bluuebunny/crossref_metadata_2025_split huggingface dataset:
Costa Rican species ofNematoctonus(anamorphic Pleurotaceae)
Authors: Koziak Alexandra T.E. , Diaz Felipe Chavarria , Diaz Joel , Garcia Maria , Janzen Daniel H. , Thorn R. Greg 
Published: September 2007

Nematoctonus (Hyphomycetes) and Hohenbuehelia (Agaricales, Pleurotaceae) are the names for the asexual and sexual stages of a genus of nematode-destroying fungi (Basidiomycota). Six morphospecies of Nematoctonus, all previously described, were isolated from fruiting bodies of Hohenbuehelia and from 439 samples of soil and organic debris collected in all 12 Holdridge life zones in Costa Rica. Nematoctonus was recorded in all but three life zones at the lowest and highest altitudes: tropical dry forest, tropical moist forest, and subalpine rain paramó. Isolates of Nematoctonus were identified by the micromorphology of their conidia and adhesive knobs, which are usually an hourglass-shaped secretory cell surrounded by a drop of mucilage. Adhesive knobs were found either exclusively on hyphae in predatory species ( Nematoctonus robustus F.R. Jones), exclusively on germinated conidia in parasitoid species ( Nematoctonus leptosporus Drechsler, Nematoctonus pachysporus Drechsler, and Nematoctonus tylosporus Drechsler) or on both hyphae and germinated conidia in a group we term “intermediate predators” ( Nematoctonus angustatus Thorn & G.L. Barron, Nematoctonus geogenius Thorn & G.L. Barron, and one monokaryotic isolate of N. robustus). Teleomorph–anamorph connections, made by culturing the anamorph from a teleomorph fruiting body, were made for N. angustatus (Hohenbuehelia angustata (Berk.) Singer), N. geogenius (Hohenbuehelia petalodes (Fr.) Schulz.), N. leptosporus (an unidentified Hohenbuehelia), and N. robustus ( Hohenbuehelia grisea (Peck) Singer).
Phylogeny of Vitaceae based on the nuclearGAI1gene sequencesThis article is one of a selection of papers presented at the symposium onVitisat the XVII International Botanical Congress held in Vienna, Austria, in 2005.
Authors: Wen Jun , Nie Ze-Long , Soejima Akiko , Meng Ying 
Published: September 2007

Phylogenetic analysis of 105 nuclear GAI1 sequences of Vitaceae provided a fairly robust phylogeny, largely congruent with the recently published chloroplast data of the family. In the GAI1 phylogeny, Cayratia Juss., Tetrastigma (Miq.) Planch., and Cyphostemma (Planch.) Alston form a clade. Cyphostemma and Tetrastigma are both monophyletic, and Cayratia is paraphyletic. Ampelopsis Michx is paraphyletic with the African Rhoicissus Planch. and the South American Cissus striata Ruiz & Pav. and its close relatives (e.g., Cissus simsiana Roem. & Schult.) nested within it. The pinnately leaved Ampelopsis forms a subclade, and the simple and palmately leaved Ampelopsis constitutes another subclade. All species of Cissus L. sampled from Asia, Africa, and Central and South America (except the C. striata complex) form a monophyletic group. Pterisanthes Blume of southeastern Asia forms a clade with the Asian Ampelocissus Planch. Vitis L. is monophyletic and forms a larger clade with the tropical Ampelocissus and Pterisanthes . Parthenocissus Planch., forms a clade with Yua C.L. Li, with each genus reportedly monophyletic. Cissus from the Old World is paraphyletic with the neotropical core Cissus nested within it. The basal grade of Cissus consists of taxa from Africa. The African-Asian biogeographic relationships are complex, with several intercontinental disjunctions. The Northern Hemisphere Ampelopsis is most closely related to the South American C. striata complex and the African Rhoicissus .
Phylogenetic analyses of Nematoctonus and Hohenbuehelia (Pleurotaceae)
Authors: Koziak Alexandra T.E. , Cheng Kei Chin , Thorn R. Greg 
Published: September 2007

Hohenbuehelia (Agaricales, Pleurotaceae) and Nematoctonus (Hyphomycetes) are the names for the sexual and asexual stages of a genus of nematode-destroying fungi (Basidiomycota). We obtained partial sequences of nuclear ribosomal DNA, including the internal transcribed spacer region and the 5′ end of the large subunit, of 37 isolates of Hohenbuehelia and Nematoctonus representing 13 of the 16 described species in Nematoctonus. Phylogenetic analyses support Hohenbuehelia–Nematoctonus as a monophyletic clade of the Pleurotaceae, within which the species were placed in five main subclades. Exclusively predatory species ( Nematoctonus brevisporus Thorn & G.L. Barron, Nematoctonus campylosporus Drechsler, Nematoctonus robustus F.R. Jones, and Nematoctonus sp. UAMH 5317) appear to be basal. In these species, adhesive knobs to capture prey are produced on their hyphae but not on their conidia. A single mycelial individual may feed on many nematodes. From these have arisen both exclusively parasitoid species ( Nematoctonus cylindrosporus Thorn & G.L. Barron, Nematoctonus leiosporus Drechsler, Nematoctonus leptosporus Drechsler, Nematoctonus pachysporus Drechsler, Nematoctonus tylosporus Drechsler), and species that we call intermediate predators ( Nematoctonus angustatus Thorn & G.L. Barron, Nematoctonus concurrens Drechsler, Nematoctonus geogenius Thorn & GL. Barron, Nematoctonus hamatus Thorn & G.L. Barron, and Nematoctonus subreniformis Thorn & G.L. Barron). Exclusively parasitoid species have conidia that germinate to form sticky knobs that attach to passing nematodes but lack adhesive knobs on the hyphae. Each mycelial individual feeds on only one nematode. Intermediate predators have adhesive knobs both on hyphae and on germinated conidia and can act in both predatory and parasitoid modes. Most morphospecies are resolved as monophyletic, but sequences of additional gene regions are required to clarify species limits within the N. angustatus – N. geogenius group.
Bidirectional transcription of a novel chimeric gene mapping to mouse chromosome Yq
Authors: Ellis Peter JI , Ferguson Lydia , Clemente Emily J , Affara Nabeel A 
Published: September 2007

Abstract

Background
The male-specific region of the mouse Y chromosome long arm (MSYq) contains three known highly multi-copy X-Y homologous gene families, Ssty1/2, Sly and Asty. Deletions on MSYq lead to teratozoospermia and subfertility or infertility, with a sex ratio skew in the offspring of subfertile MSYqdel males

Results
We report the highly unusual genomic structure of a novel MSYq locus, Orly, and a diverse set of spermatid-specific transcripts arising from copies of this locus. Orly is composed of partial copies of Ssty1, Asty and Sly arranged in sequence. The Ssty1- and Sly- derived segments are in antisense orientation relative to each other, leading to bi-directional transcription of Orly. Genome search and phylogenetic tree analysis is used to determine the order of events in mouse Yq evolution. We find that Orly is the most recent gene to arise on Yq, and that subsequently there was massive expansion in copy number of all Yq-linked genes.

Conclusion

Orly has an unprecedented chimeric structure, and generates both "forward" (Orly) and "reverse" (Orlyos) transcripts arising from the promoters at each end of the locus. The region of overlap of known Orly and Orlyos transcripts is homologous to Sly intron 2. We propose that Orly may be involved in an intragenomic conflict between mouse X and Y chromosomes, and that this process underlies the massive expansion in copy number of the genes on MSYq and their X homologues.
Generalizing Terwilliger's likelihood approach: a new score statistic to test for genetic association
Authors: el Galta Rachid , Uitte de Willige Shirley , de Visser Marieke CH , Helmer Quinta , Hsu Li , Houwing-Duistermaat Jeanine J 
Published: September 2007

Abstract

Background:
In this paper, we propose a one degree of freedom test for association between a candidate gene and a binary trait. This method is a generalization of Terwilliger's likelihood ratio statistic and is especially powerful for the situation of one associated haplotype. As an alternative to the likelihood ratio statistic, we derive a score statistic, which has a tractable expression. For haplotype analysis, we assume that phase is known.

Results:
By means of a simulation study, we compare the performance of the score statistic to Pearson's chi-square statistic and the likelihood ratio statistic proposed by Terwilliger. We illustrate the method on three candidate genes studied in the Leiden Thrombophilia Study.

Conclusion:
We conclude that the statistic follows a chi square distribution under the null hypothesis and that the score statistic is more powerful than Terwilliger's likelihood ratio statistic when the associated haplotype has frequency between 0.1 and 0.4 and has a small impact on the studied disorder. With regard to Pearson's chi-square statistic, the score statistic has more power when the associated haplotype has frequency above 0.2 and the number of variants is above five.
Deep analysis of cellular transcriptomes – LongSAGE versus classic MPSS
Authors: Hene Lawrence , Sreenu Vattipally B , Vuong Mai T , Abidi S Hussain I , Sutton Julian K , Rowland-Jones Sarah L , Davis Simon J , Evans Edward J 
Published: September 2007

Abstract

Background
Deep transcriptome analysis will underpin a large fraction of post-genomic biology. 'Closed' technologies, such as microarray analysis, only detect the set of transcripts chosen for analysis, whereas 'open' e.g. tag-based technologies are capable of identifying all possible transcripts, including those that were previously uncharacterized. Although new technologies are now emerging, at present the major resources for open-type analysis are the many publicly available SAGE (serial analysis of gene expression) and MPSS (massively parallel signature sequencing) libraries. These technologies have never been compared for their utility in the context of deep transcriptome mining.

Results
We used a single LongSAGE library of 503,431 tags and a "classic" MPSS library of 1,744,173 tags, both prepared from the same T cell-derived RNA sample, to compare the ability of each method to probe, at considerable depth, a human cellular transcriptome. We show that even though LongSAGE is more error-prone than MPSS, our LongSAGE library nevertheless generated 6.3-fold more genome-matching (and therefore likely error-free) tags than the MPSS library. An analysis of a set of 8,132 known genes detectable by both methods, and for which there is no ambiguity about tag matching, shows that MPSS detects only half (54%) the number of transcripts identified by SAGE (3,617 versus 1,955). Analysis of two additional MPSS libraries shows that each library samples a different subset of transcripts, and that in combination the three MPSS libraries (4,274,992 tags in total) still only detect 73% of the genes identified in our test set using SAGE. The fraction of transcripts detected by MPSS is likely to be even lower for uncharacterized transcripts, which tend to be more weakly expressed. The source of the loss of complexity in MPSS libraries compared to SAGE is unclear, but its effects become more severe with each sequencing cycle (i.e. as MPSS tag length increases).

Conclusion
We show that MPSS libraries are significantly less complex than much smaller SAGE libraries, revealing a serious bias in the generation of MPSS data unlikely to have been circumvented by later technological improvements. Our results emphasize the need for the rigorous testing of new expression profiling technologies.
Identification of proteins involved in the functioning of Riftia pachyptila symbiosis by Subtractive Suppression Hybridization
Authors: Sanchez Sophie , Hourdez Stéphane , Lallier François H 
Published: September 2007

AbstractBackgroundSince its discovery around deep sea hydrothermal vents of the Galapagos Rift about 30 years ago, the chemoautotrophic symbiosis between the vestimentiferan tubewormRiftia pachyptilaand its symbiotic sulfide-oxidizing γ-proteobacteria has been extensively studied. However, studies on the tubeworm host were essentially targeted, biochemical approaches. We decided to use a global molecular approach to identify new proteins involved in metabolite exchanges and assimilation by the host. We used a Subtractive Suppression Hybridization approach (SSH) in an unusual way, by comparing pairs of tissues from a single individual. We chose to identify the sequences preferentially expressed in the branchial plume tissue (the only organ in contact with the sea water) and in the trophosome (the organ housing the symbiotic bacteria) using the body wall as a reference tissue because it is supposedly not involved in metabolite exchanges in this species.ResultsWe produced four cDNA libraries: i) body wall-subtracted branchial plume library (BR-BW), ii) and its reverse library, branchial plume-subtracted body wall library (BW-BR), iii) body wall-subtracted trophosome library (TR-BW), iv) and its reverse library, trophosome-subtracted body wall library (BW-TR). For each library, we sequenced about 200 clones resulting in 45 different sequences on average in each library (58 and 59 cDNAs for BR-BW and TR-BW libraries respectively). Overall, half of the contigs matched records found in the databases with good E-values. After quantitative PCR analysis, it resulted that 16S, Major Vault Protein, carbonic anhydrase (RpCAbr), cathepsin and chitinase precursor transcripts were highly represented in the branchial plume tissue compared to the trophosome and the body wall tissues, whereas carbonic anhydrase (RpCAtr), myohemerythrin, a putative T-Cell receptor and one non identified transcript were highly specific of the trophosome tissue.ConclusionQuantitative PCR analyses were congruent with our libraries results thereby confirming the existence of tissue-specific transcripts identified by SSH. We focused our study on the transcripts we identified as the most interesting ones based on the BLAST results. Some of the keys to understanding metabolite exchanges may remain in the sequences we could not identify (hypothetical proteins and no similarity found). These sequences will have to be better studied by a longer -or complete- sequencing to check their identity, and then by verifying the expression level of the transcripts in different parts of the worm.
Optimising reproductive and child health outcomes by building evidence-based research and practice in South East Asia (SEA-ORCHID): study protocol
Authors: Henderson-Smart David J , Lumbiganon Pisake , Festin Mario R , Ho Jacqueline J , Mohammad Hakimi , McDonald Steve J , Green Sally , Crowther Caroline A ,   the SEA-ORCHID Study Group
Published: September 2007

Abstract

Background
Disorders related to pregnancy and childbirth are a major health issue in South East Asia. They represent one of the biggest health risk differentials between the developed and developing world. Our broad research question is: Can the health of mothers and babies in Thailand, Indonesia, the Philippines and Malaysia be improved by increasing the local capacity for the synthesis of research, implementation of effective interventions, and identification of gaps in knowledge needing further research?

Methods/Design
The project is a before-after study which planned to benefit from and extend existing regional and international networks. Over five years the project was designed to comprise five phases; pre-study, pre-intervention, intervention, outcome assessment and reporting/dissemination. The study was proposed to be conducted across seven project nodes: four in South East Asia and three in Australia. Each South East Asian study node was planned to be established within an existing department of obstetrics and gynaecology or neonatology and was intended to form the project coordinating centre and focus for evidence-based practice activities within that region. Nine hospitals in South East Asia planned to participate, representing a range of clinical settings. The three project nodes in Australia were intended to provide project support.
The intervention was planned to consist of capacity-strengthening activities targeted at three groups: generators of evidence, users of evidence and teachers of evidence. The primary outcome was established as changes in adherence to recommended clinical practices from baseline to completion of the project and impact on health outcomes.

Discussion
The SEA-ORCHID project was intended to improve care during pregnancy and the perinatal period of mothers and their babies in South East Asia. The possible benefits extend beyond this however, as at the end of this project there is hoped to be an existing network of South East Asian researchers and health care providers with the capacity to generalise this model to other health priority areas. It is anticipated that this project facilitate ongoing development of evidence-based practice and policy in South East Asia through attracting long-term funding, expansion into other hospitals and community-based care and the establishment of nodes in other countries.
Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer
Authors: Yu Jack X , Sieuwerts Anieta M , Zhang Yi , Martens John WM , Smid Marcel , Klijn Jan GM , Wang Yixin , Foekens John A 
Published: September 2007

Abstract

Background
Published prognostic gene signatures in breast cancer have few genes in common. Here we provide a rationale for this observation by studying the prognostic power and the underlying biological pathways of different gene signatures.

Methods
Gene signatures to predict the development of metastases in estrogen receptor-positive and estrogen receptor-negative tumors were identified using 500 re-sampled training sets and mapping to Gene Ontology Biological Process to identify over-represented pathways. The Global Test program confirmed that gene expression profilings in the common pathways were associated with the metastasis of the patients.

Results
The apoptotic pathway and cell division, or cell growth regulation and G-protein coupled receptor signal transduction, were most significantly associated with the metastatic capability of estrogen receptor-positive or estrogen-negative tumors, respectively. A gene signature derived of the common pathways predicted metastasis in an independent cohort. Mapping of the pathways represented by different published prognostic signatures showed that they share 53% of the identified pathways.

Conclusion
We show that divergent gene sets classifying patients for the same clinical endpoint represent similar biological processes and that pathway-derived signatures can be used to predict prognosis. Furthermore, our study reveals that the underlying biology related to aggressiveness of estrogen receptor subgroups of breast cancer is quite different.
The survey of serum retinol of the children aged 0~4 years in Zhejiang Province, China
Authors: Yang Rongwang , Li Rong , Mao Shujiong , Sun Liying , Huang Xinwen , Ji Chai , Zhu Zhiwei , Wu Lingling , Qin Yufeng , Zhao Zhengyan 
Published: September 2007

AbstractBackgroundVitamin A can have a positive impact on growth and development of children, but vitamin A deficiency (VAD) was found to be a public health problem in Zhejiang Province, China in 1998. There have been no studies on this topic in Zhejiang Province recently. This study was designed to evaluate the serum retinol levels of children aged 0~4 years in Zhejiang Province, southeast China. This epidemiological data will help design supplementation strategies for vitamin A in high-risk groups and improve their vitamin A status.MethodsChildren were randomly recruited for this study using a stratified sampling method. A blood sample was collected from each child. Assessment included C-reactive protein (CRP), serum retinol measured with HPLC and a questionnaire completed providing for family information and nutritional status. Logistic regression analysis was used to evaluate the risk factors for VAD in children.ResultsA group of 357 subjects aged 1 day to 4 years were recruited. The mean plasma retinol concentration was 1.653 (sd 0.47) μmol/L. There were 3.08% (11/357) of children affected with VAD, and 7.28% (26/357) of children had low vitamin A status, but none of the children showed any clinical symptoms of VAD. There was no significant difference in the levels of plasma retinol and the incidence rate of VAD between male and female children. Multivariate logistic regression analysis showed that living in urban region, having parents with good education and taking vitamin A capsule regularly prevented children from VAD, whereas being young (less than 2 years old) was a risk factor.ConclusionLow vitamin A status remains a nutritional problem in Zhejiang Province. The high-risk group in this study were young, dwelled in rural regions, had parents with poor education and did not take a regular vitamin A containing supplement.
Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation
Authors: Porter Corrine J , Matthews Jacqueline M , Mackay Joel P , Pursglove Sharon E , Schmidberger Jason W , Leedman Peter J , Pero Stephanie C , Krag David N , Wilce Matthew CJ , Wilce Jacqueline A 
Published: September 2007

Abstract

Background
Human g rowth factor r eceptor b ound protein 7 (Grb7) is an adapter protein that mediates the coupling of tyrosine kinases with their downstream signaling pathways. Grb7 is frequently overexpressed in invasive and metastatic human cancers and is implicated in cancer progression via its interaction with the ErbB2 receptor and focal adhesion kinase (FAK) that play critical roles in cell proliferation and migration. It is thus a prime target for the development of novel anti-cancer therapies. Recently, an inhibitory peptide (G7-18NATE) has been developed which binds specifically to the Grb7 SH2 domain and is able to attenuate cancer cell proliferation and migration in various cancer cell lines.

Results
As a first step towards understanding how Grb7 may be inhibited by G7-18NATE, we solved the crystal structure of the Grb7 SH2 domain to 2.1 Å resolution. We describe the details of the peptide binding site underlying target specificity, as well as the dimer interface of Grb 7 SH2. Dimer formation of Grb7 was determined to be in the μM range using analytical ultracentrifugation for both full-length Grb7 and the SH2 domain alone, suggesting the SH2 domain forms the basis of a physiological dimer. ITC measurements of the interaction of the G7-18NATE peptide with the Grb7 SH2 domain revealed that it binds with a binding affinity of Kd = ~35.7 μM and NMR spectroscopy titration experiments revealed that peptide binding causes perturbations to both the ligand binding surface of the Grb7 SH2 domain as well as to the dimer interface, suggesting that dimerisation of Grb7 is impacted on by peptide binding.

Conclusion
Together the data allow us to propose a model of the Grb7 SH2 domain/G7-18NATE interaction and to rationalize the basis for the observed binding specificity and affinity. We propose that the current study will assist with the development of second generation Grb7 SH2 domain inhibitors, potentially leading to novel inhibitors of cancer cell migration and invasion.