bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality of reporting of descriptive studies in implant dentistry. Critical aspects in design, outcome assessment and clinical relevance
Authors: Meijer Henny J.A. , Raghoebar Gerry M. 
Published: March 2012

AbstractObjectivesThe aim of this study was to conduct a review on quality of reporting on descriptive studies in implant dentistry using the STROBE Statement and to analyse possible changes in quality of reporting on descriptive studies in implant dentistry over time.Material and MethodsA hand search to select descriptive studies was carried out in seven dental journals, which were thought to have interest in the field of dental implants. Issues of the years 1990, 1995, 2000, 2005 and 2010 were screened. The STROBE Statement with 22 criteria to match was used to determine the quality of an article.ResultsTotally 4657 titles and abstracts were screened; 260 of them were found to be reporting on a descriptive study. Percentages of properly addressed items were 46% in 1990, 56% in 1995, 54% in 2000, 59% in 2005 and 70% in 2010.ConclusionFrom this review can be concluded that quality of reporting on descriptive studies in implant dentistry is low; there is some improvement from 1990 to 2010, but it does not exceed 70% coverage of the possible to address items.
Clinical research in implant dentistry: evaluation of implant‐supported restorations, aesthetic and patient‐reported outcomes
Authors: Lang Niklaus P. , Zitzmann Nicola U. ,   on behalf of Working Group 3 of the VIII European Workshop on Periodontology
Published: March 2012

AbstractThe articles discussed in working group 3 dealt with specific aspects of clinical research. In this context, the literature reporting on survival and complication rates of implant‐supported or implant‐tooth supported restorations in longitudinal studies of at least 5 years were discussed. The second aspect dealt with the evaluation of aesthetic outcomes in clinical studies and the related index systems available. Finally, the third aspect discussed dealt with patient‐reported outcome measures (PROMs). A detailed appraisal of the available methodology was presented.
Second harvest–Is there sufficient stubble for biofuel production in Australia?
Authors: Herr Alexander , O'Connell Deborah , Dunlop Michael , Unkovich Murray , Poulton Perry , Poole Michael 
Published: March 2012

AbstractIdentifying the location and amount of grain crop residues (stubble) in Australia is necessary for determining the viability of potential biofuel plant locations. We combined 22 years of crop statistics with harvest indices and land use to arrive at spatially explicit stubble productivity figures. Stubble quantities using different focal radii and from different seasons provide an insight into the feasibility of its use for bioenergy. We focus on areas where the stubble concentrations within a 50 km radius were at least 500 kt per year; the amount suggested for a viable lignocellolosic bioethanol facility. The outcome of this study has been to show, for the first time, where there are large amounts of stubble in Australia. Whether the supply of stubble is sufficiently constant over time and indeed available at a price that is economic for a biofuel plant must be subject to future work.
EXPLAINING THE LIMITS OF OLSSON'S IMPOSSIBILITY RESULT
Authors: WHEELER GREGORY 
Published: March 2012

abstractIn his groundbreaking book, Against Coherence (2005), Erik Olsson presents an ingenious impossibility theorem that appears to show that there is no informative relationship between probabilistic measures of coherence and higher likelihood of truth. Although Olsson's result provides an important insight into probabilistic models of epistemological coherence, the scope of his negative result is more limited than generally appreciated. The key issue is the role conditional independence conditions play within the witness testimony model Olsson uses to establish his result. Olsson maintains that his witness model yields charitable ceteris paribus conditions for any theory of probabilistic coherence. Not so. In fact, Olsson's model, like Bayesian witness models in general, selects a peculiar class of models that are in no way representative of the range of options available to coherence theorists. Recent positive results suggest that there is a way to develop a formal theory of coherence after all. Further, although Bayesian witness models are not conducive to the truth, they are conducive to reliability.
COHERENTISM AND JUSTIFIED INCONSISTENT BELIEFS: A SOLUTION
Authors: KVANVIG JONATHAN L. 
Published: March 2012

abstractThe most pressing difficulty coherentism faces is, I believe, the problem of justified inconsistent beliefs. In a nutshell, there are cases in which our beliefs appear to be both fully rational and justified, and yet the contents of the beliefs are inconsistent, often knowingly so. This fact contradicts the seemingly obvious idea that a minimal requirement for coherence is logical consistency. Here, I present a solution to one version of this problem.
Comparison of the Long-Term Immunogenicity of Two Pandemic Influenza A/H1N1 2009 Vaccines, the MF59-Adjuvanted and Unadjuvanted Vaccines, in Adults
Authors: Song Joon Young , Cheong Hee Jin , Seo Yu Bin , Kim In Seon , Noh Ji Yun , Heo Jung Yeon , Choi Won Suk , Lee Jacob , Kim Woo Joo 
Published: March 2012

ABSTRACTSince the first reports of the A/H1N1 virus in April 2009, the pandemic influenza virus spread globally and circulated for a long time. The primary method for the control of influenza is vaccination, but levels of influenza vaccine-induced antibody are known to decline rapidly during a 6-month period. In adults aged 18 to 64 years, we compared the long-term immunogenicity of two of the influenza A/H1N1 2009 monovalent vaccines, 3.75-μg MF59-adjuvanted vaccine and 15-μg unadjuvanted vaccine. The serum hemagglutinin inhibition (HI) titers were determined prevaccination and at 1, 6, and 10 months after vaccination. One hundred six (88.3%) of the 120 subjects were monitored for the entire 10-month period after receiving the influenza A/H1N1 2009 monovalent vaccine. There were 60 patients who received the unadjuvanted vaccine and 46 patients who received the MF59-adjuvanted vaccine. The seroprotection rates, seroconversion rates, and the geometric mean titer (GMT) folds fulfilled the criteria of the European Medicines Agency (EMA) for influenza A/California/7/2009 (H1N1) at 1 month after vaccination irrespective of the vaccine composition. Although the GMTs at 1 month postvaccination were somewhat higher in the unadjuvanted vaccine recipients than in the MF59-adjuvanted vaccine recipients, the difference was not significant (P= 0.29). The seroprotection rates at 6 and 10 months postvaccination were preserved above 70% but only in the MF59-adjuvanted vaccine recipients. In conclusion, low-dose MF59-adjuvanted influenza vaccine, even with 3.75 μg hemagglutinin antigen, might induce excellent long-term immunity that is comparable to the conventional dose of unadjuvanted vaccine among healthy adults aged 18 to 64 years.
Real-Time Molecular Epidemiology of Tuberculosis by Direct Genotyping of Smear-Positive Clinical Specimens
Authors: Alonso María , Herranz Marta , Martínez Lirola Miguel , González-Rivera Milagros , Bouza Emilio , García de Viedma Darío 
Published: March 2012

ABSTRACT

We applied MIRU-VNTR (mycobacterial interspersed repetitive-unit–variable-number tandem-repeat typing) to directly analyze the bacilli present in 61 stain-positive specimens from tuberculosis patients. A complete MIRU type (24 loci) was obtained for all but one (no amplification in one locus) of the specimens (98.4%), and the allelic values fully correlated with those obtained from the corresponding cultures. Our study is the first to demonstrate that real-time genotyping of
Mycobacterium tuberculosis
can be achieved, fully transforming the way in which molecular epidemiology techniques can be integrated into control programs.
Development of a Novel Genus-Specific Real-Time PCR Assay for Detection and Differentiation of Bartonella Species and Genotypes
Authors: Diaz Maureen H. , Bai Ying , Malania Lile , Winchell Jonas M. , Kosoy Michael Y. 
Published: March 2012

ABSTRACT

The genus
Bartonella
includes numerous species with varied host associations, including several that infect humans. Development of a molecular diagnostic method capable of detecting the diverse repertoire of
Bartonella
species while maintaining genus specificity has been a challenge. We developed a novel real-time PCR assay targeting a 301-bp region of the
ssrA
gene of
Bartonella
and demonstrated specific amplification in over 30
Bartonella
species, subspecies, and strains. Subsequent analysis of
ssrA
sequences was sufficient to discriminate
Bartonella
species and provided phylogenetic data consistent with that of
gltA
, a commonly used gene for differentiating
Bartonella
genotypes. Using this assay, we identified
Bartonella
DNA in 29% and 47% of blood specimens from elk in Wyoming and cattle in the Republic of Georgia, respectively. Sequence analysis of a subset of genotypes from elk specimens revealed a cluster most closely related to
Bartonella capreoli
, and genotypes from cattle were identified as
Bartonella bovis
, both
Bartonella
species commonly found in wild and domestic ruminants. Considering the widespread geographic distribution and infectivity potential to a variety of hosts, this assay may be an effective diagnostic method for identification of
Bartonella
infections in humans and have utility in
Bartonella
surveillance studies.
mecA
-Positive Staphylococcus aureus with Low-Level Oxacillin MIC in Taiwan
Authors: Chen Feng-Jui , Huang I-Wen , Wang Chen-Her , Chen Pei-Chen , Wang Hui-Yin , Lai Jui-Fen , Shiau Yih-Ru , Lauderdale Tsai-Ling Yang ,   TSAR Hospitals
Published: March 2012

ABSTRACT

Although the presence of
mecA
is the genotypic determinant of methicillin-resistant
Staphylococcus aureus
(MRSA), certain MRSA strains, especially community-associated MRSA (C-MRSA), can display an oxacillin MIC in the Clinical and Laboratory Standards Institute susceptible breakpoint range (≤2 μg/ml). Among 91 and 180 isolates thought to be methicillin-susceptible
S. aureus
(MSSA) with oxacillin MICs of 2 and 1 μg/ml as determined by the Sensititre broth microdilution test initially, 52 (57.1%) and 6 (3.3%), respectively, were
mecA
positive. These
mecA
-positive low-oxacillin-MIC isolates belong to the dominant Taiwan C-MRSA clone (clonal complex [CC] 59), 56 of which carried SCC
mec
type V and were
pvl
positive, and 43 of which belonged to
spa
CC t437. All 271 isolates were retested by Sensititre, as well as by Vitek II and disk diffusion (DD). Based on the oxacillin results, the sensitivities of the Sensititre, Vitek II, and DD methods were 48.3% (28/58), 46.6% (27/58), and 89.6% (52/58), respectively. Although cefoxitin was better at detecting these isolates, 12.1, 10.4, and 5.2% of these isolates were still misidentified as MSSA by Sensititre, Vitek II, and DD, respectively. These results highlight the difficulty in the accurate identification of MRSA with borderline oxacillin MICs in the CC59:SCC
mec
V clone, which likely has contributed to its spread in the health care and community settings. Since this clone has now been detected in other countries, and since other C-MRSA lineages have also been found to have low-level β-lactam resistance, the findings of the present study may be relevant to other regions. Further studies are warranted to determine the extent and clinical impact of such misidentification.
Performance of the Abbott RealTime and Roche Cobas TaqMan Hepatitis C Virus (HCV) Assays for Quantification of HCV Genotypes
Authors: LaRue Heidi , Rigali Lisa , Balada-Llasat Joan-Miquel , Pancholi Preeti 
Published: March 2012

ABSTRACT
We evaluated the Abbott RealTime (ART) and Roche Cobas TaqMan Hepatitis C virus (HCV) viral load assays for quantification of HCV genotypes in patient specimens. The ART HCV assay was a more sensitive and precise tool for accurate HCV viral load quantification across the HCV genotypes tested, especially genotype 1b.
A Protein Array Screen for Kaposi's Sarcoma-Associated Herpesvirus LANA Interactors Links LANA to TIP60, PP2A Activity, and Telomere Shortening
Authors: Shamay Meir , Liu Jianyong , Li Renfeng , Liao Gangling , Shen Li , Greenway Melanie , Hu Shaohui , Zhu Jian , Xie Zhi , Ambinder Richard F. , Qian Jiang , Zhu Heng , Hayward S. Diane 
Published: March 2012

ABSTRACT
The Kaposi's sarcoma-associated herpesvirus (KSHV) LANA protein functions in latently infected cells as an essential participant in KSHV genome replication and as a driver of dysregulated cell growth. To identify novel LANA protein-cell protein interactions that could contribute to these activities, we performed a proteomic screen in which purified, adenovirus-expressed Flag-LANA protein was incubated with an array displaying 4,192 nonredundant human proteins. Sixty-one interacting cell proteins were consistently detected. LANA interactions with high-mobility group AT-hook 1 (HMGA1), HMGB1, telomeric repeat binding factor 1 (TRF1), xeroderma pigmentosum complementation group A (XPA), pygopus homolog 2 (PYGO2), protein phosphatase 2A (PP2A)B subunit, Tat-interactive protein 60 (TIP60), replication protein A1 (RPA1), and RPA2 proteins were confirmed in coimmunoprecipitation assays. LANA-associated TIP60 retained acetyltransferase activity and, unlike human papillomavirus E6 and HIV-1 TAT proteins, LANA did not reduce TIP60 stability. The LANA-bound PP2A B subunit was associated with the PP2A A subunit but not the catalytic C subunit, suggesting a disruption of PP2A phosphatase activity. This is reminiscent of the role of simian virus 40 (SV40) small t antigen. Chromatin immunoprecipitation (ChIP) assays showed binding of RPA1 and RPA2 to the KSHV terminal repeats. Interestingly, LANA expression ablated RPA1 and RPA2 binding to the cell telomeric repeats. In U2OS cells that rely on the alternative mechanism for telomere maintenance, LANA expression had minimal effect on telomere length. However, LANA expression in telomerase immortalized endothelial cells resulted in telomere shortening. In KSHV-infected cells, telomere shortening may be one more mechanism by which LANA contributes to the development of malignancy.
Four Amino Acids of an Insect Densovirus Capsid Determine Midgut Tropism and Virulence
Authors: Multeau Cecilia , Froissart Rémy , Perrin Aurélie , Castelli Ilaria , Casartelli Morena , Ogliastro Mylène 
Published: March 2012

ABSTRACT

Densoviruses are insect parvoviruses that are orally infectious for
Lepidoptera
. To assess the mechanisms underlying their specificity and their virulence, we investigated the role of eight candidate residues in the densovirus capsid. We showed that the substitutions of four amino acids were associated with decreased virulence due to a decreased ability to cross the host midgut epithelium, without an effect on viral replication in other tissues.
Preclinical Evaluation of a Genetically Engineered Herpes Simplex Virus Expressing Interleukin-12
Authors: Markert James M. , Cody James J. , Parker Jacqueline N. , Coleman Jennifer M. , Price Kathleen H. , Kern Earl R. , Quenelle Debra C. , Lakeman Alfred D. , Schoeb Trenton R. , Palmer Cheryl A. , Cartner Samuel C. , Gillespie G. Yancey , Whitley Richard J. 
Published: March 2012

ABSTRACT

Herpes simplex virus 1 (HSV-1) mutants that lack the γ
1
34.5 gene are unable to replicate in the central nervous system but maintain replication competence in dividing cell populations, such as those found in brain tumors. We have previously demonstrated that a γ
1
34.5-deleted HSV-1 expressing murine interleukin-12 (IL-12; M002) prolonged survival of immunocompetent mice in intracranial models of brain tumors. We hypothesized that M002 would be suitable for use in clinical trials for patients with malignant glioma. To test this hypothesis, we (i) compared the efficacy of M002 to three other HSV-1 mutants, R3659, R8306, and G207, in murine models of brain tumors, (ii) examined the safety and biodistribution of M002 in the HSV-1-sensitive primate
Aotus nancymae
following intracerebral inoculation, and (iii) determined whether murine IL-12 produced by M002 was capable of activating primate lymphocytes. Results are summarized as follows: (i) M002 demonstrated superior antitumor activity in two different murine brain tumor models compared to three other genetically engineered HSV-1 mutants; (ii) no significant clinical or magnetic resonance imaging evidence of toxicity was observed following direct inoculation of M002 into the right frontal lobes of
A. nancymae
; (iii) there was no histopathologic evidence of disease in
A. nancymae
1 month or 5.5 years following direct inoculation; and (iv) murine IL-12 produced by M002 activates
A. nancymae
lymphocytes
in vitro
. We conclude that the safety and preclinical efficacy of M002 warrants the advancement of a Δγ
1
34.5 virus expressing IL-12 to phase I clinical trials for patients with recurrent malignant glioma.
Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs
Authors: Bolduc Benjamin , Shaughnessy Daniel P. , Wolf Yuri I. , Koonin Eugene V. , Roberto Francisco F. , Young Mark 
Published: March 2012

ABSTRACT

There are no known RNA viruses that infect
Archaea
. Filling this gap in our knowledge of viruses will enhance our understanding of the relationships between RNA viruses from the three domains of cellular life and, in particular, could shed light on the origin of the enormous diversity of RNA viruses infecting eukaryotes. We describe here the identification of novel RNA viral genome segments from high-temperature acidic hot springs in Yellowstone National Park in the United States. These hot springs harbor low-complexity cellular communities dominated by several species of hyperthermophilic
Archaea
. A viral metagenomics approach was taken to assemble segments of these RNA virus genomes from viral populations isolated directly from hot spring samples. Analysis of these RNA metagenomes demonstrated unique gene content that is not generally related to known RNA viruses of
Bacteria
and
Eukarya
. However, genes for RNA-dependent RNA polymerase (RdRp), a hallmark of positive-strand RNA viruses, were identified in two contigs. One of these contigs is approximately 5,600 nucleotides in length and encodes a polyprotein that also contains a region homologous to the capsid protein of nodaviruses, tetraviruses, and birnaviruses. Phylogenetic analyses of the RdRps encoded in these contigs indicate that the putative archaeal viruses form a unique group that is distinct from the RdRps of RNA viruses of
Eukarya
and
Bacteria
. Collectively, our findings suggest the existence of novel positive-strand RNA viruses that probably replicate in hyperthermophilic archaeal hosts and are highly divergent from RNA viruses that infect eukaryotes and even more distant from known bacterial RNA viruses. These positive-strand RNA viruses might be direct ancestors of RNA viruses of eukaryotes.
The Contribution of Systemic and Pulmonary Immune Effectors to Vaccine-Induced Protection from H5N1 Influenza Virus Infection
Authors: Lau Yuk-Fai , Wright Amber R. , Subbarao Kanta 
Published: March 2012

ABSTRACTLive attenuated influenza vaccines (LAIVs) are effective in providing protection against influenza challenge in animal models and in preventing disease in humans. We previously showed that LAIVs elicit a range of immune effectors and that successful induction of pulmonary cellular and humoral immunity in mice requires pulmonary replication of the vaccine virus. An upper respiratory tract immunization (URTI) model was developed in mice to mimic the human situation, in which the vaccine virus does not replicate in the lower respiratory tract, allowing us to assess the protective efficacy of an H5N1 LAIV against highly pathogenic H5N1 virus challenge in the absence of significant pulmonary immunity. Our results show that, after one dose of an H5N1 LAIV, pulmonary influenza-specific lymphocytes are the main contributors to clearance of challenge virus from the lungs and that contributions of influenza-specific enzyme-linked immunosorbent assay (ELISA) antibodies in serum and splenic CD8+T cells were negligible. Complete protection from H5N1 challenge was achieved after two doses of H5N1 LAIV and was associated with maturation of the antibody response. Although passive transfer of sera from mice that received two doses of vaccine prevented lethality in naive recipients following challenge, the mice showed significant weight loss, with high pulmonary titers of the H5N1 virus. These data highlight the importance of mucosal immunity in mediating optimal protection against H5N1 infection. Understanding the requirements for effective induction and establishment of these protective immune effectors in the respiratory tract paves the way for a more rational and effective vaccine approach in the future.
Crustal architecture of the Almada Basin, NE Brazil: an example of a non-volcanic rift segment of the South Atlantic passive margin
Authors: Gordon Andrés C. , Mohriak Webster Ueipass , Barbosa Valeria C. F. 
Published: March 2012

Abstract
The Almada Basin, located in the southern Bahia State segment of NE Brazil, shares a similar sedimentation history and stress regime with the other eastern Brazilian basins. But when considering the composition of the transitional crust, a remarkably different behaviour is observed between the Almada Basin and the other eastern Brazilian basins. The architectural elements of the basin such as the reflection Moho discontinuity, the oceanic and continental basements, and the sedimentary section, as well as the tectonic style, are discussed in this study using gravity, seismic, regional geology and well-drilling results.
The Almada Basin is part of a continental rift system that developed during the Early Cretaceous, heralding the Gondwana break-up and subsequently evolving into a passive divergent margin. Deep seismic profiles show the progressive thinning of the continental crust but there is no clear evidence of mantle exhumation.
The Almada Basin is the conjugate margin of the South Gabon Basin in West Africa. Although both basins display similar stratigraphic record and geological evolution, the rifting mechanism resulted in a considerable asymmetric break-up. The Almada Basin is floored by the Itabunas–Salvador–Curaçá Belt of the São Francisco Craton and is characterized by Palaeoproterozoic granulites in a high-angle east-dipping thrust fault regime. However, the South Gabon Basin lies on the Neoproterozoic West Congolian Belt that is made up of low- to medium-grade metamorphic rocks in a low-angle thrust tectonic regime. The Precambrian basement fabric of both the Almada and South Gabon basins is marked by lithospheric-scale discontinuities that controlled the implantation of the rift zone and the extension style during the Mesozoic. The strong basement structural inheritance can be recognized in both the geological and geophysical records.
The key architectural elements of a volcanic margin, such as large igneous provinces, seaward-dipping reflectors and the basinal syn-rift magmatism, are not recognized in the Almada Basin. Although the South Atlantic margin is mostly volcanic in the southernmost segment, the presence of these two non-volcanic segments – the southern Bahia State and the southern Gabon – are important as a record of the differences in the geotectonic process that governed the formation of the South Atlantic divergent margins.