From Reductionism to Reintegration: Solving society's most pressing problems requires building bridges between data types across the life sciences.

Decades of reductionist approaches in biology have achieved spectacular progress, but the proliferation of subdisciplines, each with its own technical and social practices regarding data, impedes the growth of the multidisciplinary and interdisciplinary approaches now needed to address pressing societal challenges. Data integration is key to a reintegrated biology able to address global issues such as climate change, biodiversity loss, and sustainable ecosystem management. We identify major challenges to data integration and present a vision for a "Data as a Service"-oriented architecture to promote reuse of data for discovery. The proposed architecture includes standards development, new tools and services, and strategies for career-development and sustainability.

Kinopus chlorellivorus gen. nov., sp. nov. (Vampyrellida, Rhizaria), a New Algivorous Protist Predator Isolated from Large-Scale Outdoor Cultures of Chlorella sorokiniana.

The large-scale culture of low-cost algal biomass can be significantly affected by microbial grazing on the algae. To minimize the impact, it is necessary to manage the predators. In this study, we describe a new genus and species of vampyrellid amoeba, Kinopus chlorellivorus, which caused the loss of Chlorella sorokiniana in large-scale cultures. We assigned it to the family Leptophryidae (Vampyrellida) based on morphology and small-subunit (SSU) rRNA gene sequence comparisons. Using transmission electron microscopy, we found spherical lucent inclusions, which have not been reported for any leptophryids or other vampyrellids. The gene sequence of SSU rRNA did not match any recognized genera or species and contained four characteristic regions. K. chlorellivorus preys on algae by engulfment. Laboratory feeding experiments confirmed that its grazing rate was as high as 131 Chlorella cells day-1 individual-1. Results of prey-range experiments demonstrated that it could consume other chlorophyte microalgae (e.g., Scenedesmus, Coelastrella, and Haematococcus) but with a strong feeding ability on Chlorella spp., with ingestion rates ranging from 2.67 to 3.15 prey predator-1 h-1 and growth rates of the amoeba ranging from 0.039 to 0.045 h-1. On the basis of its high grazing ability on Chlorella, capacity to form large populations in a short period of time, and capacity to form resistant resting stages, this contaminant has the potential to cause serious problems in large-scale Chlorella culture and should be of concern to operators of algal production facilities. IMPORTANCE The vampyrellids (Vampyrellida, Rhizaria) are a major group of predatory amoebae that have attracted significant attention because of their diversity of feeding strategies. The crucial roles they play in important processes such as suppressing soil disease and controlling aquatic algae, and as microbial contaminants in outdoor large-scale algal cultures, have also received increasing attention. In this study, a new genus and species of algivorous vampyrellid amoeba, Kinopus chlorellivorus, is described as a significant grazer responsible for losses in outdoor industrial Chlorella cultures. We found that the amoeba's detrimental effects on Chlorella cultures may be related to its specific feeding characteristics. This study provides phenotypic and genetic information on a previously unknown vampyrellid, emphasizes the impact of contaminating vampyrellids in commercial microalgal cultures, and will contribute to the development of management strategies for predicting this kind of contaminant in large-scale microalgal cultivation.

Influences of sire conception rate on pregnancy establishment in dairy cattle.

Establishment of pregnancy in cattle is complex and encompasses ovulation, fertilization, blastocyst formation and growth into an elongated conceptus, pregnancy recognition signaling, and development of the embryo and placenta. The objective here was to investigate sire influences on pregnancy establishment in cattle. First, 10 Holstein bulls were classified as high or low fertility based on their sire conception rate (SCR) value. In a field trial, pregnancy at first timed insemination was not different between high and low SCR bulls. Next, 5 of the 10 sires were phenotyped using in vitro and in vivo embryo production. There was no effect of SCR classification on in vitro embryo cleavage rate, but low SCR sires produced fewer day 8 blastocysts. In superovulated heifers, high SCR bulls produced a lower percentage of unfertilized oocytes and fewer degenerated embryos compared to low SCR bulls. Recipient heifers received three to five in vivo produced embryos from either high or low SCR sires on day 7 postestrus. Day 16 conceptus recovery and length were not different between SCR groups, and the conceptus transcriptome was not appreciably different between high and low SCR sires. The reduced ability of embryos from low SCR bulls to establish pregnancy is multifactorial and encompasses sperm fertilizing ability, preimplantation embryonic development, and development of the embryo and placenta after conceptus elongation and pregnancy recognition. These studies highlight the importance of understanding genetic contributions of the sire to pregnancy establishment that is crucial to increase reproductive efficiency in dairy cattle.

"gnparser": a powerful parser for scientific names based on Parsing Expression Grammar.

BACKGROUND: Scientific names in biology act as universal links. They allow us to cross-reference information about organisms globally. However variations in spelling of scientific names greatly diminish their ability to interconnect data. Such variations may include abbreviations, annotations, misspellings, etc. Authorship is a part of a scientific name and may also differ significantly. To match all possible variations of a name we need to divide them into their elements and classify each element according to its role. We refer to this as 'parsing' the name. Parsing categorizes name's elements into those that are stable and those that are prone to change. Names are matched first by combining them according to their stable elements. Matches are then refined by examining their varying elements. This two stage process dramatically improves the number and quality of matches. It is especially useful for the automatic data exchange within the context of "Big Data" in biology. RESULTS: We introduce Global Names Parser (gnparser). It is a Java tool written in Scala language (a language for Java Virtual Machine) to parse scientific names. It is based on a Parsing Expression Grammar. The parser can be applied to scientific names of any complexity. It assigns a semantic meaning (such as genus name, species epithet, rank, year of publication, authorship, annotations, etc.) to all elements of a name. It is able to work with nested structures as in the names of hybrids. gnparser performs with ≈99% accuracy and processes 30 million name-strings/hour per CPU thread. The gnparser library is compatible with Scala, Java, R, Jython, and JRuby. The parser can be used as a command line application, as a socket server, a web-app or as a RESTful HTTP-service. It is released under an Open source MIT license. CONCLUSIONS: Global Names Parser (gnparser) is a fast, high precision tool for biodiversity informaticians and biologists working with large numbers of scientific names. It can replace expensive and error-prone manual parsing and standardization of scientific names in many situations, and can quickly enhance the interoperability of distributed biological information.

Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora).

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.

Vernalophrys algivore gen. nov., sp. nov. (Rhizaria: Cercozoa: Vampyrellida), a New Algal Predator Isolated from Outdoor Mass Culture of Scenedesmus dimorphus.

Microbial contamination is the main cause of loss of biomass yield in microalgal cultures, especially under outdoor environmental conditions. Little is known about the identities of microbial contaminants in outdoor mass algal cultures. In this study, a new genus and species of vampyrellid amoeba, Vernalophrys algivore, is described from cultures of Scenedesmus dimorphus in open raceway ponds and outdoor flat-panel photobioreactors. This vampyrellid amoeba was a significant grazer of Scenedesmus and was frequently associated with a very rapid decline in algal numbers. We report on the morphology, subcellular structure, feeding behavior, molecular phylogeny, and life cycle. The new amoeba resembles Leptophrys in the shape of trophozoites and pseudopodia and in the mechanism of feeding (mainly by engulfment). It possesses two distinctive regions in helix E10_1 (nucleotides 117 to 119, CAA) and E23_1 (nucleotides 522 and 523, AG) of the 18S rRNA gene. It did not form a monophyletic group with Leptophrys in molecular phylogenetic trees. We establish a new genus, Vernalophrys, with the type species Vernalophrys algivore. The occurrence, impact of the amoeba on mass culture of S. dimorphus, and means to reduce vampyrellid amoeba contamination in Scenedesmus cultures are addressed. The information obtained from this study will be useful for developing an early warning system and control measures for preventing or treating this contaminant in microalgal mass cultures.

Two new species of the genus Leptomyxa (Goodey, 1915) - Leptomyxa botanica n. sp. and Leptomyxa monrepos n. sp. from the soil habitats of Northwestern Russia.

Amoebae of the genus Leptomyxa have variable morphologies and can only be reliably identified using molecular data. However, species distinction based on the 18S rRNA gene sequence is difficult due to the very low level of sequence divergence among morphologically different species. The database for other genes is much smaller, and genomic data on Leptomyxa is almost absent. In this study, we describe two new terrestrial species of the genus Leptomyxa isolated from Northwestern Russia, Leptomyxa botanica n. sp. and Leptomyxa monrepos n. sp. Both species easily adopt an expanded fan-shaped form and have a complex structure of the nucleolar material. Phylogenetic analyses show a derived status of these two species. They form a clade with Leptomyxa valladaresi. Our tree confirms that the 18S rRNA gene sequences of Leptomyxa species are split into two large clades. The morphological synapomorphies of these clades are not obvious. This analysis is complicated by the lack of reliable morphological data on many sequenced strains and probable misidentification of some isolates.

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.

An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level "supergroups," many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup "Chromalveolata" is rejected. Furthermore, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.

Afferent limb syndrome and delayed GI problems after pancreaticoduodenectomy for pancreatic cancer: single-center, 14-year experience.

BACKGROUND: There are limited data on the incidence of afferent limb syndrome and other delayed GI problems in pancreatic cancer (PaC) patients, especially among long-term survivors (>2 years). OBJECTIVE: To evaluate the incidence of afferent limb syndrome (chronic afferent limb obstruction resulting in pancreatobiliary obstruction) and delayed GI problems in PaC patients after pancreaticoduodenectomy (PD). DESIGN: Retrospective case series. SETTING: Tertiary referral center. PATIENTS: PaC patients treated with PD (N = 186) over a 14-year period (January 1995-October 2009). INTERVENTIONS: Endoscopic balloon dilation and stent placement, percutaneous biliary drainage. MAIN OUTCOME MEASUREMENTS: Incidence of afferent limb syndrome and delayed GI complications (marginal ulcers, radiation enteropathy, anastomotic strictures). RESULTS: Mean age was 63 ± 10 years; 55% of patients were male. Afferent limb syndrome was noted in 24 patients (13%). Median time to diagnosis was 1.2 years (range 0.03-12.3 years); obstruction was primarily caused by recurrent PaC (8 patients, 33%) and radiation enteropathy (9 patients, 38%). Afferent limb syndrome was more likely to develop in patients with 2 years or longer of follow-up (n = 71, [38%]) compared with patients with 2 years or less of follow-up, after controlling for age, sex, surgery type, and adjuvant treatment (adjusted odds ratio, 4.5; 95% CI, 1.8-11.7). Other delayed GI problems included radiation enteropathy (6%), marginal ulcers (5%), anastomotic strictures (4%), cholangitis/liver abscesses (5%), and GI bleeding (6%). LIMITATIONS: Retrospective, single-center study. CONCLUSIONS: GI problems, including afferent limb syndrome, are relatively common in PaC patients after surgery and adjuvant therapy. Clinicians should recognize and effectively treat these delayed GI problems, especially in long-term survivors.

Evaluating support for the current classification of eukaryotic diversity.

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification--plants, animals, fungi, and protists--have been transformed through numerous permutations into the current system of six "supergroups." The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.

Broadly sampled multigene trees of eukaryotes.

BACKGROUND: Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which have not been characterized previously, onto a well-sampled multigene genealogy, and (2) to evaluate the support for the six putative supergroups using two taxon-rich data sets and a variety of phylogenetic approaches. RESULTS: The inferred trees reveal strong support for many clades that also have defining ultrastructural or molecular characters. In contrast, we find limited to no support for most of the putative supergroups as only the 'Opisthokonta' receive strong support in our analyses. The supergroup 'Amoebozoa' has only moderate support, whereas the 'Chromalveolata', 'Excavata', 'Plantae', and 'Rhizaria' receive very limited or no support. CONCLUSION: Our analytical approach substantiates the power of increased taxon sampling in placing diverse eukaryotic lineages within well-supported clades. At the same time, this study indicates that the six supergroup hypothesis of higher-level eukaryotic classification is likely premature. The use of a taxon-rich data set with 105 lineages, which still includes only a small fraction of the diversity of microbial eukaryotes, fails to resolve deeper phylogenetic relationships and reveals no support for four of the six proposed supergroups. Our analyses provide a point of departure for future taxon- and gene-rich analyses of the eukaryotic tree of life, which will be critical for resolving their phylogenetic interrelationships.

uBioRSS: tracking taxonomic literature using RSS.

UNLABELLED: Web content syndication through standard formats such as RSS and ATOM has become an increasingly popular mechanism for publishers, news sources and blogs to disseminate regularly updated content. These standardized syndication formats deliver content directly to the subscriber, allowing them to locally aggregate content from a variety of sources instead of having to find the information on multiple websites. The uBioRSS application is a 'taxonomically intelligent' service customized for the biological sciences. It aggregates syndicated content from academic publishers and science news feeds, and then uses a taxonomic Named Entity Recognition algorithm to identify and index taxonomic names within those data streams. The resulting name index is cross-referenced to current global taxonomic datasets to provide context for browsing the publications by taxonomic group. This process, called taxonomic indexing, draws upon services developed specifically for biological sciences, collectively referred to as 'taxonomic intelligence'. Such value-added enhancements can provide biologists with accelerated and improved access to current biological content. AVAILABILITY: http://names.ubio.org/rss/

A twenty-year experience with endoscopic therapy for symptomatic primary sclerosing cholangitis.

GOALS: The current study presents 1 tertiary endoscopy center's 20-year experience using endoscopic therapy to treat patients with symptomatic primary sclerosing cholangitis (PSC). BACKGROUND: Endoscopic therapy for patients with PSC and dominant strictures has been used for more than 20 years, but there is concern that instrumenting a sclerotic biliary tree induces risks that outweigh anticipated benefits. STUDY: In this retrospective chart review, 117 patients with PSC were identified using ICD-9 codes. Patients had a mean age of 47 years (range: 15 to 86 y). Mean duration of follow-up was 8 years (range: 2 to 20 y). Of the 117 identified patients, 106 underwent endoscopic retrograde cholangiopancreatography on one or more occasions (for a total of 317 endoscopic retrograde cholangiopancreatographies), and a subset of 84 patients received endoscopic therapy for treatment of dominant strictures and/or deteriorating clinical status. Actual survival for endoscopically treated patients was compared with predicted survival using the Mayo Clinic natural history model for PSC. RESULTS: Our chart review revealed 23 recognized complications among the 317 procedures performed (7.3%), and no procedure-related deaths. Observed patient survival at years 3 and 4 was significantly higher than that predicted by the Mayo Clinic natural history model for PSC (P=0.021). CONCLUSIONS: Patients with PSC who have a deteriorating clinical course benefited from endoscopic therapy to provide drainage of bile ducts, removal of stones, and/or temporary relief from obstructions, with acceptable procedure-related complications and higher than expected 3-year and 4-year survival.

A multigene analysis of Corallomyxa tenera sp. nov. suggests its membership in a clade that includes Gromia, Haplosporidia and Foraminifera.

We combine a morphological description with a multigene analysis to assess the phylogenetic placement of a poorly known amoeboid taxon Corallomyxa within the eukaryotic tree of life. A detailed morphological analysis including transmission electron microscopy and light microscopy of Corallomyxa sp. ATCC 50975 demonstrates that this isolate is a new species, herein designated, Corallomyxa tenera sp. nov. This species possesses features of the genus, such as a multinucleate, reticulate plasmodium with localized bidirectional streaming and occasional formation of surface buds, but is differentially characterized from other species by its delicate appearance, short duration of the anastomosing reticulate network and production of round smooth-walled cysts. The new species also lacks some features found in some Corallomyxa species, including cytoplasmic condensation and an electron dense "chromocenter". A Bayesian analysis of four concatenated genes (SSU-rDNA, actin, alpha- and beta-tubulin) from a wide diversity of eukaryotes places the new species together with taxa placed in the putative supergroup 'Rhizaria'. All molecular loci refute the traditional placement of Corallomyxa within the supergroup 'Amoebozoa', which includes other Mycetozoidea and Lobosea. Maximum likelihood and Bayesian analyses of the two well-sampled genes, SSU-rDNA and actin, with increased taxon sampling of 'Rhizaria' show a close affinity of Corallomyxa with Foraminifera, Gromia and, for SSU-rDNA, Haplosporidia. We further identify a novel stem, herein designated E23-13-1, in the predicted SSU-rDNA secondary structure that supports this relationship. A hypothesis is presented for the evolution of morphological and molecular synapomorphies in a clade containing Gromia, Corallomyxa, Foraminifera and Haplosporidia.

Taxonomic informatics tools for the electronic Nomenclator Zoologicus.

Given the current trends, it seems inevitable that all biological documents will eventually exist in a digital format and be distributed across the internet. New network services and tools need to be developed to increase retrieval rates for documents and to refine data recovery. Biological data have traditionally been well managed using taxonomic principles. As part of a larger initiative to build an array of names-based network services that emulate taxonomic principles for managing biological information, we undertook the digitization of a major taxonomic reference text, Nomenclator Zoologicus. The process involved replicating the text to a high level of fidelity, parsing the content for inclusion within a database, developing tools to enable expert input into the product, and integrating the metadata and factual content within taxonomic network services. The result is a high-quality and freely available web application (http://uio.mbl.edu/NomenclatorZoologicus/) capable of being exploited in an array of biological informatics services.

The 9-day CIDR-PG protocol: Incorporation of PGF2α pretreatment into a long-term progestin-based estrus synchronization protocol for postpartum beef cows.

A pilot experiment was designed to test the hypothesis that administration of PGF2α before progestin treatment would allow for a reduced duration of progestin treatment in a long-term progestin-based estrus synchronization protocol. A modified presynchronization treatment was compared with a standard long-term controlled internal drug release (CIDR) treatment, and treatments were compared on the basis of ovarian follicular dynamics, estrous response rate, synchrony of estrus expression, and pregnancy rates resulting from timed artificial insemination (TAI) in postpartum beef cows. Estrous was synchronized for 85 cows, with cows assigned to one of two treatments based on age, days postpartum, and body condition score. Cows assigned to the 14-day CIDR-PG protocol received a CIDR insert (1.38 g progesterone) on Day 0, CIDR removal on Day 14, and administration of PGF2α (25 mg im) on Day 30. Cows assigned to the 9-day CIDR-PG protocol received PGF2α concurrent with CIDR insertion on Day 5, PGF2α concurrent with CIDR removal on Day 14, and administration of PGF2α on Day 30. In both treatments, split-time AI was performed based on estrous response. At 72 hours after PGF2α (Day 33), cows having expressed estrus received TAI; cows that failed to express estrus by 72 hours received TAI 24 hours later (96 hours after PGF2α on Day 34), with GnRH (100 µg im) administered to nonestrous cows. Estrus-detection transmitters were used from CIDR removal until AI to determine onset time of estrus expression both after CIDR removal and after PGF2α. Ovarian ultrasonography was performed at CIDR removal on Day 14, PGF2α on Day 30, and AI on Days 33 or 34. At CIDR removal on Day 14, diameter of the largest follicle present on the ovary was similar between treatments. The proportion of cows expressing estrus after CIDR removal tended to be higher (P = 0.09) among cows assigned to the 9-day CIDR-PG treatment (93%; 40 of 43) than among cows assigned to the 14-day CIDR-PG treatment (81%; 34 of 42). After PGF2α, a significantly higher proportion (P = 0.02) of cows expressed estrus after synchronization with the 9-day CIDR-PG treatment (91%; 39 of 43) than the 14-day CIDR-PG treatment (69%; 29 of 42). Consequently, pregnancy rate to TAI tended to be increased (P = 0.09) among the 9-day CIDR-PG treatment (76.7%; 33 of 43) compared with the 14-day CIDR-PG treatment (59.5%; 25 of 42). In summary, a long-term CIDR-based estrous synchronization protocol for postpartum beef cows was enhanced through administration of PGF2α at CIDR insertion and CIDR removal.

Risk of proximal colorectal neoplasia among asymptomatic patients with distal hyperplastic polyps.

PURPOSE: Many guidelines on colorectal cancer screening do not consider distal hyperplastic polyps to be a marker for proximal neoplasia. However, 11 of 17 published studies have shown an increased risk of proximal neoplasia in patients with distal hyperplastic polyps. Our goal is to assess the risk of proximal neoplasia in asymptomatic patients with distal hyperplastic polyps, compared to those with distal tubular adenomas or no distal polyps. METHODS: We assessed proximal (cecum, ascending, transverse colon and splenic flexure) and distal polyps in patients undergoing screening colonoscopy, classifying them into 3 groups: distal hyperplastic polyps only; distal adenomas with or without hyperplastic polyps; no distal polyps. The prevalence of proximal neoplasia and advanced neoplasia (polyps > or =1 cm, villous adenomas, or cancer) was compared among these groups. RESULTS: Of 2357 patients, 427 (18%) had neoplasia, including 103 (4%) with advanced neoplasia. Proximal neoplasia occurred in 175 (9%) of 1896 patients with no distal polyps, compared with 28 (12%) of 237 with distal hyperplastic polyps (P = 0.20) and 64 (29%) of 224 with distal adenomas (P <0.0001). Proximal advanced neoplasia occurred in 39 (2%) patients with no distal polyps, compared with 4 (2%) with distal hyperplastic polyps (P = 0.70) and 9 (4%) with distal adenomas (P = 0.13). CONCLUSIONS: Patients with distal hyperplastic polyps, unlike those with distal adenomas, do not exhibit an increased risk for proximal neoplasia or proximal advanced neoplasia compared to those with no distal polyps. The discovery of hyperplastic polyps on screening sigmoidoscopy should not prompt colonoscopy.

Improving the analysis of dinoflagellate phylogeny based on rDNA.

Phylogenetic studies of dinoflagellates are often conducted using rDNA sequences. In analyses to date, the monophyly of some of the major lineages of dinoflagellates remain to be demonstrated. There are several reasons for this uncertainty, one of which may be the use of models of evolution that may not closely fit the data. We constructed and examined alignments of SSU and partial LSU rRNA along with a concatenated alignment of the two molecules. The alignments showed several characteristics that may confound phylogeny reconstruction: paired helix (stem) regions that contain non-independently evolving sites, high levels of compositional heterogeneity among some of the sequences, high levels of incompatibility (homoplasy), and rate heterogeneity among sites. Taking into account these confounding factors, we analysed the data and found that the Gonyaulacales, a well-supported clade, may be the most recently diverged order. Other supported orders were, in the analysis based on SSU, the Suessiales and the Dinophysiales; however, the Gymnodiniales and Prorocentrales appeared to be polyphyletic. The Peridiniales without Heterocapsa species appeared as a monophyletic group in the analysis based on LSU; however, the support was low. The concatenated alignment did not provide a better phylogenetic resolution than the single gene alignments.

The Diversity of Eukaryotes.

The discipline of evolutionary protistology has emerged in the past 30 yr. There is as yet no agreed view of how protists are interrelated or how they should be classified. The foundations of a stable taxonomic superstructure for the protists and other eukaryotes lie in cataloging the diversity of the major monophyletic lineages of these organisms. The use of common patterns of cell organization (ultrastructural identity) seems to provide us with the most robust hypotheses of such lineages. These lineages are placed in 71 groups without identifiable sister taxa. These groups are here referred to as "major building blocks." For the first time, the compositions, ultrastructural identities, synapomorphies (where available), and subgroups of the major building blocks are summarized. More than 200 further lineages without clear identities are listed. This catalog includes all known major elements of the comprehensive evolutionary tree of protists and eukaryotes. Different approaches among protistologists to issues of nomenclature, ranking, and definitions of these groups are discussed, with particular reference to two groups-the stramenopiles and the Archezoa. The concept of "extended in-group" is introduced to refer to in-groups and the most proximate sister group and to assist in identifying the hierarchical location of taxa.

Open exchange of scientific knowledge and European copyright: The case of biodiversity information.

Background. The 7(th) Framework Programme for Research and Technological Development is helping the European Union to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme "Horizon 2020" aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights. We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information. Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation.