bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression
Authors: Krüger Manuela , Teste François P. , Laliberté Etienne , Lambers Hans , Coghlan Megan , Zemunik Graham , Bunce Michael 
Published: September 2015

AbstractEcosystem retrogression following long‐term pedogenesis is attributed to phosphorus (P) limitation of primary productivity. Arbuscular mycorrhizal fungi (AMF) enhance P acquisition for most terrestrial plants, but it has been suggested that this strategy becomes less effective in strongly weathered soils with extremely low P availability. Using next generation sequencing of the large subunit ribosomal RNA gene in roots and soil, we compared the composition and diversity of AMF communities in three contrasting stages of a retrogressive >2‐million‐year dune chronosequence in a global biodiversity hotspot. This chronosequence shows a ~60‐fold decline in total soil P concentration, with the oldest stage representing some of the most severely P‐impoverished soils found in any terrestrial ecosystem. The richness of AMF operational taxonomic units was low on young (1000's of years), moderately P‐rich soils, greatest on relatively old (~120 000 years) low‐P soils, and low again on the oldest (>2 000 000 years) soils that were lowest in P availability. A similar decline in AMF phylogenetic diversity on the oldest soils occurred, despite invariant host plant diversity and only small declines in host cover along the chronosequence. Differences in AMF community composition were greatest between the youngest and the two oldest soils, and this was best explained by differences in soil P concentrations. Our results point to a threshold in soil P availability during ecosystem regression below which AMF diversity declines, suggesting environmental filtering of AMF insufficiently adapted to extremely low P availability.
A Clustering Algorithm for Bi‐Criteria Stop Location Design with Elastic Demand
Authors: Hossein Rashidi Taha , Rey David , Jian Sisi , Waller Travis 
Published: September 2015

AbstractThis article proposes a bi‐criteria formulation to find the optimal location of light rapid transit stations in a network where demand is elastic and budget is constrained. Our model is composed of two competing objective functions seeking to maximize the total ridership and minimize the total budget allocated. In this research, demand is formulated using the random utility maximization method with variables including access time and travel time. The transit station location problem of this study is formulated using mixed integer programming and we propose a heuristic solution algorithm to solve large‐scale instances which is inspired by the problem context. The elastic demand is integrated with the optimization problem in an innovative way which facilitates the solution process. The performance of our model is evaluated on two test problems and we carry out its implementation on a real‐world instance. Due to the special shape of the Pareto front function, significant practical policy implications, in particular budget allocation, are discussed to emphasize the fact that the trade‐off between cost and benefit may result in large investments with little outcomes and vice versa.
An osteonecrosis model induced by oral bisphosphonate in ovariectomised rats
Authors: Tanaka J , Kokuryo S , Yoshiga D , Tsurushima H , Sakaguchi O , Habu M , Nishihara T , Yoshioka I , Tominaga K 
Published: September 2015

ObjectiveTo develop a model of osteonecrosis using oral bisphosphonate in ovariectomy‐induced osteoporotic rats.Materials and MethodsThirty‐six rats were subjected to ovariectomy or sham surgery. After 8 weeks, rats received oral alendronate (1.0 mg kg−1) or saline once weekly for 4 weeks; then, serum C‐telopeptide cross‐linked collagen type I levels were measured to evaluate bone metabolism. Twelve rats from each group were injected with either lipopolysaccharide or saline into the bone marrow of the mandibles and femurs, and the areas of osteonecrosis were evaluated by histomorphometry.ResultsSerum C‐telopeptide cross‐linked collagen type I levels were significantly increased in the ovariectomy group (105.1 ± 2.1 ng ml−1) compared with the sham group (78.9 ± 12.5 ng ml−1); they were significantly reduced following oral alendronate administration in the ovariectomy group (91.0 ± 4.4 ng ml−1). Following alendronate and lipopolysaccharide administration, extensive osteonecrosis was observed in the mandibles and femurs of ovariectomy (0.45 ± 0.08 mm2, 1.69 ± 0.72 mm2, respectively) and sham (1.12 ± 0.45 mm2, 1.84 ± 0.66 mm2, respectively) groups. Significantly wider osteonecrosis occurred in the mandibles of sham‐operated rats than ovariectomy rats following alendronate or lipopolysaccharide treatment.ConclusionsWe successfully developed a model of osteonecrosis in ovariectomised rats following oral bisphosphonate administration.
Will technology trample peer review in ecology? Ongoing issues and potential solutions
Authors: Peres‐Neto Pedro R. 
Published: September 2015

The classical view of peer review is that it is our primary process for assessing and judging whether research results should be published in a scholarly journal. However, the increased pressure to publish and technological developments are transforming peer review such that it is becoming a system that judges where work is published rather than whether the research is publishable (a ‘where rather than if’ process). Ecology is a field in which publication numbers puts a particular pressure on the review system. In this forum piece, I summarize the issues with the current publication system and discuss how technology is changing it, while suggesting solutions for important prior and ongoing issues with the peer review system. The view explored here is that technological developments (e.g. ease of creating journals, internet sites, storage, data generation, sharing of data and analytical code) will not eliminate peer review per se but will allow for a new set of parameters in which ethics and the optimal use of public funding will play a vital role in the evolution of the review process.SynthesisThe number of papers and journals in Ecology has increased dramatically in the past decade. I present a critical overview of our review system and proposes that pressure to publish and technological developments have transformed peer review into a system that decides “where rather than if” papers are publishable. While reviewing the current pressures and factors playing a vital role in the evolution of the review and publication systems, I propose potential solutions to deal with current and future challenges to the peer review and publication systems.
A putative TetR regulator is involved in nitric oxide stress resistance in Porphyromonas gingivalis
Authors: Boutrin M.‐C. , Yu Y. , Wang C. , Aruni W. , Dou Y. , Shi L. , Fletcher H.M. 
Published: September 2015

SummaryTo survive in the periodontal pocket, Porphyromonas gingivalis, the main causative agent of periodontal disease, must overcome oxidative and nitric oxide (NO) stress. Previously, we reported that, in the presence of NO comparable to stress conditions, the transcriptome of P. gingivalis was differentially expressed, and genes belonging to the PG1178‐81 cluster were significantly upregulated. To further evaluate their role(s) in NO stress resistance, these genes were inactivated by allelic exchange mutagenesis. Isogenic mutants P. gingivalis FLL460 (ΔPG1181::ermF) and FLL461 (ΔPG1178‐81::ermF) were black‐pigmented, with gingipain and hemolytic activities comparable to that of the wild‐type strain. Whereas the recovery of these isogenic mutants from NO stress was comparable to the wild‐type, there was increased sensitivity to hydrogen peroxide‐induced stress. RNA‐Seq analysis under conditions of NO stress showed that approximately 5 and 8% of the genome was modulated in P. gingivalis FLL460 and FLL461, respectively. The PG1178‐81 gene cluster was shown to be part of the same transcriptional unit and is inducible in response to NO stress. In the presence of NO, PG1181, a putative transcriptional regulator, was shown to bind to its own promoter region and that of several other NO responsive genes including PG0214 an extracytoplasmic function σ factor, PG0893 and PG1236. Taken together, the data suggest that PG1181 is a NO responsive transcriptional regulator that may play an important role in the NO stress resistance regulatory network in P. gingivalis.
Planning and management for sustainable coastal aquaculture development in Santa Catarina State, south Brazil
Authors: Suplicy Felipe M. , Vianna Luiz F. de Novaes , Rupp Guilherme S. , Novaes André L. T. , Garbossa Luis H. P. , de Souza Robson V. , Guzenski João , da Costa Sérgio W. , Silva Fabiano M. , dos Santos Alex A. 
Published: September 2015

AbstractMarine aquaculture of bivalve molluscs is an important economic activity in Santa Catarina State, Brazil, with more than 5000 persons directly and indirectly involved and an annual revenue of US$ 18 million in 2013. In the first decade of this activity, a lack of proper regulation imposed multiple obstacles to the sustainable management of local shellfish farming. The occupation of marine space occurred in a disorderly manner, and the unplanned development led to unfavourable conditions that threatened the sustainability of the industry. This study describes how better planning and management tools have improved governance of marine aquaculture in Santa Catarina State. The process included development of a legal framework for aquaculture planning, elaboration of local development plans with a participatory and multidisciplinary approach, development of a geographic information system to identify favourable areas and creation of a Web‐based aquaculture management system. The combined application of these actions, along with continuing extension services, is expected to contribute to the regulation of 837 shellfish farming areas, the expansion of farming activity, the mitigation of the environmental and visual impacts caused by coastal aquaculture and an increase in the public health of shellfish consumers. In this manuscript, we report an example of how the application of better planning and management of the aquaculture sector can prepare the industry for a sustainable growing cycle.
Growing older in the context of needing geriatric assessment: a qualitative study
Authors: Esbensen Bente Appel , Hvitved Ida , Andersen Hanne Elkjær , Petersen Charlotte Møller 
Published: September 2015

AimThe number of older adults will increase worldwide in the next 30 years, with many expected to develop chronic diseases and consequently require additional medical assessments and adequate care. The aim of this study was to describe how a group of older adults who need geriatric assessment experience growing older.MethodologyA qualitative study was performed. The empirical data consisted of qualitative in‐depth interviews with eight older persons referred to geriatric assessment (median age 76, range 65–86). The interviews were analysed based on Giorgi's descriptive phenomenological methodology.ResultsThe results led to an overall essence and five themes. The five themes were identified: (i) considerations to avoid weakness, (ii) compensation for the inability to perform certain activities, (iii) aides – a symbol of freedom or limitation, (iv) lifestyle considered being particularly significant and (v) considerations about the end of life as a component of growing older. The essence was defined as: illness essential for the experience of growing older and pointed to the experience of growing older that highlighted that experiencing illnesses and limitations served as reminders of their advancing age.ConclusionGrowing older while in need of comprehensive geriatric assessment led to participants feeling they were no longer able to do the same things, they used to do. Consequently, compensation became an essential part of adaption to the altered situation. Aides that helped to overcome limitations in every daily life had the status of either creating freedom or being limiting in things they wished to do. Considerations about lifestyle were focused on housing and change of dwelling. This also led to thoughts about the future and end of life. Additional research regarding accommodations in older age is warranted to offer the best solutions for older people.
Hope as an Intellectual Virtue?
Authors: Cobb Aaron D. 
Published: September 2015

AbstractHope is a ubiquitous feature of human experience, but there has been relatively little scholarship within contemporary analytic philosophy devoted to the systematic analysis of its nature and value. In the last decade, however, there has been a resurgence of interest in the study of hope and, in particular, its role in human agency. This scholarly attention reflects an ambivalence about hope's effects. While the possession of hope can have salutary consequences, it can also make the agent vulnerable to certain kinds of personal risk. The pervasiveness of hope is not a sign of its quality; only a well‐tuned hope can be a virtue. Recently, Nancy Snow has argued that hope can be an intellectual virtue. Framing her account as a contribution to regulative epistemology, she contends that the intellectual virtue of hope can (i) motivate the pursuit of important epistemic ends, (ii) create dispositions that enable the successful pursuit of these aims, and (iii) generate a method for enduring intellectual projects. In this paper, I provide a critical appraisal of Snow's account of hope as an intellectual virtue. One important implication of this critique is that hope can function as an intellectual virtue only to the extent that it has benefitted from the correcting and perfecting influence of other cognitive excellences.
Anti‐Cartesianism and Anti‐Brentanism: The Problem of Anti‐Representationalist Intentionalism
Authors: Roy Jean‐Michel 
Published: September 2015

AbstractDespite its internal divisions and the uncertainty surrounding many of its foundations, there is a growing consensus that the on‐going search for an alternative model of the mind finds a minimal theoretical identity in the pursuit of an anti‐Cartesian conception of mental phenomena. Nevertheless, this anti‐Cartesianism remains more or less explicitly committed to the neo‐Brentanian idea that intentionality is an essential feature of the mental—an idea that has prevailed since the advent of modern cognitive science in the 1950s. An issue of compatibility is thereby raised, as neo‐Brentanism arguably sides with cognitive Cartesianism. The main goal of the paper is to put into full light one specific aspect of this largely unperceived problem of compatibility by arguing that the neo‐Brentanian property of intentionality is an essentially representational one that runs counter to the salient anti‐representationalism of anti‐Cartesianism. And, that this representational essence confronts the search for alternative models of the mind of an anti‐Cartesian kind with the following theoretical issue: To what extent is it possible to devise a non‐Brentanian property of intentionality, particularly one that is fully dissociated from the property of representation? This issue is shown to be much deeper and more difficult than it looks once the nature of representation is properly apprehended; it seems to be still waiting for an answer in the current search for an alternative model of the mind, if only because it has not yet be set in fully adequate terms.
Phylogenetic relationships of nonbiting midges in the subfamilyTanypodinae (Diptera:Chironomidae) inferred from morphology
Authors: SILVA FABIO LAURINDO DA , EKREM TORBJØRN 
Published: September 2015

AbstractThe nonbiting midge subfamily Tanypodinae represents one of the most diverse lineages ofChironomidae. Despite the wide distribution and high diversity of tanypodine chironomids, the evolutionary history of the subfamily remains poorly understood. Here, we present the first phylogenetic analysis of the subfamily Tanypodinae based on morphological data. Cladistic analyses were conducted using 86 morphological characters from 115 species belonging to 54 tanypodine genera, including the eight currently recognised tribes:Anatopyniini,Clinotanypodini,Coelopyniini,Macropelopiini,Natarsiini,Pentaneurini,Procladiini andTanypodini. We use characters from fourth‐instar larvae, pupae and adults of both sexes. We examine the effects of implied weighting by reanalysing the data with varying values of concavity constant (k). Our analysis supports the monophyly ofTanypodinae withPodonominae as its sister group. All previously proposed tribes are recovered as monophyletic assemblages under a wide range of weighting factors. Under these conditions, the genusFittkauimyiais the sister group of the remaining Macropelopiini and is erected as a new monobasic tribe,Fittkauimyiinitrib.n. The tribePentaneurini is recovered as monophyletic with some internal relationships resolved. The genusParamerina, recovered as sister ofReomyia + Zavrelimyia, is formally synonymised withZavrelimyiasyn.n., based on morphological similarity in all three life stages and treated as a subgenus of the latter. Finally, the recently suggested synonymies ofGressittiusandGuassutanypuswithAlotanypusand the establishment of the subgeneraConchapelopia(Helopelopia),Macropelopia(Bethbilbeckia),Monopelopia(Cantopelopia),Thienemannimyia(Hayesomyia) andZavrelimyia(ReomyiaandSchineriella) are investigated. Our results support all proposed changes, except for the subgenus‐level status ofHelopelopiaandCantopelopia.We suggest re‐establishment ofHelopelopiaas a genus, but refrain from promoting genus‐level status ofCantopelopiaat present because the apparent sister‐relationship betweenMonopelopia + Nilotanypuslikely is due to wing vein reduction caused by miniaturisation.This published work has been registered in ZooBank,http://zoobank.org/urn:lsid:zoobank.org:pub:DF012C17‐AFB3‐4904‐83DC‐30DD94D0B376.
Non‐canonical roles for caveolin in regulation of membrane repair and mitochondria: implications for stress adaptation with age
Authors: Schilling Jan M. , Patel Hemal H. 
Published: September 2015

AbstractMany different theories of ageing have been proposed but none has served the unifying purpose of defining a molecular target that can limit the structural and functional decline associated with age that ultimately leads to the demise of the organism. We propose that the search for a molecule with these unique properties must account for regulation of the signalling efficiency of multiple cellular functions that degrade with age due to a loss of a particular protein. We suggest caveolin as one such molecule that serves as a regulator of key processes in signal transduction. We define a particular distinction between cellular senescence and ageing and propose that caveolin plays a distinct role in each of these processes. Caveolin is traditionally thought of as a membrane‐localized protein regulating signal transduction via membrane enrichment of specific signalling molecules. Ultimately we focus on two non‐canonical roles for caveolin – membrane repair and regulation of mitochondrial function – which may be novel features of stress adaptation, especially in the setting of ageing. The end result of preserving membrane structure and mitochondrial function is maintenance of homeostatic signalling, preserving barrier function, and regulating energy production for cell survival and resilient ageing.
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Association of Human Papillomavirus 31 DNA Load with Risk of Cervical Intraepithelial Neoplasia Grades 2 and 3
Authors: Liu Xia , Schiffman Mark , Hulbert Ayaka , He Zhonghu , Shen Zhenping , Koutsky Laura A. , Xi Long Fu 
Published: September 2015

ABSTRACT
The association between human papillomavirus 31 (HPV31) DNA loads and the risk of cervical intraepithelial neoplasia grades 2 and 3 (CIN2–3) was evaluated among women enrolled in the atypical squamous cells of undetermined significance (ASCUS) and low-grade squamous intraepithelial lesion (LSIL) triage study (ALTS), who were monitored semiannually over 2 years and who had HPV31 infections detected at ≥1 visit. HPV31 DNA loads in the first HPV31-positive samples and in a random set of the last positive samples from women with ≥2 HPV31-positive visits were measured by a real-time PCR assay. CIN2–3 was histologically confirmed at the same time as the first detection of HPV31 for 88 (16.6%) of 530 women. After adjustment for HPV31 lineages, coinfection with other oncogenic types, and the timing of the first positive detection, the odds ratio (OR) per 1-log-unit increase in viral loads for the risk of a concurrent diagnosis of CIN2–3 was 1.5 (95% confidence interval [CI], 1.2 to 1.9). Of 373 women without CIN2–3 at the first positive visit who had ≥1 later visit, 44 had subsequent diagnoses of CIN2–3. The initial viral loads were associated with CIN2–3 diagnosed within 6 months after the first positive visit (adjusted OR, 1.5 [95% CI, 1.0 to 2.4]) but were unrelated to CIN2–3 diagnosed later. For a random set of 49 women who were tested for viral loads at the first and last positive visits, changes in viral loads were upward and downward among women with and without follow-up CIN2–3 diagnoses, respectively, although the difference was not statistically significant. Results suggest that HPV31 DNA load levels at the first positive visit signal a short-term but not long-term risk of CIN2–3.
Blood Volume Required for Detection of Low Levels and Ultralow Levels of Organisms Responsible for Neonatal Bacteremia by Use of Bactec Peds Plus/F, Plus Aerobic/F Medium, and the BD Bactec FX System: anIn VitroStudy
Authors: Lancaster Diana P. , Friedman David F. , Chiotos Kathleen , Sullivan Kaede V. 
Published: September 2015

ABSTRACTWe used anin vitrotechnique to investigate blood volumes required to detect bacteremia and fungemia with low concentrations of an organism. At 1 to 10 CFU/ml,Escherichia coli,Staphylococcus epidermidis,Staphylococcus aureus,Listeria monocytogenes,Candida albicans, andCandida parapsilosisisolates were detected in volumes as low as 0.5 ml. Detection ofStreptococcus agalactiaeand detection of bacteremia at <1 CFU/ml were unreliable.
M-Protein Analysis of Streptococcus pyogenes Isolates Associated with Acute Rheumatic Fever in New Zealand
Authors: Williamson Deborah A. , Smeesters Pierre R. , Steer Andrew C. , Steemson John D. , Ng Adrian C. H. , Proft Thomas , Fraser John D. , Baker Michael G. , Morgan Julie , Carter Philip E. , Moreland Nicole J. 
Published: September 2015

ABSTRACT

We applied an
emm
cluster typing system to group A
Streptococcus
strains in New Zealand, including those associated with acute rheumatic fever (ARF). We observed few so-called rheumatogenic
emm
types but found a high proportion of
emm
types previously associated with pyoderma, further suggesting a role for skin infection in ARF.
A Stewardship Approach To Optimize Antimicrobial Therapy through Use of a Rapid Microarray Assay on Blood Cultures Positive for Gram-Negative Bacteria
Authors: Sothoron Conner , Ferreira Jason , Guzman Nilmarie , Aldridge Petra , McCarter Yvette S. , Jankowski Christopher A. 
Published: September 2015

ABSTRACT

A Gram-negative (GN) blood culture microarray assay with an antimicrobial stewardship program (ASP) intervention was evaluated in 126 patients with GN bacteremia. The median time to optimal therapy was shorter in the postintervention group than in the preintervention group (49.3 h versus 38.5 h, respectively;
P
= 0.0199). ASP can utilize microarray technology to decrease the time to optimal antimicrobial therapy.