bluuebunny/crossref_metadata_2025_split huggingface dataset:
Standardization of skin cleansing in vivo: part I. Development of an Automated Cleansing Device (ACiD)
Authors: Sonsmann F. K. , Strunk M. , Gediga K. , John C. , Schliemann S. , Seyfarth F. , Elsner P. , Diepgen T. L. , Kutz G. , John S. M. 
Published: October 2013

BackgroundTo date, there are no legally binding requirements concerning product testing in cosmetics. This leads to various manufacturer‐specific test methods and absent transparent information on skin cleansing products. A standardized in vivo test procedure for assessment of cleansing efficacy and corresponding barrier impairment by the cleaning process is needed, especially in the occupational context where repeated hand washing procedures may be performed at short intervals.MethodsFor the standardization of the cleansing procedure, an Automated Cleansing Device (ACiD) was designed and evaluated. Different smooth washing surfaces of the equipment for ACiD (incl. goat hair, felt, felt covered with nitrile caps) were evaluated regarding their skin compatibility.ResultsACiD allows an automated, fully standardized skin washing procedure. Felt covered with nitrile as washing surface of the rotating washing units leads to a homogenous cleansing result and does not cause detectable skin irritation, neither clinically nor as assessed by skin bioengineering methods (transepidermal water loss, chromametry).ConclusionsAutomated Cleansing Device may be useful for standardized evaluation of the cleansing effectiveness and parallel assessment of the corresponding irritancy potential of industrial skin cleansers. This will allow objectifying efficacy and safety of industrial skin cleansers, thus enabling market transparency and facilitating rational choice of products.
Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis
Authors: Narsai Reena , Devenish James , Castleden Ian , Narsai Kabir , Xu Lin , Shou Huixia , Whelan James 
Published: October 2013

SummaryOmics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or ‘expressology’, thus using and combining available information from two pre‐eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large‐scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au).
Exogenously applied muscle metabolites synergistically evoke sensations of muscle fatigue and pain in human subjects
Authors: Pollak Kelly A. , Swenson Jeffrey D. , Vanhaitsma Timothy A. , Hughen Ronald W. , Jo Daehyun , Light Kathleen C. , Schweinhardt Petra , Amann Markus , Light Alan R. 
Published: October 2013

New Findings
What is the central question of this study?
Can physiological concentrations of metabolite combinations evoke sensations of fatigue and pain when injected into skeletal muscle? If so, what sensations are evoked?
What is the main finding and its importance?
Low concentrations of protons, lactate and ATP evoked sensations related to fatigue. Higher concentrations of these metabolites evoked pain. Single metabolites evoked no sensations. This suggests that the combination of an ASIC receptor and a purinergic P2X receptor is required for signalling fatigue and pain. The results also suggest that two types of sensory neurons encode metabolites; one detects low concentrations of metabolites and signals sensations of fatigue, whereas the other detects higher levels of metabolites and signals ache and hot.
The perception of fatigue is common in many disease states; however, the mechanisms of sensory muscle fatigue are not understood. In mice, rats and cats, muscle afferents signal metabolite production in skeletal muscle using a complex of ASIC, P2X and TRPV1 receptors. Endogenous muscle agonists for these receptors are combinations of protons, lactate and ATP. Here we applied physiological concentrations of these agonists to muscle interstitium in human subjects to determine whether this combination could activate sensations and, if so, to determine how the subjects described these sensations. Ten volunteers received infusions (0.2 ml over 30 s) containing protons, lactate and ATP under the fascia of a thumb muscle, abductor pollicis brevis. Infusion of individual metabolites at maximal amounts evoked no fatigue or pain. Metabolite combinations found in resting muscles (pH 7.4 + 300 nm ATP + 1 mm lactate) also evoked no sensation. The infusion of a metabolite combination found in muscle during moderate endurance exercise (pH 7.3 + 400 nm ATP + 5 mm lactate) produced significant fatigue sensations. Infusion of a metabolite combination associated with vigorous exercise (pH 7.2 + 500 nm ATP + 10 mm lactate) produced stronger sensations of fatigue and some ache. Higher levels of metabolites (as found with ischaemic exercise) caused more ache but no additional fatigue sensation. Thus, in a dose‐dependent manner, intramuscular infusion of combinations of protons, lactate and ATP leads to fatigue sensation and eventually pain, probably through activation of ASIC, P2X and TRPV1 receptors. This is the first demonstration in humans that metabolites normally produced by exercise act in combination to activate sensory neurons that signal sensations of fatigue and muscle pain.
CONRAD—A software framework for cone‐beam imaging in radiology
Authors: Maier Andreas , Hofmann Hannes G. , Berger Martin , Fischer Peter , Schwemmer Chris , Wu Haibo , Müller Kerstin , Hornegger Joachim , Choi Jang‐Hwan , Riess Christian , Keil Andreas , Fahrig Rebecca 
Published: October 2013

Purpose:In the community of x‐ray imaging, there is a multitude of tools and applications that are used in scientific practice. Many of these tools are proprietary and can only be used within a certain lab. Often the same algorithm is implemented multiple times by different groups in order to enable comparison. In an effort to tackle this problem, the authors created CONRAD, a software framework that provides many of the tools that are required to simulate basic processes in x‐ray imaging and perform image reconstruction with consideration of nonlinear physical effects.Methods:CONRAD is a Java‐based state‐of‐the‐art software platform with extensive documentation. It is based on platform‐independent technologies. Special libraries offer access to hardware acceleration such as OpenCL. There is an easy‐to‐use interface for parallel processing. The software package includes different simulation tools that are able to generate up to 4D projection and volume data and respective vector motion fields. Well known reconstruction algorithms such as FBP, DBP, and ART are included. All algorithms in the package are referenced to a scientific source.Results:A total of 13 different phantoms and 30 processing steps have already been integrated into the platform at the time of writing. The platform comprises 74.000 nonblank lines of code out of which 19% are used for documentation. The software package is available for download athttp://conrad.stanford.edu. To demonstrate the use of the package, the authors reconstructed images from two different scanners, a table top system and a clinical C‐arm system. Runtimes were evaluated using the RabbitCT platform and demonstrate state‐of‐the‐art runtimes with 2.5 s for the 256 problem size and 12.4 s for the 512 problem size.Conclusions:As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and quantitative performance comparison between the methods of different groups.
Decay of Fecal Indicator Bacterial Populations and Bovine-Associated Source-Tracking Markers in Freshly Deposited Cow Pats
Authors: Oladeinde Adelumola , Bohrmann Thomas , Wong Kelvin , Purucker S. T. , Bradshaw Ken , Brown Reid , Snyder Blake , Molina Marirosa 
Published: October 2013

ABSTRACT

Understanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about their survival in intact cow pats deposited on pastures. We conducted a study to determine decay rates of fecal indicator bacteria (
Escherichia coli
and enterococci) and bovine-associated MST markers (CowM3, Rum-2-bac, and GenBac) in 18 freshly deposited cattle feces from three farms in northern Georgia. Samples were randomly assigned to shaded or unshaded treatment in order to determine the effects of sunlight, moisture, and temperature on decay rates. A general linear model (GLM) framework was used to determine decay rates. Shading significantly decreased the decay rate of the
E. coli
population (
P
< 0.0001), with a rate of −0.176 day
−1
for the shaded treatment and −0.297 day
−1
for the unshaded treatment. Shading had no significant effect on decay rates of enterococci, CowM3, Rum-2-bac, and GenBac (
P
> 0.05). In addition,
E. coli
populations showed a significant growth rate (0.881 day
−1
) in the unshaded samples during the first 5 days after deposition. UV-B was the most important parameter explaining the decay rate of
E. coli
populations. A comparison of the decay behaviors among all markers indicated that enterococcus concentrations exhibit a better correlation with the MST markers than
E. coli
concentrations. Our results indicate that bovine-associated MST markers can survive in cow pats for at least 1 month after excretion, and although their decay dynamic differs from the decay dynamic of
E. coli
populations, they seem to be reliable markers to use in combination with enterococci to monitor fecal pollution from pasture lands.
Extracellular Electron Transport-Mediated Fe(III) Reduction by a Community of Alkaliphilic Bacteria That Use Flavins as Electron Shuttles
Authors: Fuller Samuel J. , McMillan Duncan G. G. , Renz Marc B. , Schmidt Martin , Burke Ian T. , Stewart Douglas I. 
Published: October 2013

ABSTRACT

The biochemical and molecular mechanisms used by alkaliphilic bacterial communities to reduce metals in the environment are currently unknown. We demonstrate that an alkaliphilic (pH > 9) consortium dominated by
Tissierella
,
Clostridium
, and
Alkaliphilus
spp. is capable of using iron (Fe
3+
) as a final electron acceptor under anaerobic conditions. Iron reduction is associated with the production of a freely diffusible species that, upon rudimentary purification and subsequent spectroscopic, high-performance liquid chromatography, and electrochemical analysis, has been identified as a flavin species displaying properties indistinguishable from those of riboflavin. Due to the link between iron reduction and the onset of flavin production, it is likely that riboflavin has an import role in extracellular metal reduction by this alkaliphilic community.
Single-Cell Analyses Revealed Transfer Ranges of IncP-1, IncP-7, and IncP-9 Plasmids in a Soil Bacterial Community
Authors: Shintani Masaki , Matsui Kazuhiro , Inoue Jun-ichi , Hosoyama Akira , Ohji Shoko , Yamazoe Atsushi , Nojiri Hideaki , Kimbara Kazuhide , Ohkuma Moriya 
Published: October 2013

ABSTRACT

The conjugative transfer ranges of three different plasmids of the incompatibility groups IncP-1 (pBP136), IncP-7 (pCAR1), and IncP-9 (NAH7) were investigated in soil bacterial communities by culture-dependent and culture-independent methods.
Pseudomonas putida
, a donor of each plasmid, was mated with soil bacteria, and green fluorescent protein (GFP), encoded on the plasmid, was used as a reporter protein for successful transfer. GFP-expressing transconjugants were detected and separated at the single-cell level by flow cytometry. Each cell was then analyzed by PCR and sequencing of its 16S rRNA gene following either whole-genome amplification or cultivation. A large number of bacteria within the phylum
Proteobacteria
was identified as transconjugants for pBP136 by both culture-dependent and culture-independent methods. Transconjugants belonging to the phyla
Actinobacteria
,
Bacteroidetes
, and
Firmicutes
were detected only by the culture-independent method. Members of the genus
Pseudomonas
(class
Gammaproteobacteria
) were identified as major transconjugants of pCAR1 and NAH7 by both methods, whereas
Delftia
species (class
Betaproteobacteria
) were detected only by the culture-independent method. The transconjugants represented a minority of the soil bacteria. Although pCAR1-containing
Delftia
strains could not be cultivated after a one-to-one filter mating assay between the donor and cultivable
Delftia
strains as recipients, fluorescence
in situ
hybridization detected pCAR1-containing
Delftia
cells, suggesting that
Delftia
was a “transient” host of pCAR1.
Transferable Denitrification Capability of Thermus thermophilus
Authors: Alvarez Laura , Bricio Carlos , Blesa Alba , Hidalgo Aurelio , Berenguer José 
Published: October 2013

ABSTRACT

Laboratory-adapted strains of
Thermus
spp. have been shown to require oxygen for growth, including the model strains
T. thermophilus
HB27 and HB8. In contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. The use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. In this process, nitrate is reduced to nitrite by a reductase (Nar) that also functions as electron transporter toward nitrite and nitric oxide reductases when nitrate is scarce, effectively replacing respiratory complex III. In many
T. thermophilus
denitrificant strains, most electrons for Nar are provided by a new class of NADH dehydrogenase (Nrc). The ability to reduce nitrite to NO and subsequently to N
2
O by the corresponding Nir and Nor reductases is also strain specific. The genes encoding the capabilities for nitrate (
nar
) and nitrite (
nir
and
nor
) respiration are easily transferred between
T. thermophilus
strains by natural competence or by a conjugation-like process and may be easily lost upon continuous growth under aerobic conditions. The reason for this instability is apparently related to the fact that these metabolic capabilities are encoded in gene cluster islands, which are delimited by insertion sequences and integrated within highly variable regions of easily transferable extrachromosomal elements. Together with the chromosomal genes, these plasmid-associated genetic islands constitute the extended pangenome of
T. thermophilus
that provides this species with an enhanced capability to adapt to changing environments.
Estimating the Prevalence of Potential Enteropathogenic Escherichia coli and Intimin Gene Diversity in a Human Community by Monitoring Sanitary Sewage
Authors: Yang Kun , Pagaling Eulyn , Yan Tao 
Published: October 2013

ABSTRACT

Presently, the understanding of bacterial enteric diseases in the community and their virulence factors relies almost exclusively on clinical disease reporting and examination of clinical pathogen isolates. This study aimed to investigate the feasibility of an alternative approach that monitors potential enteropathogenic
Escherichia coli
(EPEC) and enterohemorrhagic
E. coli
(EHEC) prevalence and intimin gene (
eae
) diversity in a community by directly quantifying and characterizing target virulence genes in the sanitary sewage. The quantitative PCR (qPCR) quantification of the
eae
,
stx
1
, and
stx
2
genes in sanitary sewage samples collected over a 13-month period detected
eae
in all 13 monthly sewage samples at significantly higher abundance (93 to 7,240 calibrator cell equivalents [CCE]/100 ml) than
stx
1
and
stx
2
, which were detected sporadically. The prevalence level of potential EPEC in the sanitary sewage was estimated by calculating the ratio of
eae
to
uidA
, which averaged 1.0% (σ = 0.4%) over the 13-month period. Cloning and sequencing of the
eae
gene directly from the sewage samples covered the majority of the
eae
diversity in the sewage and detected 17 unique
eae
alleles belonging to 14 subtypes. Among them,
eae
-β2 was identified to be the most prevalent subtype in the sewage, with the highest detection frequency in the clone libraries (41.2%) and within the different sampling months (85.7%). Additionally, sewage and environmental
E. coli
isolates were also obtained and used to determine the detection frequencies of the virulence genes as well as
eae
genetic diversity for comparison.
Evaluating Gulls as Potential Vehicles of Salmonella enterica Serotype Newport (JJPX01.0061) Contamination of Tomatoes Grown on the Eastern Shore of Virginia
Authors: Gruszynski Karen , Pao Steven , Kim Chyer , Toney Denise M. , Wright Kim , Colón Ana , Engelmeyer T. , Levine Seth J. 
Published: October 2013

ABSTRACT

Salmonella enterica
serovar Newport pattern JJPX01.0061 has been identified as causing several multistate outbreaks in the last 10 years, primarily due to contamination of tomatoes grown in Virginia. The goal of this study was to evaluate gulls as a potential vehicle of
S
. Newport pattern 61 contamination for tomatoes grown on the Eastern Shore of Virginia. Gull fecal samples were collected at four sites in eastern Virginia for 3 months (May to July) in 2012, resulting in 360 samples, among which
Salmonella
was isolated from 62 samples. Twenty-two serotypes and 26 pulsed-field gel electrophoresis DNA fingerprint patterns, including
S
. Newport pattern 61, were identified. All of the patterns that were isolated multiple times, with the exception of
S
. Newport patterns JJPX01.0030 and JJPX01.0061, were clustered in time and geographical location. These results strongly suggest that both patterns of
S
. Newport are endemic to sites on the Eastern Shore where gulls were sampled. This study provides additional information regarding the epidemiology of
S
. Newport pattern 61 in Virginia and how tomatoes sold interstate may become contaminated in the field.
The Ability of Bifidobacteria To Degrade Arabinoxylan Oligosaccharide Constituents and Derived Oligosaccharides Is Strain Dependent
Authors: Rivière Audrey , Moens Frédéric , Selak Marija , Maes Dominique , Weckx Stefan , De Vuyst Luc 
Published: October 2013

ABSTRACT
Arabinoxylan oligosaccharides (AXOS) are prebiotic carbohydrates with promising health-promoting properties that stimulate the activity of specific colon bacteria, in particular bifidobacteria. However, the mechanisms by which bifidobacterial strains break down these compounds in the colon is still unknown. This study investigates AXOS consumption of a large number of bifidobacterial strains (36), belonging to 11 different species, systematically. To determine their degradation mechanisms, all strains were grown on a mixture of arabinose and xylose, xylo-oligosaccharides, and complex AXOS molecules as the sole added energy sources. Based on principal component and cluster analyses of their different arabinose substituent and/or xylose backbone consumption patterns, five clusters that were species independent could be distinguished among the bifidobacterial strains tested. In parallel, the strains were screened for the presence of genes encoding several putative AXOS-degrading enzymes, but no clear-cut correlation could be made with the different degradation mechanisms. The intra- and interspecies differences in the consumption patterns of AXOS indicate that bifidobacterial strains could avoid competition among each other or even could cooperate jointly to degrade these complex prebiotics. The knowledge gained on the AXOS degradation mechanisms in bifidobacteria can be of importance in the rational design of prebiotics with tailor-made composition and thus increased specificity in the colon.
Host Specificity and Source of Enterocytozoon bieneusi Genotypes in a Drinking Source Watershed
Authors: Guo Yaqiong , Alderisio Kerri A. , Yang Wenli , Cama Vitaliano , Feng Yaoyu , Xiao Lihua 
Published: October 2013

ABSTRACT

To assess the host specificity of
Enterocytozoon bieneusi
and to track the sources of
E. bieneusi
contamination, we genotyped
E. bieneusi
in wildlife and stormwater from the watershed of New York City's source water, using ribosomal internal transcribed spacer (ITS)-based PCR and sequence analyses. A total of 255 specimens from 23 species of wild mammals and 67 samples from stormwater were analyzed. Seventy-four (29.0%) of the wildlife specimens and 39 (58.2%) of the stormwater samples from streams were PCR positive. Altogether, 20
E. bieneusi
genotypes were found, including 8 known genotypes and 12 new ones. Sixteen and five of the genotypes were seen in animals and stormwater from the watershed, respectively, with WL4 being the most common genotype in both animals (35 samples) and stormwater (23 samples). The 20
E. bieneusi
genotypes belonged to five genogroups (groups 1, 3, 4, and 7 and an outlier), with only 23/113 (20.4%)
E. bieneusi
-positive samples belonging to zoonotic genogroup 1 and 3/20 genotypes ever being detected in humans. The two genogroups previously considered host specific, groups 3 and 4, were both detected in multiple groups of mammals. Thus, with the exception of the type IV, Peru11, and D genotypes, which were detected in only 7, 5, and 2 animals, respectively, most
E. bieneusi
strains in most wildlife samples and all stormwater samples in the watershed had no known public health significance, as these types have not previously been detected in humans. The role of different species of wild mammals in the contribution of
E. bieneusi
contamination in stormwater was supported by determinations of host-adapted
Cryptosporidium
species/genotypes in the same water samples. Data from this study indicate that the host specificity of
E. bieneusi
group 3 is broader than originally thought, and wildlife is the main source of
E. bieneusi
in stormwater in the watershed.