bluuebunny/crossref_metadata_2025_split huggingface dataset:
A quantitative approach to fluvial facies models: Methods and example results
Authors: Colombera Luca , Mountney Nigel P. , McCaffrey William D. 
Published: August 2013

AbstractTraditional facies models lack quantitative information concerning sedimentological features: this significantly limits their value as references for comparison and guides to interpretation and subsurface prediction. This paper aims to demonstrate how a database methodology can be used to generate quantitative facies models for fluvial depositional systems. This approach is employed to generate a range of models, comprising sets of quantitative information on proportions, geometries, spatial relations and grain sizes of genetic units belonging to three different scales of observation (depositional elements, architectural elements and facies units). The method involves a sequential application of filters to the knowledge base that allows only database case studies that developed under appropriate boundary conditions to contribute to any particular model. Specific example facies models are presented for fluvial environmental types categorized on channel pattern, basin climatic regime and water‐discharge regime; the common adoption of these environmental types allows a straightforward comparison with existing qualitative models. The models presented here relate to: (i) the large‐scale architecture of single‐thread and braided river systems; (ii) meandering sub‐humid perennial systems; (iii) the intermediate‐scale and small‐scale architecture of dryland, braided ephemeral systems; (iv) the small‐scale architecture of sandy meandering systems; and (v) individual architectural features of a specific sedimentary environment (a terminal fluvial system) and its sub‐environments (architectural elements). Although the quantification of architectural properties represents the main advantage over qualitative facies models, other improvements include the capacity: (i) to model on different scales of interest; (ii) to categorize the model on a variety of environmental classes; (iii) to perform an objective synthesis of many real‐world case studies; (iv) to include variability‐related and knowledge‐related uncertainty in the model; and (v) to assess the role of preservation potential by comparing ancient‐system and modern‐system data input to the model.
Mapping sub‐pixel fluvial grain sizes with hyperspatial imagery
Authors: Black Martin , Carbonneau Patrice , Church Michael , Warburton Jeff 
Published: August 2013

AbstractThis study presents an investigation of image texture approaches for mapping sub‐pixel fluvial grain‐size features from airborne imagery, allowing for the rapid acquisition of surface sand and coarse fraction (>1·41 mm) grain‐size information. Imagery at 30 mm resolution was acquired over four gravel bars from the Fraser River (British Columbia, Canada). Combined first‐order and second‐order image texture approaches (windowed standard deviation filter and the grey level co‐occurrence matrix) were used. First‐order image texture, through the application of a standard deviation filter and subsequent thresholding was used to detect the presence of surface sand, with optimal accuracy achieved at 91 ± 1·9%. A wide‐ranging parameter space investigation was used to derive optimum parameters for the grey‐level co‐occurrence matrix. Subsequently first‐order and second‐order image textures were used in multiple linear regression to achieve good calibrations with several sub‐pixel grain‐size percentiles; relative error at 1·44%, 3·18%, 6·80% and 10·6% for D5, D16, D35 and D50, respectively. The larger percentiles of D84 and D95 had relative errors of 24·7% and 29·7%, respectively. The breakdown of calibration precision for larger percentiles is attributed to a ‘pixel averaging effect’. It is concluded that multispectral imagery is not required, because sufficient image texture information can be derived from standard colour imagery. Recommendations are suggested for the application of this method to other localities and data sets, thus reducing exhaustive parameter searches in future studies.
Can Psychosocial Intervention Improve Peer and Sibling Relations Among War‐affected Children? Impact and Mediating Analyses in a Randomized Controlled Trial
Authors: Diab Marwan , Punamäki Raija‐Leena , Palosaari Esa , Qouta Samir R. 
Published: August 2013

AbstractSocial resources are considered important protectors in traumatic conditions, but few studies have analyzed their role in psychosocial interventions among war‐affected children. We examined (1) whether a psychosocial intervention (teaching recovery techniques, TRT) is effective in improving peer and sibling relations, and (2) whether these potentially improved relations mediate the intervention's impacts on children's mental health. Participants were 428 Palestinian children [10–13 (mean = 11.29, standard deviation SD = .68)‐year‐old girls (49.4 percent) and boys (50.6 percent)], who were cluster‐randomized into the TRT and wait‐list control groups. They reported the quality of peer (friendship and loneliness) and sibling (intimacy, warmth, conflict, and rivalry) relations, and posttraumatic stress, depressive and psychological distress symptoms, as well as psychosocial well‐being at baseline (T1), postintervention (T2), and six month follow‐up (T3). Results showed gender‐specific TRT intervention effects: Loneliness in peer relations reduced among boys and sibling rivalry reduced among girls. The TRT prevented the increase in sibling conflict that happened in the control group. The mediating hypothesis was partially substantiated for improved peer relations, and beneficial changes in sibling relations were generally associated with improved mental health.
Frasnian–Famennian crisis in the Malaguide Complex (Betic Cordillera, Spain)
Authors: Rodríguez‐Cañero Rosario , Martín‐Algarra Agustín 
Published: August 2013

AbstractDevonian sediments of the Malaguide Complex potentially could include the Frasnian–Famennian boundary, one of the five greatest Phanerozoic biotic crises. Conodont biofacies and microfacies of carbonate clasts from a pebbly mudstone underlying Tournaisian radiolarites allows identification, for the first time in the Malaguide Complex, of Devonian shallow marine environments laterally grading to deeper realms. The clasts yielded Frasnian conodont associations of the falsiovalis to rhenana biozones, with six biofacies that reveal different environmental conditions in their source areas. Source sediments were dismantled and redeposited within the pebbly mudstone, whose origin is tentatively related to one of the events that are associated worldwide with the Frasnian–Famennian crisis. The latter is recorded, in two equivalent Malaguide pelagic successions, by stratigraphic discontinuities, and it was, probably, tectonically and/or eustatically controlled, as in other Alpine‐Mediterranean Paleotethyan margins.
Durability of healing from spray‐applied cell therapy with human allogeneic fibroblasts and keratinocytes for the treatment of chronic venous leg ulcers: A 6‐month follow‐up
Authors: Kirsner Robert S. , Marston William A. , Snyder Robert J. , Lee Tommy D. , Cargill D. Innes , Zhang Yuxin , Dickerson Jaime E. , Slade Herbert B. 
Published: August 2013

AbstractPatients who participated in a Phase 2 trial of HP802‐247 for venous leg ulcers were invited to participate in this 24‐week follow‐up study to assess the durability of healing, document additional ulcer closures, and evaluate posttreatment safety. Consent was given by 90% (206/228), with 80% (183/228) completing all visits. Blinding was retained from the previous trial in which subjects had been randomized to vehicle or one of four cell therapy regimens. Visits were every 8 weeks. Among the 183 subjects, 43% (21/49) previously treated with cells and entering follow‐up with an open wound achieved closure, compared with 35% (7/20) previously treated with vehicle, while 10% (11/106) and 17% (3/18), respectively, experienced reopening of a previously closed wound. Subjects previously treated with cells closed more open wounds than those previously treated with vehicle (OR 1.39, 95% CI 0.47–4.10; p = 0.739), and less subjects with a previously closed wound reopened (OR 0.65, CI 0.16–2.60; p = 0.821); however, these findings were not statistically significant. At the final visit, the difference in proportion of subjects with wounds closed continued to favor the best dose from the prior trial (83% closed vs. 58%, delta 25%). Follow‐up beyond 12 weeks is necessary to evaluate the full benefit of this therapy, as treatment with cells may provide stimulus toward healing that persists for up to several weeks following the last application. The results show that the greater proportional benefit achieved by HP802‐247 relative to standard care after 12 weeks of treatment persists over a meaningful timeframe.
The comparison of two negative‐pressure wound therapy systems in a porcine model of wound healing
Authors: Davis Kathryn E. , Lafontaine Javier , Bills Jessica , Noble Deborah , Wight‐Carter Mary , Oni Georgette , Rohrich Rod J. , Lavery Lawrence A. 
Published: August 2013

AbstractThe purpose of this study was to compare two negative‐pressure wound healing systems (NPWT), −75 mmHg with a silicone‐coated (SC) dressing and −125 mmHg with polyurethane foam dressing (standard of care). In addition, this study compared the effects of two different dressing interfaces, SC dressing and gauze, with −75 mmHg pressure. For both comparisons, two groups of five pigs were evaluated over a 21‐day time course. Two excisional wounds were made on each animal and NPWT dressings were applied. A canvas saddle was constructed to hold the NPWT device so the animal had free range of the pen. Dressings were changed twice a week and wound measurements were taken. Specimens for histology and gene expression analyses were taken on day 7 and 21. These data show that there is increased expression in a few genes associated with remodeling and inflammatory processes in the NPWT‐125 with polyurethane foam as compared with the NPWT‐75 with SC dressing. These two systems, however, are equivalent with respect to wound healing, histology, and gene expression over 21 days of healing. Further, we demonstrate that there is no difference in measure of healing between the SC dressing and a basic gauze dressing.
Local blockade of glucocorticoid activation reverses stress‐ and glucocorticoid‐induced delays in cutaneous wound healing
Authors: Youm Jong‐Kyung , Park Kyungho , Uchida Yoshikazu , Chan Aegean , Mauro Theodora M. , Holleran Walter M. , Elias Peter M. 
Published: August 2013

AbstractStress slows cutaneous wound healing (WH) in an endogenous glucocorticoid (GC)‐dependent fashion. We investigated whether stress/GC‐induced delays in WH require further intracutaneous activation of endogenous GC; and whether blockade or down‐regulation of peripheral activation normalizes WH in the face of stress. Delayed WH in our motion‐restricted murine model of stress could be attributed to elevated systemic GC, because blockade of GC production (using corticotropin‐releasing factor inhibitor, antalarmin), or of peripheral binding to the GC receptor [GCr], with an antagonist, Ru‐486, normalized WH. We next investigated whether local blockade or down‐regulation of the peripheral GC‐activating enzyme, 11β‐hydroxysteroid dehydrogenase type 1 (11β‐HSD1), accelerates cutaneous WH. Topical applications of nonspecific (carbenoxolone) as well as an isoform‐specific 11β‐HSD1 inhibitor overcame stress and exogenous GC‐induced delays in WH. Moreover, two liver X receptor ligands, TO901317 and GW3695, down‐regulated expression of 11β‐HSD1, attenuating stress‐induced delays in WH. Combined inhibitor and liver X receptor ligand applications accelerated WH in the face of stress/systemic GC. Thus: (1) intracutaneous conversion of inactive‐to‐active GC accounts for stress (GC)‐induced delays in WH; and (2) blockade or down‐regulation of 11β‐HSD1 and/or GCr normalize cutaneous WH in the face of stress/GC. Local blockade or down‐regulation of cutaneous GC activation could help enhance WH in various clinical settings.
Calcium‐sensing receptor in rat vagal bronchopulmonary sensory neurons regulates the function of the capsaicin receptor TRPV1
Authors: Gu Qihai , Vysotskaya Zhanna V. , Moss II Charles R. , Kagira Martin K. , Gilbert Carolyn A. 
Published: August 2013

New findings
What is the central question of this study?Extracellular calcium‐sensing receptor (CaSR) is known to play a critical role in the maintainance of systemic calcium homeostasis. Recent studies suggest that CaSR is also involved in many biological processes unrelated to Ca2+ balance. However, the expression of CaSR and its potential interaction with transient receptor potential vanilloid receptor type 1 (TRPV1) function in bronchopulmonary afferent nerves is not known.
What is the main finding and its importance?Our immunohistochemical study demonstrated the expression of CaSR in bronchopulmonary sensory neurons. Our patch‐clamp recordings showed that strong activation of CaSR inhibits, whereas reduced CaSR function potentiates, the capsaicin‐evoked TRPV1 current in these neurons. Our data suggest that CaSR plays an integrative role in bronchopulmonary afferent signalling.
Extracellular calcium‐sensing receptor (CaSR) has been known to play a critical role in the maintainance of systemic Ca2+ homeostasis. Recent studies have shown that CaSR is also expressed in many tissues that are not directly related to plasma Ca2+ regulation, such as the central and peripheral nervous system, where the function of this receptor remains to be defined. In this study, we aimed to investigate the expression of CaSR and its potential interaction with transient receptor potential vanilloid receptor type 1 (TRPV1) in rat vagal bronchopulmonary sensory neurons. Our immunohistochemical experiments demonstrated the expression of CaSR in these sensory neurons as well as in trachea and lung parenchyma. Results from our whole‐cell patch‐clamp recordings in isolated neurons showed that strong activation of CaSR with high concentrations of its agonists, including spermine, NPS R‐568 and Ca2+, inhibited the capsaicin‐evoked whole‐cell inward current. Blockade of CaSR with its antagonists NPS 2390 and NPS 2143 significantly enhanced the capsaicin‐evoked TRPV1 current. These data suggest that CaSR is likely to be involved in the integration of primary bronchopulmonary sensory inputs in physiological and/or pathophysiological conditions.
Strong Seasonality and Interannual Recurrence in Marine Myovirus Communities
Authors: Pagarete A. , Chow C.-E. T. , Johannessen T. , Fuhrman J. A. , Thingstad T. F. , Sandaa R. A. 
Published: August 2013

ABSTRACT

The temporal community dynamics and persistence of different viral types in the marine environment are still mostly obscure. Polymorphism of the major capsid protein gene,
g23
, was used to investigate the community composition dynamics of T4-like myoviruses in a North Atlantic fjord for a period of 2 years. A total of 160 unique operational taxonomic units (OTUs) were identified by terminal restriction fragment length polymorphism (TRFLP) of the gene
g23
. Three major community profiles were identified (winter-spring, summer, and autumn), which resulted in a clear seasonal succession pattern. These seasonal transitions were recurrent over the 2 years and significantly correlated with progression of seawater temperature,
Synechococcus
abundance, and turbidity. The appearance of the autumn viral communities was concomitant with the occurrence of prominent
Synechococcus
blooms. As a whole, we found a highly dynamic T4-like viral community with strong seasonality and recurrence patterns. These communities were unexpectedly dominated by a group of persistently abundant viruses.
Pyrosequence Analysis of the
hsp65
Genes of Nontuberculous Mycobacterium Communities in Unchlorinated Drinking Water in the Netherlands
Authors: van der Wielen Paul W. J. J. , Heijnen Leo , van der Kooij Dick 
Published: August 2013

ABSTRACT

Studies have shown that certain opportunistic pathogenic species of nontuberculous mycobacteria (NTM) can be present in distributed drinking water. However, detailed information about NTM population composition in drinking water is lacking. Therefore, NTM communities in unchlorinated drinking water from the distribution system of five treatment plants in the Netherlands were characterized using 454 pyrosequencing of the
hsp65
gene. Results showed high diversities in unchlorinated drinking water, with up to 28 different NTM operational taxonomic units (OTUs) in a single sample. Each drinking water sample had a unique NTM community, and most (81.1%) OTUs were observed only once. One OTU was observed in 14 of 16 drinking water samples, indicating that this NTM species is well adapted to unchlorinated drinking water conditions. A clear influence of season, source type (groundwater, surface water), easily assimilable organic carbon (AOC) concentration, biofilm formation rate, and active biomass in treated water on the establishment of an NTM community in drinking water was not observed. Apparently, local conditions are more important for the development of a specific NTM community in the drinking water distribution system. A low (4.2%) number of
hsp65
gene sequences showed more than 97% similarity to sequences of the opportunistic pathogens
M. avium
,
M. genavense
, and
M. gordonae
. However, most (95.8%) NTM
hsp65
gene sequences were related to not-yet-described NTM species that have not been linked to disease, indicating that most NTM species in unchlorinated drinking water from distribution systems in the Netherlands have a low public health significance.
Novel Tripartite Aromatic Acid Transporter Essential for Terephthalate Uptake in Comamonas sp. Strain E6
Authors: Hosaka Masaru , Kamimura Naofumi , Toribami Shotaro , Mori Kosuke , Kasai Daisuke , Fukuda Masao , Masai Eiji 
Published: August 2013

ABSTRACT

It has been suggested that a novel type of aromatic acid transporter, which is similar to the tripartite tricarboxylate transporter (TTT), is involved in terephthalate (TPA) uptake by
Comamonas
sp. strain E6. This suggestion was based on the presence of the putative TPA-binding protein gene,
tphC
, in the TPA catabolic operon. The
tphC
gene is essential for growth on TPA and is similar to the genes encoding TTT-like substrate-binding proteins. Here we identified two sets of E6 genes,
tctBA
and
tpiBA
, which encode TTT-like cytoplasmic transmembrane proteins. Disruption of
tctA
showed no influence on TPA uptake but resulted in a complete loss of the uptake of citrate. This loss suggests that
tctA
is involved in citrate uptake. On the other hand, disruption of
tpiA
or
tpiB
demonstrated that both genes are essential for TPA uptake. Only when both
tphC
and
tpiBA
were introduced with the TPA catabolic genes into cells of a non-TPA-degrading
Pseudomonas
strain did the resting cells of the transformant acquire the ability to convert TPA. From all these results, it was concluded that the TPA uptake system consists of the TpiA-TpiB membrane components and TPA-binding TphC. Interestingly, not only was the
tpiA
mutant of E6 unable to grow on TPA or isophthalate, it also showed significant growth delays on
o
-phthalate and protocatechuate. These results suggested that the TpiA-TpiB membrane components are able to interact with multiple substrate-binding proteins. The
tpiBA
genes were constitutively transcribed as a single operon in E6 cells, whereas the transcription of
tphC
was positively regulated by TphR. TPA uptake by E6 cells was completely inhibited by a protonophore, carbonyl cyanide
m
-chlorophenyl hydrazone, indicating that the TPA uptake system requires a proton motive force.
Assessment of Survival and Body Size Variation of Culicoides imicola (Diptera: Ceratopogonidae) as Functions of “Candidatus Cardinium” (Bacteroidetes) Infection Status
Authors: Morag N. , Mullens B. A. , Gottlieb Y. 
Published: August 2013

ABSTRACT

“
Candidatus
Cardinium hertigii” (
Bacteroidetes
) is a maternally inherited endosymbiont known from several arthropods. Its mechanisms for persistence in host populations are mostly reproductive manipulation, though it has been occasionally reported to improve fitness parameters in several hosts. In
Culicoides
(Diptera: Ceratopogonidae) biting midges, the prevalence of “
Candidatus
Cardinium” infection was documented as moderate, with no detectable sex bias. We therefore investigated whether “
Candidatus
Cardinium” affects important fitness parameters, such as survival and body size, in
Culicoides imicola
, a dominant vector species. Field-collected midges were trapped and analyzed for survival under different environmental conditions and antibiotic treatment, taking into account “
Candidatus
Cardinium” infection status and parity status (i.e., parous or nulliparous). Additionally, wing lengths were measured as a proxy parameter for body size and analyzed together with “
Candidatus
Cardinium” infection data. The findings revealed no difference in survival of
Culicoides
infected with “
Candidatus
Cardinium” and that of uninfected midges in both parity states and under all tested conditions: optimal, starvation, heat, and antibiotic treatment. Beyond survival, no wing length difference was found for “
Candidatus
Cardinium”-infected versus uninfected midges. In aggregate, these findings support our conclusion that “
Candidatus
Cardinium” does not have an overt effect on the survival and size of adult
C. imicola
midges. “
Candidatus
Cardinium” may affect immature stages or may alter adult reproductive performance.
Genetically Diverse Clostridium difficile Strains Harboring Abundant Prophages in an Estuarine Environment
Authors: Hargreaves K. R. , Colvin H. V. , Patel K. V. , Clokie J. J. P. , Clokie M. R. J. 
Published: August 2013

ABSTRACT

Clostridium difficile
is the leading cause of antibiotic-associated diarrheal disease in health care settings across the world. Despite its pathogenic capacity, it can be carried asymptomatically and has been found in terrestrial and marine ecosystems outside hospital environments. Little is known about these environmental strains, and few studies have been conducted on estuarine systems. Although prophage abundance and diversity are known to occur within clinical strains, prophage carriage within environmental strains of
C. difficile
has not previously been explored. In this study, we isolated
C. difficile
from sites sampled in two consecutive years in an English estuarine system. Isolates were characterized by PCR ribotype, antibiotic resistance, and motility. The prevalence and diversity of prophages were detected by transmission electron microscopy (TEM) and a phage-specific PCR assay. We show that a dynamic and diverse population of
C. difficile
exists within these sediments and that it includes isolates of ribotypes which are associated with severe clinical infections and those which are more frequently isolated from outside the hospital environment. Prophage carriage was found to be high (75%), demonstrating that phages play a role in the biology of these strains.