bluuebunny/crossref_metadata_2025 huggingface dataset:
Deriving inherent optical property for highly turbid productive inland water from MERIS data by semi-analytical model: A case study in Taihu Lake, China
Authors: Huang C. , Chen X. , Li Y. , Yang H. , Sun D. , Le C. , Xu L.
Published: October 2017

Remote estimation of inherent optical properties was greatly challenged by significant spatial-temporal variation and the extreme complexity of bio-optical properties in inland turbid water. The multiband quasi-analytical algorithm has advantages over traditional band ratio and semi-analytical algorithm in that it is based on the remote sensing reflectance model derived from radiative transfer equation and does not need the parameterization of absorption coefficients. An improved model, which used, was developed to retrieve inherent optical properties in high turbid inland water. As a first step, the backscattering coefficient at reference wavelength [bbp(λ0)] was retrieved directly by support vector machine optimization algorithm instead of step 2 in the quasi analytical algorithm for the high correlation between bbp(λ0) and remote sensing reflectance at the near-infrared wavelength. The second step, a semi-analytical support vector machine algorithm, was used to retrieve spectral shape of bbp(λ) instead the step 4 in the quasi analytical algorithm. Part of field-measured dataset collected on November 2006, November 2007, November 2008 and April 2009 in Taihu Lake was used to train the support vector machine model, and the other part was used to test this algorithm. Results indicated that the mean square root of percentage between the derived and measured value of bbp(532 nm) was less than 3.73% and root mean square percentage of ap(442 nm) and ap(532 nm) were 15.29% and 30.45%, respectively. Furthermore, the potential application of this algorithm to MERIS data was investigated by the reduced resolution MERIS satellite image. The result shows that satellite-derived data using the support vector machine model is consistent with in situ measured data. This study advances the semi-analytical model and broadens the application of MERIS data in highly turbid inland waters.
Long-term trends in Lake Ontario's benthic macroinvertebrate community from 1994–2008
Authors: Birkett K. , Lozano S. J. , Rudstam L. G.
Published: October 2017

The benthic macroinvertebrate community of Lake Ontario was assessed through a lakewide survey in 2008. Diporeia was very rare throughout the lake at all depths in 2008, and only four of 52 locations had densities >100 m−2, all of them at depths >90 m. The maximum density of Diporeia found at any location was at 257 m−2 in 2008, which can be compared to maximum densities of 13,280 m−2 observed in 1994. Lakewide Diporeia abundance declined with an additional order of magnitude from an average of 342 m−2 in 2003 to 21 m−2 in 2008. The Quagga Mussel (D. rostriformis bugensis) dominated the benthic macroinvertebrate community in 2008, comprising over 70% of the density and 98% of the biomass. No Zebra Mussels were identified in the 2008 samples. Quagga Mussels, Oligochaetes and Chironomids were most abundant between 31 and 90 m. Sphaeriids were rare at all depths, but were more abundant at sites deeper than 90 m. Between 2003 and 2008, lakewide Dreissena abundance declined by 43% primarily due to significant declines in the 10–30 m depth region (from 6500 m−2 to 900 m−2). Dreissena did not decline significantly in the 30–90 m or over 90 m depth regions. The 2008 survey revealed a continued decline in Diporeia and Sphaeriid Clams, a replacement of Zebra Mussels by Quagga Mussels, and a decline in Quagga Mussels at depths shallower than 30 m. Oligochaetes and chironomids showed no significant changes since the 1990s.
Relative comparison and perspective on invasive species in the Laurentian and Swedish Great Lakes
Authors: Nalepa Thomas F.
Published: October 2017

The Laurentian Great Lakes and the Swedish Great Lakes both have a long history of being invaded by non-native species, although the total number reported in the former system far exceeds that in the latter. Until about the 1980s, non-native species that had the greatest ecosystem and/or socioeconomic impacts in both systems were controlled, or their negative impacts ameliorated by management actions; most prominent of these species were the Sea Lamprey and Alewife in the Laurentian Great Lakes, and Crayfish plague in the Swedish Great Lakes. In the 1980s, a number of species native to the Ponto-Caspian region were introduced into the Laurentian Great Lakes via the ballast water of transoceanic ships, and these species had significant ecosystem impacts, could not be controlled by management actions, and changed the way these lake resources were managed. Similar introductions have not occurred in the Swedish Great Lakes, but many of the same species that have impacted the Laurentian Great Lakes are spreading in European systems and in the Baltic Sea, and thus could pose an invasion risk to lakes in Sweden. Based on experiences in the Laurentian Great Lakes, it seems prudent to conduct a thorough assessment of these invaders relative to potential vectors of introduction for the Swedish Great Lakes. Also, an assessment of long-term monitoring programs is in order. Long-term data provides baseline information of the ecosystem and tracks ecosystem responses if indeed an invader becomes established.
Increased use of non-native algae species in the diet of the Green Turtle (Chelonia mydas) in a primary pasture ecosystem in Hawaii
Authors: Russell Dennis J. , Balazs George H.
Published: October 2017

The Green Turtle, Chelonia mydas, has modified its feeding behavior over the past 36 years to include the increasing abundance of non-native algae growing in the greater Kaneohe Bay area of Oahu, Hawaii. Changes in diet of the Turtles are correlated with an increase in abundance of non-native algae. Turtles are eating 135 species of marine vegetation including the following seven non-native species: Acanthophora spicifera, Hypnea musciformis, Gracilaria salicornia, Eucheuma denticulatum, Gracilaria tikvahiae, Kappaphycus striatum and Kappaphycus alvarezii. Non-native algae now represent 0.64 proportion of the Turtle diet. The present study for the additional 8 years 2005–2012, shows the utilization of non-native species for food has increased 24% since the last study that included 28 years 1976–2005. Average time for the Turtles to make the shift to non-native species is 10–12 years for the more invasive species and 20–30 years for the slower growing species. During this same time period the numbers of C. mydas, body size, and growth rates have also increased, partly due to the increased abundance of the additional non-native food items. This study verifies that the trend of Turtles eating higher amounts of non-native algae in Kaneohe Bay is now stronger than first reported in 2009.
Climate change and the impact of invasive species on aquatic ecosystems
Authors: Kernan M.
Published: October 2017

The consequences of human impacts on aquatic ecosystem activities have been far reaching. Multiple stresses affect aquatic ecosystems globally. These can adversely affect physical, chemical and ecological water status, causing change in species composition, ecosystem structure and function and biodiversity. These impacts and the capacity for managing them are further compounded by the complex nature of the interactions between stresses. In this article the focus is on the threats posed by non-native invasive species. It considers the nature of this threat and options for management, highlighting examples of invasive freshwater species in the United Kingdom. The relationship between climate change and invasive species impacts is then examined. The article is based on a keynote presentation delivered at the Marine Invasive Species: Management of ballast water and other vectors. Key lessons derived from managing freshwater ecosystems under threat of invasive species are highlighted in terms of their relevance and potential application to other systems such as those in coastal and marine areas.
Regional ocean forecasting systems and their applications: Design considerations of such a system for the South China Sea
Authors: Wang Xiaochun , Zhao Liqing , Li Zhijin , Menemenlis Dimitris
Published: October 2017

Essential components and technical details of regional ocean forecasting systems configured from the Regional Ocean Modeling System are discussed with the goal of bridging the gap between user and ocean modeling communities. Recent development of these systems and applications are also surveyed. Design considerations of such a system for the South China Sea are discussed, based on regional dynamic characteristics and potential applications.
Long-term trends in legacy contaminants in aquatic wildlife in the Hamilton Harbour Area of Concern
Authors: Hughes K. D. , de Solla S. R. , Weseloh D. V. C. , Martin P. A.
Published: October 2017

Long-term trends in contaminant exposure were examined in eggs of two aquatic-feeding species, the Herring Gull (Larus argentatus) and the Snapping Turtle (Chelydra serpentina), collected from locations within the Hamilton Harbour Area of Concern, an industrialized area historically associated with high concentrations of legacy persistent organic pollutants, metals and other compounds. Significant declines in concentrations of sum polychlorinated biphenyls, four organochlorine pesticides and 2,3,7,8-tetrachlorodibenzo-p-dioxin were evident in Herring Gull eggs collected from nesting colonies within the harbour (range in % declines = 86%–94%) and in Snapping Turtle eggs from two area of concern wetland/creek locations (range in % declines = 36%–89%) from the 1980s to 2012. Temporal trends in polychlorinated biphenyl congener profiles in eggs were examined by grouping polychlorinated biphenyl congeners according to structure-activity relationships based on their susceptibility to be metabolized by the cytochrome P450 system. Significant temporal changes in the percentages of non-metabolizable congeners (i.e. increase) and congeners metabolized by P450 1A enzymes (i.e. decrease) were evident in eggs of both species. It is not clear if these distinct temporal patterns are related to changes in metabolism following reductions in polychlorinated biphenyl burdens or changes in bioavailability of congeners in the environment. Large decreases in contaminant burdens in eggs of these two species at two different geographic scales within the area of concern (i.e. local scale for Turtles and regional scale for Gulls) are reflective of improved environmental conditions within the harbour and support their utility as top-predator wildlife bio-indicator species.
A forecast model of freak wave generations in deep water
Authors: Hu Jinpeng , Zhang Yunqiu , Huang Shuo
Published: October 2017

In ocean engineering designs, random extreme events are the most difficultly determined environmental load factors. Appearances of freak waves in the normal sea states are just such events. To reduce their potential destruction of marine structures, a forecast model is studied to predict whether freak waves occur in the wave propagation. In this model, the modified fourth-order nonlinear Schrödinger equation is employed as the deep-water wave model, which controls the evolution of complex wave envelopes. The measured wave train is set as its initial condition which needs to be changed into its corresponding complex wave envelope by use of the Hilbert transform method to be input into the wave model. During the evolution of complex wave envelope, its corresponding wave heights are estimated and compared with the definition of freak waves. If a freak wave is captured, its occurrence position and time are given. Three cases of observed, simulated and laboratory wave trains as initial conditions are performed to predict the generation of freak waves. Results show that measured wave trains can be simply and accurately input into this forecast model through the Hilbert transform method and this model can predict the generation of freak waves within some space and time in its traveling. In addition, larger groups than usual group height or length increase the probability of freak wave generation. This forecast model may provide marine activities with a safety warning in some open seas.
Effect of two macrophyte species on phytoplankton growth and water quality in a eutrophic pond
Authors: Zhao Jian-Gang , Chen Zhang-He
Published: October 2017

To evaluate the ecological restoration effect of floating and submerged macrophytes on phytoplankton inhibition and water quality improvement, an enclosure experiment was undertaken in situ including Hydrilla verticillata mono enclosure, Eichhornia crassipes mono enclosure, and H. verticillata plus E. crassipes mixed enclosure. Concentrations of total nitrogen, ammonia nitrogen, nitrate nitrogen and total phosphorus were significantly lower in the vegetated enclosures than those in the control enclosure. Eichhorniacrassipes mono enclosure had significantly lower concentrations of ammonia nitrogen and nitrate nitrogen compared to the mixed enclosure. Purification ability was higher for faster growing macrophytes. The density and biomass of the phytoplankton in the plant enclosures were lower than those in the control enclosure, while the values in the mixed enclosures were significantly higher than those in the mono enclosures. Chlorophyta were the dominant algae in all the enclosures. Pyrrophyta and Cryptophyta were the co-dominant algae in the control enclosure. Therefore, macrophytes had a significantly inhibitory effect on phytoplankton, with the mono enclosures showing a stronger inhibitory effect compared to the mixed enclosures.
Modelling phosphorus dynamics in Cootes Paradise marsh: Uncertainty assessment and implications for eutrophication management
Authors: Kim Dong-Kyun , Peller Tianna , Gozum Zoe , Theÿsmeÿer Tys , Long Tanya , Boyd Duncan , Watson Sue , Rao Y. R. , Arhonditsis George B.
Published: October 2017

Cootes Paradise marsh, a hypereutrophic wetland draining into the western end of Hamilton Harbour, Ontario, has historically been considered an important regulatory factor of the severity of local eutrophication phenomena. In this study, we present a modelling exercise that aims to draw inference on the relative contribution of various external and internal flux rates to the phosphorus budget of Cootes Paradise. We first examined the capacity of a phosphorus mass-balance model, accounting for the interplay among water column, sediments and macrophytes, to reproduce the observed total phosphorus dynamics over a 17-year period (1996–2012). Water level fluctuations were one of the key challenges for balancing the phosphorus budget during model calibration. Our analysis shows that the model satisfactorily reproduced the average seasonal patterns, as well as the year-to-year total phosphorus variability (coefficient of determination = 0.20, relative error = 26.8%, root mean square error = 62.2 μg P l−1, model efficiency = 0.15). However, our model failed to capture two years of the study period (1997 and 2007), when ambient TP levels significantly deviated from the typically prevailing conditions. Model sensitivity analysis identified the sedimentation of particulate material and diffusive reflux from sediments as two critical processes to characterize the phosphorus cycle in the wetland. Based on the current parameter specification, our model postulates that the sediments still act as a net sink, whereas macrophyte processes (respiration rates, nutrient uptake from interstitial water) appear to play a minor role. We conclude by discussing the various sources of uncertainty and additional remedial actions required in Cootes Paradise marsh to realize a shift from the current turbid-phytoplankton dominated state to its former clear-macrophyte dominated state.
Performance testing of ballast water management systems: Revisiting the interpretation of organisms ≥10 μm and ≤50 μm in minimum dimension
Authors: Kim Young-Hee , Jang Pung-Guk , Jung Seung Won , Choi Keun-Hyung
Published: October 2017

Phytoplankton are a major concern in the introduction of marine invasive species by ships. The current ballast water performance standard (Regulation D2) under the Ballast Water Convention prescribes the number of viable organisms allowed in discharged ballast water. For organisms ≥10 μm and ≤50 μm in minimum dimension, the D2 allows <10 viable organisms per ml, a size category including mostly phytoplankton. However, many phytoplankton are narrower than 10 μm but much longer than 10 μm. This discrepancy causes two major problems: firstly, ballast water management systems will not be examined for their performance at removing organisms larger than regulated by D2. Secondly, this will require higher concentrations of plankton in the challenge water to meet the required test water condition of >103 ml−1 for organisms of sizes as stipulated in the guidelines. Examination of the seasonal distribution of local Korean fresh and sea water shows that phytoplankton communities are frequently dominated by cells <10 μm in width but >10 μm in length. In addition, review of over 600 freshwater diatoms of elongated shapes reveals that more than 300 are >10 μm long, but <10 μm wide. We suggest consideration of these phytoplankton in land-based or shipboard treatment procedures and to report their treatment efficacy, in addition to reporting the performance of ballast water management systems in accordance with the D2 regulation.
A review of Hamilton Harbour beaches: Towards delisting 2020, successes and challenges
Authors: Milne Jacqui , Gilpin Sue , Fortuna John
Published: October 2017

Bayfront and Pier 4 Beaches are located in Hamilton Harbour, Ontario, Canada. Both beaches experienced health advisory postings >60% of the bathing season prior to 2005. In order to de-list Hamilton Harbour as one of 43 areas of concerns, the water quality at Bayfront and Pier 4 Beaches must meet the provincial water quality objective of 100 cfu of Escherichia coli 100 ml−1 > = 80% of the bathing season for a minimum of three consecutive years. In 2005, the Hamilton Harbour Beach Committee was formed to guide beach managers on decisions pertaining to beach remediation and E. coli mitigation. Here we discuss the various studies, projects and public outreach programs delivered by Environment Canada, the City of Hamilton and the Bay Area Restoration Council to improve beach health and move toward delisting as an Area of Concern by 2020.
Phytoplankton ecology of a culturally eutrophic embayment: Hamilton Harbour, Lake Ontario
Authors: Munawar M. , Fitzpatrick M. , Niblock H. , Kling H. , Rozon R. , Lorimer J.
Published: October 2017

Hamilton Harbour is a chronically eutrophic embayment located at the western end of Lake Ontario that has experienced many decades of agricultural, industrial, and urban contamination. It has been identified as an Area of Concern under the terms of the Great Lakes Water Quality Agreement between Canada and the United States. This study examines the ecology of the phytoplankton communities at one centrally located station during the ice-free period (May–October) of three non-consecutive years: 2002, 2004 and 2006. This was the first comprehensive study to be conducted since the 1970s. It was found that the phytoplankton communities are diverse and fluctuate throughout the year, along with changing nutrient, physical and environmental conditions. No consistent patterns of seasonal succession were observed throughout the study. Phytoflagellates including Cryptophyceae and Dinophyceae had a tendency to outnumber and out-compete other phytoplankton since they are mobile and able to seek out optimal habitats within the water column. For a highly eutrophic water body, algal biomass (annual mean ≈ 2.0 g m−3) was lower than expected and more consistent with mesotrophic conditions–an observation first made by researchers in the 1970s and attributed to the highly variable physical environment. While our study supports these earlier results, we also conclude that zooplankton grazing likely has a significant role in limiting the size of the algal standing crop. Several algal bloom events were captured during our study. In addition to the somewhat predictable blooms of Diatomeae in the spring and Cyanophyta in the summer, we also observed blooms of Cryptophyceae and Dinophyceae. In one case we observed a bloom with no dominant taxon–it contained a diverse mixture of Cryptophyceae, Euglenophyta and Dinophyceae–challenging the commonly held notion that algal blooms are essentially monocultures. Our results show that such a variable and stressed ecosystem requires frequent sampling to capture the rapid changes that occur.
Uncertainty assessment of trophic flows in Hamilton Harbour: A linear inverse modelling analysis
Authors: Hossain Monir , Stewart Thomas J. , Arhonditsis George B. , van Oevelen Dick , Minns Charles K. , Koops Marten A.
Published: October 2017

Ecopath with Ecosim has been extensively used to examine ecosystem attributes and the effects of management actions. One of the main limitations in using Ecopath to credibly guide management decisions lies in the quality and quantity of the data used. Linear Inverse Modelling treats the problem of ecosystem characterization in a rigorous mathematical way in which the foodweb is described as a (linear) function of the flows and model parameters are (inversely) derived from observed data. In this study, our thesis is that Linear Inverse Modelling can be used as a complement to Ecopath applications to evaluate our confidence in typically reported ecosystem characterizations. Based on a simplified version of a previously published foodweb topology (Hossain et al., 2012), we demonstrate that there is considerable uncertainty associated with the predicted energy flows within the ecosystem of Hamilton Harbour, Lake Ontario, Canada. Uncertainty related to external flows (e.g. respiratory and detrital flows) appears to be much higher than for internal flows associated with predator-prey relationships. Our Linear Inverse Modelling analysis reinforces earlier findings that most of the trophic flows are concentrated within the first two trophic levels, while mass fluxes at the higher trophic levels are significantly lower. The intermediate ecotrophic efficiency for zooplankton suggests that planktivorous fishes do not fully capitalize upon the available food in the system. Our model estimates that a substantial amount of the detrital material is being recycled by the microbial community within the system. Taken together with the significant detrital pool directly supporting zooplankton and oligochaetes/chironomids, this prediction is consistent with recent empirical evidence that particulate organic matter from various allochthonous or autochthonous origins constitute important components of the energy transferred to higher trophic levels. Overall, our Linear Inverse Modelling analysis offers meaningful insights that should contribute towards the development of a reliable ecosystem model for Hamilton Harbour.
Rac3 regulates breast cancer invasion and metastasis by controlling adhesion and matrix degradation
Authors: Donnelly Sara K. , Cabrera Ramon , Mao Serena P.H. , Christin John R. , Wu Bin , Guo Wenjun , Bravo-Cordero Jose Javier , Condeelis John S. , Segall Jeffrey E. , Hodgson Louis
Published: October 2017

The initial step of metastasis is the local invasion of tumor cells into the surrounding tissue. Invadopodia are actin-based protrusions that mediate the matrix degradation necessary for invasion and metastasis of tumor cells. We demonstrate that Rac3 GTPase is critical for integrating the adhesion of invadopodia to the extracellular matrix (ECM) with their ability to degrade the ECM in breast tumor cells. We identify two pathways at invadopodia important for integrin activation and delivery of matrix metalloproteinases: through the upstream recruiter CIB1 as well as the downstream effector GIT1. Rac3 activity, at and surrounding invadopodia, is controlled by Vav2 and βPIX. These guanine nucleotide exchange factors regulate the spatiotemporal dynamics of Rac3 activity, impacting GIT1 localization. Moreover, the GTPase-activating function of GIT1 toward the vesicular trafficking regulator Arf6 GTPase is required for matrix degradation. Importantly, Rac3 regulates the ability of tumor cells to metastasize in vivo. The Rac3-dependent mechanisms we show in this study are critical for balancing proteolytic activity and adhesive activity to achieve a maximally invasive phenotype.
The Association of Early Life Factors and Declining Incidence Rates of Dementia in an Elderly Population of African Americans
Authors: Hendrie Hugh C , Smith-Gamble Valerie , Lane Kathleen A , Purnell Christianna , Clark Daniel O , Gao Sujuan
Published: October 2017

Objectives

To explore the possible association of childhood residence, education levels, and occupation with declining incidence rates of dementia in 2 cohorts of elderly African Americans.

Methods

African Americans residing in Indianapolis without dementia were enrolled in 1992 and 2001 and evaluated every 2–3 years. The cohorts consist of 1,440 participants in 1992 and 1,835 participants in 2001 aged 70 years and older. Cox proportional hazard regression models were used to compare cohort differences in dementia and Alzheimer’s disease (AD) risk.

Results

The 2001 cohort had significantly decreased risk of both incident dementia and AD (hazard ratio [HR]: 0.62/0.57 for dementia/AD). Years of education was associated with decreased risk of dementia (HR = 0.93; p = .0011). A significant interaction (p = .0477) between education and childhood rural residence was found for the risk of AD that higher education level is significantly associated with reduced AD risk (HR = 0.87) in participants with childhood rural residence, but no association in those with urban upbringing. The cohort difference for dementia rates were attenuated by adjusting for the 3 risk factors but remained significant (HR = 0.75; p = .04).

Discussion

These results emphasize the importance of early life factors including rural residence and education for the risk for dementia later in life.
An architecture for genomics analysis in a clinical setting using Galaxy and Docker
Authors: Digan W , Countouris H , Barritault M , Baudoin D , Laurent-Puig P , Blons H , Burgun A , Rance B
Published: October 2017

Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker.
Abelian Arithmetic Chern–Simons Theory and Arithmetic Linking Numbers
Authors: Chung Hee-Joong , Kim Dohyeong , Kim Minhyong , Pappas Georgios , Park Jeehoon , Yoo Hwajong
Published: October 2017

Following the method of Seifert surfaces in knot theory, we define arithmetic linking numbers and height pairings of ideals using arithmetic duality theorems, and compute them in terms of $n$-th power residue symbols. This formalism leads to a precise arithmetic analogue of a “path-integral formula” for linking numbers.
Topical Review: Adherence Interventions for Youth on Gluten-Free Diets
Authors: Holbein Christina E , Carmody Julia K , Hommel Kevin A
Published: October 2017

Objective

To summarize gluten-free diet (GFD) nonadherence risk factors, nonadherence rates, and current intervention research within an integrative framework and to develop a research agenda for the development and implementation of evidence-based GFD adherence interventions.

Methods

Topical review of literature published since 2008 investigating GFD adherence in pediatric samples.

Results

Reviews of pediatric studies indicate GFD nonadherence rates ranging from 19 to 56%. There are few evidence-based, published pediatric GFD adherence interventions. Novel assessments of GFD adherence are promising but require further study. Nonmodifiable and modifiable factors within individual, family, community, and health systems domains must be considered when developing future interventions. Clinical implications are discussed.

Conclusions

Avenues for future research include development and refinement of adherence assessment tools and development of evidence-based GFD adherence interventions. Novel technologies (e.g., GFD mobile applications) require empirical study but present exciting opportunities for adherence intervention.
Temporal Occurrence and Niche Preferences of Phytophthora spp. Causing Brown Rot of Citrus in the Central Valley of California
Authors: Hao Wei , Miles Timothy D. , Martin Frank N. , Browne Gregory T. , Förster Helga , Adaskaveg James E.
Published: October 2017

Brown rot of citrus fruit is caused by several species of Phytophthora and is currently of serious concern for the California citrus industry. Two species, Phytophthora syringae and P. hibernalis, are quarantine pathogens in China, a major export market for California citrus. To maintain trade and estimate the risk of exporting a quarantine pathogen, the distribution and frequency of Phytophthora spp. causing brown rot of orange in major growing areas of California was investigated. Symptomatic fruit were collected from navel (winter to late spring) and Valencia (late spring to summer) orange orchards from 2013 to 2015. Species identification of isolates was based on morphological characteristics, random amplified polymorphic DNA banding patterns, and sequencing of the internal transcribed spacer and the partial cox2/spacer/cox1 regions from axenic cultures, or directly on DNA from fruit tissue using a multiplex TaqMan quantitative polymerase chain reaction assay. In winter samplings, the incidence of P. syringae based on the number of fruit with Phytophthora spp. detection ranged from 73.6 to 96.1% for the two counties surveyed. The remaining isolates were identified as P. citrophthora. In late spring or summer, only P. citrophthora was recovered. P. hibernalis and P. nicotianae were not detected in any fruit with brown rot symptoms. These results indicate that P. syringae is currently an important brown rot pathogen of citrus fruit in California during the cooler seasons of the year. In winter 2016 and 2017, P. syringae was recovered by pear baiting at a high incidence from leaf litter and from a small number of rhizosphere soil or root samples but not from living leaves on the tree. In contrast, P. citrophthora was rarely found in leaf litter but was commonly detected in the rhizosphere. Thus, leaf litter is a major inoculum source for P. syringae and this species occupies a distinct ecological niche.
Genetic Origins of Tetralogy of Fallot
Authors: Morgenthau Ari , Frishman William H.
Published: October 2017

Due to improved survival and clinical outcomes, congenital heart disease (CHD) is an area of growing importance within the medical community. As these patients reach adulthood and have children, there has been a growing appreciation for the increased risk of CHD among their offspring, strongly implying a genetic element. Given the growing wealth of genetic data available and these clinical implications, this review serves to reexamine the role of genetics within CHD, using Tetralogy of Fallot as a model pathology. Tetralogy of Fallot (TOF) is one of the oldest documented CHDs, with a growing prevalence of adult patients, and thus serves as an excellent model for this review. Given the complex nature of cardiac development, it is not surprising that multiple transcription factors and signaling molecules responsible for cardiogenesis have been implicated in TOF, with additional, previously nonimplicated genes being routinely reported within the literature. This review focuses on the well-characterized genes gata4, nkx2.5, jag1, foxc2, tbx5, and tbx1, which have been previously implicated in TOF. Furthermore, this article will attempt to summarize the specific clinical implications associated with the affected genes, such as right-sided aortic arches, associated syndromic presentations, and parental carrier states.
The Prognostic Implications of Two-Dimensional Speckle Tracking Echocardiography in Hypertrophic Cardiomyopathy
Authors: Zegkos Thomas , Parcharidou Despoina , Ntelios Dimitrios , Efthimiadis Georgios , Karvounis Haralambos
Published: October 2017

Two-dimensional speckle tracking echocardiography represents a novel, simple, and reproducible technique for the estimation of left ventricular myocardial deformation (strain) and the evaluation of left ventricular twist mechanics. During the last few years, its clinical and prognostic implications in cardiomyopathies and hypertrophic cardiomyopathy (HCM), in particular, have been rapidly increasing. Reduced global longitudinal strain is associated with more severe disease and confers an increased risk for major cardiac events, independently of other clinical and echocardiographic risk factors. Left ventricular dyssynchrony also seems promising as a risk factor for sudden cardiac events. With respect to left atrial mechanics, left atrial reservoir, conduit, and contractile strain may also confer an increased prognostic value for atrial fibrillation, major cardiac events, and even sudden death. Although right ventricular global longitudinal strain is impaired in HCM compared with healthy controls and individuals with physiological hypertrophy, its prognostic significance is currently unknown. Conclusively, 2-dimensional speckle tracking imaging seems promising for HCM. However, future studies are needed to incorporate this new imaging technique in the standard evaluation of an HCM individual.
Extra-glissonian Approach for Total Laparoscopic Left Hepatectomy: A Prospective Cohort Study
Authors: Chen Huan Wei , Deng Fei Wen , Hu Jian Yuan , Li Jie Yuan , Lai Eric Chun Hung , Lau Wan Yee
Published: October 2017

Laparoscopic liver resection under hemihepatic vascular inflow control has advantages over Pringle’s maneuver, especially in patients with cirrhosis. From January 2016 to August 2016, 7 patients who underwent total laparoscopic left hepatectomy under hemihepatic vascular inflow occlusion using the extra-glissonian approach were included in this study. All were hepatitis B carriers and 4 had cirrhosis. The mean operation time was 247 minutes. The mean transection time was 110 minutes. No patient needed additional Pringle’s maneuver. The mean intraoperative blood loss was 74 ml and no patient required blood transfusion. No open conversion happened. Postoperatively, no patient developed complications and there was no perioperative mortality. The mean resection margin was 2 cm. The mean hospital stay was 6 days. Upon a mean follow-up of 9 months, no patient developed tumor recurrence. The technique of total laparoscopic left hepatectomy using extra-glissonian approach was safe and feasible. The early surgical outcomes were good.
Synthesis of zeolites Na-A and Na-X from tablet compressed and calcinated coal fly ash
Authors: Hu Tao , Gao Wenyan , Liu Xin , Zhang Yifu , Meng Changgong
Published: October 2017

Zeolites Na-A and Na-X are important synthetic zeolites widely used for separation and adsorption in industry. It is of great significance to develop energy-efficient routines that can synthesize zeolites Na-A and Na-X from low-cost raw materials. Coal fly ash (CFA) is the major residue from the combustion of coal and biomass containing more than 85% SiO
2
and Al
2
O
3
, which can readily replace the conventionally used sodium silicate and aluminate for zeolite synthesis. We used Na
2
CO
3
to replace the expensive NaOH used for the calcination of CFA and showed that tablet compression can enhance the contact with Na
2
CO
3
for the activation of CFA through calcination for the synthesis of zeolites Na-A and Na-X under mild conditions. We optimized the control variables for zeolite synthesis and showed that phase-pure zeolite Na-A can be synthesized with CFA at reactant molar ratio, hydrothermal reaction temperature and reaction time of 1.3Na
2
O: 0.6Al
2
O
3
: 1SiO
2
: 38H
2
O at 80°C for 6 h, respectively, while phase-pure zeolite Na-X can be synthesized at 2.2Na
2
O: 0.2Al
2
O
3
: 1SiO
2
: 88H
2
O at 100°C for 8 h, respectively. The composition, morphology, specific surface area, vibration spectrum and thermogravimetry of synthesized Na-A and Na-X were further characterized.
A Fokker–Planck reaction model for the epitaxial growth and shape transition of quantum dots
Authors: Wei Chaozhen , Spencer Brian J.
Published: October 2017

We construct a Fokker–Planck reaction (FPR) model to investigate the dynamics of the coupled epitaxial growth and shape transition process of an array of quantum dots (QDs). The FPR model is based on a coupled system of Fokker–Planck equations wherein the distribution of each island type is governed by its own Fokker–Planck equation for growth, with reaction terms describing the shape transitions between islands of different types including asymmetric shapes. The reaction terms for the shape transitions depend on the island size and are determined from explicit calculations of the lowest barrier pathway for each shape transition. This mean-field model enables us to consider the kinetics of asymmetric shape transitions and study the evolution of island shape distributions during the coupled growth and transition process. Asymmetric metastable shapes play a crucial role in the dynamics, with asymmetric QDs comprising up to 10% of the population, and with up to 100% of the shape transitions passing through asymmetric shapes. Moreover, we find that the characteristic multimodal distribution of pyramid/dome QD coarsening can be eliminated at sufficiently high temperature and deposition rate.
Functional basis of the sexual dimorphism in the auditory fovea of the duetting bushcricketAncylecha fenestrata
Authors: Scherberich Jan , Hummel Jennifer , Schöneich Stefan , Nowotny Manuela
Published: October 2017

From mammals to insects, acoustic communication is in many species crucial for successful reproduction. In the duetting bushcricketAncylecha fenestrata, the mutual acoustic communication between males and females is asymmetrical. We investigated how those signalling disparities are reflected by sexual dimorphism of their ears. Both sexes have tympanic ears in their forelegs, but male ears possess a significantly longer crista acustica containing 35% more scolopidia. With more sensory cells to cover a similar hearing range, the male hearing organ shows a significantly expanded auditory fovea that is tuned to the dominant frequency of the female reply to facilitate phonotactic mate finding. This sex-specific auditory fovea is demonstrated in the mechanical and neuronal responses along the tonotopically organized crista acustica by laservibrometric and electrophysiological frequency mapping, respectively. Morphometric analysis of the crista acustica revealed an interrupted gradient in organ height solely within this auditory fovea region, whereas all other anatomical parameters decrease continuously from proximal to distal. Combining behavioural, anatomical, biomechanical and neurophysiological information, we demonstrate evidence of a pronounced auditory fovea as a sex-specific adaptation of an insect hearing organ for intraspecific acoustic communication.
Lactobacillus allii sp. nov. isolated from scallion kimchi
Authors: Jung Min Young , Lee Se Hee , Lee Moeun , Song Jung Hee , Chang Ji Yoon
Published: October 2017

A novel strain of lactic acid bacteria, WiKim39T, was isolated from a scallion kimchi sample consisting of fermented chili peppers and vegetables. The isolate was a Gram-positive, rod-shaped, non-motile, catalase-negative and facultatively anaerobic lactic acid bacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain WiKim39T belonged to the genus

Lactobacillus

, and shared 97.1–98.2 % pair-wise sequence similarities with related type strains,

Lactobacillus nodensis

,

Lactobacillus insicii

,

Lactobacillus versmoldensis

,

Lactobacillus tucceti

and

Lactobacillus furfuricola

. The G+C content of the strain based on its genome sequence was 35.3 mol%. The ANI values between WiKim39T and the closest relatives were lower than 80 %. Based on the phenotypic, biochemical, and phylogenetic analyses, strain WiKim39T represents a novel species of the genus

Lactobacillus

, for which the name

Lactobacillus
allii sp. nov. is proposed. The type strain is WiKim39T (=KCTC 21077T=JCM 31938T).
Hot-starting software containers for bioinformatics analyses
Authors: Zhang Pai , Hung Ling-Hong , Lloyd Wes , Yeung Ka Yee
Published: October 2017

Using software containers has become standard practice to reproducibly deploy and execute biomedical workflows on the cloud. We demonstrate that hot-starting, from containers that have been frozen after the application has already begun execution, reduces the costs of cloud computing by avoiding repetitive initialization steps. The method is widely applicable and can provide substantial savings both for small jobs and for large-scale deployments using automated schedulers.
Diffusional conductance to CO2 is the key limitation to photosynthesis in salt-stressed leaves of rice (Oryza sativa)
Authors: Wang Xiaoxiao , Wang Wencheng , Huang Jianliang , Peng Shaobing , Xiong Dongliang
Published: October 2017

Salinity significantly limits leaf photosynthesis but the photosynthetic limiting factors in salt- stressed leaves remain unclear. In the present work, photosynthetic and biochemical traits were investigated in four rice genotypes under two NaCl (0 and 150 mM) concentration to assess the stomatal, mesophyll and biochemical contributions to reduced photosynthetic rate (A) in salt stressed leaves. Our results indicated that salinity led to a decrease in A, leaf osmotic potential, electron transport rate and CO2 concentrations in the chloroplasts (Cc) of rice leaves. Decreased A in salt-stressed leaves was mainly attributable to low Cc, which was determined by stomatal and mesophyll conductance. The increased stomatal limitation was mainly related to the low leaf osmotic potential caused by soil salinity. However, the increased mesophyll limitation in salt stressed leaves was related to both osmotic stress and ion stress. These findings highlight the importance of considering mesophyll conductance when developing salinity-tolerant rice cultivars.

Abbreviations

A

photosynthetic rate

Cc, CO2

concentration at carboxylation sites

CE

apparent Rubisco activity

Chl

total chlorophyll content

Ci

intercellular CO2 concentration

ETR

electron transport rate

F0

initial fluorescence of photosystem II in darkness

Fm

maximum fluorescence of photosystem II

Fv

maximum variable fluorescence of photosystem II

Fv/Fm

maximum quantum efficiency of photosystem II

gm

mesophyll conduction

gs

stomatal conduction

Jmax

maximum electron transport rate

K

leaf K content

LMA

leaf mass per area

N

leaf N content

P

leaf P content

OP

osmotic potential

Protein

leaf total soluble protein content

qN

non-chemical quenching efficiency

Rd

day respiration

Rdark

dark respiration

Rubisco

Rubisco content

Vcmax

maximum carboxylation rate

α

leaf light absorptance efficiency

β

the distribution of electrons between PSI and PSII

Γ*

CO2 compensation point in the absence of respiration

ΦPSII

quantum efficiency of photosystem II.
Use of a Neural Circuit Probe to Validate in silico Predictions of Inhibitory Connections
Authors: Liu Honglei , Bridges Daniel , Randall Connor , Solla Sara A. , Wu Bian , Hansma Paul , Yan Xifeng , Kosik Kenneth S. , Bouchard Kristofer
Published: October 2017

Understanding how neuronal signals propagate in local network is an important step in understanding information processing. As a result, spike trains recorded with Multi-electrode Arrays (MEAs) have been widely used to study behaviors of neural connections. Studying the dynamics of neuronal networks requires the identification of both excitatory and inhibitory connections. The detection of excitatory relationships can robustly be inferred by characterizing the statistical relationships of neural spike trains. However, the identification of inhibitory relationships is more difficult: distinguishing endogenous low firing rates from active inhibition is not obvious. In this paper, we propose an in silico interventional procedure that makes predictions about the effect of stimulating or inhibiting single neurons on other neurons, and thereby gives the ability to accurately identify inhibitory causal relationships. To experimentally test these predictions, we have developed a Neural Circuit Probe (NCP) that delivers drugs transiently and reversibly on individually identified neurons to assess their contributions to the neural circuit behavior. With the help of NCP, three inhibitory connections identified by our in silico modeling were validated through real interventional experiments. Together, these methods provide a basis for mapping complete neural circuits.
The effect of abiotic and biotic stress on the salicylic acid biosynthetic pathway from mandelonitrile in peach
Authors: Agustina Bernal-Vicente , Cesar Petri , Antonio Hernández José , Pedro Diaz-Vivancos
Published: October 2017

Highlight

We show that the recently suggested third pathway for SA biosynthesis from mandelonitrile in peach is also functional under both abiotic and biotic stress conditions.

Salicylic acid (SA) plays a central role in plant responses to environmental stresses via the SA-mediated regulation of many metabolic and molecular processes. In a recent study, we suggested a third pathway for SA biosynthesis from mandelonitrile (MD) in peach plants. This pathway is alternative to the phenylalanine ammonia-lyase pathway and links SA biosynthesis and cyanogenesis. In the present work, we show that this new SA biosynthetic pathway is also functional under abiotic (salt) and biotic (Plum pox virus infection) stress conditions, although the contribution of this pathway to the SA pool does not seem to be important under such conditions. Treating peach plants with MD not only affected the SA content, but it also had a pleiotropic effect on abscisic acid and jasmonic acid levels, two well-known stress related hormones, as well as on the H2O2-related antioxidant activities. Furthermore, MD improved plant performance under the stressful conditions, probably via the activation of different signaling pathways. We have thus proven that SA is not limited to biotic stress responses, but that it also plays a role in the response to abiotic stress in peach, although the physiological functions of this new SA biosynthetic pathway from MD remain to be elucidated.

Abbreviations

ABA

abcisic acid

APX

ascorbate peroxidase

BA

benzoic acid

CAT

catalase

CNglcs

cyanogenic glycosides

MD

mandelonitrile

NPR1

non-expressor of pathogenesis-related gene

PAL

phenylalanine ammonia-lyase

Phe

phenylalanine

POX

peroxidase

PPV

Plum pox virus

SA

salicylic acid

SOD

superoxide dismutase

TRX

thioredoxins