bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental investigation of acoustic streaming in a cylindrical wave guide up to high streaming Reynolds numbers
Authors: Reyt Ida , Bailliet Hélène , Valière Jean-Christophe
Published: January 2014

Measurements of streaming velocity are performed by means of Laser Doppler Velocimetry and Particle Image Velociimetry in an experimental apparatus consisting of a cylindrical waveguide having one loudspeaker at each end for high intensity sound levels. The case of high nonlinear Reynolds number ReNL is particularly investigated. The variation of axial streaming velocity with respect to the axial and to the transverse coordinates are compared to available Rayleigh streaming theory. As expected, the measured streaming velocity agrees well with the Rayleigh streaming theory for small ReNL but deviates significantly from such predictions for high ReNL. When the nonlinear Reynolds number is increased, the outer centerline axial streaming velocity gets distorted towards the acoustic velocity nodes until counter-rotating additional vortices are generated near the acoustic velocity antinodes. This kind of behavior is followed by outer streaming cells only and measurements in the near wall region show that inner streaming vortices are less affected by this substantial evolution of fast streaming pattern. Measurements of the transient evolution of streaming velocity provide an additional insight into the evolution of fast streaming.
Identification of a Novel Membrane Transporter Mediating Resistance to Organic Arsenic in Campylobacter jejuni
Authors: Shen Zhangqi , Luangtongkum Taradon , Qiang Zhiyi , Jeon Byeonghwa , Wang Liping , Zhang Qijing
Published: January 2014

Although bacterial mechanisms involved in the resistance to inorganic arsenic are well understood, the molecular basis for organic arsenic resistance has not been described.
Campylobacter jejuni
, a major food-borne pathogen causing gastroenteritis in humans, is highly prevalent in poultry and is reportedly resistant to the arsenic compound roxarsone (4-hydroxy-3-nitrobenzenearsonic acid), which has been used as a feed additive in the poultry industry for growth promotion. In this study, we report the identification of a novel membrane transporter (named ArsP) that contributes to organic arsenic resistance in
Campylobacter
. ArsP is predicted to be a membrane permease containing eight transmembrane helices, distinct from other known arsenic transporters. Analysis of multiple
C. jejuni
isolates from various animal species revealed that the presence of an intact
arsP
gene is associated with elevated resistance to roxarsone. In addition, inactivation of
arsP
in
C. jejuni
resulted in 4- and 8-fold reductions in the MICs of roxarsone and nitarsone, respectively, compared to that for the wild-type strain. Furthermore, cloning of
arsP
into a
C. jejuni
strain lacking a functional
arsP
gene led to 16- and 64-fold increases in the MICs of roxarsone and nitarsone, respectively. Neither mutation nor overexpression of
arsP
affected the MICs of inorganic arsenic, including arsenite and arsenate, in
Campylobacter
. Moreover, acquisition of
arsP
in NCTC 11168 led to accumulation of less roxarsone than the wild-type strain lacking
arsP
. Together, these results indicate that ArsP functions as an efflux transporter specific for extrusion of organic arsenic and contributes to the resistance to these compounds in
C. jejuni
.
Ecological Dynamics of Toxic
Microcystis
spp. and Microcystin-Degrading Bacteria in Dianchi Lake, China
Authors: Zhu Lin , Wu Yanlong , Song Lirong , Gan Nanqin
Published: January 2014

Toxic cyanobacterial blooms directly threaten both human safety and the ecosystem of surface waters. The widespread occurrence of these organisms, coupled with the tumor-promoting properties of the microcystin toxins that they produce, demands action to mitigate their potential impacts and, thus, a robust understanding of their ecological dynamics. In the present work, the abundance of toxic
Microcystis
spp. and microcystin (MC)-degrading bacteria in Dianchi Lake, located in Yunnan Province, China, was studied using quantitative PCR. Samples were taken at monthly intervals from June 2010 to December 2011 at three sampling stations within this freshwater lake. Results revealed that variation in the abundance of both total
Microcystis
spp. and toxic
Microcystis
spp. exhibited similar trends during the period of the algal bloom, including the reinvasion, pelagic growth, sedimentation, and overwintering periods, and that the proportion of toxic
Microcystis
was highest during the bloom and lowest in winter. Importantly, we observed that peaks in
mlrA
gene copy numbers of MC-degrading bacteria occurred in the months following observed peaks in MC concentrations. To understand this phenomenon, we added MCs to the MC-degrading bacteria (designated strains HW and SW in this study) and found that MCs significantly enhanced
mlrA
gene copy numbers over the number for the control by a factor of 5.2 for the microcystin-RR treatment and a factor of 3.7 for the microcystin-LR treatment. These results indicate that toxic
Microcystis
and MC-degrading bacteria exert both direct and indirect effects on each other and that MC-degrading bacteria also mediate a shift from toxic to nontoxic populations of
Microcystis
.
Escherichia coli
O157:H7 Lacking the
qseBC
-Encoded Quorum-Sensing System Outcompetes the Parental Strain in Colonization of Cattle Intestines
Authors: Sharma V. K. , Casey T. A.
Published: January 2014

The
qseBC
-encoded quorum-sensing system regulates the motility of
Escherichia coli
O157:H7 in response to bacterial autoinducer 3 (AI-3) and the mammalian stress hormones epinephrine (E) and norepinephrine (NE). The
qseC
gene encodes a sensory kinase that autophosphorylates in response to AI-3, E, or NE and subsequently phosphorylates its cognate response regulator QseB. In the absence of QseC, QseB downregulates bacterial motility and virulence in animal models. In this study, we found that 8- to 10-month-old calves orally inoculated with a mixture of
E. coli
O157:H7 and its isogenic
qseBC
mutant showed significantly higher fecal shedding of the
qseBC
mutant.
In vitro
analysis revealed similar growth profiles and motilities of the
qseBC
mutant and the parental strain in the presence or absence of NE. The magnitudes of the response to NE and expression of flagellar genes
flhD
and
fliC
were also similar for the
qseBC
mutant and the parental strain. The expression of
ler
(a positive regulator of the locus of enterocyte effacement [LEE]), the
ler
-regulated
espA
gene, and the
csgA
gene (encoding curli fimbriae) was increased in the
qseBC
mutant compared to the parental strain. On the other hand, growth, motility, and transcription of
flhD
,
fliC
,
ler
,
espA
, and
csgA
were significantly reduced in the
qseBC
mutant complemented with a plasmid-cloned copy of the
qseBC
genes. Thus,
in vitro
motility and gene expression data indicate that the near-parental level of motility, ability to respond to NE, and enhanced expression of LEE and curli genes might in part be responsible for increased colonization and fecal shedding of the
qseBC
mutant in calves.
Achromobacter denitrificans
Strain YD35 Pyruvate Dehydrogenase Controls NADH Production To Allow Tolerance to Extremely High Nitrite Levels
Authors: Doi Yuki , Shimizu Motoyuki , Fujita Tomoya , Nakamura Akira , Takizawa Noboru , Takaya Naoki
Published: January 2014

We identified the extremely nitrite-tolerant bacterium
Achromobacter denitrificans
YD35 that can grow in complex medium containing 100 mM nitrite (NO
2
−
) under aerobic conditions. Nitrite induced global proteomic changes and upregulated tricarboxylate (TCA) cycle enzymes as well as antioxidant proteins in YD35. Transposon mutagenesis generated NO
2
−
-hypersensitive mutants of YD35 that had mutations at genes for aconitate hydratase and α-ketoglutarate dehydrogenase in the TCA cycle and a pyruvate dehydrogenase (Pdh) E1 component, indicating the importance of TCA cycle metabolism to NO
2
−
tolerance. A mutant in which the
pdh
gene cluster was disrupted (Δ
pdh
mutant) could not grow in the presence of 100 mM NO
2
−
. Nitrite decreased the cellular NADH/NAD
+
ratio and the cellular ATP level. These defects were more severe in the Δ
pdh
mutant, indicating that Pdh contributes to upregulating cellular NADH and ATP and NO
2
−
-tolerant growth. Exogenous acetate, which generates acetyl coenzyme A and then is metabolized by the TCA cycle, compensated for these defects caused by disruption of the
pdh
gene cluster and those caused by NO
2
−
. These findings demonstrate a link between NO
2
−
tolerance and pyruvate/acetate metabolism through the TCA cycle. The TCA cycle mechanism in YD35 enhances NADH production, and we consider that this contributes to a novel NO
2
−
-tolerating mechanism in this strain.
Identifying Beneficial Qualities of
Trichoderma parareesei
for Plants
Authors: Rubio M. Belén , Quijada Narciso M. , Pérez Esclaudys , Domínguez Sara , Monte Enrique , Hermosa Rosa
Published: January 2014

Trichoderma parareesei
and
Trichoderma reesei
(teleomorph
Hypocrea jecorina
) produce cellulases and xylanases of industrial interest. Here, the anamorphic strain T6 (formerly
T. reesei
) has been identified as
T. parareesei
, showing biocontrol potential against fungal and oomycete phytopathogens and enhanced hyphal growth in the presence of tomato exudates or plant cell wall polymers in
in vitro
assays. A
Trichoderma
microarray was used to examine the transcriptomic changes in T6 at 20 h of interaction with tomato plants. Out of a total 34,138
Trichoderma
probe sets deposited on the microarray, 250 showed a significant change of at least 2-fold in expression in the presence of tomato plants, with most of them being downregulated.
T. parareesei
T6 exerted beneficial effects on tomato plants in terms of seedling lateral root development, and in adult plants it improved defense against
Botrytis cinerea
and growth promotion under salt stress. Time course expression patterns (0 to 6 days) observed for defense-related genes suggest that T6 was able to prime defense responses in the tomato plants against biotic and abiotic stresses. Such responses undulated, with a maximum upregulation of the jasmonic acid (JA)/ethylene (ET)-related
LOX1
and
EIN2
genes and the salt tolerance
SOS1
gene at 24 h and that of the salicylic acid (SA)-related
PR-1
gene at 48 h after T6 inoculation. Our study demonstrates that the
T. parareesei
T6-tomato interaction is beneficial to both partners.
Intestinal Microbiota and Species Diversity of
Campylobacter
and
Helicobacter
spp. in Migrating Shorebirds in Delaware Bay
Authors: Ryu Hodon , Grond Kirsten , Verheijen Bram , Elk Michael , Buehler Deborah M. , Santo Domingo Jorge W.
Published: January 2014

Using 16S rRNA gene sequencing analysis, we examined the bacterial diversity and the presence of opportunistic bacterial pathogens (i.e.,
Campylobacter
and
Helicobacter
) in red knot (
Calidris canutus
;
n
= 40), ruddy turnstone (
Arenaria interpres
;
n
= 35), and semipalmated sandpiper (
Calidris pusilla
;
n
= 22) fecal samples collected during a migratory stopover in Delaware Bay. Additionally, we studied the occurrence of
Campylobacter
spp., enterococci, and waterfowl fecal source markers using quantitative PCR (qPCR) assays. Of 3,889 16S rRNA clone sequences analyzed, the bacterial community was mostly composed of
Bacilli
(63.5%),
Fusobacteria
(12.7%),
Epsilonproteobacteria
(6.5%), and
Clostridia
(5.8%). When epsilonproteobacterium-specific 23S rRNA gene clone libraries (i.e., 1,414 sequences) were analyzed, the sequences were identified as
Campylobacter
(82.3%) or
Helicobacter
(17.7%) spp. Specifically, 38.4%, 10.1%, and 26.0% of clone sequences were identified as
C. lari
(>99% sequence identity) in ruddy turnstone, red knot, and semipalmated sandpiper clone libraries, respectively. Other pathogenic species of
Campylobacter
, such as
C. jejuni
and
C. coli
, were not detected in excreta of any of the three bird species. Most
Helicobacter
-like sequences identified were closely related to
H. pametensis
(>99% sequence identity) and
H. anseris
(92% sequence identity). qPCR results showed that the occurrence and abundance of
Campylobacter
spp. was relatively high compared to those of fecal indicator bacteria, such as
Enterococcus
spp.,
E. faecalis
, and
Catellicoccus marimammalium
. Overall, the results provide insights into the complexity of the shorebird gut microbial community and suggest that these migratory birds are important reservoirs of pathogenic
Campylobacter
species.
Safety of the Surrogate Microorganism
Enterococcus faecium
NRRL B-2354 for Use in Thermal Process Validation
Authors: Kopit Lauren M. , Kim Eun Bae , Siezen Roland J. , Harris Linda J. , Marco Maria L.
Published: January 2014

Enterococcus faecium
NRRL B-2354 is a surrogate microorganism used in place of pathogens for validation of thermal processing technologies and systems. We evaluated the safety of strain NRRL B-2354 based on its genomic and functional characteristics. The genome of
E. faecium
NRRL B-2354 was sequenced and found to comprise a 2,635,572-bp chromosome and a 214,319-bp megaplasmid. A total of 2,639 coding sequences were identified, including 45 genes unique to this strain. Hierarchical clustering of the NRRL B-2354 genome with 126 other
E. faecium
genomes as well as
pbp5
locus comparisons and multilocus sequence typing (MLST) showed that the genotype of this strain is most similar to commensal, or community-associated, strains of this species.
E. faecium
NRRL B-2354 lacks antibiotic resistance genes, and both NRRL B-2354 and its clonal relative ATCC 8459 are sensitive to clinically relevant antibiotics. This organism also lacks, or contains nonfunctional copies of, enterococcal virulence genes including
acm
,
cyl
, the
ebp
operon,
esp
,
gelE
,
hyl
, IS
16
, and associated phenotypes. It does contain
scm
,
sagA
,
efaA
, and
pilA
, although either these genes were not expressed or their roles in enterococcal virulence are not well understood. Compared with the clinical strains TX0082 and 1,231,502,
E. faecium
NRRL B-2354 was more resistant to acidic conditions (pH 2.4) and high temperatures (60°C) and was able to grow in 8% ethanol. These findings support the continued use of
E. faecium
NRRL B-2354 in thermal process validation of food products.
Gut Adhesive Bacillus subtilis Spores as a Platform for Mucosal Delivery of Antigens
Authors: Tavares Batista Milene , Souza Renata D. , Paccez Juliano D. , Luiz Wilson B. , Ferreira Ewerton L. , Cavalcante Rafael C. M. , Ferreira Rita C. C. , Ferreira Luís C. S.
Published: January 2014

Bacillus subtilis
spores have been used as safe and heat-resistant antigen delivery vectors. Nonetheless, the oral administration of spores typically induces weak immune responses to the passenger antigens, which may be attributed to the fast transit through the gastrointestinal tract. To overcome this limitation, we have developed
B. subtilis
spores capable of binding to the gut epithelium by means of expressing bacterial adhesins on the spore surface. The resulting spores bound to
in vitro
intestinal cells, showed a longer transit through the mouse intestinal tract, and interacted with Peyer's patch cells. The adhesive spores increased the systemic and secreted antibody responses to the
Streptococcus mutans
P1 protein, used as a model antigen, following oral, intranasal, and sublingual administration. Additionally, P1-specific antibodies efficiently inhibited the adhesion of the oral pathogen
Streptococcus mutans
to abiotic surfaces. These results support the use of gut-colonizing
B. subtilis
spores as a new platform for the mucosal delivery of vaccine antigens.
SCO5745, a Bifunctional RNase J Ortholog, Affects Antibiotic Production in Streptomyces coelicolor
Authors: Bralley Patricia , Aseem Madiha , Jones George H.
Published: January 2014

The bacterial RNases J are considered bifunctional RNases possessing both endo- and exonucleolytic activities. We have isolated an RNase J ortholog from
Streptomyces coelicolor
encoded by the gene
sco5745
. We overexpressed a decahistidine-tagged version of SCO5745 and purified the overexpressed protein by immobilized metal ion affinity chromatography. We demonstrated the presence of both 5′-to-3′ exonucleolytic and endonucleolytic activities on the
Bacillus subtilis
thrS
transcript. Exonucleoytic activity predominated with 5′ monophosphorylated
thrS
, while endonucleolytic activity predominated with 5′ triphosphorylated
thrS
. While
sco5745
is the only RNase J allele in
S. coelicolor
, the gene is not essential. Its disruption resulted in delayed production of the antibiotic actinorhodin, overproduction of undecylprodigiosin, and diminished production of the calcium-dependent antibiotic, in comparison with the parental strain.
Expanding the Universal Medication Schedule: a patient-centred approach
Authors: Bailey Stacy Cooper , Wolf Michael S , Lopez Andrea , Russell Allison , Chen Alice Hm , Schillinger Dean , Moy Glen , Sarkar Urmimala
Published: January 2014

Objective

Improved drug labelling for chronic pill-form medications has been shown to promote patient comprehension, adherence and safety. We extended health literacy principles and included patients' perspectives to improve instructions for: (1) non-pill form, (2) short term, (3) ‘as needed,’ (4) tapered and (5) escalating dose medications.

Setting

Participants were recruited via convenience sampling from primary care clinics in Chicago, Illinois and San Francisco, California, USA.

Participants

40 adult, English-speaking participants who reported taking at least one prescription drug in the past 12 months were enrolled in the study.

Primary and secondary outcomes

Participant opinions, preferences and comprehension of standard and improved medication instructions were assessed during four iterative waves of discussion groups. Brief interviews preceding the discussion groups measured individuals’ literacy skills, sociodemographic and health characteristics.

Results

On average, participants were 46 years old, took four medications and reported two chronic health conditions. Patients varied sociodemographically; 40% were men and 33% had limited literacy skills. Patients agreed on the need for simpler terminology and specificity in instructions. Discussions addressed optimal ways of presenting numeric information, indication and duration of use information to promote comprehension and safe medication use. Consensus was reached on how to improve most of the instructions.

Conclusions

Through this patient-centred approach, we developed a set of health literacy-informed instructions for more challenging medications. Findings can inform current drug labelling initiatives and promote safe and appropriate medication use.
Trends in time to invasive examination and treatment from 2001 to 2009 in patients admitted first time with non-ST elevation myocardial infarction or unstable angina in Denmark
Authors: Mårtensson Solvej , Gyrd-Hansen Dorte , Prescott Eva , Andersen Per Kragh , Zwisler Ann-Dorthe Olsen , Osler Merete
Published: January 2014

Objective

To investigate trends in time to invasive examination and treatment for patient with first time diagnosis of non-ST elevation myocardial infarction (NSTEMI) and unstable angina during the period from 2001 to 2009 in Denmark.

Design

From 1 January 2001 to 31 December 2009 all first time hospitalisations with NSTEMI and unstable angina were identified in the National Patient Registry (n=65 909). Time from admission to initiation of coronary angiography (CAG), percutaneous coronary intervention (PCI) or coronary artery bypass graft (CABG) was calculated. We described the development in invasive examination and treatment probability (CAG, PCI and CABG at 3, 7, 10, 30 and 60 days) for the years 2001–2009, taking the competing risk of death into account using Aalen–Johansen estimators and a Fine-Gray model.

Setting

Nationwide Danish cohort.

Results

The proportion of patients receiving a CAG and PCI increased substantially over time while the proportion receiving a CABG decreased for both NSTEMI and unstable angina. For both NSTEMI and unstable angina, a significant increase in invasive examination and treatment probability at 3 days for CAG and PCI were seen especially from 2007 through to 2009. For NSTEMI, the CAG examination probability at 3 days leaped from 20% in 2007 to 32% in 2008 and 39% in 2009, and for PCI the same was true with a leap in treatment probability from 19% to 28% from 2008 to 2009.

Conclusions

In Denmark the use of CAG and PCI in treatment of NSTEMI and unstable angina has increased from 2001 to 2009, while the use of CABG has decreased. During the same period, there was a marked increase in invasive examination and treatment probability at 3 days, that is, more patients were treated faster which is in line with the political aim of reducing time to treatment.
Exploratory application of the Ages and Stages (ASQ) child development screening test in a low-income Peruvian shantytown population
Authors: Kyerematen Victoria , Hamb Averine , Oberhelman Richard A , Cabrera Lilia , Bernabe-Ortiz Antonio , Berry Susan J
Published: January 2014

Objectives

Public health research on child health is increasingly focusing on the long-term impacts of infectious diseases, malnutrition and social deprivation on child development. The objectives of this exploratory study were to (1) implement the Ages and Stages Questionnaires (ASQ) in children aged 3 months to 5 years in a low-income Peruvian population and (2) to correlate outcomes of the ASQ with risk factors such as nutritional status, diarrhoea incidence and wealth index.

Setting

Primary data collection was carried out in the Pampas de San Juan de Miraflores, a periurban low-income community in Lima, Peru.

Participants

The study population included 129 children selected through community census data, with a mean age of 22 months (SD 6.8) and with almost equal gender distribution (51% males).

Intervention

A Peruvian psychologist administered the age-appropriate (ASQ2 for participants enrolled in 2009, ASQ3 for participants enrolled in 2010). Results of the ASQ are reported separately for five scales, including Communication, Gross Motor, Fine Motor, Problem Solving and Personal-Social.

Primary and secondary outcome measures

For each scale, results are reported as normal or suspect, meaning that some milestone attainment was not evident and further evaluation is recommended.

Results

Overall, 50 of 129 children (38.7%) had suspect results for at least one of the five scales, with the highest rates of suspect results on the Communication (15.5%) and Problem Solving scales (13.9%). Higher rates of suspect outcomes were seen in older children, both overall (p=0.06) and on Problem Solving (p=0.009), and for some scales there were trends between suspect outcomes and wealth index or undernutrition.

Conclusions

The ASQ was successfully applied in a community-based study in a low-income Peruvian population, and with further validation, the ASQ may be an effective tool for identifying at-risk children in resource-poor areas of Latin America.
The PACT study protocol: a time series study investigating the impact, acceptability and cost of an integrated model for psychosocial screening, care and treatment of patients with urological and head and neck cancers
Authors: Girgis Afaf , Kelly Brian , Boyes Allison , Haas Marion , Viney Rosalie , Descallar Joseph , Candler Hayley , Bellamy Douglas , Proietto Anthony
Published: January 2014

Introduction

While there is good evidence of the effectiveness of a variety of interventions and services to prevent and/or relieve distress experienced by people affected by cancer, much of this psychosocial morbidity is undetected and untreated, with consequent exacerbated suffering, decreased satisfaction with care, impaired adherence to treatment regimens and poorer morbidity and mortality outcomes. The objective of this study is to develop, implement and assess the impact, acceptability and cost of an integrated, patient-centred Psychosocial Assessment, Care and Treatment (PACT) model of care for patients with urological and head and neck cancers.

Methods and analysis

A time series research design will be used to test the PACT model of care, newly introduced in an Australian tertiary hospital. The primary outcome is system-level impact, assessed through audit of patients’ medical records and Medicare claims for follow-up care. The secondary outcomes are impact of the model on patients' experience and healthcare professionals’ (HCPs) knowledge and confidence, assessed via patient and HCP surveys at baseline and at follow-up. Acceptability of the intervention will be assessed through HCP interviews at follow-up, and cost will be assessed from Medicare and Pharmaceutical Benefits Scheme claims information and information logged pertaining to intervention activities (eg, time spent by the newly appointed psycho-oncology staff in direct patient contact, providing training sessions, engaging in case review) and their associated costs (eg, salaries, training materials and videoconferencing).

Ethics and dissemination

Ethics approval was obtained from the Human Research Ethics Committees of Hunter New England Local Health District and the University of NSW.

Results

The results will be widely disseminated to the funding body and through peer-reviewed publications, HCP and consumer publications, oncology conferences and meetings.

Trial registration

The study is registered with the Australian New Zealand Clinical Trials Registry with registration number ACTRN12613000916741.
Holistic assessment of supportive and palliative care needs: the evidence for routine systematic questioning
Authors: Ahmed Nisar , Ahmedzai Sam H , Collins Karen , Noble Bill
Published: January 2014

There is evidence to suggest that patients with cancer and other non-malignant chronic progressive illnesses can experience distressing symptoms, or concerns, which can often remain unrecognised. There is little disagreement that routine systematic questioning is useful in identifying supportive or palliative care needs that would otherwise not be identified. The purpose of this article is to provide an overview of holistic needs assessment in the fields of supportive and palliative care and to present evidence of the value of routine systematic questioning. Systematic questioning allows needs to be identified and addressed. There is at present no standardised systematic, evidence-based holistic approach to screening patients for supportive and palliative care needs.
CCL20 mediates lipopolysaccharide induced liver injury and is a potential driver of inflammation and fibrosis in alcoholic hepatitis
Authors: Affò Silvia , Morales-Ibanez Oriol , Rodrigo-Torres Daniel , Altamirano José , Blaya Delia , Dapito Dianne H , Millán Cristina , Coll Mar , Caviglia Jorge M , Arroyo Vicente , Caballería Juan , Schwabe Robert F , Ginès Pere , Bataller Ramón , Sancho-Bru Pau
Published: January 2014

Objective

Chemokines are known to play an important role in the pathophysiology of alcoholic hepatitis (AH), a form of acute-on-chronic liver injury frequently mediated by gut derived lipopolysaccharide (LPS). In our study, we hypothesise that chemokine CCL20, one of the most upregulated chemokines in patients with AH, is implicated in the pathogenesis of AH by mediating LPS induced liver injury.

Design

CCL20 gene expression and serum levels and their correlation with disease severity were assessed in patients with AH. Cellular sources of CCL20 and its biological effects were evaluated in vitro and in vivo in chronic, acute and acute-on-chronic experimental models of carbon tetrachloride and LPS induced liver injury. RNA interference technology was used to knockdown CCL20 in vivo.

Results

CCL20 hepatic and serum levels were increased in patients with AH and correlated with the degree of fibrosis, portal hypertension, endotoxaemia, disease severity scores and short term mortality. Moreover, CCL20 expression was increased in animal models of liver injury and particularly under acute-on-chronic conditions. Macrophages and hepatic stellate cells (HSCs) were identified as the main CCL20 producing cell types. Silencing CCL20 in vivo reduced LPS induced aspartate aminotransferase and lactate dehydrogenase serum levels and hepatic proinflammatory and profibrogenic genes. CCL20 induced proinflammatory and profibrogenic effects in cultured primary HSCs.

Conclusions

Our results suggest that CCL20 upregulation is strongly associated with LPS and may not only represent a new potential biomarker to predict outcome in patients with AH but also an important mediator linking hepatic inflammation, injury and fibrosis in AH.
MINIMAL CURVATURE-CONSTRAINED PATHS IN THE PLANE WITH A CONSTRAINT ON ARCS WITH OPPOSITE ORIENTATIONS
Authors: GROSSMAN P. A. , BRAZIL M. , RUBINSTEIN J. H. , THOMAS D. A.
Published: January 2014

The declines that provide vehicle access in an underground mine are typically designed as paths formed by concatenating line segments and circular arcs. In order to reduce wear on the ore trucks and the road surfaces and to enhance driver safety, such paths may be subject to a further constraint: each pair of consecutive arcs with opposite orientations must be separated by a straight line segment of at least a certain specified length. In order to reduce the construction and operational costs of the mine, it is desirable to minimize the lengths of such paths between any given pair of directed points. Some necessary and sufficient conditions are obtained for paths of this form to be locally or globally minimal with respect to length. In particular, it is shown that there is always a globally minimal path that contains at most four circular arcs.
INDIVIDUAL-BASED COMPUTATIONAL MODEL USED TO EXPLAIN 2009 PANDEMIC H1N1 IN RURAL CAMPUS COMMUNITY
Authors: MILLER LYDIA , JONES THERESE , MORGAN MINDY , LAPIN SERGEY , SCHWARTZ ELISSA J.
Published: January 2014

In the beginning of fall semester 2009, over 2,000 students contacted the student health service at Washington State University to report symptoms of influenza. The epidemic in Pullman, WA made national news, and many speculated on the severity and extent of the disease spread. Analysis of data from the influenza A(H1N1)pdm09 epidemic in Pullman, WA offers an opportunity to gain insights into characteristics of this rural campus community outbreak. In this study, an individual-based stochastic epidemic simulation model was used with the data to estimate infection parameters and make projections of the number of symptomatic individuals that would result given a variety of plausible scenarios. The parameters that were estimated include the number of individuals initially infected and the basic reproductive ratio (R0). The model was then used to predict the magnitude of infection with vaccination, isolation and quarantine. The results show that the best single intervention strategy is vaccination, and the reduction in infection is greatest when vaccination, isolation and quarantine are used simultaneously.
STUDY OF EXCITED NUCLEONS AND THEIR STRUCTURE
Authors: BURKERT VOLKER D.
Published: January 2014

Recent advances in the study of excited nucleons are discussed. Much of the progress has been achieved due to the availability of high precision meson production data in the photoproduction and electroproduction sectors, the development of multi-channel partial wave analysis techniques, and advances in Lattice QCD with predictions of the full excitation spectrum.
HADRONIC REACTIONS IN A DYNAMICAL COUPLED-CHANNEL MODEL
Authors: RÖNCHEN DEBORAH
Published: January 2014

The reactions πN → πN, ηN, KΛ and KΣ are described in a combined analysis, based on the Jülich dynamical coupled-channel framework. Unitarity, analyticity and other general requirements of the S-matrix are preserved in this Lagrangian-based, field-theoretical approach. The reliable extraction of resonance parameters is possible in terms of poles and residues.
N*(1920)(1/2+) STATE IN THE $NK\bar{K}$ SYSTEM
Authors: XIE JU-JUN , MARTÍNEZ TORRES A. , OSET E.
Published: January 2014

We study the three body [Formula: see text] system by using the fixed center approximation to the Faddeev equations, taking the interaction between N and [Formula: see text], N and K, and [Formula: see text] and K from the chiral unitary approach. Our results suggest that a [Formula: see text] hadron state, with spin-parity JP = 1/2+, and mass around 1920 MeV, can be formed.
THE POSSIBLE DI-OMEGA DIBARYON IN QUARK CLUSTER MODEL
Authors: DAI L. R. , LIU J. , YUAN L.
Published: January 2014

The mixing of scalar mesons is introduced into the baryon-baryon system in the chiral SU(3) quark model to further dynamically investigate the Di-omega state by using the same parameters as those in reasonably describing the experimental hyperon-nucleon and nucleon-nucleon scattering data. Two different mixings of scalar mesons, the ideal mixing and 19° mixing, are discussed, and compared with no mixing. The results show that it is still deeply bound state if 19° mixing is adopted, the same as those of no mixing. However, for ideal mixing, the binding energy is reduced quite a lot, yet it is still a bound state.
A surrogate competition approach to enhancing game-based learning
Authors: Chen Zhi-Hong , Chen Sherry Y.
Published: January 2014

Competition is useful in game-based learning, although it can also generate negative influences. To expand the potential for competition models in game-based learning, this study proposes the notion of surrogate competition, which eliminates direct competition between students. Such surrogates could be employed as buffers so that the competition between students is more relaxed. To explore the possible benefits of a surrogate approach to competition, the My-Pet-My-Arena system has been developed and evaluated. Two empirical studies were conducted to examine the effects of the surrogate competition. The results revealed that surrogate competition enhanced students’ learning achievement as well as increased their motivation. Furthermore, the surrogate competition might also assist students in attributing competitive failures to a lack of effort. Working from the results obtained in these two studies, a general model of surrogate competition is proposed to help designers implement forms of surrogate competition in other systems for game-based learning.
A survey of software aging and rejuvenation studies
Authors: Cotroneo Domenico , Natella Roberto , Pietrantuono Roberto , Russo Stefano
Published: January 2014

Software aging
is a phenomenon plaguing many long-running complex software systems, which exhibit performance degradation or an increasing failure rate. Several strategies based on the proactive
rejuvenation
of the software state have been proposed to counteract software aging and prevent failures. This survey article provides an overview of studies on Software Aging and Rejuvenation (SAR) that have appeared in major journals and conference proceedings, with respect to the statistical approaches that have been used to forecast software aging phenomena and to plan rejuvenation, the kind of systems and aging effects that have been studied, and the techniques that have been proposed to rejuvenate complex software systems. The analysis is useful to identify key results from SAR research, and it is leveraged in this article to highlight trends and open issues.
Software rejuvenation scheduling using accelerated life testing
Authors: Zhao Jing , Jin Yuliang , Trivedi Kishor S. , Jr. Rivalino Matias , Wang Yanbin
Published: January 2014

A number of studies have reported the phenomenon of “Software aging”, caused by resource exhaustion and characterized by progressive software performance degradation. In this article, we carry out an experimental study of software aging and rejuvenation for an on-line bookstore application, following the standard configuration of TPC-W benchmark. While real website is used for the bookstore, the clients are emulated. In order to reduce the time to application failures caused by memory leaks, we use the accelerated life testing (ALT) approach. We then select the Weibull time to failure distribution at normal level, to be used in a semi-Markov process, to compute the optimal software rejuvenation trigger interval. Since the validation of optimal rejuvenation trigger interval with emulated browsers will take an inordinate long time, we develop a simulation model to validate the ALT experimental results, and also estimate the steady-state availability to cross-validate the results of the semi-Markov availability model.
Software aging in the eucalyptus cloud computing infrastructure
Authors: Araujo Jean , Matos Rubens , Alves Vandi , Maciel Paulo , Souza F. Vieira de , Jr. Rivalino Matias , Trivedi Kishor S.
Published: January 2014

The need for high reliability, availability and performance has significantly increased in modern applications, that handle rapidly growing demands while providing uninterruptible services. Cloud computing systems fundamentally provide access to large pools of data and computational resources. Eucalyptus is a software framework largely used to implement private clouds and hybrid-style Infrastructure as a Service. It implements the Amazon Web Service (AWS) API, allowing interoperability with other AWS-based services. This article investigates the software aging effects in the Eucalyptus framework, considering workloads composed of intensive requests for remote storage attachment and virtual machine instantiations. We found problems that may be harmful to system dependability and performance, specifically regarding to RAM memory and swap space exhaustion, besides highly excessive CPU utilization by the virtual machines. We also present an approach that applies time series analysis to schedule rejuvenation, so as to reduce the downtime by predicting the proper moment to perform the rejuvenation. We experimentally evaluate our approach using an Eucalyptus test bed. The results show that our approach achieves higher availability, when compared to a threshold-triggered rejuvenation method based on continuous monitoring of resources utilization.
Robust learning approach for neuro-inspired nanoscale crossbar architecture
Authors: Chabi Djaafar , Querlioz Damien , Zhao Weisheng , Klein Jacques-Olivier
Published: January 2014

Scaling beyond CMOS require a new combination of computing paradigm and new devices. In this context, memristor are often considered as best candidate to implement efficiently synapses in hardware neural networks. In this article, we analyze the impact of memristor parameter variability. We build an analytical model of the global reliability at the crossbar level. It is based on a supervised learning method with multilayer and redundancy extensions. Comparisons with Monte Carlo simulations of small neural network validate our analytical model. It can be used to extrapolate directly the reliability of large-scale neural system. Our extrapolations show that high defect rate and important parameter variability can be handle efficiency with a moderate amount of redundancy.
Workload assignment considering NBTI degradation in multicore systems
Authors: Sun Jin , Lysecky Roman , Shankar Karthik , Kodi Avinash , Louri Ahmed , Roveda Janet
Published: January 2014

With continuously shrinking technology, reliability issues such as Negative Bias Temperature Instability (NBTI) has resulted in considerable degradation of device performance, and eventually the short mean-time-to-failure (MTTF) of the whole multicore system. This article proposes a new workload balancing scheme based on device-level fractional NBTI model to balance the workload among active cores while relaxing stressed ones. Starting with NBTI-induced threshold voltage degradation, we define a concept of Capacity Rate (CR) as an indication of one core's ability to accept workload. Capacity rate captures core's performance variability in terms of delay and power metrics under the impact of NBTI aging. The proposed workload balancing framework employs the capacity rates as workload constraints, applies a Dynamic Zoning (DZ) algorithm to group cores into zones to process task flows, and then uses Dynamic Task Scheduling (DTS) to allocate tasks in each zone with balanced workload and minimum communication cost. Experimental results on a 64-core system show that by allowing a small part of the cores to relax over a short time period, the proposed methodology improves multicore system yield (percentage of core failures) by 20%, while extending MTTF by 30% with insignificant degradation in performance (less than 3%).
GPU code generation for ODE-based applications with phased shared-data access patterns
Authors: Hagiescu Andrei , Liu Bing , Ramanathan R. , Palaniappan Sucheendra K. , Cui Zheng , Chattopadhyay Bipasa , Thiagarajan P. S. , Wong Weng-Fai
Published: January 2014

We present a novel code generation scheme for GPUs. Its key feature is the platform-aware generation of a heterogeneous pool of threads. This exposes more data-sharing opportunities among the concurrent threads and reduces the memory requirements that would otherwise exceed the capacity of the on-chip memory. Instead of the conventional strategy of focusing on exposing as much parallelism as possible, our scheme leverages on the phased nature of memory access patterns found in many applications that exhibit massive parallelism. We demonstrate the effectiveness of our code generation strategy on a computational systems biology application. This application consists of computing a Dynamic Bayesian Network (DBN) approximation of the dynamics of signalling pathways described as a system of Ordinary Differential Equations (ODEs). The approximation algorithm involves (i) sampling many (of the order of a few million) times from the set of initial states, (ii) generating trajectories through numerical integration, and (iii) storing the statistical properties of this set of trajectories in Conditional Probability Tables (CPTs) of a DBN via a prespecified discretization of the time and value domains. The trajectories can be computed in parallel. However, the intermediate data needed for computing them, as well as the entries for the CPTs, are too large to be stored locally. Our experiments show that the proposed code generation scheme scales well, achieving significant performance improvements on three realistic signalling pathways models. These results suggest how our scheme could be extended to deal with other applications involving systems of ODEs.
Fast modulo scheduler utilizing patternized routes for coarse-grained reconfigurable architectures
Authors: Kim Wonsub , Choi Yoonseo , Park Haewoo
Published: January 2014

Coarse-Grained Reconfigurable Architectures (CGRAs) present a potential of high compute throughput with energy efficiency. A CGRA consists of an array of Functional Units (FUs), which communicate with each other through an interconnect network containing transmission nodes and register files. To achieve high performance from the software solutions mapped onto CGRAs, modulo scheduling of loops is generally employed. One of the key challenges in modulo scheduling for CGRAs is to explicitly handle routings of operands from a source to a destination operations through various routing resources. Existing modulo schedulers for CGRAs are slow because finding a valid routing is generally a searching problem over a large space, even with the guidance of well-defined cost metrics. Applications in traditional embedded multimedia domains are regarded as relatively tolerant to a slow compile time in exchange for a high-quality solution. However, many rapidly growing domains of applications, such as 3D graphics, require a fast compilation. Entrances of CGRAs to these domains have been blocked mainly due to their long compile time. We attack this problem by utilizing patternized routes, for which resources and time slots for a success can be estimated in advance when a source operation is placed. By conservatively reserving predefined resources at predefined time slots, future routings originating from the source operation are guaranteed. Experiments on a real-world 3D graphics benchmark suite show that our scheduler improves the compile time up to 6,000 times while achieving an average 70% throughputs of the state-of-the-art CGRA modulo scheduler, the Edge-centric Modulo Scheduler (EMS).
Unsolved problems in visibility graphs of points, segments, and polygons
Authors: Ghosh Subir K. , Goswami Partha P.
Published: January 2014

In this survey article, we present open problems and conjectures on visibility graphs of points, segments, and polygons along with necessary backgrounds for understanding them.
Synchronous programming in audio processing
Authors: Barkati Karim , Jouvelot Pierre
Published: January 2014

The adequacy of a programming language to a given software project or application domain is often considered a key factor of success in software development and engineering, even though little theoretical or practical information is readily available to help make an informed decision. In this article, we address a particular version of this issue by comparing the adequacy of general-purpose synchronous programming languages to more Domain-Specific Languages (DSLs) in the field of computer music. More precisely, we implemented and tested the same lookup table oscillator example program, one of the most classical algorithms for sound synthesis, using a selection of significant synchronous programming languages, half of which designed as specific music languages—Csound, Pure Data, SuperCollider, ChucK, Faust—and the other half being general synchronous formalisms—Signal, Lustre, Esterel, Lucid Synchrone and C with the OpenMP Stream Extension (Matlab/Octave is used for the initial specification). The advantages of these two approaches are discussed, providing insights to language designers and possibly software developers of both communities regarding programming languages design for the audio domain.
Using grammars for pattern recognition in images
Authors: Pedro Ricardo Wandré Dias , Nunes Fátima L. S. , Machado-Lima Ariane
Published: January 2014

Grammars are widely used to describe string languages such as programming and natural languages and, more recently, biosequences. Moreover, since the 1980s grammars have been used in computer vision and related areas. Some factors accountable for this increasing use regard its relatively simple understanding and its ability to represent some semantic pattern models found in images, both spatially and temporally. The objective of this article is to present an overview regarding the use of syntactic pattern recognition methods in image representations in several applications. To achieve this purpose, we used a systematic review process to investigate the main digital libraries in the area and to document the phases of the study in order to allow the auditing and further investigation. The results indicated that in some of the studies retrieved, manually created grammars were used to comply with a particular purpose. Other studies performed a learning process of the grammatical rules. In addition, this article also points out still unexplored research opportunities in the literature.
The Antithrombotic Effects of Statins
Authors: Phillip Owens A. , Mackman Nigel
Published: January 2014

Hypercholesterolemia is considered the primary risk factor for cardiovascular disease. An estimated 200 million prescriptions are issued per year for statins to treat hypercholesterolemia. Importantly, statins have additional beneficial effects independent of their effects on lipids. Recent studies have shown that statins reduce thrombosis via multiple pathways, including inhibiting platelet activation and reducing the pathologic expression of the procoagulant protein tissue factor. Many of the antithrombotic effects of statins are attributed to inhibiting prenylation of RhoA and effects on other intracellular signaling molecules such as NF-κB and KLF2. These antithrombotic activities of statins likely contribute to the ability of statins to reduce the incidence of cardiovascular death.