Word learning,phonological short-term memory,phonotactic probability and long-term memory: towards an integrated framework

Word learning is studied in a multitude of ways, and it is often not clear what the relationship is between different phenomena. In this article, we begin by outlining a very simple functional framework that despite its simplicity can serve as a useful organizing scheme for thinking about various types of studies of word learning. We then review a number of themes that in recent years have emerged as important topics in the study of word learning, and relate them to the functional framework, noting nevertheless that these topics have tended to be somewhat separate areas of study. In the third part of the article, we describe a recent computational model and discuss how it offers a framework that can integrate and relate these various topics in word learning to each other. We conclude that issues that have typically been studied as separate topics can perhaps more fruitfully be thought of as closely integrated, with the present framework offering several suggestions about the nature of such integration.     

An integrated network visualization framework towards metabolic engineering applications

Background

Over the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). These methods provided insight on the functioning of microbial metabolism and played a key role in the design of genetic modifications that can lead to strains of industrial interest. On the other hand, in the context of Systems Biology research, biological network visualization has reinforced its role as a core tool in understanding biological processes. However, it has been scarcely used to foster ME related methods, in spite of the acknowledged potential.

Results

In this work, an open-source software that aims to fill the gap between ME and metabolic network visualization is proposed, in the form of a plugin to the OptFlux ME platform. The framework is based on an abstract layer, where the network is represented as a bipartite graph containing minimal information about the underlying entities and their desired relative placement. The framework provides input/output support for networks specified in standard formats, such as XGMML, SBGN or SBML, providing a connection to genome-scale metabolic models. An user-interface makes it possible to edit, manipulate and query nodes in the network, providing tools to visualize diverse effects, including visual filters and aspect changing (e.g. colors, shapes and sizes). These tools are particularly interesting for ME, since they allow overlaying phenotype simulation results or elementary flux modes over the networks.

Conclusions

The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0420-0) contains supplementary material, which is available to authorized users.     

A meta-analysis of cambium phenology and growth: linear and non-linear patterns in conifers of the northern hemisphere

Background and Aims

Ongoing global warming has been implicated in shifting phenological patterns such as the timing and duration of the growing season across a wide variety of ecosystems. Linear models are routinely used to extrapolate these observed shifts in phenology into the future and to estimate changes in associated ecosystem properties such as net primary productivity. Yet, in nature, linear relationships may be special cases. Biological processes frequently follow more complex, non-linear patterns according to limiting factors that generate shifts and discontinuities, or contain thresholds beyond which responses change abruptly. This study investigates to what extent cambium phenology is associated with xylem growth and differentiation across conifer species of the northern hemisphere.

Methods

Xylem cell production is compared with the periods of cambial activity and cell differentiation assessed on a weekly time scale on histological sections of cambium and wood tissue collected from the stems of nine species in Canada and Europe over 1–9 years per site from 1998 to 2011.

Key Results

The dynamics of xylogenesis were surprisingly homogeneous among conifer species, although dispersions from the average were obviously observed. Within the range analysed, the relationships between the phenological timings were linear, with several slopes showing values close to or not statistically different from 1. The relationships between the phenological timings and cell production were distinctly non-linear, and involved an exponential pattern

Conclusions

The trees adjust their phenological timings according to linear patterns. Thus, shifts of one phenological phase are associated with synchronous and comparable shifts of the successive phases. However, small increases in the duration of xylogenesis could correspond to a substantial increase in cell production. The findings suggest that the length of the growing season and the resulting amount of growth could respond differently to changes in environmental conditions.     

Assessment of thyroid function: towards an integrated laboratory--clinical approach

Laboratory assessment of thyroid function is now often initiated with a low pre-test probability, by clinicians who may not have a detailed knowledge of current methodology or testing strategies. Skilled laboratory staff can significantly enhance the choice of appropriate tests and the accuracy of clinical response; such involvement requires both appropriate training and relevant information from the clinician. Measurement of the serum thyroid stimulating hormone (TSH) concentration with an assay of adequate sensitivity is now the cornerstone of thyroid function testing; for untreated populations at risk of primary thyroid dysfunction, a normal TSH concentration rules out an abnormality with a high degree of certainty. However, in several important situations, most notably pituitary abnormalities and early treatment of thyroid dysfunction, serum TSH can give a misleading indication of thyroid status. An abnormal TSH concentration alone is never an adequate basis for initiation of treatment, which should be based on the typical relationship between trophic and target gland hormones, based on serum TSH and an estimate of serum free thyroxine (T4). Six basic assumptions, some clinical, some laboratory-based, need to be considered, together with the relevant limiting conditions, for reliable use of this relationship. Current methods of free T4 estimation remain imperfect, especially during critical illness. Diagnostic approach differs significantly between initial diagnosis and follow-up of treated thyroid dysfunction. In some situations, serum triiodothyronine (T3) is also required, but serum T3 lacks sensitivity for diagnosis of hypothyroidism, and has poor specificity during non-thyroidal illness. Where assay results are anomalous, most atypical findings can be resolved by attention to the clinical context, without further investigation.     

Connectivity and invasive species management: towards an integrated landscape approach

Invasive plants and animals are a major cause of global biodiversity loss. Invasive Species Management (ISM) helps conserve localized populations and ecosystems, but rarely have its potential benefits been explored at the landscape scale. We explore how ISM can enhance landscape connectivity, and how its incorporation into conservation planning algorithms could help design optimal reserve networks. Conversely, conservation planning and connectivity modelling can optimize targeting of ISM, achieving benefits for a wider range of taxa and ecological processes, without the need for additional resources. Empirical research must investigate the spatial pattern of benefits from ISM, and when to target priority conservation sites or the areas (matrix) between them. By bolstering populations within—and increasing connectivity between—focal patches, ISM should move beyond conserving individual sites to creating functionally connected networks of conservation areas.     

From mechanisms to function: an integrated framework of animal innovation

Animal innovations range from the discovery of novel food types to the invention of completely novel behaviours. Innovations can give access to new opportunities, and thus enable innovating agents to invade and create novel niches. This in turn can pave the way for morphological adaptation and adaptive radiation. The mechanisms that make innovations possible are probably as diverse as the innovations themselves. So too are their evolutionary consequences. Perhaps because of this diversity, we lack a unifying framework that links mechanism to function. We propose a framework for animal innovation that describes the interactions between mechanism, fitness benefit and evolutionary significance, and which suggests an expanded range of experimental approaches. In doing so, we split innovation into factors (components and phases) that can be manipulated systematically, and which can be investigated both experimentally and with correlational studies. We apply this framework to a selection of cases, showing how it helps us ask more precise questions and design more revealing experiments.     

Quality of oral health services in residential care: towards an evaluation framework

Background: There is widespread neglect of oral healthcare, and uncertainty about how best to organise and evaluate the impact of oral health services in long‐term care (LTC) facilities. Consequently, there is need for an evaluation framework to improve and account for the quality of oral healthcare in the facilities. Objectives: This paper: (i) identifies basic concepts of quality of care and evaluation in healthcare; (ii) reviews the methods used to evaluate the operation and effectiveness of oral healthcare in LTC facilities and (iii) recommends change to assure oral health‐related quality and accountability for frail elders. Method: A literature review provided insights to the theoretical basis and practical applications for assessing the quality of healthcare relevant to oral healthcare for frail elders. Results: Oral health‐related programmes in LTC facilities could be improved by using a combination of quality assurance and health programme evaluation that: (i) engages everyone involved; (ii) seeks multiple attributes of quality; (iii) evaluates the structure, process or activities, and outcome of the oral health programme; (iv) uses formative and summative methods to provide both quantitative and qualitative evidence of care and (v) transfers new knowledge for appropriate consideration and action. Conclusions: This theoretical framework can be applied in dentistry in LTC to provide an assessment model specific to oral healthcare for frail elders in residential care.     

A survey of motif discovery methods in an integrated framework

Background  

There has been a growing interest in computational discovery of regulatory elements, and a multitude of motif discovery methods have been proposed. Computational motif discovery has been used with some success in simple organisms like yeast. However, as we move to higher organisms with more complex genomes, more sensitive methods are needed. Several recent methods try to integrate additional sources of information, including microarray experiments (gene expression and ChlP-chip). There is also a growing awareness that regulatory elements work in combination, and that this combinatorial behavior must be modeled for successful motif discovery. However, the multitude of methods and approaches makes it difficult to get a good understanding of the current status of the field.     

Maintaining and restoring hydrologic habitat connectivity in mediterranean streams: an integrated modeling framework

Hydrologic alterations designed to provide a stable water supply and to prevent flooding are commonly used in mediterranean-climate river (med-rivers) basins, and these alterations have led to habitat loss and significant declines in aquatic biodiversity. Often the health of freshwater ecosystems depends on maintaining and recovering hydrologic habitat connectivity, which includes structural components related to the physical landscape, functionality of flow dynamics, and an understanding of species habitat requirements for movement, reproduction, and survival. To advance our understanding of hydrologic habitat connectivity and benefits of habitat restoration alternatives we provide: (1) a review of recent perspectives on hydrologic connectivity, including quantitative methods; and (2) a modeling framework to quantify the effects of restoration on hydrologic habitat connectivity. We then illustrate this approach through a case study on lateral hydrologic habitat connectivity that results from channel restoration scenarios using scenarios with different historic and climate-change flows to restore fish floodplain habitat in a med-river, the San Joaquin River, California. Case study results show that in addition to the channel alterations, higher flows are required to recover significant flooded habitat area, especially given reductions in flows expected under climate change. These types of studies will help the planning for restoration of hydrologic habitat connectivity in med-rivers, a critical step for mediterranean species recovery.     

The Genome Sequence DataBase: towards an integrated functional genomics resource.

During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data collections, and provide new methods and tools to access and analyze data. Data quality has been improved by extensive curation of certain data fields necessary for maintaining data collections and for using certain tools. Data quality has also been increased by improvements to the suite of programs that import data from the International Nucleotide Sequence Database Collaboration (IC). The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within the last year, allowing public access to this valuable resource of expressed sequences. Data access was improved by the addition of the Sequence Viewer, a platform-independent graphical viewer for GSDB sequence data. This tool has also been integrated with other searching and data retrieval tools. A BLAST homology search service was also made available, allowing researchers to search all of the data, including the unique data, that are available from GSDB. These improvements are designed to make GSDB more accessible to users, extend the rich searching capability already present in GSDB, and to facilitate the transition to an integrated system containing many different types of biological data.     

Indicators for biodiversity and ecosystem services: towards an improved framework for ecosystems assessment

Ecosystem assessment and monitoring requires the development and application of suitable indicators, i.e. they need to be (i) reliable and capable of simplifying complex relationships, (ii) quantifiable and transparent in order to enable an easy communication, and (iii) fit for the purpose of indication. These requirements are scarcely fulfilled in current ecosystem assessment and monitoring efforts to address the requirements of international biodiversity conventions. Here we present and test a set of seven criteria towards an improved framework for ecosystems indication with particular emphasis on the indication of biodiversity and ecosystem services: purpose of indication, indicator type according to the EEA’s Driver-Pressure-State-Impact-Response scheme, direct/indirect linkages to biodiversity and ecosystem services, spatial scale and scalability across scales, applicability of benchmarks/reference values, availability of data and protocols, and applicability of remote sensing. The criteria are tested using 24 indicators of ecosystem assessment and monitoring at the global, continental and regional scale. Based on the general trends revealed by our evaluation, we present recommendations to streamline and improve ecosystem indication with respect to international biodiversity conventions. The implementation of our recommendations does require concerted international effort, comparable, for instance, to the implementation of the Water Framework Directive in Europe.     

Flowers as sensory billboards: progress towards an integrated understanding of floral advertisement

This paper explores the landscape of integrated sensory signals that are produced by flowers, and the contextual information that modulates pollinator responses to such signals. Chiloglottis orchids are pollinated by mimicking the pheromone and posture of female thynnine wasps, but floral height provides the context within which male wasps respond to these signals. The odor and appearance of carrion attract blowflies to Helicodiceros inflorescences, but flies are more likely to enter the floral chamber when heat is present as a contextual cue. Finally, fragrance, UV-visual cues and echo fingerprints are redundant signals that Glossophaga bats can use to find flowers, depending on prior experience and the photic environment.     

The maize two-dimensional gel protein database: towards an integrated genome analysis program

This paper describes the first maize database of proteins separated by two-dimensional electrophoresis. Fifty-six coleoptile proteins and 18 leaf proteins from two maize lines were partially microsequenced. Thirty-six proteins (49%) displayed high similarity with database proteins. Nine of these proteins, representing five different functions, had never been described in maize. No conclusive function could be found for 45 polypeptides (61% of the microsequenced proteins). In addition, an alternative identification method, based on amino acid analysis, allowed candidates to be proposed for 17 proteins out of 44 additional proteins analyzed in the coleoptiles. These results are stored in a database which also includes, when available, genetic information about the chromosomal location of structural genes and regulatory factors of proteins. This database is being used in the context of a project on the genetic mapping of the expressed genome in maize.