bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential contributions of plant Dicer‐like proteins to antiviral defences against potato virus X in leaves and roots
Authors: Andika Ida Bagus , Maruyama Kazuyuki , Sun Liying , Kondo Hideki , Tamada Tetsuo , Suzuki Nobuhiro 
Published: January 2015

SummaryMembers of the plant Dicer‐like (DCL) protein family are the critical components of the RNA‐silencing pathway that mediates innate antiviral defence. The distinct antiviral role of each individual DCL protein has been established with mostly based on observations of aerial parts of plants. Thus, although the roots are closely associated with the life cycle of many plant viruses, little is known about the antiviral activities of DCL proteins in roots. We observed that antiviral silencing strongly inhibits potato virus X (PVX) replication in roots of some susceptible Solanaceae species. Silencing of the DCL4 homolog in Nicotiana benthamiana partially elevated PVX replication levels in roots. In Arabidopsis thaliana, which was originally considered a non‐host plant of PVX, high levels of PVX accumulation in inoculated leaves were achieved by inactivation of DCL4, while in the upper leaves and roots, it required the additional inactivation of DCL2. In transgenic A. thaliana carrying the PVX amplicon with a green fluorescent protein (GFP) gene insertion in the chromosome (AMP243 line), absence of DCL4 enabled high levels of PVX‐GFP accumulation in various aerial organs but not in the roots, suggesting that DCL4 is critical for intracellular antiviral silencing in shoots but not in roots, where it can be functionally compensated by other DCL proteins. Together, the high level of functional redundancies among DCL proteins may contribute to the potent antiviral activities against PVX replication in roots.
Molecular Underpinnings of Synaptic Vesicle Pool Heterogeneity
Authors: Crawford Devon C. , Kavalali Ege T. 
Published: January 2015

AbstractNeuronal communication relies on chemical synaptic transmission for information transfer and processing. Chemical neurotransmission is initiated by synaptic vesicle fusion with the presynaptic active zone resulting in release of neurotransmitters. Classical models have assumed that all synaptic vesicles within a synapse have the same potential to fuse under different functional contexts. In this model, functional differences among synaptic vesicle populations are ascribed to their spatial distribution in the synapse with respect to the active zone. Emerging evidence suggests, however, that synaptic vesicles are not a homogenous population of organelles, and they possess intrinsic molecular differences and differential interaction partners. Recent studies have reported a diverse array of synaptic molecules that selectively regulate synaptic vesicles' ability to fuse synchronously and asynchronously in response to action potentials or spontaneously irrespective of action potentials. Here we discuss these molecular mediators of vesicle pool heterogeneity that are found on the synaptic vesicle membrane, on the presynaptic plasma membrane, or within the cytosol and consider some of the functional consequences of this diversity. This emerging molecular framework presents novel avenues to probe synaptic function and uncover how synaptic vesicle pools impact neuronal signaling.
Tariff‐tax Reforms in Large Economies
Authors: Ganelli Giovanni , Tervala Juha 
Published: January 2015

AbstractThis paper studies tariff‐tax reforms in a two‐region global New Keynesian model composed of a developing and an advanced region. In our baseline calibration, a revenue‐neutral reform that lowers tariffs in developing countries can reduce domestic welfare. The reason is that the increase in developing countries welfare due to higher output is dominated by the welfare losses stemming from the deterioration of the terms of trade. On the other hand, the reform increases output and welfare in the advanced countries and in the world as a whole. The effects that we highlight have not been studied in previous contributions to the literature, which looks at tariff‐tax reforms using a small open economy framework. Nominal rigidities have important implications for adjustment dynamics in our model. In the case of a ‘point‐for‐point’ reform, for example, price stickiness implies that the international dynamics of output is reversed compared to a revenue‐neutral reform.
The 24th annual meeting of the European Tissue Repair Society (ETRS) in Edinburgh, Scotland
Authors: Shaw Tanya J. , Lippens Evi 
Published: January 2015

AbstractFrom the 10th to 12th of September 2014, in the midst of the Scottish Independence debate, the European Tissue Repair Society descended on Edinburgh for their 24th Annual Meeting. In the beautiful and historic setting of the Royal College of Surgeons of Scotland, Professors David Thomas (Chair), Phil Stephens, Chris Lloyd, and their teams from Cardiff hosted an educational and inspiring program.
ACOUSTICAL STANDARDS NEWS
Authors: Blaeser Susan B. , Schomer Paul D. 
Published: January 2015

American National Standards (ANSI Standards) developed by Accredited Standards Committees S1, S2, S3, S3/SC 1, and S12 in the areas of acoustics, mechanical vibration and shock, bioacoustics, animal bioacoustics, and noise, respectively, are published by the Acoustical Society of America (ASA). In addition to these standards, ASA publishes catalogs of Acoustical Standards, both National and International. To receive copies of the latest Standards catalogs, please contact Susan B. Blaeser.
Comments are welcomed on all material in Acoustical Standards News.
This Acoustical Standards News section in JASA, as well as the National and International Catalogs of Acoustical Standards, and other information on the Standards Program of the Acoustical Society of America, are available via the ASA home page: http://acousticalsociety.org.
Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon
Authors: Hernández Marcela , Dumont Marc G. , Yuan Quan , Conrad Ralf 
Published: January 2015

ABSTRACT

Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH
4
, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with
13
CO
2
for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with
13
C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to
Proteobacteria
(13 OTUs) and
Verrucomicrobia
(8 OTUs). These OTUs were affiliated with the
Alphaproteobacteria
,
Betaproteobacteria
, and
Deltaproteobacteria
classes of
Proteobacteria
and the “
Spartobacteria
” and
Opitutae
classes of
Verrucomicrobia
. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment.
Syntrophic Growth of Desulfovibrio alaskensis Requires Genes for H
2
and Formate Metabolism as Well as Those for Flagellum and Biofilm Formation
Authors: Krumholz Lee R. , Bradstock Peter , Sheik Cody S. , Diao Yiwei , Gazioglu Ozcan , Gorby Yuri , McInerney Michael J. 
Published: January 2015

ABSTRACT

In anaerobic environments, mutually beneficial metabolic interactions between microorganisms (syntrophy) are essential for oxidation of organic matter to carbon dioxide and methane. Syntrophic interactions typically involve a microorganism degrading an organic compound to primary fermentation by-products and sources of electrons (i.e., formate, hydrogen, or nanowires) and a partner producing methane or respiring the electrons via alternative electron accepting processes. Using a transposon gene mutant library of the sulfate-reducing
Desulfovibrio alaskensis
G20, we screened for mutants incapable of serving as the electron-accepting partner of the butyrate-oxidizing bacterium,
Syntrophomonas wolfei
. A total of 17 gene mutants of
D. alaskensis
were identified as incapable of serving as the electron-accepting partner. The genes identified predominantly fell into three categories: membrane surface assembly, flagellum-pilus synthesis, and energy metabolism. Among these genes required to serve as the electron-accepting partner, the glycosyltransferase, pilus assembly protein (
tadC
), and flagellar biosynthesis protein showed reduced biofilm formation, suggesting that each of these components is involved in cell-to-cell interactions. Energy metabolism genes encoded proteins primarily involved in H
2
uptake and electron cycling, including a rhodanese-containing complex that is phylogenetically conserved among sulfate-reducing
Deltaproteobacteria
. Utilizing an mRNA sequencing approach, analysis of transcript abundance in wild-type axenic and cocultures confirmed that genes identified as important for serving as the electron-accepting partner were more highly expressed under syntrophic conditions. The results imply that sulfate-reducing microorganisms require flagellar and outer membrane components to effectively couple to their syntrophic partners; furthermore, H
2
metabolism is essential for syntrophic growth of
D. alaskensis
G20.
The Global Regulator CodY in Streptococcus thermophilus Controls the Metabolic Network for Escalating Growth in the Milk Environment
Authors: Lu W. W. , Wang Y. , Wang T. , Kong J. 
Published: January 2015

ABSTRACT

CodY is a transcriptional regulator conserved in the low-GC group of Gram-positive bacteria. In this work, we demonstrated the presence in
Streptococcus thermophilus
ST2017 of a functional member of the CodY family of global regulatory proteins,
S. thermophilus
CodY (CodY
St
). The CodY
St
regulon was identified by transcriptome analysis; it consisted predominantly of genes involved in amino acid metabolism but also included genes involved in several other cellular processes, including carbon metabolism, nutrient transport, and stress response. It was revealed that CodY
St
repressed the transformation of the central metabolic pathway to amino acid metabolism and improved lactose utilization. Furthermore, the glutamate dehydrogenase gene (
gdhA
), repressed by CodY
St
, was suggested to coordinate the interconversion between carbon metabolism and amino acid metabolism and to play an important role on the optimal growth of
S. thermophilus
ST2017 in milk. A conserved CodY
St
box [AA(T/A)(A/T)TTCTGA(A/C)AATT] was indeed required for
in vitro
binding of CodY
St
to the target regions of DNA. These results provided evidence for the function of CodY
St
, by which this strain coordinately regulates its various metabolic pathways so as to adapt to the milk environment.
Anthranilate Deteriorates the Structure of Pseudomonas aeruginosa Biofilms and Antagonizes the Biofilm-Enhancing Indole Effect
Authors: Kim Soo-Kyoung , Park Ha-Young , Lee Joon-Hee 
Published: January 2015

ABSTRACT

Anthranilate and indole are alternative degradation products of tryptophan, depending on the bacterial species. While indole enhances the biofilm formation of
Pseudomonas aeruginosa
, we found that anthranilate, the tryptophan degradation product of
P. aeruginosa
, had an opposite effect on
P. aeruginosa
biofilm formation, in which anthranilate deteriorated the mushroom structure of biofilm. The anthranilate effect on biofilm formation was differentially exerted depending on the developmental stage and the presence of shear force. Anthranilate slightly accelerated the initial attachment of
P. aeruginosa
at the early stage of biofilm development and appeared to build more biofilm without shear force. But anthranilate weakened the biofilm structure in the late stage, deteriorating the mushroom structure of biofilms with shear force to make a flat biofilm. To investigate the interplay of anthranilate with indole in biofilm formation, biofilms were cotreated with anthranilate and indole, and the results showed that anthranilate antagonized the biofilm-enhancing effect of indole. Anthranilate was able to deteriorate the preformed biofilm. The effect of anthranilate and indole on biofilm formation was quorum sensing independent. AntR, a regulator of anthranilate-degrading metabolism was synergistically activated by cotreatment with anthranilate and indole, suggesting that indole might enhance biofilm formation by facilitating the degradation of anthranilate. Anthranilate slightly but significantly affected the cyclic diguaniylate (c-di-GMP) level and transcription of major extracellular polysaccharide (Psl, Pel, and alginate) operons. These results suggest that anthranilate may be a promising antibiofilm agent and antagonize the effect of indole on
P. aeruginosa
biofilm formation.
Extrahuman Epidemiology of Acinetobacter baumannii in Lebanon
Authors: Rafei Rayane , Hamze Monzer , Pailhoriès Hélène , Eveillard Matthieu , Marsollier Laurent , Joly-Guillou Marie-Laure , Dabboussi Fouad , Kempf Marie 
Published: January 2015

ABSTRACT

The presence of
Acinetobacter baumannii
outside hospitals is still a controversial issue. The objective of our study was to explore the extrahospital epidemiology of
A. baumannii
in Lebanon. From February 2012 to October 2013, a total of 73 water samples, 51 soil samples, 37 raw cow milk samples, 50 cow meat samples, 7 raw cheese samples, and 379 animal samples were analyzed by cultural methods for the presence of
A. baumannii
. Species identification was performed by
rpoB
gene sequencing. Antibiotic susceptibility was investigated, and the
A. baumannii
population was studied by two genotyping approaches: multilocus sequence typing (MLST) and
bla
OXA-51
sequence-based typing (SBT).
A. baumannii
was detected in 6.9% of water samples, 2.7% of milk samples, 8.0% of meat samples, 14.3% of cheese samples, and 7.7% of animal samples. All isolates showed a susceptible phenotype against most of the antibiotics tested and lacked carbapenemase-encoding genes, except one that harbored a
bla
OXA-143
gene. MLST analysis revealed the presence of 36 sequence types (STs), among which 24 were novel STs reported for the first time in this study.
bla
OXA-51
SBT showed the presence of 34 variants, among which 21 were novel and all were isolated from animal origins. Finally, 30 isolates had new partial
rpoB
sequences and were considered putative new
Acinetobacter
species. In conclusion, animals can be a potential reservoir for
A. baumannii
and the dissemination of new emerging carbapenemases. The roles of the novel animal clones identified in community-acquired infections should be investigated.
Long-Term Study of Vibrio parahaemolyticus Prevalence and Distribution in New Zealand Shellfish
Authors: Cruz C. D. , Hedderley D. , Fletcher G. C. 
Published: January 2015

ABSTRACT

The food-borne pathogen
Vibrio parahaemolyticus
has been reported as being present in New Zealand (NZ) seawaters, but there have been no reported outbreaks of food-borne infection from commercially grown NZ seafood. Our study determined the current incidence of
V. parahaemolyticus
in NZ oysters and Greenshell mussels and the prevalence of
V. parahaemolyticus
tdh
and
trh
strains. Pacific (235) and dredge (21) oyster samples and mussel samples (55) were obtained from commercial shellfish-growing areas between December 2009 and June 2012. Total
V. parahaemolyticus
numbers and the presence of pathogenic genes
tdh
and
trh
were determined using the FDA most-probable-number (MPN) method and confirmed using PCR analysis. In samples from the North Island of NZ,
V. parahaemolyticus
was detected in 81% of Pacific oysters and 34% of mussel samples, while the numbers of
V. parahaemolyticus
tdh
and
trh
strains were low, with just 3/215 Pacific oyster samples carrying the
tdh
gene.
V. parahaemolyticus
organisms carrying
tdh
and
trh
were not detected in South Island samples, and
V. parahaemolyticus
was detected in just 1/21 dredge oyster and 2/16 mussel samples. Numbers of
V. parahaemolyticus
organisms increased when seawater temperatures were high, the season when most commercial shellfish-growing areas are not harvested. The numbers of
V. parahaemolyticus
organisms in samples exceeded 1,000 MPN/g only when the seawater temperatures exceeded 19°C, so this environmental parameter could be used as a trigger warning of potential hazard. There is some evidence that the total
V. parahaemolyticus
numbers increased compared with those reported from a previous 1981 to 1984 study, but the analytical methods differed significantly.
Severe colic mimicking intussusception: a new phenomenon
Authors: El-Gohary Mohamed Amin 
Published: January 2015

ObjectiveTo highlight a new phenomenon that we have encountered in children during the past 5 years. Children in this group have a pathognomonic clinical picture of sudden acute severe abdominal colic during which the child is continuously screaming for 1–2 min. All these patients were initially diagnosed on clinical and ultrasonographic grounds as acute intussusception. Careful interpretation of the radiological findings revealed faecal impaction of the terminal ileum and caecum.DesignThis is a retrospective study looking at children presenting between 2009 and 2014 with acute severe abdominal colic pain. These were 11 patients aged 9 months to 5 years. We reviewed our experience in the management and diagnosis of these patients.ResultAll patients were diagnosed initially as intussusception, which was confirmed by ultrasonography (US). US revealed an appearance mimicking intussusception, 3 cases of which were intermittent. This US appearance proved to be a hard stool filling the terminal ileum. In all patients, abdominal X-ray revealed stool at the right side of the colon filling the caecum. Diagnostic gastrografin enemas that were performed in four patients excluded intussusception and confirmed stool at the caecum and ascending colon. In none of those patients had contrast passed into the terminal ileum. There was dramatic response to fleet and/or gastrografin enemas. Five patients required a second dose of enema and two patients required three doses.ConclusionsWe highlight a new phenomenon of severe abdominal pain caused by faecal impaction of the terminal ileum and caecum. Increased awareness of this condition helps to avoid unnecessary investigations and/or surgical exploration.
Inter-rater reliability of J-point location and measurement of the magnitude of ST segment elevation at the J-point on ECGs of STEMI patients by emergency department doctors
Authors: Lim Hoon Chin Steven , Salandanan Edgar Azada , Phillips Rachel , Tan Jun Guan , Hezan Muhammad Azmi 
Published: January 2015

Introduction and objectivesIdentification of the J-point and measurement of ST segment elevation at the J-point are important for the diagnosis of ST-elevation myocardial infarction (STEMI). We conducted a study to determine the inter-rater reliability (IRR) of J-point location and measurement of the magnitude of ST elevation at the J-point on ECGs of patients with STEMI by emergency department (ED) doctors.Subjects and methodsEach participant examined 20 STEMI ECGs during a 1-month period in 2013. The participants were required to locate the J-point by selecting the small 1 mm square within which the J-point is located and measure the magnitude of ST elevation at the J-point identified (rounded up to the nearest 0.5 mm). The intraclass correlation coefficient (ICC) was calculated to assess the IRR.ResultsThirty doctors participated. The ICC assessing the degree to which all participants provided agreement in their assessment of the location of J-points across ECGs was 0.85 (95% CI 0.75 to 0.93), which is in the excellent range. The ICC for assessing the magnitude of ST elevation was 0.97 (95% CI 0.94 to 0.98), indicating excellent agreement as well.ConclusionsED doctors show a high level of agreement when determining the location of J-points and measuring the magnitude of ST elevation at those J-points on ECGs of patients with STEMI. The findings support the measurement of ST segment elevation at the J-point in STEMI cases and should be regarded as a consistent standard to avoid confusion.
An evaluation of demographic factors affecting performance in a paediatric membership multiple-choice examination
Authors: Menzies Lara , Minson Susan , Brightwell Alexandra , Davies-Muir Anna , Long Andrew , Fertleman Caroline 
Published: January 2015

ABSTRACT

Objective
To determine if demographic factors are associated with outcome in a multiple-choice, electronically marked paediatric postgraduate examination.

Method
Retrospective analysis of pass rates of UK trainees sitting Membership of the Royal College of Paediatrics and Child Health (MRCPCH) part 1B from 2007 to 2011. Data collected by the RCPCH from examination candidates were analysed to assess the effects of gender, age, and country and university of medical qualification on examination outcome.

Results
At first attempt at MRCPCH part 1B, the overall pass rate from 2007 to 2011 was 843/2056 (41.0%). In univariate analysis, passing the examination was associated with being a UK graduate (649/1376 (47.2%)) compared with being an international medical graduate (130/520 (25.0%)) (OR 2.68 (95% CI 2.14 to 3.36), p&lt;0.001). There was strong evidence that the proportion of candidates passing the examination differed for graduates of the 19 different UK medical schools (Fisher's exact test p&lt;0.001). In multivariate logistic regression analysis, after adjustment for age, sex and whether the part 1A examination was taken concurrently, being a UK graduate was still strongly associated with passing the examination (OR 3.17 (95% CI 2.41 to 4.17), p&lt;0.001). UK graduates performed best at 26–27 years of age (52.4% pass rate), whereas overseas graduates performed best at ≥38 years of age (50.8% pass rate).

Conclusions
MRCPCH part 1B outcome was related to place of primary medical qualification, with a significantly lower pass rate for international medical graduates compared with UK graduates, as well as significant variation in examination outcome between graduates from different UK medical schools. These data may be used to guide new initiatives to improve support and education for these trainees and to inform development of undergraduate curricula and help trainees prepare more successfully for postgraduate examinations.