Long-term data on invaders: when the fox is away, the mink will play

Studies of the effects and population dynamics of invasive species typically cover only short time periods. However, populations of invasive species interact with native species, and these interactions may have strong effects on invaders’ populations and effects over time. We present and analyze long-term data on invasive American mink (Neovison vison), native red fox (Vulpes vulpes), and mountain hare (Lepus timidus) in Sweden. The mink’s population dynamics followed a pattern of logistic growth from the late 1930s to the late 1970s. In the early 1980s, however, the population tripled, then declined sharply. We suggest that the mink’s population tripling was caused by a drastic decline in red fox populations, which caused terrestrial prey to increase. Later recovery of the fox population reversed the trend and caused the mink population’s recent decline. Our study shows that species interactions between native and invasive species, and therefore biotic resistance, can change dramatically over time.     

Accuracy of administrative claims data for polypectomy

Background:

The frequency of polypectomy is an important indicator of quality assurance for population-based colorectal cancer screening programs. Although administrative databases of physician claims provide population-level data on the performance of polypectomy, the accuracy of the procedure codes has not been examined. We determined the level of agreement between physician claims for polypectomy and documentation of the procedure in endoscopy reports.

Methods:

We conducted a retrospective cohort study involving patients aged 50–80 years who underwent colonoscopy at seven study sites in Montréal, Que., between January and March 2007. We obtained data on physician claims for polypectomy from the Régie de l’Assurance Maladie du Québec (RAMQ) database. We evaluated the accuracy of the RAMQ data against information in the endoscopy reports.

Results:

We collected data on 689 patients who underwent colonoscopy during the study period. The sensitivity of physician claims for polypectomy in the administrative database was 84.7% (95% confidence interval [CI] 78.6%–89.4%), the specificity was 99.0% (95% CI 97.5%–99.6%), concordance was 95.1% (95% CI 93.1%–96.5%), and the kappa value was 0.87 (95% CI 0.83–0.91).

Interpretation:

Despite providing a reasonably accurate estimate of the frequency of polypectomy, physician claims underestimated the number of procedures performed by more than 15%. Such differences could affect conclusions regarding quality assurance if used to evaluate population-based screening programs for colorectal cancer. Even when a high level of accuracy is anticipated, validating physician claims data from administrative databases is recommended.Population-based screening programs for colorectal cancer rely heavily on the performance of colonoscopy as either the initial examination or as the follow-up to a positive screening by virtual colonography, double-contrast barium enema or fecal occult blood testing. Colonoscopy is the only screening examination accepted at 10-year intervals among people at average risk without significant polyps found. It allows direct visualization of the entire colon and rectum and permits removal of adenomatous polyps, precursors of colorectal cancer. The frequency of polypectomy is an important indicator of quality assurance for colorectal cancer screening programs.In the province of Quebec, physicians are reimbursed for medical services by the Régie de l’Assurance Maladie du Québec (RAMQ), the government agency responsible for administering the provincial health insurance plan. Physicians receive additional remuneration for performing a polypectomy if they include the procedure code in their claim.Data from physician claims databases are commonly used in health services research,^1–7 even though the data are collected for administrative purposes and physician reimbursement. Procedure codes in physician claims databases are presumed to have a very high level of agreement with data in medical charts.⁸ A physician making a claim will need to submit the diagnostic code and, when applicable, the procedure code. Studies that rely on physician claims databases can be divided into those that examine the diagnostic codes entered and those that examine the procedure codes entered. Few studies have attempted to validate procedure codes, and often not as the primary study objective.^9–14We conducted a study to determine the level of agreement between physician claims for polypectomy and documentation of the procedure in endoscopy reports.     

Phytosociological data give biased estimates of species richness

Abstract. Large phytosociological data sets of three types of grassland and three types of forest vegetation from the Czech Republic were analysed with a focus on plot size used in phytosociological sampling and on the species‐area relationship. The data sets included 12975 relevés, sampled by different authors in different parts of the country between 1922 and 1999. It was shown that in the grassland data sets, the relevés sampled before the 1960s tended to have a larger plot size than the relevés made later on. No temporal variation in plot sizes used was detected in forest relevés. Species‐area curves fitted to the data showed unnatural shapes, with levelling‐off or even decrease in plot sizes higher than average. This distortion is explained by the subjective, preferential method of field sampling used in phytosociology. When making relevés in species‐poor vegetation, researchers probably tend to use larger plots in order to include more species. The reason for this may be that a higher number of species gives a higher probability of including presumed diagnostic species, so that the relevé can be more easily classified in the Braun‐Blanquet classification system. This attitude of phytosociologists has at least two consequences: (1) in phytosociological data bases species‐poor vegetation types are underrepresented or relevés are artificially biased towards higher species richness; (2) the suitability of phytosociological data for species richness estimation is severely limited.     

Use of administrative claims data for comparative effectiveness research of rheumatoid arthritis treatments

Observational studies, particularly those using large administrative claims databases, have become increasingly popular sources of comparative effectiveness or comparative safety research. Studies using claims data often face challenges and criticisms due to the lack of certain clinical information, such as lifestyle risk factors, disease severity, and questionable accuracy of disease diagnoses. A novel, claims-based algorithm to evaluate the clinical effectiveness of rheumatoid arthritis medications has been developed and its performance seems promising, although further validation is needed.     

Xanthomonas oryzae pv. oryzae XopQ protein suppresses rice immune responses through interaction with two 14-3-3 proteins but its phospho-null mutant induces rice immune responses and interacts with another 14-3-3 protein

Many bacterial phytopathogens employ effectors secreted through the type-III secretion system to suppress plant innate immune responses. The Xanthomonas type-III secreted non-TAL effector protein Xanthomonas outer protein Q (XopQ) exhibits homology to nucleoside hydrolases. Previous work indicated that mutations which affect the biochemical activity of XopQ fail to affect its ability to suppress rice innate immune responses, suggesting that the effector might be acting through some other pathway or mechanism. In this study, we show that XopQ interacts in yeast and in planta with two rice 14-3-3 proteins, Gf14f and Gf14g. A serine to alanine mutation (S65A) of a 14-3-3 interaction motif in XopQ abolishes the ability of XopQ to interact with the two 14-3-3 proteins and to suppress innate immunity. Surprisingly, the S65A mutant gains the ability to interact with a third 14-3-3 protein that is a negative regulator of innate immunity. The XopQS65A mutant is an inducer of rice immune responses and this property is dominant over the wild-type function of XopQ. Taken together, these results suggest that XopQ targets the rice 14-3-3 mediated immune response pathway and that its differential phosphorylation might enable interaction with alternative 14-3-3 proteins.     

Complexity of rice Hsp100 gene family: lessons from rice genome sequence data

Elucidation of genome sequence provides an excellent platform to understand detailed complexity of the various gene families. Hsp100 is an important family of chaperones in diverse living systems. There are eight putative gene loci encoding for Hsp100 proteins in Arabidopsis genome. In rice, two full-length Hsp100 cDNAs have been isolated and sequenced so far. Analysis of rice genomic sequence by in silico approach showed that two isolated rice Hsp100 cDNAs correspond to Os05g44340 and Os02g32520 genes in the rice genome database. There appears to be three additional proteins (encoded by Os03g31300, Os04g32560 and Os04g33210 gene loci) that are variably homologous to Os05g44340 and Os02g32520 throughout the entire amino acid sequence. The above five rice Hsp100 genes show significant similarities in the signature sequences known to be conserved among Hsp100 proteins. While Os05g44340 encodes cytoplasmic Hsp100 protein, those encoded by the other four genes are predicted to have chloroplast transit peptides.     

Both carboxy-terminal tails of alpha- and beta-tubulin are essential, but either one will suffice

Microtubules (MTs) are organized into distinct systems essential for cell shape, movement, intracellular transport, and division. Electron crystallographic analyses provide little information about how MTs produce diverse structures and functions, perhaps because they failed to visualize the last 10 residues of the alpha- and the last 18 of the beta-tubulin C-terminal tails (CTTs), which likely play a role in MT diversity. CTTs define conserved, nonallelic isotypes in mammals, are major sites of posttranslational modifications (PTMs), are binding sites for microtubule-associated proteins (MAPs), and determine MT motor processivity. Using mutagenesis and homologous gene replacement in Tetrahymena thermophila, we analyzed mutations, deletions, tail switches, and tail duplications of alpha- and beta-tubulin CTTs. We demonstrate that a tail is required for the essential function of both alpha- and beta-tubulin. However, the two tails are interchangeable, and cells grow normally with either an alpha or a beta tail on both tubulins. In addition, an alpha gene containing a duplicated alpha C terminus rescues a lethal mutant lacking all known posttranslational modification sites on the beta C terminus but cannot rescue deletion of the beta tail. Thus, tubulin tails have a second essential function that is not associated with posttranslational modification.     

Dispersal kernel of green rice leafhopper estimated from truncated data

Characterizing dispersal kernels from truncated data is important for managing and predicting population dynamics. We used mark-recapture data from 10 previously published replicated experiments at three host plant development stages (seedling, tillering, and heading) to estimate parameters of the normal and exponential dispersal kernels for green rice leafhopper, Nephotettix cincticeps (Uhler). We compared classic statistical methods for estimating untruncated distribution parameters from truncated data with maximum likelihood (MLE) and the method of statistical moments for simulated and empirical data. Simulations showed that both methods provided accurate parameter estimates with similar precision. The method of moments is algebraically complex, but simple to calculate, while the MLE methods require numerical solutions of nonlinear equations. Simulations also showed that accurate, precise estimates of the parameters of the untruncated distributions could be attained even under severe truncation with sufficient numbers of recaptures. Both diffusivity and the exponential mean were higher with later plant growth stage, showing that insects moved farther and faster at the heading stage. Precision of the estimates was not strongly related to percent capture, size of the experimental field, or the number of leafhoppers captured. The leptokurtic exponential kernel fit the data better than the normal kernel for all the experiments. These results support an alternative explanation for the strong density-dependent population regulation of this species at the heading stage. Instead of leafhopper density per se, the increase in movement at this stage could integrate the populations in the separate fields, leveling densities throughout the landscape.     

基于EST数据的水稻基因表达大规模初步分析

EST序列代表了组织基因表达的转录信号,本研究尝试开发简单高效的大规模EST分析方法,从NCBI下载水稻(Oryza sativa)的所有EST序列并进行分析以获取水稻发育过程基因表达的重要信息。通过进行blast比对和phrap拼接分析,及利用Unix文本过滤方法,从EST序列拼接获得了3万多个重叠群序列。进一步将重叠群序列与NCBI核酸数据库进行比对获得了各个序列的注释信息。从重叠群的组织表达初步挖掘中发现花药的表达数量最多,为下一步探讨水稻发育器官特异表达基因调控打下了重要基础。     

"Change yourself and the whole world will become kinder": Russian activists for reproductive health and the limits of claims making for women

This article views reproductive health activism as a fruitful site for analyzing the cultural logics through which legitimate claims for women's needs become expressed and circumscribed. It begins from the observation that in the United States and Britain, reproductive health has been a key arena for feminist political claims and struggles for women's rights, bodily integrity, access to health care, and demands for authority in relations with experts. These concerns and struggles have not, however, emerged in all postsocialist contexts, and new activism in Russia reveals strikingly different agendas. Innovative groups of health providers seeking to increase women's access to birth control methods and safe sex, home birth opportunities, and improved health services work outside of feminist perspectives and reject political paths for change. By examining the ideological inspirations, cultural logics, and political-economic constraints shaping the outreach work of Russian health practitioners, the article explains how and why health activism became a site for personal "spiritual" revival and the strengthening of nuclear families. It also explores how conditions following the collapse of socialism have further legitimized activists' rejection of political agendas for change.     

The one that did not get away: individual assignment using microsatellite data detects a case of fishing competition fraud

Assignment of an individual to the population from which it most probably originated based on its multilocus genotype has been widely applied in recent years. In this study, individual assignment based on microsatellite data was used to identify a case of fishing competition fraud. Despite the fact that the true population of origin was most probably not among the reference populations, recent modifications of the assignment tests were used in confidently excluding (p < 0.0001) the possibility of a 5.5 kg salmon (Salmo salar) originating from the fishing competition location, Lake Saimaa (south-east Finland). In fact, the probability of the suspect salmon originating from one of the regions that supply most of Finland's fish markets was found to be over 600 times higher than it originating from Lake Saimaa. When presented with this evidence, the offender confessed to purchasing the salmon at a local fish shop and criminal charges were laid. This study emphasizes the potential practical application of the individual assignment procedure, in particular the usefulness of confidently excluding populations as the origin of an individual. A similar strategy could be also used, for example in suspected cases of illegal poaching, in order to assign or exclude individuals from originating from a claimed population.     

Additional data for nuclear DNA give new insights into the phylogenetic position of Sorex granarius within the Sorex araneus group

Many species contain genetic lineages that are phylogenetically intermixed with those of other species. In the Sorex araneus group, previous results based on mtDNA and Y chromosome sequence data showed an incongruent position of Sorex granarius within this group. In this study, we explored the relationship between species within the S. araneus group, aiming to resolve the particular position of S. granarius. In this context, we sequenced a total of 2447 base pairs (bp) of X-linked and nuclear genes from 47 individuals of the S. araneus group. The same taxa were also analyzed within a Bayesian framework with nine autosomal microsatellites. These analyses revealed that all markers apart from mtDNA showed similar patterns, suggesting that the problematic position of S. granarius is best explained by an incongruent behavior by mtDNA. Given their close phylogenetic relationship and their close geographic distribution, the most likely explanation for this pattern is past mtDNA introgression from S. araneus race Carlit to S. granarius.