bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Note: Preliminary investigations into the use of a functionalised polymer to reduce diffusion in Fricke gel dosimeters
Authors: Smith S. T. , Masters K.‐S. , Hosokawa K. , Blinco J. P. , Crowe S. B. , Kairn T. , Trapp J. V. 
Published: November 2015

Purpose:A modification of the existing PVA‐FX hydrogel has been made to investigate the use of a functionalised polymer in a Fricke gel dosimetry system to decrease Fe3+ diffusion.Methods:The chelating agent, xylenol orange, was chemically bonded to the gelling agent, polyvinyl alcohol (PVA) to create xylenol orange functionalised PVA (XO‐PVA). A gel was created from the XO‐PVA (20% w/v) with ferrous sulfate (0.4 mM) and sulfuric acid (50 mM).Results:This resulted in an optical density dose sensitivity of 0.014 Gy−1, an auto‐oxidation rate of 0.0005 h−1, and a diffusion rate of 0.129 mm2 h−1; an 8% reduction compared to the original PVA‐FX gel, which in practical terms adds approximately 1 h to the time span between irradiation and accurate read‐out.Conclusions:Because this initial method of chemically bonding xylenol orange to polyvinyl alcohol has inherently low conversion, the improvement on existing gel systems is minimal when compared to the drawbacks. More efficient methods of functionalising polyvinyl alcohol with xylenol orange must be developed for this system to gain clinical relevance.
Prior image based temporally constrained reconstruction algorithm for magnetic resonance guided high intensity focused ultrasound
Authors: Prakash Jaya , Todd Nick , Yalavarthy Phaneendra K. 
Published: November 2015

Purpose:A prior image based temporally constrained reconstruction (PITCR) algorithm was developed for obtaining accurate temperature maps having better volume coverage, and spatial, and temporal resolution than other algorithms for highly undersampled data in magnetic resonance (MR) thermometry.Methods:The proposed PITCR approach is an algorithm that gives weight to the prior image and performs accurate reconstruction in a dynamic imaging environment. The PITCR method is compared with the temporally constrained reconstruction (TCR) algorithm using pork muscle data.Results:The PITCR method provides superior performance compared to the TCR approach with highly undersampled data. The proposed approach is computationally expensive compared to the TCR approach, but this could be overcome by the advantage of reconstructing with fewer measurements. In the case of reconstruction of temperature maps from 16% of fully sampled data, the PITCR approach was 1.57× slower compared to the TCR approach, while the root mean square error using PITCR is 0.784 compared to 2.815 with the TCR scheme.Conclusions:The PITCR approach is able to perform more accurate reconstructions of temperature maps compared to the TCR approach with highly undersampled data in MR guided high intensity focused ultrasound.
3D liver segmentation using multiple region appearances and graph cuts
Authors: Peng Jialin , Hu Peijun , Lu Fang , Peng Zhiyi , Kong Dexing , Zhang Hongbo 
Published: November 2015

Purpose:Efficient and accurate 3D liver segmentations from contrast‐enhanced computed tomography (CT) images play an important role in therapeutic strategies for hepatic diseases. However, inhomogeneous appearances, ambiguous boundaries, and large variance in shape often make it a challenging task. The existence of liver abnormalities poses further difficulty. Despite the significant intensity difference, liver tumors should be segmented as part of the liver. This study aims to address these challenges, especially when the target livers contain subregions with distinct appearances.Methods:The authors propose a novel multiregion‐appearance based approach with graph cuts to delineate the liver surface. For livers with multiple subregions, a geodesic distance based appearance selection scheme is introduced to utilize proper appearance constraint for each subregion. A special case of the proposed method, which uses only one appearance constraint to segment the liver, is also presented. The segmentation process is modeled with energy functions incorporating both boundary and region information. Rather than a simple fixed combination, an adaptive balancing weight is introduced and learned from training sets. The proposed method only calls initialization inside the liver surface. No additional constraints from user interaction are utilized.Results:The proposed method was validated on 50 3D CT images from three datasets, i.e., Medical Image Computing and Computer Assisted Intervention (MICCAI) training and testing set, and local dataset. On MICCAI testing set, the proposed method achieved a total score of 83.4 ± 3.1, outperforming nonexpert manual segmentation (average score of 75.0). When applying their method to MICCAI training set and local dataset, it yielded a mean Dice similarity coefficient (DSC) of 97.7% ± 0.5% and 97.5% ± 0.4%, respectively. These results demonstrated the accuracy of the method when applied to different computed tomography (CT) datasets. In addition, user operator variability experiments showed its good reproducibility.Conclusions:A multiregion‐appearance based method is proposed and evaluated to segment liver. This approach does not require prior model construction and so eliminates the burdens associated with model construction and matching. The proposed method provides comparable results with state‐of‐the‐art methods. Validation results suggest that it may be suitable for the clinical use.
Hydrocarbon-Degrading Bacteria Exhibit a Species-Specific Response to Dispersed Oil while Moderating Ecotoxicity
Authors: Overholt Will A. , Marks Kala P. , Romero Isabel C. , Hollander David J. , Snell Terry W. , Kostka Joel E. 
Published: November 2015

ABSTRACT

The Deepwater Horizon blowout in April 2010 represented the largest accidental marine oil spill and the largest release of chemical dispersants into the environment to date. While dispersant application may provide numerous benefits to oil spill response efforts, the impacts of dispersants and potential synergistic effects with crude oil on individual hydrocarbon-degrading bacteria are poorly understood. In this study, two environmentally relevant species of hydrocarbon-degrading bacteria were utilized to quantify the response to Macondo crude oil and Corexit 9500A-dispersed oil in terms of bacterial growth and oil degradation potential. In addition, specific hydrocarbon compounds were quantified in the dissolved phase of the medium and linked to ecotoxicity using a U.S. Environmental Protection Agency (EPA)-approved rotifer assay. Bacterial treatment significantly and drastically reduced the toxicity associated with dispersed oil (increasing the 50% lethal concentration [LC
50
] by 215%). The growth and crude oil degradation potential of
Acinetobacter
were inhibited by Corexit by 34% and 40%, respectively; conversely, Corexit significantly enhanced the growth of
Alcanivorax
by 10% relative to that in undispersed oil. Furthermore, both bacterial strains were shown to grow with Corexit as the sole carbon and energy source. Hydrocarbon-degrading bacterial species demonstrate a unique response to dispersed oil compared to their response to crude oil, with potentially opposing effects on toxicity. While some species have the potential to enhance the toxicity of crude oil by producing biosurfactants, the same bacteria may reduce the toxicity associated with dispersed oil through degradation or sequestration.
Divergent Evolution of the repFII Replicon of IncF Plasmids Carrying Cytotoxic Necrotizing Factor
cnf2
, Cytolethal Distending Toxin
cdtIII
, and
f17Ae
Fimbrial Variant Genes in Type 2 Necrotoxigenic Escherichia coli Isolates from Calves
Authors: Bihannic Morgan , Haenni Marisa , Oswald Eric , Madec Jean-Yves 
Published: November 2015

ABSTRACT

Among the pathovars of
Escherichia coli
in cattle, necrotoxigenic
E. coli
(NTEC) is defined by the production of cytotoxic necrotizing factors (CNFs). In particular, type 2 NTEC (NTEC2) strains are frequent in diarrheic and septicemic calves and usually coproduce CNF type 2 (CNF2), cytolethal distending toxin type III (CDTIII), and fimbrial adhesins of the F17 family, whose genetic determinants have frequently been reported on the same Vir-like plasmid. In this study, we investigated the genetic environment of the
cnf2
,
f17Ae
, and
cdtIII
genes in a collection of fecal
E. coli
isolates recovered from 484 French and 58 Iranian calves. In particular, we highlighted the spread of
cnf2
,
f17Ae
, and
cdtIII
on similar 150-kb IncF plasmids harboring the newly assigned repFII replicon allele F74 in NTEC2 isolates. Interestingly, this 150-kb IncF plasmid differed from the 140-kb IncF plasmid harboring the newly assigned repFII replicon allele F75 and carrying
cnf2
alone. These results suggest two divergent lineages of
cnf2
-carrying IncF plasmids depending on the presence of the
f17Ae
and
cdtIII
genes. This partition was observed in
E. coli
strains of unrelated backgrounds, suggesting two different evolutionary paths of
cnf2
-carrying IncF plasmids rather than divergent evolutions of NTEC2 clones. The driving forces for such divergent evolutions are not known, and further studies are required to clarify the selection of plasmid subtypes spreading virulence determinants in
E. coli
, in particular, plasmids of the IncF family.
Application of the Environmental Relative Moldiness Index in Finland
Authors: Täubel Martin , Karvonen Anne M. , Reponen Tiina , Hyvärinen Anne , Vesper Stephen , Pekkanen Juha 
Published: November 2015

ABSTRACT

The environmental relative moldiness index (ERMI) metric was previously developed to quantify mold contamination in U.S. homes. This study determined the applicability of the ERMI for quantifying mold and moisture damage in Finnish residences. Homes of the LUKAS2 birth cohort in Finland were visually inspected for moisture damage and mold, and vacuumed floor dust samples were collected. An ERMI analysis including 36 mold-specific quantitative PCR assays was performed on the dust samples (
n
= 144), and the ERMI metric was analyzed against inspection-based observations of moisture damage and mold. Our results show that the ERMI was significantly associated with certain observations of visible mold in Finnish homes but not with moisture damage. Several mold species occurred more frequently and at higher levels in Finnish than in U.S. homes. Modification of the ERMI toward Finnish conditions, using a subsample of LUKAS2 homes with and without moisture damage, resulted in a simplified metric based on 10 mold species. The Finnish ERMI (FERMI) performed substantially better in quantifying moisture and mold damage in Finnish homes, showing significant associations with various observations of visible mold, strongest when the damage was located in the child's main living area, as well as with mold odor and moisture damage. As shown in Finland, the ERMI as such is not equally well usable in different climates and geographic regions but may be remodeled to account for local outdoor and indoor fungal conditions as well as for moisture damage characteristics in a given country.
The Extracellular Wall-Bound β-
N
-Acetylglucosaminidase from Lactobacillus casei Is Involved in the Metabolism of the Human Milk Oligosaccharide Lacto-
N
-Triose
Authors: Bidart Gonzalo N. , Rodríguez-Díaz Jesús , Yebra María J. 
Published: November 2015

ABSTRACT

Human milk oligosaccharides (HMOs) are considered to play a key role in establishing and maintaining the infant gut microbiota. Lacto-
N
-triose forms part of both type 1 and type 2 HMOs and also of the glycan moieties of glycoproteins. Upstream of the previously characterized gene cluster involved in lacto-
N
-biose and galacto-
N
-biose metabolism from
Lactobacillus casei
BL23, there are two genes,
bnaG
and
manA
, encoding a β-
N
-acetylglucosaminidase precursor and a mannose-6-phosphate isomerase, respectively. In this work, we show that
L. casei
is able to grow in the presence of lacto-
N
-triose as a carbon source. Inactivation of
bnaG
abolished the growth of
L. casei
on this oligosaccharide, demonstrating that BnaG is involved in its metabolism. Interestingly, whole cells of a
bnaG
mutant were totally devoid of β-
N
-acetylglucosaminidase activity, suggesting that BnaG is an extracellular wall-attached enzyme. In addition to hydrolyzing lacto-
N
-triose into
N
-acetylglucosamine and lactose, the purified BnaG enzyme also catalyzed the hydrolysis of 3′-
N
-acetylglucosaminyl-mannose and 3′-
N
-acetylgalactosaminyl-galactose.
L. casei
can be cultured in the presence of 3′-
N
-acetylglucosaminyl-mannose as a carbon source, but, curiously, the
bnaG
mutant strain was not impaired in its utilization. These results indicate that the assimilation of 3′-
N
-acetylglucosaminyl-mannose is independent of BnaG. Enzyme activity and growth analysis with a
manA
-knockout mutant showed that ManA is involved in the utilization of the mannose moiety of 3′-
N
-acetylglucosaminyl-mannose. Here we describe the physiological role of a β-
N
-acetylglucosaminidase in lactobacilli, and it supports the metabolic adaptation of
L. casei
to the
N
-acetylglucosaminide-rich gut niche.
Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage
Authors: Ferrocino Ilario , Greppi Anna , La Storia Antonietta , Rantsiou Kalliopi , Ercolini Danilo , Cocolin Luca 
Published: November 2015

ABSTRACT

Beef burgers were stored at 4°C in a vacuum in nisin-activated antimicrobial packaging. Microbial ecology analyses were performed on samples collected between days 0 and 21 of storage to discover the population diversity. Two batches were analyzed using RNA-based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. The active packaging retarded the growth of the total viable bacteria and lactic acid bacteria. Culture-independent analysis by pyrosequencing of RNA extracted directly from meat showed that
Photobacterium phosphoreum
,
Lactococcus piscium
,
Lactobacillus sakei
, and
Leuconostoc carnosum
were the major operational taxonomic units (OTUs) shared between control and treated samples. Beta diversity analysis of the 16S rRNA sequence data and RNA-DGGE showed a clear separation between two batches based on the microbiota. Control samples from batch B showed a significant high abundance of some taxa sensitive to nisin, such as
Kocuria rhizophila
,
Staphylococcus xylosus
,
Leuconostoc carnosum
, and
Carnobacterium divergens
, compared to control samples from batch A. However, only from batch B was it possible to find a significant difference between controls and treated samples during storage due to the active packaging. Predicted metagenomes confirmed differences between the two batches and indicated that the use of nisin-based antimicrobial packaging can determine a reduction in the abundance of specific metabolic pathways related to spoilage. The present study aimed to assess the viable bacterial communities in beef burgers stored in nisin-based antimicrobial packaging, and it highlights the efficacy of this strategy to prolong beef burger shelf life.
Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation
Authors: García-Fraile Paula , Benada Oldrich , Cajthaml Tomáš , Baldrian Petr , Lladó Salvador 
Published: November 2015

ABSTRACT

Understanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55
T
, which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55
T
include
Bryocella elongata
SN10
T
(95.4% identity),
Acidicapsa ligni
WH120
T
(95.2% identity), and
Telmatobacter bradus
TPB6017
T
(95.0% identity), revealing that strain S55
T
should be classified within the phylum
Acidobacteria
, subdivision 1. Strain S55
T
is a rod-like bacterium that grows at acidic pH (3 to 6). Its phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicate that strain S55
T
corresponds to a new genus within the phylum
Acidobacteria
; thus, we propose the name
Terracidiphilus gabretensis
gen. nov., sp. nov. (strain S55
T
= NBRC 111238
T
= CECT 8791
T
). This strain produces extracellular enzymes implicated in the degradation of plant-derived biopolymers. Moreover, analysis of the genome sequence of strain S55
T
also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55
T
being expressed in the forest soil, especially during winter. Our results suggest an important contribution of
T. gabretensis
S55
T
in the carbon cycle in the
Picea abies
coniferous forest.
Three-decade neurological and neurocognitive follow-up of HIV-1-infected patients on best-available antiretroviral therapy in Finland
Authors: Heikinheimo T , Poutiainen E , Salonen O , Elovaara I , Ristola M 
Published: November 2015

ObjectivesIs it possible to live without neurocognitive or neurological symptoms after being infected with HIV for a very long time? These study patients with decades-long HIV infection in Finland were observed in this follow-up study during three time periods: 1986–1990, in 1997 and in 2013.SettingPatients from greater Helsinki area were selected from outpatient's unit of infectious diseases.ParticipantsThe study included 80 HIV patients. Patients with heavy alcohol consumption, central nervous system disorder or psychiatric disease were excluded.Primary and secondary outcome measuresThe patients underwent neurological and neuropsychological examinations, MRI of the brain and laboratory tests, including blood CD4 cells and plasma HIV-1 RNA. Neuropsychological examination included several measures: subtests of Wechsler Adult Intelligence Scale, Wechsler Memory Scale-Revised, list learning, Stroop and Trail-Making-B test. The Beck Depression Inventory and Fatigue Severity Scale were also carried out. The obtained data from the three time periods were compared with each other.ResultsOwing to high mortality among the original 80 patients, eventually, 17 participated in all three examinations performed between 1986 and 2013. The time from the HIV diagnosis was 27 (23–30) years. Blood CD4 cells at the diagnosis were 610 (29–870) cells/mm3, and the nadir CD4 168 (4–408) cells/mm3. The time on combined antiretroviral treatment was 13 (5–17) years. 9 patients suffered from fatigue, 5 had polyneuropathy and 3 had lacunar cerebral infarcts. There was a subtle increase of brain atrophy in 2 patients. Mild depressive symptoms were common. The neuropsychological follow-up showed typical age-related cognitive changes. No HIV-associated dementia features were detected.ConclusionsPolyneuropathy, fatigue and mild depression were common, but more severe neurological abnormalities were absent. These long-term surviving HIV-seropositive patients, while on best-available treatment, showed no evidence of HIV-associated neurocognitive disorder in neuropsychological and neuroradiological evaluations.
Barriers faced by healthcare professionals when managing falls in older people in Kuala Lumpur, Malaysia: a qualitative study
Authors: Loganathan Annaletchumy , Ng Chirk Jenn , Tan Maw Pin , Low Wah Yun 
Published: November 2015

ObjectiveTo explore the barriers faced by healthcare professionals (HCPs) in managing falls among older people (aged above 60 years) who have a high risk of falling.Research designThe study used a qualitative methodology, comprising 10 in-depth interviews and two focus group discussions. A semistructured topic guide was used to facilitate the interviews, which were audio recorded, transcribed verbatim and checked for accuracy. Data were analysed thematically using WeftQDA software.Participants20 HCPs who managed falls in older people.SettingThis study was conducted at the Primary Care Clinic in the University Malaya Medical Centre (UMMC), Malaysia.ResultsFour categories of barriers emerged—these were related to perceived barriers for older people, HCPs’ barriers, lack of caregiver support and healthcare system barriers. HCPs perceived that older people normalised falls, felt stigmatised, were fatalistic, as well as in denial regarding falls-related advice. HCPs themselves trivialised falls and lacked the skills to manage falls. Rehabilitation was impeded by premature decisions to admit older people to nursing homes. Lastly, there was a lack of healthcare providers as well as a dearth of fall education and training on fall prevention for HCPs.ConclusionsThis study identified barriers that explain poor fall management in older people with a high risk of falls. The lack of structured fall prevention guidelines and insufficient training in fall management made HCPs unable to advise patients on how to prevent falls. The findings of this study warrant evidence-based structured fall prevention intervention targeted to patients as well as to HCPs.
Ranolazine for the treatment of chronic stable angina: a cost-effectiveness analysis from the UK perspective
Authors: Coleman Craig I , Freemantle Nick , Kohn Christine G 
Published: November 2015

ObjectivesTo estimate the cost-effectiveness of ranolazine when added to standard-of-care (SoC) antianginals compared with SoC alone in patients with stable coronary disease experiencing ≥3 attacks/week.SettingAn economic model utilising a UK health system perspective, a 1-month cycle-length and a 1-year time horizon.ParticipantsPatients with stable coronary disease experiencing ≥3 attacks/week starting in 1 of 4 angina frequency health states based on Seattle Angina Questionnaire Angina Frequency (SAQAF) scores (100=no; 61–99=monthly; 31–60=weekly; 0–30=daily angina).InterventionRanolazine added to SoC or SoC alone. Patients were allowed to transition between SAQAF states (first cycle only) or death (any cycle) based on probabilities derived from the randomised, controlled Efficacy of Ranolazine in Chronic Angina trial and other studies. Patients not responding to ranolazine in month 1 (not improving ≥1 SAQAF health state) discontinued ranolazine and were assumed to behave like SoC patients.Primary and secondary outcomes measuresCosts (£2014) and quality-adjusted life-years (QALYs) for patients receiving and not receiving ranolazine.ResultsRanolazine patients lived a mean of 0.701 QALYs at a cost of £5208. Those not receiving ranolazine lived 0.662 QALYs at a cost of £5318. The addition of ranolazine to SoC was therefore a dominant economic strategy. The incremental cost-effectiveness ratio was sensitive to ranolazine cost; exceeding £20 000/QALY when ranolazine's cost was >£203/month. Ranolazine remained a dominant strategy when indirect costs were included and mortality rates were assumed to increase with worsening severity of SAQAF health states. Monte Carlo simulation found ranolazine to be a dominant strategy in ∼71% of 10 000 iterations.ConclusionsAlthough UK-specific data on ranolazine's efficacy and safety are lacking, our analysis suggest ranolazine added to SoC in patients with weekly or daily angina is likely cost-effective from a UK health system perspective.