A swarm pattern transformation method based on macroscopic parameter operations

The work reported in this paper is motivated by biomimetic inspiration - the transformation of patterns. The major issue addressed is the development of feasible methods for transformation based on a macroscopic tool. The general requirement for the feasibility of the transformation method is determined by classifying pattern formation approaches an their characteristics. A formal definition for pattern transformation is provided and four special cases namely, elementary and geometric transformation based on repositioning all and some robotic agents are introduced. A feasible method for transforming patterns geometrically, based on the macroscopic parameter operation of a swarm is considered. The transformation method is applied to a swarm model which lends itself to the transformation technique. Simulation studies are developed to validate the feasibility of the approach, and do indeed confirm the approach.

RKHS-Methods at Series Summation for Software Implementation

Reproducing Kernel Hilbert Space (RKHS) and Reproducing Transformation Methods for Series Summation that allow analytically obtaining alternative representations for series in the finite form are developed.

Transformation of Medicago truncatula with the arginine decarboxylase gene to modify polyamine metabolism toward water deficit resistance

Dissertation submitted to obtain a Ph.D. (Doutoramento) degree in Biology at the Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa

Development of a subject-specific musculoskeletal shoulder model : inverse and forward dynamics applications

A prevalência de pessoas que referem dor no complexo articular do ombro, com concomitante limitação na capacidade para realizar atividades da vida diária, é elevada. Estes níveis de prevalência sobrecarregam quer os utentes, como a própria sociedade. A evidência científica atual indicia a existência de uma relação entre as alterações da articulação escápulo-torácica e as patologias associadas à articulação gleno-umeral. A capacidade de quantificar, cinemática e cineticamente, as disfunções ao nível das articulações escápulo-torácica e gleno-umeral, é algo de enorme importância, quer para a comunidade biomecânica, como para a clínica. No decorrer dos trabalhos desta tese foi desenvolvido, através do software OpenSim, um modelo tridimensional músculo-esquelético do complexo articular do ombro que inclui a representação do tórax/coluna, clavícula, omoplata, úmero, rádio, cúbito e articulações que permitem os movimentos relativos desses segmentos, assim como, 16 músculos e 4 ligamentos. Com um total de 11 graus de liberdade, incluindo um novo modelo articular escápulo-torácico, os resultados demonstram que este é capaz de reconstruir de forma precisa e rápida os movimentos escápulo-torácicos e glenoumerais, recorrendo para tal, à cinemática inversa, e à dinâmica inversa e direta. Conta ainda com um método de transformação inovador para determinar, com base nas especificidades dos sujeitos, os locais de inserção muscular. As principais motivações subjacentes ao desenvolvimento desta tese foram contribuir para o aprofundar do atual conhecimento sobre as disfunções do complexo articular do ombro e, simultaneamente, proporcionar à comunidade clínica uma ferramenta biomecânica de livre acesso com o intuito de melhor suportar as decisões clínicas e dessa forma concorrer para uma prática mais efetiva.

Modeling and simulating a mathematical tool for multi-robot pattern transformation

The work reported in this paper is motivated by the need to investigate general methods for pattern transformation. A formal definition for pattern transformation is provided and four special cases namely, elementary and geometric transformation based on repositioning all and some agents in the pattern are introduced. The need for a mathematical tool and simulations for visualizing the behavior of a transformation method is highlighted. A mathematical method based on the Moebius transformation is proposed. The transformation method involves discretization of events for planning paths of individual robots in a pattern. Simulations on a particle physics simulator are used to validate the feasibility of the proposed method.

Modeling and simulating a mathematical tool for multi-robot pattern transformation

The work reported in this paper is motivated by the need to investigate general methods for pattern transformation. A formal definition for pattern transformation is provided and four special cases namely, elementary and geometric transformation based on repositioning all and some agents in the pattern are introduced. The need for a mathematical tool and simulations for visualizing the behavior of a transformation method is highlighted. A mathematical method based on the Moebius transformation is proposed. The transformation method involves discretization of events for planning paths of individual robots in a pattern. Simulations on a particle physics simulator are used to validate the feasibility of the proposed method.

Perspective transformation: Women in long-term recovery from alcohol abuse

Objective. The purpose of this study was to determine the meaning of personal transformation for twenty women in long term, stable recovery from alcohol abuse; to identify themes or patterns of this recovery, and; to determine the extent to which they experienced the phenomenon of perspective transformation. ^ Method. Volunteers were recruited by advertisement, word of mouth, and through a closed circuit web based broadcast. A descriptive, exploratory study, which analyzed perspective transformation from the standpoint of five action phases, was conducted. Data was collected using in-depth personal interviews and questionnaires. Subjects' responses were analyzed by qualitative methods. Triangulation was performed on the grouped data comparing the interviews to the data produced by the questionnaires. Quantitative analysis of questionnaire items explored behavioral changes experienced before and after alcoholism recovery. ^ Results. Five phases of recovery were identified. Phase I which involved recognition that alcohol was a problem and change might be possible took several years during which 3 major transitions occurred: (1) from often being alienated to having relationships with family and friends; (2) from daily upheavals to eventually a more peaceful existence, and; (3) from denial that alcohol was a problem to acceptance and willingness to change. Recovery was often seen in a spiritual context, which also required ongoing support. During Phase II there was an assessment of self, others, and the environment which revealed a pattern of intense unhappiness and negative feelings toward self and others with a disregard for cultural norms. Phase III revealed a period of desperation as life became unmanageable, but gradual willingness to accept support and guidance and a desire to improve self and help others. This led to improvement of existing role performance and the willingness to try out new roles. In Phase IV there was a pattern of personal growth which included: the establishment of boundaries, setting priorities, a willingness to place others' needs above their own, acceptance of responsibility, and learning to cope without alcohol, often with the use of tools learned in AA. During Phase V, many experienced knowledge of frailties but growing respect for self and others, with an improved ability to function in giving relationships. Implications for Prevention and Recovery: Early education concerning addiction and recovery may play a crucial role in prevention and early recovery, as it did for children of women in this study. Recovery requires persistent effort and organized support. ^

Effects of strontium ranelate and alendronate on bone microstructure in women with osteoporosis. Results of a 2-year study.

A Strontium ranelate appears to influence more than alendronate distal tibia bone microstructure as assessed by high-resolution peripheral quantitative computed tomography (HR-pQCT), and biomechanically relevant parameters as assessed by micro-finite element analysis (mu FEA), over 2 years, in postmenopausal osteoporotic women.Introduction Bone microstructure changes are a target in osteoporosis treatment to increase bone strength and reduce fracture risk.Methods Using HR-pQCT, we investigated the effects on distal tibia and radius microstructure of strontium ranelate (SrRan; 2 g/day) or alendronate (70 mg/week) for 2 years in postmenopausal osteoporotic women. This exploratory randomized, double-blind trial evaluated HR-pQCT and FEA parameters, areal bone mineral density (BMD), and bone turnover markers.Results In the intention-to-treat population (n = 83, age: 64 +/- 8 years; lumbar T-score: -2.8 +/- 0.8 [DXA]), distal tibia Cortical Thickness (CTh) and Density (DCort), and cancellous BV/TV increased by 6.3%, 1.4%, and 2.5%, respectively (all P < 0.005), with SrRan, but not with alendronate (0.9%, 0.4%, and 0.8%, NS) (P < 0.05 for all above between-group differences). Difference for CTh evaluated with a distance transformation method was close to significance (P = 0.06). The estimated failure load increased with SrRan (+2.1%, P < 0.005), not with alendronate (-0.6%, NS) (between-group difference, P < 0.01). Cortical stress was lower with SrRan (P < 0.05); both treatments decreased trabecular stress. At distal radius, there was no between-group difference other than DCort (P < 0.05). Bone turnover markers decreased with alendronate; bALP increased (+21%) and serum-CTX-I decreased (-1%) after 2 years of SrRan (between-group difference at each time point for both markers, P < 0.0001). Both treatments were well tolerated.Conclusions Within the constraints of HR-pQCT method, and while a possible artefactual contribution of strontium cannot be quantified, SrRan appeared to influence distal tibia bone microstructure and FEA-determined biomechanical parameters more than alendronate. However, the magnitude of the differences is unclear and requires confirmation with another method.

Methods for Region Based Paper Surface Roughness Measurement

Paperin pinnan karheus on yksi paperin laatukriteereistä. Sitä mitataan fyysisestipaperin pintaa mittaavien laitteiden ja optisten laitteiden avulla. Mittaukset vaativat laboratorioolosuhteita, mutta nopeammille, suoraan linjalla tapahtuville mittauksilla olisi tarvetta paperiteollisuudessa. Paperin pinnan karheus voidaan ilmaista yhtenä näytteelle kohdistuvana karheusarvona. Tässä työssä näyte on jaettu merkitseviin alueisiin, ja jokaiselle alueelle on laskettu erillinen karheusarvo. Karheuden mittaukseen on käytetty useita menetelmiä. Yleisesti hyväksyttyä tilastollista menetelmää on käytetty tässä työssä etäisyysmuunnoksen lisäksi. Paperin pinnan karheudenmittauksessa on ollut tarvetta jakaa analysoitava näyte karheuden perusteella alueisiin. Aluejaon avulla voidaan rajata näytteestä selvästi karheampana esiintyvät alueet. Etäisyysmuunnos tuottaa alueita, joita on analysoitu. Näistä alueista on muodostettu yhtenäisiä alueita erilaisilla segmentointimenetelmillä. PNN -menetelmään (Pairwise Nearest Neighbor) ja naapurialueiden yhdistämiseen perustuvia algoritmeja on käytetty.Alueiden jakamiseen ja yhdistämiseen perustuvaa lähestymistapaa on myös tarkasteltu. Segmentoitujen kuvien validointi on yleensä tapahtunut ihmisen tarkastelemana. Tämän työn lähestymistapa on verrata yleisesti hyväksyttyä tilastollista menetelmää segmentoinnin tuloksiin. Korkea korrelaatio näiden tulosten välillä osoittaa onnistunutta segmentointia. Eri kokeiden tuloksia on verrattu keskenään hypoteesin testauksella. Työssä on analysoitu kahta näytesarjaa, joidenmittaukset on suoritettu OptiTopolla ja profilometrillä. Etäisyysmuunnoksen aloitusparametrit, joita muutettiin kokeiden aikana, olivat aloituspisteiden määrä ja sijainti. Samat parametrimuutokset tehtiin kaikille algoritmeille, joita käytettiin alueiden yhdistämiseen. Etäisyysmuunnoksen jälkeen korrelaatio oli voimakkaampaa profilometrillä mitatuille näytteille kuin OptiTopolla mitatuille näytteille. Segmentoiduilla OptiTopo -näytteillä korrelaatio parantui voimakkaammin kuin profilometrinäytteillä. PNN -menetelmän tuottamilla tuloksilla korrelaatio oli paras.

Die aeroelastische Stabilitätsanalyse – ein praxisnaher Ansatz zur intervalltheoretischen Betrachtung von Modellierungsunsicherheiten am Flugzeug

Die Untersuchung des dynamischen aeroelastischen Stabilitätsverhaltens von Flugzeugen erfordert sehr komplexe Rechenmodelle, welche die wesentlichen elastomechanischen und instationären aerodynamischen Eigenschaften der Konstruktion wiedergeben sollen. Bei der Modellbildung müssen einerseits Vereinfachungen und Idealisierungen im Rahmen der Anwendung der Finite Elemente Methode und der aerodynamischen Theorie vorgenommen werden, deren Auswirkungen auf das Simulationsergebnis zu bewerten sind. Andererseits können die strukturdynamischen Kenngrößen durch den Standschwingungsversuch identifiziert werden, wobei die Ergebnisse Messungenauigkeiten enthalten. Für eine robuste Flatteruntersuchung müssen die identifizierten Unwägbarkeiten in allen Prozessschritten über die Festlegung von unteren und oberen Schranken konservativ ermittelt werden, um für alle Flugzustände eine ausreichende Flatterstabilität sicherzustellen. Zu diesem Zweck wird in der vorliegenden Arbeit ein Rechenverfahren entwickelt, welches die klassische Flatteranalyse mit den Methoden der Fuzzy- und Intervallarithmetik verbindet. Dabei werden die Flatterbewegungsgleichungen als parameterabhängiges nichtlineares Eigenwertproblem formuliert. Die Änderung der komplexen Eigenlösung infolge eines veränderlichen Einflussparameters wird mit der Methode der numerischen Fortsetzung ausgehend von der nominalen Startlösung verfolgt. Ein modifizierter Newton-Iterations-Algorithmus kommt zur Anwendung. Als Ergebnis liegen die berechneten aeroelastischen Dämpfungs- und Frequenzverläufe in Abhängigkeit von der Fluggeschwindigkeit mit Unschärfebändern vor.

A mathematical model, implementation and study of a swarm system

The work reported in this paper is motivated towards the development of a mathematical model for swarm systems based on macroscopic primitives. A pattern formation and transformation model is proposed. The pattern transformation model comprises two general methods for pattern transformation, namely a macroscopic transformation method and a mathematical transformation method. The problem of transformation is formally expressed and four special cases of transformation are considered. Simulations to confirm the feasibility of the proposed models and transformation methods are presented. Comparison between the two transformation methods is also reported.

The sl(2) affine Toda model coupled to the matter: solitons and confinement

The so-called conformal affine Toda theory coupled to the matter fields (CATM), associated to the (s) over capl(2) affine Lie algebra, is studied. The conformal symmetry is fixed by setting a connection to zero, then one defines an off-critical model, the affine Toda model coupled to the matter (ATM). Using the dressing transformation method we construct the explicit forms of the two-soliton classical solutions, and show that a physical bound soliton-antisoliton pair (breather) does not exist. Moreover, we verify that these solutions share some features of the sine-Gordon (massive Thirring) solitons, and satisfy the classical equivalence of topological and Noether currents in the ATM model. We show, using bosonization techniques that the ATM theory decouples into a sine-Gordon model and a free scalar. Imposing the Noether and topological currents equivalence as a constraint, one can show that the ATM model leads to a bag model like mechanism for the confinement of the color charge inside the sine-Gordon solitons (baryons).

Tau-functions and dressing transformations for zero-curvature affine integrable equations

The solutions of a large class of hierarchies of zero-curvature equations that includes Toda- and KdV-type hierarchies are investigated. All these hierarchies are constructed from affine (twisted or untwisted) Kac-Moody algebras g. Their common feature is that they have some special vacuum solutions corresponding to Lax operators lying in some Abelian (up to the central term) subalgebra of g; in some interesting cases such subalgebras are of the Heisenberg type. Using the dressing transformation method, the solutions in the orbit of those vacuum solutions are constructed in a uniform way. Then, the generalized tau-functions for those hierarchies are defined as an alternative set of variables corresponding to certain matrix elements evaluated in the integrable highest-weight representations of g. Such definition of tau-functions applies for any level of the representation, and it is independent of its realization (vertex operator or not). The particular important cases of generalized mKdV and KdV hierarchies as well as the Abelian and non-Abelian affine Toda theories are discussed in detail. © 1997 American Institute of Physics.

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to “reproducibility maps” that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one’s own laboratory.

T-strand integration in maize protoplasts after codelivery of a T-DNA substrate and virulence genes

We describe a plant protoplast transformation method that provides transformants with a simple pattern of integration of a foreign gene. The approach is to deliver into plant protoplasts by direct gene transfer the Agrobacterium virulence genes virD1 and virD2 with or without virE2, together with a target plasmid containing a gene of interest flanked by Agrobacterium T-DNA border repeat sequences of 25 bp. We present evidence of T-DNA formation in maize protoplasts and its integration into the maize genome. The frequency of VirD1-VirD2-mediated integration events was about 20–35% of the total number of transformants. The addition of virE2 doubled the transformation efficiency. The method described here is of sufficient efficiency and simplicity to be useful for the production of transgenic plants with single-copy well-defined transgenic inserts.