bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing and coupling a water quality and a fisheries ecosystem model of the Chesapeake Bay for the exploratory assessment of resource management strategies
Authors: Townsend Howard 
Published: May 2013

Abstract
The Chesapeake Bay (CB) is the North America's largest estuary and is a highly productive ecosystem. State and Federal agencies have been working for over two decades to implement ecosystem-based management (EBM), which will allow the understanding of the impacts of cumulative stressors and enable decision-making that incorporates trade-offs in ecosystem goods and services. To effectively move towards EBM, models that account for bottom-up (e.g. eutrophication) as well as top-down (e.g. fisheries harvest) drivers are necessary. One step towards the integrated analysis of ecosystem stressors is to integrate the existing models that capture bottom-up and top-down effects. In this paper, the efforts of integrating the CB fisheries ecosystem model and the water quality model are described. Specifically, to achieve the integration of these two models, the methods for (i) model comparisons and (ii) model coupling outlined in a report by the CB Scientific and Technical Advisory Committee are implemented for this paper. Comparative analyses of the two models were performed to assess the model structure uncertainty. Broad indirect coupling of these models allows connections between water quality and commercially and recreationally important species to be made and used to assess trade-offs between water quality management goals and fisheries management goals.
Genetic engineering of rotaviruses by reverse genetics
Authors: Komoto Satoshi , Taniguchi Koki 
Published: May 2013

ABSTRACTThe rotavirus genome is composed of 11 gene segments of dsRNA. A recent breakthrough in the field of rotaviruses is the development of a reverse genetics system for generating recombinant rotaviruses possessing a gene segment derived from cloned cDNA. Although this approach is a helper virus‐driven system that is technically limited and gives low levels of recombinant viruses, it allows alteration of the rotavirus genome, thus contributing to our understanding of these medically important viruses. So far, this approach has successfully been applied to three of the 11 viral segments in our laboratory and others, and the efficiency of recovery of recombinant viruses has been improved. However, we are still waiting for the development of a helper virus‐free reverse genetics system for generating an infectious rotavirus entirely from cDNAs, as has been achieved for other members of the Reoviridae family.
Risk avoidance in sympatric large carnivores: reactive or predictive?
Authors: Broekhuis Femke , Cozzi Gabriele , Valeix Marion , McNutt John W. , Macdonald David W. 
Published: May 2013

Summary

Risks of predation or interference competition are major factors shaping the distribution of species. An animal's response to risk can either be reactive, to an immediate risk, or predictive, based on preceding risk or past experiences. The manner in which animals respond to risk is key in understanding avoidance, and hence coexistence, between interacting species.
We investigated whether cheetahs (Acinonyx jubatus), known to be affected by predation and competition by lions (Panthera leo) and spotted hyaenas (Crocuta crocuta), respond reactively or predictively to the risks posed by these larger carnivores.
We used simultaneous spatial data from Global Positioning System (GPS) radiocollars deployed on all known social groups of cheetahs, lions and spotted hyaenas within a 2700 km2 study area on the periphery of the Okavango Delta in northern Botswana. The response to risk of encountering lions and spotted hyaenas was explored on three levels: short‐term or immediate risk, calculated as the distance to the nearest (contemporaneous) lion or spotted hyaena, long‐term risk, calculated as the likelihood of encountering lions and spotted hyaenas based on their cumulative distributions over a 6‐month period and habitat‐associated risk, quantified by the habitat used by each of the three species.
We showed that space and habitat use by cheetahs was similar to that of lions and, to a lesser extent, spotted hyaenas. However, cheetahs avoided immediate risks by positioning themselves further from lions and spotted hyaenas than predicted by a random distribution.
Our results suggest that cheetah spatial distribution is a hierarchical process, first driven by resource acquisition and thereafter fine‐tuned by predator avoidance; thus suggesting a reactive, rather than a predictive, response to risk.
Nonlinear variation of stream–forest linkage along a stream‐size gradient: an assessment using biogeochemical proxies of in‐stream fine particulate organic matter
Authors: Sakamaki Takashi , Richardson John S. 
Published: May 2013

Summary
Spatial scale of processes is necessary information to design appropriate ecosystem research and management. In‐stream ecological processes are tightly linked with their adjacent terrestrial environment and impacted by modifications of riparian environments, particularly in small, forested streams. Quantitative understanding of how the dynamic coupling of these adjacent ecosystems varies along stream continua is necessary to enhance stream research and management.
In temperate, forest‐dominated watersheds of British Columbia, Canada, we examined the stream–forest linkage along a stream‐size gradient based on biogeochemical analysis of fine particulate organic matter retained in streambed sediment (FPOMS). We analysed FPOMS at 48 stations in 14 cobble‐bed streams from 2·2 to 39 m bankfull widths during summer low‐flow conditions and tested their relationships with local, forest‐related, environmental factors (light penetration, benthic coarse POM biomass, riparian‐soil properties) along the stream‐size gradient.
Carbon/nitrogen ratio of FPOMS (FPOMS‐C/N) was distinctly lower in stream bankfull widths larger than an estimated threshold around 7·6 m and corresponded with decrease in N/chlorophyll a of FPOMS and inorganic nitrogen concentration. We found significant linkages of FPOMS‐C/N with local streamside environments in streams narrower than the threshold (but not in widths <~3 m). For wider streams, reduced canopy cover was likely to enhance in‐stream nitrogen cycling by algae and consistently lowered FPOMS‐C/N regardless of streamside environment. These indicate a nonlinear attenuation of the strength of linkage between in‐stream biogeochemical processes and forest‐related environments along the stream‐size gradient.
Synthesis and applications. The relationship of biogeochemical proxies of in‐stream fine particulate organic matter with local environments can be a practical tool for measuring the strength of stream‐forest linkage. Furthermore, regional‐ and stream‐specific threshold stream widths dividing in‐stream biogeochemical regimes can be an important landmark for ecologists and managers to refine designs for stream research and management at appropriate spatial scales. For stream widths narrower than a threshold, reach‐scale linkages between stream and terrestrial environments can be a major focus, and riparian conditions need to be carefully managed to protect stream habitats. For stream widths wider than a threshold, catchment impacts on streams at larger spatial scales would be a more important focus.
Effect of nisin‐producing Lactococcus lactis starter cultures on the inhibition of two pathogens in ripened cheeses
Authors: Bello Barbara Dal , Zeppa Giuseppe , Bianchi Daniela M , Decastelli Lucia , Traversa Amaranta , Gallina Silvia , Coisson Jean Daniel , Locatelli Monica , Travaglia Fabiano , Cocolin luca 
Published: May 2013

The effect of Lactococcus lactis nisin‐producing strains, isolated from Italian fermented foods, on the survival of two foodborne pathogens namely Listeria monocytogenes and Staphylococcus aureus was investigated in experimental cheese production. One of the three Lactobacillus lactis nisin innoculated as starters, Lactobacillus lactis 41FL1 lowered S. aureus count by 1.73 log colony‐forming units (cfu)/g within the first 3 days, reaching the highest reduction, 3.54 log cfu/g, by the end of ripening period of 60 days. There was no effect on L. monocytogenes. The application of L. lactis 41FL1 as bioprotective culture in controlling S. aureus shows considerable promise.
Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2013–31 March 2013
Authors:   Molecular Ecology Resources Primer Development Consortium, Arias M. C. , Atteke Christiane , Augusto S. C. , Bailey J. , Bazaga Pilar , Beheregaray Luciano B. , Benoit Laure , Blatrix Rumsaïs , Born Céline , Brito R. M. , Chen Hai‐kui , Covarrubias Sara , de Vega Clara , Djiéto‐Lordon Champlain , Dubois Marie‐Pierre , Francisco F. O. , García Cristina , Gonçalves P. H. P. , González Clementina , Gutiérrez‐Rodríguez Carla , Hammer Michael P. , Herrera Carlos M. , Itoh H. , Kamimura S. , Karaoglu H. , Kojima S. , Li Shou‐Li , Ling Hannah J. , Matos‐Maraví Pável F. , McKey Doyle , Mezui‐M'Eko Judicaël , Ornelas Juan Francisco , Park R. F. , Pozo María I. , Ramula Satu , Rigueiro Cristina , Sandoval‐Castillo Jonathan , Santiago L. R. , Seino Miyuki M. , Song Chang‐Bing , Takeshima H. , Vasemägi Anti , Wellings C. R. , Yan Ji , Yu‐Zhou Du , Zhang Chang‐Rong , Zhang Tian‐Yun 
Published: May 2013

AbstractThis article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross‐tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii.
Optimizing preservation protocols to extract high‐quality RNA from different tissues of echinoderms for next‐generation sequencing
Authors: Pérez‐Portela Rocío , Riesgo Ana 
Published: May 2013

AbstractTranscriptomic information provides fundamental insights into biological processes. Extraction of quality RNA is a challenging step, and preservation and extraction protocols need to be adjusted in many cases. Our objectives were to optimize preservation protocols for isolation of high‐quality RNA from diverse echinoderm tissues and to compare the utility of parameters as absorbance ratios and RIN values to assess RNA quality. Three different tissues (gonad, oesophagus and coelomocytes) were selected from the sea urchin Arbacia lixula. Solid tissues were flash‐frozen and stored at −80 °C until processed. Four preservation treatments were applied to coelomocytes: flash freezing and storage at −80 °C, RNAlater and storage at −20 °C, preservation in TRIzol reagent and storage at −80 °C and direct extraction with TRIzol from fresh cells. Extractions of total RNA were performed with a modified TRIzol protocol for all tissues. Our results showed high values of RNA quantity and quality for all tissues, showing nonsignificant differences among them. However, while flash freezing was effective for solid tissues, it was inadequate for coelomocytes because of the low quality of the RNA extractions. Coelomocytes preserved in RNAlater displayed large variability in RNA integrity and insufficient RNA amount for further isolation of mRNA. TRIzol was the most efficient system for stabilizing RNA which resulted on high RNA quality and quantity. We did not detect correlation between absorbance ratios and RNA integrity. The best strategies for assessing RNA integrity was the visualization of 18S rRNA and 28S rRNA bands in agarose gels and estimation of RIN values with Agilent Bioanalyzer chips.
Propafenone Versus Vernakalant for Conversion of Recent‐Onset Atrial Fibrillation
Authors: Conde Diego , Costabel Juan Pablo , Aragon Martin , Lambardi Florencia , Klein Andrés , Corrales Barbosa Andrea , Trivi Marcelo , Giniger Alberto 
Published: May 2013

SummaryIntroductionAn oral loading dose of propafenone 600 mg is used in our center as in other places around the world for conversion of recent‐onset atrial fibrillation (AF) in patients without structural heart disease. Vernakalant is a novel, safe, and effective drug used intravenously and has proved to be more rapid in converting recent‐onset AF to sinus rhythm compared with placebo and amiodarone. There is no study that compares vernakalant with propafenone. The aim of our study is to compare the time taken for conversion of recent‐onset AF in patients treated with vernakalant and propafenone.MethodsThirty‐six hemodynamically stable patients with recent‐onset AF without structural heart disease were prospectively included. A single oral dose of propafenone 600 mg was administered to 19 patients and 17 received intravenous vernakalant. Clinical and laboratory variables, conversion rate, and time to conversion were recorded.ResultsBaseline characteristics were similar in both groups. Time to conversion to sinus rhythm was of 166 min (120–300) in the propafenone group versus 9 min (6–18) in the vernakalant group (P = 0.0001). Conversion rate was of 78% in the propafenone group at 8 h and of 93% in the vernakalant group at 2 h; yet, this difference was not statistically significant (P = 0.4). Time to conversion had a direct impact in hospital stay, which was 43% shorter in the vernakalant group (P = 0.0001).ConclusionTime to conversion of AF to sinus rhythm was significantly shorter in the vernakalant group compared with the propafenone group and was associated with shorter hospital stay.
Low body mass index is associated with impaired quality of life in patients with rheumatoid arthritis
Authors: Fukuda Wataru , Omoto Atsushi , Ohta Tamaki , Majima Saori , Kimura Toshihiro , Tanaka Toru , Kohno Masataka , Kawahito Yutaka 
Published: May 2013

AbstractAimTo investigate the relationship between quality of life (QOL) and rheumatoid chachesia, malnutrition in patients with rheumatoid arthritis (RA).MethodsEuroQol Group 5‐Dimension Self‐Report Questionnaire (EQ5D) and Japanese Health Assessment Questionnaire (JHAQ) scores, body mass index (BMI), arm muscle area (AMA) and clinical indicators were measured in 385 RA patients. One‐way analysis of variance for obtained data was conducted among three groups: 131 with low BMI (< 20), 163 with moderate (20–25) and 91 with high BMI (≥25). Then multiple regression analyses for JHAQ and EQ5D scores with nutritional and clinical indicators as independent variables were performed.ResultsEQ5D and JHAQ scores were significantly lower and higher, respectively, in the low BMI group than those in the moderate BMI group. Clinical indicators including doses of corticosteroid were similar among the three groups except for disease duration. Disease activity score (DAS) 28, disease duration, C‐reactive protein and AMA were significant variables in the regression model for EQ5D.ConclusionLow BMI deteriorates the QOL of RA patients. Muscle protein loss apparently leads to a reduction in BMI and QOL.
Global Income Inequality in Numbers: in History and Now
Authors: Milanovic Branko 
Published: May 2013

AbstractThis article presents an overview of calculations of global inequality, recently and over the long term, and outlines the main controversies and political and philosophical implications of the findings. It focuses in particular on the winners and losers of the most recent episode of globalization, from 1988 to 2008. It suggests that the period has witnessed the first decline in inequality between world citizens since the Industrial Revolution. However, the decline can be sustained only if countries' mean incomes continue to converge (as they have been doing during the past ten years) and if internal (within‐country) inequalities, which are already high, are kept in check. Mean‐income convergence would also reduce the huge ‘citizenship premium’ that is enjoyed today by the citizens of rich countries.
Assessing species occurrence and species‐specific use patterns of bais (forest clearings) in Central Africa with camera traps
Authors: Gessner Julia , Buchwald Rainer , Wittemyer George 
Published: May 2013

AbstractThe impacts of increasing resource extraction on biodiversity in the Central African rainforest are largely unknown, in part due to the lack of baseline data on species occurrence across the basin. Natural forest clearings (bais) in this region are key habitats for a variety of vertebrates and offer opportunities for monitoring species distribution. Information on species composition, however, is lacking from the majority of areas (except for long‐term study sites). Approaches and protocols for short‐term bai assessments can greatly advance such baseline knowledge. This study demonstrates that camera traps provide an effective method for species inventories (species occurrence and temporal activity patterns) and monitoring at bais across the broader region. In comparison with direct observational studies, they performed especially well regarding rare and nocturnal species. Camera traps during sampling sessions of 4 weeks or less recorded previously undocumented, and 65–94% of the mammals known to use each of seven Central African bais. Results indicate that many mammal species, in particular African forest elephants (Loxodonta africana cyclotis), visit bais preferentially at night. This underlines the urgent need for monitoring tools providing both diurnal and nocturnal data to provide baseline data that address conservation and management objectives.
An analysis of structure: biomass structure relationships for characteristic species of the western Kalahari, Botswana
Authors: Meyer Thoralf , D'Odorico Paolo , Okin Greg S. , Shugart Herman H. , Caylor Kelly K. , O'Donnell Frances C. , Bhattachan Abi , Dintwe Kebonyethata 
Published: May 2013

AbstractSavannah ecosystems are important carbon stocks on the Earth, and their quantification is crucial for understanding the global impact of climate and land‐use changes in savannahs. The estimation of aboveground/belowground plant biomass requires tested allometric relationships that can be used to determine total plant biomass as a function of easy‐to‐measure morphological indicators. Despite recent advances in savannah ecology, research on allometric relations in savannahs remains confined to a few site‐specific studies where basal area is typically used as the main morphometric parameter with plant biomass. We investigate allometric relations at four sites along a 950‐km transect in the Kalahari across mean rainfall gradient 170 mm yr−1–550 mm yr−1. Using data from 342 harvested trees/shrubs, we relate basal area, height and crown diameter to aboveground biomass. These relationships are strongest in trees and weakest in small shrubs. Strong allometric relationships are also determined for morphologically similar groups of woody vegetation. We show that crown diameter can be used as an alternative to basal area in allometric relationships with plant biomass. This finding may enhance the ability to determine aboveground biomass over large areas using high‐resolution aerial or satellite imagery without requiring ground‐based measurements of basal area.
Five‐year oncological outcomes of endoscopic extraperitoneal radical prostatectomy (EERPE) for prostate cancer: results from a medium‐volume UK centre
Authors: McNeill S. Alan , Good Daniel W. , Stewart Grant D. , Stolzenburg Jens‐Uwe 
Published: May 2013

Objective
To determine the 5‐year oncological outcomes of endoscopic extraperitoneal radical prostatectomy (EERPE) from a medium‐volume centre, thereby providing much needed data on outcomes from the UK.
Patients and Methods
From January 2006 to January 2012, 575 patients underwent EERPE for localized prostate cancer, performed by a single surgeon who had completed a modular training programme.
Follow‐up was as per local hospital policy and data were collected in our prospective database.
A retrospective review of patient demographics, prostate‐specific antigen (PSA) levels, pathological T stages, Gleason scores, surgical margin status and biochemical recurrence (BCR) data was performed. BCR was defined as PSA >0.2 μg/L.
Results
The mean (range) patient age was 62 (40.3–76.5) years and the mean (range) follow‐up was 30 (12–72) months. The median (interquartile range [IQR]) operating time was 135 (120–170) min and the median (IQR) blood loss was 200 (100–250) mL.
Of the 575 patients, 135 (23.5%) had positive surgical margins (PSMs). The PSM rate for pT2 disease was 66/406 patients (16.3%) and for pT3 disease it was 68/168 patients (40.5%). Overall BCR‐free survival at 5‐years was 81.5%.
Multivariate Cox analysis showed that PSMs, Gleason score, D'Amico risk category and pT stage were independent predictors of BCR‐free survival.
Conclusions
This assessment of the oncological results of EERPE, which included the surgical learning curve, shows that the adoption of EERPE after mentored fellowship training translates into mid‐term oncological outcomes in line with those of retropubic/transperitoneal laparoscopic approaches and with large‐volume centres worldwide which have pioneered laparoscopic radical prostatectomy.
The study shows that EERPE in a medium‐volume second generation laparoscopic centre (that introduced EERPE after adequate training in pioneering centres) produces results with good 5‐year oncological outcomes, similar to those of other major series, for patients in the UK.
The Relative Importance of Fungal Infection, Conspecific Density and Environmental Heterogeneity for Seedling Survival in a Dominant Tropical Tree
Authors: Chanthorn Wirong , Caughlin Trevor , Dechkla Sukhum , Brockelman Warren Y. 
Published: May 2013

AbstractA gap remains in our understanding of how host‐specific fungal pathogens impact negative density dependence (NDD). Here, we investigated survival ofCinnamomum subaveniumMiq. seedlings, the dominant canopy species in a seasonal tropical evergreen forest, Thailand. It is infected by a host‐specific fungus that is easily identifiable in the field. We quantified the effects of conspecific seedling and adult density on fungal infection and seedling survival over a wide range of environmental heterogeneity in elevation, understory vegetation and presence of forest gaps. Generalized linear mixed models (GLMMs) for seedling survival revealed that fungal infection significantly reduced survival and had the strongest effect on seedling survival as compared with conspecific density and environmental heterogeneity. Adult conspecific density was not, however, significantly correlated with the probability of infection, and conspecific seedling density was positively associated with increased infection only at high elevations. In contrast to infection, we found a significant positive correlation between conspecific seedling density and the probability of seedling survival. Consequently, our results demonstrate that fungal infection can have major impacts on seedling survival, but not in a manner consistent with localNDDeffects on seedlings, as assumed in the Janzen–Connell hypothesis. Our study provides an example of how quantifying the interaction between environmental heterogeneity and a host‐specific plant‐pathogen can yield unexpected insights into the dynamics of seedling populations. The combined effects of host‐specific pathogens and environmental heterogeneity on survival of dominant seedling species may ultimately provide a chance for rarer species to recruit.