bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear Magnetic Resonance Structure of the Nucleic Acid-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 3
Authors: Serrano Pedro , Johnson Margaret A. , Chatterjee Amarnath , Neuman Benjamin W. , Joseph Jeremiah S. , Buchmeier Michael J. , Kuhn Peter , Wüthrich Kurt 
Published: October 2009

ABSTRACTThe nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand β-sheet holding two α-helices of three and four turns that are oriented antiparallel to the β-strands. Two antiparallel two-strand β-sheets and two 310-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of theSaccharomyces cerevisiaeVts1p protein, although the two proteins do not share a common globular fold.
Microarray Analysis of
Paramecium bursaria
Chlorella Virus 1 Transcription
Authors: Yanai-Balser Giane M. , Duncan Garry A. , Eudy James D. , Wang Dong , Li Xiao , Agarkova Irina V. , Dunigan David D. , Van Etten James L. 
Published: October 2009

ABSTRACT

Paramecium bursaria
chlorella virus 1 (PBCV-1), a member of the family
Phycodnaviridae
, is a large double-stranded DNA, plaque-forming virus that infects the unicellular green alga
Chlorella
sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)-containing RNAs obtained from cells at seven time points after virus infection. The results led to the following conclusions: (i) the PBCV-1 replication cycle is temporally programmed and regulated; (ii) 360 (99%) of the arrayed PBCV-1 CDSs were expressed at some time in the virus life cycle in the laboratory; (iii) 227 (62%) of the CDSs were expressed before virus DNA synthesis begins; (iv) these 227 CDSs were grouped into two classes: 127 transcripts disappeared prior to initiation of virus DNA synthesis (considered early), and 100 transcripts were still detected after virus DNA synthesis begins (considered early/late); (v) 133 (36%) of the CDSs were expressed after virus DNA synthesis begins (considered late); and (vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor, aphidicolin, prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 life cycle.
Transmission of Pandemic H1N1 Influenza Virus and Impact of Prior Exposure to Seasonal Strains or Interferon Treatment
Authors: Steel John , Staeheli Peter , Mubareka Samira , García-Sastre Adolfo , Palese Peter , Lowen Anice C. 
Published: October 2009

ABSTRACT
Novel swine-origin influenza viruses of the H1N1 subtype were first detected in humans in April 2009. As of 12 August 2009, 180,000 cases had been reported globally. Despite the fact that they are of the same antigenic subtype as seasonal influenza viruses circulating in humans since 1977, these viruses continue to spread and have caused the first influenza pandemic since 1968. Here we show that a pandemic H1N1 strain replicates in and transmits among guinea pigs with similar efficiency to that of a seasonal H3N2 influenza virus. This transmission was, however, partially disrupted when guinea pigs had preexisting immunity to recent human isolates of either the H1N1 or H3N2 subtype and was fully blocked through daily intranasal administration of interferon to either inoculated or exposed animals. Our results suggest that partial immunity resulting from prior exposure to conventional human strains may blunt the impact of pandemic H1N1 viruses in the human population. In addition, the use of interferon as an antiviral prophylaxis may be an effective way to limit spread in at-risk populations.
A Novel Bipartite Double-Stranded RNA Mycovirus from the White Root Rot Fungus
Rosellinia necatrix
: Molecular and Biological Characterization, Taxonomic Considerations, and Potential for Biological Control
Authors: Chiba Sotaro , Salaipeth Lakha , Lin Yu-Hsin , Sasaki Atsuko , Kanematsu Satoko , Suzuki Nobuhiro 
Published: October 2009

ABSTRACT

White root rot, caused by the ascomycete
Rosellinia necatrix
, is a devastating disease worldwide, particularly in fruit trees in Japan. Here we report on the biological and molecular properties of a novel bipartite double-stranded RNA (dsRNA) virus encompassing dsRNA-1 (8,931 bp) and dsRNA-2 (7,180 bp), which was isolated from a field strain of
R. necatrix
, W779. Besides the strictly conserved 5′ (24 nt) and 3′ (8 nt) terminal sequences, both segments show high levels of sequence similarity in the long 5′ untranslated region of approximately 1.6 kbp. dsRNA-1 and -2 each possess two open reading frames (ORFs) named ORF1 to -4. Although the protein encoded by 3′-proximal ORF2 on dsRNA-1 shows sequence identities of 22 to 32% with RNA-dependent RNA polymerases from members of the families
Totiviridae
and
Chrysoviridae
, the remaining three virus-encoded proteins lack sequence similarities with any reported mycovirus proteins. Phylogenetic analysis showed that the W779 virus belongs to a separate clade distinct from those of other known mycoviruses. Purified virions ∼50 nm in diameter consisted of dsRNA-1 and -2 and a single major capsid protein of 135 kDa, which was shown by peptide mass fingerprinting to be encoded by dsRNA-1 ORF1. We developed a transfection protocol using purified virions to show that the virus was responsible for reduction of virulence and mycelial growth in several host strains. These combined results indicate that the W779 virus is a novel bipartite dsRNA virus with potential for biological control (virocontrol), named
Rosellinia necatrix megabirnavirus 1
(RnMBV1), that possibly belongs to a new virus family.
Role of Scavenger Receptor Class B Type I in Hepatitis C Virus Entry: Kinetics and Molecular Determinants
Authors: Catanese Maria Teresa , Ansuini Helenia , Graziani Rita , Huby Thierry , Moreau Martine , Ball Jonathan K. , Paonessa Giacomo , Rice Charles M. , Cortese Riccardo , Vitelli Alessandra , Nicosia Alfredo 
Published: October 2009

ABSTRACT
Scavenger receptor class B type I (SR-BI) is an essential receptor for hepatitis C virus (HCV) and a cell surface high-density-lipoprotein (HDL) receptor. The mechanism of SR-BI-mediated HCV entry, however, is not clearly understood, and the specific protein determinants required for the recognition of the virus envelope are not known. HCV infection is strictly linked to lipoprotein metabolism, and HCV virions may initially interact with SR-BI through associated lipoproteins before subsequent direct interactions of the viral glycoproteins with SR-BI occur. The kinetics of inhibition of cell culture-derived HCV (HCVcc) infection with an anti-SR-BI monoclonal antibody imply that the recognition of SR-BI by HCV is an early event of the infection process. Swapping and single-substitution mutants between mouse and human SR-BI sequences showed reduced binding to the recombinant soluble E2 (sE2) envelope glycoprotein, thus suggesting that the SR-BI interaction with the HCV envelope is likely to involve species-specific protein elements. Most importantly, SR-BI mutants defective for sE2 binding, although retaining wild-type activity for receptor oligomerization and binding to the physiological ligand HDL, were impaired in their ability to fully restore HCVcc infectivity when transduced into an SR-BI-knocked-down Huh-7.5 cell line. These findings suggest a specific and direct role for the identified residues in binding HCV and mediating virus entry. Moreover, the observation that different regions of SR-BI are involved in HCV and HDL binding supports the hypothesis that new therapeutic strategies aimed at interfering with virus/SR-BI recognition are feasible.
Gap junction hemichannels contribute to the generation of diarrhoea during infectious enteric disease
Authors: Guttman Julian Andrew , En-Ju Lin Ann , Li Yuling , Bechberger John , Naus Christian C , Vogl A Wayne , Finlay B Brett 
Published: October 2009

ObjectiveThe attaching and effacing (A/E) pathogens enterohaemorrhagic Escherichia coli, enteropathogenic E coli and Citrobacter rodentium colonise intestinal tracts, attach to enterocytes, collapse infected cell microvilli and alter numerous host cell processes during infection. Enterocyte alterations result in numerous small molecules being released from host cells that likely contribute to diarrhoeal phenotypes observed during these infections. One possible route for small molecules to be released from intestinal cells may be through functional gap junction hemichannels. Here we examine the involvement of these hemichannels during the diarrhoeal disease caused by A/E pathogens in vivo.DesignMice were infected with the diarrhoea-causing murine A/E pathogen C rodentium for 7 days. Connexin43 (Cx43) protein levels and immunolocalisation in the colon were initially used to determine alterations during A/E bacterial infections in vivo. Connexin mimetic peptides and connexin permeable tracer molecules were used to gage the presence and function of unpaired connexin hemichannels. The role of Cx43 in diarrhoea generation was assessed by comparing infections of wild-type mice to Cx43 mutant mice and determining the water abundance in the colonic luminal material.ResultsWe demonstrate that Cx43 protein levels are increased in colonocytes during in vivo A/E bacterial infections, resulting in functionally open connexon hemichannels in apical membranes of infected cells. Moreover, infected Cx43 +/− mice do not suffer from diarrhoeal disease.ConclusionsThis study provides the first evidence that functional connexon hemichannels can occur in the intestine and are a novel molecular mechanism of water release during infectious diarrhoea.
The impact of constructive feedback on training in gastrointestinal endoscopy using high-fidelity virtual-reality simulation: a randomised controlled trial
Authors: Kruglikova Irina , Grantcharov Teodor P , Drewes Asbjorn M , Funch-Jensen Peter 
Published: October 2009

BackgroundRecently, virtual reality computer simulators have been used to enhance traditional endoscopy teaching. Previous studies have demonstrated construct validity of these systems and transfer of virtual skills to the operating room. However, to date no simulator-training curricula have been designed and there is very little evidence on the impact of external feedback on acquisition of endoscopic skills.The aim of the present study was to assess the impact of external feedback on the learning curves on a VR colonoscopy simulator using inexperienced trainees.Materials and methods22 trainees, without colonoscopy experience were randomised to a group which received structured feedback provided by an experienced supervisor and a controlled group. All participants performed 15 repetitions of task 3 from the Introduction colonoscopy module of the Accu Touch Endoscopy simulator. Retention/transfer tests on simulator were performed 4–6 weeks after the last repetition. The proficiency levels were based on the performance of eight experienced colonoscopists.ResultsAll subjects were able to complete the procedure on the simulator. There were no perforations in the feedback group versus seven in the non-feedback group. Subjects in the feedback group reached expert proficiency levels in percentage of mucosa visualised and time to reach the caecum significantly faster compared with the control group. None of the groups demonstrated significant degradation of performance in simulator retention/transfer tests.ConclusionConcurrent feedback given by supervisor concur an advantage in acquisition of basic colonoscopy skills and achieving of proficiency level as compared to independent training.
Acute enterovirus infection followed by myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and viral persistence: Figure 1
Authors: Chia J , Chia A , Voeller M , Lee T , Chang R 
Published: October 2009

AimsEnteroviruses are well-known causes of acute respiratory and/or gastrointestinal infections and non-specific flu-like illness. Although enterovirus protein, RNA and non-cytopathic viruses have been demonstrated in the stomach biopsies of patients with myalgia encephalomyelitis/chronic fatigue syndrome (ME/CFS), causality for chronic diseases is difficult to establish without having well-documented cases of acute enterovirus infections. The aim of this study was to link acute enteroviral infection to viral persistence in patients with ME/CFS.MethodPatients admitted to the hospital with acute febrile illnesses were screened for enteroviral infections. Acutely infected patients were followed longitudinally, and those who developed symptoms of ME/CFS underwent oesophagogastroduodenoscopy and biopsies of the antrum to document viral persistence by immunoperoxidase staining for viral protein and viral RNA assay.ResultsThree representative patients with different manifestations of acute enterovirus infections progressed to have chronic symptoms of ME/CFS. Persistent viral infection was demonstrated in the antrum years later.ConclusionAfter acute infections, enteroviruses can persist in patients resulting in manifestation of ME/CFS. Chronic enterovirus infection in an immunocompetent host may be an example of a stalemate between attenuated, intracellular viruses and an ineffective immune response.
Integrated back and forward analysis of rock slope stability and rockslide runout at Afternoon Creek, Washington
Authors: Strouth Alex , Eberhardt Erik 
Published: October 2009

Hazard assessments involving large rock slopes are often problematic, given the influence of geology on failure kinematics and the subsequent influence of the failure kinematics on the rockslide runout. The 2003 Afternoon Creek rockslide in northwest Washington is one such example, where 750 000 m3 of rock slid from a steep ridge harmlessly into Afternoon Creek. However, topographic and structural controls at the source area unexpectedly redirected a small volume (<10%) down the opposite side of the ridge along a much steeper travel path, impacting the highway below. Postfailure investigations indicate that the slope still presents a danger. To address this, a framework was developed that links back analyses with forward modelling of failure initiation and runout. Field mapping and data collection were specifically tailored for these analyses. Advanced numerical modelling was used to assess likely rockslide source areas, volumes, and controlling features. These were then used to guide a series of three-dimensional runout simulations to model rockslide travel path, reach, and velocities. The results show that a rockslide originating from the ridge could occur again and that the topography would again direct a small percentage of material down the backside which would reach the highway below.
THE SI* MODELING FRAMEWORK: METAMODEL AND APPLICATIONS
Authors: ZANNONE NICOLA 
Published: October 2009

Security Requirements Engineering is emerging spurred by the realization that security must be dealt from the early phases of the system development process. Modeling languages in this field are challenging as they must provide concepts appropriate in order to talk about security within an organization. In previous work we introduced the SI* modeling language tailored to capture security aspects of socio-technical systems. SI* is founded on four main notions, namely supervision, permission, delegation, and trust. In this paper, we present the SI* metamodel. We also present some frameworks and methodologies founded on this modeling language for the analysis of security and dependability requirements as well as the exploration of design alternatives and the generation of skeletons of secure business processes. The paper also presents a development environment that uses the SI* metamodel as its basis core.
ENTREPRENEURIAL UNIVERSITY, TRANSFER TECHNOLOGY AND FUNDING: AN EMPIRICAL ANALYSIS
Authors: LOPEZ SARA FERNÁNDEZ , OTERO LUÍS , RODEIRO DAVID , RODRÍGUEZ ALFONSO 
Published: October 2009

Universities are now responsible for economic and social development. This new mission is transforming the traditional university into an entrepreneurial university. This entrepreneurial activity has mainly been carried out by transferring technology to industry, in particular, by patenting.The objective of this paper is to understand why some Spanish universities are more successful than others at patenting. In order to determine the factors that influence the patenting activity, we used a sample made up of 47 Spanish Public On-Campus Universities existing in 2003. Firstly, we applied the Poisson model. Secondly, after finding overdispersion in the data, the two approximations of the binomial negative were estimated (NEGBIN I and NEGBIN II). Lastly, we compared the results obtained with the three regression models.The results show that university patents are significantly positively associated with research funding, university size, technology transfer experience and resources and scientific areas with a greater market orientation. On the contrary, our results support the idea that university's research quality has a negative effect on the patent outputs.This study contributes to the literature on university patenting activity. First, there are no similar empirical studies about Spanish universities. Second, our findings provide quantitative evidence of the importance of funding research and university support policies in patent production. As a consequence, we can set out several policies to improve the dissemination of scientific knowledge and technology transfer activities.
On the Iron-ores of Exmoor
Authors: Smyth Warington W. 
Published: October 2009

Much attention has been bestowed, during the last seven years, on the exploration of veins of iron-ore in that hilly tract of country in Devonshire and West Somersetshire, which extends from Ilfracombe on the west, to near Bridgewater on the east. Its dominant points, on Exmoor, rise to an elevation of from 1400 to 1600 feet above the level of the sea, whilst the greater part of the region in question is of so considerable a height, that the deeply-cut valleys, or combes, through which the numerous streams find their way to the craggy coast, have long earned a deserved celebrity for the landscape-scenery of North Devon.
The district in which, at intervals, iron mines have been opened, is a belt of about five miles in width and about thirty in length, forming a part of the “Greywacke Group” of Sir H. De la Beche*, and of the equivalents of the “Plymouth Group” and a portion of the “Dartmouth Group” of the Devonian series, as described by Sedgwick†.
If, from Linton, where the lower beds of the range may be examined, the observer travel southward, he will pass over a constantly ascending series of strata, and about Simonsbath, on Exmoor, will reach the line of irregular lenticular deposits of limestone, which, trending from Combe Martin by Challacombe, through the midst of Exmoor, to Cutcombe and Treborough, furnish an indication of the general strike of the district, and a supposed parallel to the more massive limestones of Plymouth. To the north
On some Outline-drawings and Photographs of the Skull of the
Zygomaturus trilobus
, Macleay (
Nototherium
, Owen?)
Authors: Owen  
Published: October 2009

Sir R.I. Murchison placed in my hands a few days ago seven photographs, three of which are stereoscopic, of , perhaps, the most extraordinary mammalian fossil yet discovered in Australia.
These photographs, with a brief printed notice of their subject by Wm. Sharpe Macleay, Esq., F.R.S., and some MS. notes by J.D. Macdonald, M.D., R.N., had been transmitted to Sir Roderick by his Excellency the Governor Sir W. Denison, from Sydney, New South Wales ; and it is by the desire of Sir Roderick Murchison that I now bring the subject under the notice of the Geological Society of London, to whom Sir Roderick desires to present the Photographs, on the part of His Excellency, Sir Wm. Denison.
I had, some weeks previously, received from my friend and correspondent, George Bennette, Esq., F.L.S., of Sydney, New south wales accompanying outlines of the same fossil skull, made by him on the reception of the specimen by the authorities of the Australian Museum at Sydney, and I had penned notes of my comparisons of this sketches before receiving the photographs and descritions of the fossil skull from Sir Roderick I. Muschison.
Mr. Macleay's description appears in a Report on "Donations to the Australian Museum during August, 1857," published in a Sydney newspaper of about the same date. It is as follows:—

“Fossil Skull of a new marsupial animal, which bears a nearer approach to
Diprotodon
than to any other known genus. The size was apparently that of a large ox; and the
On the Mode of Formation of Volcanic Cones and Craters
Authors: Scrope G. Poulett 
Published: October 2009

In a paper read before the Society in April 1856, I called attention to this subject*. I should have thought further recurrence to it unnecessary had it not been that, in the first part of the fourth volume of Baron Humboldt's ‘Kosmos’ of which a translation has recently issued from the press, under the superintendence of General Sabine), that distinguished author, while treating very fully of volcanic action, gives the unqualified support of his great authority to the theory of upheaval as contradistinguished from that of eruption in reference to the origin of volcanic cones and craters,—a theory which, in common with Sir Charles Lyell, M. Constant Prévost, and many others, I believe to be not merely erroneous, but destructive of all clearness of apprehension as to the part which volcanic action has really played in the structural arrangement of the earth's surface.
I think I shall be justified in this last observation in the opinion of any person who will peruse with attention Baron Humboldt's work, and endeavour to realize some definite idea of what the author considers volcanic action to be—how cones or craters are formed—how lava-currents conduct themselves when expelled under varying circumstances upon the earth's surface—what volcanic mountains, or what portions of any such, are the product of eruption and accumulation, and what of the mere mechanical upheaval in mass of preexisting beds. The whole subject is rendered indistinct, and I will venture to say unintelligible, by the author's adheson to the theory of “Cones and