bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viruses and the cellular RNA decay machinery
Authors: Gaglia Marta Maria , Glaunsinger Britt A. 
Published: May 2010

AbstractThe ability to control cellular and viral gene expression, either globally or selectively, is central to a successful viral infection, and it is also crucial for the host to respond and eradicate pathogens. In eukaryotes, regulation of message stability contributes significantly to the control of gene expression and plays a prominent role in the normal physiology of a cell as well as in its response to environmental and pathogenic stresses. Not surprisingly, emerging evidence indicates that there are significant interactions between the eukaryotic RNA turnover machinery and a wide variety of viruses. Interestingly, in many cases viruses have evolved mechanisms not only to evade eradication by these pathways, but also to manipulate them for enhanced viral replication and gene expression. Given our incomplete understanding of how many of these pathways are normally regulated, viruses should be powerful tools to help deconstruct the complex networks and events governing eukaryotic RNA stability. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms
RNA in Disease and Development > RNA in Disease
RNase MRP and disease
Authors: Mattijssen Sandy , Welting Tim J. M. , Pruijn Ger J. M. 
Published: May 2010

AbstractThe human RNase MRP complex consists of a catalytic RNA and several protein components. RNase MRP is a ubiquitously expressed eukaryotic endoribonuclease that cleaves various RNAs, including ribosomal, messenger, and mitochondrial RNAs, in a highly specific fashion. In several autoimmune diseases autoantibodies targeting RNase MRP have been found. These so‐called anti‐Th/To autoantibodies, which most frequently can be detected in the sera of scleroderma patients, are directed to several protein components of the RNase MRP and the evolutionarily related RNase P complex. It is not yet known whether the anti‐Th/To immune response is an epiphenomenon or whether these autoantibodies play a role in the pathophysiology of the disease. The gene encoding the RNase MRP RNA was the first nuclear non‐coding RNA gene demonstrated to be associated with a genetic disease. Mutations in this gene are causing the highly pleiotropic disease cartilage‐hair hypoplasia (CHH). CHH patients are characterized by a short stature, hypoplastic hair, and short limbs. In addition, they show a predisposition to lymphomas and other cancers and suffer from defective T‐cell immunity. Since the identification of the first CHH‐associated mutations in 2001, many distinct mutations have been found in different patients. These mutations either affect the structure of the RNase MRP RNA or are located in the promoter region and reduce the expression levels. In this review article we will, after describing the biochemical aspects of RNase MRP, discuss the targeting of RNase MRP in autoimmunity and the role of mutations in the RNase MRP RNA gene in CHH. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

RNA-Based Catalysis > RNA‐Mediated Cleavage
Translation > Ribosome Biogenesis
RNA Turnover and Surveillance > Regulation of RNA Stability
RNA in Disease and Development > RNA in Disease
2,6‐Bis(pyrazol‐3‐yl)pyridine as Meridional Capping Ligand: Synthesis, Characterization, and Crystal Structure of the First Corresponding Hexanuclear Iron(III) Complex
Authors: Plaul Daniel , Spielberg Eike T. , Plass Winfried 
Published: May 2010

AbstractBased on the 2,6‐bis(pyrazol‐3‐yl)pyridine ligand (H2bpp) the hexanuclear iron(III) complex [Fe6(bpp)4(μ3‐O)2(μ‐OMe)3(μ‐OH)Cl2] (1) was synthesized. The reaction with iron(II) chloride and additional pyridine leads to the exclusive formation of the complex through self‐assembly process. Six octahedrally coordinated iron atoms are linked through the pyrazolido groups of four H2bpp ligands. These are further linked through bridging hydroxido, methoxido, and oxido groups. The complex has been characterized by IR spectroscopy, ESI mass spectrometry, elemental analysis and X‐ray crystallography. Temperature‐dependent magnetic measurements indicate strong antiferromagnetic exchange interaction between the high‐spin iron(III) ions within the complex, which leads to an S = 0 spin ground state. As a result of the two Fe3(μ3‐O) fragments two frustrated exchange pathways are present. In addition the properties of H2bpp as a potential capping ligand for the synthesis of heteroleptic trinuclear complexes based on the triaminoguanidine core is investigated.
Perioperative change in white blood cell count predicts outcome of hepatic resection for hepatocellular carcinoma
Authors: Fujiwara Yuki , Shiba Hiroaki , Furukawa Kenei , Iida Tomonori , Sakamoto Taro , Gocho Takeshi , Wakiyama Shigeki , Hirohara Shoichi , Ishida Yuichi , Misawa Takeyuki , Ohashi Toya , Yanaga Katsuhiko 
Published: May 2010

AbstractBackgroundIn spite of improvements in surgical management, hepatocellular carcinoma (HCC) still recurs after operation in 60–70% of patients. Therefore, we investigated the relation between perioperative change in white blood cell count (WBC) and tumor recurrence as well as survival in patients with HCC after hepatic resection.MethodsSubjects were 53 patients who underwent elective hepatic resection for HCC. We retrospectively examined the relation between perioperative change in WBC and recurrence of HCC as well as overall survival.ResultsAdvanced tumor stage and increasing of WBC on postoperative day (POD) 1 were positively associated with worse disease‐free survival rate on both univariate and multivariate analysis (p < 0.05). Advanced tumor stage, increasing of WBC on POD 1, and blood transfusion were positively associated with worse overall survival rate on univariate analysis (p < 0.05), while change in WBC was the only independent factor on multivariate analysis (p < 0.05).ConclusionsPerioperative change in WBC after elective hepatic resection for HCC is positively associated with recurrence and worse survival.
Mitochondrial fatty acid oxidation disorders: clinical presentation of long‐chain fatty acid oxidation defects before and after newborn screening
Authors: Spiekerkoetter Ute 
Published: May 2010

AbstractThe different long‐chain fatty acid oxidation defects present with similar heterogeneous clinical phenotypes of different severity. Organs mainly affected comprise the heart, liver, and skeletal muscles. All symptoms are reversible with sufficient energy supply. In some long‐chain fatty acid oxidation defects, disease‐specific symptoms occur. Only in disorders of the mitochondrial trifunctional protein (TFP) complex, including long‐chain 3‐hydroxyacyl‐coenzyme A (CoA) dehydrogenase (LCHAD) deficiency, neuropathy and retinopathy develop that are progressive and irreversible despite current treatment measures. In most long‐chain fatty acid oxidation defects, no clear genotype–phenotype correlation exists due to molecular heterogeneity. However, some isolated mutations have been identified to be associated with only mild phenotypes, e.g., the V243A mutation in very‐long‐chain acyl‐CoA dehydrogenase (VLCAD) deficiency. LCHAD deficiency is due to the prevalent homozygous 1528G>C mutation and presents with heterogeneous clinical phenotypes, suggesting the importance of other environmental and genetic factors. For some disorders, it was shown that residual enzyme activity measured in fibroblasts or lymphocytes correlated with severity of clinical phenotype. Implementation of newborn screening has significantly reduced morbidity and mortality of long‐chain fatty acid oxidation defects. However, the severest forms of TFP deficiency are still highly associated with neonatal death. Newborn screening also identifies a great number of mildly affected patients who may never develop clinical symptoms throughout life. However, later‐onset exercise‐induced myopathic symptoms remain characteristic clinical features of long‐chain fatty acid oxidation defects. Disease prevalence has increased with newborn screening.
An Analysis of Nursing Diagnoses for Patients Undergoing Procedures in a Brazilian Interventional Radiology Suite
Authors: Viegas Liza de Souza , Turrini Ruth Natalia Teresa , da Silva Bastos Cerullo Josinete Aparecida 
Published: May 2010

AbstractInnovations in minimally invasive surgery have led to more procedures being performed in the interventional radiology suite. It, therefore, is essential that nurses in radiology departments be competent to care for all types of patients. Use of nursing classification systems can improve care by providing standardized language for documentation. We conducted a project that involved 25 patients undergoing interventional radiology procedures between August and October 2006 in São Paulo, Brazil, to identify the most frequent North American Nursing Diagnosis Association (NANDA) nursing diagnoses used and then compared the NANDA diagnoses to Perioperative Nursing Data Set diagnoses. The most frequent nursing diagnoses in the participants were anxiety, chronic pain, inefficient tissue perfusion–peripheral, deficient knowledge, and risk for falls. These results are similar to diagnoses that have been reported in outpatient centers. The NANDA and Perioperative Nursing Data Set diagnoses were found to be similar.
Best Practices for Minimally Invasive Procedures
Authors: Ulmer Brenda C. 
Published: May 2010

AbstractTechniques and instrumentation for minimally invasive surgical procedures originated in gynecologic surgery, but the benefits of surgery with small incisions or no incisions at all have prompted the expansion of these techniques into numerous specialties. Technologies such as robotic assistance, single‐incision laparoscopic surgery, natural orifice transluminal endoscopic surgery, and video‐assisted thoracoscopic surgery have led to the continued expansion of minimally invasive surgery into new specialties. With this expansion, perioperative nurses and other members of the surgical team are required to continue to learn about new technology and instrumentation, as well as the techniques and challenges involved in using new technology, to help ensure the safety of their patients. This article explores the development of minimally invasive procedures and offers suggestions for increasing patient safety.
Measuring practitioner/therapist effects in randomised trials of low back pain and neck pain interventions in primary care settings
Authors: Lewis Martyn , Morley Stephen , van der Windt Danielle A.W.M. , Hay Elaine , Jellema Petra , Dziedzic Krysia , Main Chris J. 
Published: May 2010

AbstractIn psychological health treatment studies it has been shown that differences between therapists account for some of the non‐specific effect of treatment but this phenomenon has not so far systematically been investigated in musculoskeletal disorders. In this study we evaluated and compared the size and potential influence of the ‘practitioner effect’ (or ‘therapist effect’) in three randomised treatment trials of low back pain and neck pain patients in primary care. We calculated the proportion of variance in outcomes attributable to differences across practitioners, i.e. the practitioner–variance partition coefficient (p–vpc). As measures of outcome, we focused on self‐reported disability as the primary outcome, but we also investigated assessed psychological outcomes. The p–vpc for the disability measures ranged from 2.6% to 7.1% across trials and time points (post treatment and follow up). Estimates differed between treatment subgroups within trials; being highest in treatment subgroups assigned to psychosocial‐based interventions. A ‘practitioner effect’ does exist and is more pronounced in treatments involving greater psychosocial emphasis. This has implications for both practice and research in this clinical area. It highlights the importance of patient–practitioner interactions, and the need to address practitioner effects in designing and analysing outcome studies in low back pain and neck pain in primary care.
Statistical challenges for genome-wide association studies of suicidality using family data
Authors: Lasky-Su J. , Lange C. 
Published: May 2010

AbstractThe etiology of suicide is complex in nature with both environmental and genetic causes that are extremely diverse. This extensive heterogeneity weakens the relationship between genotype and phenotype and as a result, we face many challenges when studying the genetic etiology of suicide. We are now in the midst of a genetics revolution, where genotyping costs are decreasing and genotyping speed is increasing at a fast rate, allowing genetic association studies to genotype thousands to millions of SNPs that cover the entire human genome. As such, genome-wide association studies (GWAS) are now the norm. In this article we address several statistical challenges that occur when studying the genetic etiology of suicidality in the age of the genetics revolution. These challenges include: (1) the large number of statistical tests; (2) complex phenotypes that are difficult to quantify; and (3) modest genetic effect sizes. We address these statistical issues in the context of family-based study designs. Specifically, we discuss several statistical extensions of family-based association tests (FBATs) that work to alleviate these challenges. As our intention is to describe how statistical methodology may work to identify disease variants for suicidality, we avoid the mathematical details of the methodologies presented.
Study of Completed Archaeal Genomes and Proteomes: Hypothesis of Strong Mutational AT Pressure Existed in Their Common Predecessor
Authors: Khrustalev Vladislav V. , Barkovsky Eugene V. 
Published: May 2010

Abstract
The number of completely sequenced archaeal genomes has been sufficient for a large-scale bioinformatic study. We have conducted analyses for each coding region from 36 archaeal genomes using the original CGS algorithm by calculating the total GC content (G+C), GC content in first, second and third codon positions as well as in fourfold and twofold degenerated sites from third codon positions, levels of arginine codon usage (Arg2: AGA/G; Arg4: CGX), levels of amino acid usage and the entropy of amino acid content distribution. In archaeal genomes with strong GC pressure, arginine is coded preferably by GC-rich Arg4 codons, whereas in most of archaeal genomes with G+C&lt;0.6, arginine is coded preferably by AT-rich Arg2 codons. In the genome of Haloquadratum walsbyi, which is closely related to GC-rich archaea, GC content has decreased mostly in third codon positions, while Arg4&gt;&gt;Arg2 bias still persists. Proteomes of archaeal species carry characteristic amino acid biases: levels of isoleucine and lysine are elevated, while levels of alanine, histidine, glutamine and cytosine are relatively decreased. Numerous genomic and proteomic biases observed can be explained by the hypothesis of previously existed strong mutational AT pressure in the common predecessor of all archaea.
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
Authors: Wang Dapeng , Zhang Yubin , Zhang Zhang , Zhu Jiang , Yu Jun 
Published: May 2010

Abstract
We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5’ to 3’ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.
More on Moore on ‘Existence’
Authors: Tully R.E. 
Published: May 2010

G.E. Moore divided his well-known essay, “Is Existence a Predicate?” into two parts. The first has become famous as an early example of “ordinary language” analysis, while the second (a mere 2½ pages) has been universally neglected, for what appear to be several obvious reasons:(1) Moore's arguments in Part I are forthright and seem decisive. He deploys grammar and logic to show how the sentence ‘Tame tigers exist’ differs from ‘Tame tigers growl’, and thus to answer convincingly the question posed by the essay's title. By contrast, the arguments of Part II are compressed, tentative and obscure. It seems neither an obvious nor a needed sequel to Part I.
Perception
Authors: Odegard Douglas 
Published: May 2010

I Shall offer a realist theory of perception which in an important sense is neither direct nor representational nor causal.Let us say that we directly perceive something if perceiving it enables us to know of its existence without having evidence of its existence. In this sense, direct perception allows us to have “direct knowledge” of what we perceive. For example, I see after-images directly, since I can know of their existence without having visual evidence of their existence. I do not have to look at them with my eyes. Granted, I do need evidence in order to know that they are after-images; but not in order to know of their existence as colours or shapes. Also, I do have to see them in order to know that they exist. But this is not a condition of having evidence. It is only a condition of their existence, which in turn is a truth condition of my knowing.
Kierkegaard on philosophy
Authors: Johnson Ralph H. 
Published: May 2010

At The end of the Concluding Unscientific Postscript, in the Appendix entitled “For an Understanding with the Reader,” Johannes Climacus, the pseudonymous author, renders the following verdict:So then the book is superfluous; let no one therefore take the pains to appeal to it as an authority; for he who thus appeals to it has eo ipso misunderstood it.
Diagnosing the causes of territory abandonment by the Endangered Egyptian vulture Neophron percnopterus: the importance of traditional pastoralism and regional conservation
Authors: Mateo-Tomás Patricia , Olea Pedro P. 
Published: May 2010

AbstractIdentifying threats to declining species and prescribing ways of preventing their extinction are basic challenges for biodiversity conservation. We analysed the causes underlying the loss of territories of the Endangered Egyptian vulture Neophron percnopterus in a key population at the north-western edge of its distribution in Europe by developing multi-scale models that combined factors from nest site to landscape. We used generalized linear models and an information-theoretic approach to identify the optimal combination of scales and resolutions that could explain territorial abandonment. Those models combining nest-site and landscape scales considerably improved prediction ability compared to those considering only one scale. The best combined model had a high predictive ability (96.9% of correctly classified cases). Small cliffs at high altitudes in rugged areas with declining livestock (especially of sheep and goats) increased the likelihood of territory abandonment. Our findings highlight the importance of developing region-specific multi-scale models to determine reliably the factors driving territory loss and of designing effective conservation strategies accordingly. Conservation measures for the studied population should be developed at two spatial scales. At the smaller scale it is necessary to closely control nest sites to avoid direct disturbances. At a larger scale it is essential to implement policies that can support traditional pastoralism.
Prior residency does not always pay off – co-infections inDaphnia
Authors: LOHR JENNIFER N. , YIN MINGBO , WOLINSKA JUSTYNA 
Published: May 2010

SUMMARYThe epidemiological and ecological processes which govern the success of multiple-species co-infections are as yet unresolved. Here we investigated prior versus late residency within hosts, meaning which parasite contacts the host first, to determine if the outcomes of intra-host competition are altered. We infected a single genotype of the waterfleaDaphnia galeatawith both the intestinal protozoanCaullerya mesniliand the haemolymph fungusMetschnikowiasp. (single genotype of each parasite species), as single infections, simultaneous co-infections and as sequential co-infections, with each parasite given 4 days prior residency. Simultaneous co-infections were significantly more virulent than both single infections and sequential co-infections, as measured by a decreased host life span and fecundity. Further, in addition to theDaphniahost, the parasites also suffered fitness decreases in simultaneous co-infections, as measured by spore production. The sequential co-infections, however, had mixed effects:C. mesnilibenefited from prior residency, whereasMetschnikowiasp. experienced a decline in fitness. Our results show that multiple-species co-infections ofDaphniamay be more virulent than single infections, and that prior residency does not always provide a competitive advantage.
Molecular characterization ofNeospora caninumMAG1, a dense granule protein secreted into the parasitophorous vacuole, and associated with the cyst wall and the cyst matrix
Authors: GUIONAUD CHRISTOPHE , HEMPHILL ANDREW , MEVISSEN MEIKE , ALAEDDINE FERIAL 
Published: May 2010

SUMMARYInNeospora caninumandToxoplasma gondii, the parasitophorous vacuole (PV) is synthesized at the time of infection. During tachyzoite-to-bradyzoite stage conversion, the PV is later transformed into a tissue cyst that allows parasites to survive in their host for extended periods of time. We report on the characterization of NcMAG1, theN. caninumorthologue ofT. gondiiMAG1 (matrix antigen 1; TgMAG1). The 456 amino acid predicted NcMAG1 protein is 54% identical to TgMAG1. By immunoblotting, a rabbit antiserum raised against recombinant NcMAG1 detected a major product of ~67 kDa in extracts ofN. caninumtachyzoite-infected Vero cells, which was stained more prominently in extracts of infected Vero cells treated to inducein vitrobradyzoite conversion. Immunofluorescence and TEM localized the protein mainly within the cyst wall and the cyst matrix. In both tachyzoites and bradyzoites, NcMAG1 was associated with the parasite dense granules. Comparison between NcMAG1 and TgMAG1 amino acid sequences revealed that the C-terminal conserved regions exhibit 66% identity, while the N-terminal variable regions exhibit only 32% identity. Antibodies against NcMAG1-conserved region cross-reacted with the orthologuous protein inT. gondiibut those against the variable region did not. This indicates that the variable region possesses unique antigenic characteristics.
A new mechanism for science-policy transfer and biodiversity governance?
Authors: SOBERON JORGE M. , SARUKHAN JOSE K. 
Published: May 2010

SUMMARYNew initiatives are being proposed to create knowledge-transfer mechanisms between biodiversity science and so-called ‘decision makers’ that are apparently ignoring some of the significant differences to which biodiversity governance is subject at different scales. Shifting scales seriously change the rules of knowledge transfer; some implications of this are explored. Appropriate scope and focus are vital for international initiatives. There is no substitute for the full development of local capacities, and the multinational lending agencies interested in the conservation of biodiversity, the achievement of the Millennium Development Goals, and others should support such national efforts and establish regional training facilities to help generate the human and basic institutional capacities needed.