bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variations in Posidonia oceanica meadow structure along the coast of the Dugi Otok Island (eastern Adriatic Sea)
Authors: Kru΂ić Petar 
Published: June 2008

Although the anthropogenic impact on Posidonia oceanica meadows in the Mediterranean Sea has been studied over the last few decades, the data about the status of this endemic magnoliophyte are scarcer from the Adriatic Sea. Samples of P. oceanica meadows were collected in June and July 2004 using SCUBA diving at 8 sites in the area of the Dugi Otok Island, all at depths of 10 m. The meadow's shoot density was measured, and shoots were collected to be examined and compared through number of leaves per shoot, leaf surface per shoot, leaf area index, number and biomass of taxa of epiphytic flora. Significant differences in P. oceanica meadow structure were found among investigated sites, especially between sites in the vicinity of the fish farm and the other sites. Meadow density decreased at sites in the Dugi Otok channel and the main impact factors seem to be the input of organic matter, originating from the fish cages and sewage input. These human activities are a source of nutrient pollution and stimulate blooms of phytoplankton and higher algae. The sea grass meadow vitality seems to be more negatively affected in the channel. The highest values of shoot density were recorded at investigated sites VR and ME at the outer part of the Dugi Otok Island. The shoot density was very low at site FU, situated in the channel. Biomass of the epiphytic algae exhibited the highest values at the site FU, while at the other investigated sites the values were significantly lower. Concerning the epiphytic macroflora, a total of 55 taxa of epiphytic macroalgae were identified and the class Rhodophyta dominated in all samples. The present study shows the high differences in morphological and structural characteristics of Posidonia oceanica meadows among various sites with and without anthropogenic influence.
Addressing legal and political barriers to global pharmaceutical access: Options for remedying the impact of the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) and the imposition of TRIPS-plus standards
Authors: COHEN-KOHLER JILLIAN CLARE , FORMAN LISA , LIPKUS NATHANIEL 
Published: June 2008

AbstractDespite myriad programs aimed at increasing access to essential medicines in the developing world, the global drug gap persists. This paper focuses on the major legal and political constraints preventing implementation of coordinated global policy solutions – particularly, the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) and bilateral and regional free trade agreements. We argue that several policy and research routes should be taken to mitigate the restrictive impact of TRIPS and TRIPS-plus rules, including greater use of TRIPS flexibilities, advancement of human rights, and an ethical framework for essential medicines distribution, and a broader campaign that debates the legitimacy of TRIPS and TRIPS-plus standards themselves.
Willingness to pay for alternative policies for patients with Alzheimer’s Disease
Authors: NEGRÍN MIGUEL A. , PINILLA JAIME , LEÓN CARMELO J. 
Published: June 2008

AbstractThis paper focuses on eliciting the willingness to pay (WTP) for policy measures aimed at improving the health care offered to patients suffering from Alzheimer’s disease (AD). We utilize a discrete choice experiment (DCE) approach for the elicitation of the preferences of the general population for three alternative policies: home care, day care centres, and medium or long-stay centres. The results show that these policies are significantly valued across the surveyed population. The monthly WTP per hour of home care is estimated as €4 per individual, while the monthly WTP values for full population coverage in day centres and medium–long-stay centres are estimated as €0.43 and €0.42 respectively. We compare the results of classical and Bayesian estimation methods, and conclude that the latter provide a better representation of the heterogeneity in the sample. The results are significant for health care, as they enable policymakers to identify the social demand for such services, as well as the relative economic values placed on the alternative policy measures.
Consumer-directed health care: promise or puffery?
Authors: CALLAHAN DANIEL 
Published: June 2008

AbstractConsumer-directed health care (CDHC) is one of the basic ideas that has emerged in recent years as a way of bringing greater efficiency and cost control into health care. Its principal aims are to give patients greater control over their care, economically as well as medically, and to improve competition among providers to increase the range of patient control. Its roots are American, bespeaking a cultural suspicion of government, a worry about rising costs, and an appeal to the popularity of choice in almost all matters, now including health care. CDHC also bespeaks the ideology of market ideology, drawing on both market concepts in economics and a push by American conservatives (particularly President George W. Bush) to privatize as much of American health care as possible). It draws particularly on the business community as a source of ideas and inspiration, assuming that if choice and competition work well in the commercial sector, it will work equally well in health care. A fundamental question, however, is not simply how well business models might work, but also whether thinking of the patient as a savvy consumer could ever make full sense in the face of complicated, emotionally charged illnesses and complex decision-making situations. Skepticism is in order.
Using Student Article Presentations for Evidence-Based Practice and Evidence-Based Education
Authors: Hester Eva Jackson 
Published: June 2008

Abstract
Increased attention to evidence-based practice (EBP) within the profession has required more emphasis on research studies used in graduate courses. Instructors are now faced with determining effective methods for incorporating and documenting the inclusion of research aspects of EBP. This paper discusses the importance of incorporating EBP research aspects within the framework of evidence-based education (EBE) by using student article presentations.
“Two First Authors”: Defining and Evaluating Collaborative Partnership
Authors: Jackson Catherine , Seymour Patricia J. 
Published: June 2008

Abstract
Models of academic collaboration typically assume roles dictated by experience or seniority. Our experience as two new faculty members engaged in a long-term curriculum revision project led us to a partnership-type of collaboration, the “two first authors” model. This model required us to assume flexible roles with regard to workload and participation at various points in the project. Although this model of collaboration does not meet traditional expectations for evaluating faculty roles in academic projects, the intellectual and practical benefits became clear throughout the progress of our work. We encourage instructors, researchers and reviewers to explicitly identify their assumptions and expectations regarding collaboration, and to explore options related to establishing fluid roles for members of a collaborative team.
Evidence-Based Analysis of Formative Assessment
Authors: Levey Sandra 
Published: June 2008

Abstract
This study examined evidence for the effectiveness of one approach to formative assessment based on students' anonymous reports of material that was “best learned” and “least learned” at the end of each lecture. Responses to “least learned” information were covered in subsequent lectures or were placed on Blackboard. Two graduate classes' judgments of the effectiveness of this approach to formative assessment were examined, along with the specific topics that were reported to present the most difficulty according to their reports of “least learned” information. Two classes participated in this study: 20 students in the first class and 21 in the second. Students were presented with a questionnaire that contained a Likert Scale that asked if this approach led to (a) better understanding of course material, (b) better coverage by the instructor, (c) appreciation of anonymity, (d) asking more questions, and (e) more confidence in asking questions. There was no significant difference between the responses to the questionnaire for the first class and the second class. Students reported benefits of formative assessment which provides an ongoing and evidence-based analysis of learning skills.
Student Self-Directed Professional Development as a Formative Assessment Skill
Authors: Cascella Paul W. , Vogel Donald A. 
Published: June 2008

Abstract
While professional development is most typically thought of as continuing education beyond the master’s degree, we have formulated a process for master’s degree students in speech-language pathology to identify and self-evaluate their own professional development. Current standards for preparing graduate students in speech-language pathology focus primarily on introducing students to an extensive array of academic and clinical topics (e.g., disorders, conditions, service delivery models, evidence-based practice). However, indirect support for self-directed professional development can be found in two CAA standards, Standard 3.1B (i.e., “breadth and depth of the scope of practice”) and Standard 4.2 (i.e., reasonable accommodations). The authors describe a series of self-reflection activities that are integrated within speech-language pathology course work for the purpose of fostering professional development at the preservice level. Student comments and outcomes to date are described.
FIRMA: a method for detection of alternative splicing from exon array data
Authors: Purdom E. , Simpson K. M. , Robinson M. D. , Conboy J. G. , Lapuk A. V. , Speed T.P. 
Published: June 2008

Abstract
Motivation: Analyses of EST data show that alternative splicing is much more widespread than once thought. The advent of exon and tiling microarrays means that researchers now have the capacity to experimentally measure alternative splicing on a genome wide level. New methods are needed to analyze the data from these arrays.
Results: We present a method, finding isoforms using robust multichip analysis (FIRMA), for detecting differential alternative splicing in exon array data. FIRMA has been developed for Affymetrix exon arrays, but could in principle be extended to other exon arrays, tiling arrays or splice junction arrays. We have evaluated the method using simulated data, and have also applied it to two datasets: a panel of 11 human tissues and a set of 10 pairs of matched normal and tumor colon tissue. FIRMA is able to detect exons in several genes confirmed by reverse transcriptase PCR.
Availability: R code implementing our methods is contributed to the package aroma.affymetrix.
Contact: epurdom@stat.berkeley.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
On correcting the overestimation of the permutation-based false discovery rate estimator
Authors: Jiao Shuo , Zhang Shunpu 
Published: June 2008

AbstractMotivation: Recent attempts to account for multiple testing in the analysis of microarray data have focused on controlling the false discovery rate (FDR), which is defined as the expected percentage of the number of false positive genes among the claimed significant genes. As a consequence, the accuracy of the FDR estimators will be important for correctly controlling FDR. Xie et al. found that the standard permutation method of estimating FDR is biased and proposed to delete the predicted differentially expressed (DE) genes in the estimation of FDR for one-sample comparison. However, we notice that the formula of the FDR used in their paper is incorrect. This makes the comparison results reported in their paper unconvincing. Other problems with their method include the biased estimation of FDR caused by over- or under-deletion of DE genes in the estimation of FDR and by the implicit use of an unreasonable estimator of the true proportion of equivalently expressed (EE) genes. Due to the great importance of accurate FDR estimation in microarray data analysis, it is necessary to point out such problems and propose improved methods.Results: Our results confirm that the standard permutation method overestimates the FDR. With the correct FDR formula, we show the method of Xie et al. always gives biased estimation of FDR: it overestimates when the number of claimed significant genes is small, and underestimates when the number of claimed significant genes is large. To overcome these problems, we propose two modifications. The simulation results show that our estimator gives more accurate estimation.Contact: szhang3@unl.edu
Database indexing for production MegaBLAST searches
Authors: Morgulis Aleksandr , Coulouris George , Raytselis Yan , Madden Thomas L. , Agarwala Richa , Schäffer Alejandro A. 
Published: June 2008

Abstract
Motivation: The BLAST software package for sequence comparison speeds up homology search by preprocessing a query sequence into a lookup table. Numerous research studies have suggested that preprocessing the database instead would give better performance. However, production usage of sequence comparison methods that preprocess the database has been limited to programs such as BLAT and SSAHA that are designed to find matches when query and database subsequences are highly similar.
Results: We developed a new version of the MegaBLAST module of BLAST that does the initial phase of finding short seeds for matches by searching a database index. We also developed a program makembindex that preprocesses the database into a data structure for rapid seed searching. We show that the new ‘indexed MegaBLAST’ is faster than the ‘non-indexed’ version for most practical uses. We show that indexed MegaBLAST is faster than miBLAST, another implementation of BLAST nucleotide searching with a preprocessed database, for most of the 200 queries we tested. To deploy indexed MegaBLAST as part of NCBI'sWeb BLAST service, the storage of databases and the queueing mechanism were modified, so that some machines are now dedicated to serving queries for a specific database. The response time for such Web queries is now faster than it was when each computer handled queries for multiple databases.
Availability: The code for indexed MegaBLAST is part of the blastn program in the NCBI C++ toolkit. The preprocessor program makembindex is also in the toolkit. Indexed MegaBLAST has been used in production on NCBI's Web BLAST service to search one version of the human and mouse genomes since October 2007. The Linux command-line executables for blastn and makembindex, documentation, and some query sets used to carry out the tests described below are available in the directory: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/indexed_megablast
Contact: schaffer@helix.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Biodiversity of North Sea fish: why do the politicians care but marine scientists appear oblivious to this issue?
Authors: Greenstreet Simon P. R. 
Published: June 2008

AbstractGreenstreet, S. P. R. 2008. Biodiversity of North Sea fish: why do the politicians care but marine scientists appear oblivious to this issue? – ICES Journal of Marine Science, 65: 1515–1519. Political drivers underpinning the development of an Ecosystem Approach to Marine Management (EAMM) focus on conserving and restoring biodiversity. However, the Element of Ecological Quality for Fish Communities that emerged from the 2002 Bergen North Sea Ministerial Conference relates to “Changes in the proportion of large fish and hence the average weight and average maximum length of the fish community”. How did this apparent change in direction arise? Responding to advice requests from OSPAR, ICES established seven criteria for identifying “state” indicators capable of supporting indicator-based management. Application of these criteria underlined the merits of indicators of fish size, whereas diversity indices performed poorly against four of the criteria. These difficulties are examined here. Far from being oblivious to the issue of biodiversity, marine scientists recognized that they were not in a position to recommend Ecological Quality Objectives (EcoQOs) for fish biodiversity that would have relied on the use of biodiversity indicators. The use of indicators of size structure, for which the theoretical foundation was better developed, allowed the continued development of an EAMM in the short term. However, if the issue of biodiversity is to be addressed in the longer term, then shortcomings associated with the use of biodiversity indicators need to be addressed.
Changes in spawning-stock structure and recruitment pattern of red mullet, Mullus barbatus, after a trawl ban in the Gulf of Castellammare (central Mediterranean Sea)
Authors: Fiorentino F. , Badalamenti F. , D’Anna G. , Garofalo G. , Gianguzza P. , Gristina M. , Pipitone C. , Rizzo P. , Fortibuoni T. 
Published: June 2008

Abstract
Fiorentino, F., Badalamenti, F., D’Anna, G., Garofalo, G., Gianguzza, P., Gristina, M., Pipitone, C., Rizzo, P., and Fortibuoni, T. 2008. Changes in spawning-stock structure and recruitment pattern of red mullet, Mullus barbatus, after a trawl ban in the Gulf of Castellammare (central Mediterranean Sea). – ICES Journal of Marine Science, 65: 1175–1183. The increase in biomass of red mullet, Mullus barbatus, in the Gulf of Castellammare (northwestern Sicily, central Mediterranean) after a 14-year trawl ban, prompted us to compare the spawning-stock structure and the recruitment pattern before and after the closure. Datasets obtained from three experimental trawl surveys were available before the ban (April and September 1985; April–May 1986) and four post-ban (September and November 2004; March and May 2005). Spawning-stock biomass increased significantly after the ban. Moreover, females at depths >50 m in the post-ban period were larger than those collected before the ban at the same depth. The recruitment pattern of the population also changed. Notably, recruit numbers increased and recruitment occurs over a broader period. The increase in biomass after the trawl ban seems to be the result of a combination of different processes, mainly associated with the lowering of fishing mortality. A positive trend in sea surface temperature in the area may have played a role too.
Folding kinetics and thermodynamics of Pseudomonas syringae effector protein AvrPto provide insight into translocation via the type III secretion system
Authors: Dawson Jennifer E. , Nicholson Linda K. 
Published: June 2008

AbstractIn order to infect their hosts, many Gram‐negative bacteria translocate agents of infection, called effector proteins, through the type III secretion system (TTSS) into the host cytoplasm. This process is thought to require at least partial unfolding of these agents, raising the question of how an effector protein might unfold to enable its translocation and then refold once it reaches the host cytoplasm. AvrPto is a well‐studied effector protein of Pseudomonas syringae pv tomato. The presence of a readily observed unfolded population of AvrPto in aqueous solution and the lack of a known secretion chaperone make it ideal for studying the kinetic and thermodynamic characteristics that facilitate translocation. Application of Nzz exchange spectroscopy revealed a global, two‐state folding equilibrium with 16% unfolded population, a folding rate of 1.8 s−1, and an unfolding rate of 0.33 s−1 at pH 6.1. TrAvrPto stability increases with increasing pH, with only 2% unfolded population observed at pH 7.0. The R1 relaxation of TrAvrPto, which is sensitive to both the global anisotropy of folded TrAvrPto and slow exchange between folded and unfolded conformations, provided independent verification of the global kinetic rate constants. Given the acidic apoplast in which the pathogen resides and the more basic host cytoplasm, these results offer an intriguing mechanism by which the pH dependence of stability and slow folding kinetics of AvrPto would allow efficient translocation of the unfolded form through the TTSS and refolding into its functional folded form once inside the host.
Taxonomic studies of Pterostichus ishikawai Nemoto (Coleoptera: Carabidae)
Authors: SASAKAWA Kôji , KIM Jung‐Lark , KIM Jong‐Kuk , KUBOTA Kôhei 
Published: June 2008

AbstractA macrocephalic pterostichine carabid, Pterostichus ishikawai Nemoto, endemic to the Korean Peninsula, is taxonomically revised based mainly on the membranous parts of the genitalia (male endophallus and female vagina). Two species are separated from P. ishikawai (type locality: Mount Taebaegsan) and newly described: P. ishikawaioides (type locality: Mount Sobaeksan) and P. jiricola (type locality: Mount Jirisan). Since comparative male genital morphology does not support monophyly for these three species, the two novel species should be treated as distinct species, not subspecies of P. ishikawai.
Performance of clones and morphs of two cereal aphids on wheat plants with high and low nitrogen content
Authors: KHAN Mahfuza , PORT Gordon 
Published: June 2008

AbstractThe great variability of the aphid life cycle and their tendency for host alternation gives rise to aphid clones and morphs. Inter‐ and intraclonal variability may be observed in the responses of aphids to various environmental factors. In this study we aimed to evaluate the influence of intrinsic factors (clone and morph type) on the intrinsic rate of increase (rm) of the English grain aphid, Sitobion avenae (Fabricius), and the bird cherry‐oat aphid, Rhopalosiphum padi (Linnaeus). For each species four apterous clones were collected from established laboratory colonies and compared to assess their relative fitness on high‐ and low‐nitrogen wheat plants under laboratory conditions. The clones had significantly different intrinsic rates of increase on high‐ and low‐nitrogen plants. All R. padi clones had a higher intrinsic rate of increase and mean relative growth rate than S. avenae. Experiments were also conducted to compare the mean fecundity of apterous and alate morphs of S. avenae and R. padi clones on high‐ and low‐nitrogen wheat plants. On high‐nitrogen plants the apterous morphs of S. avenae clones had significantly higher mean fecundity than alate morphs. There were no significant differences between the mean fecundity of alate morphs of the same species on high‐ and low‐nitrogen plants. The results support the idea of better fitness of specific clones/morphs on certain host plants due to higher and lower intrinsic rates of increase.