bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cupping artifact correction and automated classification for high‐resolution dedicated breast CT images
Authors: Yang Xiaofeng , Wu Shengyong , Sechopoulos Ioannis , Fei Baowei 
Published: October 2012

Purpose:To develop and test an automated algorithm to classify the different tissues present in dedicated breast CT images.Methods:The original CT images are first corrected to overcome cupping artifacts, and then a multiscale bilateral filter is used to reduce noise while keeping edge information on the images. As skin and glandular tissues have similar CT values on breast CT images, morphologic processing is used to identify the skin mask based on its position information. A modified fuzzy C‐means (FCM) classification method is then used to classify breast tissue as fat and glandular tissue. By combining the results of the skin mask with the FCM, the breast tissue is classified as skin, fat, and glandular tissue. To evaluate the authors’ classification method, the authors use Dice overlap ratios to compare the results of the automated classification to those obtained by manual segmentation on eight patient images.Results:The correction method was able to correct the cupping artifacts and improve the quality of the breast CT images. For glandular tissue, the overlap ratios between the authors’ automatic classification and manual segmentation were 91.6% ± 2.0%.Conclusions:A cupping artifact correction method and an automatic classification method were applied and evaluated for high‐resolution dedicated breast CT images. Breast tissue classification can provide quantitative measurements regarding breast composition, density, and tissue distribution.
Incidence of Staphylococcus aureus and Analysis of Associated Bacterial Communities on Food Industry Surfaces
Authors: Gutiérrez Diana , Delgado Susana , Vázquez-Sánchez Daniel , Martínez Beatriz , Cabo Marta López , Rodríguez Ana , Herrera Juan J. , García Pilar 
Published: October 2012

ABSTRACT

Biofilms are a common cause of food contamination with undesirable bacteria, such as pathogenic bacteria.
Staphylococcus aureus
is one of the major bacteria causing food-borne diseases in humans. A study designed to determine the presence of
S. aureus
on food contact surfaces in dairy, meat, and seafood environments and to identify coexisting microbiota has therefore been carried out. A total of 442 samples were collected, and the presence of
S. aureus
was confirmed in 6.1% of samples. Sixty-three
S. aureus
isolates were recovered and typed by random amplification of polymorphic DNA (RAPD). Profiles were clustered into four groups which were related to specific food environments. All isolates harbored some potential virulence factors such as enterotoxin production genes, biofilm formation-associated genes, antibiotic resistance, or lysogeny. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints of bacterial communities coexisting with
S. aureus
revealed the presence of bacteria either involved in food spoilage or of concern for food safety in all food environments. Food industry surfaces could thus be a reservoir for
S. aureus
forming complex communities with undesirable bacteria in multispecies biofilms. Uneven microbiological conditions were found in each food sector, which indicates the need to improve hygienic conditions in food processing facilities, particularly the removal of bacterial biofilms, to enhance the safety of food products.
A New Bacterial Disease on Mandevilla sanderi, Caused by Pseudomonas savastanoi: Lessons Learned for Bacterial Diversity Studies
Authors: Eltlbany Namis , Prokscha Zsa-Zsa , Castañeda-Ojeda M. Pilar , Krögerrecklenfort Ellen , Heuer Holger , Wohanka Walter , Ramos Cayo , Smalla Kornelia 
Published: October 2012

ABSTRACT

Leaf lesions of
Mandevilla sanderi
were shown to be caused by
Pseudomonas savastanoi
. While BOX fingerprints were similar for
P. savastanoi
isolates from different host plants, plasmid restriction patterns and sequencing of plasmid-located pathogenicity determinants revealed that
Mandevilla
isolates contained similar plasmids distinct from those of other isolates. A
repA
-based detection method was established.
Ethylene Glycol Metabolism by Pseudomonas putida
Authors: Mückschel Björn , Simon Oliver , Klebensberger Janosch , Graf Nadja , Rosche Bettina , Altenbuchner Josef , Pfannstiel Jens , Huber Armin , Hauer Bernhard 
Published: October 2012

ABSTRACT

In this study, we investigated the metabolism of ethylene glycol in the
Pseudomonas putida
strains KT2440 and JM37 by employing growth and bioconversion experiments, directed mutagenesis, and proteome analysis. We found that strain JM37 grew rapidly with ethylene glycol as a sole source of carbon and energy, while strain KT2440 did not grow within 2 days of incubation under the same conditions. However, bioconversion experiments revealed metabolism of ethylene glycol by both strains, with the temporal accumulation of glycolic acid and glyoxylic acid for strain KT2440. This accumulation was further increased by targeted mutagenesis. The key enzymes and specific differences between the two strains were identified by comparative proteomics. In
P. putida
JM37, tartronate semialdehyde synthase (Gcl), malate synthase (GlcB), and isocitrate lyase (AceA) were found to be induced in the presence of ethylene glycol or glyoxylic acid. Under the same conditions, strain KT2440 showed induction of AceA only. Despite this difference, the two strains were found to use similar periplasmic dehydrogenases for the initial oxidation step of ethylene glycol, namely, the two redundant pyrroloquinoline quinone (PQQ)-dependent enzymes PedE and PedH. From these results we constructed a new pathway for the metabolism of ethylene glycol in
P. putida
. Furthermore, we conclude that
Pseudomonas putida
might serve as a useful platform from which to establish a whole-cell biocatalyst for the production of glyoxylic acid from ethylene glycol.
A Novel
meso
-Diaminopimelate Dehydrogenase from Symbiobacterium thermophilum: Overexpression, Characterization, and Potential for
d
-Amino Acid Synthesis
Authors: Gao Xiuzhen , Chen Xi , Liu Weidong , Feng Jinhui , Wu Qiaqing , Hua Ling , Zhu Dunming 
Published: October 2012

ABSTRACT

meso
-Diaminopimelate dehydrogenase (
meso
-DAPDH) is an NADP
+
-dependent enzyme which catalyzes the reversible oxidative deamination on the
d
-configuration of
meso
-2,6-diaminopimelate to produce
l
-2-amino-6-oxopimelate. In this study, the gene encoding a
meso
-diaminopimelate dehydrogenase from
Symbiobacterium thermophilum
was cloned and expressed in
Escherichia coli
. In addition to the native substrate
meso
-2,6-diaminopimelate, the purified enzyme also showed activity toward
d
-alanine,
d
-valine, and
d
-lysine. This enzyme catalyzed the reductive amination of 2-keto acids such as pyruvic acid to generate
d
-amino acids in up to 99% conversion and 99% enantiomeric excess. Since
meso
-diaminopimelate dehydrogenases are known to be specific to
meso
-2,6-diaminopimelate, this is a unique wild-type
meso
-diaminopimelate dehydrogenase with a more relaxed substrate specificity and potential for
d
-amino acid synthesis. The enzyme is the most stable
meso
-diaminopimelate dehydrogenase reported to now. Two amino acid residues (F146 and M152) in the substrate binding sites of
S. thermophilum meso
-DAPDH different from the sequences of other known
meso
-DAPDHs were replaced with the conserved amino acids in other
meso
-DAPDHs, and assay of wild-type and mutant enzyme activities revealed that F146 and M152 are not critical in determining the enzyme's substrate specificity. The high thermostability and relaxed substrate profile of
S. thermophilum meso
-DAPDH warrant it as an excellent starting enzyme for creating effective
d
-amino acid dehydrogenases by protein engineering.
Probing the Role of Sigma π Interaction and Energetics in the Catalytic Efficiency of Endo-1,4-β-Xylanase
Authors: Singh Raushan Kumar , Tiwari Manish Kumar , Kim In-Won , Chen Zhilei , Lee Jung-Kul 
Published: October 2012

ABSTRACT

Chaetomium globosum
endo-1,4-β-xylanase (XylCg) is distinguished from other xylanases by its high turnover rate (1,860 s
−1
), the highest ever reported for fungal xylanases. One conserved amino acid, W48, in the substrate binding pocket of wild-type XylCg was identified as an important residue affecting XylCg's catalytic efficiency.
Novel Bacterial Community Associated with 500-Year-Old Unpreserved Archaeological Wood from King Henry VIII's Tudor Warship the Mary Rose
Authors: Preston Joanne , Watts Joy E. M. , Jones Mark 
Published: October 2012

ABSTRACT

A 500-year-old unpreserved
Mary Rose
sample, historically containing an iron bolt, was analyzed using enrichment cultures and 16S sequencing. The novel community of bacteria present demonstrates a biological pathway of Fe and S oxidation and a range of acid-generating metabolisms, with implications for preservation and biogeochemical cycling.
Lactate and Acrylate Metabolism by Megasphaera elsdenii under Batch and Steady-State Conditions
Authors: Prabhu Rupal , Altman Elliot , Eiteman Mark A. 
Published: October 2012

ABSTRACT

The growth of
Megasphaera elsdenii
on lactate with acrylate and acrylate analogues was studied under batch and steady-state conditions. Under batch conditions, lactate was converted to acetate and propionate, and acrylate was converted into propionate. Acrylate analogues 2-methyl propenoate and 3-butenoate containing a terminal double bond were similarly converted into their respective saturated acids (isobutyrate and butyrate), while crotonate and lactate analogues 3-hydroxybutyrate and (
R
)-2-hydroxybutyrate were not metabolized. Under carbon-limited steady-state conditions, lactate was converted to acetate and butyrate with no propionate formed. As the acrylate concentration in the feed was increased, butyrate and hydrogen formation decreased and propionate was increasingly generated, while the calculated ATP yield was unchanged.
M. elsdenii
metabolism differs substantially under batch and steady-state conditions. The results support the conclusion that propionate is not formed during lactate-limited steady-state growth because of the absence of this substrate to drive the formation of lactyl coenzyme A (CoA) via propionyl-CoA transferase. Acrylate and acrylate analogues are reduced under both batch and steady-state growth conditions after first being converted to thioesters via propionyl-CoA transferase. Our findings demonstrate the central role that CoA transferase activity plays in the utilization of acids by
M. elsdenii
and allows us to propose a modified acrylate pathway for
M. elsdenii
.
Genome Sequence of Pichia kudriavzevii M12, a Potential Producer of Bioethanol and Phytase
Authors: Chan Giek Far , Gan Han Ming , Ling How Lie , Rashid Noor Aini Abdul 
Published: October 2012

ABSTRACT

A draft genome sequence of
Pichia kudriavzevii
M12 is presented here. The genome reveals the presence of genes encoding enzymes involved in xylose utilization and the pentose phosphate pathway for bioethanol production. Strain M12 is also a potential producer of phytases, enzymes useful in food processing and agriculture.
Monitoring fitness levels and detecting implications for health in a French population: an observational study
Authors: Nassif Hala , Sedeaud Adrien , Abidh Elisa , Schipman Julien , Tafflet Muriel , Deschamps Thibault , Maillet Hervé , Ovigneur Hervé , Desgorces François-Denis , Toussaint Jean-François 
Published: October 2012

ObjectiveTo analyse the physical fitness of a large sample of the French population across different ages.DesignObservational cross-sectional study.SettingData were collected from the Athletic Track and Field Federation, which organised events dedicated to measuring physical fitness. The events took place in 22 regions between 2006 and 2010.ParticipantsFrench volunteer citizens (N=31 349) aged between 4 and 80 years old who participated in events dedicated to measuring physical fitness.Primary and secondary outcome measuresWe assessed the results of the following fitness tests: 20 m shuttle run, standing broad jump, repeated squat jump, 4×10 m shuttle run, speed, flexibility and push-ups in relation to age and body mass index (BMI) using Spearman's rho, a one-way analysis of variance. A bi-exponential model was used to represent the performance with age.ResultsOur major results showed higher performances for men and for subjects with normal BMI at all age groups except for the flexibility test. BMI was strongly correlated across all ages with physical fitness p<0.0001. Furthermore, through bi-exponential model, a mean peak performance was identified at 26.32 years of age for men and 22.18 years of age for women.ConclusionsPhysical fitness assessment using a simple series of tests on the general population offers an important indicator of health status. The possibility of observing the evolution of fitness levels with time provides an important monitoring method from a public health perspective. Further research is needed to reinforce and evaluate the approach.
The effect of healthcare delivery privatisation on avoidable mortality: longitudinal cross-regional results from Italy, 1993–2003
Authors: Quercioli Cecilia , Messina Gabriele , Basu Sanjay , McKee Martin , Nante Nicola , Stuckler David 
Published: October 2012

BackgroundDuring the 1990s, Italy privatised a significant portion of its healthcare delivery. The authors compared the effectiveness of private and public sector healthcare delivery in reducing avoidable mortality (deaths that should not occur in the presence of effective medical care).MethodsThe authors calculated the average rate of change in age-standardised avoidable mortality rates in 19 of Italy's regions from 1993 to 2003. Multivariate regression models were used to analyse the relationship between rates of change in avoidable mortality and levels of spending on public versus private healthcare delivery, controlling for potential demographic and economic confounders.ResultsGreater spending on public delivery of health services corresponded to faster reductions in avoidable mortality rates. Each €100 additional public spending per capita on NHS delivery was independently associated with a 1.47% reduction in the rate of avoidable mortality (p=0.003). In contrast, spending on private sector services had no statistically significant effect on avoidable mortality rates (p=0.557). A higher percentage of spending on private sector delivery was associated with higher rates of avoidable mortality (p=0.002). The authors found that neither public nor private sector delivery spending was significantly associated with non-avoidable mortality rates, plausibly because non-avoidable mortality is insensitive to healthcare services.ConclusionPublic spending was significantly associated with reductions in avoidable mortality rates over time, while greater private sector spending was not at the regional level in Italy.
Cancer-Associated Fibroblasts Drive the Progression of Metastasis through both Paracrine and Mechanical Pressure on Cancer Tissue
Authors: Karagiannis George S. , Poutahidis Theofilos , Erdman Susan E. , Kirsch Richard , Riddell Robert H. , Diamandis Eleftherios P. 
Published: October 2012

Abstract
Neoplastic cells recruit fibroblasts through various growth factors and cytokines. These “cancer-associated fibroblasts” (CAF) actively interact with neoplastic cells and form a myofibroblastic microenvironment that promotes cancer growth and survival and supports malignancy. Several products of their paracrine signaling repertoire have been recognized as tumor growth and metastasis regulators. However, tumor-promoting cell signaling is not the only reason that makes CAFs key components of the “tumor microenvironment,” as CAFs affect both the architecture and growth mechanics of the developing tumor. CAFs participate in the remodeling of peritumoral stroma, which is a prerequisite of neoplastic cell invasion, expansion, and metastasis. CAFs are not present peritumorally as individual cells but they act orchestrated to fully deploy a desmoplastic program, characterized by “syncytial” (or collective) configuration and altered cell adhesion properties. Such myofibroblastic cohorts are reminiscent of those encountered in wound-healing processes. The view of “cancer as a wound that does not heal” led to useful comparisons between wound healing and tumorigenesis and expanded our knowledge of the role of CAF cohorts in cancer. In this integrative model of cancer invasion and metastasis, we propose that the CAF-supported microenvironment has a dual tumor-promoting role. Not only does it provide essential signals for cancer cell dedifferentiation, proliferation, and survival but it also facilitates cancer cell local invasion and metastatic phenomena. Mol Cancer Res; 10(11); 1403–18. ©2012 AACR.
Planning estimates for the provision of core mental health services in Queensland 2007 to 2017
Authors: Harris Meredith G , Buckingham William J , Pirkis Jane , Groves Aaron , Whiteford Harvey 
Published: October 2012

Objective: To derive planning estimates for the provision of public mental health services in Queensland 2007–2017. Method: We used a five-step approach that involved: (i) estimating the prevalence and severity of mental disorders in Queensland, and the number of people at each level of severity treated by health services; (ii) benchmarking the level and mix of specialised mental health services in Queensland against national data; (iii) examining 5-year trends in Queensland public sector mental health service utilisation; (iv) reviewing Australian and international planning benchmarks; and (v) setting resource targets based on the results of the preceding four steps. Best available evidence was used where possible, supplemented by value judgements as required. Results: Recommended resource targets for inpatient service were: 20 acute beds per 100,000 population, consistent with national average service provision but 13% above Queensland provision in 2005; and 10 non-acute beds per 100,000, 65% below Queensland levels in 2005. Growth in service provision was recommended for all other components. Adult residential rehabilitation service targets were 10 clinical 24-hour staffed beds per 100,000, and 18 non-clinical beds per 100,000. Supported accommodation targets were 35 beds per 100,000 in supervised hostels and 35 places per 100,000 in supported public housing. A direct care clinical workforce of 70 FTE per 100,000 for ambulatory care services was recommended. Fifteen per cent of total mental health funding was recommended for community support services provided by non-government organisations. Conclusions: The recommended targets pointed to specific areas for priority in Queensland, notably the need for additional acute inpatient services for older persons and expansion of clinical ambulatory care, residential rehabilitation and supported accommodation services. The development of nationally agreed planning targets for public mental health services and the mental health community support sector were identified as priorities.
Choosing Colors for Map Display Icons Using Models of Visual Search
Authors: Shive Joshua , Francis Gregory 
Published: October 2012

Objective: We show how to choose colors for icons on maps to minimize search time using predictions of a model of visual search. Background: The model analyzes digital images of a search target (an icon on a map) and a search display (the map containing the icon) and predicts search time as a function of target-distractor color distinctiveness and target eccentricity. Method: We parameterized the model using data from a visual search task and performed a series of optimization tasks to test the model’s ability to choose colors for icons to minimize search time across icons. Map display designs made by this procedure were tested experimentally. In a follow-up experiment, we examined the model’s flexibility to assign colors in novel search situations. Results: The model fits human performance, performs well on the optimization tasks, and can choose colors for icons on maps with novel stimuli to minimize search time without requiring additional model parameter fitting. Conclusion: Models of visual search can suggest color choices that produce search time reductions for display icons. Application: Designers should consider constructing visual search models as a low-cost method of evaluating color assignments.
The Impact of Transfer Setup on the Performance of Independent Wheelchair Transfers
Authors: Toro Maria Luisa , Koontz Alicia M. , Cooper Rory A. 
Published: October 2012

Objective: The aim of this study was to determine how selected environmental factors affect transfers and to compare our results to the Americans with Disabilities Act Accessibility Guidelines (ADAAG). Background: Few data are available to support standards development related to transfers in the built environment. Method: Participants were 120 wheeled mobility device (WMD) users who transferred to and from a modular transfer station that consisted of a height-adjustable platform with a lateral grab bar, optional obstacle to the transfer, and an optional height-adjustable front grab bar. Maximum and minimum vertical heights of the transfer surface, maximum gap distance between the WMD and transfer surface, grab bar use, and WMD space needs were recorded. Results: The 95th percentile lowest and highest heights attained were similar to the median WMD seat-to-floor height (56 cm). We found that 42% (47/113) could not perform a transfer with the obstacle present. Participants transferred higher when the front grab bar was added to the setup ( p = .005) and higher and lower with the front grab bar than without it when the obstacle was present in the setup ( p = .003 and p = .005, respectively). We found that 95% of participants performed a transfer across an 8.9-cm gap. ADAAG recommendations fall short for the height and clear-space needs of the 50th-percentile WMD users. Conclusion: Revisions concerning transfer heights, gaps, clear spaces, and grab bar heights are necessary to make transfers more accessible to WMD users. Application: The data will be used to revise the guidelines related to transfers and to enable designers and engineers to create an environment that is more accessible.