bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a soft tissue filler by ex vivo confocal microscopy and Raman spectroscopy in a case of adverse reaction to the filler
Authors: Cinotti E. , Perrot J. L. , Labeille B. , Boukenter A. , Ouerdane Y. , Cosmo P. , Douchet C. , Grivet D. , Cambazard F. 
Published: July 2014

BackgroundSoft tissue fillers are usually identified in the skin using the conventional histopathologic examination. Ex vivo RCM has been used in one case and Raman spectroscopy (RS), which has been recently applied for the identification of skin foreign bodies, has never been employed for fillers. We report the use of both these new techniques, ex vivo RCM and RS, to confirm the diagnosis of adverse reaction to a soft tissue filler and to identify its composition.MethodsWe excised a skin nodule suspicious of adverse reaction to soft tissue filler, and we performed an ex vivo reflectance confocal microscopy (RCM) and an histopathologic examination, followed by a RS analysis.ResultsEx vivo RCM showed numerous hypo‐reflective microspheres in the dermis that corresponded to rounded vacuoles at histopathologic examination, suggestive of polymethylmethacrylate (PMMA). RS showed a series of peaks at 600, 813, 970 1252, 1450, 1728, and 2951 cm−1 in correspondence to the microspheres, confirming the presence of PMMA.ConclusionThese results suggest that ex vivo RCM and RS are additional tools to conventional histopathologic examination to characterize soft tissue fillers in case of adverse reaction. RCM has the advantage compared with the histopathologic examination that can be extemporaneously performed on a fresh surgical specimen. RS allow a precise chemical identification of the filler.
Acute UVB‐induced epidermal changes assessed by multiphoton laser tomography
Authors: Koehler M. J. , Kellner K. , Hipler U.‐C. , Kaatz M. 
Published: July 2014

BackgroundIn vivo multiphoton tomography (MPT) of human skin has become a valuable tool for non‐invasive examination of morphological and biophysical skin properties and their alterations. So far, skin changes after UVB irradiation were mainly evaluated clinically and histologically. The present study aimed at non‐invasive imaging of histological changes during acute UVB irradiation by multiphoton laser tomography.MethodsIn 10 volunteers, five areas were irradiated once with an erythematous UVB dose. Multiphoton measurements were performed four times, i.e. before irradiation (baseline), and 24, 48 and 72 h after irradiation, respectively. The data were evaluated for changes of epidermal pleomorphy, spongiosis, pigmentation and thickness.ResultsThe four parameters were altered significantly by acute UVB irradiation, i.e. epidermal pleomorphy, spongiosis, pigmentation and thickness increased within 72 h after irradiation.ConclusionThus, the study has shown that typical epidermal changes induced by acute UVB irradiation can be evaluated by MPT.
Endoplasmic reticulum aminopeptidase 1 function and its pathogenic role in regulating innate and adaptive immunity in cancer and major histocompatibility complex class I‐associated autoimmune diseases
Authors: Fruci D. , Romania P. , D'Alicandro V. , Locatelli F. 
Published: July 2014

AbstractMajor histocompatibility complex (MHC) class I molecules present antigenic peptides on the cell surface to alert natural killer (NK) cells and CD8+ T cells for the presence of abnormal intracellular events, such as virus infection or malignant transformation. The generation of antigenic peptides is a multistep process that ends with the trimming of N‐terminal extensions in the endoplasmic reticulum (ER) by aminopeptidases ERAP1 and ERAP2. Recent studies have highlighted the potential role of ERAP1 in reprogramming the immunogenicity of tumor cells in order to elicit innate and adaptive antitumor immune responses, and in conferring susceptibility to autoimmune diseases in predisposed individuals. In this review, we will provide an overview of the current knowledge about the role of ERAP1 in MHC class I antigen processing and how its manipulation may constitute a promising tool for cancer immunotherapy and treatment of MHC class I‐associated autoimmune diseases.
The origin of Lake Cheko and the 1908 Tunguska Event recorded by forest trees
Authors: Gasperini Luca , Stanghellini Carlo , Serra Romano 
Published: July 2014

AbstractSeveral lines of evidence indicate that Cheko, a small lake close to the epicentre of the 1908 Tunguska Event (TE), fills a crater left behind by a fragment of the Tunguska Cosmic Body that impacted the ground downrange of the main explosion. It is thought that over 80 million trees were flattened or burnt as a consequence of the TE. However, a small number of trees in the devastated area survived the explosion and recorded in their growth‐ring patterns the environmental changes that followed this event. Some of those trees were found around Lake Cheko, ~10 km NW of the inferred TE epicentre. We analysed new data from the floor of Lake Cheko, including seismic‐reflection profiles, side‐scan sonar and video images, as well as dendrochronological evidence in tree samples collected along the shores, to test the hypothesis of a 1908 formation of the lake.
The condensin complexes play distinct roles to ensure normal chromosome morphogenesis during meiotic division in Arabidopsis
Authors: Smith Sarah J. , Osman Kim , Franklin F. Christopher H. 
Published: July 2014

SummaryMeiosis is a specialized cell division essential for sexual reproduction. During meiosis the chromosomes are highly organized, and correct chromosome architecture is required for faithful segregation of chromosomes at anaphase I and II. Condensin is involved in chromosome organization during meiotic and mitotic cell divisions. Three condensin subunits, AtSMC4 and the condensin I and II specific subunits AtCAP‐D2 and AtCAP‐D3, respectively, have been studied for their role in meiosis. This has revealed that both the condensin I and condensin II complexes are required to maintain normal structural integrity of the meiotic chromosomes during the two nuclear divisions. Their roles appear functionally distinct in that condensin I is required to maintain normal compaction of the centromeric repeats and 45S rDNA, whereas loss of condensin II was associated with extensive interchromosome connections at metaphase I. Depletion of condensin is also associated with a slight reduction in crossover formation, suggesting a role during meiotic prophase I.
A 3D MR‐acquisition scheme for nonrigid bulk motion correction in simultaneous PET‐MR
Authors: Kolbitsch Christoph , Prieto Claudia , Tsoumpas Charalampos , Schaeffter Tobias 
Published: July 2014

Purpose:Positron emission tomography (PET) is a highly sensitive medical imaging technique commonly used to detect and assess tumor lesions. Magnetic resonance imaging (MRI) provides high resolution anatomical images with different contrasts and a range of additional information important for cancer diagnosis. Recently, simultaneous PET‐MR systems have been released with the promise to provide complementary information from both modalities in a single examination. Due to long scan times, subject nonrigid bulk motion, i.e., changes of the patient's position on the scanner table leading to nonrigid changes of the patient's anatomy, during data acquisition can negatively impair image quality and tracer uptake quantification. A 3D MR‐acquisition scheme is proposed to detect and correct for nonrigid bulk motion in simultaneously acquired PET‐MR data.Methods:A respiratory navigated three dimensional (3D) MR‐acquisition with Radial Phase Encoding (RPE) is used to obtain T1‐ and T2‐weighted data with an isotropic resolution of 1.5 mm. Healthy volunteers are asked to move the abdomen two to three times during data acquisition resulting in overall 19 movements at arbitrary time points. The acquisition scheme is used to retrospectively reconstruct dynamic 3D MR images with different temporal resolutions. Nonrigid bulk motion is detected and corrected in this image data. A simultaneous PET acquisition is simulated and the effect of motion correction is assessed on image quality and standardized uptake values (SUV) for lesions with different diameters.Results:Six respiratory gated 3D data sets with T1‐ and T2‐weighted contrast have been obtained in healthy volunteers. All bulk motion shifts have successfully been detected and motion fields describing the transformation between the different motion states could be obtained with an accuracy of 1.71 ± 0.29 mm. The PET simulation showed errors of up to 67% in measured SUV due to bulk motion which could be reduced to less than 10% with the proposed motion compensation approach.Conclusions:A MR acquisition scheme which yields both high resolution 3D anatomical data and highly accurate nonrigid motion information without an increase in scan time is presented. The proposed method leads to a strong improvement in both MR and PET image quality and ensures an accurate assessment of tracer uptake.
Dose‐to‐water conversion for the backscatter‐shielded EPID: A frame‐based method to correct for EPID energy response to MLC transmitted radiation
Authors: Zwan Benjamin J. , King Brian W. , O'Connor Daryl J. , Greer Peter B. 
Published: July 2014

Purpose:To develop a frame‐by‐frame correction for the energy response of amorphous silicon electronic portal imaging devices (a‐Si EPIDs) to radiation that has transmitted through the multileaf collimator (MLC) and to integrate this correction into the backscatter shielded EPID (BSS‐EPID) dose‐to‐water conversion model.Methods:Individual EPID frames were acquired using a Varian frame grabber and iTools acquisition software then processed using in‐house software developed inMATLAB. For each EPID image frame, the region below the MLC leaves was identified and all pixels in this region were multiplied by a factor of 1.3 to correct for the under‐response of the imager to MLC transmitted radiation. The corrected frames were then summed to form a corrected integrated EPID image. This correction was implemented as an initial step in the BSS‐EPID dose‐to‐water conversion model which was then used to compute dose planes in a water phantom for 35 IMRT fields. The calculated dose planes, with and without the proposed MLC transmission correction, were compared to measurements in solid water using a two‐dimensional diode array.Results:It was observed that the integration of the MLC transmission correction into the BSS‐EPID dose model improved agreement between modeled and measured dose planes. In particular, the MLC correction produced higher pass rates for almost all Head and Neck fields tested, yielding an average pass rate of 99.8% for 2%/2 mm criteria. A two‐sample independentt‐test and fisher F‐test were used to show that the MLC transmission correction resulted in a statistically significant reduction in the mean and the standard deviation of the gamma values, respectively, to give a more accurate and consistent dose‐to‐water conversion.Conclusions:The frame‐by‐frame MLC transmission response correction was shown to improve the accuracy and reduce the variability of the BSS‐EPID dose‐to‐water conversion model. The correction may be applied as a preprocessing step in any pretreatment portal dosimetry calculation and has been shown to be beneficial for highly modulated IMRT fields.
Germination of Aspergillus niger Conidia Is Triggered by Nitrogen Compounds Related to
l
-Amino Acids
Authors: Hayer Kimran , Stratford Malcolm , Archer David B. 
Published: July 2014

ABSTRACT

Conidial germination is fundamentally important to the growth and dissemination of most fungi. It has been previously shown (K. Hayer, M. Stratford, and D. B. Archer, Appl. Environ. Microbiol. 79:6924–6931, 2013,
http://dx.doi.org/10.1128/AEM.02061-13
), using sugar analogs, that germination is a 2-stage process involving triggering of germination and then nutrient uptake for hyphal outgrowth. In the present study, we tested this 2-stage germination process using a series of nitrogen-containing compounds for the ability to trigger the breaking of dormancy of
Aspergillus niger
conidia and then to support the formation of hyphae by acting as nitrogen sources. Triggering and germination were also compared between
A. niger
and
Aspergillus nidulans
using 2-deoxy-
d
-glucose (trigger),
d
-galactose (nontrigger in
A. niger
but trigger in
A. nidulans
), and an N source (required in
A. niger
but not in
A. nidulans
). Although most of the nitrogen compounds studied served as nitrogen sources for growth, only some nitrogen compounds could trigger germination of
A. niger
conidia, and all were related to
l
-amino acids. Using
l
-amino acid analogs without either the amine or the carboxylic acid group revealed that both the amine and carboxylic acid groups were essential for an
l
-amino acid to serve as a trigger molecule. Generally, conidia were able to sense and recognize nitrogen compounds that fitted into a specific size range. There was no evidence of uptake of either triggering or nontriggering compounds over the first 90 min of
A. niger
conidial germination, suggesting that the germination trigger sensors are not located within the spore.
Functional and Structural Responses of Hyporheic Biofilms to Varying Sources of Dissolved Organic Matter
Authors: Wagner Karoline , Bengtsson Mia M. , Besemer Katharina , Sieczko Anna , Burns Nancy R. , Herberg Erik R. , Battin Tom J. 
Published: July 2014

ABSTRACT

Headwater streams are tightly connected with the terrestrial milieu from which they receive deliveries of organic matter, often through the hyporheic zone, the transition between groundwater and streamwater. Dissolved organic matter (DOM) from terrestrial sources (that is, allochthonous) enters the hyporheic zone, where it may mix with DOM from
in situ
production (that is, autochthonous) and where most of the microbial activity takes place. Allochthonous DOM is typically considered resistant to microbial metabolism compared to autochthonous DOM. The composition and functioning of microbial biofilm communities in the hyporheic zone may therefore be controlled by the relative availability of allochthonous and autochthonous DOM, which can have implications for organic matter processing in stream ecosystems. Experimenting with hyporheic biofilms exposed to model allochthonous and autochthonous DOM and using 454 pyrosequencing of the 16S rRNA (targeting the “active” community composition) and of the 16S rRNA gene (targeting the “bulk” community composition), we found that allochthonous DOM may drive shifts in community composition whereas autochthonous DOM seems to affect community composition only transiently. Our results suggest that priority effects based on resource-driven stochasticity shape the community composition in the hyporheic zone. Furthermore, measurements of extracellular enzymatic activities suggest that the additions of allochthonous and autochthonous DOM had no clear effect on the function of the hyporheic biofilms, indicative of functional redundancy. Our findings unravel possible microbial mechanisms that underlie the buffering capacity of the hyporheic zone and that may confer stability to stream ecosystems.
Gammaproteobacterial Methanotrophs Dominate Cold Methane Seeps in Floodplains of West Siberian Rivers
Authors: Oshkin Igor Y. , Wegner Carl-Eric , Lüke Claudia , Glagolev Mikhail V. , Filippov Illiya V. , Pimenov Nikolay V. , Liesack Werner , Dedysh Svetlana N. 
Published: July 2014

ABSTRACT

A complex system of muddy fluid-discharging and methane (CH
4
)-releasing seeps was discovered in a valley of the river Mukhrinskaya, one of the small rivers of the Irtysh Basin, West Siberia. CH
4
flux from most (90%) of these gas ebullition sites did not exceed 1.45 g CH
4
h
−1
, while some seeps emitted up to 5.54 g CH
4
h
−1
. The δ
13
C value of methane released from these seeps varied between −71.1 and −71.3‰, suggesting its biogenic origin. Although the seeps were characterized by low
in situ
temperatures (3.5 to 5°C), relatively high rates of methane oxidation (15.5 to 15.9 nmol CH
4
ml
−1
day
−1
) were measured in mud samples. Fluorescence
in situ
hybridization detected 10
7
methanotrophic bacteria (MB) per g of mud (dry weight), which accounted for up to 20.5% of total bacterial cell counts. Most (95.8 to 99.3%) methanotroph cells were type I (gammaproteobacterial) MB. The diversity of methanotrophs in this habitat was further assessed by pyrosequencing of
pmoA
genes, encoding particulate methane monooxygenase. A total of 53,828
pmoA
gene sequences of seep-inhabiting methanotrophs were retrieved and analyzed. Nearly all of these sequences affiliated with type I MB, including the
Methylobacter-Methylovulum-Methylosoma
group, lake cluster 2, and several as-yet-uncharacterized methanotroph clades. Apparently, microbial communities attenuating methane fluxes from these local but strong CH
4
sources in floodplains of high-latitude rivers have a large proportion of potentially novel, psychrotolerant methanotrophs, thereby providing a challenge for future isolation studies.
A Desaturase Gene Involved in the Formation of 1,14-Nonadecadiene in Synechococcus sp. Strain PCC 7002
Authors: Mendez-Perez Daniel , Herman Nicolaus A. , Pfleger Brian F. 
Published: July 2014

ABSTRACT

The marine cyanobacterium
Synechococcus
sp. strain PCC 7002 synthesizes two alkenes, 1-nonadecene and 1,14-nonadecadiene. Whereas the genetic basis for the biosynthesis of the terminal double bond in both alkenes has been characterized, the origin of the internal double bond in 1,14-nonadecadiene has not. In this study, we demonstrate that a gene encoding an uncharacterized desaturase is involved in the formation of the internal double bond of 1,14-nonadecadiene. Further, at low temperatures, the desaturase gene is essential for growth, and in wild-type cells the levels of 1,14-nonadecadiene increase relative to that of cells grown at 38°C. These data suggest that 1,14-nonadecadiene plays a role in responding to cold stress.
Screening of a Leptospira biflexa Mutant Library To Identify Genes Involved in Ethidium Bromide Tolerance
Authors: Pětrošová Helena , Picardeau Mathieu 
Published: July 2014

ABSTRACT

Leptospira
spp. are spirochete bacteria comprising both pathogenic and free-living species. The saprophyte
L. biflexa
is a model bacterium for studying leptospiral biology due to relative ease of culturing and genetic manipulation. In this study, we constructed a library of 4,996 random transposon mutants in
L. biflexa
. We screened the library for increased susceptibility to the DNA intercalating agent, ethidium bromide (EtBr), in order to identify genetic determinants that reduce
L. biflexa
susceptibility to antimicrobial agents. By phenotypic screening, using subinhibitory EtBr concentrations, we identified 29 genes that, when disrupted via transposon insertion, led to increased sensitivity of the bacteria to EtBr. At the functional level, these genes could be categorized by function as follows: regulation and signaling (
n
= 11), transport (
n
= 6), membrane structure (
n
= 5), stress response (
n
= 2), DNA damage repair (
n
= 1), and other processes (
n
= 3), while 1 gene had no predicted function. Genes involved in transport (including efflux pumps) and regulation (two-component systems, anti-sigma factor antagonists, etc.) were overrepresented, demonstrating that these genes are major contributors to EtBr tolerance. This finding suggests that transport genes which would prevent EtBr to enter the cell cytoplasm are critical for EtBr resistance. We identified genes required for the growth of
L. biflexa
in the presence of sublethal EtBr concentration and characterized their potential as antibiotic resistance determinants. This study will help to delineate mechanisms of adaptation to toxic compounds, as well as potential mechanisms of antibiotic resistance development in pathogenic
L. interrogans
.
Microbial Community Stratification Controlled by the Subseafloor Fluid Flow and Geothermal Gradient at the Iheya North Hydrothermal Field in the Mid-Okinawa Trough (Integrated Ocean Drilling Program Expedition 331)
Authors: Yanagawa Katsunori , Breuker Anja , Schippers Axel , Nishizawa Manabu , Ijiri Akira , Hirai Miho , Takaki Yoshihiro , Sunamura Michinari , Urabe Tetsuro , Nunoura Takuro , Takai Ken 
Published: July 2014

ABSTRACT

The impacts of lithologic structure and geothermal gradient on subseafloor microbial communities were investigated at a marginal site of the Iheya North hydrothermal field in the Mid-Okinawa Trough. Subsurface marine sediments composed of hemipelagic muds and volcaniclastic deposits were recovered through a depth of 151 m below the seafloor at site C0017 during Integrated Ocean Drilling Program Expedition 331. Microbial communities inferred from 16S rRNA gene clone sequencing in low-temperature hemipelagic sediments were mainly composed of members of the
Chloroflexi
and deep-sea archaeal group. In contrast, 16S rRNA gene sequences of marine group I
Thaumarchaeota
dominated the microbial phylotype communities in the coarse-grained pumiceous gravels interbedded between the hemipelagic sediments. Based on the physical properties of sediments such as temperature and permeability, the porewater chemistry, and the microbial phylotype compositions, the shift in the physical properties of the sediments is suggested to induce a potential subseafloor recharging flow of oxygenated seawater in the permeable zone, leading to the generation of variable chemical environments and microbial communities in the subseafloor habitats. In addition, the deepest section of sediments under high-temperature conditions (∼90°C) harbored the sequences of an uncultivated archaeal lineage of hot water crenarchaeotic group IV that may be associated with the high-temperature hydrothermal fluid flow. These results indicate that the subseafloor microbial community compositions and functions at the marginal site of the hydrothermal field are highly affected by the complex fluid flow structure, such as recharging seawater and underlying hydrothermal fluids, coupled with the lithologic transition of sediments.
FLP-FRT-Based Method To Obtain Unmarked Deletions of
CHU
_
3237
(
porU
) and Large Genomic Fragments of Cytophaga hutchinsonii
Authors: Wang Ying , Wang Zhiquan , Cao Jing , Guan Zhiwei , Lu Xuemei 
Published: July 2014

ABSTRACT

Cytophaga hutchinsonii
is a widely distributed cellulolytic bacterium in the phylum
Bacteroidetes
. It can digest crystalline cellulose rapidly without free cellulases or cellulosomes. The mechanism of its cellulose utilization remains a mystery. We developed an efficient method based on a linear DNA double-crossover and FLP-FRT recombination system to obtain unmarked deletions of both single genes and large genomic fragments in
C. hutchinsonii
. Unmarked deletion of
CHU
_
3237
(
porU
), an ortholog of the C-terminal signal peptidase of a type IX secretion system (T9SS), resulted in defects in colony spreading, cellulose degradation, and protein secretion, indicating that it is a component of the T9SS and that T9SS plays an important role in cellulose degradation by
C. hutchinsonii
. Furthermore, deletions of four large genomic fragments were obtained using our method, and the sizes of the excised fragments varied from 9 to 19 kb, spanning from 6 to 22 genes. The customized FLP-FRT method provides an efficient tool for more rapid progress in the cellulose degradation mechanism and other physiological aspects of
C. hutchinsonii
.