bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eosinophilic esophagitis in children following cardiac transplantation: Association with post‐transplant lymphoproliferative disorder and other transplant outcomes
Authors: Kindel Steven J. , Joy Brian F. , Pahl Elfriede , Wald Eric L. 
Published: June 2014

AbstractAlthough cardiac transplantation is life‐saving, morbidities from immunosuppression are significant. EoE is a complication of calcineurin inhibitors following liver transplant causing feeding intolerance, weight loss, vomiting, and dysphagia. There are limited reports of EoE following heart transplantation. We performed a retrospective single‐center review of pediatric cardiac transplant patients from 2000 to 2010. A case–control analysis of patients with and without EoE was performed evaluating heart transplantation outcomes such as rates of rejection, CAV, PTLD, and graft loss. Eighty‐six transplants were performed in 84 patients; 34 (40%) underwent diagnostic endoscopy, and 10 (12%) had EoE. Median time to diagnosis of EoE was 3.7 yr (IQR: 2.0–5.2). There were no differences in demographics or use of induction medications between patients with or without EoE. Patients with EoE had fewer episodes of treated rejection (1.0 vs. 2.5; p = 0.04). Four of 10 (40%) EoE patients had PTLD compared with only 2/24 (8%) of those without EoE (p = 0.048; OR 7.33 [95% CI: 1.1–50.2]). There were no differences in CAV or graft loss between groups. EoE should be considered as a cause of GI symptoms in children after cardiac transplantation and may be associated with fewer rejection episodes and increased rates of PTLD, thus representing a marker of over‐immunosuppression.
Automatic reconstruction of regular buildings using a shape‐based balloon snake model
Authors: Yari Diako , Mokhtarzade Mehdi , Ebadi Hamid , Ahmadi Salman 
Published: June 2014

AbstractBuildings are regarded as the most prominent man‐made objects: hence, their automatic extraction from aerial and satellite images has attracted the interest of photogrammetric research communities. In this paper, a balloon snake, a well‐known active contour model, was developed for the precise extraction of building boundaries. Traditional active contours are highly sensitive to image data and are problematic when building boundaries are weakened, usually due to occlusions. To improve the efficiency of the traditional balloon snake model, a shape‐based balloon snake model was introduced where knowledge about the expected geometrical shape of buildings was modelled and applied to the traditional snake representation. Implementation of the proposed algorithm confirmed its efficiency in the precise extraction of building boundaries. Experimental results and the qualitative and quantitative evaluations demonstrate the potential of the proposed shape‐based balloon snake model and its superiority over traditional models.
Labour Markets, Care Regimes and Foreign Care Worker Policies in East Asia
Authors: Song Jiyeoun 
Published: June 2014

AbstractThis article analyzes the politics of foreign care worker policies in Japan, Korea and Taiwan. In the face of socio‐demographic challenges, these countries have responded differently to the increasing demand for hiring foreign care workers, creating distinct policies with respect to the origins of the foreign care workforce, the size of the foreign care workforce in the labour market, and job specifications. In this article, I argue that the interaction of female employment patterns, the public provision (or lack) of social care, and labour market policies in the care service sector determines the diverging political pathways of foreign care worker policies in these three countries over the past two decades.
New fossil Progonocimicidae (Hemiptera: Coleorrhyncha: Progonocimicoidea) from the Upper Mesozoic of northeastern China, with a phylogeny of Coleorrhyncha
Authors: DONG QIUPING , YAO YUNZHI , REN DONG 
Published: June 2014

AbstractA new Progonocimicidae species, Cicadocoris anisomeridis sp.n., with asymmetrical tegmina is described from the Middle Jurassic Jiulongshan Formation in northeastern China. This is the fifth report of Coleorrhyncha from China. A cladistic analysis based on a combination of fossil and extant taxa clarifies the phylogenetic status of the new fossils and allows the reconstruction of inter‐subfamily relationships within the suborder Coleorrhyncha. Coleorrhyncha is monophyletic and divided into two main clades. Progonocimicidae comprises a monophyletic lineage, to which the new fossils belong. The broadly conceived Progonocimicinae and Cicadocorinae, as recognized by earlier authors, are not supported. The monophyly of the family Karabasiidae is also not supported, and its two constituent subfamilies Hoploridiinae and Karabasiinae are raised to family rank. Hoploridiidae is found to be sister group to all extant moss bugs, and Karabasiidae is found to be the monophyletic sister group to Hoploridiidae + all extant moss bugs.This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:30BC0498‐3B8A‐4650‐BC9D‐02A0C8D870B2.
Preservation of Re‐Os isotope signatures in pyrite throughout low‐T, high‐P eclogite facies metamorphism
Authors: van Acken David , Su Wen , Gao Jun , Creaser Robert A. 
Published: June 2014

AbstractPyrite in LT–HP eclogites from the western Tianshan orogenic belt yields a Re‐Os age of 378.1 ± 8.9 Ma, which is 30–70 Ma older than ages previously obtained for the same rocks using the Rb–Sr, Sm–Nd, Ar–Ar, U–Pb, and Lu–Hf isotope systems. The Tianshan LT–HP eclogite experienced temperatures of up to ~570 °C combined with pressures of up to 2.1 GPa during metamorphism. These conditions are below the transition of pyrite to pyrrhotite, which defines both pyrite stability and possibly its closure temperature for Re‐Os. Pyrite can preserve Re‐Os signatures through eclogite facies peak metamorphic conditions, and thus allow determination of the formation age of pyrite in the protolith.
Modularity of nearly ordinary 2-adic residually dihedral Galois representations
Authors: Allen Patrick B. 
Published: June 2014

AbstractWe prove modularity of some two-dimensional,$\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}2$-adic Galois representations over a totally real field that are nearly ordinary at all places above$2$and that are residually dihedral. We do this by employing the strategy of Skinner and Wiles, using Hida families, together with the$2$-adic patching method of Khare and Wintenberger. As an application we deduce modularity of some elliptic curves over totally real fields that have good ordinary or multiplicative reduction at places above $2$.
Syntaxin‐binding domain of Kv2.1 is essential for the expression of apoptotic K+ currents
Authors: McCord Meghan C. , Kullmann Paul H. , He Kai , Hartnett Karen A. , Horn John P. , Lotan Ilana , Aizenman Elias 
Published: June 2014

Key points
K+ efflux through newly membrane‐inserted voltage‐gated Kv2.1 K+ channels precedes neuronal apoptosis.
In this study, we show that the binding site of the soluble N‐ethylmaleimide‐sensitive factor attachment protein receptor (SNARE) protein syntaxin on Kv2.1 (a 110 amino acid C‐terminal domain of Kv2.1, termed C1a) is required for the enhancement of apoptotic K+ currents.
Expression of a Kv2.1‐derived C1a peptide prevents Kv2.1/syntaxin binding, oxidant‐induced, enhanced K+ currents and cell death without substantially affecting electrical properties of neurons.
Data suggest that syntaxin binds within the most distal 50 amino acids of the C1a domain of Kv2.1.
Disrupting Kv2.1/syntaxin binding may represent a new tactic for suppressing injurious K+ efflux, which is a ubiquitous requirement of apoptotic signalling cascades in neurons.
AbstractIntracellular signalling cascades triggered by oxidative injury can lead to upregulation of Kv2.1 K+ channels at the plasma membrane of dying neurons. Membrane incorporation of new channels is necessary for enhanced K+ efflux and a consequent reduction of intracellular K+ that facilitates apoptosis. We showed previously that the observed increase in K+ currents is a soluble N‐ethylmaleimide‐sensitive factor attachment protein receptor (SNARE)‐mediated process, and that the SNARE protein syntaxin binds directly to Kv2.1 channels. In the present study, we tested whether disrupting the interaction of Kv2.1 and syntaxin promoted the survival of cortical neurons following injury. Syntaxin is known to bind to Kv2.1 in a domain comprising amino acids 411–522 of the channel's cytoplasmic C terminus (C1a). Here we show that this domain is required for the apoptotic K+ current enhancement. Moreover, expression of an isolated, Kv2.1‐derived C1a peptide is sufficient to suppress the injury‐induced increase in currents by interfering with Kv2.1/syntaxin binding. By subdividing the C1a peptide, we were able to localize the syntaxin binding site on Kv2.1 to the most plasma membrane‐distal residues of C1a. Importantly, expression of this peptide segment in neurons prevented the apoptotic K+ current enhancement and cell death following an oxidative insult, without greatly impairing baseline K+ currents or normal electrical profiles of neurons. These results establish that binding of syntaxin to Kv2.1 is crucial for the manifestation of oxidant‐induced apoptosis, and thereby reveal a potential new direction for therapeutic intervention in the treatment of neurodegenerative disorders.
RANS Modeling of Accelerating Boundary Layers
Authors: Oriji Ugochukwu R. , Karimisani Sahand , Tucker Paul G. 
Published: June 2014

Abstract
A numerical investigation of accelerated boundary layers (BL) has been performed using linear and nonlinear eddy viscosity models (EVM). The acceleration parameters (KS) investigated the range between 1.5 × 10−6 and 3.0 × 10−6. The one-equation (k-l), Spalart Allmaras (SA), and the two-equation Menter Shear Stress Transport (SST) and Chien models in their standard forms are found to be insensitive to acceleration. Nevertheless, proposed modifications for the SA, Chien, and the k-l models significantly improved predictions. The major improvement was achieved by modifying the damping functions in these models and also an analogous source term, E, for the Chien model. Encouraging agreement with measurements is found using the Launder Sharma (LS), cubic and explicit algebraic stress models (EASM) in their standard forms. The cubic model best predicted the turbulence quantities. Investigations confirm that it is practical for Reynolds-Average Navier–Stokes (RANS) models to capture reversion from the turbulent to laminar state albeit for equilibrium sink type flows.
Microbial Successions Are Associated with Changes in Chemical Profiles of a Model Refrigerated Fresh Pork Sausage during an 80-Day Shelf Life Study
Authors: Benson Andrew K. , David Jairus R. D. , Gilbreth Stefanie Evans , Smith Gordon , Nietfeldt Joseph , Legge Ryan , Kim Jaehyoung , Sinha Rohita , Duncan Christopher E. , Ma Junjie , Singh Indarpal 
Published: June 2014

ABSTRACT

Fresh pork sausage is produced without a microbial kill step and therefore chilled or frozen to control microbial growth. In this report, the microbiota in a chilled fresh pork sausage model produced with or without an antimicrobial combination of sodium lactate and sodium diacetate was studied using a combination of traditional microbiological methods and deep pyrosequencing of 16S rRNA gene amplicons. In the untreated system, microbial populations rose from 10
2
to 10
6
CFU/g within 15 days of storage at 4°C, peaking at nearly 10
8
CFU/g by day 30. Pyrosequencing revealed a complex community at day 0, with taxa belonging to the
Bacilli
,
Gammaproteobacteria
,
Betaproteobacteria
,
Actinobacteria
,
Bacteroidetes
, and
Clostridia
. During storage at 4°C, the untreated system displayed a complex succession, with species of
Weissella
and
Leuconostoc
that dominate the product at day 0 being displaced by species of
Pseudomonas
(
P. lini
and
P. psychrophila
) within 15 days. By day 30, a second wave of taxa (
Lactobacillus graminis
,
Carnobacterium divergens
,
Buttiauxella brennerae
,
Yersinia mollaretti
, and a taxon of
Serratia
) dominated the population, and this succession coincided with significant chemical changes in the matrix. Treatment with lactate-diacetate altered the dynamics dramatically, yielding a monophasic growth curve of a single species of
Lactobacillus
(
L. graminis
), followed by a uniform selective die-off of the majority of species in the population. Of the six species of
Lactobacillus
that were routinely detected,
L. graminis
became the dominant member in all samples, and its origins were traced to the spice blend used in the formulation.
Uptake and Metabolism of
N
-Acetylglucosamine and Glucosamine by Streptococcus mutans
Authors: Moye Zachary D. , Burne Robert A. , Zeng Lin 
Published: June 2014

ABSTRACT

Glucosamine and
N
-acetylglucosamine are among the most abundant sugars on the planet, and their introduction into the oral cavity via the diet and host secretions, and through bacterial biosynthesis, provides oral biofilm bacteria with a source of carbon, nitrogen, and energy. In this study, we demonstrated that the dental caries pathogen
Streptococcus mutans
possesses an inducible system for the metabolism of
N
-acetylglucosamine and glucosamine. These amino sugars are transported by the phosphoenolpyruvate:sugar phosphotransferase system (PTS), with the glucose/mannose enzyme II permease encoded by
manLMN
playing a dominant role. Additionally, a previously uncharacterized gene product encoded downstream of the
manLMN
operon, ManO, was shown to influence the efficiency of uptake and growth on
N
-acetylglucosamine and, to a lesser extent, glucosamine. A transcriptional regulator, designated NagR, was able to bind the promoter regions
in vitro
, and repress the expression
in vivo
, of the
nagA
and
nagB
genes, encoding
N
-acetylglucosamine-6-phosphate deacetylase and glucosamine-6-phosphate deaminase, respectively. The binding activity of NagR could be inhibited by glucosamine-6-phosphate
in vitro
. Importantly, in contrast to the case with certain other
Firmicutes
, the gene for
de novo
synthesis of glucosamine-6-phosphate in
S. mutans
,
glmS
, was also shown to be regulated by NagR, and NagR could bind the
glmS
promoter region
in vitro
. Finally, metabolism of these amino sugars by
S. mutans
resulted in the production of significant quantities of ammonia, which can neutralize cytoplasmic pH and increase acid tolerance, thus contributing to enhanced persistence and pathogenic potential.
Epithelial Adhesion Mediated by Pilin SpaC Is Required for Lactobacillus rhamnosus GG-Induced Cellular Responses
Authors: Ardita Courtney S. , Mercante Jeffrey W. , Kwon Young Man , Luo Liping , Crawford Madelyn E. , Powell Domonica N. , Jones Rheinallt M. , Neish Andrew S. 
Published: June 2014

ABSTRACT

Lactobacillus rhamnosus
GG is a widely used probiotic, and the strain's salutary effects on the intestine have been extensively documented. We previously reported that strain GG can modulate inflammatory signaling, as well as epithelial migration and proliferation, by activating NADPH oxidase 1-catalyzed generation of reactive oxygen species (ROS). However, how strain GG induces these responses is unknown. Here, we report that strain GG's probiotic benefits are dependent on the bacterial-epithelial interaction mediated by the SpaC pilin subunit. By comparing strain GG to an isogenic mutant that lacks SpaC (strain GGΩ
spaC
), we establish that SpaC is necessary for strain GG to adhere to gut mucosa, that SpaC contributes to strain GG-induced epithelial generation of ROS, and that SpaC plays a role in strain GG's capacity to stimulate extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) signaling in enterocytes. In addition, we show that SpaC is required for strain GG-mediated stimulation of cell proliferation and protection against radiologically inflicted intestinal injury. The identification of a critical surface protein required for strain GG to mediate its probiotic influence advances our understanding of the molecular basis for the symbiotic relationship between some commensal bacteria of the gut lumen and enterocytes. Further insights into this relationship are critical for the development of novel approaches to treat intestinal diseases.
Following Pathogen Development and Gene Expression in a Food Ecosystem: the Case of a Staphylococcus aureus Isolate in Cheese
Authors: Fleurot Isabelle , Aigle Marina , Fleurot Renaud , Darrigo Claire , Hennekinne Jacques-Antoine , Gruss Alexandra , Borezée-Durant Elise , Delacroix-Buchet Agnès 
Published: June 2014

ABSTRACT

Human intoxication or infection due to bacterial food contamination constitutes an economic challenge and a public health problem. Information on the
in situ
distribution and expression of pathogens responsible for this risk is to date lacking, largely because of technical bottlenecks in detecting signals from minority bacterial populations within a complex microbial and physicochemical ecosystem. We simulated the contamination of a real high-risk cheese with a natural food isolate of
Staphylococcus aureus
, an enterotoxin-producing pathogen responsible for food poisoning. To overcome the problem of a detection limit in a solid matrix, we chose to work with a fluorescent reporter (superfolder green fluorescent protein) that would allow spatiotemporal monitoring of
S. aureus
populations and targeted gene expression. The combination of complementary techniques revealed that
S. aureus
localizes preferentially on the cheese surface during ripening. Immunochemistry and confocal laser scanning microscopy enabled us to visualize, in a single image, dairy bacteria and pathogen populations, virulence gene expression, and the toxin produced. This procedure is readily applicable to other genes of interest, other bacteria, and different types of food matrices.
Daily Expression Pattern of Protein-Encoding Genes and Small Noncoding RNAs in Synechocystis sp. Strain PCC 6803
Authors: Beck Christian , Hertel Stefanie , Rediger Anne , Lehmann Robert , Wiegard Anika , Kölsch Adrian , Heilmann Beate , Georg Jens , Hess Wolfgang R. , Axmann Ilka M. 
Published: June 2014

ABSTRACT

Many organisms harbor circadian clocks with periods close to 24 h. These cellular clocks allow organisms to anticipate the environmental cycles of day and night by synchronizing circadian rhythms with the rising and setting of the sun. These rhythms originate from the oscillator components of circadian clocks and control global gene expression and various cellular processes. The oscillator of photosynthetic cyanobacteria is composed of three proteins, KaiA, KaiB, and KaiC, linked to a complex regulatory network.
Synechocystis
sp. strain PCC 6803 possesses the standard cyanobacterial
kaiABC
gene cluster plus multiple
kaiB
and
kaiC
gene copies and antisense RNAs for almost every
kai
transcript. However, there is no clear evidence of circadian rhythms in
Synechocystis
sp. PCC 6803 under various experimental conditions. It is also still unknown if and to what extent the multiple
kai
gene copies and
kai
antisense RNAs affect circadian timing. Moreover, a large number of small noncoding RNAs whose accumulation dynamics over time have not yet been monitored are known for
Synechocystis
sp. PCC 6803. Here we performed a 48-h time series transcriptome analysis of
Synechocystis
sp. PCC 6803, taking into account periodic light-dark phases, continuous light, and continuous darkness. We found that expression of functionally related genes occurred in different phases of day and night. Moreover, we found day-peaking and night-peaking transcripts among the small RNAs; in particular, the amounts of
kai
antisense RNAs correlated or anticorrelated with those of their respective
kai
target mRNAs, pointing toward the regulatory relevance of these antisense RNAs. Surprisingly, we observed that the amounts of 16S and 23S rRNAs in this cyanobacterium fluctuated in light-dark periods, showing maximum accumulation in the dark phase. Importantly, the amounts of all transcripts, including small noncoding RNAs, did not show any rhythm under continuous light or darkness, indicating the absence of circadian rhythms in
Synechocystis
.
Identification of Mn(II)-Oxidizing Bacteria from a Low-pH Contaminated Former Uranium Mine
Authors: Akob Denise M. , Bohu Tsing , Beyer Andrea , Schäffner Franziska , Händel Matthias , Johnson Carol A. , Merten Dirk , Büchel Georg , Totsche Kai Uwe , Küsel Kirsten 
Published: June 2014

ABSTRACTBiological Mn oxidation is responsible for producing highly reactive and abundant Mn oxide phases in the environment that can mitigate metal contamination. However, little is known about Mn oxidation in low-pH environments, where metal contamination often is a problem as the result of mining activities. We isolated two Mn(II)-oxidizing bacteria (MOB) at pH 5.5 (Duganellaisolate AB_14 andAlbidiferaxisolate TB-2) and nine strains at pH 7 from a former uranium mining site. Isolate TB-2 may contribute to Mn oxidation in the acidic Mn-rich subsoil, as a closely related clone represented 16% of the total community. All isolates oxidized Mn over a small pH range, and isolates from low-pH samples only oxidized Mn below pH 6. Two strains with different pH optima differed in their Fe requirements for Mn oxidation, suggesting that Mn oxidation by the strain found at neutral pH was linked to Fe oxidation. Isolates tolerated Ni, Cu, and Cd and produced Mn oxides with similarities to todorokite and birnessite, with the latter being present in subsurface layers where metal enrichment was associated with Mn oxides. This demonstrates that MOB can be involved in the formation of biogenic Mn oxides in both moderately acidic and neutral pH environments.
DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies
Authors: Hugerth Luisa W. , Wefer Hugo A. , Lundin Sverker , Jakobsson Hedvig E. , Lindberg Mathilda , Rodin Sandra , Engstrand Lars , Andersson Anders F. 
Published: June 2014

ABSTRACT

The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571–1579, 2011,
http://dx.doi.org/10.1038/ismej.2011.41
), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.