Leaf palatability and decomposability increase during a 200‐year‐old post‐cultural woody succession in New Zealand

Question: How do aggregate trait values and functional diversity of leaf traits linked to palatability and decomposability change during a woody post‐cultural succession spanning 200 years? Location: Coastal Marlborough, South Island, New Zealand. Methods: The biomass of all woody species was determined in 32 20‐m × 20‐m plots ranging from 10 to 200 years in time since last disturbance. Species abundances were combined with data on leaf nutrient, secondary metabolite and structural carbohydrate content to calculate biomass‐weighted trait means (i.e. aggregate trait values) and functional diversity index values for each plot. Aggregate trait values and functional diversity were regressed on successional age and total live above‐ground carbon content to examine functional shifts with succession and one consequence of succession – increasing above‐ground carbon. Results: Almost all significant regressions between aggregate trait values and both successional age and above‐ground carbon indicated a shift toward increased leaf palatability and decomposability during succession. The relationships were all non‐linear, with aggregate trait value shifts occurring relatively early in the successional sequence. There was weak evidence for an increase in functional richness with succession, but this was a secondary effect relative to the shifts in aggregate trait values. Conclusions: These results are in direct contrast with studies of the early stages of herbaceous post‐cultural successions from grasslands to shrublands, which have found a shift towards communities of decreasing palatability and decomposability, suggesting that functional shifts in woody succession may be fundamentally different.     

Visual contrast sensitivity in patients with impairment of functional independence after stroke

ABSTRACT: BACKGROUND: Stroke has been considered a serious public health problem in many countries, accounting for complex disorders involving perception, such as visual, cognitive and functional deficits. The impact of stroke on the visual perception of individuals with impairments in functional independence was investigated. METHODS: We measured changes in functional independence and visual function in 40 patients with stroke (M = 52.3, SD = 0.65) and 10 controls (M = 52.5, SD = 0.66). The patients were divided into four subgroups following the Barthel Index (Group A: 20--35, serious dependence; Group B: 40--55, moderate dependence; Group C: 60--95, mild dependence; and Group D: 100 points, independence). Visual function was evaluated using the Contrast Sensitivity Function (CSF). The contrast threshold was measured using a temporal, two-alternative, forced-choice psychophysical method. RESULTS: The results show significant differences in CSF between healthy volunteers and patients with stroke (F (1.56) = 151.2, p < 0.001) for all frequencies (F (2.56) = 125.96, p < 0.001). The results also show that patients with low functional independence had lower contrast sensitivity than those with greater functional independence (F (3.56) = 344.82, p < 0.001). CONCLUSIONS: An association exists between CSF and a worsening in the functional potential for performing daily living activities. Our results suggest that the CSF can be used as a diagnostic tool to analyze visual function associated with deficits in functional independence after stroke. These findings should be considered across the continuum of care for these patients.     

An object model and database for functional genomics

MOTIVATION: Large-scale functional genomics analysis is now feasible and presents significant challenges in data analysis, storage and querying. Data standards are required to enable the development of public data repositories and to improve data sharing. There is an established data format for microarrays (microarray gene expression markup language, MAGE-ML) and a draft standard for proteomics (PEDRo). We believe that all types of functional genomics experiments should be annotated in a consistent manner, and we hope to open up new ways of comparing multiple datasets used in functional genomics. RESULTS: We have created a functional genomics experiment object model (FGE-OM), developed from the microarray model, MAGE-OM and two models for proteomics, PEDRo and our own model (Gla-PSI-Glasgow Proposal for the Proteomics Standards Initiative). FGE-OM comprises three namespaces representing (i) the parts of the model common to all functional genomics experiments; (ii) microarray-specific components; and (iii) proteomics-specific components. We believe that FGE-OM should initiate discussion about the contents and structure of the next version of MAGE and the future of proteomics standards. A prototype database called RNA And Protein Abundance Database (RAPAD), based on FGE-OM, has been implemented and populated with data from microbial pathogenesis. AVAILABILITY: FGE-OM and the RAPAD schema are available from http://www.gusdb.org/fge.html, along with a set of more detailed diagrams. RAPAD can be accessed by registration at the site.     

Models for loosely linked gene duplicates suggest lengthy persistence of both copies

Consider the appearance of a duplicate copy of a gene at a locus linked loosely, if at all, to the locus at which the gene is usually found. If all copies of the gene are subject to non-functionalizing mutations, then two fates are possible: loss of functional copies at the duplicate locus (loss of duplicate expression), or loss of functional copies at the original locus (map change). This paper proposes a simple model to address the probability of map change, the time taken for a map change and/or loss of duplicate expression, and considers where in the spectrum between loss of duplicate expression and map change such a duplicate complex is likely to be found. The findings are: the probability of map change is always half the reciprocal of the population size N, the time for a map change to occur is order NlogN generations, and that there is a marked tendency for duplicates to remain near equi-frequency with the gene at the original locus for a large portion of that time. This is in excellent agreement with simulations.     

Effect of hamstring-emphasized resistance training on hamstring:quadriceps strength ratios

A decreased hamstring:quadriceps (H:Q) ratio may put the hamstrings and anterior cruciate ligament (ACL) at increased risk of injury. Therefore, the purpose of this study was to evaluate H:Q ratios of 12 female National Collegiate Athletic Association soccer players, and to test the effects of a 6-week strength training program on these ratios. Each subject completed 2 practice sessions before a pretest. Subjects then completed 6 weeks of strength training that included the addition of 2 hamstring specific exercises, followed by a posttest. Peak torque during concentric and eccentric actions for both hamstrings and quadriceps was measured with an isokinetic dynamometer. Each muscle action was tested at 3 angular velocities in the following order: concentric 240, 180, and 60 degrees x s(-1) and eccentric 60, 180, and 240 degrees x s(-1). The H:Q strength ratio was evaluated using concentric muscle actions (concentric hamstrings:concentric quadriceps). This method is commonly used and is thus called the conventional ratio. Because concentric actions do not occur simultaneously in opposing muscles, a more functional assessment compares eccentric hamstring actions to concentric quadriceps actions. This functional ratio was also analyzed. Mean conventional and functional H:Q ratio data were analyzed using separate analysis of variance procedures with repeated measures on all factors (2 [Test] x 2 [Leg] x 3 [Angular Velocity]). The results revealed a significant main effect for factor (F test) with the functional ratio (p < 0.05) but not for the conventional ratio. The mean functional ratio increased from 0.96 +/- 0.09 in pretest to 1.08 +/- 0.11 in posttest. These results suggest that 6 weeks of strength training that emphasizes hamstrings is sufficient to significantly increase the functional ratio. The functional ratio after training exceeded 1.0, which is specifically recommended for prevention of ACL injuries.     

The development of a method for functional assessment of dentures

Aims: To design and validate a method of assessing complete dentures from a functional standpoint. Subjects: A random sample of 40 complete denture wearers took part in the study. Setting: A university clinical department of prosthetic dentistry. Intervention: We undertook a pilot study to refine the protocol and criteria. All participants and their dentures were examined by two authors independently, with no prior knowledge of the patients'complaints. Design: We defined nine clinical factors of functional quality and applied criteria with binary scoring. We analysed the scores for these factors for inter‐rater reliability. Results: The method proved simple to apply and took less than 5 minutes to complete. The inter‐examiner agreement for all factors was 86% to 100% giving Kappa scores of 0.64 to 1.00 (all Good or Very Good). Conclusions: This study successfully demonstrates that the technique, which we call the Functional Assessment of Dentures (FAD), can give good inter‐examiner reliability. It can therefore be used separately as a routine diagnostic tool and to investigate the relationship between denture qualities and functional ‘outcome’ such as difficulty eating or dietary selection.     

Review of published studies of kidney,liver, and gastrointestinal birth defects in fetal alcohol spectrum disorders

OBJECTIVE: Review of published studies of birth defects of the renal, liver, and gastrointestinal organ systems in subjects with fetal alcohol spectrum disorders (FASD). METHOD: We searched PubMed ( http://www.pubmed.gov ) using the following terms: fetal alcohol syndrome and: gastrointestinal tract, kidney, liver, and congenital abnormalities for all years and English only citations. RESULTS: We located 12 studies of FASD and defects of or functional impairments for the liver, 12 of renal abnormalities, and only two with gastrointestinal defects. We did not identify specific patterns of malformations or functional deficits for any of the three organ systems. The existing literature suggests a series of nonspecific outcomes in FASD. CONCLUSIONS: Fetal alcohol spectrum disorder includes a diagnostic category of alcohol‐related birth defects which is clinically difficult to apply. This study adds to the existing literature on birth defects in FASD which is still very limited. The categorical diagnosis of alcohol‐related birth defects requires additional research to determine if a specific pattern of organ specific abnormalities or functional deficits emerges in subjects with FASD. Birth Defects Research (Part A), 2009. © 2009 Wiley‐Liss, Inc.     

DER: An algorithm for comparing species diversity between assemblages

There is no single diversity index that adequately summarises species diversity, since this is a multidimensional concept and hence should be quantified using a compound statistical measure. Here, we present the DER algorithm, available as an R package on CRAN and as an RWizard application on http://www.ipez.es/RWizard. This algorithm provides tools for differentiating assemblages on the basis of five compounds of diversity: rarity, heterogeneity, evenness, taxonomic/phylogenetic diversity and functional diversity. For all the samples, the algorithm calculates a total of 39 of the indices most often used. All indices of all samples are transformed to a scale range of between 0 and 1, and the algorithm calculates the polar coordinates of all samples with all possible combinations for all five groups of indices. Thus, for each combination, an index of rarity, heterogeneity (species richness is included in this group), evenness, taxonomic/phylogenetic diversity and functional diversity is used for each group to calculate the polar coordinates of all samples. When the polar coordinates of the samples are obtained for each combination, the convex hull and the mean Euclidean distance between samples are calculated. The algorithm selects the combination of indices with the highest value of the mean between convex hull and mean Euclidean distance between samples; priority is therefore given to maximising dispersion between the samples. The polar coordinates of the selected combination are depicted using a diagram from which it is possible to determine the differences in terms of rarity, heterogeneity, evenness, taxonomic/phylogenetic diversity and functional diversity between assemblages.     

ELISA: Structure-Function Inferences based on statistically significant and evolutionarily inspired observations

The problem of functional annotation based on homology modeling is primary to current bioinformatics research. Researchers have noted regularities in sequence, structure and even chromosome organization that allow valid functional cross-annotation. However, these methods provide a lot of false negatives due to limited specificity inherent in the system. We want to create an evolutionarily inspired organization of data that would approach the issue of structure-function correlation from a new, probabilistic perspective. Such organization has possible applications in phylogeny, modeling of functional evolution and structural determination. ELISA (Evolutionary Lineage Inferred from Structural Analysis, http://romi.bu.edu/elisa) is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function "neighborhoods". The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). We introduce a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.Availability: The database is available at http://romi.bu.edu/elisa.     

Inferring sub-cellular localization through automated lexical analysis

MOTIVATION: The SWISS-PROT sequence database contains keywords of functional annotations for many proteins. In contrast, information about the sub-cellular localization is available for only a few proteins. Experts can often infer localization from keywords describing protein function. We developed LOCkey, a fully automated method for lexical analysis of SWISS-PROT keywords that assigns sub-cellular localization. With the rapid growth in sequence data, the biochemical characterisation of sequences has been falling behind. Our method may be a useful tool for supplementing functional information already automatically available. RESULTS: The method reached a level of more than 82% accuracy in a full cross-validation test. Due to a lack of functional annotations, we could infer localization for fewer than half of all proteins in SWISS-PROT. We applied LOCkey to annotate five entirely sequenced proteomes, namely Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Arabidopsis thaliana (plant) and a subset of all human proteins. LOCkey found about 8000 new annotations of sub-cellular localization for these eukaryotes.     

Hierarchical tree snipping: clustering guided by prior knowledge

MOTIVATION: Hierarchical clustering is widely used to cluster genes into groups based on their expression similarity. This method first constructs a tree. Next this tree is partitioned into subtrees by cutting all edges at some level, thereby inducing a clustering. Unfortunately, the resulting clusters often do not exhibit significant functional coherence. RESULTS: To improve the biological significance of the clustering, we develop a new framework of partitioning by snipping--cutting selected edges at variable levels. The snipped edges are selected to induce clusters that are maximally consistent with partially available background knowledge such as functional classifications. Algorithms for two key applications are presented: functional prediction of genes, and discovery of functionally enriched clusters of co-expressed genes. Simulation results and cross-validation tests indicate that the algorithms perform well even when the actual number of clusters differs considerably from the requested number. Performance is improved compared with a previously proposed algorithm. AVAILABILITY: A java package is available at http://www.cs.bgu.ac.il/~dotna/ TreeSnipping     

VIS-O-BAC: exploratory visualization of functional genome studies from bacteria

SUMMARY: The visualization-aided exploration of complex datasets will allow the research community to formulate novel functional hypotheses leading to a better understanding of biological processes at all levels. Therefore, we have developed a web resource termed VIS-O-BAC designed for the functional investigation of expression data for model systems, such as bacterial pathogens based on a graphical display. Genome-scale datasets derived from typical 'omic' approaches can directly be explored with respect to three biologically relevant aspects, the genome structure (operon organization), the organization of genes in pathways (KEGG) and the gene function with Gene Ontology (GO) terms. The integrated viewers can be used in parallel and combine expression data and functional annotations from different external data repositories. The graphical visualizations evidently accelerate both the validation of regulatory information and the detection of affected biological processes. AVAILABILITY: http://leger2.gbf.de/cgi-bin/vis-o-bac.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Assessing the relative contribution of functional divergence and guild aggregation to overall functional structure of species assemblages

The study of functional structure in species assemblages emphasizes the detection of significant guild aggregation patterns. Thus, protocols based on intensive resampling of empirical data have been proposed to assess guild structure. Such protocols obtain the frequency distribution of a given functional similarity metric, and identify a threshold value (often the 95th percentile) beyond which clusters in a functional dendrogram are considered as significant guilds (using one-tailed tests). An alternative approach sequentially searches for significant differences between clusters at decreasing levels of similarity in a dendrogram until one is detected, then assumes that all subsequent nodes should also be significant. Nevertheless, these protocols do not test both the significance and sign of deviations from random at all levels of functional similarity within a dendrogram. Here, we propose a new bootstrapping approach that: (1) overcomes such pitfalls by performing two-tailed tests for each node in a dendrogram of functional similarity after separately determining their respective sample distributions, and (2) enables the quantification of the relative contribution of guild aggregation and functional divergence to the overall functional structure of the entire assemblage. We exemplify this approach by using long-term data on guild dynamics in a vertebrate predator assemblage of central Chile. Finally, we illustrate how the interpretation of functional structure is improved by applying this new approach to the data set available.     

Associations between Depressive State and Impaired Higher-Level Functional Capacity in the Elderly with Long-Term Care Requirements

Depressive state has been reported to be significantly associated with higher-level functional capacity among community-dwelling elderly. However, few studies have investigated the associations among people with long-term care requirements. We aimed to investigate the associations between depressive state and higher-level functional capacity and obtain marginal odds ratios using propensity score analyses in people with long-term care requirements. We conducted a cross-sectional study based on participants aged ≥65 years (n = 545) who were community dwelling and used outpatient care services for long-term preventive care. We measured higher-level functional capacity, depressive state, and possible confounders. Then, we estimated the marginal odds ratios (i.e., the change in odds of impaired higher-level functional capacity if all versus no participants were exposed to depressive state) by logistic models using generalized linear models with the inverse probability of treatment weighting (IPTW) for propensity score and design-based standard errors. Depressive state was used as the exposure variable and higher-level functional capacity as the outcome variable. The all absolute standardized differences after the IPTW using the propensity scores were <10% which indicated negligible differences in the mean or prevalence of the covariates between non-depressive state and depressive state. The marginal odds ratios were estimated by the logistic models with IPTW using the propensity scores. The marginal odds ratios were 2.17 (95%CI: 1.13–4.19) for men and 2.57 (95%CI: 1.26–5.26) for women. Prevention of depressive state may contribute to not only depressive state but also higher-level functional capacity.     

茄子功能性雄性不育的遗传及其与果紫色基因连锁关系的研究

采用新育成的茄子功能性雄性不育系uGA 1-MS和2个栽培品种,进行双亲本杂交世代遗传试验,发现F_1和B_2代植株皆雄性正常,B_2和F_2代可育株和不育株呈1:1和3:1分离,表明茄子功能性雄性不育性状由单隐性基因支配,用基因符号fms表示。连锁测验数据表明基因+/fms与果紫色基因X/x紧密连锁。预期该雄性不育性可在茄子杂种优势育种和种子生产上加以利用。