bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards an index of all known species: the Catalogue of Life, its rationale, design and use
Authors: CACHUELA‐PALACIO Monalisa 
Published: September 2008

AbstractThe Catalogue of Life, created by Species 2000 and the Integrated Taxonomic Information System, has the ambitious aim of creating a uniform and validated index of the world's known species for use as a practical tool in inventorying and monitoring biodiversity worldwide. This is achieved by accessing an array of taxonomic databases created and made available by individual, project and institutional custodians through taxonomic and biodiversity initiatives. A standard data set is delivered for every known species, drawn from Species 2000 contributing databases. Data are provided to the Species 2000 Philippine office, compiled annually and published in CD‐ROM format. Species 2000 also includes the Species Locator Service, which gives a responsible opinion as to the actual species currently recognized by taxonomists and their accepted names, and the Name Service that assists users in checking the spelling and original publication details for a wider range of names, including species not yet incorporated in the Species Locator Service. The Species Locator Service is available as the Dynamic Checklist, which is used to search for the scientific name of an organism online, and the Annual Checklist, which is a stable index produced once a year and is available on CD‐ROM and online. Catalogue of Life currently covers more than 272 000 species and 32 000 infraspecies, with 181 000 synonyms. It has 217 000 common names, 87 000 references and 20 contributing databases that encompass all known animals, plants, fungi and microorganisms.
Brief report on the status of Kozlov's pika, Ochotona koslowi (Büchner), in the east Kunlun mountains of China
Authors: LI Weidong , ZHANG Huibin , LIU Zhihu 
Published: September 2008

AbstractKoslov's pika, Ochotona koslowi (Büchner), was surveyed in western China. This endangered species is poorly known. We determined that it is a burrowing pika, and lives in social family groups at high densities. It primarily occupies high‐elevation cold grassland vegetation. It appears to have a high reproductive rate. More emphasis should be placed on research into this unique species in China.
The actuality of Lamarck: towards the bicentenary of his Philosophic Zoologique
Authors: POR Francis Dov 
Published: September 2008

AbstractLamarck, a son of the age of natural philosophy and revolutionary ideas, turned to zoology, the field in which he made his major impact, in his old age. By then, the world had already shifted towards a different intellectual atmosphere and, due to this anachronism, he was snubbed and even ridiculed by the mainstream neo‐Darwinists. Yet his basic ideas about the active role of organisms in and the progressive unraveling of evolution stubbornly survived along the academic fringes and, more importantly, among the humanistic writers. Recent developments in genetic inheritance, embryology, immunology and behavioral studies vindicate, at least in part, the 200‐year‐old vision of Lamarck.
Spectral numbers in Floer theories
Authors: Usher Michael 
Published: September 2008

AbstractThe chain complexes underlying Floer homology theories typically carry a real-valued filtration, allowing one to associate to each Floer homology class a spectral number defined as the infimum of the filtration levels of chains representing that class. These spectral numbers have been studied extensively in the case of Hamiltonian Floer homology by Oh, Schwarz and others. We prove that the spectral number associated to any nonzero Floer homology class is always finite, and that the infimum in the definition of the spectral number is always attained. In the Hamiltonian case, this implies that what is known as the ‘nondegenerate spectrality’ axiom holds on all closed symplectic manifolds. Our proofs are entirely algebraic and apply to any Floer-type theory (including Novikov homology) satisfying certain standard formal properties. The key ingredient is a theorem about the existence of best approximations of arbitrary elements of finitely generated free modules over Novikov rings by elements of prescribed submodules with respect to a certain family of non-Archimedean metrics.
Lakshmibai–Seshadri paths of level-zero shape and one-dimensional sums associated to level-zero fundamental representations
Authors: Naito Satoshi , Sagaki Daisuke 
Published: September 2008

AbstractWe give an interpretation of the energy function and classically restricted one-dimensional sums associated to tensor products of level-zero fundamental representations of quantum affine algebras in terms of Lakshmibai–Seshadri paths of level-zero shape.
Primary Clearance of Murine Gammaherpesvirus 68 by PKCθ−/−CD8 T Cells Is Compromised in the Absence of Help from CD4 T Cells
Authors: Dias Peter , Shea Ashley L. , Inglis Chandra , Giannoni Francesca , Lee Lian Ni , Sarawar Sally R. 
Published: September 2008

ABSTRACTCD4 T cells are dispensable for acute control of murine gammaherpesvirus 68 (MHV-68) but are necessary for effective long-term control of the virus by CD8 T cells. In contrast, protein kinase C θ (PKCθ) is not essential for either acute or long-term viral control. However, we found that while either CD4 or CD8 T cells could mediate the clearance of MHV-68 from the lungs of PKCθ+/+mice, PKCθ−/−mice depleted of either subset failed to clear the virus. These data suggest that there are two alternative pathways for MHV-68 clearance, one dependent on CD4 T cells and the other on PKCθ. Protection mediated by the latter appears to be short-lived. These observations may help to explain the differential requirement for PKCθ in various models of CD8 T-cell activation and differences in the costimulatory requirements for acute and long-term viral control.
Identification of a Movement Protein of the
Tenuivirus
Rice Stripe Virus
Authors: Xiong Ruyi , Wu Jianxiang , Zhou Yijun , Zhou Xueping 
Published: September 2008

ABSTRACT

Rice stripe virus (RSV) is the type member of the genus
Tenuivirus
. RSV has four single-stranded RNAs and causes severe disease in rice fields in different parts of China. To date, no reports have described how RSV spreads within host plants or the viral and/or host factor(s) required for tenuivirus movement. We investigated functions of six RSV-encoded proteins using
trans
-complementation experiments and biolistic bombardment. We demonstrate that NSvc4, encoded by RSV RNA4, supports the intercellular trafficking of a movement-deficient
Potato virus X
in
Nicotiana benthamiana
leaves. We also determined that upon biolistic bombardment or agroinfiltration, NSvc4:enhanced green fluorescent protein (eGFP) fusion proteins localize predominantly near or within the walls of onion and tobacco epidermal cells. In addition, the NSvc4:eGFP fusion protein can move from initially bombarded cells to neighboring cells in
Nicotiana benthamiana
leaves. Immunocytochemistry using tissue sections from RSV-infected rice leaves and an RSV NSvc4-specific antibody showed that the NSvc4 protein accumulated in walls of RSV-infected leaf cells. Gel retardation assays revealed that the NSvc4 protein interacts with single-stranded RNA in vitro, a common feature of many reported plant viral movement proteins (MPs). RSV NSvc4 failed to interact with the RSV nucleocapsid protein using yeast two-hybrid assays. Taken together, our data indicate that RSV NSvc4 is likely an MP of the virus. This is the first report describing a tenuivirus MP.
Hypophosphataemia at a large academic hospital in South Africa
Authors: Hoffmann M , Zemlin A E , Meyer W P , Erasmus R T 
Published: September 2008

Aim:The aim of this study was to determine the most common causes of hypophosphataemia (⩽0.5 mmol/l) in a hospital population in order to identify patient groups at risk of developing the condition.Methods:The study was conducted at Tygerberg Hospital, a tertiary care centre in the Western Cape, South Africa. All patients identified with a phosphate level ⩽0.5 mmol/l during an 18-month period were included in the study. Medical records of these patients were reviewed.Results:Of all the requests received for serum phosphate determination by the laboratory, 2% (861 out of 45 394 requests) were ⩽0.5 mmol/l. Thirty per cent (30%; n = 189) of the patients in the study population died during their hospital stay. Most (45%; n = 278) of the patients with low phosphate levels occurred in an intensive care setting, whereas 10% (n = 63) were most likely due to refeeding, and 6% (n = 35) had neoplastic disease. Sepsis was implicated as a contributing factor in 26% (n = 162).Conclusion:Severe hypophosphataemia is associated with a very high mortality (30%, n = 189). Patients with a high risk of developing hypophosphataemia include those in an intensive care unit (ICU), patients suffering from neoplastic diseases, possible refeeding syndrome and septic patients. Regular phosphate determination is recommended in these patients to facilitate early diagnosis of hypophosphataemia.
Overexpression of von Hippel-Lindau protein in skeletal muscles of patients with chronic obstructive pulmonary disease
Authors: Jatta K , Eliason G , Portela-Gomes G M , Grimelius L , Caro O , Nilholm L , Sirjsö A , Piehl-Aulin K , Abdel-Halim S M 
Published: September 2008

Background:A significant number of patients with chronic obstructive pulmonary disease (COPD) exhibit skeletal muscle wasting and decreased capillary area formation, which correlate with increased mortality.Aim:To determine the molecular mechanisms mediating decreased capillary formation in COPD.Methods:24 patients with COPD and 12 matching controls were recruited. Patients with COPD were classified into mild, moderate and severe groups according to GOLD (global initiative for chronic obstructive lung disease) criteria. Biopsy specimens were obtained from the tibialis anterior muscle. Fibre typing and capillary formation, together with messenger RNA (mRNA) expression of hypoxia-inducible factors (HIF1α and HIF3α), vascular endothelial growth factors (VEGF-A, VEGF-B and VEGF-C isoforms) and von Hippel-Lindau (VHL) protein, were determined. VHL expression and localisation were further studied by immunohistochemistry.Results:Skeletal muscle capillary formation decreased significantly with increasing disease severity. Compared with controls, a tendency to mRNA overexpression of HIF1α, HIF3α and VEGF isoforms was observed in mild and moderate COPD, which decreased at the severe stage. In contrast, skeletal muscle biopsy samples from patients with COPD exhibited significant overexpression of VHL at both the mRNA and protein level by immunohistochemistry. VHL protein was further determined to be localised to satellite cells.Conclusions:Overexpression of VHL was identified in the skeletal muscle of patients with COPD. Increased VHL activity may have a negative effect on transduction of the hypoxic signal and may contribute to decreased capillarisation in skeletal muscles of patients with COPD.
Human herpes virus 6 in archival cardiac tissues from children with idiopathic dilated cardiomyopathy or congenital heart disease
Authors: Comar M , D’Agaro P , Campello C , Poli A , Breinholt J P , Towbin J A , Vatta M 
Published: September 2008

Objective:To explore the possible role of human herpes virus 6 (HHV-6) in cardiac disorders in childhood in a retrospective study on archival specimens of explanted hearts.Methods:16 children (median age at transplantation 11.0 years) with idiopathic dilated cardiomyopathy (DCM) and 19 children (median age at transplantation 1.0 year) with congenital heart disease (CHD), previously found to be negative for other cardiotropic viruses such as enteroviruses, adenovirus, parvovirus B19, cytomegalovirus and Epstein–Barr virus, were tested for HHV-6 by quantitative real-time PCR and by genotyping. In addition, HHV-7/8 infection was investigated by qualitative PCR.Results:HHV-6 B variant was detected in 11 of 35 samples (31.4%) with a mean viral load of 3.1×102 copies/μg of DNA. When assessed by heart disorder, the prevalence was different in the two groups (43.7% in DCM and 21% in CHD) while the mean viral loads were similar. In a logistic multivariate analysis HHV-6 was independently associated with DCM, taking CHD as reference and adjusting for age (best estimate: OR = 6.94; 95% CI 1.00 to 49.85; p = 0.05).Conclusions:Although the clinical significance of the results is unknown, HHV-6 B genome is frequently detected in explanted hearts from children with DCM and to a lesser extent with CHD, thus adding evidence for HHV-6 cardiac involvement.
ON KHOVANOV'S COBORDISM THEORY FOR $\mathfrak{su}_3$ KNOT HOMOLOGY
Authors: MORRISON SCOTT , NIEH ARI 
Published: September 2008

We reconsider the [Formula: see text] link homology theory defined by Knovanov in [9] and generalized by Mackaay and Vaz in [15]. With some slight modifications, we describe the theory as a map from the planar algebra of tangles to a planar algebra of complexes of "cobordisms with seams" (actually, a "canopolis"), making it local in the sense of Bar-Natan's local [Formula: see text] theory of [2]. We show that this "seamed cobordism canopolis" decategorifies to give precisely what you had both hope for and expect: Kuperberg's [Formula: see text] spider defined in [14]. We conjecture an answer to an even more interesting question about the decategorification of the Karoubi envelope of our cobordism theory. Finally, we describe how the theory is actually completely computable, and give a detailed calculation of the [Formula: see text] homology of the (2,n) torus knots.
A Key Role for Cyclic AMP-Responsive Element Binding Protein in Hypoxia-Mediated Activation of the Angiogenesis Factor CCN1 (CYR61) in Tumor Cells
Authors: Meyuhas Ronit , Pikarsky Eli , Tavor Einat , Klar Avihu , Abramovitch Rinat , Hochman Jacob , Lago Tal Goshen , Honigman Alik 
Published: September 2008

AbstractHypoxia is a prominent feature of solid tumors known to contribute to malignant progression and therapeutic resistance. Cancer cells adapt to hypoxia using various pathways, allowing tumors to thrive in a low oxygen state. Induction of new blood vessel formation via the secretion of proangiogenic factors is one of the main adaptive responses engaged by tumor cells under hypoxic conditions. Hypoxia-inducible factor 1 (HIF-1) is a transcription factor that plays a pivotal role in mediating such responses. In addition, several other transcription factors have also been implicated in hypoxic gene regulation, either independently or in cooperation with HIF-1. In this work, we show that the expression of the angiogenesis-related, immediate early gene CCN1 (formerly known as CYR61), considered to be involved in tumor growth and invasiveness, is enhanced upon hypoxia stress primarily in a protein kinase A and cyclic AMP-responsive element binding protein (CREB) and CRE–dependent manner in various cell lines. The hypoxia-mediated activation of the CCN1 promoter is independent of HIF-1 and HIF-2, as shown by small interfering RNA knockdown. We identify the cis element in the mouse CCN1 promoter responsible for CREB binding to be one of two partial CRE sites present in the promoter. Moreover, we report for the first time that CREB-mediated CCN1 transcription is enhanced in hypoxic regions of tumors in vivo. Identifying and characterizing the molecular mechanisms that govern the response of tumors to hypoxia may be instrumental to identify the tumors that will respond favorably to inhibition of angiogenesis and thus lead to the development of treatments that could complement hypoxia-inducing treatment modalities. (Mol Cancer Res 2008;6(9):1397–409)
The Circadian Gene NPAS2, a Putative Tumor Suppressor, Is Involved in DNA Damage Response
Authors: Hoffman Aaron E. , Zheng Tongzhang , Ba Yue , Zhu Yong 
Published: September 2008

Abstract
Apart from regulating sleep and wakefulness, the circadian system may play an important role in other biological processes, including pathways involved in tumorigenesis. Two genetic association studies recently conducted by our lab have shown that a missense mutation in neuronal PAS domain protein 2 (NPAS2), a core circadian gene and transcriptional regulator, is significantly associated with risk of breast cancer and non–Hodgkin's lymphoma. Our current functional analyses provide the first in vitro evidence further demonstrating that cells with RNA interference–mediated depletion of NPAS2 fail to exhibit the expected cell cycle delay in response to mutagen treatment. DNA repair capacity, as measured by the comet assay, is also impaired. Moreover, a pathway-based PCR expression array of genes important for DNA damage signaling showed that knockdown of NPAS2 significantly represses the expression of several cell cycle and DNA repair genes. Thus, NPAS2 may play a role in tumorigenesis by affecting expression of cancer-related genes and could be considered a novel tumor suppressor. (Mol Cancer Res 2008;6(9):1461–8)
Repression of the Desmocollin 2 Gene Expression in Human Colon Cancer Cells Is Relieved by the Homeodomain Transcription Factors Cdx1 and Cdx2
Authors: Funakoshi Shinsuke , Ezaki Toshihiko , Kong Jianping , Guo Rong Jun , Lynch John P. 
Published: September 2008

Abstract
Desmosomes are intracellular junctions that provide strong cell-cell adhesion in epithelia and cardiac muscle. Their disruption causes several human diseases and contributes to the epithelial-to-mesenchymal transition observed in cancer. Desmocollin 2 (DSC2) is a cadherin superfamily member and a critical component of desmosomes found in intestinal epithelium. However, the mechanism regulating DSC2 gene expression in intestinal cells is not known. Cdx1 and Cdx2 are homeodomain transcription factors that regulate intestine-specific gene expression. Cdx expression in the past has been associated with the induction of desmosomes. We now show that the DSC2 gene is a transcriptional target for Cdx1 and Cdx2. Colon cancer cell lines retaining Cdx2 expression typically express DSC2. Restoration of Cdx expression in Colo 205 cells induced DSC2 mRNA and protein and the formation of desmosomes. The 5′-flanking region of the DSC2 promoter contains two consensus Cdx-binding sites. Electrophoretic mobility shift assays show that Cdx1 and Cdx2 bind these sites in vitro, and chromatin immunoprecipitation confirmed Cdx2 binding in vivo. DSC2 promoter truncations established that these regions are Cdx responsive. The truncations also identify a region of the promoter in which potent transcriptional repressors act. This repressor activity is relieved by Cdx binding. We conclude that the homeodomain transcription factors Cdx1 and Cdx2 regulate DSC2 gene expression in intestinal epithelia by reversing the actions of a transcriptional repressor. The regulation of desmosomal junctions by Cdx contributes to normal intestinal epithelial columnar morphology and likely antagonizes the epithelial-to-mesenchymal transition necessary for the metastasis of colon cancer cells in humans. (Mol Cancer Res 2008;6(9):1478–90)
Sox7 Is an Independent Checkpoint for β-Catenin Function in Prostate and Colon Epithelial Cells
Authors: Guo Lizheng , Zhong Diansheng , Lau Stephen , Liu Xiuju , Dong Xue-Yuan , Sun Xiaodong , Yang Vincent W. , Vertino Paula M. , Moreno Carlos S. , Varma Vijay , Dong Jin-Tang , Zhou Wei 
Published: September 2008

Abstract
The presence of somatic β-catenin mutations in some prostate cancers implies that aberrant WNT signaling is involved in the cancer development. Although β-catenin stability is regulated by a multicomponent destruction complex, mutational alterations of β-catenin or other components of the destruction complexes are rare in prostate tumors. Therefore, β-catenin may be regulated by another protein in the prostate. In fact, recent linkage and somatic deletion analyses in prostate cancers reveal a 1.4-Mb candidate tumor suppressor locus on 8p23.1, which includes the Sox7 gene. Here we show that Sox7 protein expression was indeed down-regulated in 47% (15 of 32) of prostate adenocarcinomas. In addition, Sox7 mRNA was down-regulated in 60% of snap-frozen tumors. This down-regulation was found to be due to tumor-specific promoter hypermethylation, which was present in 48% (10 of 21) of primary prostate tumors and 44% (11 of 25) of prostate cancer cell lines/xenografts. We discovered that Sox7 protein physically interacts with β-catenin and suppresses β-catenin–mediated transcription by depleting active β-catenin. Furthermore, in HCT116 colorectal cancer cell lines with Sox7 inactivation, ectopic Sox7 expression suppressed cell proliferation and inhibited transcription that was activated by an endogenous mutant β-catenin. Although nearly all colorectal cancers contain mutations in β-catenin or adenomatous polyposis coli/axin, epigenetic silencing of Sox7 was still observed. These data suggest that Sox7 is a tumor suppressor that functions as an independent checkpoint for β-catenin transcriptional activity. Inactivation of Sox7 could promote the development of a majority of colorectal tumors and approximately half of prostate tumors. (Mol Cancer Res 2008;6(9):1421–10)
Autoubiquitination of BCA2 RING E3 Ligase Regulates Its Own Stability and Affects Cell Migration
Authors: Amemiya Yutaka , Azmi Peter , Seth Arun 
Published: September 2008

Abstract
Accumulating evidence suggests that ubiquitination plays a role in cancer by changing the function of key cellular proteins. Previously, we isolated BCA2 gene from a library enriched for breast tumor mRNAs. The BCA2 protein is a RING-type E3 ubiquitin ligase and is overexpressed in human breast tumors. In order to deduce the biochemical and biological function of BCA2, we searched for BCA2-binding partners using human breast and fetal brain cDNA libraries and BacterioMatch two-hybrid system. We identified 62 interacting partners, the majority of which were found to encode ubiquitin precursor proteins including ubiquitin C and ubiquitin A-52. Using several deletion and point mutants, we found that the BCA2 zinc finger (BZF) domain at the NH2 terminus specifically binds ubiquitin and ubiquitinated proteins. The autoubiquitination activity of BCA2, RING-H2 mutant, BZF mutant, and various lysine mutants of BCA2 were investigated. Our results indicate that the BCA2 protein is strongly ubiquitinated and no ubiquitination is detected with the BCA2 RING-H2 mutant, indicating that the RING domain is essential for autoubiquitination. Mutation of the K26 and K32 lysines in the BZF domain also abrogated autoubiquitination activity. Interestingly, mutation of the K232 and K260 lysines in and near the RING domain resulted in an increase in autoubiquitination activity. Additionally, in cellular migration assays, BCA2 mutants showed altered cell motility compared with wild-type BCA2. On the basis of these findings, we propose that BCA2 might be an important factor regulating breast cancer cell migration/metastasis. We put forward a novel model for BCA2 E3 ligase–mediated cell regulation. (Mol Cancer Res 2008;6(9):1385–96)