Information theory analysis of Australian humpback whale song

Songs produced by migrating whales were recorded off the coast of Queensland, Australia, over six consecutive weeks in 2003. Forty-eight independent song sessions were analyzed using information theory techniques. The average length of the songs estimated by correlation analysis was approximately 100 units, with song sessions lasting from 300 to over 3100 units. Song entropy, a measure of structural constraints, was estimated using three different methodologies: (1) the independently identically distributed model, (2) a first-order Markov model, and (3) the nonparametric sliding window match length (SWML) method, as described by Suzuki et al. [(2006). “Information entropy of humpback whale song,” J. Acoust. Soc. Am. 119, 1849–1866]. The analysis finds that the song sequences of migrating Australian whales are consistent with the hierarchical structure proposed by Payne and McVay [(1971). “Songs of humpback whales,” Science 173, 587–597], and recently supported mathematically by Suzuki et al. (2006) for singers on the Hawaiian breeding grounds. Both the SWML entropy estimates and the song lengths for the Australian singers in 2003 were lower than that reported by Suzuki et al. (2006) for Hawaiian whales in 1976–1978; however, song redundancy did not differ between these two populations separated spatially and temporally. The average total information in the sequence of units in Australian song was approximately 35 bits/song. Aberrant songs (8%) yielded entropies similar to the typical songs

Earlier age of dementia onset and shorter survival times in dementia patients with diabetes

Diabetes is a risk factor for dementia, but relatively little is known about the epidemiology of the association. A retrospective population study using Western Australian hospital inpatient, mental health outpatient, and death records was used to compare the age at index dementia record (proxy for onset age) and survival outcomes in dementia patients with and without preexisting diabetes (n = 25,006; diabetes, 17.3%). Inpatient records from 1970 determined diabetes history in this study population with incident dementia in years 1990–2005. Dementia onset and death occurred an average 2.2 years and 2.6 years earlier, respectively, in diabetic compared with nondiabetic patients. Age-specific mortality rates were increased in patients with diabetes. In an adjusted proportional hazard model, the death rate was increased with long-duration diabetes, particularly with early age onset dementia. In dementia diagnosed before age 65 years, those with a ≥15-year history of diabetes died almost twice as fast as those without diabetes (hazard ratio = 1.9, 95% confidence interval: 1.3, 2.9). These results suggest that, in patients with diabetes, dementia onset occurs on average 2 years early and survival outcomes are generally poorer. The effect of diabetes on onset, survival, and mortality is greatest when diabetes develops before middle age and after 15 years’ diabetes duration. The impact of diabetes on dementia becomes progressively attenuated in older age groups

Ratio-Based Analysis of Differential mRNA Processing and Expression of a Polyadenylation Factor Mutant pcfs4 Using Arabidopsis Tiling Microarray

US National Institutes of Health [1R15GM07719201A1]; US National Science Foundation [IOS-0817818]; Ohio Plant Biotech Consortium; National Natural Science Foundation of China [60774033]; Specialized Research Fund for the Doctoral Program of Higher EducatiBackground: Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized in recent years. Arabidopsis polyadenylation factor PCFS4 was shown to function in leaf development and in flowering time control. The function of PCFS4 in controlling flowering time was correlated with the alternative polyadenylation of FCA, a flowering time regulator. However, genetic evidence suggested additional targets of PCFS4 that may mediate its function in both flowering time and leaf development. Methodology/Principal Findings: To identify further targets, we investigated the whole transcriptome of a PCFS4 mutant using Affymetrix Arabidopsis genomic tiling 1.0R array and developed a data analysis pipeline, termed RADPRE (Ratio-based Analysis of Differential mRNA Processing and Expression). In RADPRE, ratios of normalized probe intensities between wild type Columbia and a pcfs4 mutant were first generated. By doing so, one of the major problems of tiling array data-variations caused by differential probe affinity-was significantly alleviated. With the probe ratios as inputs, a hierarchy of statistical tests was carried out to identify differentially processed genes (DPG) and differentially expressed genes (DEG). The false discovery rate (FDR) of this analysis was estimated by using the balanced random combinations of Col/pcfs4 and pcfs4/Col ratios as inputs. Gene Ontology (GO) analysis of the DPGs and DEGs revealed potential new roles of PCFS4 in stress responses besides flowering time regulation. Conclusion/Significance: We identified 68 DPGs and 114 DEGs with FDR at 1% and 2%, respectively. Most of the 68 DPGs were subjected to alternative polyadenylation, splicing or transcription initiation. Quantitative PCR analysis of a set of DPGs confirmed that most of these genes were truly differentially processed in pcfs4 mutant plants. The enriched GO term "regulation of flower development'' among PCFS4 targets further indicated the efficacy of the RADPRE pipeline. This simple but effective program is available upon request

Mid- and Late-Life Diabetes in Relation to the Risk of Dementia: A Population-Based Twin Study

OBJECTIVE—We aimed to verify the association between diabetes and the risk of dementia, Alzheimer's disease, and vascular dementia in twins and to explore whether genetic and early-life environmental factors could contribute to this association

Diabetes Is Associated with Cerebrovascular but not Alzheimer\u27s Disease Neuropathology

INTRODUCTION: The relationship of diabetes to specific neuropathologic causes of dementia is incompletely understood. METHODS: We used logistic regression to evaluate the association between diabetes and infarcts, Braak neurofibrillary tangle stage, and neuritic plaque score in 2365 autopsied persons. In a subset of \u3e1300 persons with available cognitive data, we examined the association between diabetes and cognition using Poisson regression. RESULTS: Diabetes increased odds of brain infarcts (odds ratio [OR] = 1.57, P \u3c .0001), specifically lacunes (OR = 1.71, P \u3c .0001), but not Alzheimer\u27s disease neuropathology. Diabetes plus infarcts was associated with lower cognitive scores at end of life than infarcts or diabetes alone, and diabetes plus high level of Alzheimer\u27s neuropathologic changes was associated with lower mini-mental state examination scores than the pathology alone. DISCUSSION: This study supports the conclusions that diabetes increases the risk of cerebrovascular but not Alzheimer\u27s disease pathology, and at least some of diabetes\u27 relationship to cognitive impairment may be modified by neuropathology

Mobility, Expansion and Management of a Multi-Species Scuba Diving Fishery in East Africa

Background: Scuba diving fishing, predominantly targeting sea cucumbers, has been documented to occur in an uncontrolled manner in the Western Indian Ocean and in other tropical regions. Although this type of fishing generally indicates a destructive activity, little attention has been directed towards this category of fishery, a major knowledge gap and barrier to management. Methodology and Principal Findings: With the aim to capture geographic scales, fishing processes and social aspects the scuba diving fishery that operate out of Zanzibar was studied using interviews, discussions, participant observations and catch monitoring. The diving fishery was resilient to resource declines and had expanded to new species, new depths and new fishing grounds, sometimes operating approximately 250 km away from Zanzibar at depths down to 50 meters, as a result of depleted easy-access stock. The diving operations were embedded in a regional and global trade network, and its actors operated in a roving manner on multiple spatial levels, taking advantage of unfair patron-client relationships and of the insufficient management in Zanzibar. Conclusions and Significance: This study illustrates that roving dynamics in fisheries, which have been predominantly addressed on a global scale, also take place at a considerably smaller spatial scale. Importantly, while proposed management of the sea cucumber fishery is often generic to a simplified fishery situation, this study illustrates

Genetic Architecture of Hybrid Male Sterility in Drosophila: Analysis of Intraspecies Variation for Interspecies Isolation

Background: The genetic basis of postzygotic isolation is a central puzzle in evolutionary biology. Evolutionary forces causing hybrid sterility or inviability act on the responsible genes while they still are polymorphic, thus we have to study these traits as they arise, before isolation is complete. Methodology/Principal Findings: Isofemale strains of D. mojavensis vary significantly in their production of sterile F 1 sons when females are crossed to D. arizonae males. We took advantage of the intraspecific polymorphism, in a novel design, to perform quantitative trait locus (QTL) mapping analyses directly on F1 hybrid male sterility itself. We found that the genetic architecture of the polymorphism for hybrid male sterility (HMS) in the F1 is complex, involving multiple QTL, epistasis, and cytoplasmic effects. Conclusions/Significance: The role of extensive intraspecific polymorphism, multiple QTL, and epistatic interactions in HMS in this young species pair shows that HMS is arising as a complex trait in this system. Directional selection alone would be unlikely to maintain polymorphism at multiple loci, thus we hypothesize that directional selection is unlikely to be the only evolutionary force influencing postzygotic isolation

X chromosomal regulation in flies: when less is more

In Drosophila, dosage compensation of the single male X chromosome involves upregulation of expression of X linked genes. Dosage compensation complex or the male specific lethal (MSL) complex is intimately involved in this regulation. The MSL complex members decorate the male X chromosome by binding on hundreds of sites along the X chromosome. Recent genome wide analysis has brought new light into X chromosomal regulation. It is becoming increasingly clear that although the X chromosome achieves male specific regulation via the MSL complex members, a number of general factors also impinge on this regulation. Future studies integrating these aspects promise to shed more light into this epigenetic phenomenon

Diabetes and the Risk of Multi-System Aging Phenotypes: A Systematic Review and Meta-Analysis

[[abstract]]Background: Observational studies suggested an association between diabetes and the risk of various geriatric conditions (i.e., cognitive impairment, dementia, depression, mobility impairment, disability, falls, and urinary incontinence). However, the magnitude and impact of diabetes on older adults have not been reviewed. Methodology/Principal Findings: MEDLINE and PSYCINFO databases were searched through November 2007 for published studies, supplemented by manual searches of bibliographies of key articles. Population-based, prospective cohort studies that reported risk of geriatric outcomes in relation to diabetes status at baseline were selected. Two authors independently extracted the data, including study population and follow-up duration, ascertainment of diabetes status at baseline, outcomes of interest and their ascertainment, adjusted covariates, measures of association, and brief results. Fifteen studies examined the association of DM with cognitive dysfunction. DM was associated with a faster decline in cognitive function among older adults. The pooled adjusted risk ratio (RR) for all dementia when persons with DM were compared to those without was 1.47 (95% CI, 1.25 to 1.73). Summary RRs for Alzheimer's disease and vascular dementia comparing persons with DM to those without were 1.39 (CI, 1.16 to 1.66) and 2.38 (CI, 1.79 to 3.18), respectively. Four of 5 studies found significant association of DM with faster mobility decline and incident disability. Two studies examined the association of diabetes with falls in older women. Both found statistically significant associations. Insulin users had higher RR for recurrent falls. One study for urinary incontinence in older women found statistically significant associations. Two studies for depression did not suggest that DM was an independent predictor of incident depression. Conclusions/Significance: Current evidence supports that DM is associated with increased risk for selected geriatric conditions. Clinicians should increase their awareness and provide appropriate care. Future research is required to elucidate the underlying pathological pathway. 2009 Lu et al