bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pond shutdown as a strategy for preventing outbreaks of white spot disease in shrimp farms in Mexico
Authors: Hernandez‐Llamas Alfredo , Magallon‐Barajas Francisco J. , Perez‐Enriquez Ricardo , Cabanillas‐Ramos Julio , Esparza‐Leal Hector M. , Portillo‐Clark Guillermo 
Published: June 2013

AbstractPond shutdown is a strategy used to eliminate residual pathogens. For 2005–2011, we analysed the relationship between the prevalence of white spot disease (WSD) and the length of pond shutdown (LPS) and discussed its effectiveness for the prevention of WSD in Mexico. The LPS increased significantly from 2.1 months in 2005 to 3.1 months in 2011. The prevalence of WSD diminished significantly from 2005 to 2009, but no evidence of diminution was found when 2010 and 2011 were included in the time series. A χ2‐test for trend indicated that the prevalence of WSD diminished significantly as LPS increased in 2005 through to 2009 and 2005 through to 2011 (P < 0.05). When analysed on an annual basis, the prevalence decreased significantly in relation with LPS in 2006 (P = 0.048), 2007 (P = 0.002), 2008 (P = 0.0001) and 2009 (P = 0.001); no evidence for decreasing the prevalence occurred in 2005 (P = 0.1), 2010 (P = 0.17) or 2011 (P = 0.52). The χ2‐test adjusted for confounding indicated that decreases in prevalence in 2005 to 2009 could be attributed to increases of LPS rather than confounding variables such as increased resistance of shrimp, diminished virulence and improved cultivation practices. We discuss the possible relationship between the warm water temperatures in the Gulf of California and increases in the prevalence of WSD. We conclude that LPS has been an adequate management strategy for preventing WSD, supporting recent compulsory measures taken by the Mexican government to improve biosecurity in shrimp farms.
Dynamic self‐thinning model for sessile animal populations with multilayered distribution
Authors: Fuentes‐Santos Isabel , Cubillo Alhambra M. , Fernández‐Reiriz María José , Labarta Uxío 
Published: June 2013

AbstractThe main drawback of the traditional self‐thinning model is how time is handled. Self‐thinning (ST) has been formally recognized as a dynamic process, while the current ST models have not included the temporal effect. This restricts the analysis to the average competitive behaviour of the population and produces a biased estimation of the self‐thinning parameters. In this study, we extend the dynamic ST model introduced by Roderick and Barnes (2004) to the analysis of multilayered sessile animal populations. For this purpose, we incorporate the number of layers and the density per layer into the dynamical approach. The performance of the dynamic model was checked and compared with the classical ST model through the analysis of mussel populations grown at different density treatments. Unlike the traditional model, the dynamical approach detected the effect of culture density on the competitive behaviour of individuals and allowed to analyse the temporal evolution of intraspecific competition by estimating the ST exponent trajectory. Moreover, this approach provided an ecological interpretation of any possible value of the ST exponent. Thus, our results support the use of the dynamic model in the analysis of self‐thinning in sessile animal multilayered populations. The estimation of the ST exponent trajectory reflects the dynamic nature of the ST process, providing a more realistic description of population dynamics than the traditional model.
Chlorite meniscus cement – implications for diagenetic mineral growth after oil emplacement
Authors: Friis Henrik , Molenaar Nicolaas , Varming Thomas 
Published: June 2013

AbstractThe possible influence on diagenesis of oil migration into reservoir sandstones is important for understanding their development. Although many studies have addressed the question of continued growth of diagenetic minerals after oil emplacement, there is little clear evidence of the timing of mineral growth relative to oil emplacement, nor of the possible mechanisms of continued mineral growth. This study presents an example of continued cementation by pore‐lining chlorite during and after the migration of oil into a Palaeocene turbidite sandstone reservoir near the Faroe Islands. Chlorite developed in two different textures. One texture occurs on framework grain surfaces adjacent to open pore space in contact with oil. The other texture occurs close to framework grain contacts where contact with oil appears to have been prevented by residual pore‐water menisci. The meniscus crystals are larger than those from open pore, implying that diagenetic clay mineral growth has continued after oil emplacement.
Monte Carlo investigation of the increased radiation deposition due to gold nanoparticles using kilovoltage and megavoltage photons in a 3D randomized cell model
Authors: Douglass Michael , Bezak Eva , Penfold Scott 
Published: June 2013

Purpose:Investigation of increased radiation dose deposition due to gold nanoparticles (GNPs) using a 3D computational cell model during x‐ray radiotherapy.Methods:Two GNP simulation scenarios were set up in Geant4; a single 400 nm diameter gold cluster randomly positioned in the cytoplasm and a 300 nm gold layer around the nucleus of the cell. Using an 80 kVp photon beam, the effect of GNP on the dose deposition in five modeled regions of the cell including cytoplasm, membrane, and nucleus was simulated. Two Geant4 physics lists were tested: the default Livermore and custom built Livermore/DNA hybrid physics list. 106 particles were simulated at 840 cells in the simulation. Each cell was randomly placed with random orientation and a diameter varying between 9 and 13 μm. A mathematical algorithm was used to ensure that none of the 840 cells overlapped. The energy dependence of the GNP physical dose enhancement effect was calculated by simulating the dose deposition in the cells with two energy spectra of 80 kVp and 6 MV. The contribution from Auger electrons was investigated by comparing the two GNP simulation scenarios while activating and deactivating atomic de‐excitation processes in Geant4.Results:The physical dose enhancement ratio (DER) of GNP was calculated using the Monte Carlo model. The model has demonstrated that the DER depends on the amount of gold and the position of the gold cluster within the cell. Individual cell regions experienced statistically significant (p < 0.05) change in absorbed dose (DER between 1 and 10) depending on the type of gold geometry used. The DER resulting from gold clusters attached to the cell nucleus had the more significant effect of the two cases (DER ∼ 55). The DER value calculated at 6 MV was shown to be at least an order of magnitude smaller than the DER values calculated for the 80 kVp spectrum. Based on simulations, when 80 kVp photons are used, Auger electrons have a statistically insignificant (p < 0.05) effect on the overall dose increase in the cell. The low energy of the Auger electrons produced prevents them from propagating more than 250–500 nm from the gold cluster and, therefore, has a negligible effect on the overall dose increase due to GNP.Conclusions:The results presented in the current work show that the primary dose enhancement is due to the production of additional photoelectrons.
Provenance and Geographic Spread of St. Louis Encephalitis Virus
Authors: Kopp Anne , Gillespie Thomas R. , Hobelsberger Daniel , Estrada Alejandro , Harper James M. , Miller Richard A. , Eckerle Isabella , Müller Marcel A. , Podsiadlowski Lars , Leendertz Fabian H. , Drosten Christian , Junglen Sandra 
Published: June 2013

ABSTRACTSt. Louis encephalitis virus (SLEV) is the prototypic mosquito-borne flavivirus in the Americas. Birds are its primary vertebrate hosts, but amplification in certain mammals has also been suggested. The place and time of SLEV emergence remain unknown. In an ecological investigation in a tropical rainforest in Palenque National Park, Mexico, we discovered an ancestral variant of SLEV inCulex nigripalpusmosquitoes. Those SLEV-Palenque strains form a highly distinct phylogenetic clade within the SLEV species. Cell culture studies of SLEV-Palenque versus epidemic SLEV (MSI-7) revealed no growth differences in insect cells but a clear inability of SLEV-Palenque to replicate in cells from birds, cotton rats, and free-tailed bats permissive for MSI-7 replication. Only cells from nonhuman primates and neotropical fruit bats were moderately permissive. Phylogeographic reconstruction identified the common ancestor of all epidemic SLEV strains to have existed in an area between southern Mexico and Panama ca. 330 years ago. Expansion of the epidemic lineage occurred in two waves, the first representing emergence near the area of origin and the second involving almost parallel appearances of the virus in the lower Mississippi and Amazon delta regions. Early diversification events overlapped human habitat invasion during the post-Columbian era. Several documented SLEV outbreaks, such as the 1964 Houston epidemic or the 1990 Tampa epidemic, were predated by the arrival of novel strains between 1 and 4 years before the outbreaks. Collectively, our data provide insight into the putative origins of SLEV, suggesting that virus emergence was driven by human invasion of primary rainforests.IMPORTANCESt. Louis encephalitis virus (SLEV) is the prototypic mosquito-transmitted flavivirus of the Americas. Unlike the West Nile virus, which we know was recently introduced into North America from the Old World, the provenience of SLEV is obscure. In an ecological investigation in a primary rainforest area of Palenque National Park, Mexico, we have discovered an ancestral variant of SLEV. The ancestral virus was much less active than the epidemic virus in cell cultures, reflecting its incomplete adaptation to hosts encountered outside primary rainforests. Knowledge of this virus enabled a spatiotemporal reconstruction of the common ancestor of all SLEVs and how the virus spread from there. We can infer that the cosmopolitan SLEV lineage emerged from Central America in the 17th century, a period of post-Columbian colonial history marked by intense human invasion of primary rainforests. Further spread followed major bird migration pathways over North and South America.
Light Regulation of Swarming Motility in Pseudomonas syringae Integrates Signaling Pathways Mediated by a Bacteriophytochrome and a LOV Protein
Authors: Wu Liang , McGrane Regina S. , Beattie Gwyn A. 
Published: June 2013

ABSTRACT

The biological and regulatory roles of photosensory proteins are poorly understood for nonphotosynthetic bacteria. The foliar bacterial pathogen
Pseudomonas syringae
has three photosensory protein-encoding genes that are predicted to encode the blue-light-sensing LOV (light, oxygen, or voltage) histidine kinase (LOV-HK) and two red/far-red-light-sensing bacteriophytochromes, BphP1 and BphP2. We provide evidence that LOV-HK and BphP1 form an integrated network that regulates swarming motility in response to multiple light wavelengths. The swarming motility of
P. syringae
B728a deletion mutants indicated that LOV-HK positively regulates swarming motility in response to blue light and BphP1 negatively regulates swarming motility in response to red and far-red light. BphP2 does not detectably regulate swarming motility. The histidine kinase activity of each LOV-HK and BphP1 is required for this regulation based on the loss of complementation upon mutation of residues key to their kinase activity. Surprisingly, mutants lacking both
lov
and
bphP1
were similar in motility to a
bphP1
single mutant in blue light, indicating that the loss of
bphP1
is epistatic to the loss of
lov
and also that BphP1 unexpectedly responds to blue light. Moreover, whereas expression of
bphP1
did not alter motility under blue light in a
bphP1
mutant, it reduced motility in a mutant lacking
lov
and
bphP1
, demonstrating that LOV-HK positively regulates motility by suppressing negative regulation by BphP1. These results are the first to show cross talk between the LOV protein and phytochrome signaling pathways in bacteria, and the similarity of this regulatory network to that of photoreceptors in plants suggests a possible common ancestry.

IMPORTANCE
Photosensory proteins enable organisms to perceive and respond to light. The biological and ecological roles of these proteins in nonphotosynthetic bacteria are largely unknown. This study discovered that a blue-light-sensing LOV (light, oxygen, or voltage) protein and a red/far-red-light-sensing bacteriophytochrome both regulate swarming motility in the foliar pathogen
Pseudomonas syringae
. These proteins form an integrated signaling network in which the bacteriophytochrome represses swarming motility in response to red, far-red, and blue light, and LOV positively regulates swarming motility by suppressing bacteriophytochrome-mediated blue-light signaling. This is the first example of cross talk between LOV and phytochrome signaling pathways in bacteria, which shows unexpected similarity to photoreceptor signaling in plants.
Helicobacter pylori VacA Suppresses Lactobacillus acidophilus-Induced Interferon Beta Signaling in Macrophages via Alterations in the Endocytic Pathway
Authors: Weiss Gudrun , Forster Sam , Irving Aaron , Tate Michelle , Ferrero Richard L. , Hertzog Paul , Frøkiær Hanne , Kaparakis-Liaskos Maria 
Published: June 2013

ABSTRACT

Helicobacter pylori
causes chronic gastritis and avoids elimination by the immune system of the infected host. The commensal bacterium
Lactobacillus acidophilus
has been suggested to exert beneficial effects as a supplement during
H. pylori
eradication therapy. In the present study, we applied whole-genome microarray analysis to compare the immune responses induced in murine bone marrow-derived macrophages (BMDMs) stimulated with
L. acidophilus
,
H. pylori
, or both bacteria in combination. While
L. acidophilus
induced a Th1-polarizing response characterized by high expression of interferon beta (IFN-β) and interleukin 12 (IL-12),
H. pylori
strongly induced the innate cytokines IL-1β and IL-1α. In BMDMs prestimulated with
L. acidophilus
,
H. pylori
blocked the expression of
L. acidophilus
-induced IFN-β and IL-12 and suppressed the expression of key regulators of the Rho, Rac, and Cdc42 GTPases. The inhibition of
L. acidophilus
-induced IFN-β was independent of
H. pylori
viability and the virulence factor CagPAI; however, a vacuolating cytotoxin (
vacA
) mutant was unable to block IFN-β. Confocal microscopy demonstrated that the addition of
H. pylori
to
L. acidophilus
-stimulated BMDMs redirects intracellular processing, leading to an accumulation of
L. acidophilus
in the endosomal and lysosomal compartments. Thus, our findings indicate that
H. pylori
inhibits the development of a strong Th1-polarizing response in BMDMs stimulated with
L. acidophilus
by blocking the production of IFN-β in a VacA-dependent manner. We suggest that this abrogation is caused by a redirection of the endocytotic pathway in the processing of
L. acidophilus
.

IMPORTANCE
Approximately half of the world’s population is infected with
Helicobacter pylori
. The factors that allow this pathogen to persist in the stomach and cause chronic infections have not yet been fully elucidated. In particular, how
H. pylori
avoids killing by macrophages, one of the main types of immune cell underlying the epithelium, remains elusive. Here we have shown that the
H. pylori
virulence factor VacA plays a key role by blocking the activation of innate cytokines induced by the probiotic
Lactobacillus acidophilus
in macrophages and suppresses the expression of key regulators required for the organization and dynamics of the intracellular cytoskeleton. Our results identify potential targets for the treatment of
H. pylori
infection and vaccination, since specific inhibition of the toxin VacA possibly allows the activation of an efficient immune response and thereby eradication of
H. pylori
in the host.
PLK1 and YY1 interaction in follicular lymphoma is associated with unfavourable outcome
Authors: Sandison Harriet E , Usher Suzanne , Karimiani Ehsan G , Ashton Garry , Menasce Lia P , Radford John A , Linton Kim , Byers Richard J 
Published: June 2013

AimsYing Yang 1 (YY1) is a transcription factor involved in both proliferation and apoptosis. It is prognostic in follicular lymphoma (FL), increased protein levels being associated with favourable outcome. PLK1 is a critical regulator of mitosis, playing a role in spindle formation and in regulation of the G2/M cell cycle checkpoint. PLK1 phosphorylates YY1 at the G2/M checkpoint with activation of YY1 and resultant progression from G2 into mitosis.MethodsThis study aims to investigate possible molecular coexpression and interaction of YY1 with PLK1 in FL using Duolink II in situ proximity ligation assay (PLA) in 51 FL samples in a tissue microarray.ResultsPositive PLA signals were present at variable frequency and Kaplan-Meier analysis showed association of signal frequency above the median with unfavourable outcome (p=0.0270). PLA signals were localised to the nuclear edge, with only one signal per cell, suggesting PLK1 and YY1 coexpression at the centrosome. In a minority of cells, two very close PLA signals were present in a single cell, and occasionally, there was a strong ring of semi-confluent fluorescent PLA signals round the nucleus of non-dividing cells, while rarely events were observed in the cytoplasm surrounding dividing cells.ConclusionsThe results confirm association of YY1 and PLK1 with outcome in FL and suggest coexpression at the centrosome. Given the reported interaction of YY1 with PLK1 at the centriole and promotion of cell division at the G2/M checkpoint, the results would concord with the known association of higher proliferation with poor outcome in FL.
Short‐Term Effects of Land Leveling on Irrigation‐Related Some Soil Properties in a Clay Loam Soil
Authors: Öztekin Tekin 
Published: June 2013

There are few studies conducted on the short‐term effects of land leveling on soil water holding capacity. The objectives of this study were to analyze the short‐term effects of land leveling on the magnitudes, variances, spatial variability, and distributions of surface (0–20 cm) and subsurface (20–40 cm) soil properties of bulk density, field capacity, permanent wilting point, water holding capacity and particle size fractions. The study was conducted in a 1.2 ha field with clay loam soil located on the low terraces of Yesilirmak River, Tokat, Turkey. According to the paired t‐test results, water holding capacity, and bulk density significantly increased, while permanent wilting point (P ≤ 0.001) and field capacity (P ≤ 0.05) significantly decreased for surface soil due to land leveling. The reasons for the increases in WHC values in both cut and fill areas (29%, and 12%, resp.) of surface soil are look like the much more decreases in PWP values than those of FC values and the increases in BD values. The moderate positive linear relationship between the surface soil clay contents and cut depths through cut areas (r = 0.64) was also determined in this study.
Effects of Dietary Weight Loss and Exercise on Insulin-Like Growth Factor-I and Insulin-Like Growth Factor-Binding Protein-3 in Postmenopausal Women: A Randomized Controlled Trial
Authors: Mason Caitlin , Xiao Liren , Duggan Catherine , Imayama Ikuyo , Foster-Schubert Karen E. , Kong Angela , Campbell Kristin L. , Wang Ching-Yun , Alfano Catherine M. , Blackburn George L. , Pollack Michael , McTiernan Anne 
Published: June 2013

AbstractHigh levels of insulin-like growth factor (IGF)-I may increase the risk of common cancers in humans. We hypothesized that weight loss induced by diet and/or exercise would reduce IGF-I in postmenopausal women. Four hundred and thirty nine overweight or obese [body mass index (BMI) ≥ 25 kg/m2] women (50–75 years) were randomly assigned to: (i) exercise (N = 117), (ii) dietary weight loss (N = 118), (iii) diet + exercise (N = 117), or (iv) control (N = 87). The diet intervention was a group-based program with a 10% weight loss goal. The exercise intervention was 45 minutes/day, 5 days/week of moderate-to-vigorous intensity activity. Fasting serum IGF-I and IGF-binding protein (IGFBP)-3 were measured at baseline and 12 months by radioimmunoassay. Higher baseline BMI was associated with lower IGF-I and IGF-I/IGFBP-3 molar ratio. Although no significant changes in either IGF-I or IGFBP-3 were detected in any intervention arm compared with control, the IGF-I/IGFBP-3 ratio increased significantly in the diet (+5.0%, P &lt; 0.01) and diet + exercise (+5.4%, P &lt; 0.01) groups compared with control. Greater weight loss was positively associated with change in both IGF-I (Ptrend = 0.017) and IGF-I/IGFBP-3 ratio (Ptrend &lt; 0.001) in the diet group, but inversely with change in IGFBP-3 in the diet + exercise group (Ptrend = 0.01). No consistent interaction effects with baseline BMI were detected. Modified IGF-I bioavailability is unlikely to be a mechanism through which caloric restriction reduces cancer risk in postmenopausal women. Cancer Epidemiol Biomarkers Prev; 22(8); 1457–63. ©2013 AACR.
Serum Insulin-like Growth Factor-I Level Is an Independent Predictor of Recurrence and Survival in Early Hepatocellular Carcinoma: A Prospective Cohort Study
Authors: Cho Eun Ju , Lee Jeong-Hoon , Yoo Jeong-Ju , Choi Won-Mook , Lee Min Jong , Cho Yuri , Lee Dong Hyeon , Lee Yun Bin , Kwon Jung Hee , Yu Su Jong , Lee Jeong Min , Suh Kyung-Suk , Kim Kion , Kim Yoon Jun , Yoon Jung-Hwan , Kim Chung Yong , Lee Hyo-Suk 
Published: June 2013

Abstract
Purpose: Insulin-like growth factor-I (IGF-I) reflects hepatic synthetic function and plays an important role in the development and progression of various cancers. In this study, we investigated whether pretreatment serum IGF-I levels predict time-to-recurrence (TTR) and overall survival (OS) in patients with early-stage hepatocellular carcinoma after curative treatment.
Experimental Design: Consecutive patients with hepatocellular carcinoma who had undergone surgical resection, radiofrequency ablation, or percutaneous ethanol injection as curative treatments of early hepatocellular carcinoma were included from two prospective cohorts and the training set (n = 101) and the validation set (n = 91) were established. Serum samples were collected before treatment and the levels of IGF-I and IGF-binding protein-3 (IGFBP-3) were analyzed with regard to their associations with recurrence and survival.
Results: In the training set, patients with low IGF-I levels showed significantly shorter TTR [median, 14.6 months; 95% confidence interval (CI), 1.8–27.5] than patients with high IGF-I levels (median, 50.8 months; 95% CI, 36.9–64.7; P &lt; 0.001) during a median follow-up period of 52.4 months. In the multivariate analysis, low levels of IGF-I were an independent predictor of recurrence (HR, 2.49; 95% CI, 1.52–4.08; P &lt; 0.001). Furthermore, together with high-serum α-fetoprotein and multiple tumors, low levels of IGF-I remained an independent predictor of poorer survival (HR, 8.00; 95% CI, 1.94–33.01; P = 0.004). Applied to the independent validation set, low-serum IGF-I levels maintained their prognostic value for shorter TTR and OS.
Conclusions: Low-baseline IGF-I levels independently correlated with shorter TTR and poorer survival in patients with early-stage hepatocellular carcinoma after curative treatment. Clin Cancer Res; 19(15); 4218–27. ©2013 AACR.