Nested dictionary learning for hierarchical organization of imagery and text

A tree-based dictionary learning model is developed for joint analysis of imagery and associated text. The dictionary learning may be applied directly to the imagery from patches, or to general feature vectors extracted from patches or superpixels (using any existing method for image feature extraction). Each image is associated with a path through the tree (from root to a leaf), and each of the multiple patches in a given image is associated with one node in that path. Nodes near the tree root are shared between multiple paths, representing image characteristics that are common among different types of images. Moving toward the leaves, nodes become specialized, representing details in image classes. If available, words (text) are also jointly modeled, with a path-dependent probability over words. The tree structure is inferred via a nested Dirichlet process, and a retrospective stick-breaking sampler is used to infer the tree depth and width.

Phylogeny and the hierarchical organization of plant diversity

R. H. Whittaker's idea that plant diversity can be divided into a hierarchy of spatial components from alpha at the within-habitat scale through beta for the turnover of species between habitats to gamma along regional gradients implies the underlying existence of alpha, beta, and gamma niches. We explore the hypothesis that the evolution of a, (3, and gamma niches is also hierarchical, with traits that define the a niche being labile, while those defining a and 7 niches are conservative. At the a level we find support for the hypothesis in the lack of close significant phylogenetic relationship between meadow species that have similar a niches. In a second test, a niche overlap based on a variety of traits is compared between congeners and noncongeners in several communities; here, too, there is no evidence of a correlation between a niche and phylogeny. To test whether beta and gamma niches evolve conservatively, we reconstructed the evolution of relevant traits on evolutionary trees for 14 different clades. Tests against null models revealed a number of instances, including some in island radiations, in which habitat (beta niche) and elevational maximum (an aspect of the gamma niche) showed evolutionary conservatism.

Time-dependent hierarchical organization of spatial working memory: a transcranial magnetic stimulation study

The performance of memory-guided saccades with two different delays (3 and 30 s of memorization) was studied in seven healthy subjects. Double-pulse transcranial magnetic stimulation (dTMS) with an interstimulus interval of 100 ms was applied over the right dorsolateral prefrontal cortex (DLPFC) early (1 s after target presentation) and late (28 s after target presentation). Early stimulation significantly increased in both delays the percentage of error in amplitude (PEA) of contralateral memory-guided saccades compared to the control experiment without stimulation. dTMS applied late in the delay had no significant effect on PEA. Furthermore, we found a significantly smaller effect of early stimulation in the long-delay paradigm. These results suggest a time-dependent hierarchical organization of the spatial working memory with a functional dominance of DLPFC during the early memorization, independent from the memorization delay. For a long memorization delay, however, working memory seems to have an additional, DLPFC-independent component.

From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers

DNA-grafted supramolecular polymers (SPs) allow the programmed organization of DNA in a highly regular, one-dimensional array. Oligonucleotides are arranged along the edges of pyrene-based helical polymers. Addition of complementary oligonucleotides triggers the assembly of individual nanoribbons resulting in the development of extended supramolecular networks. Network formation is enabled by cooperative coaxial stacking interactions of terminal GC base pairs. The process is accompanied by structural changes in the pyrene polymer core that can be followed spectroscopically. Network formation is reversible, and disassembly into individual ribbons is realized either via thermal denaturation or by addition of a DNA separator strand.

Hierarchical carbon nanowire microarchitectures made by plasma-assisted pyrolysis of photoresist

We present a new approach for the fabrication and integration of vertically aligned forests of amorphous carbon nanowires (CNWs), using only standard lithography, oxygen plasma treatment, and thermal processing. The simplicity and scalability of this process, as well as the hierarchical organization of CNWs, provides a potential alternative to the use of carbon nanotubes and graphene for applications in microsystems and high surface area materials. The CNWs are highly branched at the nanoscale, and novel hierarchical microstructures with CNWs connected to a solid amorphous core are made by controlling the plasma treatment time. By multilayer processing we demonstrate deterministic joining of CNW micropillars into 3D sensing networks. Finally we show that these networks can be chemically functionalized and used for measurement of DNA binding with increased sensitivity. © 2011 American Chemical Society.

Toward a hierarchical concept of plant stress

A number of attempts have been made to obtain a clear definition of biological stress. However, in spite of the efforts, some controversies on the concept of plant stress remain. The current versions are centered either on the cause (stress factor) or on the effect (stress response) of environmental stress. The objective of this study was to contribute to the definition of stress, using a hierarchical approach. Thus, we have performed an analysis of the most usual stress concepts and tested the relevance of considering different observation scales in a study on plant response to water deficit. Seedlings of Eucalyptus grandis were grown in vitro at water potentials ranging from -0.16 to -0.6 MPa, and evaluated according to growth and biochemical parameters. Data were analyzed through principal component analysis (PCA), which pointed to a hierarchical organization in plant responses to environmental disturbances. Growth parameters (height and dry weight) are more sensitive to water deficit than biochemical ones (sugars, proline, and protein), suggesting that higher hierarchical levels were more sensitive to environmental constraints than lower hierarchical ones. We suggest that before considering an environmental fluctuation as stressful, it is necessary to take into account different levels of plant response, and that the evaluation of the effects of environmental disturbances on an organism depends on the observation scale being used. Hence, a more appropriate stress concept should consider the hierarchical organization of the biological systems, not only for a more adequate theoretical approach, but also for the improvement of practical studies on plants under stress.

A multiscale study on the structural and mechanical properties of the luffa sponge from Luffa cylindrica plant

Cellular materials that are often observed in biological systems exhibit excellent mechanical properties at remarkably low densities. Luffa sponge is one of such materials with a complex interconnecting porous structure. In this paper, we studied the relationship between its structural and mechanical properties at different levels of its hierarchical organization from a single fiber to a segment of whole sponge. The tensile mechanical behaviors of three single fibers were examined by an Instron testing machine and the ultrastructure of a fractured single fiber was observed in a scanning electronic microscope. Moreover, the compressive mechanical behaviors of the foam-like blocks from different locations of the sponge were examined. The difference of the compressive stress-strain responses of four sets of segmental samples were also compared. The result shows that the single fiber is a porous composite material mainly consisting of cellulose fibrils and lignin/hemicellulose matrix, and its Young's modulus and strength are comparable to wood. The mechanical behavior of the block samples from the hoop wall is superior to that from the core part. Furthermore, it shows that the influence of the inner surface on the mechanical property of the segmental sample is stronger than that of the core part; in particular, the former's Young's modulus, strength and strain energy absorbed are about 1.6 times higher. The present work can improve our understanding of the structure-function relationship of the natural material, which may inspire fabrication of new biomimetic foams with desirable mechanical efficiency for further applications in anti-crushing devices and super-light sandwich panels.

Kansallisvaltion teräsmiehestä valtakunnan sovittelijaksi : Poliisikulttuurin psykohistorialliset solmukohdat 1930-1997

From Steely Nation-State Superman to Conciliator of Economical Global Empire – A Psychohistory of Finnish Police Culture 1930-1997 My study concerns the way police culture has changed within the societal changes in Finnish society between 1930 and 1997. The method of my study was psycho-historical and post-structural analysis. The research was conducted by examining the psycho-historical plateaus traceable within Finnish police culture. I made a social diagnosis of the autopoietic relationship between the power-holders of Finnish society and the police (at various levels of hierarchical organization). According to police researcher John P. Crank, police culture should be understood as the cognitive processes behind the actions of the police. Among these processes are the values, beliefs, rituals, customs and advice which standardize their work and the common sense of policemen. According to Crank, police culture is defined by a mindset which thinks, judges and acts according to its evaluations filtered by its own preliminary comprehension. Police culture consists of all the unsaid assumptions of being a policeman, the organizational structures of police, official policies, unofficial ways of behaviour, forms of arrest, procedures of practice and different kinds of training habits, attitudes towards suspects and citizens, and also possible corruption. Police culture channels its members’ feelings and emotions. Crank says that police culture can be seen in how policemen express their feelings. He advises police researchers to ask themselves how it feels to be a member of the police. Ethos has been described as a communal frame for thought that guides one’s actions. According to sociologist Martti Grönfors, the Finnish mentality of the Protestant ethic is accentuated among Finnish policemen. The concept of ethos expresses very well the self-made mentality as an ethical tension which prevails in police work between communal belonging and individual freedom of choice. However, it is significant that it is a matter of the quality of relationships, and that the relationship is always tied to the context of the cultural history of dealing with one’s anxiety. According to criminologist Clifford Shearing, the values of police culture act as subterranean processes of the maintenance of social power in society. Policemen have been called microcosmic mediators, or street corner politicians. Robert Reiner argues that at the level of self-comprehension, policemen disparage the dimension of politics in their work. Reiner points out that all relationships which hold a dimension of power are political. Police culture has also been called a canteen culture. This idea expresses the day-to-day basis of the mentality of taking care of business which policing produces as a necessity for dealing with everyday hardships. According to police researcher Timo Korander, this figurative expression embodies the nature of police culture as a crew culture which is partly hidden from police chiefs who are at a different level. This multitude of standpoints depicts the diversity of police cultures. According to Reiner, one should not see police culture as one monolithic whole; instead one should assess it as the interplay of individuals negotiating with their environment and societal power networks. The cases analyzed formed different plateaus of study. The first plateau was the so-called ‘Rovaniemi arson’ case in the summer of 1930. The second plateau consisted of the examinations of alleged police assaults towards the Communists during the Finnish Continuation War of 1941 to 1944 and the threats that societal change after the war posed to Finnish Society. The third plateau was thematic. Here I investigated how using force towards police clients has changed culturally from the 1930s to the 1980s. The fourth plateau concerned with the material produced by the Security Police detectives traced the interaction between Soviet KGB agents and Finnish politicians during the long 1970s. The fifth plateau of larger changes in Finnish police culture then occurred during the 1980s as an aftermath of the former decade. The last, sixth plateau of changing relationships between policing and the national logic of action can be seen in the murder of two policemen in the autumn of 1997. My study shows that police culture has transformed from a “stone cold” steely fixed identity towards a more relational identity that tries to solve problems by negotiating with clients instead of using excessive force. However, in this process of change there is a traceable paradox in Finnish policing and police culture. On the one hand, policemen have, at the practical level, constructed their policing identity by protecting their inner self in their organizational role at work against the projections of anger and fear in society. On the other hand, however, they have had to safeguard themselves at the emotional level against the predominance of this same organizational role. Because of this dilemma they must simultaneously construct both a distance from their own role as police officers and the role of the police itself. This makes the task of policing susceptible to the political pressures of society. In an era of globalization, and after the heyday of the welfare state, this can produce heightened challenges for Finnish police culture.

Control aspects in proportionality Markov manpower systems

In this paper, the control aspects of a hierarchical organization under the influence of "proportionality" policies are analyzed. Proportionality policies are those that restrict the recruitment to every level of the hierarchy (except the bottom most level or base level) to be in strict proportion to the promotions into that level. Both long term and short term control analysis have been discussed. In long term control the specific roles of the parameters of the system with regard to control of the shape and size of the system have been analyzed and yield suitable control strategies. In short term control, the attainability of a target or goal structure within a specific time from a given initial structure has been analyzed and yields the required recruitment strategies. The theoretical analyses have been illustrated with computational examples and also with real world data.

Control aspects in proportionality Markov manpower systems

In this paper, the control aspects of a hierarchical organization under the influence of "proportionality" policies are analyzed. Proportionality policies are those that restrict the recruitment to every level of the hierarchy (except the bottom most level or base level) to be in strict proportion to the promotions into that level. Both long term and short term control analysis have been discussed. In long term control the specific roles of the parameters of the system with regard to control of the shape and size of the system have been analyzed and yield suitable control strategies. In short term control, the attainability of a target or goal structure within a specific time from a given initial structure has been analyzed and yields the required recruitment strategies. The theoretical analyses have been illustrated with computational examples and also with real world data. The control of such proportionality systems is then compared with that of the general systems (which do not follow such policies) with some significant conclusions. The control relations of such proportionality systems are found to be simpler and more practically feasible than those of general Markov systems, which do not have such restrictions. Such proportionality systems thus not only retain and match the flexibility of general Markov systems but also have the added advantage of simpler and more practically feasible controls. The proportionality policies hence act as an alternative and more practicably feasible means of control. (C) 2004 Elsevier Inc. All rights reserved.

Glioblastoma-Specific Protein Interaction Network Identifies PP1A and CSK21 as Connecting Molecules between Cell Cycle-Associated Genes

Glioblastoma (GBM; grade IV astrocytoma) is a very aggressive form of brain cancer with a poor survival and few qualified predictive markers. This study integrates experimentally validated genes that showed specific upregulation in GBM along with their protein-protein interaction information. A system level analysis was used to construct GBM-specific network. Computation of topological parameters of networks showed scale-free pattern and hierarchical organization. From the large network involving 1,447 proteins, we synthesized subnetworks and annotated them with highly enriched biological processes. A careful dissection of the functional modules, important nodes, and their connections identified two novel intermediary molecules CSK21 and protein phosphatase 1 alpha (PP1A) connecting the two subnetworks CDC2-PTEN-TOP2A-CAV1-P53 and CDC2-CAV1-RB-P53-PTEN, respectively. Real-time quantitative reverse transcription-PCR analysis revealed CSK21 to be moderately upregulated and PP1A to be overexpressed by 20-fold in GBM tumor samples. Immunohistochemical staining revealed nuclear expression of PP1A only in GBM samples. Thus, CSK21 and PP1A, whose functions are intimately associated with cell cycle regulation, might play key role in gliomagenesis. Cancer Res; 70(16); 6437-47. (C)2010 AACR.

Root system traits of Norway spruce, Scots pine, and silver birch in mixed boreal forests: an analysis of root architecture, morphology, and anatomy

The aim of this thesis was to unravel the functional-structural characteristics of root systems of Betula pendula Roth., Picea abies (L.) Karst., and Pinus sylvestris L. in mixed boreal forest stands differing in their developmental stage and site fertility. The root systems of these species had similar structural regularities: horizontally-oriented shallow roots defined the horizontal area of influence, and within this area, each species placed fine roots in the uppermost soil layers, while sinker roots defined the maximum rooting depth. Large radial spread and high ramification of coarse roots, and the high specific root length (SRL) and root length density (RLD) of fine roots indicated the high belowground competitiveness and root plasticity of B. pendula. Smaller radial root spread and sparser branching of coarse roots, and low SRL and RLD of fine roots of the conifers could indicate their more conservative resource use and high association with and dependence on ectomycorrhiza-forming fungi. The vertical fine root distributions of the species were mostly overlapping, implying the possibility for intense belowground competition for nutrients. In each species, conduits tapered and their frequency increased from distal roots to the stem, from the stem to the branches, and to leaf petioles in B. pendula. Conduit tapering was organ-specific in each species violating the assumptions of the general vascular scaling model (WBE). This reflects the hierarchical organization of a tree and differences between organs in the relative importance of transport, safety, and mechanical demands. The applied root model was capable of depicting the mass, length and spread of coarse roots of B. pendula and P. abies, and to the lesser extent in P. sylvestris. The roots did not follow self-similar fractal branching, because the parameter values varied within the root systems. Model parameters indicate differences in rooting behavior, and therefore different ecophysiological adaptations between species.

Communities in complex networks

The study of complex networks has attracted the attention of the scientific community for many obvious reasons. A vast number of systems, from the brain to ecosystems, power grid, and the Internet, can be represented as large complex networks, i.e, assemblies of many interacting components with nontrivial topological properties. The link between these components can describe a global behaviour such as the Internet traffic, electricity supply service, market trend, etc. One of the most relevant topological feature of graphs representing these complex systems is community structure which aims to identify the modules and, possibly, their hierarchical organization, by only using the information encoded in the graph topology. Deciphering network community structure is not only important in order to characterize the graph topologically, but gives some information both on the formation of the network and on its functionality.

Sobre sofrimento e terapêuticas em um ambulatório público de saúde mental

Este trabalho tem por objetivo apresentar concepções de sofrimento e terapêuticas dos usuários de um ambulatório de Saúde Mental de um posto de saúde localizado na zona norte do Rio de Janeiro. Estas concepções, calcadas num universo holista e hierárquico de valor, contrastam com as concepções de sofrimento, pessoa e terapêuticas próprias das práticas psi, indissociáveis da perspectiva individualista que lhe deu origem, cuja concepção de pessoa é calcada na experiência de uma interioridade psicológica, dotada de liberdade de escolha, autonomia, apontando, consequentemente, para concepções acerca do adoecimento e da terapêutica bastante diferentes daquelas próprias a uma configuração hierárquica de valores. Nesse sentido, discutem-se as repercussões que essas diferenças trazem para o estabelecimento de uma relação terapêutica. Observou-se que as concepções de sofrimento e a terapêutica dos entrevistados situam-se na configuração do nervoso, na qual aspectos físicos e morais da perturbação estão imbricados de forma indissociável. Na medida em que eles se auto-representam a partir de suas relações familiares e laborativas, a construção do que seja perturbação está referida a essa relacionalidade, que lhes confere uma identidade numa organização hierárquica. A psicoterapia é também englobada por essa mesma lógica, sendo deslocada do seu sentido individualista original, para ser ressignificada à luz do modelo físico-moral da perturbação e da relacionalidade própria à configuração do nervoso. Dessa forma, entende-se a psicoterapia como conversa que visa o desabafo, botar para fora os problemas, assim como forma de pensar em outras coisas que não o problema, duas estratégias consideradas terapêuticas na configuração do nervoso.