Phytohormone collaboration: zooming in on auxin-brassinosteroid interactions.

Similar to animal hormones, classic plant hormones are small organic molecules that regulate physiological and developmental processes. In development, this often involves the regulation of growth through the control of cell size or division. The plant hormones auxin and brassinosteroid modulate both cell expansion and proliferation and are known for their overlapping activities in physiological assays. Recent molecular genetic analyses in the model plant Arabidopsis suggest that this reflects interdependent and often synergistic action of the two hormone pathways. Such pathway interactions probably occur through the combinatorial regulation of common target genes by auxin- and brassinosteroid-controlled transcription factors. Moreover, auxin and brassinosteroid signaling and biosynthesis and auxin transport might be linked by an emerging upstream connection involving calcium-calmodulin and phosphoinositide signaling.

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and paralogy relationships, and in the detection of relevant evolutionary events such as gene family expansions and contractions, horizontal gene transfer, recombination or incomplete lineage sorting. Similarly, given the plurality of evolutionary histories among genes encoded in a given genome, there is a need for the combined analysis of genome-wide collections of phylogenetic trees (phylomes). Here, we introduce a new release of PhylomeDB (http://phylomedb.org), a public repository of phylomes. Currently, PhylomeDB hosts 120 public phylomes, comprising >1.5 million maximum likelihood trees and multiple sequence alignments. In the current release, phylogenetic trees are annotated with taxonomic, protein-domain arrangement, functional and evolutionary information. PhylomeDB is also a major source for phylogeny-based predictions of orthology and paralogy, covering >10 million proteins across 1059 sequenced species. Here we describe newly implemented PhylomeDB features, and discuss a benchmark of the orthology predictions provided by the database, the impact of proteome updates and the use of the phylome approach in the analysis of newly sequenced genomes and transcriptomes.

Zooming and creeping.

Producida en colaboración con el Museo de Historia Natural de Londres, se estudia al animal más rápido y al más lento en tierra, mar y aire y se pregunta si la velocidad o la lentitud puede ser una ventaja en el mundo natural. También se ocupa de cómo los vientos de gran velocidad, chocan con el agua e incluso cómo un aparentemente pacífico río puede cambiar drásticamente el paisaje de la naturaleza.

Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite

Most ice in nature forms because of impurities which boost the exceedingly low nucleation rate of pure supercooled water. However, the microscopic details of ice nucleation on these substances remain largely unknown. Here, we have unraveled the molecular mechanism and the kinetics of ice formation on kaolinite, a clay mineral playing a key role in climate science. We find that the formation of ice at strong supercooling in the presence of this clay is about 20 orders of magnitude faster than homogeneous freezing. The critical nucleus is substantially smaller than that found for homogeneous nucleation and, in contrast to the predictions of classical nucleation theory (CNT), it has a strong two-dimensional character. Nonetheless, we show that CNT describes correctly the formation of ice at this complex interface. Kaolinite also promotes the exclusive nucleation of hexagonal ice, as opposed to homogeneous freezing where a mixture of cubic and hexagonal polytypes is observed.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

High-magnification vascular imaging to reject false-positive sites in situ during Hexvix® fluorescence cystoscopy.

Fluorescence imaging for detection of non-muscle-invasive bladder cancer is based on the selective production and accumulation of fluorescing porphyrins-mainly, protoporphyrin IX-in cancerous tissues after the instillation of Hexvix®. Although the sensitivity of this procedure is very good, its specificity is somewhat limited due to fluorescence false-positive sites. Consequently, magnification cystoscopy has been investigated in order to discriminate false from true fluorescence positive findings. Both white-light and fluorescence modes are possible with the magnification cystoscope, allowing observation of the bladder wall with magnification ranging between 30× for standard observation and 650×. The optical zooming setup allows adjusting the magnification continuously in situ. In the high-magnification (HM) regime, the smallest diameter of the field of view is 600 microns and the resolution is 2.5 microns when in contact with the bladder wall. With this cystoscope, we characterized the superficial vascularization of the fluorescing sites in order to discriminate cancerous from noncancerous tissues. This procedure allowed us to establish a classification based on observed vascular patterns. Seventy-two patients subject to Hexvix® fluorescence cystoscopy were included in the study. Comparison of HM cystoscopy classification with histopathology results confirmed 32?33 (97%) cancerous biopsies and rejected 17?20 (85%) noncancerous lesions.

High-magnification vascular imaging to reject false-positive sites in situ during Hexvix® fluorescence cystoscopy

Fluorescence imaging for detection of non-muscle-invasive bladder cancer is based on the selective production and accumulation of fluorescing porphyrins-mainly, protoporphyrin IX-in cancerous tissues after the instillation of Hexvix®. Although the sensitivity of this procedure is very good, its specificity is somewhat limited due to fluorescence false-positive sites. Consequently, magnification cystoscopy has been investigated in order to discriminate false from true fluorescence positive findings. Both white-light and fluorescence modes are possible with the magnification cystoscope, allowing observation of the bladder wall with magnification ranging between 30× for standard observation and 650×. The optical zooming setup allows adjusting the magnification continuously in situ. In the high-magnification (HM) regime, the smallest diameter of the field of view is 600 microns and the resolution is 2.5 microns when in contact with the bladder wall. With this cystoscope, we characterized the superficial vascularization of the fluorescing sites in order to discriminate cancerous from noncancerous tissues. This procedure allowed us to establish a classification based on observed vascular patterns. Seventy-two patients subject to Hexvix® fluorescence cystoscopy were included in the study. Comparison of HM cystoscopy classification with histopathology results confirmed 32/33 (97%) cancerous biopsies and rejected 17/20 (85%) noncancerous lesions.

Deviations of Governance In IT Multi-Sourcing: A Case Study

IT outsourcing (ITO) refers to the shift of IT/IS activities from internal to external of an organization. In prior research, the governance of ITO is recognized with persistent strategic importance for practice, because it is tightly related to ITO success. Under the rapid transformation of global market, the evolving practice of ITO requires updated knowledge on effective governance. However, research on ITO governance is still under developed due to the lack of integrated theoretical frameworks and the variety of empirical settings besides dyadic client-vendor relationships. Especially, as multi-sourcing has become an increasingly common practice in ITO, its new governance challenges must be attended by both ITO researchers and practitioners. To address this research gap, this study aims to understand multi-sourcing governance with an integrated theoretical framework incorporating both governance structure and governance mechanisms. The focus is on the emerging deviations among formal, perceived and practiced governance. With an interpretive perspective, a single case study is conducted with mixed methods of Social Network Analysis (SNA) and qualitative inquiries. The empirical setting embraces one client firm and its two IT suppliers for IT infrastructure services. The empirical material is analyzed at three levels: within one supplier firm, between the client and one supplier, and among all three firms. Empirical evidences, at all levels, illustrate various deviations in governance mechanisms, with which emerging governance structures are shaped. This dissertation contributes to the understanding of ITO governance in three domains: the governance of ITO in general, the governance of multi-sourcing in particular, and research methodology. For ITO governance in general, this study has identified two research strands of governance structure and governance mechanisms, and integrated both concepts under a unified framework. The composition of four research papers contributes to multi-sourcing research by illustrating the benefits of zooming in and out across the multilateral relationships with different aspects and scopes. Methodologically, the viability and benefit of mixed-method is illustrated and confirmed for both researchers and practitioners.

Le livre sous la loupe : Nouvelles formes d’écriture électronique

Les fichiers qui accompagnent le document incluent une archive .jar du zoom-éditeur (qui peut être lancé via un browser) et des exemples de z-textes réalisés avec ce logiciel.

Effets d’un dispositif de formation exploitant des vidéos d’exemples de pratiques sur le développement d’une compétence professionnelle chez des enseignants du primaire

Cette recherche avait pour objectif d’évaluer l’effet du dispositif de formation « Zoom sur l’expertise pédagogique », ou, plus précisément, d’évaluer l’effet d’un parcours de formation créé grâce à ce dispositif et intégrant des exemples de pratiques sur vidéo sur les apprentissages et les intentions de changement de pratique d’un groupe d’enseignants du primaire relativement à la compétence professionnelle « Piloter des situations d’enseignement-apprentissage ». La réforme des programmes scolaires, qui s’installe progressivement depuis 2001, modifie considérablement les orientations en matière d’apprentissage et d’enseignement. Sa réussite repose notamment sur l’appropriation de nouvelles compétences professionnelles souvent difficiles à développer pour le personnel enseignant. À ces besoins de formation, les modalités de formation continue proposées ne semblaient répondre que partiellement. Le dispositif a été développé dans le but de soutenir le personnel enseignant dans l’appropriation de ce renouveau pédagogique et propose de nouvelles stratégies de formation basées principalement sur l’observation et l’analyse d’exemples de pratiques sur vidéo et enrichis de divers outils stimulant la réflexion sur la pratique. Sa conception s’inscrit dans un contexte d’émergence d’initiatives similaires. Néanmoins, beaucoup de questions restaient en suspens quant aux effets réels de ces dispositifs sur le développement professionnel des enseignants. Afin de réaliser une évaluation de ce dispositif, nous avons créé un parcours de formation que six enseignants ont réalisé. Ces personnes ont ensuite participé à deux entrevues semi-dirigées et ont partagé les notes prises durant la formation. Un cadre théorique a été développé, permettant de dégager trois questions de recherche : « Quels ont été les effets du dispositif de formation sur les savoirs relatifs aux composantes de la compétence ciblée ? » ; « Quels ont été les effets du dispositif de formation sur les intentions de changement de pratique des enseignants ? » ; « Comment améliorer le dispositif pour mieux soutenir le développement professionnel des enseignants ? ». Ce cadre a par la suite guidé l’analyse et l’interprétation des données recueillies. Une quantité substantielle d’informations a été obtenue permettant de mieux comprendre et documenter le rôle d’un tel dispositif de formation en ligne et des vidéos qui le composent. Nous avons pu confirmer leur effet positif sur le développement professionnel. Nous retenons notamment que les enseignants sont en mesure de mieux définir les composantes de la compétence ciblée par la formation, ils ont confirmé leur sentiment d’avoir appris, ils ont tous exprimé l'intention d’apporter des changements dans leur pratique. Tous ont grandement apprécié le parcours et ses vidéos, notamment la possibilité qu’elles leur offraient de s’identifier à des pairs et d’envisager des pistes de mise en application plus concrètes de leurs nouvelles connaissances. Par ailleurs, les commentaires et les suggestions des participants ont permis de dégager des pistes d’amélioration telles que la diminution de la quantité de vidéos, du nombre d’éléments de compétence présentés, ou l’augmentation de compléments pédagogiques accompagnant les vidéos. Ces pistes devraient toutefois être précisées et étudiées ce qui génère de nouvelles questions de recherches.

An integrated assessment of resource use strategies in the Borana pastoral system of southern Ethiopia

In the pastoral production systems, mobility remains the main technique used to meet livestock’s fodder requirements. Currently, with growing challenges on the pastoral production systems, there is urgent need for an in-depth understanding of how pastoralists continue to manage their grazing resources and how they determine their mobility strategies. This study examined the Borana pastoralists’ regulation of access to grazing resources, mobility practices and cattle reproductive performances in three pastoral zones of Borana region of southern Ethiopia. The central objective of the study was to contribute to the understanding of pastoral land use strategies at a scale relevant to their management. The study applied a multi-scalar methodological approach that allowed zooming in from communal to individual herd level. Through participatory mapping that applied Google Earth image print out as visual aid, the study revealed that the Borana pastoralists conceptualized their grazing areas as distinctive grazing units with names, borders, and specific characteristics. This knowledge enables the herders to communicate the condition of grazing resources among themselves in a precise way which is important in management of livestock mobility. Analysis of grazing area use from the participatory maps showed that the Borana pastoralists apportion their grazing areas into categories that are accessed at different times of the year (temporal use areas). This re-organization is an attempt by the community to cope with the prevailing constraints which results in fodder shortages especially during the dry periods. The re-organization represents a shift in resource use system, as the previous mobility practice across the ecologically varied zones of the rangelands became severely restricted. Grazing itineraries of 91 cattle herds for over 16 months obtained using the seasonal calendar interviews indicated that in the areas with the severest mobility constraints, the herders spent most of their time in the year round use areas that are within close proximity to the settlements. A significant change in mobility strategy was the disallowing of foora practice by the communities in Dirre and Malbe zones in order to reduce competition. With the reduction in mobility practices, there is a general decline in cattle reproductive parameters with the areas experiencing the severest constraints showing the least favourable reproductive performances. The study concludes that the multi-scalar methodology was well suited to zoom into pastoral grazing management practices from communal to individual herd levels. Also the loss of mobility in the Borana pastoral system affects fulfilment of livestock feed requirements thus resulting in reduced reproductive performances and herd growth potentials. While reversal of the conditions of the situations in the Borana rangelands is practically unfeasible, the findings from this research underscore the need to protect the remaining pastoral lands since the pastoral production system remains the most important livelihood option for the majority of the Borana people. In this regards the study emphasises the need to adopt and domesticate regional and international policy frameworks such as that proposed by the African Union in 2010.

Ka-Map: an interactive web-mapping application

ka-Map ("ka" as in ka-boom!) is an open source project that is aimed at providing a javascript API for developing highly interactive web-mapping interfaces using features available in modern web browsers. ka-Map currently has a number of interesting features. It sports the usual array of user interface elements such as: interactive, continuous panning without reloading the page; keyboard navigation options (zooming, panning); zooming to pre-set scales; interactive scalebar, legend and keymap support; optional layer control on client side; server side tile caching

Remote presence: supporting deictic gestures through a handheld multi-touch device

This thesis argues on the possibility of supporting deictic gestures through handheld multi-touch devices in remote presentation scenarios. In [1], Clark distinguishes indicative techniques of placing-for and directing-to, where placing-for refers to placing a referent into the addressee’s attention, and directing-to refers to directing the addressee’s attention towards a referent. Keynote, PowerPoint, FuzeMeeting and others support placing-for efficiently with slide transitions, and animations, but support limited to none directing-to. The traditional “pointing feature” present in some presentation tools comes as a virtual laser pointer or mouse cursor. [12, 13] have shown that the mouse cursor and laser pointer offer very little informational expressiveness and do not do justice to human communicative gestures. In this project, a prototype application was implemented for the iPad in order to explore, develop, and test the concept of pointing in remote presentations. The prototype offers visualizing and navigating the slides as well as “pointing” and zooming. To further investigate the problem and possible solutions, a theoretical framework was designed representing the relationships between the presenter’s intention and gesture and the resulting visual effect (cursor) that enables the audience members to interpret the meaning of the effect and the presenter’s intention. Two studies were performed to investigate people’s appreciation of different ways of presenting remotely. An initial qualitative study was performed at The Hague, followed by an online quantitative user experiment. The results indicate that subjects found pointing to be helpful in understanding and concentrating, while the detached video feed of the presenter was considered to be distracting. The positive qualities of having the video feed were the emotion and social presence that it adds to the presentations. For a number of subjects, pointing displayed some of the same social and personal qualities [2] that video affords, while less intensified. The combination of pointing and video proved to be successful with 10-out-of-19 subjects scoring it the highest while pointing example came at a close 8-out-of-19. Video was the least preferred with only one subject preferring it. We suggest that the research performed here could provide a basis for future research and possibly be applied in a variety of distributed collaborative settings.

Accuracy of zoomed digital image in the detection of periodontal bone defect: in vitro study

Objectives: (1) To evaluate the intraobserver agreement related to image interpretation and (2) to compare the accuracy of 100%, 200% and 400% zoomed digital images in the detection of simulated periodontal bone defects.Methods: Periodontal bone defects were created in 60 pig hemi-mandibles with slow-speed burs 0.5 mm, 1.0 mm, 1.5 mm, 2.0 mm and 3.0 mm in diameter. 180 standardized digital radiographs were made using Schick sensor and evaluated at 100%, 200% and 400% zooming. The intraobserver agreement was estimated by Kappa statistic (kappa). For the evaluation of diagnostic accuracy receiver operating characteristic (ROC) analysis was performed followed by chi-square test to compare the areas under ROC curves according to each level of zooming.Results: For 100%, 200% and 400% zooming the intraobserver agreement was moderate (kappa = 0.48, kappa = 0.54 and kappa = 0.43, respectively) and there were similar performances in the discrimination capacity, with ROC areas of 0.8611 (95% CI: 0.7660-0.9562), 0.8600 (95% CI: 0.7659-0.9540), and 0.8368 (95% CI: 0.7346-0.9390), respectively, with no statistical significant differences (chi(2)-test; P = 0.8440).Conclusions: A moderate intraobserver agreement was observed in the classification of periodontal bone defects and the 100%, 200% and 400% zoomed digital images presented similar performances in the detection of periodontal bone defects.