Architectural Rules Research Articles

Modulating Heterologous Gene Expression with Portable mRNA-Stabilizing 5'-UTR Sequences.

RNA half-lives are frequently perceived as depending on too many variables, and transcript stability is generally missed as a checkpoint amenable to manipulation in synthetic designs. In this work, the contribution of mRNA stability to heterologous protein production levels in E.coli has been inspected. To this end, we capitalized on the wealth of information available on intrinsic mRNA stability determinants, four of which were formatted as portable modules consisting of 5'-untranslated regions (UTRs). The cognate DNA sequences were then assembled in a genetic frame in which mRNA stability endowed by the UTRs was the only variable to run expression of sfGFP. Reporter output and Northern blot-based measurements of absolute mRNA half-lives revealed that such UTRs were found to keep intact their ability to modulate transcript stability when excised from their natural context and placed as the upstream region of the reporter gene. By keeping transcription fixed and combining different UTRs with a constant ribosomal binding site, we showed that mRNA decay can be made the limiting constituent of the overall gene expression flow. Moreover, the data indicated that manipulating mRNA stability had little effect on expression noise in the corresponding population. Finally, augmented heterologous expression brought about by mRNA stability did not make cells more vulnerable to resource-consuming stresses. The tangible result of this work was a collection of well-characterized mRNA-stabilizing sequences that can be composed along with other expression signals in any construct following the assembly rules of the Standard European Vector Architecture (SEVA) format.

The WGB method to recover implemented architectural rules

Context: The identification of architectural rules, which specify allowed dependencies among architectural modules, is a key challenge in software architecture recovery. Existing approaches either retrieve a large set of rules, compromising their practical use, or are limited to supporting the understanding of such rules, which are manually recovered.Objective: To propose and evaluate a method to recover architectural rules, focusing on those implemented in the source code, which may differ from planned or conceptual rules.Method: We propose the WGB method, which analyzes dependencies among architectural modules as a graph, adding weights that correspond to the proposed module dependency strength (MDS) metric and identifies the set of implemented architectural rules by solving a mathematical optimization problem. We evaluated our method with a case study and an empirical study that compared rules extracted by the method with the conceptual architecture and source code dependencies of six systems. These comparisons considered efficiency and effectiveness of our method.Results: Regarding efficiency, our method took 45.55 s to analyze the largest system evaluated. Considering effectiveness, our method captured package dependencies as extracted rules with a reduction of 87.6%, on average, to represent this information. Using allowed architectural dependencies as a reference point (but not a gold standard), provided rules achieved 37.1% of precision and 37.8% of recall.Conclusion: Our empirical evaluation shows that the implemented architectural rules recovered by our method consist of abstract representations of (a large number of) module dependencies, providing a concise view of dependencies that can be inspected by developers to identify occurrences of architectural violations and undocumented rules.

Supporting the analyzability of architectural component models - empirical findings and tool support

This article discusses the understandability of component models that are frequently used as central views in architectural descriptions of software systems. We empirically examine how different component level metrics and the participants’ experience and expertise can be used to predict the understandability of those models. In addition, we develop a tool that supports applying the obtained empirical findings in practice. Our results show that the prediction models have a large effect size, which means that their prediction strength is of high practical significance. The participants’ experience plays an important role in the prediction but the obtained models are not as accurate as the models that use the component level metrics. The developed tools combine the DSL-based architecture abstraction approach with the obtained empirical findings. While the DSL-based architecture abstraction approach enables software architects to keep source code and architecture consistent, the metrics extensions enable them, while working with the DSL, to continuously judge and improve the analyzability of architectural component models based on the understandability of their individual components they create with the DSL. Provided metrics extensions can also help in assessing how much each architectural rule used to specify the DSL affects the understandability of a component which enables for instance finding the rules that contribute the most to a limited understandability. Finally, our approach supports change impact analysis, i.e., the identification of changes that affect different analyzability levels of the component models. We studied the applicability of our approach in a case study of an existing open source system.

FACADE SEGMENTATION WITH A STRUCTURED RANDOM FOREST

Abstract. In this paper we present a bottom-up approach for the semantic segmentation of building facades. Facades have a predefined topology, contain specific objects such as doors and windows and follow architectural rules. Our goal is to create homogeneous segments for facade objects. To this end, we have created a pixelwise labeling method using a Structured Random Forest. According to the evaluation of results for two datasets with the classifier we have achieved the above goal producing a nearly noise-free labeling image and perform on par or even slightly better than the classifier-only stages of state-of-the-art approaches. This is due to the encoding of the local topological structure of the facade objects in the Structured Random Forest. Additionally, we have employed an iterative optimization approach to select the best possible labeling.

The scaling of the hydraulic architecture in poplar leaves.

Although much is known about the hydraulics of xylem, the hydraulic interconnectivity and dimensional scaling of phloem with respect to xylem in leaves has not been adequately studied to test alternative hydraulic architectural rules such as da Vinci's rule or Murray's rule, or physiological models such as Münch's Pressure Flow hypothesis. Using confocal and electron microscopy as well as mathematical analyses, we examined the hydraulic architecture of the mature leaves of the model species Populus tremula×alba across all seven hierarchical orders of the vascular branching. We show that: phloem and xylem conductive areas increase from minor to major veins; the sum of the conductive areas for each vein order increases exponentially from major to minor veins; the volume of individual sieve tube and vessel members increases from minor to major veins; and phloem conductive area scales isometrically with respect to xylem area across all vein orders. The application of first principles to our data shows that conductive areas scale according to da Vinci's rule and not according to Murray's rule, and that the phloem network in poplar leaves can generate the pressure gradient envisioned in Münch's hypothesis.

An unusual elbow muscle in the red howler monkey: does it deserve invention of a new name musculus contrahens cubiti?

During dissection of a juvenile specimen of howler monkey (Alouatta seniculus), we discovered a supernumerary muscle. This muscle originates from the lateral epicondyle of the humerus, distal to the m. brahioradialis and beneath the m. extensor carpi radialis longus, and runs deeply to insert on the proximal part of the radius adjacent to the m. supinator.To determine homology of the unusual muscle, we compared it with the known abnormal extra muscles in the group of preaxial forearm extensors in humans and other primates, as well as other mammals. The only similar muscle is the so-called m. brachioradialis accessorius, which is very rarely found in humans medial to the n. radialis r. superficialis. Both in howlers and humans, its unique topological interrelations with the n. radialis suggest that this muscle is fundamentally different from all surrounding forearm extensors including the proper m. brachioradialis. At the same time, its innervation by the n. radialis confirms that it is a true extensor, contrary to the reptilian m. tractor radii.The general problem of identifying homology of anomalies and novelties is considered. As the enigmatic muscle departs from rules of myological architecture of the tetrapod forelimb, we failed to establish its general homology and, instead, suggest naming it as m. contrahens cubiti. This means that the muscle acts as the elbow flexor although it intimately belongs to extensors.

The Comparative Study of Privacy in Designing Qajar Dynasty Isfahan`s Houses and Malaysia`s Traditional Houses

Privacy is taken from cultural and religious values and belief which are among the rules of the traditional residential architecture which have been shown in different ways in traditional architecture in different ways. Lots of valuable characteristics of the traditional Iranian houses prove the fact that Iranian people kept privacy; nowadays with the penetration of western architectural culture and after Qajar dynasty, a reflection of that style is rarely seen in contemporary residential architecture. This survey is to analyze privacy layering in Iranian architectural houses and as a religious value by the use of the mentioned method (observation, interview, and studying the maps) in the traditional sample of Malaysia as the comparative sample and then compared with the other Malaysian samples. By taking the nature of the objective of the research into considerations, the research method is comparative case study based on qualitative approach. Results of this survey have shown that privacy in different layers were designed for keeping people`s independence, and providing the mental and psychological peace of the family member which is completely consistent with Islamic sources; there are some similarities and difference between the Malaysian sample and two samples of the early and late of Qajar period. The conclusion of this study shows the existence of extrovert privacy pattern in Malaysian houses and also existence of introvert privacy pattern in Qajar houses and different spatial categorizations; the privacy keeping principle and approaches in contemporary architecture is applicable.Keywords: Privacy, Hierarchy, Being introvert, Isfahan`s Qajar Houses, Traditional Malaysian house.

Integrated Structural–Architectural Design for Interactive Planning

AbstractTraditionally, building floor plans are designed by architects with their usability, functionality and architectural aesthetics in mind; however, the structural properties of the distribution of load‐bearing walls and columns are usually not taken into account at this stage. In this paper, we propose a novel approach for the design of architectural floor plans by integrating structural layout analysis directly into the planning process. In order to achieve this, we introduce a planning tool which interactively enforces checks for structural stability of the current design, and which on demand proposes how to stabilize it if necessary. Technically, our solution contains an interactive architectural modelling framework as well as a constrained optimization module where both are based on respective architectural rules. Using our tool, an architect can predict already in a very early planning stage whose designs are structurally sound such that later changes due to stability reasons can be prevented. We compare manually computed solutions with optimal results of our proposed automated design process in order to show how much our proposed system can help architects to improve the process of laying out structural models optimally.

A Semantic Modelling Framework-Based Method for Building Reconstruction from Point Clouds

Over the past few years, there has been an increasing need for semantic information in automatic city modelling. However, due to the complexity of building structure, the semantic reconstruction of buildings is still a challenging task because it is difficult to extract architectural rules and semantic information from the data. To improve the insufficiencies, we present a semantic modelling framework-based approach for automated building reconstruction using the semantic information extracted from point clouds or images. In this approach, a semantic modelling framework is designed to describe and generate the building model, and a workflow is established for extracting the semantic information of buildings from an unorganized point cloud and converting the semantic information into the semantic modelling framework. The technical feasibility of our method is validated using three airborne laser scanning datasets, and the results are compared with other related works comprehensively, which indicate that our approach can simplify the reconstruction process from a point cloud and generate 3D building models with high accuracy and rich semantic information.

Selective synaptic remodeling of amygdalocortical connections associated with fear memory.

Neural circuits underlying auditory fear conditioning have been extensively studied. Here we identified a previously unexplored pathway from the lateral amygdala (LA) to the auditory cortex (ACx) and found that selective silencing of this pathway using chemo- and optogenetic approaches impaired fear memory retrieval. Dual-color in vivo two-photon imaging of mouse ACx showed pathway-specific increases in the formation of LA axon boutons, dendritic spines of ACx layer 5 pyramidal cells, and putative LA-ACx synaptic pairs after auditory fear conditioning. Furthermore, joint imaging of pre- and postsynaptic structures showed that essentially all new synaptic contacts were made by adding new partners to existing synaptic elements. Together, these findings identify an amygdalocortical projection that is important to fear memory expression and is selectively modified by associative fear learning, and unravel a distinct architectural rule for synapse formation in the adult brain.

© Montreal's Cité-Jardin du Tricentenaire Transformation: The Role of the PIIA as a Tool for Resilience

This research focuses on the impact of the implementation of a by-law in a residential area, Montreal's garden city, la Cite-Jardin du Tricentenaire. The City of Montreal has implemented a set of specific architectural and environmental rules (PIIA, a Plan for Architectural Integration and Establishment) in order to protect and preserve the unique character of this Garden City built during the 1940's. In the general plan, Montreal designated the area as an exceptional site for preservation, a natural urban area and an authentic neighbourhood inspired by Ebenezer Howard's Garden City. In spite of the requirements of the PIIA for la Cite-Jardin, the recommendations of the Heritage Council of Montreal and the pressure exerted by the Residents' Association, a neutral observer might well conclude that not enough has been done to preserve the unique character of this neighborhood nor to prevent major transformations. The signs of decline in the quality of this heritage neighborhood have continued unabated during the 2010's: (1) significant enlargement of original houses, (2) demolition of heritage houses and reconstruction with only minimal, superficial similarities and (3) destruction of mature trees and replacement with suburban-style landscaping. While similar in some respects to the process of gentrification, the demographic changes underway in the Cite-Jardin are being produced by newcomers of a similar social class to the original residents but with a distinctly lower sensitivity to heritage architecture and community norms. Our research project aims to understand the effect of the PIIA as a potential catalyst for resilience in a case study, the Cite-Jardin du Tricentenaire community. Given the decentralized structure of the City of Montreal, bylaws governing the community are the responsibility of the Borough of Rosemont-La Petite-Patrie. This paper focuses principally on documentary analysis and interviews with borough officials designed to substantiate the theoretical structure underlying our approach.

Engineering of synthetic, stress-responsive yeast promoters.

Advances in synthetic biology and our understanding of the rules of promoter architecture have led to the development of diverse synthetic constitutive and inducible promoters in eukaryotes and prokaryotes. However, the design of promoters inducible by specific endogenous or environmental conditions is still rarely undertaken. In this study, we engineered and characterized a set of strong, synthetic promoters for budding yeast Saccharomyces cerevisiae that are inducible under acidic conditions (pH ≤ 3). Using available expression and transcription factor binding data, literature on transcriptional regulation, and known rules of promoter architecture we improved the low-pH performance of the YGP1 promoter by modifying transcription factor binding sites in its upstream activation sequence. The engineering strategy outlined for the YGP1 promoter was subsequently applied to create a response to low pH in the unrelated CCW14 promoter. We applied our best promoter variants to low-pH fermentations, enabling ten-fold increased production of lactic acid compared to titres obtained with the commonly used, native TEF1 promoter. Our findings outline and validate a general strategy to iteratively design and engineer synthetic yeast promoters inducible to environmental conditions or stresses of interest.

TRADITIONAL ARCHITECTURE ECO-SYSTEMS IN IRAN, THE WAY OF THE SUSTAINABLE ARCHITECTURE

Ponte Academic JournalJul 2016, Volume 72, Issue 7 TRADITIONAL ARCHITECTURE ECO-SYSTEMS IN IRAN, THE WAY OF THE SUSTAINABLE ARCHITECTUREAuthor(s): Zahra Ghomi-AviliJ. Ponte - Jul 2016 - Volume 72 - Issue 7 doi: 10.21506/j.ponte.2016.7.12 Abstract:This paper discusses issues related Sustainability and Iranian traditional architecture. Sustainable architecture has a main role in the world of architecture nowadays. In any parts of the world architects try to suggest new methods for sustainability. Accordingly, traditional Iranian architecture, it is observed that Iranian architectural characteristics conform to the rules of sustainable architecture and can obtain sustainability in modern architecture by being reveled by certain features of traditional Iranian one. The aim of this research is to demonstrate traditional architecture in Hot-Arid climate and humid and rainy region which embraces the southern shores of the Caspian Sea of Iran as tow samples of sustainable architecture. Result of this paper; show that considering the experience in traditional architecture of hot-aired regions, it is possible to create an environmental and sustainable architecture for todays and future in Iran. By suggesting new ways to transfer sustainable elements in our modern buildings we could have the best choice for our generation both in energy and in culture. Download full text:Check if you have access through your login credentials or your institution Username Password

Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification.

Background Various groups of flowering plants reveal profound (‘saltational’) changes of their bauplans (architectural rules) as compared with related taxa. These plants are known as morphological misfits that appear as rather large morphological deviations from the norm. Some of them emerged as morphological key innovations (perhaps ‘hopeful monsters’) that gave rise to new evolutionary lines of organisms, based on (major) genetic changes.Scope This pictorial report places emphasis on released bauplans as typical for bladderworts (Utricularia, approx. 230 secies, Lentibulariaceae) and river-weeds (Podostemaceae, three subfamilies, approx. 54 genera, approx. 310 species). Bladderworts (Utricularia) are carnivorous, possessing sucking traps. They live as submerged aquatics (except for their flowers), as humid terrestrials or as epiphytes. Most Podostemaceae are restricted to rocks in tropical river-rapids and waterfalls. They survive as submerged haptophytes in these extreme habitats during the rainy season, emerging with their flowers afterwards. The recent scientific progress in developmental biology and evolutionary history of both Lentibulariaceae and Podostemaceae is summarized.Conclusions Lentibulariaceae and Podostemaceae follow structural rules that are different from but related to those of more typical flowering plants. The roots, stems and leaves – as still distinguishable in related flowering plants – are blurred (‘fuzzy’). However, both families have stable floral bauplans. The developmental switches to unusual vegetative morphologies facilitated rather than prevented the evolution of species diversity in both families. The lack of one-to-one correspondence between structural categories and gene expression may have arisen from the re-use of existing genetic resources in novel contexts. Understanding what developmental patterns are followed in Lentibulariaceae and Podostemaceae is a necessary prerequisite to discover the genetic alterations that led to the evolution of these atypical plants. Future molecular genetic work on morphological misfits such as bladderworts and river-weeds will provide insight into developmental and evolutionary aspects of more typical vascular plants.

Five Years of Software Architecture Checking: A Case Study of Eclipse

Over time, source code tends to drift from the intended software architecture, often resulting in the loss of desired software qualities. To help keep code aligned with the intended architecture, the developers of core parts of the open source Eclipse platform introduced API Tools to express and check architectural rules. Researchers analyzed five years of Eclipse architecture-checking reports that API Tools produced. They investigated what kinds of rules the developers found helpful to check, how code diverged from the intended architecture, and how the developers dealt with architectural violations over time. This article is part of a special issue on Software Architecture.

A design-by-contract approach to recover the architectural style from run-time misbehaviour

We propose to control the reconfigurations of applications leading to an erroneous state by exploiting its architectural model. Our work relies on Architectural Design Rewriting (ADR, for short) which is a rule-based formal framework for modelling (the evolution of) software architectures. We equip the reconfiguration rules of an ADR architecture with pre- and post-conditions expressed in a simple logic; a pre-condition constraints the applicability of a rule while a post-condition specifies the properties expected of the resulting graphs. We give an algorithm to compute the weakest pre-condition out of a rule and its post-condition. On top of this algorithm, we design a simple methodology that allows us to select which rules can be applied at the architectural level to reconfigure a system so to regain its architectural style when it becomes compromised by unexpected run-time reconfigurations.

The evolution of architecture.

The article discusses the genetic aspects of the evolution of animal architecture. Topics include the wide variety of intricate nests and homes built by birds, mammals, and social insects, such as Macrotermes bellicosus termites, studies by Jesse N. Weber and Hopi E. Hoekstra on the genetics of architecture in the field mouse genus Peromyscus, and the design of more efficient cities based on computer programs that follow the same architectural rules as social insects.

El escenario de la calidad en la Universidad española: de dónde venimos y hacia dónde vamos

Revista Electronica Interuniversitaria de Formacion del Profesorado, vol. 17, no. 3, pp. 1-16

Architectured bimetallic laminates by roll bonding: bonding mechanisms and applications

Manufacturing of bimetallic laminates (<2 mm) with an internal architecture by roll bonding allows to obtain a compromise of conflicting properties. Two applications are considered: copper–steel–copper sheets for high power electronic component substrates and lightweight aluminium–steel–aluminium laminates for structural, electromagnetic applications in power generation and for electromagnetic compatibility. They have in common an architecture, with three-dimensional percolating networks of two metals produced with a sufficient precision. The bonding mechanisms are investigated through microstructural and thermomechanical characterisation of the assemblies produced. Roll bonding fills the voids in a central component by plastic deformation and creates the bonds by cold welding. It may be followed or preceded by surface and heat treatments with the objective to improve the cold welding and to relieve the internal stress state. Architectural rules to optimise the properties of the two-phase laminates in view of the applications may be guided by finite element models combining physical and thermomechanical aspects.

Penerapan Linq(Language Integrated Query) Untuk Implementasi Aplikasi Perpustakaan

LINQ is new technology to create even window or web application. This research focus on how to implemented LINQ at Library application. The application is compiled by following a three-layer architecture rule, which is known as 'three tier'. A 'Three tier' architecture is divided into three parts, they are data tier, business tier, and presentation tier. Data tier is data in the form of a database, business tier is data in the form of services which consists of different functions that consumes the data tier, and the last one is presentation tier which takes the form of applications interface that consumes business tier.The stored information will be consumed through a special class called business logic class that will handle various operations, such as insert, update, and delete the data book. LINQ is needed to create this business logic class that allows data access and aims to facilitate query to all types of data such as Object, XML, databases, etc. This LINQ enables a programming language which is used on the Microsoft NET framework has a native query capabilities towards the data. The LINQ statement is written using C#.net with Visual Studio 2010 and DevExprees 2012 with SQLServer database. The system design uses UML. The result is library application using LINQ framework. Kata Kunci : Library application, LINQ, LINQ to SQL, Web service, WCF, SOA, Prototype.