pinecone/core-2020-05-10-deduplication huggingface dataset:
Computation of protein geometry and its applications: Packing and
  function prediction

This chapter discusses geometric models of biomolecules and geometric
constructs, including the union of ball model, the weigthed Voronoi diagram,
the weighted Delaunay triangulation, and the alpha shapes. These geometric
constructs enable fast and analytical computaton of shapes of biomoleculres
(including features such as voids and pockets) and metric properties (such as
area and volume). The algorithms of Delaunay triangulation, computation of
voids and pockets, as well volume/area computation are also described. In
addition, applications in packing analysis of protein structures and protein
function prediction are also discussed.Comment: 32 pages, 9 figure
Panofsky on Physics, Politics, and Peace: Pief Remembers

Wolfgang K.H. Panofsky is a prominent physicist who has been an active contributor to elementary particle physics, accelerator building, and laboratory administration as well as to international security policy and arms control. This volume is a somewhat unorthodox memoir. In Panofsky’s words: "This volume contains an unsystematic account of my past work; it is not intended to be an autobiography in the conventional meaning of the term. It is not even remotely a scholarly description of the momentous developments in which I was able to participate; rather it is a recital of memorable episodes, borrowing from the compulsory preface of facetious British history: ‘History is not what you thought. It is what you can remember.’ " Pie
The Teacher's Role in Implementing Cooperative Learning in the Classroom.

The teacher’s role in implementing cooperative learning in the classroom provides a comprehensive overview of the theories, research outcomes, challenges and issues in guided cooperative learning. In many chapters there are clear guidelines and discussion about how cooperative learning practices can be embedded into classroom curricula. This volume also provides an overview of the major research and theoretical perspectives that underpin the development of cooperative learning, outlines how specific small group experiences can promote interaction, thinking and learning, discusses key roles teachers’ play in promoting student discourse, and demonstrates how interaction style among students and teachers is crucial in facilitating discussion, problem-solving, and learning
Semaphorin signals in cell adhesion and cell migration: functional role and molecular mechanisms

Cell migration is pivotal in embryo development and in the adult. During development a wide range of progenitor cells travel over long distances before undergoing terminal differentiation. Moreover, the morphogenesis of epithelial tissues and of the cardiovascular system involves remodelling compact cell layers and sprouting of new tubular branches. In the adult, cell migration is essential for leucocytes involved in immune response. Furthermore, invasive and metastatic cancer cells have the distinctive ability to overcome normal tissue boundaries, travel in and out of blood vessels, and settle down in heterologous tissues. Cell migration normally follows strict guidance cues, either attractive, or inhibitory and repulsive. Semaphorins are a wide family of signals guiding cell migration during development and in the adult. Recent findings have established that semaphorin receptors, the plexins, govern cell migration by regulating integrin-based cell substrate adhesion and actin cytoskeleton dynamics, via specific monomeric GTPases. Plexins furthermore recruit tyrosine kinases in receptor complexes, which allows switching between multiple signaling pathways and functional outcomes. In this article, we will review the functional role of semaphorins in cell migration and the implicated molecular mechanisms controlling cell adhesion.status: publishe
Atomic commitment in transactional DHTs

We investigate the problem of atomic commit in transactional database systems\ud
built on top of Distributed Hash Tables. DHTs provide a decentralized way to\ud
store and look up data. To solve the atomic commit problem we propose to\ud
use an adaption of Paxos commit as a non-blocking algorithm. We exploit the\ud
symmetric replication technique existing in the DKS DHT to determine which\ud
nodes are necessary to execute the commit algorithm. By doing so we achieve a\ud
lower number of communication rounds and a reduction of meta-data in contrast\ud
to traditional Three-Phase-Commit protocols. We also show how the proposed\ud
solution can cope with dynamism due to churn in DHTs. Our solution works\ud
correctly relying only on an inaccurate failure detection of node failure which is\ud
necessary for systems running over the Internet
Exercise-induced respiratory muscle work: Effects on blood flow, fatigue and performance

This is the post print version of this article. The official published version can be obtained from the link below.In healthy subjects, heavy intensity endurance exercise places substantial demands on the respiratory muscles as breathing frequency, ventilation and the work of breathing rise over time. In the highly trained subject working at high absolute work rates, the ventilatory demand often causes varying degrees of expiratory flow limitation, sometimes accompanied by lung hyperinflation and, therefore, increased elastic work of breathing. Time-dependant increases in effort perceptions for both dyspnea and limb discomfort accompany these increased ventilatory demands. Similar responses to endurance exercise but at much lower exercise intensities also occur in patients with COPD and CHF. Note that these responses significantly influence exercise performance times in both health and disease. This effect was demonstrated by the marked reductions in the rate of rise of effort perceptions and the enhanced exercise performance times elicited by unloading the respiratory muscles using pressure support ventilation or proportional assist mechanical ventilation. In healthy fit subjects, unloading the inspiratory work of breathing by about one half increased performance by an average of 14% (Harms et al. 2000), and in CHF and COPD patients performance time more than doubled with respiratory muscle unloading (O’Donnell et al. 2001). Why are effort perceptions of limb discomfort markedly reduced and exercise performance increased when the respiratory muscles are unloaded? Our hypothesis is shown in Fig. 1
Ontology engineering in virtual breeding environments

This paper proposes a new method for managing the use of ontologies in the context of a Virtual Breeding Environment. This research work focus is on the dissolution phase of a Virtual  Enterprise or Collaborative  Network, whereontology segmentation  techniques  are  user to enrich  the  VBE's  ontology library.  Firstly,  an overview of the process  of  ontology composition  and decomposition is given and the ontology  library system  adopted  described.Then, the ontologies' ranking  and classification method is described,explaining a set of metrics inspired in social network approaches. Finally, the results of preliminary tests are discussed
Virtual power producers integration into MASCEM

All over the world Distributed Generation is seen as a valuable help to get cleaner and more efficient electricity. Under this context distributed generators, owned by different decentralized players can provide a significant amount of the electricity generation. To get negotiation power and advantages of scale economy, these players can be aggregated giving place to a new concept: the Virtual Power Producer. Virtual Power Producers are multi-technology and multi-site heterogeneous entities. Virtual Power Producers should adopt organization and management methodologies so that they can make Distributed Generation a really profitable activity, able to participate in the market. In this paper we address the integration of Virtual Power Producers into an electricity market simulator –MASCEM – as a coalition of distributed producers
Distributed design of product oriented manufacturing systems

Manufacturing leanness and agility are requirements of today’s manufacturing
systems. Leanness call for a best fit of the manufacturing systems to products,
therefore requiring product oriented manufacturing systems (POMS).
Manufacturing agility can be achieved through easy systems reconfiguration to
fit changing manufacturing requirements, which may mean dynamically
configuring POMS. For this a suitable design system is required. Due to
complexity of this design, and to the need for using suitable design methods,
which may not be available locally, distributed sources of design services can
be used. This paper presents and describes a prototype of a Distributed Design
system for POMS based on a POMS design methodology and distributed
suppliers of design services
Toward the QoS Support in 4G Wireless Systems

This paper presents a novel approach to support Quality of Service for wireless multimedia applications in the context of 4G wireless systems. Adopting a Service Oriented Architecture, it is inspired to Open Wireless Architectures (OWA), building a suitable framework over the top of the heterogeneous wireless MACs. It lets to enhance the existing QoS support provided by standard MAC protocols and it uses the contract model to guarantee QoS, taking into account the applications requests. It negotiates dynamically Application Level Contracts which will be translated seamlessly in Resource Level Contracts for the underlying network services. It receives the feedback by underlying network services to adjust the scheduling algorithms and policies to provide soft guarantees. The framework comprises QoS Manager, Admission Control, Enhanced Scheduler, Predictor and Feedback System. In particular, the QoS manager component is a middleware between applications and lower network layers and it is able to dynamically manage available resources under different load conditions in a transparent manner to application level
Cue and Sensor Fusion for Independent Moving Objects Detection and Description in Driving Scenes

In this study we present an approach to detecting, describing and tracking independently moving objects (IMOs) independently moving object, IMO in stereo video sequences acquired by on-board cameras on a moving vehicle.
In the proposed model only three sensors are used: stereovision,speedometer and LIDAR (Light Detection and Ranging) Light Detection and Ranging, LIDAR. The IMOs detected by vision are matched with obstacles provided by LIDAR. In the case of a successful matching, the descriptions of the IMOs (distance, relative speed and acceleration) are provided by ACC (Adaptive Cruise Control) Adaptive Cruise Control, ACC LIDAR sensor, or otherwise these descriptions are estimated based on vision. Absolute speed of the IMO is evaluated using its relative velocity and egospeed provided by the speedometer. Preliminary results indicate the generalization ability of the proposed system.status: publishe
A Power-Efficient Methodology for Mapping Applications on Multi-Processor System-on-Chip Architectures

This work introduces an application mapping methodology and case study for multi-processor on-chip architectures. Starting from the description of an application in standard sequential code (e.g. in C), first the application is profiled, parallelized when possible, then its components are moved to hardware implementation when necessary to satisfy performance and power constraints. After mapping, with the use of hardware objects to handle concurrency, the application power consumption can be further optimized by a task-based scheduler for the\ud
remaining software part, without the need for operating system support. The key contributions of this work are: a methodology for high-level hardware/software partitioning that allows the designer to use the same code for both hardware and\ud
software models for simulation, providing nevertheless preliminary estimations for timing and power consumption; and a task-based scheduling algorithm that does not require operating system support. The methodology has been applied to\ud
the co-exploration of an industrial case study: an MPEG4 VGA real-time encoder
Swarm and entropic modeling for landmine detection robots

Even at the dawn of the 21st century, landmines still pose a global threat. Buried just inches below the surface, combatants and noncombatants alike are all at risk of stepping on a mine. Their very nature is such that these furtive weapons do not discriminate, making it an urgent task to tackle the problem. According to the U.S.State Department [1], based on an estimate reported just a few years ago, there are well over 100 million anti-personnel mines around the world. The existence of these passive weapons causes a disruption in the development of already impoverished regions, as well as maiming or killing countless innocent passers-by. Since the ratification of the anti-personnel mine total ban treaty in 1997, their detection, removal, and elimination have become a top priority. Nevertheless, at the current rate, given the manpower and the man-hours that could be dedicated to the removal of these sleeping arms, it would take centuries. The concerns regarding the speed of removal and safety of the disposers eventually bring us to the discussion of the proposed method. Nature already provided good solutions to manage groups of less able beings: fish schools, ant swarms, animal packs, bird flocks, and so on.With the growing desire of humans to create intelligent systems, these biosystems are being thoroughly inspected [3-10] and implemented [11-14] in various studies. In this study a robotic agent is referred to as a drone, the group of robotic agents is referred to as a swarm, and the agent with mapping abilities is referred to as the alpha drone
Semidefinite Representation of the $k$-Ellipse

The $k$-ellipse is the plane algebraic curve consisting of all points whose
sum of distances from $k$ given points is a fixed number. The polynomial
equation defining the $k$-ellipse has degree $2^k$ if $k$ is odd and degree
$2^k{-}\binom{k}{k/2}$ if $k$ is even. We express this polynomial equation as
the determinant of a symmetric matrix of linear polynomials. Our representation
extends to weighted $k$-ellipses and $k$-ellipsoids in arbitrary dimensions,
and it leads to new geometric applications of semidefinite programming.Comment: 16 pages, 5 figure
Cognition in Rodents

Cognition is a loosely defined term with divergent meanings in different disciplines and species. In human psychology, ‘cognition’ is often used in reference to concepts such as ‘mind’ or ‘higher mental functions’. However, in more general terms, ‘cognition’ is regularly used to refer to all manner of information organization by the brain: from collection, to processing, to storage and recognition or recall. Whereas ‘cognition’ would seem to permeate all mental functions, including subjective perception and innate responses, ‘cognitive ability’ has a slightly more specific connotation – something more akin to intelligence or information-processing ability. Thus, ‘cognition’ deals with mental process structure and ‘cognitive abilities’ with natural variations impinging upon functioning at the higher end of that structure. Although the term ‘cognition’ sometimes subsumes or substitutes ‘cognitive ability’ in the literature, understanding this methodological distinction allows us to read across the two fields without the misunderstandings that classical cognitive psychologists have sometimes shown for cognitive ability research
Exploring Environmental Services Incentive Policies for the Philippine Rice Sector: The Case of Intra-Species Agro Biodiversity Conservation

This paper considers a hypothetical scheme of green payments to induce inter-specific agrobiodiversity in the context of Philippine rice farming. We empirically estimate a model of farmer behavior and then simulate the consequences of alternative (hypothetical) PES schemes under a fixed budget constraint. We find that, under this particular application, there is a clear trade-off between the two policy goals of enhancing biodiversity and poverty reduction. Even the totally untargeted lump-sum subsidy would have a larger poverty reduction impact than would the first-best conservation subsidy payment scheme. Therefore, policymakers would be required to strike a delicate balance between the two competing policy objectives. In addition, there is also a clear trade-off between the efficiency of targeted conservation payment and the information requirement for implementing subsidy schemes.
A low cost coarse/fine piezoelectrically actuated microgripper with force measurement adapted to EUPASS control structure.

Over the last few years the demand for miniature objects and devices has continuously increased. So the need for MEMS (Micro Electro Mechanical Systems) and MOEMS (Micro Opto Electro Mechanical Systems) in various fields has become more and more important. New micromanipulation technologies must be developed that take into account the specificities of MEMS and MOEMS. For performing manipulation tasks, gripping is one of the fundamental functions. In this paper, the design and the control of a microgripper dedicated to very high precision tasks are presented. The LAB (Laboratoire d'Automatique de Besançon) has developped a microgripper based on the piezoelectric properties (1). This gripper is equipped with a precise sensor for force measurement. Force measurement is very important in order to avoid damaging or destroying the fragile object. Various approaches we used to model and calibrate the microgripper. The control of the gripper is done using the EUPASS Control Structure (6)
A Classification and Coding System for Micro-Assembly

This paper presents the development of a standard classification and coding
system for micro-scale assembled devices that can link micro-assembly concepts and
technologies to the attributes of the assembly components and their interrelationships
that define the assembled device/product. The proposed system is based on an n-digit
coding of both individual parts as well as the assembly. The coding scheme identifies a
form code, a material code and a process code for both parts and the assembly and then
partitions each into the relevant attributes. A specific example of coding of the parts of a
miniature spin bearing has been considered to illustrate the applicability of the coding
system.status: publishe
Gene and repetitive sequence annotation in the Triticeae

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes
Cytogenetics of melanoma and nonmelanoma skin cancer

Cytogenetic analysis of melanoma and nonmelanoma skin cancers has revealed recurrent aberrations, the frequency of which is reflective of malignant potential. Highly aberrant karyotypes are seen in melanoma, squamous cell carcinoma, solar keratosis and Merkel cell carcinoma with more stable karyotypes seen in basal cell carcinoma, keratoacanthoma, Bowen's disease, dermatofibrosarcomaprotuberans and cutaneous lymphomas. Some aberrations were common amongst a number of skin cancer types including rearrangements and numerical abnormalities of chromosome 1, -3p, +3q, partial or entire trisomy 6, trisomy 7, +8q, -9p, +9q, partial or entire loss of chromosome 10, -17p, + 17q and partial or entire gain of chromosome 20. Combination of cytogenetic analysis with other molecular genetic techniques has enabled the identification of not only aberrant chromosomal regions, but also the genes that contribute to a malignant phenotype. This review provides a comprehensive summary of the pertinent cytogenetic aberrations associated with a variety of melanoma and nonmelanoma skin cancers.Full Tex
Molecular biology of malignant melanoma

El pdf es la versión post-print.The incidence of melanoma has increased more rapidly than any other type of cancer. In this review, we summarize the most important genetic alterations that contribute to the development of malignant melanoma. Our knowledge of the genetic and biological events involved in the genesis and progression of this disease has been benefited from the evolvement of a wealth of genetically engineered animal models. Hopefully, the understanding generated by all these studies will contribute to develop new therapeutic strategies to handle this fatal malignancy. © 2008 Springer New York.Work in our laboratory has been funded by the Spanish Ministry of Education (grant SAF2004-04902 to MQ) and Fides and Medical Research Funds (grant PI05626 to PM-D). MP is funded by the company Digna Biotech. PM-D is funded by the >Ramón y Cajal> program.Peer Reviewe