Search

Citation patterns were examined for Worm et al. 2006 (Science 314∶787–790), a high-impact paper that focused on relationships between marine biodiversity and ecosystem services. This paper sparked much controversy through its projection, highlighted in the press release, that all marine fisheries would be collapsed by 2048. Analysis of 664 citing papers revealed that only a small percentage (11%) referred to the 2048 projection, while 39% referred to fisheries collapse in general, and 40% to biodiversity and ecosystem services. The 2048 projection was mentioned more often in papers published soon after the original paper, in low-impact journals, and in journals outside of fields that would be expected to focus on biodiversity. Citing papers also mentioned the 2048 projection more often if they had few authors (28% of single-author papers vs. 2% of papers with 10 or more authors). These factors suggest that the more knowledgeable the authors of citing papers were about the controversy over the 2048 projection, the less likely they were to refer to it. A noteworthy finding was that if the original authors were also involved in the citing papers, they rarely (1 of 55 papers, 2%) mentioned the 2048 projection. Thus the original authors have emphasized the broader concerns about biodiversity loss, rather than the 2048 projection, as the key result of their study. [ABSTRACT FROM AUTHOR]

Quantifying the impact of a scholarly paper is of great significance, yet the effect of geographical distance of cited papers has not been explored. In this paper, we examine 30,596 papers published in Physical Review C, and identify the relationship between citations and geographical distances between author affiliations. Subsequently, a relative citation weight is applied to assess the impact of a scholarly paper. A higher-order weighted quantum PageRank algorithm is also developed to address the behavior of multiple step citation flow. Capturing the citation dynamics with higher-order dependencies reveals the actual impact of papers, including necessary self-citations that are sometimes excluded in prior studies. Quantum PageRank is utilized in this paper to help differentiating nodes whose PageRank values are identical. [ABSTRACT FROM AUTHOR]

Paper mulberry, Broussonetia papyrifera (L.) L’Hér. ex Vent. (Moraceae), a dioecious species, was transported by humans from Taiwan to the islands of Remote Oceania. Its introduction and cultivation in Remote Oceania was intentional due to its cultural importance as a fiber source for barkcloth textiles. The aim of this study was to explore the genetic diversity and structure of paper mulberry populations within Remote Oceania in order to infer dispersal patterns that may reflect past human interaction among island groups. We present the integrated analysis of 380 samples (313 contemporary and 67 herbarium specimens) collected in Near and Remote Oceania. Genetic characterization was based on a set of ten microsatellites developed for B. papyrifera and complemented with the analysis of the ribosomal internal transcribed spacer ITS-1 sequence, a sex marker and the chloroplast ndhF–rpl32 intergenic spacer. Microsatellite data identify a total of 64 genotypes, despite this being a clonally propagated crop, and show three major dispersal hubs within Remote Oceania, centered on the islands of Fiji, Tonga, and Pitcairn. Of 64 genotypes identified, 55 correspond to genotypes associated to female-sexed plants that probably descend from plants introduced by the prehistoric Austronesian-speaking voyagers. The ratio of accessions to genotypes between herbarium and contemporary samples, suggests recent loss of genetic diversity. In addition to the chloroplast haplotypes described previously, we detected two new haplotypes within Remote Oceania both originating in Taiwan. This is the first study of a commensal species to show genetic structuring within Remote Oceania. In spite of the genetic bottleneck, the presence of only one sex, a timespan of less than 5000 years, and asexual propagation of this crop in Remote Oceania, we detect genetic diversity and regional structuring. These observations suggest specific migration routes between island groups within Remote Oceania. [ABSTRACT FROM AUTHOR]

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks. [ABSTRACT FROM AUTHOR]

Cooperation among kin is common in animal societies. Kin groups may form by individuals directly discriminating relatives based on kin recognition cues, or form passively through natal philopatry and limited dispersal. We describe the genetic landscape for a primitively eusocial wasp, Polistes dominula, and ask whether individuals choose cooperative partners that are nearby and/or that are genetic relatives. Firstly, we genotyped an entire sub-population of 1361 wasps and found genetic structuring on an extremely fine scale: the probability of finding genetic relatives decreases exponentially within just a few meters of an individual’s nest. At the same time, however, we found a lack of genetic structuring between natural nest aggregations within the population. Secondly, in a separate dataset where ~2000 wasps were genotyped, we show that wasps forced experimentally to make a new nest choice tended to choose new nests near to their original nests, and that these nests tended to contain some full sisters. However, a significant fraction of wasps chose nests that did not contain sisters, despite sisters being present in nearby nests. Although we cannot rule out a role for direct kin recognition or natal nest-mate recognition, our data suggest that kin groups may form via a philopatric rule-of-thumb, whereby wasps simply select groups and nesting sites that are nearby. The result is that most subordinate helpers obtain indirect fitness benefits by breeding cooperatively. [ABSTRACT FROM AUTHOR]

Open access publication rates have been steadily increasing over time. In spite of this growth, academics in low income settings struggle to gain access to the full canon of research literature. While the vast majority of open access repositories and funding organizations with open access policies are based in high income countries, the geographic patterns of open access publication itself are not well characterized. In this study, we developed a computational approach to better understand the topical and geographical landscape of open access publications in the biomedical research literature. Surprisingly, we found a strong negative correlation between country per capita income and the percentage of open access publication. Open access publication rates were particularly high in sub-Saharan Africa, but vastly lower in the Middle East and North Africa, South Asia, and East Asia and the Pacific. These effects persisted when considering papers only bearing authors from within each region and income group. However, papers resulting from international collaborations did have a higher percentage of OA than single-country papers, and inter-regional collaboration increased OA publication for all world regions. There was no clear relationship between the number of open access policies in a region and the percentage of open access publications in that region. To understand the distribution of open access across topics of biomedical research, we examined keywords that were most enriched and depleted in open access papers. Keywords related to genomics, computational biology, animal models, and infectious disease were enriched in open access publications, while keywords related to the environment, nursing, and surgery were depleted in open access publications. This work identifies geographic regions and fields of research that could be priority areas for open access advocacy. The finding that open access publication rates are highest in sub-Saharan Africa and low income countries suggests that factors other than open access policy strongly influence authors’ decisions to make their work openly accessible. The high proportion of OA resulting from international collaborations indicates yet another benefit of collaborative research. Certain applied fields of medical research, notably nursing, surgery, and environmental fields, appear to have a greater proportion of fee-for-access publications, which presumably creates barriers that prevent researchers and practitioners in low income settings from accessing the literature in those fields. [ABSTRACT FROM AUTHOR]

The lack of management experience at the landscape scale and the limited feasibility of experiments at this scale have increased the use of scenario modeling to analyze the effects of different management actions on focal species. However, current modeling approaches are poorly suited for the analysis of viability in dynamic landscapes. Demographic (e.g., metapopulation) models of species living in these landscapes do not incorporate the variability in spatial patterns of early successional habitats, and landscape models have not been linked to population viability models. We link a landscape model to a metapopulation model and demonstrate the use of this model by analyzing the effect of forest management options on the viability of the Sharp-tailed Grouse ( ) in the Pine Barrens region of northwestern Wisconsin (U.S.A.). This approach allows viability analysis based on landscape dynamics brought about by processes such as succession, disturbances, and silviculture. The landscape component of the model (LANDIS) predicts forest landscape dynamics in the form of a time series of raster maps. We combined these maps into a time series of patch structures, which formed the dynamic spatial structure of the metapopulation component (RAMAS). Our results showed that the viability of Sharp-tailed Grouse was sensitive to landscape dynamics and demographic variables such as fecundity and mortality. Ignoring the landscape dynamics gave overly optimistic results, and results based only on landscape dynamics (ignoring demography) lead to a different ranking of the management options than the ranking based on the more realistic model incorporating both landscape and demographic dynamics. Thus, models of species in dynamic landscapes must consider habitat and population dynamics simultaneously. [ABSTRACT FROM AUTHOR]

Although land preservation and promotion of successful regeneration are important conservation actions, their ability to increase population growth rates of slow-growing, long-lived trees is limited. We investigated the demography of Taxus floridana Nutt., a rare understory conifer, in three populations in different ravine forests spanning its entire geographic range along the Apalachicola River Bluffs in northern Florida (U.S.A.). We examined spatial and temporal patterns in demographic parameters and projected population growth rates by using four years of data on the recruitment and survival of seedlings and established stems, and on diameter growth from cross-sections of dead stems. All populations experienced a roughly 10-fold increase in seedling recruitment in 1996 compared with other years. The fates of seedlings and stems between 8 and 16 mm differed among populations. The fates of stems in two other size classes (the 2- to 4-mm class and the 4- to 8-mm class) differed among both populations and years. Individual stems in all populations exhibited similarly slow growth rates. Stochastic matrix models projected declines in all populations. Stochastic matrix analysis revealed the high elasticity of a measure of stochastic population growth rate to perturbations in the stasis of large reproductive stems for all populations. Additional analyses also indicated that occasional episodes of high recruitment do not greatly affect population growth rates. Conservation efforts directed at long-lived, slow-growing rare plants like Taxus floridana should both protect established reproductive individuals and further enhance survival of individuals in other life-history stages, such as juveniles, that often do not appear to contribute greatly to population growth rates. [ABSTRACT FROM AUTHOR]

Background: In large-scale epidemiology, bloodspot sampling by fingerstick onto filter paper has many advantages, including ease and low costs of collection, processing and transport. We describe the development of an enzyme-linked immunoassay (ELISA) for quantifying insulin from dried blood spots and demonstrate its application in a large trial. Methods: We adapted an existing commercial kit (Mercodia Human Insulin ELISA, 10-1113-01) to quantify insulin from two 3-mm diameter discs (≈6 µL of blood) punched from whole blood standards and from trial samples. Paediatricians collected dried blood spots in a follow-up of 13,879 fasted children aged 11.5 years (interquartile range 11.3–11.8 years) from 31 trial sites across Belarus. We quantified bloodspot insulin levels and examined their distribution by demography and anthropometry. Results: Mean intra-assay (n = 157) coefficients of variation were 15% and 6% for ‘low’ (6.7 mU/L) and ‘high’ (23.1 mU/L) values, respectively; the respective inter-assay values (n = 33) were 23% and 11%. The intraclass correlation coefficient between 50 paired whole bloodspot versus serum samples, collected simultaneously, was 0.90 (95% confidence interval 0.85 to 0.95). Bloodspot insulin was stable for at least 31 months at −80°C, for one week at +30°C and following four freeze-thaw cycles. Paediatricians collected a median of 8 blood spots from 13,487 (97%) children. The geometric mean insulin (log standard deviation) concentrations amongst 12,812 children were 3.0 mU/L (1.1) in boys and 4.0 mU/L (1.0) in girls and were positively associated with pubertal stage, measures of central and peripheral adiposity, height and fasting glucose. Conclusions: Our simple and convenient bloodspot assay is suitable for the measurement of insulin in very small volumes of blood collected on filter paper cards and can be applied to large-scale epidemiology studies of the early-life determinants of circulating insulin.

Due to significant advances in instrumentation, many previously specialized techniques have become "routine" in user facilities. However, detailed knowledge held by experts has often not been relayed to general users, so they often rely on entry-level information, basic principles, and comparison with literature results for data analysis. As a result, major errors in the data analysis of multiple surface and material analysis techniques, including in x-ray photoelectron spectroscopy (XPS), have been appearing in the scientific literature. Representative examples of serious errors in XPS data analysis are shown in this work. We suggest that surface and material analysis, and perhaps even science in general, are in a state of "pre-crisis." We use two (logistic) models from population biology to suggest that bad analyses self-correct if they remain below a critical number. However, beyond a threshold, the literature can become useless because of the perpetuation of faulty analyses and concomitant loss of its self-correcting ability. XPS is used by scientists in many communities because of the power of the technique and high-quality instrumentation that is commercially available. Those who make new surfaces and materials face unique challenges because of the large number of surface and material analytical techniques that are often needed to characterize their materials. Graduate students and post-docs are often provided with only minimal instruction on using surface and material characterization methods. High fees for instruments may affect both the quality and the quantity of the data people collect. The Prisoner's Dilemma is a model from game theory that describes situations with reward structures that encourage uncooperative behavior and lead to suboptimal outcomes. However, the outcomes of Prisoner's Dilemma are not inevitable—their consequences change if their reward structures change. The current system does not appear to incentivize detailed learning of surface and material characterization techniques and careful material characterization. Prisoner's dilemmas appear to lead to other undesirable consequences in science. The concerns raised in this work suggest that many manuscripts are incompletely reviewed at present. The different stakeholders in this problem, including authors, research advisers, subject matter experts, reviewers, scientists who notice examples of faulty data analysis, editors, journals and publishers, funding agencies, scientific societies, leaders at universities and research centers, and instrument vendors, can improve the current situation. This work provides specific recommendations for each of these stakeholders. For example, we believe that authors are primarily responsible for the correctness of their work, not reviewers or editors; we question the wisdom of listing the names of the editor and reviewers on a paper; we are grateful for the significant contributions that have been made by subject matter experts to produce standards and tutorial information; the high cost of instrument time at some institutions may limit student access and result in suboptimal analyses; staff scientists often need to be better recognized for their intellectual contributions to studies; publishers may wish to allow selective reviewing of specific sections of papers related to material characterization; the reviewing at some open access journals may be inadequate; while it had its shortcomings, the pre-open access model of publishing incentivized the production and publication of high-quality work; audits of the products (scientific papers) of funding agencies may be necessary; collaboration needs to be encouraged to a greater extent at some institutions; and instrument vendors should not suggest to potential customers that surface characterization, e.g., by XPS, is trivial or simple. [ABSTRACT FROM AUTHOR]

Environmental stochasticity and climate affect outcomes in evolutionary games, which can thereby affect biological diversity. Our maximum likelihood (ML) estimates of replicator dynamics for morph frequency data from control (25 years) and three experimentally perturbed populations (14 years) of side-blotched lizards yield a 3 × 3 payoff matrix in the generalized Rock-Paper-Scissors family; it has intransitive best replies, and each strategy is its own worst reply. ML estimates indicate significant interactive effects of density and temperature on morph frequency. Implied dynamics feature a powerful interior attractor and recover (for the first time) observed 4-5 year oscillations. Our evolutionary experiment on morph frequency confirms that oscillations are driven by frequency dependent selection, but climate entrains the cycles across the perturbed and control populations within 10 generations. Applying the model across the species range, we find that climate also accounts for morph fixation and mating system diversity, suggesting climate may similarly impact ecosystem diversity. [ABSTRACT FROM AUTHOR]

Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA. [ABSTRACT FROM AUTHOR]

We address the question why papers dealing with the ecology of primates are so sparsely represented in the general ecological literature. A literature analyses based on entries in Web of Science and PrimateLit reveals that despite a large number of papers published on primates in general and on the ecology of primates, only a very small fraction of these papers is published in high-ranking international ecological journals. We discuss a number of potential reasons for the disproportion and highlight the problems associated with experimental research on wild primates and constraints on sample size as major issues. [ABSTRACT FROM AUTHOR]

Recently, computational Grids have proven to be a good solution for processing large-scale, computation intensive problems. However, the heterogeneity, dynamics of resources and diversity of applications requirements have always been important factors affecting their performance. In response to these challenges, this work first builds a Grid job scheduling architecture that can dynamically monitor Grid computing center resources and make corresponding scheduling decisions. Second, a Grid job model is proposed to describe the application requirements. Third, this paper studies the characteristics of commercial interconnection networks used in Grids and forecast job transmission time. Fourth, this paper proposes an application-aware job scheduling mechanism (AJSM) that includes periodic scheduling flow and a heuristic application-aware deadline constraint job scheduling algorithm. The rigorous performance evaluation results clearly demonstrate that the proposed application-aware job scheduling mechanism can successful schedule more Grid jobs than the existing algorithms. For successful scheduled jobs, our proposed AJSM method is the best algorithm for job average processing time and makespan. [ABSTRACT FROM AUTHOR]

The article presents the author's views on the theory of conservation biology. He states that wildlife biologists have reinforced the perception of conservation biology as a theoretical discipline. The author feels that conservation biology, being recognized as a formal discipline for 10 years, still feels the growing pains of an emerging discipline. The discipline of "conservation biology" has inherited a wealth of existing theory from its parent disciplines such as population biology.

Introduction: Respondent-driven sampling (RDS) offers a recruitment strategy for hard-to-reach populations. However, RDS faces logistical and theoretical challenges that threaten efficiency and validity in settings worldwide. We present innovative adaptations to conventional RDS to overcome barriers encountered in recruiting a large, representative sample of men who have sex with men (MSM) who travel internationally. Methods: Novel methodological adaptations for the “International Travel Research to Inform Prevention” or “I-TRIP” study were offering participants a choice between electronic and paper coupons referrals for recruitment and modifying the secondary incentives structure from small cash amounts to raffle entries for periodic large cash prize raffle drawings. Staged referral limit increases from 3 to 10 referrals and progressive addition of 70 seeds were also implemented. Results: There were 501 participants enrolled in up to 13 waves of growth. Among participants with a choice of referral methods, 81% selected electronic referrals. Of participants who were recruited electronically, 90% chose to remain with electronic referrals when it was their turn to recruit. The mean number of enrolled referrals was 0.91 for electronic referrals compared to 0.56 for paper coupons. Median referral lag time, i.e., the time interval between when recruiters were given their referrals and when a referred individual enrolled in the study, was 20 days (IQR 10–40) for electronic referrals, 20 days (IQR 8–58) for paper coupons, 20 days (IQR 10–41) for raffle entries and 33 days (IQR 16–148) for small cash incentives. Conclusions: The recruitment of MSM who travel internationally required maximizing known flexible tools of RDS while at the same time necessitating innovations to increase recruitment efficiency. Electronic referrals emerged as a major advantage in recruiting this hard-to-reach population who are of high socio-economic status, geographically diffuse and highly mobile. These enhancements may improve the performance of RDS in target populations with similar characteristics. [ABSTRACT FROM AUTHOR]

The publication, in 1958, of Charles Elton's book The ecology of invasions by animals and plants launched the systematic study of biological invasions. Invasion ecology has grown to become an important multi-disciplinary subfield of ecology with growing links to many other disciplines. This paper examines the citation history of Elton's book using the Web of Science. We also examine Elton's influence in shaping the current research agenda in invasion ecology, for which we use the 28 papers in a special issue of Diversity and Distributions (Volume 14: 2) as a representative sample. After 50 years, Elton's book remains the most cited single source in the field (> 1500 citations), and is cited more often every year (> 100 times) than any other invasion-related publication, including influential papers in journals. Most citations to Elton's book refer to particular topics/concepts covered in the book, rather than citing it as a general reference about invasions. The shift in the distribution of topics/concepts cited with reference to Elton over time follows the same trend as for biogeography and ecology in general (increasing emphasis on analytical studies, multi-scale analyses, multi-disciplinary studies, etc.). Some topics emphasized by Elton are still the focus of current research (dispersal and spread of invasive organisms, impact on biodiversity, role of disturbance and enemy release) but several prominent themes in modern studies were not addressed by Elton. The emergence of new themes can be attributed to a general change in approach and emphasis underpinning research questions in conservation biogeography and applied ecology over the last half century (risk analysis, multi-scale comparisons, propagule pressure, experimental approaches) and to the recent emergence and increasing availability of large data sets on the distribution of introduced species and to the emergence of key technologies (e.g. geographic information systems, modelling techniques, including niche-based modelling, and molecular methods). Half a century after its publication, Charles Elton's book on invasions remains influential, but massive changes in the status of invasions and other environmental issues worldwide, together with advances in technology, are reshaping the game rules and priorities of invasion ecology. [ABSTRACT FROM AUTHOR]

Dispersal knowledge is essential for conservation management, and demand is growing. But are we accumulating dispersal knowledge at a pace that can meet the demand? To answer this question we tested for changes in dispersal data collection and use over time. Our systematic review of 655 conservation-related publications compared five topics: climate change, habitat restoration, population viability analysis, land planning (systematic conservation planning) and invasive species. We analysed temporal changes in the: (i) questions asked by dispersal-related research; (ii) methods used to study dispersal; (iii) the quality of dispersal data; (iv) extent that dispersal knowledge is lacking, and; (v) likely consequences of limited dispersal knowledge. Research questions have changed little over time; the same problems examined in the 1990s are still being addressed. The most common methods used to study dispersal were occupancy data, expert opinion and modelling, which often provided indirect, low quality information about dispersal. Although use of genetics for estimating dispersal has increased, new ecological and genetic methods for measuring dispersal are not yet widely adopted. Almost half of the papers identified knowledge gaps related to dispersal. Limited dispersal knowledge often made it impossible to discover ecological processes or compromised conservation outcomes. The quality of dispersal data used in climate change research has increased since the 1990s. In comparison, restoration ecology inadequately addresses large-scale process, whilst the gap between knowledge accumulation and growth in applications may be increasing in land planning. To overcome apparent stagnation in collection and use of dispersal knowledge, researchers need to: (i) improve the quality of available data using new approaches; (ii) understand the complementarities of different methods and; (iii) define the value of different kinds of dispersal information for supporting management decisions. Ambitious, multi-disciplinary research programs studying many species are critical for advancing dispersal research. [ABSTRACT FROM AUTHOR]

Drawing on the theory of social action in organizational and institutional sociology, this paper examines the behavioral consequences of plural logics of action. It addresses the question based on the empirical case of plural medical systems that are composed of both biomedicine and alternative medicine. Applying mixed methods of a cross-national panel data analysis and a content analysis of medical journal articles, it finds that plural systems affect health outcomes negatively when tensions between biomedicine and alternative medicine are unaddressed. In contrast, plural systems produce tangible health benefits when biomedicine and alternative medicine are coordinated through government policies or by health care organizations/professionals. This paper proposes plurality coordination as an important mechanism that modifies the behavioral consequences of plural logics. This proposition contributes to providing theoretical answers to the sociological puzzle that plural logics of action produce inconsistent behavioral consequences. [ABSTRACT FROM AUTHOR]

Phylogenetic comparative methods are becoming increasingly popular for investigating evolutionary patterns and processes. However, these methods are not infallible - they suffer from biases and make assumptions like all other statistical methods., Unfortunately, although these limitations are generally well known in the phylogenetic comparative methods community, they are often inadequately assessed in empirical studies leading to misinterpreted results and poor model fits. Here, we explore reasons for the communication gap dividing those developing new methods and those using them., We suggest that some important pieces of information are missing from the literature and that others are difficult to extract from long, technical papers. We also highlight problems with users jumping straight into software implementations of methods (e.g. in r) that may lack documentation on biases and assumptions that are mentioned in the original papers., To help solve these problems, we make a number of suggestions including providing blog posts or videos to explain new methods in less technical terms, encouraging reproducibility and code sharing, making wiki-style pages summarising the literature on popular methods, more careful consideration and testing of whether a method is appropriate for a given question/data set, increased collaboration, and a shift from publishing purely novel methods to publishing improvements to existing methods and ways of detecting biases or testing model fit. Many of these points are applicable across methods in ecology and evolution, not just phylogenetic comparative methods. [ABSTRACT FROM AUTHOR]

Co-diagnosis of HIV and tuberculosis presents a treatment dilemma. Starting both treatments at the same time can cause a flood of immune response called immune reconstitution inflammatory syndrome (IRIS) which can be lethal. But, how long to delay HIV treatment is less understood. In 2011, based on the conclusions of three separate studies, WHO recommended starting HIV treatment earlier for those with later HIV disease progression. This paper conducts a replication study of one of the three studies, by Havlir and colleagues. Using their publicly available data, we were able to replicate most of the results presented in the original paper. In our measurement and estimation analyses we use different estimation techniques to assess the robustness of the results. We find that adjusting for loss to follow-up does not affect the main results of the paper. However, an ANCOVA estimation and an instrumental variable model weaken the main result of the paper of better outcomes with early HIV treatment only for those who are sicker, reducing significance from the 5% to the 10% level. A change-point analysis also detects no changes in effect by timing of HIV treatment initiation or different thresholds of CD4 count for the primary outcome. This result suggests that the choice of start time for HIV treatment initiation should be based on other factors including potential drug interactions, overlapping side effects, a high pill burden and severity of illness rather than CD4 threshold and preset timeframes. While we caution against overgeneralizing, the result of this replication is aligned with more recent studies that show no evidence that early initiation of HIV treatment reduces mortality for any patients. [ABSTRACT FROM AUTHOR]

This paper uses text data mining to identify long-term developments in tourism academic research from the perspectives of thematic focus, geography, and gender of tourism authorship. Abstracts of papers published in the period of 1970–2017 in high-ranking tourist journals were extracted from the Scopus database and served as data source for the analysis. Fourteen subject areas were identified using the Latent Dirichlet Allocation (LDA) text mining approach. LDA integrated with GIS information allowed to obtain geography distribution and trends of scholarly output, while probabilistic methods of gender identification based on social network data mining were used to track gender dynamics with sufficient confidence. The findings indicate that, while all 14 topics have been prominent from the inception of tourism studies to the present day, the geography of scholarship has notably expanded and the share of female authorship has increased through time and currently almost equals that of male authorship. [ABSTRACT FROM AUTHOR]

Objective: Irrational use of antimicrobial agents for preventing postoperative SSIs is a common phenomenon in China, which results in more bacterial resistance, higher hospital infection rates, extra costs of antimicrobial agents. The aim of the study is to evaluate the effect of Drug Rational Usage Guidelines System (DRUGS) on the surgeon's prescription behavior of antimicrobial agents. Methods: 10 common surgical operations which included 1543 cases (where 778 cases using paper-based guidelines and 765 cases using DRUGS) were selected and their demographic and clinical data were collected. The selected operations include thyroid resection, breast mass resection, myomectomy, etc. The evaluation criteria were antibiotic administrative categories, the time of initial dose, duration of administration, length of stay, the costs of antibiotics, SSIs and drug adverse reactions(ADR). Results: The antimicrobial agents were mostly administrated within 0.5 h to 2 h before incision, 656 patients (85.75%) were intervened with DRUGS and 256 (32.90%) with paper-based guidelines according to the protocol. For the clean wounds incision, 547 patients (91.62%) were within 24 h of withdrawal antibiotics with using paper-based guidelines versus 91 (14.79%) with using DRUGS. A total of 19 kinds of antibiotics were used in the 1543 cases. The leading three on the list of frequency were piperacillin and sulbactam sodium, cefathiamidine and cefoperazone. While after the intervention, the list of frequency changed to cefazolin, cefathiamidine, cefoperazone. The average hospital stay was (7.00±4.31)d with paper-based guidelines and (2.54±1.57)d with DRUGS, respectively. The average cost of antibiotics was ¥(3481.36±2584.46) with paper-based guidelines and ¥(1693.39±1478.27) with DRUGS, respectively. However, there were no significant differences in the incidence of SSIs and ADR between two groups. Conclusion: In this study, the increased availability of antibiotic guidelines at the time of drug ordering, combined with DRUGS, was associated with an enhanced surgeon adherence to guidelines. [ABSTRACT FROM AUTHOR]

This document is an introduction to a special issue of the Journal of Biological Dynamics dedicated to the memory of Abdul-Aziz Yakubu, a mathematician known for his contributions to population biology. The papers in this issue cover a range of topics in mathematical biology, including discrete-time and continuous-time models used to study real-life phenomena in population biology and ecology. The articles were reviewed by independent reviewers and cover subjects such as nutrient-phytoplankton-oysters systems, host-parasitoid systems, predator-prey systems, disease spread, and the modeling of various diseases. The guest editors express their gratitude to the authors and reviewers for their contributions. [Extracted from the article]

An investigation in a randomized population-based Swedish study with 564 participants aged 18-80 years showed that mean physical activity levels obtained using short message service (SMS) by means of cell phones (n = 171) were equal to corresponding levels obtained when sending identical questions by web (n = 182) or paper (n = 211). The response rates were similar for the SMS, web and paper groups. [ABSTRACT FROM AUTHOR]

Little is known about bacterial dynamics in the oligotrophic ocean, particularly about its cultivable population. We examined the abundance of total and cultivable bacteria in relation to changes in biogeochemical conditions in the eastern Atlantic Ocean with special regard to Vibrio spp., a group of bacteria that can cause diseases in human and aquatic organisms. Surface, deep water and plankton samples (<20 µm, 20-55 µm and >55 µm) were collected between 50° N and 24° S. Chlorophyll-a was very low (<0.3 µg l-1) in most areas of the nutrient-poor Atlantic, except at a few locations near upwelling regions. In surface water, dissolved organic carbon (DOC) and nitrogen (DON) concentrations were 64-95 µM C and 2-10 µM N accounting for ≥90% and ≥76% of total organic C and N, respectively. DOC and DON gradually decreased to ~45 µM C and <5 µM N in the bottom water while dissolved inorganic nutrients (Si, P, N) increased with depth. In the surface layer, culture independent total bacteria, represented by 4'-6-diamidino-2-phenylindole (DAPI) counts, ranged mostly between 107 and 108 cells l-1, while cultivable bacterial counts (CBC) and Vibrio spp. were found at concentrations of 104-107 and 10⊃2-105 colony forming units (CFU) l-1, respectively. Most bacteria (>99 %) were found in the nanoplankton fraction (<20 µm), however, bacterial abundance did not correlate with suspended particulates (chlorophyll-a, particulate organic C and N). Instead, we found a highly significant correlation between bacterial abundance and temperature (p < 0.001) and a significant correlation with DOC and DON. Among the cultivable bacteria, the abundance of Vibrio was also highly significantly correlated with DOC and DON (p<0.0005 and p<0.005, respectively). In cold waters of the mid-pelagic and abyssal zones, CBC was 50 to 100-times lower than in the surface layer; however, cultivable Vibrio spp. could be isolated from the bathypelagic zone and even near the seafloor (average ~10CFU l-1). In contrast, DAPI counts revealed a homogenous distribution of the non-cultivable bacterial population throughout the oceanic depths. Our study indicates that Vibrio and other bacteria may largely depend on dissolved organic matter to survive in nutrient-poor oceanic habitats, without being associated with plankton or particles. [ABSTRACT FROM AUTHOR]

Online submission and review of manuscripts is now required. Please follow the instructions for authors given below. When your manuscript has been prepared in accordance with these instructions, please access the following web site:. You must selectFunctional Ecologywhen you log on to the online submission site. [ABSTRACT FROM AUTHOR]

This paper presents a novel method on the optimization of bi-objective Flexible Job-shop Scheduling Problem (FJSP) under stochastic processing times. The robust counterpart model and the Non-dominated Sorting Genetic Algorithm II (NSGA-II) are used to solve the bi-objective FJSP with consideration of the completion time and the total energy consumption under stochastic processing times. The case study on GM Corporation verifies that the NSGA-II used in this paper is effective and has advantages to solve the proposed model comparing with HPSO and PSO+SA. The idea and method of the paper can be generalized widely in the manufacturing industry, because it can reduce the energy consumption of the energy-intensive manufacturing enterprise with less investment when the new approach is applied in existing systems. [ABSTRACT FROM AUTHOR]

Background: Floating catchment methods have recently been applied to identify priority regions for Automated External Defibrillator (AED) deployment, to aid in improving Out of Hospital Cardiac Arrest (OHCA) survival. This approach models access as a supply-to-demand ratio for each area, targeting areas with high demand and low supply for AED placement. These methods incorporate spatial covariates on OHCA occurrence, but do not provide precise AED locations, which are critical to the initial intent of such location analysis research. Exact AED locations can be determined using optimisation methods, but they do not incorporate known spatial risk factors for OHCA, such as income and demographics. Combining these two approaches would evaluate AED placement impact, describe drivers of OHCA occurrence, and identify areas that may not be appropriately covered by AED placement strategies. There are two aims in this paper. First, to develop geospatial models of OHCA that account for and display uncertainty. Second, to evaluate the AED placement methods using geospatial models of accessibility. We first identify communities with the greatest gap between demand and supply for allocating AEDs. We then use this information to evaluate models for precise AED location deployment. Methods: Case study data set consisted of 2802 OHCA events and 719 AEDs. Spatial OHCA occurrence was described using a geospatial model, with possible spatial correlation accommodated by introducing a conditional autoregressive (CAR) prior on the municipality-level spatial random effect. This model was fit with Integrated Nested Laplacian Approximation (INLA), using covariates for population density, proportion male, proportion over 65 years, financial strength, and the proportion of land used for transport, commercial, buildings, recreation, and urban areas. Optimisation methods for AED locations were applied to find the top 100 AED placement locations. AED access was calculated for current access and 100 AED placements. Priority rankings were then given for each area based on their access score and predicted number of OHCA events. Results: Of the 2802 OHCA events, 64.28% occurred in rural areas, and 35.72% in urban areas. Additionally, over 70% of individuals were aged over 65. Supply of AEDs was less than demand in most areas. Priority regions for AED placement were identified, and access scores were evaluated for AED placement methodology by ranking the access scores and the predicted OHCA count. AED placement methodology placed AEDs in areas with the highest priority, but placed more AEDs in areas with more predicted OHCA events in each grid cell. Conclusion: The methods in this paper incorporate OHCA spatial risk factors and OHCA coverage to identify spatial regions most in need of resources. These methods can be used to help understand how AED allocation methods affect OHCA accessibility, which is of significant practical value for communities when deciding AED placements. [ABSTRACT FROM AUTHOR]

This paper re-examines health-growth relationship using an unbalanced panel of 17 advanced economies for the period 1870–2013 and employs panel generalised method of moments estimator that takes care of endogeneity issues, which arise due to reverse causality. We utilise macroeconomic data corresponding to inflation, government expenditure, trade and schooling in sample countries that takes care of omitted variable bias in growth regression. With alternate model specifications, we show that population health proxied by life expectancy exert a positive and significant effect on both real income per capita as well as growth. Our results are in conformity with the existing empirical evidence on the relationship between health and economic growth, they, however, are more robust due to the presence of long-term data, appropriate econometric procedure and alternate model specifications. We also show a strong role of endogeneity in driving standard results in growth empirics. In addition to life expectancy, other constituent of human capital, education proxied by schooling is also positively associated with real per capita income. Policy implication that follows from this paper is that per capita income can be boosted through focussed policy attention on population health. The results, however, posit differing policy implications for advanced and developing economies. [ABSTRACT FROM AUTHOR]

Ensembles are a well established machine learning paradigm, leading to accurate and robust models, predominantly applied to predictive modeling tasks. Ensemble models comprise a finite set of diverse predictive models whose combined output is expected to yield an improved predictive performance as compared to an individual model. In this paper, we propose a new method for learning ensembles of process-based models of dynamic systems. The process-based modeling paradigm employs domain-specific knowledge to automatically learn models of dynamic systems from time-series observational data. Previous work has shown that ensembles based on sampling observational data (i.e., bagging and boosting), significantly improve predictive performance of process-based models. However, this improvement comes at the cost of a substantial increase of the computational time needed for learning. To address this problem, the paper proposes a method that aims at efficiently learning ensembles of process-based models, while maintaining their accurate long-term predictive performance. This is achieved by constructing ensembles with sampling domain-specific knowledge instead of sampling data. We apply the proposed method to and evaluate its performance on a set of problems of automated predictive modeling in three lake ecosystems using a library of process-based knowledge for modeling population dynamics. The experimental results identify the optimal design decisions regarding the learning algorithm. The results also show that the proposed ensembles yield significantly more accurate predictions of population dynamics as compared to individual process-based models. Finally, while their predictive performance is comparable to the one of ensembles obtained with the state-of-the-art methods of bagging and boosting, they are substantially more efficient. [ABSTRACT FROM AUTHOR]

The three papers included in this special issue represent a set of presentations in an invited session on disease ecology at the 2005 Spring Meeting of the Eastern North American Region of the International Biometric Society. The papers each address statistical estimation and inference for particular components of different disease processes and, taken together, illustrate the breadth of statistical issues arising in the study of the ecology and public health impact of disease. As an introduction, we provide a very brief overview of the area of “disease ecology”, a variety of synonyms addressing different aspects of disease ecology, and present a schematic structure illustrating general components of the underlying disease process, data collection issues, and different disciplinary perspectives ranging from microbiology to public health surveillance. [ABSTRACT FROM AUTHOR]

The article presents various articles published in the journal for the past decade. The first year of the publication of the journal which was in 1999 featured the article which tackles vigorous hybrids of landscape and traditional ecosystem ecology. Meanwhile in 1998 an article which evaluated approaches used for landscape pattern analysis had become the most highly article. Moreover, in 2002 an article was also published which analyzed the effects of exotic plant invasion on soil nutrient cycles.

Changes in urban residential density represent an important issue in terms of land consumption, the conservation of ecosystems, air quality and related human health problems, as well as the consequential challenges for urban and regional planning. It is the decline of residential densities, in particular, that has often been used as the very definition of sprawl, describing a phenomenon that has been extensively studied in the United States and in Western Europe. Whilst these studies provide valuable insights into urbanization processes, only a handful of them have reflected the uneven dynamics of simultaneous urban growth and shrinkage, using residential density changes as a key indicator to uncover the underlying dynamics. This paper introduces a contrasting analysis of recent developments in both de- and re-concentration, defined as decreasing or increasing residential densities, respectively. Using a large sample of European cities, it detects differences in density changes between successional population growth/decline. The paper shows that dedensification, found in some large cities globally, is not a universal phenomenon in growing urban areas; neither the increasing disproportion between a declining demand for and an increasing supply of residential areas nor actual concentration processes in cities were found. Thus, the paper provides a new, very detailed perspective on (de)densification in both shrinking and growing cities and how they specifically contribute to current land take in Europe. [ABSTRACT FROM AUTHOR]

The dispatching of hydro-thermal system is a nonlinear programming problem with multiple constraints and high dimensions and the solution techniques of the model have been a hotspot in research. Based on the advantage of that the artificial bee colony algorithm (ABC) can efficiently solve the high-dimensional problem, an improved artificial bee colony algorithm has been proposed to solve DHTS problem in this paper. The improvements of the proposed algorithm include two aspects. On one hand, local search can be guided in efficiency by the information of the global optimal solution and its gradient in each generation. The global optimal solution improves the search efficiency of the algorithm but loses diversity, while the gradient can weaken the loss of diversity caused by the global optimal solution. On the other hand, inspired by genetic algorithm, the nectar resource which has not been updated in limit generation is transformed to a new one by using selection, crossover and mutation, which can ensure individual diversity and make full use of prior information for improving the global search ability of the algorithm. The two improvements of ABC algorithm are proved to be effective via a classical numeral example at last. Among which the genetic operator for the promotion of the ABC algorithm’s performance is significant. The results are also compared with those of other state-of-the-art algorithms, the enhanced ABC algorithm has general advantages in minimum cost, average cost and maximum cost which shows its usability and effectiveness. The achievements in this paper provide a new method for solving the DHTS problems, and also offer a novel reference for the improvement of mechanism and the application of algorithms. [ABSTRACT FROM AUTHOR]

Introduction: Despite evidence of the high prevalence of antibiotic resistant infections in developing countries, studies on the clinical and economic impact of antibiotic resistance (ABR) to inform interventions to contain its emergence and spread are limited. The aim of this study was to analyze the published literature on the clinical and economic implications of ABR in developing countries. Methods: A systematic search was carried out in Medline via PubMed and Web of Sciences and included studies published from January 01, 2000 to December 09, 2016. All papers were considered and a quality assessment was performed using the Newcastle-Ottawa quality assessment scale (NOS). Results: Of 27 033 papers identified, 40 studies met the strict inclusion and exclusion criteria and were finally included in the qualitative and quantitative analysis. Mortality was associated with resistant bacteria, and statistical significance was evident with an odds ratio (OR) 2.828 (95%CI, 2.231–3.584; p = 0.000). ESKAPE pathogens was associated with the highest risk of mortality and with high statistical significance (OR 3.217; 95%CIs; 2.395–4.321; p = 0.001). Eight studies showed that ABR, and especially antibiotic-resistant ESKAPE bacteria significantly increased health care costs. Conclusion: ABR is associated with a high mortality risk and increased economic costs with ESKAPE pathogens implicated as the main cause of increased mortality. Patients with non-communicable disease co-morbidities were identified as high-risk populations. [ABSTRACT FROM AUTHOR]

This paper is a contribution to the modeling–methodological development of the application of mathematical systems theory in population biology. A discrete-time nonlinear Leslie-type model is considered, where both the reproduction and survival rates decrease as the total population size increases. In this context, the monitoring problem means that, from the observation of the size of certain age classes as a function of time, we want to recover (estimate) the whole state process (i.e., the time-dependent size of the rest of the classes). First, for the linearization approach, conditions for the existence and asymptotic stability of a positive equilibrium are obtained, then the discrete-time observer design method is applied to estimate an unknown state trajectory near the equilibrium, where we could observe a single age class. It is also shown how the observer design can be used to detect an unknown change in the environment that affects the population dynamics. The environmental change is supposed to be generated by additional dynamics (exosystem). Now, the Leslie-type model is extended with this exosystem, and the observer design is applied to this extended system. In this way, an estimation can be obtained for different (constant or periodic) environmental changes as well. [ABSTRACT FROM AUTHOR]