bluuebunny/crossref_metadata_2025 huggingface dataset:
Typicality, Graded Membership, and Vagueness
Authors: Hampton James A.
Published: October 2010

This paper addresses theoretical problems arising from the vagueness of language terms, and intuitions of the vagueness of the concepts to which they refer. It is argued that the central intuitions of prototype theory are sufficient to account for both typicality phenomena and psychological intuitions about degrees of membership in vaguely defined classes. The first section explains the importance of the relation between degrees of membership and typicality (or goodness of example) in conceptual categorization. The second and third section address arguments advanced by , and , that the two notions of degree of membership and typicality must relate to fundamentally different aspects of conceptual representations. A version of prototype theory—the Threshold Model—is proposed to counter these arguments and three possible solutions to the problems of logical selfcontradiction and tautology for vague categorizations are outlined. In the final section graded membership is related to the social construction of conceptual boundaries maintained through language use.
The Role of Prior Experience in Language Acquisition
Authors: Lany Jill , Gómez Rebecca L. , Gerken Lou Ann
Published: October 2010

Learners exposed to an artificial language recognize its abstract structural regularities when instantiated in a novel vocabulary (e.g., ; ). We asked whether such sensitivity accelerates subsequent learning, and enables acquisition of more complex structure. In Experiment 1, pre‐exposure to a category‐induction language of the form aX bY sped subsequent learning when the language is instantiated in a different vocabulary. In Experiment 2, while naíve learners did not acquire an acX bcY language, in which aX and bY co‐occurrence regularities were separated by a c‐element, prior experience with an aX bY language provided some benefit. In Experiment 3 we replicated this finding with a 24‐hour delay between learning phases, and controlled for prior experience with the aX bY language's prosodic and phonological characteristics. These findings suggest that learners, and the structure they can acquire, change as a function of experience.
Semantic Boost on Episodic Associations: An Empirically‐Based Computational Model
Authors: Silberman Yaron , Bentin Shlomo , Miikkulainen Risto
Published: October 2010

Words become associated following repeated co‐occurrence episodes. This process might be further determined by the semantic characteristics of the words. The present study focused on how semantic and episodic factors interact in incidental formation of word associations. First, we found that human participants associate semantically related words more easily than unrelated words; this advantage increased linearly with repeated co‐occurrence. Second, we developed a computational model, SEMANT, suggesting a possible mechanism for this semantic‐episodic interaction. In SEMANT, episodic associations are implemented through lateral connections between nodes in a pre‐existent self‐organized map of word semantics. These connections are strengthened at each instance of concomitant activation, proportionally with the amount of the overlapping activity waves of activated nodes. In computer simulations SEMANT replicated the dynamics of associative learning in humans and led to testable predictions concerning normal associative learning as well as impaired learning in a diffuse semantic system like that characteristic of schizophrenia.
The cell biology of touch
Authors: Lumpkin Ellen A. , Marshall Kara L. , Nelson Aislyn M.
Published: October 2010

The sense of touch detects forces that bombard the body’s surface. In metazoans, an assortment of morphologically and functionally distinct mechanosensory cell types are tuned to selectively respond to diverse mechanical stimuli, such as vibration, stretch, and pressure. A comparative evolutionary approach across mechanosensory cell types and genetically tractable species is beginning to uncover the cellular logic of touch reception.
Impacts of Free Trade Agreements on Agricultural Trade Creation and Trade Diversion
Authors: Sun Lin , Reed Michael R.
Published: October 2010

This paper evaluates agricultural trade creation and diversion effects of the most important free trade agreements (FTAs). Trade creation and diversion effects are estimated using a Poisson Pseudo‐Maximum‐Likelihood (PPML) estimator with various fixed effects to deal with heteroskedasticity and zero trade observations. The analysis finds that PPML estimation is preferred to OLS and the estimated impacts of FTAs are different if zero trade observations are considered. The ASEAN‐China preferential trade agreement, EU‐15, EU‐25, and Southern African Development Community agreements have generated large increases in agricultural trade among their members.
SmashCommunity: a metagenomic annotation and analysis tool
Authors: Arumugam Manimozhiyan , Harrington Eoghan D. , Foerstner Konrad U. , Raes Jeroen , Bork Peer
Published: October 2010

Summary: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses.

Availability: SmashCommunity source code and documentation are available at http://www.bork.embl.de/software/smash

Contact:  bork@embl.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
MiRonTop: mining microRNAs targets across large scale gene expression studies
Authors: Le Brigand Kevin , Robbe-Sermesant Karine , Mari Bernard , Barbry Pascal
Published: October 2010

Summary: Current challenges in microRNA (miRNA) research are to improve the identification of in vivo mRNA targets and clarify the complex interplay existing between a specific miRNA and multiple biological networks. MiRonTop is an online java web tool that integrates DNA microarrays or high-throughput sequencing data to identify the potential implication of miRNAs on a specific biological system. It allows a rapid characterization of the most pertinent mRNA targets according to several existing miRNA target prediction approaches. It also provides useful representations of the enrichment scores according to the position of the target site along the 3′-UTR, where the contribution of the sites located in the vicinity of the stop codon and of the polyA tail can be clearly highlighted. It provides different graphs of miRNA enrichment associated with up- or down-regulated transcripts and different summary tables about selections of mRNA targets and their functional annotations by Gene Ontology.

Availability:  http://www.microarray.fr:8080/miRonTop/index

Contact:  barbry@ipmc.cnrs.fr
Interactional and functional centrality in transcriptional co-expression networks
Authors: Prifti Edi , Zucker Jean-Daniel , Clément Karine , Henegar Corneliu
Published: October 2010

Motivation: The noisy nature of transcriptomic data hinders the biological relevance of conventional network centrality measures, often used to select gene candidates in co-expression networks. Therefore, new tools and methods are required to improve the prediction of mechanistically important transcriptional targets.

Results: We propose an original network centrality measure, called annotation transcriptional centrality (ATC) computed by integrating gene expression profiles from microarray experiments with biological knowledge extracted from public genomic databases. ATC computation algorithm delimits representative functional domains in the co-expression network and then relies on this information to find key nodes that modulate propagation of functional influences within the network. We demonstrate ATC ability to predict important genes in several experimental models and provide improved biological relevance over conventional topological network centrality measures.

Availability: ATC computational routine is implemented in a publicly available tool named FunNet (www.funnet.info)

Contact:  edi.prifti@crc.jussieu.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Clinical, neuroradiological and genetic findings in pontocerebellar hypoplasia
Authors: Namavar Yasmin , Barth Peter G. , Kasher Paul R. , van Ruissen Fred , Brockmann Knut , Bernert Günther , Writzl Karin , Ventura Karen , Cheng Edith Y. , Ferriero Donna M. , Basel-Vanagaite Lina , Eggens Veerle R. C. , Krägeloh-Mann Ingeborg , De Meirleir Linda , King Mary , Graham John M. , von Moers Arpad , Knoers Nine , Sztriha Laszlo , Korinthenberg Rudolf , Consortium PCH , Dobyns William B. , Baas Frank , Poll-The Bwee Tien
Published: October 2010

Pontocerebellar hypoplasia is a group of autosomal recessive neurodegenerative disorders with prenatal onset. The common characteristics are cerebellar hypoplasia with variable atrophy of the cerebellum and the ventral pons. Supratentorial involvement is reflected by variable neocortical atrophy, ventriculomegaly and microcephaly. Mutations in the transfer RNA splicing endonuclease subunit genes (TSEN54, TSEN2, TSEN34) were found to be associated with pontocerebellar hypoplasia types 2 and 4. Mutations in the mitochondrial transfer RNA arginyl synthetase gene (RARS2) were associated with pontocerebellar hypoplasia type 6. We studied a cohort of 169 patients from 141 families for mutations in these genes, of whom 106 patients tested positive for mutations in one of the TSEN genes or the RARS2 gene. In order to delineate the neuroradiological and clinical phenotype of patients with mutations in these genes, we compared this group with 63 patients suspected of pontocerebellar hypoplasia who were negative on mutation analysis. We found a strong correlation (P < 0.0005) between TSEN54 mutations and a dragonfly-like cerebellar pattern on magnetic resonance imaging, in which the cerebellar hemispheres are flat and severely reduced in size and the vermis is relatively spared. Mutations in TSEN54 are clinically associated with dyskinesia and/or dystonia and variable degrees of spasticity, in some cases with pure generalized spasticity. Nonsense or splice site mutations in TSEN54 are associated with a more severe phenotype of more perinatal symptoms, ventilator dependency and early death. In addition, we present ten new mutations in TSEN54, TSEN2 and RARS2. Furthermore, we show that pontocerebellar hypoplasia type 1 together with elevated cerebrospinal fluid lactate may be caused by RARS2 mutations.
Absence of obesity paradox in patients with chronic heart failure and diabetes mellitus: a propensity‐matched study
Authors: Adamopoulos Chris , Meyer Philippe , Desai Ravi V. , Karatzidou Kyparissi , Ovalle Fernando , White Michel , Aban Inmaculada , Love Thomas E. , Deedwania Prakash , Anker Stefan D. , Ahmed Ali
Published: October 2010

Aims

Obesity is paradoxically associated with survival benefit in patients with chronic heart failure (HF). However, obesity complicates the management of diabetes mellitus (DM), which is common in HF. Yet, little is known about the impact of obesity in HF patients with DM. Therefore, we examined the association between obesity and outcomes in propensity‐matched cohorts of HF patient with and without DM.

Methods and results

Of the 7788 participants with chronic mild to moderate HF in the Digitalis Investigation Group trial, 7379 were non‐cachectic [body mass index (BMI) ≥20 kg/m2] at baseline. Of these, 2153 (29%) had DM, of whom 798 (37%) were obese (BMI ≥30 kg/m2). Of the 5226 patients without DM, 1162 (22%) were obese. Propensity scores for obesity were used to separately assemble 636 pairs of obese and non‐obese patients with DM and 770 pairs of obese and non‐obese patients without DM, who were balanced on 32 baseline characteristics. Among matched patients with DM, all‐cause mortality occurred in 38 and 39% of obese and non‐obese patients, respectively [hazard ratio (HR) when obesity was compared with no obesity 0.99; 95% confidence interval (CI) 0.80–1.22; P = 0.915]. Among matched patients without DM, all‐cause mortality occurred in 23 and 27% obese and non‐obese patients, respectively (HR associated with obesity 0.77; 95% CI 0.61–0.97; P = 0.025).

Conclusion

In patients with chronic mild to moderate HF and DM, obesity confers no paradoxical survival benefit. Whether intentional weight loss may improve outcomes in these patients needs to be investigated in future prospective studies.
Rebuilding depleted fish stocks: the good, the bad, and, mostly, the ugly
Authors: Murawski Steven A.
Published: October 2010

Murawski, S. A. 2010. Rebuilding depleted fish stocks: the good, the bad, and, mostly, the ugly. – ICES Journal of Marine Science, 67: 1830–1840. Recovery of depleted fish populations has become an important theme in national and international negotiations and commitments regarding sustainability. Although up to 63% of fish stocks worldwide may be in need of rebuilding, only 1% are currently classified as “rebuilding”, and fewer yet have been “rebuilt”. Recent history in stock recovery provides a rich source of examples of rebuilding plans across a spectrum of execution (“good”, “bad”, “ugly”, and “in progress”). Of 24 depleted stocks with formal plans that successfully reduced the fishing mortality, all but one exhibited signs of recovery. The median instantaneous annual rate of biomass recovery (0.16) was similar to the rate of depletion (−0.14) experienced, but stocks with more vulnerable life histories recovered substantially slower than they had been depleted. Most successful rebuilding programmes have incorporated substantial, measurable reductions in fishing mortality at the onset, rather than relying on incremental small reductions over time. A particularly vexing issue is the differential pace of recovery among relatively productive and unproductive components of mixed-species fisheries. Rebuilding the majority of stocks classified worldwide as “overfished” will take a more effective, consistent, and politically supported stock-recovery paradigm, if society is eventually to meet its articulated sustainability goals for global fisheries.
Shell strength and fishing damage to the smooth clam (Callista chione): simulating impacts caused by bivalve dredging
Authors: Vasconcelos Paulo , Morgado-André António , Morgado-André Carlos , Gaspar Miguel B.
Published: October 2010

Vasconcelos, P., Morgado-André, A., Morgado-André, C., and Gaspar, M. B. 2011. Shell strength and fishing damage to the smooth clam (Callista chione): simulating impacts caused by bivalve dredging. – ICES Journal of Marine Science, 68: 32–42. The smooth clam Callista chione is exploited by a fleet of dredgers along the southwestern coast of Portugal and suffers from a high incidence of shell damage. The force required to break C. chione shells in relation to fishing impacts and dredge damage is quantified. Fishing trials and shell-strength measurements (compression and compaction experiments) were performed to determine whether shell damage was attributable to the direct impact of the dredge teeth or to sediment compaction. A three-dimensional model of C. chione was subjected to simulated force by the finite element method. Analyses of damage areas and breakage patterns revealed two groups of samples, one containing the samples from compression experiments and another with the samples from dredging and compaction experiments, suggesting that most shell damage was attributable to compaction within the sediment. Information is provided to help improve the design of bivalve dredges, by increasing both length and angle of the dredge teeth, which would reduce the compaction force and distribute it differentially within the sediment, forcing upward movement of the bivalves.
In the Eye of the Beholder: The Effect of Rater Variability and Different Rating Scales on QTL Mapping
Authors: Poland Jesse A. , Nelson Rebecca J.
Published: October 2010

The agronomic importance of developing durably resistant cultivars has led to substantial research in the field of quantitative disease resistance (QDR) and, in particular, mapping quantitative trait loci (QTL) for disease resistance. The assessment of QDR is typically conducted by visual estimation of disease severity, which raises concern over the accuracy and precision of visual estimates. Although previous studies have examined the factors affecting the accuracy and precision of visual disease assessment in relation to the true value of disease severity, the impact of this variability on the identification of disease resistance QTL has not been assessed. In this study, the effects of rater variability and rating scales on mapping QTL for northern leaf blight resistance in maize were evaluated in a recombinant inbred line population grown under field conditions. The population of 191 lines was evaluated by 22 different raters using a direct percentage estimate, a 0-to-9 ordinal rating scale, or both. It was found that more experienced raters had higher precision and that using a direct percentage estimation of diseased leaf area produced higher precision than using an ordinal scale. QTL mapping was then conducted using the disease estimates from each rater using stepwise general linear model selection (GLM) and inclusive composite interval mapping (ICIM). For GLM, the same QTL were largely found across raters, though some QTL were only identified by a subset of raters. The magnitudes of estimated allele effects at identified QTL varied drastically, sometimes by as much as threefold. ICIM produced highly consistent results across raters and for the different rating scales in identifying the location of QTL. We conclude that, despite variability between raters, the identification of QTL was largely consistent among raters, particularly when using ICIM. However, care should be taken in estimating QTL allele effects, because this was highly variable and rater dependent.
The aesthetics of water and land: a promising concept for managing scarce water resources under climate change
Authors: Tielbörger Katja , Fleischer Aliza , Menzel Lucas , Metz Johannes , Sternberg Marcelo
Published: October 2010

The eastern Mediterranean faces a severe water crisis: water supply decreases due to climate change, while demand increases due to rapid population growth. The GLOWA Jordan River project generates science-based management strategies for maximizing water productivity under global climate change. We use a novel definition of water productivity as the full range of services provided by landscapes per unit blue (surface) and green (in plants and soil) water. Our combined results from climatological, ecological, economic and hydrological studies suggest that, in Israel, certain landscapes provide high returns as ecosystem services for little input of additional blue water. Specifically, cultural services such as recreation may by far exceed that of food production. Interestingly, some highly valued landscapes (e.g. rangeland) appear resistant to climate change, making them an ideal candidate for adaptive land management. Vice versa, expanding irrigated agriculture is unlikely to be sustainable under global climate change. We advocate the inclusion of a large range of ecosystem services into integrated land and water resources management. The focus on cultural services and integration of irrigation demand will lead to entirely different but productive water and land allocation schemes that may be suitable for withstanding the problems caused by climate change.
How uncertain are climate model projections of water availability indicators across the Middle East?
Authors: Hemming Debbie , Buontempo Carlo , Burke Eleanor , Collins Mat , Kaye Neil
Published: October 2010

The projection of robust regional climate changes over the next 50 years presents a considerable challenge for the current generation of climate models. Water cycle changes are particularly difficult to model in this area because major uncertainties exist in the representation of processes such as large-scale and convective rainfall and their feedback with surface conditions. We present climate model projections and uncertainties in water availability indicators (precipitation, run-off and drought index) for the 1961–1990 and 2021–2050 periods. Ensembles from two global climate models (GCMs) and one regional climate model (RCM) are used to examine different elements of uncertainty. Although all three ensembles capture the general distribution of observed annual precipitation across the Middle East, the RCM is consistently wetter than observations, especially over the mountainous areas. All future projections show decreasing precipitation (ensemble median between −5 and −25%) in coastal Turkey and parts of Lebanon, Syria and Israel and consistent run-off and drought index changes. The Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) GCM ensemble exhibits drying across the north of the region, whereas the Met Office Hadley Centre work Quantifying Uncertainties in Model ProjectionsAtmospheric (QUMP-A) GCM and RCM ensembles show slight drying in the north and significant wetting in the south. RCM projections also show greater sensitivity (both wetter and drier) and a wider uncertainty range than QUMP-A. The nature of these uncertainties suggests that both large-scale circulation patterns, which influence region-wide drying/wetting patterns, and regional-scale processes, which affect localized water availability, are important sources of uncertainty in these projections. To reduce large uncertainties in water availability projections, it is suggested that efforts would be well placed to focus on the understanding and modelling of both large-scale processes and their teleconnections with Middle East climate and localized processes involved in orographic precipitation.
Water and society in Jordan and Israel today: an introductory overview
Authors: Black Emily
Published: October 2010

Increasing population levels and demand for water have led to a global water shortage, with more than one billion people unable to access safe drinking water. The Middle East is particularly vulnerable to water stress because of its dense population, variable climate and vulnerable groundwater resources. In Jordan, for example, if current trends in population continue, the water per capita will halve—putting the country in the category of having an absolute water shortage. This opening paper summarizes the climate and hydrology of Jordan and Israel, describes how water is managed at a national level in Jordan and reflects briefly on the broader international context.
Global Gene Profiling of Laser-Captured Pollen Mother Cells Indicates Molecular Pathways and Gene Subfamilies Involved in Rice Meiosis
Authors: Tang Xiang , Zhang Zhi-Yong , Zhang Wen-Juan , Zhao Xing-Ming , Li Xuan , Zhang Dong , Liu Qiao-Quan , Tang Wei-Hua
Published: October 2010

Pollen mother cells (PMCs) represent a critical early stage in plant sexual reproduction in which the stage is set for male gamete formation. Understanding the global molecular genetics of this early meiotic stage has so far been limited to whole stamen or floret transcriptome studies, but since PMCs are a discrete population of cells in developmental synchrony, they provide the potential for precise transcriptome analysis and for enhancing our understanding of the transition to meiosis. As a step toward identifying the premeiotic transcriptome, we performed microarray analysis on a homogenous population of rice (Oryza sativa) PMCs isolated by laser microdissection and compared them with those of tricellular pollen and seedling. Known meiotic genes, including OsSPO11-1, PAIR1, PAIR2, PAIR3, OsDMC1, OsMEL1, OsRAD21-4, OsSDS, and ZEP1, all showed preferential expression in PMCs. The Kyoto Encyclopedia of Genes and Genomes pathways significantly enriched in PMC-preferential genes are DNA replication and repair pathways. Our genome-wide survey showed that, in the buildup to meiosis, PMCs accumulate the molecular machinery for meiosis at the mRNA level. We identified 1,158 PMC-preferential genes and suggested candidate genes and pathways involved in meiotic recombination and meiotic cell cycle control. Regarding the developmental context for meiosis, the DEF-like, AGL2-like, and AGL6-like subclades of MADS box transcription factors are PMC-preferentially expressed, the trans-zeatin type of cytokinin might be preferentially synthesized, and the gibberellin signaling pathway is likely active in PMCs. The ubiquitin-mediated proteolysis pathway is enriched in the 127 genes that are expressed in PMCs but not in tricellular pollen or seedling.
Past and current tendency for facial flushing after a small dose of alcohol is a marker for increased risk of upper aerodigestive tract cancer in Japanese drinkers
Authors: Yokoyama Akira , Yokoyama Tetsuji , Omori Tai
Published: October 2010

(Cancer Sci 2010; 101: 2497–2498)
Reply to Span et al.: Mammaglobin RT‐qPCR for breast cancer metastasis detection in sentinel lymph nodes
Authors: Liu Yan‐Hui , Xu Fang‐Ping , Liao Ning , Li Li , Zhang Guo‐chun , Zhuang Heng‐Guo
Published: October 2010

(Cancer Sci 2010; 101: 2502)
Decreased bone density in men on methadone maintenance therapy
Authors: Grey Andrew , Rix‐Trott Karla , Horne Anne , Gamble Greg , Bolland Mark , Reid Ian R.
Published: October 2010

Aims Opioid use may impact adversely upon skeletal health. Participants in methadone maintenance programmes commonly have prolonged exposure to opioids. We sought to determine whether participants in a methadone maintenance programme have evidence of altered bone mineral density (BMD) and bone turnover.

Design Cross‐sectional study of people taking methadone maintenance therapy (MMT).

Setting Clinical research centre.

Participants Eighty‐three people (48 men, 35 women) who had taken MMT for a median (interquartile range) of 11 (6–16) years. Comparison data were from both a normative database and control subjects recruited and assessed at the same location as the participants taking MMT.

Measurements BMD at lumbar spine, total hip and total body; biochemical markers of bone turnover.

Findings In men taking MMT, BMD was lower than normal at each skeletal site [mean, 95% confidence intervalZ‐score −1.1 (−1.6 to −0.7) at the lumbar spine, −1.0 (−1.3 to −0.7) at the total hip, and −1.1 (−1.4 to −0.8) at the total body,P < 0.001 at each site]. BMD in the women taking MMT was not different from control values. Bone turnover was within the normal range in both genders. Serum testosterone was lower in the men taking MMT than in controls.

Conclusions BMD is lower than normal throughout the skeleton in men, but not women, taking MMT. Assessment of skeletal health, including estimation of absolute fracture risk, should be undertaken in men participating in methadone maintenance programmes.
The impact of elective knee/hip replacement surgery and thromboprophylaxis with rivaroxaban or dalteparin on thrombin generation
Authors: Green Laura , Lawrie Andrew S. , Patel Shelain , Hossain Fahad , Chitolie Andrew , Mackie Ian J. , Haddad Fares S. , Machin Samuel J.
Published: October 2010

Total hip/knee replacement surgeries are associated with an increased risk of venous thromboembolism and post‐operative thromboprophylaxis has become standard treatment. This study aimed to: (i) assess the impact of hip/knee replacement surgery on ex vivo thrombin generation (TG), prothrombin fragments 1 + 2 (F1 + 2), thrombin‐antithrombin complexes (TAT) and D‐dimer; (ii) compare the anticoagulant effects of dalteparin and rivaroxaban on TG 24 h after surgery. Haemostatic variables were assessed in plasma samples of 51 patients taken pre‐operatively, peri‐operatively, and 24 h post‐operatively. Prophylaxis, once a day, with dalteparin or rivaroxaban, starting 6–8 h post‐operatively, was administered in 25 (14 knee/11 hip) and 26 patients (13 knee/13 hip) respectively. TG, F1 + 2, TAT and D‐dimer increased during surgery. Dalteparin patients showed a variable TG response 24 h after surgery: conversely, the effect of rivaroxaban on TG was consistent across individuals. Good correlation was seen between rivaroxaban levels and TG‐lag‐time (rs = 0·46, P = 0·01); TG‐time‐to‐Peak (rs = 0·53, P = 0·005); TG‐peak‐thrombin (rs = −0·59, P = 0·001); and TG‐velocity‐index‐rate (rs = −0·61, P = 0·0009). Patients who received rivaroxaban showed a greater decrease of TG, F1 + 2 and TAT (but not D‐dimer) than those on dalteparin. TG increases during hip/knee replacement surgery. Rivaroxaban inhibits TG more than dalteparin at 24 h after surgery.
Freshwater conservation planning: an introduction
Authors: TURAK EREN , LINKE SIMON
Published: October 2010

1. Global freshwater biodiversity is facing rapid decline. Freshwater conservation planning aims to reduce this decline by efficiently prioritising conservation actions.

2. This Special Issue presents nine papers from five continents demonstrating a wide range of approaches to spatial prioritisation for freshwater conservation and two papers that explore directions for research and implementation in conservation planning.

3. Despite an emphasis on running waters and data‐rich regions, these papers collectively offer a wide range of perspectives for advancing the science and practice of systematic conservation planning across freshwater realms, including data‐poor regions and standing‐water ecosystems.
Fostering real‐world clinical mental health research
Authors: Cleary Michelle , Hunt Glenn E , Walter Garry , Jackson Debra
Published: October 2010

Aims and objectives.  In this article, we identify key aspects for enhancing real‐world research in mental health care clinical settings and broadly discuss some practicalities and issues that must be considered beforehand.

Background.  Practice which is evidence‐based uses interventions or treatment methods that are supported by research findings for their quality and efficacy. Modern mental health settings endorse evidence‐based practice and welcome the development of innovative, evidence‐based approaches to care. Often, however, research findings are inaccessible, inconclusive, inconsistent, contradictory and overwhelming in sheer volume. Further, where there is no evidence, the absence of evidence is frequently mistaken for evidence of absence of the effectiveness of services.

Design.  Discursive paper.

Method.  The main themes expressed in the literature were collated by the authors into themes, and their relevance to the development of real‐world clinical mental health research is summarised with the aid of a vignette.

Conclusions.  Ideally, research should be part of mainstream activities and as such constitute core business. Staff in mental health services should be encouraged to be research productive, and prospective clinical researchers should consider linking their studies to higher research degree programmes so that they can access resources, support and expertise to sustain motivation and morale.

Relevance to clinical practice.  For research findings to make the leap to evidence‐based practice, the research needs to include real‐world consumers and families typical of clinical practice supported by clinically relevant outcomes. Clinical and research leaders should create opportunities for academic and clinical nurses to collaborate in research, and researchers should ensure that clinically relevant outcomes are presented in ways that are meaningful and accessible to clinicians.
Defining the role of a FYVE domain in the localization and activity of a cAMP phosphodiesterase implicated in osmoregulation in Trypanosoma cruzi
Authors: Schoijet Alejandra C. , Miranda Kildare , Medeiros Lia Carolina Soares , de Souza Wanderley , Flawiá Mirtha M. , Torres Héctor N. , Pignataro Omar P. , Docampo Roberto , Alonso Guillermo D.
Published: October 2010

Intracellular levels of cyclic nucleotide second messengers are regulated predominantly by a large superfamily of phosphodiesterases (PDEs). Trypanosoma cruzi, the causative agent of Chagas disease, encodes four different PDE families. One of these PDEs, T. cruzi PDE C2 (TcrPDEC2) has been characterized as a FYVE domain containing protein. Here, we report a novel role for TcrPDEC2 in osmoregulation in T. cruzi and reveal the relevance of its FYVE domain. Our data show that treatment of epimastigotes with TcrPDEC2 inhibitors improves their regulatory volume decrease, whereas cells overexpressing this enzyme are unaffected by the same inhibitors. Consistent with these results, TcrPDEC2 localizes to the contractile vacuole complex, showing strong labelling in the region corresponding to the spongiome. Furthermore, transgenic parasites overexpressing a truncated version of TcrPDEC2 without the FYVE domain show a failure in its targeting to the contractile vacuole complex and a marked decrease in PDE activity, supporting the importance of this domain to the localization and activity of TcrPDEC2. Taking together, the results here presented are consistent with the importance of the cyclic AMP signalling pathway in regulatory volume decrease and implicate TcrPDEC2 as a specifically localized PDE involved in osmoregulation in T. cruzi.
Feasibility and reliability of classifying gross motor function among children with cerebral palsy using population‐based record surveillance
Authors: Benedict Ruth E. , Patz Jean , Maenner Matthew J. , Arneson Carrie L. , Yeargin‐Allsopp Marshalyn , Doernberg Nancy S. , Van Naarden Braun Kim , Kirby Russell S. , Durkin Maureen S.
Published: October 2010

Benedict RE, Patz J, Maenner MJ, Arneson CL, Yeargin‐Allsopp M, Doernberg NS, Van Naarden Braun K, Kirby RS, Durkin MS. Feasibility and reliability of classifying gross motor function among children with cerebral palsy using population‐based record surveillance. Paediatric and Perinatal Epidemiology 2010.

For conditions with wide‐ranging consequences, such as cerebral palsy (CP), population‐based surveillance provides an estimate of the prevalence of case status but only the broadest understanding of the impact of the condition on children, families or society. Beyond case status, information regarding health, functional skills and participation is necessary to fully appreciate the consequences of the condition. The purpose of this study was to assess the feasibility and reliability of enhancing population‐based surveillance by classifying gross motor function (GMF) from information available in medical records of children with CP.

We assessed inter‐rater reliability of two GMF classification methods, one the Gross Motor Function Classification System (GMFCS) and the other a 3‐category classification of walking ability: (1) independently, (2) with handheld mobility device, or (3) limited or none. Two qualified clinicians independently reviewed abstracted evaluations from medical records of 8‐year‐old children residing in southeast Wisconsin, USA who were identified as having CP (n = 154) through the Centers for Disease Control and Prevention's Autism and Developmental Disabilities Monitoring Network. Ninety per cent (n = 138) of the children with CP had information in the record after age 4 years and 108 (70%) had adequate descriptions of gross motor skills to classify using the GMFCS. Agreement was achieved on 75.0% of the GMFCS ratings (simple kappa = 0.67, 95% confidence interval [95% CI 0.57, 0.78], weighted kappa = 0.83, [95% CI 0.77, 0.89]). Among case children for whom walking ability could be classified (n = 117), approximately half walked independently without devices and one‐third had limited or no walking ability. Across walking ability categories, agreement was reached for 94% (simple kappa = 0.90, [95% CI 0.82, 0.96], weighted kappa = 0.94, [95% CI 0.89, 0.98]).

Classifying GMF in the context of active records‐based surveillance is feasible and reliable. Future surveillance efforts that include functional level among children with cerebral palsy may provide important information for monitoring the impact of the condition for programmatic and policy purposes.
A new filter that accurately mimics the solar UV‐B spectrum using standard UV lamps: the photochemical properties, stabilization and use of the urate anion liquid filter
Authors: SAMPATH‐WILEY PRIYA , JAHNKE LELAND S.
Published: October 2010

The physiological effects unique to solar ultraviolet (UV)‐B exposure (280–315 nm) are difficult to accurately replicate in the laboratory. This study evaluates the effectiveness of the sodium urate anion in a liquid filter that yields a spectrum nearly indistinguishable from the solar UV‐B spectrum while filtering the emissions of widely used UV‐B lamps. The photochemical properties and stability of this filter are examined and weighed against a typical spectrum of ground‐level solar UV‐B radiation. To test the effectiveness of this filter, light‐saturated photosynthetic oxygen evolution rates were measured following exposure to UV‐B filtered either by this urate filter or the widely used cellulose acetate (CA) filter. The ubiquitous marine Chlorophyte alga Dunaliella tertiolecta was tested under identical UV‐B flux densities coupled with ecologically realistic fluxes of UV‐A and visible radiation for 6 and 12 h exposures. These results indicate that the urate‐filtered UV‐B radiation yields minor photosynthetic inhibition when compared with exposures lacking in UV‐B. This is in agreement with published experiments using solar radiation. In sharp contrast, radiation filtered by CA filters produced large inhibition of photosynthesis.
Intraindividual variability in Sinonamuropteridae forewing venation (Grylloblattida; Late Carboniferous): taxonomic and nomenclatural implications
Authors: CUI YINGYING , BÉTHOUX OLIVIER , REN DONG
Published: October 2010

The family Sinonamuropteridae has been erected for nine fossil insect species from the Late Carboniferous Tupo Formation (Ningxia, China), each represented by a single isolated forewing. The family has been assigned to the order Diaphanopterodea (extinct palaeopteran order). We investigated the forewing venation pattern and its variability in this family based on an abundant collection from the same locality. Based on new data on Chelopterum peregrinumCarpenter, 1950 (Grylloblattida; Lower Permian; Wellington Formation, U.S.A.) and the new material, we demonstrate that the nine sinonamuropteridaean species form a single one: Sinonamuropteris ningxiaensisPeng et al., 2005. The following genera are considered as synonyms of Sinonamuropteris: SeparatonervaPeng et al., 2005syn.n., CombonervaPeng et al., 2005syn.n. and TectonervaPeng et al., 2005syn.n. The following species (all with Peng et al., 2005, as their authority) are considered as synonyms of S. ningxiaensis: Separatonerva longasyn.n., Separatonerva qilianshanensissyn.n., Combonerva granulatasyn.n., Combonerva huangheensissyn.n., Tectonerva longovatasyn.n., Sinonamuropsis zhongweiensissyn.n., Sinonamuropsis rugoverrucosasyn.n., Sinonamuropsis xiaheyanensissyn.n. The family must be assigned to the neopteran order Grylloblattida.
Temperature controls nuclear import of Tam3 transposase in Antirrhinum
Authors: Fujino Kaien , Hashida Shin‐nosuke , Ogawa Takashi , Natsume Tomoko , Uchiyama Takako , Mikami Tetsuo , Kishima Yuji
Published: October 2010

It has been proposed that environmental stimuli can activate transposable elements (TEs), whereas few substantial mechanisms have been shown so far. The class‐II element Tam3 from Antirrhinum majus exhibits a unique property of low‐temperature‐dependent transposition (LTDT). LTDT has proved invaluable in developing the gene isolation technologies that have underpinned much of modern plant developmental biology. Here, we reveal that LTDT involves differential subcellular localization of the Tam3 transposase (TPase) in cells grown at low (15°C) and high (25°C) temperatures. The mechanism is associated with the nuclear import of Tam3 TPase in Antirrhinum cells. At high temperature, the nuclear import of Tam3 TPase is severely restricted in Antirrhinum cells, whereas at low temperature, the nuclear localization of Tam3 TPase is observed in about 20% of the cells. However, in tobacco BY‐2 and Allium cepa (onion) cells, Tam3 TPase is transported into most nuclei. In addition to three nuclear localization signals (NLSs), the Tam3 TPase is equipped with a nuclear localization inhibitory domain (NLID), which functions to abolish nuclear import of the TPase at high temperature in Antirrhinum. NLID in Tam3 TPase is considered to interact with Antirrhinum‐specific factor(s). The host‐specific regulation of the nuclear localization of transposase represents a new repertoire controlling class‐II TEs.
Two putatively homoeologous wheat genes mediate recognition of SnTox3 to confer effector‐triggered susceptibility to Stagonospora nodorum
Authors: Zhang Zengcui , Friesen Timothy L. , Xu Steven S. , Shi Gongjun , Liu Zhaohui , Rasmussen Jack B. , Faris Justin D.
Published: October 2010

The pathogen Stagonospora nodorum produces multiple effectors, also known as host‐selective toxins (HSTs), that interact with corresponding host sensitivity genes in an inverse gene‐for‐gene manner to cause the disease Stagonospora nodorum blotch (SNB) in wheat. In this study, a sensitivity gene was identified in Aegilops tauschii, the diploid D‐genome donor of common wheat. The gene was mapped to the short arm of chromosome 5D and mediated recognition of the effector SnTox3, which was previously shown to be recognized by the wheat gene Snn3 on chromosome arm 5BS. Comparative mapping suggested that Snn3 and the gene on 5DS are probably homoeologous and derived from a common ancestor. Therefore, we propose to designate these genes as Snn3‐B1 and Snn3‐D1, respectively. Compatible Snn3‐D1–SnTox3 interactions resulted in more severe necrosis in both effector infiltration and spore inoculation experiments than compatible Snn3‐B1–SnTox3 interactions, indicating that Snn3‐B1 and Snn3‐D1 may have different affinities in SnTox3 recognition or signal transduction. Wheat bin‐mapped expressed sequence tags and good levels of collinearity among the wheat Snn3 regions, rice (Oryza sativa), and Brachypodium distachyon were exploited for saturation and fine mapping of the Snn3‐D1 locus. Markers delineating the Snn3‐D1 locus to a 1.4 cM interval will be useful for initiating positional cloning. Further characterization of how these homoeologous genes mediate recognition of the same pathogen effector should enhance understanding of host manipulation by necrotrophic pathogens in causing disease.
Behavioural Interactions and Hormones in Naturally and Hatchery‐Spawned Chinook Salmon
Authors: Garner Shawn R. , Madison Barry N. , Bernier Nicholas J. , Neff Bryan D.
Published: October 2010

Artificial breeding programmes commonly lead to domestication, which is associated with many behavioural differences that can reduce the success of animals released into natural environments. To better understand the factors contributing to domestication, we used a captive population of Chinook salmon (Oncorhynchus tshawytscha) to partition hormonal and behavioural differences to effects of the breeding method and rearing environment. We compared 9‐mo‐old juveniles from three lines that shared a common genetic background: (1) the Channel line produced by natural spawning and reared in a low‐density environment with a natural substrate for approx. 6 mo before being transferred to the hatchery; (2) the Hatchery line produced by artificial spawning; and (3) the Transfer line produced by natural spawning but reared in the hatchery from the eyed‐egg stage. Plasma concentrations of 11‐ketotestosterone (11‐KT) and cortisol were measured in groups of 150 fish and again after 4 d of social interactions in groups of six fish. There was no difference in 11‐KT among lines in large groups, but in small groups, Transfer fish had lower 11‐KT concentrations and were significantly less aggressive than both Channel and Hatchery fish. Regardless of group size, concentrations of the stress hormone cortisol were nearly twofold higher in Channel fish than in Hatchery and Transfer fish. Furthermore, the elevated cortisol concentrations in Channel fish were associated with 35% lower feeding rates than in the other two lines. Our study details complex behavioural and hormonal responses to breeding method and rearing environment in juvenile salmon.
Sounds Modulate Males’ Aggressiveness in a Cichlid Fish
Authors: Bertucci Frédéric , Beauchaud Marilyn , Attia Joël , Mathevon Nicolas
Published: October 2010

Acoustic signals are produced in many fish species during agonistic or courtship interactions. A way to test the biological role of these sounds is the use of acoustic playback experiments. However, sounds are usually associated with visual displays and playback experiments performed in fish so far, often failed to match acoustic and visual stimuli. To avoid this mismatch issue, we experimentally separated or coupled visual and acoustic channels to test the role of sounds produced during male–male aggressive interactions in a cichlid fish, Metriaclima zebra. Results show that aggressive behaviour is based on visual stimuli and that acoustic signals alone never trigger aggression. Furthermore, the association between visual and acoustic channels lowers the level of aggressiveness found when fish can only interact visually. This suggests that acoustic signals used during a dispute may complement visual displays to modulate males’ behaviour by reducing their aggressiveness and the risk of escalated fights.
Continuous and intermittent transcranial magnetic theta burst stimulation modify tactile learning performance and cortical protein expression in the rat differently
Authors: Mix Annika , Benali Alia , Eysel Ulf T. , Funke Klaus
Published: October 2010

Repetitive transcranial magnetic stimulation (rTMS) can modulate cortical excitability in a stimulus‐frequency‐dependent manner. Two kinds of theta burst stimulation (TBS) [intermittent TBS (iTBS) and continuous TBS (cTBS)] modulate human cortical excitability differently, with iTBS increasing it and cTBS decreasing it. In rats, we recently showed that this is accompanied by changes in the cortical expression of proteins related to the activity of inhibitory neurons. Expression levels of the calcium‐binding protein parvalbumin (PV) and of the 67‐kDa isoform of glutamic acid decarboxylase (GAD67) were strongly reduced following iTBS, but not cTBS, whereas both increased expression of the 65‐kDa isoform of glutamic acid decarboxylase. In the present study, to investigate possible functional consequences, we applied iTBS and cTBS to rats learning a tactile discrimination task. Conscious rats received either verum or sham rTMS prior to the task. Finally, to investigate how rTMS and learning effects interact, protein expression was determined for cortical areas directly involved in the task and for those either not, or indirectly, involved. We found that iTBS, but not cTBS, improved learning and strongly reduced cortical PV and GAD67 expression. However, the combination of learning and iTBS prevented this effect in those cortical areas involved in the task, but not in unrelated areas. We conclude that the improved learning found following iTBS is a result of the interaction of two effects, possibly in a homeostatic manner: a general weakening of inhibition mediated by the fast‐spiking interneurons, and re‐established activity in those neurons specifically involved in the learning task, leading to enhanced contrast between learning‐induced and background activity.