Systematic expression profiling of the mouse transcriptome using RIKEN cDNA mircoarrays

The number of known mRNA transcripts in the mouse has been greatly expanded by the RIKEN Mouse Gene Encyclopedia project. Validation of their reproducible expression in a tissue is an important contribution to the study of functional genomics. In this report, we determine the expression profile of 57,931 clones on 20 mouse tissues using cDNA microarrays. Of these 57,931 clones, 22,928 clones correspond to the FANTOM2 clone set. The set represents 20,234 transcriptional units (TUs) out of 33,409 TUs in the FANTOM2 set. We identified 7206 separate clones that satisfied stringent criteria for tissue-specific expression. Gene Ontology terms were assigned for these 7206 clones, and the proportion of 'molecular function' ontology for each tissue-specific clone was examined. These data will provide insights into the function of each tissue. Tissue-specific gene expression profiles obtained using our cDNA microarrays were also compared with the data extracted from the GNF Expression Atlas based on Affymetrix microarrays. One major outcome of the RIKEN transcriptome analysis is the identification of numerous nonprotein-coding mRNAs. The expression profile was also used to obtain evidence of expression for putative noncoding RNAs. In addition, 1926 clones (70%) of 2768 clones that were categorized as unknown EST, and 1969 (58%) clones of 3388 clones that were categorized as unclassifiable were also shown to be reproducibly expressed.

Quality of life instruments in studies of menorrhagia: a systematic review

BACKGROUND: The use of quality of life (QoL) instruments in menorrhagia research is increasing but there is concern that not enough emphasis is placed on patient-focus in these measurements, i.e. on issues which are of importance to patients and reflect their experiences and concerns (clinical face validity). The objective was to assess the quality of QoL instruments in studies of menorrhagia. STUDY DESIGN: A systematic review of published research. Papers were identified through MEDLINE (1966-April 2000), EMBASE (1980-April 2000), Science Citation Index (1981-April 2000), Social Science Citation Index (1981-April 2000), CINAHL (1982-1999) and PsychLIT (1966-1999), and by manual searching of bibliographies of known primary and review articles. Studies were selected if they assessed women with menorrhagia for life quality, either developing QoL instruments or applying them as an outcome measure. Selected studies were assessed for quality of their QoL instruments, using a 17 items checklist including 10 items for clinical face validity (issues of relevance to patients' expectations and concerns) and 7 items for measurement properties (such as reliability, responsiveness, etc.). RESULTS: A total of 19 articles, 8 on instrument development and 11 on application, were included in the review. The generic Short Form 36 Health Survey Questionnaire (SF36) was used in 12/19 (63%) studies. Only two studies developed new specific QoL instruments for menorrhagia but they complied with 7/17 (41%) and 10/17 (59%) of the quality criteria. Quality assessment showed that only 7/19 (37%) studies complied with more than half the criteria for face validity whereas 17/19 (90%) studies complied with more than half of the criteria for measurement properties (P = 0.0001). CONCLUSION: Among existing QoL instruments, there is good compliance with the quality criteria for measurement properties but not with those for clinical face validity. There is a need to develop methodologically sound disease specific QoL instruments in menorrhagia focussing both on face validity and measurement properties.

Quality of life instruments in studies of menorrhagia: a systematic review

BACKGROUND: The use of quality of life (QoL) instruments in menorrhagia research is increasing but there is concern that not enough emphasis is placed on patient-focus in these measurements, i.e. on issues which are of importance to patients and reflect their experiences and concerns (clinical face validity). The objective was to assess the quality of QoL instruments in studies of menorrhagia. STUDY DESIGN: A systematic review of published research. Papers were identified through MEDLINE (1966-April 2000), EMBASE (1980-April 2000), Science Citation Index (1981-April 2000), Social Science Citation Index (1981-April 2000), CINAHL (1982-1999) and PsychLIT (1966-1999), and by manual searching of bibliographies of known primary and review articles. Studies were selected if they assessed women with menorrhagia for life quality, either developing QoL instruments or applying them as an outcome measure. Selected studies were assessed for quality of their QoL instruments, using a 17 items checklist including 10 items for clinical face validity (issues of relevance to patients' expectations and concerns) and 7 items for measurement properties (such as reliability, responsiveness, etc.). RESULTS: A total of 19 articles, 8 on instrument development and 11 on application, were included in the review. The generic Short Form 36 Health Survey Questionnaire (SF36) was used in 12/19 (63%) studies. Only two studies developed new specific QoL instruments for menorrhagia but they complied with 7/17 (41%) and 10/17 (59%) of the quality criteria. Quality assessment showed that only 7/19 (37%) studies complied with more than half the criteria for face validity whereas 17/19 (90%) studies complied with more than half of the criteria for measurement properties (P = 0.0001). CONCLUSION: Among existing QoL instruments, there is good compliance with the quality criteria for measurement properties but not with those for clinical face validity. There is a need to develop methodologically sound disease specific QoL instruments in menorrhagia focussing both on face validity and measurement properties.

Systematic review of Late Jurassic sauropods from the Museu Geológico collections (Lisboa, Portugal)

The Museu Geológico collections house some of the first sauropod references of the Lusitanian Basin Upper Jurassic record, including the Lourinhasaurus alenquerensis and Lusotitan atalaiensis lectotypes, previously considered as new species of the Apatosaurus and Brachiosaurus genera, respectively. Several fragmentary specimens have been classical referred to those taxa, but the most part of these systematic attributions are not supported herein, excluding a caudal vertebra from Maceira (MG 8804) considered as cf. Lusotitan atalaiensis. From the material housed in the Museu Geológico were identified basal eusauropods (indeterminate eusauropods and turiasaurs) and neosauropods (indeterminate neosauropods, diplodods and camarasaurids and basal titanosauriforms). Middle caudal vertebrae with lateral fossae, ventral hollow border by pronounced ventrolateral crests and quadrangular cross-section suggest for the presence of diplodocine diplodocids in north area of the Lusitanian Basin Central Sector during the Late Jurassic. A humerus collected from Praia dos Frades (MG 4976) is attributed to cf. Duriatitan humerocristatus suggesting the presence of shared sauropod forms between the Portugal and United Kingdom during the Late Jurassic. Duriatitan is an indeterminate member of Eusauropoda and the discovery of new material in both territories is necessary to confirm this systematic approach. The studied material is in according with the previous recorded paleobiodiversity for the sauropod clade during the Portuguese Late Jurassic, which includes basal eusauropods (including turiasaurs), diplodocids and macronarians (including camarasaurids and basal titanosauriforms).

A review on systematic and taxonomic of the Persian Gulf fish species, based on geographical distribution pattern and habitat diversity, using by GIS

During the period from 2011 - 2015 with the aim of this study was to systematically review and in particular the revised classification of the Persian Gulf (and the Strait of Hormuz) and to obtain new information about the final confirmed list of fish species of Iranian waters of the Persian Gulf (and Hormuz Strait), samples of museums, surveys and sampling, and comparative study of all available sources and documentation was done. Classification systematic of sharks and batoids and bony fishes. Based on the results, the final list of approved fish of the Persian Gulf (including the Strait of Hormuz and Gulf of Oman border region) are 907 species in 157 families, of which 93 species of fish with 28 cartilaginous families (including 18 families with 60 species and 10 families with 34 species of shark and batoids); and 129 families with 814 species of bony fishes are. The presence of 11 new family with only one representative species in the area include Veliferidae, Zeidae, Sebastidae, Stomiidae, Dalatiidae, Zanclidae, Pempheridae, Lophiidae Kuhliidae, Etmoptridae and Chlorophthalmidae also recently introduced and approved. The two families based Creediidae Clinidae and their larvae samples for newly identified area. 62 families with mono-species and 25 families with more than 10 species are present including Gobiidae (53), Carangide (48), Labride (41), Blenniidae (34), Apogonidae (32) and Lutjanidae (31) of bony fishes, Carcharhinidae (26) of sharks and Dasyatidae (12) in terms of number of species of batoids most families to have their data partitioning. Also, 13 species as well as endemic species introduced the Persian Gulf and have been approved in terms of geographical expansion of the Persian Gulf are unique to the area.Two species of the family Poeciliidae and Cyprinodontidae have species of fresh water to the brackish coastal habitats have found a way;in addition to 11 types of families Carcharhinidae, Clupeidae, Chanidae, Gobidae, Mugilidae, Sparidae also as a species, with a focus on freshwater river basins in the south of the country have been found. In this study, it was found that out of 907 species have been reported from the study area, 294 species (32.4 %) to benthic habitats (Benthic habitats) and 613 species (67.6 %) in pelagic habitats (Pelagic habitats) belong. Coral reefs and rocky habitats in the range of benthic fish (129 species - 14.3 %) and reef associated fishes in the range of pelagic fishes (432 species – 47.8 %), the highest number and percentage of habitat diversity (Species habitats) have been allocated. As well as fish habitats with sea grass and algae beds in benthic habitat (17 species- 1.9 %) and pelagic - Oceanic (Open sea) in the whole pelagic fish (30 species – 3.3 %), the lowest number and percentage of habitat diversity into account. From the perspective of animal geography (Zoogeography) and habitat overlaps and similarities (Habitat overlapping) fish fauna of the Persian Gulf compared with other similar seas (tropical and subtropical, and warm temperate) in the Indian Ocean area - calm on the surface, based on the presence of certain species that the fish fauna of the Persian Gulf to the Red Sea and the Bay of Bengal (East Arabian Sea) compared to other regions in the Indian Ocean (Pacific) is closer (about 50%), and the Mediterranean (East area) and The Hawaiian Islands have the lowest overlap and similarity of habitat and species (about 10%).

A systematic review of environmental correlates of obesity-related dietary behaviors in youth

There is increasing interest in the role the environment plays in shaping the dietary behavior of youth, particularly in the context of obesity prevention. An overview of environmental factors associated with obesity-related dietary behaviors among youth is needed to inform the development of interventions. A systematic review of observational studies on environmental correlates of energy, fat, fruit/ vegetable, snack/fast food and soft drink intakes in children (4–12 years) and adolescents (13–18 years) was conducted. The results were summarized using the analysis grid for environments linked to obesity. The 58 papers reviewed mostly focused on sociocultural and economical–environmental factors at the household level. The most consistent associations were found between parental intake and children’s fat, fruit/vegetable intakes, parent and sibling intake with adolescent’s energy and fat intakes and parental education with adolescent’s fruit/ vegetable intake. A less consistent but positive association was found for availability and accessibility on children’s fruit/vegetable intake. Environmental factors are predominantly studied at the household level and focus on sociocultural and economic aspects. Most consistent associations were found for parental influences (parental intake and education).More studies examining environmental factors using longitudinal study designs and validated measures are needed for solid evidence to inform interventions.

Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

Entrepreneurial bricolage : towards systematic empirical testing

The behavioral theory of “entrepreneurial bricolage” attempts to understand what entrepreneurs do when faced with resource constraints. Most research about bricolage, defined as “making do by applying combinations of the resources at hand to new problems and opportunities” (Baker & Nelson 2005: 333), has been qualitative and inductive (Garud & Karnoe, 2003). Although this has created a small body of rich descriptions and interesting insights, little deductive theory has been developed and the relationship between bricolage and firm performance has not been systematically tested. In particular, prior research has suggested bricolage can have both beneficial and harmful effects. Ciborra’s (1996) study of Olivetti suggested that bricolage helped Olivetti to adapt, but simultaneously constrained firm effectiveness. Baker & Nelson (2005) suggested that bricolage may be harmful at very high levels, but more helpful if used judiciously. Other research suggests that firm innovativeness may play an important role in shaping the outcomes of bricolage (Anderson 2008). In this paper, we theorize and provide preliminary test of the bricolage-performance relationship and how it is affected by firm innovativeness.

Does venture opportunity variation matter? investigating systematic process differences between innovative and imitative new ventures

The central thesis in the article is that the venture creation process is different for innovative versus imitative ventures. This holds up; the pace of the process differs by type of venture as do, in line with theory-based hypotheses, the effects of certain human capital (HC) and social capital (SC) predictors. Importantly, and somewhat unexpectedly, the theoretically derived models using HC, SC, and certain controls are relatively successful explaining progress in the creation process for the minority of innovative ventures, but achieve very limited success for the imitative majority. This may be due to a rationalistic bias in conventional theorizing and suggests that there is need for considerable theoretical development regarding the important phenomenon of new venture creation processes. Another important result is that the building up of instrumental social capital, which we assess comprehensively and as a time variant construct, is important for making progress with both types of ventures, and increasingly, so as the process progresses. This result corroborates with stronger operationalization and more appropriate analysis method what previously published research has only been able to hint at.

Incomplete pregnancy and risk of ovarian cancer : results from two Australian case-control studies and systematic review

Although full-term pregnancies reduce the risk of ovarian cancer, it has not been conclusively established whether incomplete pregnancies also influence risk. We investigated the relationship between a history of incomplete pregnancy and incident epithelial ovarian cancer among over 4,500 women who participated in two large Australian population-based case-control studies in 1990-1993 and 2002-2005. They provided responses to detailed questions about their reproductive histories and other personal factors. Summary odds ratios (OR) and confidence intervals (CI) derived from each study using the same covariates were aggregated. We found no significant associations between the number of incomplete pregnancies and ovarian cancer, for parous (OR = 0.98, 95% CI: 0.89, 1.08) or nulliparous (OR = 1.06, 95% CI: 0.75, 1.48) women, nor for the number of spontaneous or induced abortions and ovarian cancer for parous women (OR = 0.95, 95% CI 0.82, 1.09; OR = 1.08, 95% CI: 0.86, 1.36) or nulliparous women (OR = 1.2, 95% CI: 0.6, 2.4; OR = 0.8, 95% CI: 0.47, 1.38), respectively. A systematic review of 37 previous studies of the topic confirmed our findings that a history of incomplete pregnancy does not influence a woman’s risk of epithelial ovarian cancer.

Integrated versus non-integrated management and care for clients with co-occurring mental health and substance use disorders : a qualitative systematic review of randomised controlled trials

The purpose of this paper is to conduct a qualitative review of randomised controlled trials in relation to the treatment of adults with co-occurring mental health and substance use disorder (MH/SUD). In particular, integrated approaches are compared with non-integrated approaches to treatment. Ten articles were identified for inclusion in the review. The findings are equivocal with regard to the superior efficacy of integrated approaches to treatment, although the many limitations of the studies need to be considered in our understanding of this finding. Clearly, this is an extremely challenging client group to engage and maintain in intervention research, and the complexity and variability of the problems render control particularly difficult. The lack of available evidence to support the superiority of integration is discussed in relation to these challenges. Much remains to be investigated with regard to integrated management and care for people with co-occurring and MH/SUD, particularly for specific combinations of dual diagnosis and giving consideration to the level of inter-relatedness between the disorders.

The use of narrative text for injury surveillance research : a systematic review

Objective: To summarise the extent to which narrative text fields in administrative health data are used to gather information about the event resulting in presentation to a health care provider for treatment of an injury, and to highlight best practise approaches to conducting narrative text interrogation for injury surveillance purposes.----- Design: Systematic review----- Data sources: Electronic databases searched included CINAHL, Google Scholar, Medline, Proquest, PubMed and PubMed Central.. Snowballing strategies were employed by searching the bibliographies of retrieved references to identify relevant associated articles.----- Selection criteria: Papers were selected if the study used a health-related database and if the study objectives were to a) use text field to identify injury cases or use text fields to extract additional information on injury circumstances not available from coded data or b) use text fields to assess accuracy of coded data fields for injury-related cases or c) describe methods/approaches for extracting injury information from text fields.----- Methods: The papers identified through the search were independently screened by two authors for inclusion, resulting in 41 papers selected for review. Due to heterogeneity between studies metaanalysis was not performed.----- Results: The majority of papers reviewed focused on describing injury epidemiology trends using coded data and text fields to supplement coded data (28 papers), with these studies demonstrating the value of text data for providing more specific information beyond what had been coded to enable case selection or provide circumstantial information. Caveats were expressed in terms of the consistency and completeness of recording of text information resulting in underestimates when using these data. Four coding validation papers were reviewed with these studies showing the utility of text data for validating and checking the accuracy of coded data. Seven studies (9 papers) described methods for interrogating injury text fields for systematic extraction of information, with a combination of manual and semi-automated methods used to refine and develop algorithms for extraction and classification of coded data from text. Quality assurance approaches to assessing the robustness of the methods for extracting text data was only discussed in 8 of the epidemiology papers, and 1 of the coding validation papers. All of the text interrogation methodology papers described systematic approaches to ensuring the quality of the approach.----- Conclusions: Manual review and coding approaches, text search methods, and statistical tools have been utilised to extract data from narrative text and translate it into useable, detailed injury event information. These techniques can and have been applied to administrative datasets to identify specific injury types and add value to previously coded injury datasets. Only a few studies thoroughly described the methods which were used for text mining and less than half of the studies which were reviewed used/described quality assurance methods for ensuring the robustness of the approach. New techniques utilising semi-automated computerised approaches and Bayesian/clustering statistical methods offer the potential to further develop and standardise the analysis of narrative text for injury surveillance.

Recruiting older adults to health research studies : a systematic review

Objective: To provide a systematic review of papers comparing the effectiveness of different strategies to recruit older adults (aged 50 years and over) to participate in health research studies, to guide successful recruitment in future research. Methods: Four major databases were searched for papers published between 1995 and 2008 with: target group aged 50 years or over; participants allocated to receive one of two or more recruitment strategies; and an outcome measure of response rate or enrolment in study. Results: Twelve papers were included in the review. Conclusion: For postal questionnaires, recruitment strategies used with older adults had comparable outcomes to those used to recruit from the general population. For other types of studies, strategies involving face-to-face contact may be more effective than indirect methods, but this needs to be balanced against feasibility. Overall, little evidence on the topic exists and more rigorous investigation is necessary.