bluuebunny/crossref_metadata_2025_split huggingface dataset:
Change Detection Within Pipeline ROWs: Environmental Change Analysis Using High Resolution Satellite Imagery
Authors: Huisman Otto , Gharibi Arash 
Published: January 2016

One of the major concerns for pipeline operators is to efficiently monitor the events happening over the pipeline corridor, or right-of-way (ROW). Monitoring of the ROW is an important part of ensuring the safe and efficient transportation of oil and gas. Events occurring within this zone require rapid assessment and, if necessary, mitigation. These events could be physical intrusions such as encroachment from growing settlements, impact of vegetation, pipeline leakage or geo-environmental hazards.
Analysis of satellite imagery can provide an efficient and low cost solution to access and quantify change across the ROW. Examining these events over a periodic interval requires implementation of specific methods that can support the on-going monitoring and decision making practices. In this context, satellite remote sensing images can provide a low cost and efficient solution for monitoring the physical and environmental impacts over the ROW of pipeline system.
This paper reports on the development of a methodological approach for environmental change analysis using high resolution satellite images that can help decision making in pipeline systems. Analysis results and maps produced during this work provide an insight into landcover change over the study area and expected to support in on-going pipeline management practices.
Two methods, Vegetation index differencing and post classification comparison have been implemented to identify change areas in the Taranaki region of the North Island of New Zealand. Vegetation index differencing with NDVI shows increase or decrease of overall vegetation within the study area. Special focus was given on large area increase and decrease with area threshold value above 0.2 hectare.
Detailed analysis of change was conducted with post classification comparison method that uses land cover classification results of year 2010 and 2013. An overall change of 10% has been observed throughout the study area with large area change of approximately 5%. Results obtained from post classification comparison method were further analyzed with 6 focus areas and compared with the existing soil data and rainfall data.
The methods adopted during this study are expected to provide a base for environmental change analysis in similar pipeline corridors to support decision making.
Results of a Mitigation Technique Used to Reduce Pipeline Strains in Unstable Slopes
Authors: Contreras Maria F. , Pereira Ordoñez Mauricio , Hernández Jon , Vergara Carlos 
Published: January 2016

The OCENSA pipeline system crosses a wide range of geological zones, finding different stability problems. Those problems related with landslides are stabilized with different kinds of geotechnical works within the pipeline maintenance programs, but sometimes these problems reach big dimensions making very difficult to stabilize them, so mitigation techniques are necessary in order to guarantee the pipe integrity.
A mitigation technique using EPS (Expanded Poly-Styrene) blocks is being used in the OCENSA pipeline system (Colombia) in order to reduce the buried pipe response due to soil displacements during landslide events and in creeping slopes. OCENSA is the first operator in Latin America using this technique. Prior to the use of this technique, numerical modeling studies were done with the support of SOLSIN S.A.S. These studies were focused on determining the viability and effectiveness of the proposed technique.
The purpose of the EPS blocks is to constitute a low-density fill with very low Young modulus reducing the soil-pipeline interaction forces. These blocks are located near the landslide limits in both, the stable and un-stable zones in order to reduce the stiffness of the materials around the pipe. These blocks allow the pipe to move beyond the landslide limits, reducing the bending strains. The extension of the EPS backfill is determined by means of the geotechnical investigation of the place in study and using the in-line inspection tools data to determine the length of the pipe affected by the soil movement.
In this paper, three case studies are presented in which the proposed mitigation technique effectiveness was proved. In this part, data analyses coming from the in line inspection program was done.
The inertial tool data showed that the EPS blocks had a significant effect on the pipe response, reducing the total strains compared with those obtained with a normal backfill. This technique can be used to reduce the frequency of the strain-relief excavations in unstable slopes. That means a cost reduction in the pipe maintenance activities and a more efficient integrity management program.
Mutational Analysis of Quinolone Resistance Protein QnrVC7 Provides Novel Insights into the Structure-Activity Relationship of Qnr Proteins
Authors: Po Kathy Hiu Laam , Chan Edward Wai Chi , Chen Sheng 
Published: January 2016

ABSTRACT

This study assessed the functional importance of residues located at the i
−2
position of face 4 of the tandem repeat loops of the quinolone resistance protein QnrVC7 through mutagenesis studies. The i
−2
position of face 4 on different coils required residues with different natures. Some substitutions reduced the protective activity of QnrVC7, while some of them increased it. These findings advanced our understanding on the detailed structural organization and functional requirements of Qnr proteins.
Survey of Carbapenemase-Producing Enterobacteriaceae in Companion Dogs in Madrid, Spain
Authors: González-Torralba Ana , Oteo Jesús , Asenjo Alejandra , Bautista Verónica , Fuentes Elisabeth , Alós Juan-Ignacio 
Published: January 2016

ABSTRACT

We found a low prevalence (0.6%) of carbapenemase-producing
Enterobacteriaceae
(CPE) in fecal microbiota of companion dogs. A single VIM-1-producing
Klebsiella pneumoniae
isolate belonging to sequence type (ST) 2090 was detected.
bla
VIM-1
was carried on a class 1 integron and an untypeable ∼48-kb plasmid. Emergence and spread of CPE in this group of animals may be a threat to public health in human and veterinary medicine. This finding supports the need for active surveillance studies in companion animals that live close to humans, as interspecies transmission may occur within the same household.
In Vitro
Antiviral Activity and Resistance Profile Characterization of the Hepatitis C Virus NS5A Inhibitor Ledipasvir
Authors: Cheng Guofeng , Tian Yang , Doehle Brian , Peng Betty , Corsa Amoreena , Lee Yu-Jen , Gong Ruoyu , Yu Mei , Han Bin , Xu Simin , Dvory-Sobol Hadas , Perron Michel , Xu Yili , Mo Hongmei , Pagratis Nikos , Link John O. , Delaney William 
Published: January 2016

ABSTRACT

Ledipasvir (LDV; GS-5885), a component of Harvoni (a fixed-dose combination of LDV with sofosbuvir [SOF]), is approved to treat chronic hepatitis C virus (HCV) infection. Here, we report key preclinical antiviral properties of LDV, including
in vitro
potency,
in vitro
resistance profile, and activity in combination with other anti-HCV agents. LDV has picomolar antiviral activity against genotype 1a and genotype 1b replicons with 50% effective concentration (EC
50
) values of 0.031 nM and 0.004 nM, respectively. LDV is also active against HCV genotypes 4a, 4d, 5a, and 6a with EC
50
values of 0.11 to 1.1 nM. LDV has relatively less
in vitro
antiviral activity against genotypes 2a, 2b, 3a, and 6e, with EC
50
values of 16 to 530 nM.
In vitro
resistance selection with LDV identified the single Y93H and Q30E resistance-associated variants (RAVs) in the NS5A gene; these RAVs were also observed in patients after a 3-day monotherapy treatment.
In vitro
antiviral combination studies indicate that LDV has additive to moderately synergistic antiviral activity when combined with other classes of HCV direct-acting antiviral (DAA) agents, including NS3/4A protease inhibitors and the nucleotide NS5B polymerase inhibitor SOF. Furthermore, LDV is active against known NS3 protease and NS5B polymerase inhibitor RAVs with EC
50
values equivalent to those for the wild type.
bla
NDM-5
-Bearing IncFII-Type Plasmids of Klebsiella pneumoniae Sequence Type 147 Transmitted by Cross-Border Transfer of a Patient
Authors: Shin Juyoun , Baek Jin Yang , Cho Sun Young , Huh Hee Jae , Lee Nam Yong , Song Jae-Hoon , Chung Doo Ryeon , Ko Kwan Soo 
Published: January 2016

ABSTRACT

The two plasmids extracted from
Klebsiella pneumoniae
sequence type 147 (ST147) isolates were analyzed. The first isolate was obtained from a patient transferred from United Arab Emirates to South Korea. The second isolate was obtained from a Korean patient and was suspected to be transmitted from the first patient. Sequences of two plasmids were almost the same, and genetic structures, including
bla
NDM-5
, of these plasmids were similar to plasmids of NDM-1-producing
Escherichia coli
ST131 isolates found in Europe.
Regulatory Mutations Impacting Antibiotic Susceptibility in an Established Staphylococcus aureus Biofilm
Authors: Atwood Danielle N. , Beenken Karen E. , Lantz Tamara L. , Meeker Daniel G. , Lynn William B. , Mills Weston B. , Spencer Horace J. , Smeltzer Mark S. 
Published: January 2016

ABSTRACT

We previously determined the extent to which mutations of different
Staphylococcus aureus
regulatory loci impact biofilm formation as assessed under
in vitro
conditions. Here we extend these studies to determine the extent to which those regulatory loci that had the greatest effect on biofilm formation also impact antibiotic susceptibility. The experiments were done under
in vitro
and
in vivo
conditions using two clinical isolates of
S. aureus
(LAC and UAMS-1) and two functionally diverse antibiotics (daptomycin and ceftaroline). Mutation of the staphylococcal accessory regulator (
sarA
) or
sigB
was found to significantly increase susceptibilities to both antibiotics and in both strains in a manner that could not be explained by changes in the MICs. The impact of a mutation in
sarA
was comparable to that of a mutation in
sigB
and greater than the impact observed with any other mutant. These results suggest that therapeutic strategies targeting
sarA
and/or
sigB
have the greatest potential to facilitate the ability to overcome the intrinsic antibiotic resistance that defines
S. aureus
biofilm-associated infections.
First Characterization of CTX-M-15-Producing Escherichia coli Strains Belonging to Sequence Type (ST) 410, ST224, and ST1284 from Commercial Swine in South America
Authors: Silva Ketrin C. , Moreno Marina , Cabrera Carlos , Spira Beny , Cerdeira Louise , Lincopan Nilton , Moreno Andrea M. 
Published: January 2016

ABSTRACT

We report for the first time the isolation of CTX-M-15-producing
Escherichia coli
strains belonging to sequence type (ST) 410, ST224, and ST1284 in commercial swine in Brazil. The
bla
CTX-M-15
gene was located on F-::A9::B1 and C1::A9::B1 IncF-type plasmids, surrounded by a new genetic context comprising the IS
26
insertion sequence truncated with the IS
Ecp1
element upstream of
bla
CTX-M-15
. These results reveal that commercial swine have become a new reservoir of CTX-M-15-producing bacteria in South America.
Functions of VPA1418 and VPA0305 Catalase Genes in Growth of Vibrio parahaemolyticus under Oxidative Stress
Authors: Chen Ching-Lian , Fen Shin-yuan , Chung Chun-Hui , Yu Shu-Chuan , Chien Cheng-Lun , Wong Hin-chung 
Published: January 2016

ABSTRACT

The marine foodborne enteropathogen
Vibrio parahaemolyticus
has four putative catalase genes. The functions of two
katE
-homologous genes,
katE1
(VPA1418) and
katE2
(VPA0305), in the growth of this bacterium were examined using gene deletion mutants with or without complementary genes. The growth of the mutant strains in static or shaken cultures in a rich medium at 37°C or at low temperatures (12 and 4°C), with or without competition from
Escherichia coli
, did not differ from that of the parent strain. When 175 μM extrinsic H
2
O
2
was added to the culture medium, bacterial growth of the Δ
katE1
strain was delayed and growth of the Δ
katE1
Δ
katE2
and Δ
katE1
Δ
ahpC1
double mutant strains was completely inhibited at 37°C for 8 h. The sensitivity of the Δ
katE1
strain to the inhibition of growth by H
2
O
2
was higher at low incubation temperatures (12 and 22°C) than at 37°C. The determined gene expression of these catalase and
ahpC
genes revealed that
katE1
was highly expressed in the wild-type strain at 22°C under H
2
O
2
stress, while the
katE2
and
ahpC
genes may play an alternate or compensatory role in the Δ
katE1
strain. This study demonstrated that
katE1
encodes the chief functional catalase for detoxifying extrinsic H
2
O
2
during logarithmic growth and that the function of these genes was influenced by incubation temperature.
Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH
Authors: Hüpeden Jennifer , Wegen Simone , Off Sandra , Lücker Sebastian , Bedarf Yvonne , Daims Holger , Kühn Carsten , Spieck Eva 
Published: January 2016

ABSTRACTThe functioning of recirculation aquaculture systems (RAS) is essential to maintain water quality for fish health, and one crucial process here is nitrification. The investigated RAS was connected to a rainbow trout production system and operated at an average temperature of 13°C and pH 6.8. Community analyses of the nitrifying biofilm revealed a coexistence ofNitrospiraandNitrotoga, and it is hypothesized that a slightly acidic pH in combination with lower temperatures favors the growth of the latter. Modification of the standard cultivation approach toward lower pH values of 5.7 to 6.0 resulted in the successful enrichment (99% purity) ofNitrotogasp. strain HW29, which had a 16S rRNA sequence similarity of 99.0% toNitrotoga arctica. Reference cultures ofNitrospira defluviiand the novelNitrotogasp. HW29 were used to confirm differentiation of these nitrite oxidizers in distinct ecological niches.Nitrotogasp. HW29 revealed pH and temperature optima of 6.8 and 22°C, respectively, whereasNitrospira defluviidisplayed the highest nitrite oxidation rate at pH 7.3 and 32°C. We report here the occurrence ofNitrotogaas one of the main nitrite-oxidizing bacteria in freshwater aquaculture systems and indicate that a slightly acidic pH, in addition to temperatures below 20°C, can be applied as a selective isolation criterion for this microorganism.
Depletion of Phagocytic Cells during Nonlethal Plasmodium yoelii Infection Causes Severe Malaria Characterized by Acute Renal Failure in Mice
Authors: Terkawi Mohamad Alaa , Nishimura Maki , Furuoka Hidefumi , Nishikawa Yoshifumi 
Published: January 2016

ABSTRACT

In the current study, we examined the effects of depletion of phagocytes on the progression of
Plasmodium yoelii
17XNL infection in mice. Strikingly, the depletion of phagocytic cells, including macrophages, with clodronate in the acute phase of infection significantly reduced peripheral parasitemia but increased mortality. Moribund mice displayed severe pathological damage, including coagulative necrosis in liver and thrombi in the glomeruli, fibrin deposition, and tubular necrosis in kidney. The severity of infection was coincident with the increased sequestration of parasitized erythrocytes, the systematic upregulation of inflammation and coagulation, and the disruption of endothelial integrity in the liver and kidney. Aspirin was administered to the mice to minimize the risk of excessive activation of the coagulation response and fibrin deposition in the renal tissue. Interestingly, treatment with aspirin reduced the parasite burden and pathological lesions in the renal tissue and improved survival of phagocyte-depleted mice. Our data imply that the depletion of phagocytic cells, including macrophages, in the acute phase of infection increases the severity of malarial infection, typified by multiorgan failure and high mortality.
Characterization of RNA Helicase CshA and Its Role in Protecting mRNAs and Small RNAs of Staphylococcus aureus Strain Newman
Authors: Kim Samin , Corvaglia Anna-Rita , Léo Stefano , Cheung Ambrose , Francois Patrice 
Published: January 2016

ABSTRACT

The toxin MazF
sa
in
Staphylococcus aureus
is a sequence-specific endoribonuclease that cleaves the majority of the mRNAs
in vivo
but spares many essential mRNAs (e.g.,
secY
mRNA) and, surprisingly, an mRNA encoding a regulatory protein (i.e.,
sarA
mRNA). We hypothesize that some mRNAs may be protected by RNA-binding protein(s) from degradation by MazF
sa
. Using heparin-Sepharose-enriched fractions that hybridized to
sarA
mRNA on Northwestern blots, we identified among multiple proteins the DEAD box RNA helicase CshA (NWMN_1985 or SA1885) by mass spectroscopy. Purified CshA exhibits typical RNA helicase activities, as exemplified by RNA-dependent ATPase activity and unwinding of the DNA-RNA duplex. A severe growth defect was observed in the
cshA
mutant compared with the parent when grown at 25°C but not at 37°C. Activation of MazF
sa
in the
cshA
mutant resulted in lower CFU per milliliter accompanied by a precipitous drop in viability (∼40%) compared to those of the parent and complemented strains. NanoString analysis reveals diminished expression of a small number of mRNAs and 22 small RNAs (sRNAs) in the
cshA
mutant versus the parent upon MazF
sa
induction, thus implying protection of these RNAs by CshA. In the case of the sRNA teg049 within the
sarA
locus, we showed that the protective effect was likely due to transcript stability as revealed by reduced half-life in the
cshA
mutant versus the parent. Accordingly, CshA likely stabilizes selective mRNAs and sRNAs
in vivo
and as a result enhances
S. aureus
survival upon MazF
sa
induction during stress.
Regulation of Expression of Uropathogenic Escherichia coli Nonfimbrial Adhesin TosA by PapB Homolog TosR in Conjunction with H-NS and Lrp
Authors: Engstrom Michael D. , Mobley Harry L. T. 
Published: January 2016

ABSTRACT

Urinary tract infections (UTIs) are a major burden to human health. The overwhelming majority of UTIs are caused by uropathogenic
Escherichia coli
(UPEC) strains. Unlike some pathogens, UPEC strains do not have a fixed core set of virulence and fitness factors but do have a variety of adhesins and regulatory pathways. One such UPEC adhesin is the nonfimbrial adhesin TosA, which mediates adherence to the epithelium of the upper urinary tract. The
tos
operon is AT rich, resides on pathogenicity island
aspV
, and is not expressed under laboratory conditions. Because of this, we hypothesized that
tosA
expression is silenced by H-NS. Lrp, based on its prominent function in the regulation of other adhesins, is also hypothesized to contribute to
tos
operon regulation. Using a variety of
in vitro
techniques, we mapped both the
tos
operon promoter and TosR binding sites. We have now identified TosR as a dual regulator of the
tos
operon, which could control the
tos
operon in association with H-NS and Lrp. H-NS is a negative regulator of the
tos
operon, and Lrp positively regulates the
tos
operon. Exogenous leucine also inhibits Lrp-mediated
tos
operon positive regulation. In addition, TosR binds to the
pap
operon, which encodes another important UPEC adhesin, P fimbria. Induction of TosR synthesis reduces production of P fimbria. These studies advance our knowledge of regulation of adhesin expression associated with uropathogen colonization of a host.
MyD88 Mediates Instructive Signaling in Dendritic Cells and Protective Inflammatory Response during Rickettsial Infection
Authors: Bechelli Jeremy , Smalley Claire , Zhao Xuemei , Judy Barbara , Valdes Patricia , Walker David H. , Fang Rong 
Published: January 2016

ABSTRACTSpotted fever group rickettsiae cause potentially life-threatening infections throughout the world. Several members of the Toll-like receptor (TLR) family are involved in host response to rickettsiae, and yet the mechanisms by which these TLRs mediate host immunity remain incompletely understood. In the present study, we found that host susceptibility of MyD88−/−mice to infection withRickettsia conoriiorRickettsia australiswas significantly greater than in wild-type (WT) mice, in association with severely impaired bacterial clearancein vivo.R. australis-infected MyD88−/−mice showed significantly lower expression levels of gamma interferon (IFN-γ), interleukin-6 (IL-6), and IL-1β, accompanied by significantly fewer inflammatory infiltrates of macrophages and neutrophils in infected tissues, than WT mice. The serum levels of IFN-γ, IL-12, IL-6, and granulocyte colony-stimulating factor were significantly reduced, while monocyte chemoattractant protein 1, macrophage inflammatory protein 1α, and RANTES were significantly increased in infected MyD88−/−mice compared to WT mice. Strikingly,R. australisinfection was incapable of promoting increased expression of MHC-IIhighand production of IL-12p40 in MyD88−/−bone marrow-derived dendritic cells (BMDCs) compared to WT BMDCs, although costimulatory molecules were upregulated in both types of BMDCs. Furthermore, the secretion levels of IL-1β byRickettsia-infected BMDCs and in the sera of infected mice were significantly reduced in MyD88−/−mice compared to WT controls, suggesting thatin vitroandin vivoproduction of IL-1β is MyD88 dependent. Taken together, our results suggest that MyD88 signaling mediates instructive signals in DCs and secretion of IL-1β and type 1 immune cytokines, which may account for the protective inflammatory response during rickettsial infection.
The Variable Region of Pneumococcal Pathogenicity Island 1 Is Responsible for Unusually High Virulence of a Serotype 1 Isolate
Authors: Harvey Richard M. , Trappetti Claudia , Mahdi Layla K. , Wang Hui , McAllister Lauren J. , Scalvini Alexandra , Paton Adrienne W. , Paton James C. 
Published: January 2016

ABSTRACT

Streptococcus pneumoniae
is the leading infectious cause of death in children in the world. However, the mechanisms that drive the progression from asymptomatic colonization to disease are poorly understood. Two virulence-associated genomic accessory regions (ARs) were deleted in a highly virulent serotype 1 clinical isolate (strain 4496) and examined for their contribution to pathogenesis. Deletion of a prophage encoding a platelet-binding protein (PblB) resulted in reduced adherence, biofilm formation, reduced initial infection within the lungs, and a reduction in the number of circulating platelets in infected mice. However, the region's overall contribution to the survival of mice was not significant. In contrast, deletion of the variable region of pneumococcal pathogenicity island 1 (vPPI1) was also responsible for a reduction in adherence and biofilm formation but also reduced survival and invasion of the pleural cavity, blood, and lungs. While the 4496ΔPPI1 strain induced higher expression of the genes encoding interleukin-10 (IL-10) and CD11b in the lungs of challenged mice than the wild-type strain, very few other genes exhibited altered expression. Moreover, while the level of IL-10 protein was increased in the lungs of 4496ΔPPI1 mutant-infected mice compared to strain 4496-infected mice, the levels of gamma interferon (IFN-γ), CXCL10, CCL2, and CCL4 were not different in the two groups. However, the 4496ΔPPI1 mutant was found to be more susceptible than the wild type to phagocytic killing by a macrophage-like cell line. Therefore, our data suggest that vPPI1 may be a major contributing factor to the heightened virulence of certain serotype 1 strains, possibly by influencing resistance to phagocytic killing.