bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep‐burial alteration of early‐diagenetic carbonate concretions formed in Palaeozoic deep‐marine greywackes and mudstones (Bardo Unit, Sudetes Mountains, Poland)
Authors: Bojanowski Maciej J. , Barczuk Andrzej , Wetzel Andreas 
Published: December 2013

AbstractCarbonate concretions formed in bathyal and deeper settings have been studied less frequently than those formed in shallow‐marine deposits. Similarly, concretions affected by catagenetic conditions have rarely been reported. Calcite concretions in deep‐marine mudstones and greywackes of the Bardo Unit (Sudetes Mountains, Poland) formed during early diagenesis and were buried to significant depths. Petrographic and geochemical (elemental and stable C and O isotopic) analyses document their formation close to the sediment–water interface, prior to mechanical compaction within the sulphate reduction zone and their later burial below the oil window. Although the concretions were fully formed during early diagenesis, the effects of increased temperature and interaction with late‐diagenetic interstitial fluids can be discerned. During maximum burial, the concretions underwent thorough recrystallization that caused alteration of fabric and elemental and O isotope composition. The initial finely crystalline cement was replaced by more coarsely crystalline, sheaf‐like, poikilotopic calcite in the concretions. These large calcite crystals engulf and partially replace unstable detrital constituents. The extremely low δ18O values (down to −21·2‰ Vienna Pee Dee Belemnite) in the concretions are the result of the increased temperature in combination with alteration of volcanic glass, both causing a significant18O‐depletion of bicarbonate dissolved in the interstitial fluids. Recrystallization led to uniform O isotope ratios in the concretions, but did not affect the C isotope signature. The δ13C values of the late‐diagenetic cements precipitated in the greywacke and in cracks cutting through concretions imply crystallization in the catagenetic zone and decarboxylation as a source of the bicarbonate. These late‐diagenetic processes took place in a supposedly overpressured setting, as suggested by clastic dykes and hydrofractures that cut through both concretions and host rock. All of these features show how the effects of early and late diagenesis can be distinguished in such rocks.
Information Rich GIS Dissemination in Disconnected Environments
Authors: Johnston William , Banerjee Nilanjan , Cothren Jackson , Parkerson James P. 
Published: December 2013

AbstractInformation‐rich maps are today rendered from powerful back‐end servers. Unfortunately, there may be circumstances in which access to such Internet‐resident web services is infeasible or unreliable. These disconnected environments can theoretically occur during major power outages, malicious attacks on communications infrastructure, natural disasters, or in remote operating environments. One might also envision applications in which a disconnected service is preferred over Internet‐resident services, such as when the local internet service is overloaded with traffic, making communication though it difficult. To this end, this article presents a software stack (a map stack) that can serve GIS information from low power embedded nodes. The system combines a spatially enabled SQL database, location‐based routing, and multi‐scale map rendering to serve information‐rich GIS data on common hand‐held devices at minimal energy consumption. The maps are rendered on browsers on off‐the‐shelf mobile devices such as smart phones and tablets. The system also provides a crowd sourced capability where end users can annotate maps with up‐to‐date information on the scene of the natural disaster. We have prototyped a fully functional map stack on a battery powered Gumstix Overo air platform. We show that the map stack is a highly extensible platform that provides low latency, and low energy dissemination of maps during a natural disaster.
Semantically Enriching an Open Source Sensor Observation Service Implementation for Accessing Heterogeneous Environmental Data Sources
Authors: Hilbring Désirée , Moumtzidou Anastasia , Moßgraber Jürgen , Vrochidis Stefanos 
Published: December 2013

AbstractMany kinds of environmental data are nowadays publicly available, but spread over the web. This article discusses using the Sensor Observation Service (SOS) standard of the Open Geospatial Consortium (OGC) as a common interface for providing data from heterogeneous sources which can be integrated to a user tailored environmental information system. In order to allow for providing user‐tailored and problem‐specific information the adjusted SOS is augmented by a semantic layer which maps the environmental information to ontology concepts. The necessary information fusion from different domains and data types lead to several specific requirements for the SOS. Addressing these requirements we have implemented a SOS which still conforms to the OGC SOS 1.0.0 standard specification. The developed SOS has been integrated in a publicly available demonstrator of our personalized environmental information system. Additionally this article discusses future consequences for the SOS, caused by the recently published SOS 2.0 specification.
Lack of isocitrate lyase in Chlamydomonas leads to changes in carbon metabolism and in the response to oxidative stress under mixotrophic growth
Authors: Plancke Charlotte , Vigeolas Helene , Höhner Ricarda , Roberty Stephane , Emonds‐Alt Barbara , Larosa Véronique , Willamme Remi , Duby Franceline , Onga Dhali David , Thonart Philippe , Hiligsmann Serge , Franck Fabrice , Eppe Gauthier , Cardol Pierre , Hippler Michael , Remacle Claire 
Published: November 2013

SummaryIsocitrate lyase is a key enzyme of the glyoxylate cycle. This cycle plays an essential role in cell growth on acetate, and is important for gluconeogenesis as it bypasses the two oxidative steps of the tricarboxylic acid (TCA) cycle in which CO2 is evolved. In this paper, a null icl mutant of the green microalga Chlamydomonas reinhardtii is described. Our data show that isocitrate lyase is required for growth in darkness on acetate (heterotrophic conditions), as well as for efficient growth in the light when acetate is supplied (mixotrophic conditions). Under these latter conditions, reduced acetate assimilation and concomitant reduced respiration occur, and biomass composition analysis reveals an increase in total fatty acid content, including neutral lipids and free fatty acids. Quantitative proteomic analysis by 14N/15N labelling was performed, and more than 1600 proteins were identified. These analyses reveal a strong decrease in the amounts of enzymes of the glyoxylate cycle and gluconeogenesis in parallel with a shift of the TCA cycle towards amino acid synthesis, accompanied by an increase in free amino acids. The decrease of the glyoxylate cycle and gluconeogenesis, as well as the decrease in enzymes involved in β–oxidation of fatty acids in the icl mutant are probably major factors that contribute to remodelling of lipids in the icl mutant. These modifications are probably responsible for the elevation of the response to oxidative stress, with significantly augmented levels and activities of superoxide dismutase and ascorbate peroxidase, and increased resistance to paraquat.
Jasmonate‐dependent modifications of the pectin matrix during potato development function as a defense mechanism targeted by Dickeya dadantii virulence factors
Authors: Taurino Marco , Abelenda Jose A. , Río‐Alvarez Isabel , Navarro Cristina , Vicedo Begonya , Farmaki Theodora , Jiménez Pedro , García‐Agustín Pilar , López‐Solanilla Emilia , Prat Salomé , Rojo Enrique , Sánchez‐Serrano José J. , Sanmartín Maite 
Published: November 2013

SummaryThe plant cell wall constitutes an essential protection barrier against pathogen attack. In addition, cell‐wall disruption leads to accumulation of jasmonates (JAs), which are key signaling molecules for activation of plant inducible defense responses. However, whether JAs in return modulate the cell‐wall composition to reinforce this defensive barrier remains unknown. The enzyme 13–allene oxide synthase (13–AOS) catalyzes the first committed step towards biosynthesis of JAs. In potato (Solanum tuberosum), there are two putative St13–AOS genes, which we show here to be differentially induced upon wounding. We also determine that both genes complement an Arabidopsis aos null mutant, indicating that they encode functional 13–AOS enzymes. Indeed, transgenic potato plants lacking both St13–AOS genes (CoAOS1/2 lines) exhibited a significant reduction of JAs, a concomitant decrease in wound‐responsive gene activation, and an increased severity of soft rot disease symptoms caused by Dickeya dadantii. Intriguingly, a hypovirulent D. dadantii pel strain lacking the five major pectate lyases, which causes limited tissue maceration on wild‐type plants, regained infectivity in CoAOS1/2 plants. In line with this, we found differences in pectin methyl esterase activity and cell‐wall pectin composition between wild‐type and CoAOS1/2 plants. Importantly, wild‐type plants had pectins with a lower degree of methyl esterification, which are the substrates of the pectate lyases mutated in the pel strain. These results suggest that, during development of potato plants, JAs mediate modification of the pectin matrix to form a defensive barrier that is counteracted by pectinolytic virulence factors from D. dadantii.
Distinct Pseudomonas type‐III effectors use a cleavable transit peptide to target chloroplasts
Authors: Li Guangyong , Froehlich John E. , Elowsky Christian , Msanne Joseph , Ostosh Andrew C. , Zhang Chi , Awada Tala , Alfano James R. 
Published: December 2013

SummaryThe pathogen Pseudomonas syringae requires a type‐III protein secretion system and the effector proteins it injects into plant cells for pathogenesis. The primary role for P. syringae type‐III effectors is the suppression of plant immunity. The P. syringae pv. tomato DC3000 HopK1 type‐III effector was known to suppress the hypersensitive response (HR), a programmed cell death response associated with effector‐triggered immunity. Here we show that DC3000 hopK1 mutants are reduced in their ability to grow in Arabidopsis, and produce reduced disease symptoms. Arabidopsis transgenically expressing HopK1 are reduced in PAMP‐triggered immune responses compared with wild‐type plants. An N‐terminal region of HopK1 shares similarity with the corresponding region in the well‐studied type‐III effector AvrRps4; however, their C‐terminal regions are dissimilar, indicating that they have different effector activities. HopK1 is processed in planta at the same processing site found in AvrRps4. The processed forms of HopK1 and AvrRps4 are chloroplast localized, indicating that the shared N‐terminal regions of these type‐III effectors represent a chloroplast transit peptide. The HopK1 contribution to virulence and the ability of HopK1 and AvrRps4 to suppress immunity required their respective transit peptides, but the AvrRps4‐induced HR did not. Our results suggest that a primary virulence target of these type‐III effectors resides in chloroplasts, and that the recognition of AvrRps4 by the plant immune system occurs elsewhere. Moreover, our results reveal that distinct type‐III effectors use a cleavable transit peptide to localize to chloroplasts, and that targets within this organelle are important for immunity.
Development of a Highly Sensitive and Specific Blastomycosis Antibody Enzyme Immunoassay Using Blastomyces dermatitidis Surface Protein BAD-1
Authors: Richer Sarah M. , Smedema Melinda L. , Durkin Michelle M. , Brandhorst T. Tristan , Hage Chadi A. , Connolly Patricia A. , Leland Diane S. , Davis Thomas E. , Klein Bruce S. , Wheat L. Joseph 
Published: November 2013

ABSTRACTSerologic tests for antibodies toBlastomyces dermatitidisare not thought to be useful for the diagnosis of blastomycosis, in part due to the low sensitivity of immunodiffusion and complement fixation. Earlier studies have shown that the enzyme immunoassay improves the sensitivity of antibody detection for the diagnosis of blastomycosis. Microplates coated with theB. dermatitidissurface protein BAD-1 were used for testing sera from patients with proven blastomycosis or histoplasmosis and controls. Semiquantification was accomplished by using standards containing human anti-B. dermatitidisantibodies. The antibodies were detected in 87.8% of the patients with blastomycosis by the enzyme immunoassay compared to 15.0% by immunodiffusion. The specificities were 99.2% for patients with nonfungal infections and healthy subjects and 94.0% for patients with histoplasmosis. The results were highly reproducible on repeat testing. When combined with antigen testing, antibody testing improved the sensitivity from 87.8% to 97.6%. Enzyme immunoassay detection of antibodies against BAD-1 is highly specific, has greatly improved sensitivity over immunodiffusion, and may identify cases with negative results by antigen testing. This assay has the potential to aid in the diagnosis of blastomycosis.
Whole-Genome Sequences of Two Beak and Feather Disease Viruses in the Endangered Swift Parrot (
Lathamus discolor
)
Authors: Sarker Subir , Ghorashi Seyed A. , Forwood Jade K. , Raidal Shane R. 
Published: November 2013

ABSTRACT

Two complete genomes of beak and feather disease virus (BFDV) were characterized from
Lathamus discolor
, the Australian swift parrot. This is the first report of BFDV complete genome sequences in this host. The completed BFDV genomes consist of 1,984 nucleotides encoding two open reading frames with 99.7% pairwise nucleotide identity.
Complete Genome Sequence of a Novel Iflavirus from the Transcriptome of
Halyomorpha halys
, the Brown Marmorated Stink Bug
Authors: Sparks Michael E. , Gundersen-Rindal Dawn E. , Harrison Robert L. 
Published: November 2013

ABSTRACT

We report the genome sequence of a novel iflavirus recovered from the transcriptome of a colony of the brown marmorated stink bug,
Halyomorpha halys
. The genome is 9,263 nucleotides (nt) and contains an open reading frame (ORF) encoding a 3,017-amino-acid polyprotein.
Genome Sequence of
Mycoplasma parvum
(Formerly Eperythrozoon parvum), a Diminutive Hemoplasma of the Pig
Authors: do Nascimento Naíla C. , dos Santos Andrea P. , Chu Yuefeng , Guimaraes Ana M. S. , Pagliaro Apryl , Messick Joanne B. 
Published: November 2013

ABSTRACT

We report the complete genome sequence of
Mycoplasma parvum
strain Indiana. Its circular chromosome is 564,395 bp, which is smaller than that of
Mycoplasma genitalium
, which was previously considered the smallest member of the
Mollicutes
. Comparative analyses of the genomes of
M. parvum
and
Mycoplasma suis
will provide novel insights into the molecular basis of their virulence.
Draft Genome Sequence of Lactobacillus jensenii Strain MD IIE-70(2)
Authors: Karlyshev Andrey V. , Nadarajah Sindhujan , Abramov Vyacheslav M. 
Published: November 2013

ABSTRACT

A draft genome sequence of
Lactobacillus jensenii
strain MD IIE-70(2) was determined using Ion PGM technology. The reads were mapped to a reference strain and assembled using a combination of tools. The genetic features revealed in this study will assist in understanding the probiotic properties of
Lactobacillus
bacteria.
Recurrent Melioidosis in the Darwin Prospective Melioidosis Study: Improving Therapies Mean that Relapse Cases Are Now Rare
Authors: Sarovich Derek S. , Ward Linda , Price Erin P. , Mayo Mark , Pitman Matthew C. , Baird Robert W. , Currie Bart J. 
Published: November 2013

ABSTRACT

The Darwin Prospective Melioidosis Study has documented 785 melioidosis cases over 23 years. Recurrent melioidosis occurred in 39/679 (5.7%) patients surviving initial infection; 29 patients suffered relapse of the original infection, and 10 presented with a new
Burkholderia pseudomallei
infection. With improved therapy, relapse has become rare in recent years.
Diagnosis of Prosthetic Joint Infection by Use of PCR-Electrospray Ionization Mass Spectrometry
Authors: Greenwood-Quaintance Kerryl E. , Uhl James R. , Hanssen Arlen D. , Sampath Rangarajan , Mandrekar Jayawant N. , Patel Robin 
Published: November 2013

ABSTRACT

We compared PCR-electrospray ionization mass spectrometry (PCR-ESI/MS) to culture using sonicate fluid from 431 subjects with explanted knee (
n
= 270) or hip (
n
= 161) prostheses. Of these, 152 and 279 subjects had prosthetic joint infection (PJI) and aseptic failure, respectively. The sensitivities for detecting PJI were 77.6% for PCR-ESI/MS and 69.7% for culture (
P
= 0.0105). The specificities were 93.5 and 99.3%, respectively (
P
= 0.0002).
Rescue of a Recombinant Machupo Virus from Cloned cDNAs and
In Vivo
Characterization in Interferon (αβ/γ) Receptor Double Knockout Mice
Authors: Patterson Michael , Seregin Alexey , Huang Cheng , Kolokoltsova Olga , Smith Jennifer , Miller Milagros , Smith Jeanon , Yun Nadezhda , Poussard Allison , Grant Ashley , Tigabu Bersabeh , Walker Aida , Paessler Slobodan 
Published: November 2013

ABSTRACT

Machupo virus (MACV) is the etiological agent of Bolivian hemorrhagic fever (BHF), a reemerging and neglected tropical disease associated with high mortality. The prototypical strain of MACV, Carvallo, was isolated from a human patient in 1963, but minimal
in vitro
and
in vivo
characterization has been reported. To this end, we utilized reverse genetics to rescue a pathogenic MACV from cloned cDNAs. The recombinant MACV (rMACV) had
in vitro
growth properties similar to those of the parental MACV. Both viruses caused similar disease development in alpha/beta and gamma interferon receptor knockout mice, including neurological disease development and high mortality. In addition, we have identified a novel murine model with mortality and neurological disease similar to BHF disease reported in humans and nonhuman primates.
The N-Terminal Domain of PA from Bat-Derived Influenza-Like Virus H17N10 Has Endonuclease Activity
Authors: Tefsen Boris , Lu Guangwen , Zhu Yaohua , Haywood Joel , Zhao Lili , Deng Tao , Qi Jianxun , Gao George F. 
Published: November 2013

ABSTRACT
Influenza imposes a great burden on society, not only in its seasonal appearance that affects both humans and domesticated animals but also through the constant threat of potential pandemics. Migratory birds are considered to be the reservoir hosts for influenza viruses, but other animals must also be considered. The recently identified influenza-like virus genome, from H17N10 in bats, was shown to be markedly different from genomes of other known influenza viruses, as both its surface glycoproteins hemagglutinin (HA) and neuraminidase (NA) do not have canonical functions. However, no studies on other individual proteins from this particular virus have been reported until now. Here, we describe the structure of the N-terminal domain of PA from H17N10 influenza-like virus at 2.7-Å resolution and show that it has a fold similar to those of homologous PA domains present in more familiar influenza A virus strains. Moreover, we demonstrate that it possesses endonuclease activity and that the histidine residue in the active site is essential for this activity. Although this particular influenza virus subtype is probably not infectious for humans (even its virus state has not been confirmed in bats, as only the genome has been sequenced), reassortment of canonical influenza viruses with certain segments from H17N10 cannot be ruled out at this stage. Therefore, further studies are urgently needed for the sake of influenza prevention and control.
Palmitoylation and p8-Mediated Human T-Cell Leukemia Virus Type 1 Transmission
Authors: Edwards Dustin , Fukumoto Risaku , de Castro-Amarante Maria Fernanda , Alcantara Luiz Carlos Junior , Galvão-Castro Bernardo , Washington Parks Robyn , Pise-Masison Cynthia , Franchini Genoveffa 
Published: November 2013

ABSTRACT

The
orf-I
gene of human T-cell leukemia type 1 (HTLV-1) encodes p8 and p12 and has a conserved cysteine at position 39. p8 and p12 form disulfide-linked dimers, and only the monomeric forms of p8 and p12 are palmitoylated. Mutation of cysteine 39 to alanine (C39A) abrogated dimerization and palmitoylation of both proteins. However, the ability of p8 to localize to the cell surface and to increase cell adhesion and viral transmission was not affected by the C39A mutation.
The Singular Quest for a Universal Tree of Life
Authors: Sapp Jan , Fox George E. 
Published: December 2013

SUMMARYCarl Woese developed a unique research program, based on rRNA, for discerning bacterial relationships and constructing a universal tree of life. Woese's interest in the evolution of the genetic code led to him to investigate the deep roots of evolution, develop the concept of the progenote, and conceive of theArchaea. In so doing, he and his colleagues at the University of Illinois in Urbana revolutionized microbiology and brought the classification of microbes into an evolutionary framework. Woese also provided definitive evidence for the role of symbiosis in the evolution of the eukaryotic cell while underscoring the importance of lateral gene transfer in microbial evolution. Woese and colleagues' proposal of three fundamental domains of life was brought forward in direct conflict with the prokaryote-eukaryote dichotomy. Together with several colleagues and associates, he brought together diverse evidence to support the rRNA evidence for the fundamentally tripartite nature of life. This paper aims to provide insight into his accomplishments, how he achieved them, and his place in the history of biology.
Pneumothorax occurring after nasogastric tube removal
Authors: Paul Vishesh , Shenoy Amith , Kupfer Yizhak , Tessler Sidney 
Published: December 2013

An 85-year-old woman with failure to thrive due to poor oral intake was admitted owing to dehydration. A nasogastric (NG) tube was inserted for the initiation of enteral feedings. The tube position was confirmed by gastric auscultation after insufflating air through the tube. A chest X-ray revealed that the NG tube traversed the right main stem bronchus with its tip ending in the right costophrenic angle adjacent to the pleura. No pneumothorax was identified. The tube was removed and a short while later the patient developed mild chest discomfort. A repeat chest X-ray revealed significant pneumothorax on the right side. She was treated conservatively with 100% oxygen with successful resolution of the pneumothorax.