bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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 &lt;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 &gt;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 &lt;10 μm in width but &gt;10 μm in length. In addition, review of over 600 freshwater diatoms of elongated shapes reveals that more than 300 are &gt;10 μm long, but &lt;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 &gt;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 &gt; = 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.
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

Abstract

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

Abstract
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

AbstractFollowing 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

Abstract

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.
Hot-starting software containers for bioinformatics analyses
Authors: Zhang Pai , Hung Ling-Hong , Lloyd Wes , Yeung Ka Yee 
Published: October 2017

AbstractUsing 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.AbbreviationsAphotosynthetic rateCc, CO2concentration at carboxylation sitesCEapparent Rubisco activityChltotal chlorophyll contentCiintercellular CO2 concentrationETRelectron transport rateF0initial fluorescence of photosystem II in darknessFmmaximum fluorescence of photosystem IIFvmaximum variable fluorescence of photosystem IIFv/Fmmaximum quantum efficiency of photosystem IIgmmesophyll conductiongsstomatal conductionJmaxmaximum electron transport rateKleaf K contentLMAleaf mass per areaNleaf N contentPleaf P contentOPosmotic potentialProteinleaf total soluble protein contentqNnon-chemical quenching efficiencyRdday respirationRdarkdark respirationRubiscoRubisco contentVcmaxmaximum carboxylation rateαleaf light absorptance efficiencyβthe distribution of electrons between PSI and PSIIΓ*CO2 compensation point in the absence of respirationΦPSIIquantum 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

AbstractUnderstanding 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

HighlightWe show that the recently suggested third pathway for SA biosynthesis from mandelonitrile in peach is also functional under both abiotic and biotic stress conditions.AbstractSalicylic 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.AbbreviationsABAabcisic acidAPXascorbate peroxidaseBAbenzoic acidCATcatalaseCNglcscyanogenic glycosidesMDmandelonitrileNPR1non-expressor of pathogenesis-related genePALphenylalanine ammonia-lyasePhephenylalaninePOXperoxidasePPVPlum pox virusSAsalicylic acidSODsuperoxide dismutaseTRXthioredoxins
Finite-sample genome-wide regression p-values (GWRPV) with a non-normally distributed phenotype
Authors: Connor Gregory , O’Neill Michael 
Published: October 2017

AbstractThis paper derives the exact finite-sample p-value for univariate regression of a quantitative phenotype on individual genome markers, relying on a mixture distribution for the dependent variable. The p-value estimator conventionally used in existing genome-wide association study (GWAS) regressions assumes a normally-distributed dependent variable, or relies on a central limit theorem based approximation. The central limit theorem approximation is unreliable for GWAS regression p-values, and measured phenotypes often have markedly non-normal distributions. A normal mixture distribution better fits observed phenotypic variables, and we provide exact small-sample p-values for univariate GWAS regressions under this flexible distributional assumption. We illustrate the adjustment using a years-of-education phenotypic variable.