Speciation by host switch in brood parasitic indigobirds

A growing body of empirical and theoretical work supports the plausibility of sympatric speciation(1-3), but there remain few examples in which all the essential components of the process are well understood. The African indigobirds Vidua spp. are host-specific brood parasites. Indigobird nestlings are reared along with host young, and mimic the mouth markings of their respective hosts(4-6). As adults, male indigobirds mimic host song(4-7), whereas females use these songs to choose both their mates and the nests they parasitize(8). These behavioural mechanisms promote the cohesion of indigobird populations associated with a given host species, and provide a mechanism for reproductive isolation after a new host is colonized. Here we show that all indigobird species are similar genetically, but are significantly differentiated in both mitochondrial haplotype and nuclear allele frequencies. These data support a model of recent sympatric speciation. In contrast to the cuckoo Cuculus canorus, in which only female lineages are faithful to specific hosts(9,10), host switches have led to speciation in indigobirds because both males and females imprint on their hosts(8,11).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62510/1/nature01863.pd

A User-Friendly Hybrid Sparse Matrix Class in C++

When implementing functionality which requires sparse matrices, there are numerous storage formats to choose from, each with advantages and disadvantages. To achieve good performance, several formats may need to be used in one program, requiring explicit selection and conversion between the formats. This can be both tedious and error-prone, especially for non-expert users. Motivated by this issue, we present a user-friendly sparse matrix class for the C++ language, with a high-level application programming interface deliberately similar to the widely used MATLAB language. The class internally uses two main approaches to achieve efficient execution: (i) a hybrid storage framework, which automatically and seamlessly switches between three underlying storage formats (compressed sparse column, coordinate list, Red-Black tree) depending on which format is best suited for specific operations, and (ii) template-based meta-programming to automatically detect and optimise execution of common expression patterns. To facilitate relatively quick conversion of research code into production environments, the class and its associated functions provide a suite of essential sparse linear algebra functionality (eg., arithmetic operations, submatrix manipulation) as well as high-level functions for sparse eigendecompositions and linear equation solvers. The latter are achieved by providing easy-to-use abstractions of the low-level ARPACK and SuperLU libraries. The source code is open and provided under the permissive Apache 2.0 license, allowing unencumbered use in commercial products

Diabetes mellitus and prostate cancer risk among older men: population-based case–control study

We investigate the relation between diabetes mellitus and risk of prostate cancer among older (age 65–79 years) men in a population-based case–control study of 407 incident histologically confirmed cases registered in the South Carolina Central Cancer Registry between 1999 and 2001 (70.6% response rate); controls were 393 men identified through the Health Care Financing Administration Medicare beneficiary file for South Carolina in 1999 (63.8% response rate). After adjusting for age, race, and prostate cancer screening in the past 5 years, a history of diabetes mellitus was associated with a reduced risk of prostate cancer (adjusted odds ratio (aOR)¼0.64; 95% confidence interval (CI)¼0.45, 0.91). The protective effect was stronger for those with complications associated with diabetes (aOR¼0.61; 95% CI¼0.42, 0.90) and for African-American men (aOR¼0.36; 95% CI¼0.21, 0.62). Additional research is needed to understand the biologic mechanisms by which diabetes may influence prostate cancer risk; genetic factors may play an important role in understanding this association

Monounsaturated fats and immune function

Animal studies suggest that olive oil is capable of modulating functions of cells of the immune system in a manner similar to, albeit weaker than, fish oils. There is some evidence that the effects of olive oil on immune function in animal studies are due to oleic acid rather than to trace elements or antioxidants. Importantly, several studies have demonstrated effects of oleic acid-containing diets on in vivo immune responses. In contrast, consumption of a monounsaturated fatty acid (MUFA)-rich diet by humans does not appear to bring about a general suppression of immune cell functions. The effects of this diet in humans are limited to decreasing aspects of adhesion of peripheral blood mononuclear cells, although there are trends towards decreases in natural killer cell activity and proliferation. The lack of a clear effect of MUFA in humans may be attributable to the higher level of monounsaturated fat used in the animal studies, although it is ultimately of importance to examine the effects of intakes which are in no way extreme. The effects of MUFA on adhesion molecules are potentially important, since these molecules appear to have a role in the pathology of a number of diseases involving the immune system. This area clearly deserves further exploration

Physical activity for people living with dementia: carer outcomes and side effects from the perspectives of professionals and family carers

Adherence to physical activity is challenging for people living with dementia, and largely dependent on carers' involvement. Carers are likely to support physical activity based on their perceived balance between benefits and potential side effects of such intervention for both patients and themselves. Professionals also have a role in terms of optimising such interventions not only for people with dementia but also their carers.publishe

Proline-rich antimicrobial peptide, PR-39 gene transduction altered invasive activity and actin structure in human hepatocellular carcinoma cells

PR-39 is an endogenous proline-rich antimicrobial peptide which induces the synthesis of syndecan-1, a transmembrane heparan sulphate proteoglycan involved in cell-to-matrix interactions and wound healing. Previously, we revealed that the expression of syndecan-1 was reduced in human hepatocellular carcinomas with high metastatic potential and speculated that syndecan-1 played an important role in inhibition of invasion and metastasis. It is assumed that a modification of this process with PR-39 and syndecan-1 may result in a new strategy by which it can inhibit the invasion and metastasis. Therefore, we transduced a gene of PR-39 into human hepatocellular carcinoma cell line HLF, which shows a low expression of syndecan-1 and a high in vitro invasive activity, and examined whether this procedure could reduce the invasive activity of tumour cells. In two transfectants with PR-39 gene, the syndecan-1 expression was induced and the invasive activity in type I collagen-coated chamber was inhibited. Moreover, these transfectants showed the suppression of motile activity assayed by phagokinetic tracks in addition to the disorganization of actin filaments observed by a confocal imaging system. In contrast, five transfectants with syndecan-1 gene in the HLF cells revealed suppression of invasive activity but did not alter the motile activity and actin structures of the cell. These results suggest that PR-39 has functions involved in the suppression of motile activity and alteration of actin structure on human hepatocellular carcinoma cells in addition to the suppression of invasive activity which might result from the induction of syndecan-1 expression. © 1999 Cancer Research Campaig

The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences

<p>Abstract</p> <p>Background</p> <p>Enormous molecular sequence data have been accumulated over the past several years and are still exponentially growing with the use of faster and cheaper sequencing techniques. There is high and widespread interest in using these data for phylogenetic analyses. However, the amount of data that one can retrieve from public sequence repositories is virtually impossible to tame without dedicated software that automates processes. Here we present a novel bioinformatics pipeline for downloading, formatting, filtering and analyzing public sequence data deposited in GenBank. It combines some well-established programs with numerous newly developed software tools (available at <url>http://software.zfmk.de/</url>).</p> <p>Results</p> <p>We used the bioinformatics pipeline to investigate the phylogeny of the megadiverse insect order Hymenoptera (sawflies, bees, wasps and ants) by retrieving and processing more than 120,000 sequences and by selecting subsets under the criteria of compositional homogeneity and defined levels of density and overlap. Tree reconstruction was done with a partitioned maximum likelihood analysis from a supermatrix with more than 80,000 sites and more than 1,100 species. In the inferred tree, consistent with previous studies, "Symphyta" is paraphyletic. Within Apocrita, our analysis suggests a topology of Stephanoidea + (Ichneumonoidea + (Proctotrupomorpha + (Evanioidea + Aculeata))). Despite the huge amount of data, we identified several persistent problems in the Hymenoptera tree. Data coverage is still extremely low, and additional data have to be collected to reliably infer the phylogeny of Hymenoptera.</p> <p>Conclusions</p> <p>While we applied our bioinformatics pipeline to Hymenoptera, we designed the approach to be as general as possible. With this pipeline, it is possible to produce phylogenetic trees for any taxonomic group and to monitor new data and tree robustness in a taxon of interest. It therefore has great potential to meet the challenges of the phylogenomic era and to deepen our understanding of the tree of life.</p

Split-based computation of majority-rule supertrees

<p>Abstract</p> <p>Background</p> <p>Supertree methods combine overlapping input trees into a larger supertree. Here, I consider split-based supertree methods that first extract the split information of the input trees and subsequently combine this split information into a phylogeny. Well known split-based supertree methods are matrix representation with parsimony and matrix representation with compatibility. Combining input trees on the same taxon set, as in the consensus setting, is a well-studied task and it is thus desirable to generalize consensus methods to supertree methods.</p> <p>Results</p> <p>Here, three variants of majority-rule (MR) supertrees that generalize majority-rule consensus trees are investigated. I provide simple formulas for computing the respective score for bifurcating input- and supertrees. These score computations, together with a heuristic tree search minmizing the scores, were implemented in the python program PluMiST (Plus- and Minus SuperTrees) available from <url>http://www.cibiv.at/software/plumist</url>. The different MR methods were tested by simulation and on real data sets. The search heuristic was successful in combining compatible input trees. When combining incompatible input trees, especially one variant, MR(-) supertrees, performed well.</p> <p>Conclusions</p> <p>The presented framework allows for an efficient score computation of three majority-rule supertree variants and input trees. I combined the score computation with a heuristic search over the supertree space. The implementation was tested by simulation and on real data sets and showed promising results. Especially the MR(-) variant seems to be a reasonable score for supertree reconstruction. Generalizing these computations to multifurcating trees is an open problem, which may be tackled using this framework.</p

Outcome analysis following removal of locking plate fixation of the proximal humerus

<p>Abstract</p> <p>Background</p> <p>Concerning surgical management experience with locking plates for proximal humeral fractures has been described with promising results. Though, distinct hardware related complaints after fracture union are reported. Information concerning the outcome after removal of hardware from the proximal humerus is lacking and most studies on hardware removal are focused on the lower extremity. Therefore the aim of this study was to analyze the functional short-term outcome following removal of locking plate fixation of the proximal humerus.</p> <p>Methods</p> <p>Patients undergoing removal of a locking plate of the proximal humerus were prospectively followed. Patients were subdivided into the following groups: Group HI: symptoms of hardware related subacromial impingement, Group RD: persisting rotation deficit, Group RQ: patients with request for a hardware removal. The clinical (Constant-Murley score) and radiologic (AP and axial view) follow-up took place three and six months after the operation. To evaluate subjective results, the Medical Outcomes Study Short Form-36 (SF-36), was completed.</p> <p>Results</p> <p>59 patients were included. The mean length of time with the hardware in place was 15.2 ± 3.81 months. The mean of the adjusted overall Constant score before hardware removal was 66.2 ± 25.2% and increased significantly to 73.1 ± 22.5% after 3 months; and to 84.3 ± 20.6% after 6 months (p < 0.001). The mean of preoperative pain on the VAS-scale before hardware removal was 5.2 ± 2.9, after 6 months pain in all groups decreased significantly (p < 0.001). The SF-36 physical component score revealed a significant overall improvement in both genders (p < 0.001) at six months.</p> <p>Conclusion</p> <p>A significant improvement of clinical outcome following removal was found. However, a general recommendation for hardware removal is not justified, as the risk of an anew surgical and anesthetic procedure with all possible complications has to be carefully taken into account. However, for patients with distinct symptoms it might be justified.</p