bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re‐evaluating transarterial chemoembolization for the treatment of Hepatocellular Carcinoma: Consensus recommendations and review by an International Expert Panel
Authors: Cheng Ann Lii , Amarapurkar Deepak , Chao Yee , Chen Pei‐Jer , Geschwind Jean‐François , Goh Khean L. , Han Kwang‐Hyub , Kudo Masatoshi , Lee Han Chu , Lee Rheun‐Chuan , Lesmana Laurentius A. , Lim Ho Yeong , Paik Seung Woon , Poon Ronnie T. , Tan Chee‐Kiat , Tanwandee Tawesak , Teng Gaojun , Park Joong‐Won 
Published: September 2013

AbstractPatients with unresectable hepatocellular carcinoma (HCC) usually receive transarterial chemoembolization (TACE) or systemic therapies with intermediate and advanced‐stage disease. However, intermediate‐stage HCC patients often have unsatisfactory clinical outcomes with repeated TACE and there is considerable uncertainty surrounding the criteria for repeating or stopping TACE treatment. In July 2012, an Expert Panel Opinion on Interventions in Hepatocellular Carcinoma (EPOIHCC) was re‐convened in Shanghai in an attempt to provide a consensus on the practice of TACE, particularly in regard to evaluating TACE ‘failure’. To that end, current clinical practice throughout Asia was reviewed in detail including safety and efficacy data on TACE alone as well as in combination with targeted systemic therapies for intermediate HCC. This review summarizes the evidence discussed at the meeting and provides expert recommendations regarding the use of TACE for unresectable intermediate‐stage HCC. A key consensus of the Expert Panel was that the current definitions of TACE failure are not useful in differentiating between situations where TACE is no longer effective in controlling disease locally vs. systemically. By redefining these concepts, it may be possible to provide a clearer indication of when TACE should be repeated and more importantly, when TACE should be discontinued.
Seasonal dynamics of fungal communities in a temperate oak forest soil
Authors: Voříšková Jana , Brabcová Vendula , Cajthaml Tomáš , Baldrian Petr 
Published: September 2013

Summary

Fungi are the agents primarily responsible for the transformation of plant‐derived carbon in terrestrial ecosystems. However, little is known of their responses to the seasonal changes in resource availability in deciduous forests, including photosynthate allocation below ground and seasonal inputs of fresh litter.

Vertical stratification of and seasonal changes in fungal abundance, activity and community composition were investigated in the litter, organic and upper mineral soils of a temperate Quercus petraea forest using ergosterol and extracellular enzyme assays and amplicon 454‐pyrosequencing of the rDNA‐ITS region.

Fungal activity, biomass and diversity decreased substantially with soil depth. The highest enzyme activities were detected in winter, especially in litter, where these activities were followed by a peak in fungal biomass during spring. The litter community exhibited more profound seasonal changes than did the community in the deeper horizons. In the litter, saprotrophic genera reached their seasonal maxima in autumn, but summer typically saw the highest abundance of ectomycorrhizal taxa. Although the composition of the litter community changes over the course of the year, the mineral soil shows changes in biomass.

The fungal community is affected by season. Litter decomposition and phytosynthate allocation represent important factors contributing to the observed variations.
The Political Economy of Policy Gridlock inSouthKorea: The Case of theLeeMyung‐bak Government's Green Growth Policy
Authors: Heo Inhye 
Published: September 2013

This article analyzes the occurrence, development, results, and special features of policy gridlock inSouthKorea's green growth (GG) policy from a political–economic perspective. Analysis is based on the claim that the relationships that the government has formed with other relevant policy actors—including the National Assembly, market players, and civil society—underpin the critical political–economic causes of the gridlock. Research results show that the characteristics of the relationships that the government has formed with those actors, as well as the complex interactions among them (such as intervening in other actor–government relationships and pursuing either conflict or cooperation with one another), have functioned as direct causes of policy gridlock. Based on these findings, the article explores the theoretical implications of the study of policy gridlock and the comparative international implications for global efforts towardGG, while consideringSouthKorea's intermediate position in the globalGGcommunity.Related ArticlesHarris,Paul.2008. “.”Politics & Policy36():914‐943.http://onlinelibrary.wiley.com/doi/10.1111/j.1747‐1346.2008.00145.x/abstractLevine,Stephen.2007. “.”Politics & Policy35():102‐135.Kane,John,Hui‐ChiehLoy, andHaigPatapan.2010. “.”Politics & Policy38():381‐394.http://onlinelibrary.wiley.com/doi/10.1111/j.1747‐1346.2010.00240.x/abstractRelated Media.2009. “.”http://www.youtube.com/watch?v=rP6KE‐NDDJE.2008. “.”http://www.democracynow.org/2008/8/7/south_koreans_fill_streets_of_seoulKosch O'Donnell,Jill.2011. “” . June 15.http://asiafoundation.org/in‐asia/2011/06/15/koreas‐97‐billion‐dollar‐question‐what‐is‐green‐growth/
Insights into the Mode of Action of Benzyl Isothiocyanate on Campylobacter jejuni
Authors: Dufour Virginie , Stahl Martin , Rosenfeld Eric , Stintzi Alain , Baysse Christine 
Published: September 2013

ABSTRACT

Campylobacter jejuni
is a widespread pathogen responsible for most of the food-borne gastrointestinal diseases in Europe. The use of natural antimicrobial molecules is a promising alternative to antibiotic treatments for pathogen control in the food industry. Isothiocyanates are natural antimicrobial compounds, which also display anticancer activity. Several studies described the chemoprotective effect of isothiocyanates on eukaryotic cells, but the antimicrobial mechanism is still poorly understood. We investigated the early cellular response of
C. jejuni
to benzyl isothiocyanate by both transcriptomic and physiological approaches. The transcriptomic response of
C. jejuni
to benzyl isothiocyanate showed upregulation of heat shock response genes and an impact on energy metabolism. Oxygen consumption was progressively impaired by benzyl isothiocyanate treatment, as revealed by high-resolution respirometry, while the ATP content increased soon after benzyl isothiocyanate exposition, which suggests a shift in the energy metabolism balance. Finally, benzyl isothiocyanate induced intracellular protein aggregation. These results indicate that benzyl isothiocyanate affects
C. jejuni
by targeting proteins, resulting in the disruption of major metabolic processes and eventually leading to cell death.
Resistance to Quorum-Quenching Compounds
Authors: García-Contreras Rodolfo , Maeda Toshinari , Wood Thomas K. 
Published: September 2013

ABSTRACT
Bacteria have the remarkable ability to communicate as a group in what has become known as quorum sensing (QS), and this trait has been associated with important bacterial phenotypes, such as virulence and biofilm formation. Bacteria also have an incredible ability to evolve resistance to all known antimicrobials. Hence, although inhibition of QS has been hailed as a means to reduce virulence in a manner that is impervious to bacterial resistance mechanisms, this approach is unlikely to be a panacea. Here we review the evidence that bacteria can evolve resistance to quorum-quenching compounds.
Tomato Fruit and Seed Colonization by Clavibacter michiganensis subsp. michiganensis through External and Internal Routes
Authors: Tancos Matthew A. , Chalupowicz Laura , Barash Isaac , Manulis-Sasson Shulamit , Smart Christine D. 
Published: September 2013

ABSTRACT

The Gram-positive bacterium
Clavibacter michiganensis
subsp.
michiganensis
, causal agent of bacterial wilt and canker of tomato, is an economically devastating pathogen that inflicts considerable damage throughout all major tomato-producing regions. Annual outbreaks continue to occur in New York, where
C. michiganensis
subsp.
michiganensis
spreads via infected transplants, trellising stakes, tools, and/or soil. Globally, new outbreaks can be accompanied by the introduction of contaminated seed stock; however, the route of seed infection, especially the role of fruit lesions, remains undefined. In order to investigate the modes of seed infection, New York
C. michiganensis
subsp.
michiganensis
field strains were stably transformed with a gene encoding enhanced green fluorescent protein (eGFP). A constitutively eGFP-expressing virulent
C. michiganensis
subsp.
michiganensis
isolate, GCMM-22, was used to demonstrate that
C. michiganensis
subsp.
michiganensis
could not only access seeds systemically through the xylem but also externally through tomato fruit lesions, which harbored high intra- and intercellular populations. Active movement and expansion of bacteria into the fruit mesocarp and nearby xylem vessels followed, once the fruits began to ripen. These results highlight the ability of
C. michiganensis
subsp.
michiganensis
to invade tomato fruits and seeds through multiple entry routes.
Efficient Production of Bacillus thuringiensis Cry1AMod Toxins under Regulation of
cry3Aa
Promoter and Single Cysteine Mutations in the Protoxin Region
Authors: García-Gómez Blanca I. , Sánchez Jorge , Martínez de Castro Diana L. , Ibarra Jorge E. , Bravo Alejandra , Soberón Mario 
Published: September 2013

ABSTRACT

Bacillus thuringiensis
Cry1AbMod toxins are engineered versions of Cry1Ab that lack the amino-terminal end, including domain I helix α-1 and part of helix α-2. This deletion improves oligomerization of these toxins in solution in the absence of cadherin receptor and counters resistance to Cry1A toxins in different lepidopteran insects, suggesting that oligomerization plays a major role in their toxicity. However, Cry1AbMod toxins are toxic to
Escherichia coli
cells, since the
cry1A
promoter that drives its expression in
B. thuringiensis
has readthrough expression activity in
E. coli
, making difficult the construction of these CryMod toxins. In this work, we show that Cry1AbMod and Cry1AcMod toxins can be cloned efficiently under regulation of the
cry3A
promoter region to drive its expression in
B. thuringiensis
without expression in
E. coli
cells. However, p3A-Cry1Ab(c)Mod construction promotes the formation of Cry1AMod crystals in
B. thuringiensis
cells that were not soluble at pH 10.5 and showed no toxicity to
Plutella xylostella
larvae. Cysteine residues in the protoxin carboxyl-terminal end of Cry1A toxins have been shown to be involved in disulfide bond formation, which is important for crystallization. Six individual cysteine substitutions for serine residues were constructed in the carboxyl-terminal protoxin end of the p3A-Cry1AbMod construct and one in the carboxyl-terminal protoxin end of p3A-Cry1AcMod. Interestingly, p3A-Cry1AbMod C654S and C729S and p3A-Cry1AcMod C730S recover crystal solubility at pH 10.5 and toxicity to
P. xylostella
. These results show that combining the
cry3A
promoter expression system with single cysteine mutations is a useful system for efficient expression of Cry1AMod toxins in
B. thuringiensis
.
Isolation of Butanol- and Isobutanol-Tolerant Bacteria and Physiological Characterization of Their Butanol Tolerance
Authors: Kanno Manabu , Katayama Taiki , Tamaki Hideyuki , Mitani Yasuo , Meng Xian-Ying , Hori Tomoyuki , Narihiro Takashi , Morita Naoki , Hoshino Tamotsu , Yumoto Isao , Kimura Nobutada , Hanada Satoshi , Kamagata Yoichi 
Published: September 2013

ABSTRACT

Despite their importance as a biofuel production platform, only a very limited number of butanol-tolerant bacteria have been identified thus far. Here, we extensively explored butanol- and isobutanol-tolerant bacteria from various environmental samples. A total of 16 aerobic and anaerobic bacteria that could tolerate greater than 2.0% (vol/vol) butanol and isobutanol were isolated. A 16S rRNA gene sequencing analysis revealed that the isolates were phylogenetically distributed over at least nine genera:
Bacillus
,
Lysinibacillus
,
Rummeliibacillus
,
Brevibacillus
,
Coprothermobacter
,
Caloribacterium
,
Enterococcus
,
Hydrogenoanaerobacterium
, and
Cellulosimicrobium
, within the phyla
Firmicutes
and
Actinobacteria
. Ten of the isolates were phylogenetically distinct from previously identified butanol-tolerant bacteria. Two relatively highly butanol-tolerant strains CM4A (aerobe) and GK12 (obligate anaerobe) were characterized further. Both strains changed their membrane fatty acid composition in response to butanol exposure, i.e., CM4A and GK12 exhibited increased saturated and cyclopropane fatty acids (CFAs) and long-chain fatty acids, respectively, which may serve to maintain membrane fluidity. The gene (
cfa
) encoding CFA synthase was cloned from strain CM4A and expressed in
Escherichia coli
. The recombinant
E. coli
showed relatively higher butanol and isobutanol tolerance than
E. coli
without the
cfa
gene, suggesting that
cfa
can confer solvent tolerance. The exposure of strain GK12 to butanol by consecutive passages even enhanced the growth rate, indicating that yet-unknown mechanisms may also contribute to solvent tolerance. Taken together, the results demonstrate that a wide variety of butanol- and isobutanol-tolerant bacteria that can grow in 2.0% butanol exist in the environment and have various strategies to maintain structural integrity against detrimental solvents.
Clonal Variants of Plasmodium falciparum Exhibit a Narrow Range of Rolling Velocities to Host Receptor CD36 under Dynamic Flow Conditions
Authors: Herricks Thurston , Avril Marion , Janes Joel , Smith Joseph D. , Rathod Pradipsinh K. 
Published: September 2013

ABSTRACTCytoadhesion ofPlasmodium falciparumparasitized red blood cells (pRBCs) has been implicated in the virulence of malaria infection. Cytoadhesive interactions are mediated by the protein family ofPlasmodium falciparumerythrocyte membrane protein 1 (PfEMP1). The PfEMP1 family is under strong antibody and binding selection, resulting in extensive sequence and size variation of the extracellular domains. Here, we investigated cytoadhesion of pRBCs to CD36, a common receptor ofP. falciparumfield isolates, under dynamic flow conditions. Isogeneic parasites, predominantly expressing single PfEMP1 variants, were evaluated for binding to recombinant CD36 under dynamic flow conditions using microfluidic devices. We tested if PfEMP1 size (number of extracellular domains) or sequence variation affected the pRBC-CD36 interaction. Our analysis showed that clonal parasite variants varied ∼5-fold in CD36 rolling velocity despite extensive PfEMP1 sequence polymorphism. In addition, adherent pRBCs exhibited a characteristic hysteresis in rolling velocity at microvascular flow rates, which was accompanied by changes in pRBC shape and may represent important adaptations that favor stable binding.
Genome Sequence of Salt-Tolerant Bacillus safensis Strain VK, Isolated from Saline Desert Area of Gujarat, India
Authors: Kothari V. V. , Kothari R. K. , Kothari C. R. , Bhatt V. D. , Nathani N. M. , Koringa P. G. , Joshi C. G. , Vyas B. R. M. 
Published: September 2013

ABSTRACT

Bacillus safensis
strain VK was isolated from the rhizosphere of a cumin plant growing in the saline desert of Radhanpar, Gujarat, India. Here, we provide the 3.68-Mb draft genome sequence of
B. safensis
VK, which might provide information about the salt tolerance and genes encoding enzymes for the strain's plant growth-promoting potential.
Draft Whole-Genome Sequence of VIM-1-Producing Multidrug-Resistant Enterobacter cloacae EC_38VIM1
Authors: Villa Jennifer , Viedma Esther , Otero Joaquín R. , Chaves Fernando 
Published: September 2013

ABSTRACT

The VIM-1-producing multidrug-resistant strain
Enterobacter cloacae
was isolated from blood culture. The strain showed multiple resistances to clinically used antibiotics, including all β-lactams, fluoroquinolones, aminoglycosides, and sulfonamides. Sequence analysis showed the presence of 14 genes associated with resistance to antibiotics, including the metallo-β-lactamase VIM-1 gene, which was located in a class 1 integron.
Draft Genome Sequence of
Cladonia macilenta
KoLRI003786, a Lichen-Forming Fungus Producing Biruloquinone
Authors: Park Sook-Young , Choi Jaeyoung , Kim Jung A , Jeong Min-Hye , Kim Soonok , Lee Yong-Hwan , Hur Jae-Seoun 
Published: September 2013

ABSTRACT

The lichen-forming fungus
Cladonia macilenta
strain KoLRI003786 is capable of producing an acetylcholinesterase inhibitor, biruloquinone, which effectively prevents neurodegeneration in Alzheimer's disease. Laying the foundation to unravel the biruloquinone biosynthetic pathway, we present the 37.11-Mb draft genome sequence of strain KoLRI003786.
Draft Genome Sequences of Helicobacter pylori Strains HPARG63 and HPARG8G, Cultured from Patients with Chronic Gastritis and Gastric Ulcer Disease
Authors: Armitano Rita Inés , Zerbetto De Palma Gerardo , Matteo Mario José , Revale Santiago , Romero Soledad , Traglia Germán Matías , Catalano Mariana 
Published: September 2013

ABSTRACT

Helicobacter pylori
colonizes the human gastric mucosa, leading to a spectrum of gastric diseases in susceptible populations. Here we announce the draft genome sequences of strains HPARG8G and HPARG63. The data for both genome sequences provide insights regarding the diversity in gene content and rearrangement of the genomic islands commonly harbored by
H. pylori
.
Characterization of Fructose 1,6-Bisphosphatase and Sedoheptulose 1,7-Bisphosphatase from the Facultative Ribulose Monophosphate Cycle Methylotroph Bacillus methanolicus
Authors: Stolzenberger Jessica , Lindner Steffen N. , Persicke Marcus , Brautaset Trygve , Wendisch Volker F. 
Published: September 2013

ABSTRACT

The genome of the facultative ribulose monophosphate (RuMP) cycle methylotroph
Bacillus methanolicus
encodes two bisphosphatases (GlpX), one on the chromosome (GlpX
C
) and one on plasmid pBM19 (GlpX
P
), which is required for methylotrophy. Both enzymes were purified from recombinant
Escherichia coli
and were shown to be active as fructose 1,6-bisphosphatases (FBPases). The FBPase-negative
Corynebacterium glutamicum
Δ
fbp
mutant could be phenotypically complemented with
glpX
C
and
glpX
P
from
B. methanolicus
. GlpX
P
and GlpX
C
share similar functional properties, as they were found here to be active as homotetramers
in vitro
, activated by Mn
2+
ions and inhibited by Li
+
, but differed in terms of the kinetic parameters. GlpX
C
showed a much higher catalytic efficiency and a lower

K
m

for fructose 1,6-bisphosphate (86.3 s
−1
mM
−1
and 14 ± 0.5 μM, respectively) than GlpX
P
(8.8 s
−1
mM
−1
and 440 ± 7.6 μM, respectively), indicating that GlpX
C
is the major FBPase of
B. methanolicus
. Both enzymes were tested for activity as sedoheptulose 1,7-bisphosphatase (SBPase), since a SBPase variant of the ribulose monophosphate cycle has been proposed for
B. methanolicus
. The substrate for the SBPase reaction, sedoheptulose 1,7-bisphosphate, could be synthesized
in vitro
by using both fructose 1,6-bisphosphate aldolase proteins from
B. methanolicus
. Evidence for activity as an SBPase could be obtained for GlpX
P
but not for GlpX
C
. Based on these
in vitro
data, GlpX
P
is a promiscuous SBPase/FBPase and might function in the RuMP cycle of
B. methanolicus
.
Predicting a biliary aetiology in paediatric acute pancreatitis
Authors: Coffey Michael J , Nightingale Scott , Ooi Chee Y 
Published: September 2013

ObjectiveAcute biliary pancreatitis (ABP) is a common cause of pancreatitis which may require timely intervention. We aimed to identify routine laboratory parameters for early prediction of biliary aetiology in paediatric acute pancreatitis (AP).DesignA retrospective review of children with AP (January 2000–July 2011) was performed at two tertiary paediatric hospitals in New South Wales, Australia. Predictors of ABP using laboratory parameters (measured within 48 h of presentation) were determined using a multivariate logistic regression model and evaluated.ResultsOf the 131 pancreatitis episodes reviewed, 21 (16%) were biliary-related. Raised serum lipase, alkaline phosphatase, γ-glutamyl transpeptidase (GGT), alanine aminotransferase (ALT) and aspartate aminotransferase were associated with biliary aetiology (all p<0.0016) on univariate analysis. In multiple logistic regression, serum GGT ≥40 U/L, ALT ≥150 U/L, and lipase ≥15×the upper limit of normal (ULN) were predictive of ABP. To improve clinical applicability, the predictive performance when at least two of the three ABP predictors (coined the ‘biliary pancreatitis triad’) were satisfied was evaluated. The triad performed with a specificity, sensitivity, positive predictive value and negative predictive value of 95, 89, 76 and 98%, respectively.ConclusionsThe biliary pancreatitis triad of serum GGT ≥40 U/L, ALT ≥150 U/L and lipase ≥15×ULN within 48 h of presentation may be used as simple clinical predictors of ABP in children. Children with values falling below 2 or 3 of these thresholds are very unlikely to have AP due to a biliary cause.
Return to play following injury: whose decision should it be?
Authors: Shrier Ian , Safai Parissa , Charland Lyn 
Published: September 2013

BackgroundReturn-to-play (RTP) decision-making is required for every injured athlete. However, these decisions often lead to conflict between sport medicine professionals, athletes, coaches and sport associations. This study explores differences in professionals’ opinion about which criteria should be used for RTP decisions, and who is best able to evaluate them.MethodsWe surveyed Canadian sport medicine physicians, physiotherapists, athletic therapists, chiropractors, massage therapists, athletes, coaches and representatives from three sport associations. The 10 min online survey asked respondents to rate criteria as mandatory to irrelevant on a five-point Likert scale, and to indicate which profession was best able to evaluate the criteria.ResultsIn general, medical doctors, physiotherapists and athletic therapists were considered best able to assess factors related to risk of injury and complications from injury. Each clinician group (except sport massage therapists) generally believed their own profession has the best capacity to evaluate the criteria. Athletes, coaches and sport associations were considered to have the best capacity to assess factors related to competition (desire, psychological and financial impact and loss of competitive standing). There remained considerable heterogeneity both between and within stakeholder groups.ConclusionsWe found that differences in approach to RTP decisions were generally greater within versus between-stakeholder groups. If shared decision-making is to become the norm in clinical sport medicine, we need to begin a discussion on which discrepancies are due to lack of training (resolved through education) or scientific knowledge (resolved through research) or simply reflect the divergence of personal/societal values.