bluuebunny/crossref_metadata_2025_split huggingface dataset:
From Yuppies to Yupps: Family Gentrifiers Consuming Spaces and Re‐inventing Cities
Authors: Karsten Lia 
Published: March 2014

AbstractThis is a study of family consumption in an upgraded Amsterdam neighbourhood. It aims to unravel the relationship between the increase of middle‐class families and the establishing of new family‐related consumption spaces, both commercial and public. Based on observations and interviews in Amsterdam, we identify an increase in family and child directed consumption spaces. They reflect parental wishes to continue their former childless lifestyle, the need to combine work and care, and the wish to educate children in a wide range of skills. The more intensive consumption of parks and sidewalks reveals new practices of public parenting in urban contexts. It is argued that the transformation from childless yuppie to young urban professional parent (yupp) not only goes along with new consumption cultures but also with the production of a new city. This re‐invented city has potentials for age and gender equality, however unequal class relations appear to continue.
Acute enteritis associated with Coxsackievirus A19 in a kidney transplant patient
Authors: Melica G. , Langlois A.‐L. , Le Goff J. , Viglietti D. , Glotz D. , Molina J.‐M. , Peraldi M.‐N. 
Published: March 2014

AbstractDiarrhea is a frequent complication after kidney transplantation, with an incidence rate between 22% and 51%. In many cases, the cause remains unknown. We describe here the first case, to our knowledge, of persistent diarrhea associated with Coxsackievirus A19 (CVA19) in a kidney transplant recipient. The patient was a 46‐year‐old man who received a deceased‐donor kidney. He experienced delayed graft function because of donor kidney donation after circulatory determination of death. Maintenance immunosuppression consisted of low‐dose cyclosporine, high‐dose mycophenolate mofetil (MMF) (3 g/day), and prednisone (10 mg/day). He had severe diarrhea for 2 weeks associated with acute renal failure. No pathogens were found in the stool cultures. Enterovirus detection was positive by real‐time polymerase chain reaction, and sequence analysis found CVA19 (from Enterovirus C group). Area under the curve of MMF was 48 mg.h/L. Because of the persistence of diarrhea, MMF was stopped and replaced by azathioprine. The diarrhea disappeared, but serum creatinine did not return to baseline. CVA19 rarely causes gastroenteritis. This case illustrates that MMF is not always the direct cause of diarrhea, and that new clinical infectious diseases will be detected with the expansion of molecular‐based DNA diagnostics.
MHF1 plays Fanconi anaemia complementation group M protein (FANCM)‐dependent and FANCM‐independent roles in DNA repair and homologous recombination in plants
Authors: Dangel Natalie J. , Knoll Alexander , Puchta Holger 
Published: March 2014

SummaryFanconi anaemia complementation group M protein (FANCM), a component of the human Fanconi anemia pathway, acts as DNA translocase that is essential during the repair of DNA interstrand cross‐links. The DNA‐damage‐binding function of FANCM is strongly enhanced by the histone fold‐containing FANCM‐associated protein MHF1. We identified a single homologue of MHF1 in the genome of Arabidopsis thaliana. Similar to the loss of AtFANCM, the loss of AtMHF1 leads to several meiotic defects, such as chromosome bridges between bivalents and an unequal distribution of chromosomes. Moreover, MHF1, together with FANCM, is involved in interstrand cross‐link repair in plants. This phenotype is detectable only in double mutants of the RecQ helicase and BLM homologue RECQ4A, which appears to function in a parallel pathway to the FANCM/MHF1 complex. However, in somatic cells, FANCM has an MHF1‐independent function in replicative repair in a parallel pathway to the endonuclease MUS81. Furthermore, MHF1 is required for efficient somatic homologous recombination (HR) – a role antagonistic to FANCM. FANCM and RECQ4A define two parallel pathways of HR suppression in Arabidopsis. Hyperrecombination in the fancm but not the recq4A mutant can be abolished by MHF1 mutations. This finding indicates that MHF1 and FANCM act at different steps of a single, common, HR pathway.
Effects of acute hypoxia on cerebrovascular responses to carbon dioxide
Authors: Ogoh Shigehiko , Nakahara Hidehiro , Ueda Shinya , Okazaki Kazunobu , Shibasaki Manabu , Subudhi Andrew W. , Miyamoto Tadayoshi 
Published: March 2014

New Findings
What is the central question of this study?
In acute hypoxia, the reduction in arterial CO2 tension due to the hypoxic ventilatory response (respiratory chemoreflex) stimulates cerebral vasoconstriction, which opposes the degree of hypoxic cerebral vasodilatation. The aim was to examine this interaction further. Specifically, we questioned whether arterial CO2 tension‐mediated effects on cerebrovascular regulation are attenuated during acute hypoxia.
What is the main finding and its importance?
Cerebrovascular CO2 reactivity and CO2‐mediated effects on dynamic cerebral autoregulation were attenuated during acute hypoxia. These findings suggest that blunted cerebrovascular responses to CO2 may limit the degree of CO2‐mediated vasoconstriction to help maintain adequate cerebral blood flow for cerebral O2 homeostasis during acute hypoxia.
In normoxic conditions, a reduction in arterial carbon dioxide tension causes cerebral vasoconstriction, thereby reducing cerebral blood flow and modifying dynamic cerebral autoregulation (dCA). It is unclear to what extent these effects are altered by acute hypoxia and the associated hypoxic ventilatory response (respiratory chemoreflex). This study tested the hypothesis that acute hypoxia attenuates arterial CO2 tension‐mediated regulation of cerebral blood flow to help maintain cerebral O2 homeostasis. Eight subjects performed three randomly assigned respiratory interventions following a resting baseline period, as follows: (1) normoxia (21% O2); (2) hypoxia (12% O2); and (3) hypoxia with wilful restraint of the respiratory chemoreflex. During each intervention, 0, 2.0, 3.5 or 5.0% CO2 was sequentially added (8 min stages) to inspired gas mixtures to assess changes in steady‐state cerebrovascular CO2 reactivity and dCA. During normoxia, the addition of CO2 increased internal carotid artery blood flow and middle cerebral artery mean blood velocity (MCA Vmean), while reducing dCA (change in phase = −0.73 ± 0.22 rad, P = 0.005). During acute hypoxia, internal carotid artery blood flow and MCA Vmean remained unchanged, but cerebrovascular CO2 reactivity (internal carotid artery, P = 0.003; MCA Vmean, P = 0.031) and CO2‐mediated effects on dCA (P = 0.008) were attenuated. The effects of hypoxia were not further altered when the respiratory chemoreflex was restrained. These findings support the hypothesis that arterial CO2 tension‐mediated effects on the cerebral vasculature are reduced during acute hypoxia. These effects could limit the degree of hypocapnic vasoconstriction and may help to regulate cerebral blood flow and cerebral O2 homeostasis during acute periods of hypoxia.
Monte Carlo simulation of a quantum noise limited Čerenkov detector based on air‐spaced light guiding taper for megavoltage x‐ray imaging
Authors: Teymurazyan A. , Rowlands J. A. , Pang G. 
Published: March 2014

Purpose:Electronic Portal Imaging Devices (EPIDs) have been widely used in radiation therapy and are still needed on linear accelerators (Linacs) equipped with kilovoltage cone beam CT (kV‐CBCT) or MRI systems. Our aim is to develop a new high quantum efficiency (QE) Čerenkov Portal Imaging Device (CPID) that is quantum noise limited at dose levels corresponding to a single Linac pulse.Methods:Recently a new concept of CPID for MV x‐ray imaging in radiation therapy was introduced. It relies on Čerenkov effect for x‐ray detection. The proposed design consisted of a matrix of optical fibers aligned with the incident x‐rays and coupled to an active matrix flat panel imager (AMFPI) for image readout. A weakness of such design is that too few Čerenkov light photons reach the AMFPI for each incident x‐ray and an AMFPI with an avalanche gain is required in order to overcome the readout noise for portal imaging application. In this work the authors propose to replace the optical fibers in the CPID with light guides without a cladding layer that are suspended in air. The air between the light guides takes on the role of the cladding layer found in a regular optical fiber. Since air has a significantly lower refractive index (∼1 versus 1.38 in a typical cladding layer), a much superior light collection efficiency is achieved.Results:A Monte Carlo simulation of the new design has been conducted to investigate its feasibility. Detector quantities such as quantum efficiency (QE), spatial resolution (MTF), and frequency dependent detective quantum efficiency (DQE) have been evaluated. The detector signal and the quantum noise have been compared to the readout noise.Conclusions:Our studies show that the modified new CPID has a QE and DQE more than an order of magnitude greater than that of current clinical systems and yet a spatial resolution similar to that of current low‐QE flat‐panel based EPIDs. Furthermore it was demonstrated that the new CPID does not require an avalanche gain in the AMFPI and is quantum noise limited at dose levels corresponding to a single Linac pulse.
Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island
Authors: Zhang Xing Xing , Guo Hui Juan , Wang Rui , Sui Xin Hua , Zhang Yan Ming , Wang En Tao , Tian Chang Fu , Chen Wen Xin 
Published: March 2014

ABSTRACT

The genus
Bradyrhizobium
has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among
Bradyrhizobium
strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (
SMc00019
,
thrA
, and
truA
). This was also supported by analyses of eight genes outside the symbiosis island (“off-island” genes;
SMc00019
,
thrA
,
truA
,
fabB
,
glyA
,
phyR
,
exoN
, and
hsfA
). However, seven genes inside the symbiosis island (“island” genes;
nifA
,
nifH
,
nodC
,
nodV
,
fixA
,
trpD
, and
rhcC2
) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by
Bradyrhizobium japonicum
,
Bradyrhizobium diazoefficiens
,
Bradyrhizobium huanghuaihaiense
,
Bradyrhizobium liaoningense
,
Bradyrhizobium daqingense
,
Bradyrhizobium
sp. I,
Bradyrhizobium
sp. III, and
Bradyrhizobium
sp. IV) was not found in
Bradyrhizobium yuanmingense
,
Bradyrhizobium
sp. II, or
Bradyrhizobium elkanii
. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.
Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine Samples by Using High-Throughput Sequencing Analyses of PCR-Amplified DNA Polymerase and Major Capsid Protein Genes
Authors: Clerissi Camille , Grimsley Nigel , Ogata Hiroyuki , Hingamp Pascal , Poulain Julie , Desdevises Yves 
Published: March 2014

ABSTRACT

Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in
Prasinovirus
genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of
Prasinovirus
diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.
Safely Coupling Livestock and Crop Production Systems: How Rapidly Do Antibiotic Resistance Genes Dissipate in Soil following a Commercial Application of Swine or Dairy Manure?
Authors: Marti Romain , Tien Yuan-Ching , Murray Roger , Scott Andrew , Sabourin Lyne , Topp Edward 
Published: March 2014

ABSTRACT

Animal manures recycled onto crop production land carry antibiotic-resistant bacteria. The present study evaluated the fate in soil of selected genes associated with antibiotic resistance or genetic mobility in field plots cropped to vegetables and managed according to normal farming practice. Referenced to unmanured soil, fertilization with swine or dairy manure increased the relative abundance of the gene targets
sul1
,
erm
(B),
str
(B),
int1
, and IncW
repA
. Following manure application in the spring of 2012, gene copy number decayed exponentially, reaching background levels by the fall of 2012. In contrast, gene copy number following manure application in the fall of 2012 or spring of 2013 increased significantly in the weeks following application and then declined. In both cases, the relative abundance of gene copy numbers had not returned to background levels by the fall of 2013. Overall, these results suggest that under conditions characteristic of agriculture in a humid continental climate, a 1-year period following a commercial application of raw manure is sufficient to ensure that an additional soil burden of antibiotic resistance genes approaches background. The relative abundance of several gene targets exceeded background during the growing season following a spring application or an application done the previous fall. Results from the present study reinforce the advisability of treating manure prior to use in crop production systems.
Arsenic(V) Reduction in Relation to Iron(III) Transformation and Molecular Characterization of the Structural and Functional Microbial Community in Sediments of a Basin-Fill Aquifer in Northern Utah
Authors: Mirza Babur S. , Muruganandam Subathra , Meng Xianyu , Sorensen Darwin L. , Dupont R. Ryan , McLean Joan E. 
Published: March 2014

ABSTRACT

Basin-fill aquifers of the Southwestern United States are associated with elevated concentrations of arsenic (As) in groundwater. Many private domestic wells in the Cache Valley Basin, UT, have As concentrations in excess of the U.S. EPA drinking water limit. Thirteen sediment cores were collected from the center of the valley at the depth of the shallow groundwater and were sectioned into layers based on redoxmorphic features. Three of the layers, two from redox transition zones and one from a depletion zone, were used to establish microcosms. Microcosms were treated with groundwater (GW) or groundwater plus glucose (GW+G) to investigate the extent of As reduction in relation to iron (Fe) transformation and characterize the microbial community structure and function by sequencing 16S rRNA and arsenate dissimilatory reductase (
arrA
) genes. Under the carbon-limited conditions of the GW treatment, As reduction was independent of Fe reduction, despite the abundance of sequences related to
Geobacter
and
Shewanella
, genera that include a variety of dissimilatory iron-reducing bacteria. The addition of glucose, an electron donor and carbon source, caused substantial shifts toward domination of the bacterial community by
Clostridium
-related organisms, and As reduction was correlated with Fe reduction for the sediments from the redox transition zone. The
arrA
gene sequencing from microcosms at day 54 of incubation showed the presence of 14 unique phylotypes, none of which were related to any previously described
arrA
gene sequence, suggesting a unique community of dissimilatory arsenate-respiring bacteria in the Cache Valley Basin.
Clostridium botulinum Strains Producing BoNT/F4 or BoNT/F5
Authors: Raphael Brian H. , Bradshaw Marite , Kalb Suzanne R. , Joseph Lavin A. , Lúquez Carolina , Barr John R. , Johnson Eric A. , Maslanka Susan E. 
Published: March 2014

ABSTRACT

Botulinum neurotoxin type F (BoNT/F) may be produced by
Clostridium botulinum
alone or in combination with another toxin type such as BoNT/A or BoNT/B. Type F neurotoxin gene sequences have been further classified into seven toxin subtypes. Recently, the genome sequence of one strain of
C. botulinum
(Af84) was shown to contain three neurotoxin genes (
bont
/
F4
,
bont
/
F5
, and
bont
/
A2
). In this study, eight strains containing
bont
/
F4
and seven strains containing
bont
/
F5
were examined. Culture supernatants produced by these strains were incubated with BoNT/F-specific peptide substrates. Cleavage products of these peptides were subjected to mass spectral analysis, allowing detection of the BoNT/F subtypes present in the culture supernatants. PCR analysis demonstrated that a plasmid-specific marker (PL-6) was observed only among strains containing
bont
/
F5
. Among these strains, Southern hybridization revealed the presence of an approximately 242-kb plasmid harboring
bont
/
F5
. Genome sequencing of four of these strains revealed that the genomic backgrounds of strains harboring either
bont
/
F4
or
bont
/
F5
are diverse. None of the strains analyzed in this study were shown to produce BoNT/F4 and BoNT/F5 simultaneously, suggesting that strain Af84 is unusual. Finally, these data support a role for the mobility of a
bont
/
F5
-carrying plasmid among strains of diverse genomic backgrounds.
Diversity of the Lactic Acid Bacterium and Yeast Microbiota in the Switch from Firm- to Liquid-Sourdough Fermentation
Authors: Di Cagno Raffaella , Pontonio Erica , Buchin Solange , De Angelis Maria , Lattanzi Anna , Valerio Francesca , Gobbetti Marco , Calasso Maria 
Published: March 2014

ABSTRACT

Four traditional type I sourdoughs were comparatively propagated (28 days) under firm (dough yield, 160) and liquid (dough yield, 280) conditions to mimic the alternative technology options frequently used for making baked goods. After 28 days of propagation, liquid sourdoughs had the lowest pH and total titratable acidity (TTA), the lowest concentrations of lactic and acetic acids and free amino acids, and the most stable density of presumptive lactic acid bacteria. The cell density of yeasts was the highest in liquid sourdoughs. Liquid sourdoughs showed simplified microbial diversity and harbored a low number of strains, which were persistent.
Lactobacillus plantarum
dominated firm sourdoughs over time.
Leuconostoc lactis
and
Lactobacillus brevis
dominated only some firm sourdoughs, and
Lactobacillus sanfranciscensis
persisted for some time only in some firm sourdoughs.
Leuconostoc citreum
persisted in all firm and liquid sourdoughs, and it was the only species detected in liquid sourdoughs at all times; it was flanked by
Leuconostoc mesenteroides
in some sourdoughs.
Saccharomyces cerevisiae
,
Candida humilis
,
Saccharomyces servazzii
,
Saccharomyces bayanus-Kazachstania
sp., and
Torulaspora delbrueckii
were variously identified in firm and liquid sourdoughs. A total of 197 volatile components were identified through purge and trap–/solid-phase microextraction–gas chromatography-mass spectrometry (PT–/SPME–GC-MS). Aldehydes, several alcohols, and some esters were at the highest levels in liquid sourdoughs. Firm sourdoughs mainly contained ethyl acetate, acetic acid, some sulfur compounds, and terpenes. The use of liquid fermentation would change the main microbial and biochemical features of traditional baked goods, which have been manufactured under firm conditions for a long time.
Rapid TaqMan-Based Quantification of Chlorophyll
d
-Containing Cyanobacteria in the Genus Acaryochloris
Authors: Behrendt Lars , Nielsen Jeppe L. , Sørensen Søren J. , Larkum Anthony W. D. , Winther Jakob R. , Kühl Michael 
Published: March 2014

ABSTRACT

Reports of the chlorophyll (Chl)
d
-containing cyanobacterium
Acaryochloris
have accumulated since its initial discovery in 1996. The majority of this evidence is based on amplification of the gene coding for the 16S rRNA, and due to the wide geographical distribution of these sequences, a global distribution of
Acaryochloris
species was suggested. Here, we present a rapid, reliable, and cost-effective TaqMan-based quantitative PCR (qPCR) assay that was developed for the specific detection of
Acaryochloris
species in complex environmental samples. The TaqMan probe showed detection limits of ∼10 16S rRNA gene copy numbers based on standard curves consisting of plasmid inserts. DNA from five
Acaryochloris
strains, i.e., MBIC11017, CCMEE5410, HICR111A, CRS, and Awaji-1, exhibited amplification efficiencies of >94% when tested in the TaqMan assay. When used on complex natural communities, the TaqMan assay detected the presence of
Acaryochloris
species in four out of eight samples of crustose coralline algae (CCA), collected from temperate and tropical regions. In three out of these TaqMan-positive samples, the presence of Chl
d
was confirmed via high-performance liquid chromatography (HPLC), and corresponding cell estimates of
Acaryochloris
species amounted to 7.6 × 10
1
to 3.0 × 10
3
per mg of CCA. These numbers indicate a substantial contribution of Chl
d
-containing cyanobacteria to primary productivity in endolithic niches. The new TaqMan assay allows quick and easy screening of environmental samples for the presence of
Acaryochloris
species and is an important tool to further resolve the global distribution and significance of this unique oxyphototroph.
The Canonical Twin-Arginine Translocase Components Are Not Required for Secretion of Folded Green Fluorescent Protein from the Ancestral Strain of Bacillus subtilis
Authors: Snyder Anthony J. , Mukherjee Sampriti , Glass J. Kyle , Kearns Daniel B. , Mukhopadhyay Suchetana 
Published: March 2014

ABSTRACT

Cellular processes, such as the digestion of macromolecules, phosphate acquisition, and cell motility, require bacterial secretion systems. In
Bacillus subtilis
, the predominant protein export pathways are Sec (generalized secretory pathway) and Tat (twin-arginine translocase). Unlike Sec, which secretes unfolded proteins, the Tat machinery secretes fully folded proteins across the plasma membrane and into the medium. Proteins are directed for Tat-dependent export by N-terminal signal peptides that contain a conserved twin-arginine motif. Thus, utilizing the Tat secretion system by fusing a Tat signal peptide is an attractive strategy for the production and export of heterologous proteins. As a proof of concept, we expressed green fluorescent protein (GFP) fused to the PhoD Tat signal peptide in the laboratory and ancestral strains of
B. subtilis
. Secretion of the Tat-GFP construct, as well as secretion of proteins in general, was substantially increased in the ancestral strain. Furthermore, our results show that secreted, fluorescent GFP could be purified directly from the extracellular medium. Nonetheless, export was not dependent on the known Tat secretion components or the signal peptide twin-arginine motif. We propose that the ancestral strain contains additional Tat components and/or secretion regulators that were abrogated following domestication.