temperatures in the range of 140–180 °C and pressures in the range of 3–5 MPa of H2 were studied and it was concluded that higher temperatures and pressures had a positive effect in order to
maximize the production of hexitols. The developed kinetic model predicted with high accuracy the concentration of the different compounds involved in the proposed reaction pathway and served to calculate the reaction rate constant and activation energy values for the different steps of the catalytic process.Este trabajo forma parte del proyecto de investigación: CTQ2015- 64892-R (MINECO/FEDER
Precipitated iron: a limit on gettering efficacy in multicrystalline silicon

A phosphorus diffusion gettering model is used to examine the efficacy of a standard gettering process on interstitial and precipitated iron in multicrystalline silicon. The model predicts a large concentration of precipitated iron remaining after standard gettering for most as-grown iron distributions. Although changes in the precipitated iron distribution are predicted to be small, the simulated post-processing interstitial iron concentration is predicted to depend strongly on the as-grown distribution of precipitates, indicating that precipitates must be considered as internal sources of contamination during processing. To inform and validate the model, the iron distributions before and after a standard phosphorus diffusion step are studied in samples from the bottom, middle, and top of an intentionally Fe-contaminated laboratory ingot. A census of iron-silicide precipitates taken by synchrotron-based X-ray fluorescence microscopy confirms the presence of a high density of iron-silicide precipitates both before and after phosphorus diffusion. A comparable precipitated iron distribution was measured in a sister wafer after hydrogenation during a firing step. The similar distributions of precipitated iron seen after each step in the solar cell process confirm that the effect of standard gettering on precipitated iron is strongly limited as predicted by simulation. Good agreement between the experimental and simulated data supports the hypothesis that gettering kinetics is governed by not only the total iron concentration but also by the distribution of precipitated iron. Finally, future directions based on the modeling are suggested for the improvement of effective minority carrier lifetime in multicrystalline silicon solar cells
Two-stream instability in quasi-one-dimensional Bose-Einstein
  condensates

We apply a kinetic model to predict the existence of an instability mechanism
in elongated Bose-Einstein condensates. Our kinetic description, based on the
Wigner formalism, is employed to highlight the existence of unstable Bogoliubov
waves that may be excited in the counterpropagation configuration. We identify
a dimensionless parameter, the Mach number at T = 0, that tunes different
regimes of stability. We also estimate the magnitude of the main parameters at
which two-stream instability is expected to be observed under typical
experimental conditions.Comment: 4 page
Tailoring Non-Compact Spin Chains

We study three-point correlation functions of local operators in planar
$\mathcal{N}=4$ SYM at weak coupling using integrability. We consider
correlation functions involving two scalar BPS operators and an operator with
spin, in the so called SL(2) sector. At tree level we derive the corresponding
structure constant for any such operator. We also conjecture its one loop
correction. To check our proposals we analyze the conformal partial wave
decomposition of known four-point correlation functions of BPS operators. In
perturbation theory, we extract from this decomposition sums of structure
constants involving all primaries of a given spin and twist. On the other hand,
in our integrable setup these sum rules are computed by summing over all
solutions to the Bethe equations. A perfect match is found between the two
approaches.Comment: 2 figure
A statistical theory of polymer network degradation

A statistical theory was proposed for the degradation (random scission of chains) of a network having f-functional nodes in the case where all chains contain equireactive groups and a chain scission event does not create new groups or suppress more than one group. Closedform relations were established between the conversion ratio of the degradation process and the crosslink density. Emphasis was put on the value of the conversion ratio for which the gel disappears. Some limited cases already considered in the literature were recovered, but a general solution was proposed for networks having any number of reactive groups per chain, be it uniform or not, and for conversion ratios up to the degelation point. The results were applied successfully to recent experiments regarding the hydrolysis of a polyester
Plastisol Gelation and Fusion Rheological Aspects

This study deals with the rheological aspects of poly-vinyl chloride (PVC) plastisol gelation and fusion processes in foamable formulations. Here, such processes are simulated by temperature-programmed experiment (5 K min−1) in which complex viscosity components are continuously recorded. Nineteen samples based on a PVC-VAC (vinyl acetate 95/5) copolymer with 100 phr plasticizer have been studied, differing only by the plasticizer structure. The sample shear modulus increases continuously with temperature until a maximum, long time after the end of the dissolution process as characterized by DSC. The temperature at the maximum varies between 345 and 428 K with a clear tendency to increase almost linearly with the plasticizer molar mass, and to vary with the flexibility and the degree of branching of the plasticizer molecule. The shear modulus increase is interpreted in terms of progressive “welding” of swelled particles by polymer chain reptation. The plasticizer nature would mainly affect the friction parameter of chain diffusio
A review of contemporary work on the ethics of ambient assisted living technologies for people with dementia

Ambient assisted living (AAL) technologies can provide assistance and support to persons with dementia. They might allow them the possibility of living at home for longer whilst maintaining their comfort and security as well as offering a way towards reducing the huge economic and personal costs forecast as the incidence of dementia increases worldwide over coming decades. However, the development, introduction and use of AAL technologies also trigger serious ethical issues. This paper is a systematic literature review of the on-going scholarly debate about these issues. More specifically, we look at the ethical issues involved in research and development (R&D), clinical experimentation, and clinical application of AAL technologies for people with dementia and related stakeholders. In the discussion we focus on: 1) the value of the goals of AAL technologies, 2) the special vulnerability of persons with dementia in their private homes, 3) the complex question of informed consent for the usage of AAL technologies
Large bipartite Bell violations with dichotomic measurements

In this paper we introduce a simple and natural bipartite Bell scenario, by considering the correlations between two parties defined by general measurements in one party and dichotomic ones in the other. We show that unbounded Bell violations can be obtained in this context. Since such violations cannot occur when both parties use dichotomic measurements, our setting can be considered as the simplest one where this phenomenon can be observed. Our example is essentially optimal in terms of the outputs and the Hilbert space dimension