bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of boron on the performance of automotive brake
Authors: Muzathik A. , Nizam Y. , Ahmad M. , Nik W.
Published: February 2014

Friction material in an automotive brake system plays an important role for effective and safe brake performance. A single material has never been sufficient to solve performance related issues. Current research aimed to examine properties of Boron mixed brake pads by comparing them with the commercial brake pads. Friction coefficient of Boron mixed brake pads and commercial brake pads were significantly different and increased with the increase in surface roughness. The abrupt reduction of friction coefficient is more significant in commercial brake pad samples than in Boron mixed brake pad formulations. Fade occurred in commercial brake pad sample at lower temperatures. Boron formulations are more stable than their commercial counterparts.
Comparison of Experimental and Computational Fluid Dynamics (CFD) Studies of Slug Flow in a Vertical 90° Bend
Authors: Abdulkadir M. , Hernandez-Perez V. , Lo S. , Lowndes I. S. , Azzopardi B. J.
Published: February 2014

This paper presents the results of comparison of experimental and CFD studies of slug flow in a vertical 90° bend using validated models. For the experimental part, Electrical Capacitance Tomography (ECT), Wire Mesh Tomography (WMS), and high-speed videos were used to monitor an air-silicone oil mixture flowing in a vertical 90o bend. The ECT probes were mounted before the bend whilst the WMS was positioned either immediately upstream or immediately downstream of the bend. The downstream pipe was maintained horizontal whilst the upstream pipe was maintained vertical. The bend (R/D = 2.3) was made of transparent acrylic resin. Parallel to the experiments, simulations were carried out for same experiment set-up using the commercial software package Star-CD and Star-CCM+. The condition was simulated with the Volume of Fluid (VOF) model. The simulation predictions were validated against the experimental data. A reasonably good agreement was observed for the results of the experiment and CFD.
Effects of Atmospheric Dynamics on CO2 Seepage at Mammoth Mountain, California USA
Authors: Ogretim Egemen , Crandall Dustin , Gray Donald D. , Bromhal Grant S.
Published: February 2014

In the past few decades, atmospheric effects on the variation of seepage from soil have been studied in disciplines such as volcanology, environmental protection, safety and health hazard avoidance. Recently, monitoring of potential leakage from the geologic sequestration of carbon has been added to this list. Throughout these diverse fields, barometric pumping and presence of steady winds are the two most commonly investigated atmospheric factors. These two factors have the effect of pumping gas into and out of the unsaturated zone, and sweeping the gas in the porous medium. This study focuses on two new factors related to atmosphere in order to explain the CO2 seepage anomalies observed at the Horseshoe Lake tree kill near Mammoth Mountain, CA, where the temporal variation of seepage due to a storm event could not be explained by the two commonly studied effects. First, the interaction of the lower atmospheric dynamics and the ground topography is considered for its effect on the seepage variation over an area that is linked through high-porosity, high-permeability soils and/or fracture networks. Second, the regional pressure fronts that impose significant pressure oscillation over an area are studied. The comparison of the computer simulation results with the experimental measurements suggests that the seepage anomaly observed at the Horseshoe Lake Tree Kill could be due to the unsteady effects caused by regional pressure fronts.
Comment on ‘Lower Bounds to Future Sea-Level Rise’
Authors: Hunter John
Published: February 2014

The paper Lower Bounds to Future Sea-Level Rise (Parker, 2013) bears many similarities to an earlier one (Parker et al., 2013). In particular, the first pair of equations in both papers are almost identical and wrong, as pointed out by Hunter (2013). In addition, a crucial statement in the Abstract suggests that present observations of sea-level rise show no acceleration and therefore cast doubt on present projections of sea-level rise; this conclusion has previously been shown to be false (Hunter and Brown, 2013). It should be noted that this is by no means a comprehensive exploration of all the possible errors in Parker's paper.
Experimental and Numerical Investigation of Hydrodynamic Response of Spar with Wind Turbine under Random Waves
Authors: Nallayarasu S. , Saravanapriya S.
Published: February 2014

In this paper, experimental and numerical investigation on the motion response of Spar with wind turbine subjected to random waves are presented and discussed. The studies were carried out for three different cases: (a) Spar with wind turbine subjected to waves when the turbine blades are in stationary condition; (b) Spar with wind turbine in operating condition under calm sea state; (c) Spar with wind turbine subjected to waves when the turbine blades are in operating condition. The numerical investigation was carried out using hydrodynamic software Ansys AQWA. The influence of the turbine blade rotation on the motion response of the Spar was investigated and the responses of the system under random waves were presented in terms of statistical values. The experimental results and the results obtained from numerical investigation matches reasonably well. The motion response of the system has increased by about 30%, 20% and 25% for surge, heave and pitch respectively, for turbine blades in rotating condition when compared with Spar with wind turbine in stationary condition.
MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data
Authors: Barturen Guillermo , Rueda Antonio , Oliver José L. , Hackenberg Michael
Published: February 2014

Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling of the methylation levels is done from the alignments. A huge effort has been made to quickly and correctly align the reads and many different algorithms and programs to do this have been created. However, the second step is just as crucial and non-trivial, but much less attention has been paid to the final inference of the methylation states. Important error sources do exist, such as sequencing errors, bisulfite failure, clonal reads, and single nucleotide variants.

We developed MethylExtract, a user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources. MethylExtract detects variation (SNVs – Single Nucleotide Variants) in a similar way to VarScan, a very sensitive method extensively used in SNV and genotype calling based on non-bisulfite-treated reads. The usefulness of MethylExtract is shown by means of extensive benchmarking based on artificial bisulfite-treated reads and a comparison to a recently published method, called Bis-SNP.

MethylExtract is able to detect SNVs within High-Throughput Sequencing experiments of bisulfite treated DNA at the same time as it generates high quality methylation maps. This simultaneous detection of DNA methylation and sequence variation is crucial for many downstream analyses, for example when deciphering the impact of SNVs on differential methylation. An exclusive feature of MethylExtract, in comparison with existing software, is the possibility to assess the bisulfite failure in a statistical way. The source code, tutorial and artificial bisulfite datasets are available at http://bioinfo2.ugr.es/MethylExtract/ and http://sourceforge.net/projects/methylextract/, and also permanently accessible from 10.5281/zenodo.7144.
Typification of Linnaean names in Malvaceae for the Italian flora
Authors: Iamonico Duilio , Peruzzi Lorenzo
Published: February 2014

The typification of the six Linnaean names Gossypium hirsutum, Hibiscus pentacarpos, H. trionum, Lavatera lusitanica, L. micans and Malva crispa var. verticillata is discussed. The names are lectotypified using specimens from Clifford, Linnaeus and Van Royen Herbaria and illustrations from Zannichelli and Morison.
Phylogeny and taxonomy of Syngonanthus and Comanthera (Eriocaulaceae): Evidence from expanded sampling
Authors: Echternacht Livia , Sano Paulo Takeo , Bonillo Céline , Cruaud Corinne , Couloux Arnaud , Dubuisson Jean-Yves
Published: February 2014

Comanthera and Syngonanthus (Eriocaulaceae) are monocotyledonous herbs that occur mainly in neotropical savannas in the Guiana Shield and in southeastern Brazil, with a few species in Africa. Phylogenetic relationships in Syngonanthus and Comanthera are still unresolved and have not yet been assessed using a broad and comprehensive sampling. The present study aimed to test the monophyly of both genera and their putative infrageneric taxa and to evaluate their taxonomy and supporting synapomorphies in the light of a resolved phylogeny. The resulting phylogenetic hypotheses were then used to infer the biogeographical histories of the taxa, especially in Brazil. Molecular analyses based on plastid (trnL‐F, psbA‐trnH) and nuclear (ITS) markers using parsimony and Bayesian inference were conducted on 62 species belonging to the ingroup. Syngonanthus s.l. (composed of Syngonanthus, Philodice and Comanthera), Syngonanthus s.str. (including Philodice), Comanthera and both of its subgenera were retrieved as monophyletic, strongly supported by molecular and morphological apomorphies. However Syngonanthus sect. Carphocephalus appeared polyphyletic, and its species were embedded within a paraphyletic S. sect. Syngonanthus. Within Comanthera, clades restricted to equatorial savannas appeared to be sisters to clades restricted to southeastern Brazil, especially in the Espinhaço Range, with a disjunct pattern between Bahia and Minas Gerais states. Within Syngonanthus s.str., Andean and African species appeared embedded in Brazilian clades, but resolution and support within the genus must be improved in future research.
Dates of publication of the “Journal de Botanique/ Ботаническiй журналъ (St.-Petersburg)” (1906–1909)
Authors: Doweld Alexander B.
Published: February 2014

Precise dates of publication for issues of the Journal de Botanique  Ботаническiй журналъ (St. Petersburg), published in 1906–1909 by the former Imperial St.‐Petersburg Society of Naturalists are provided as a supplement to precise publication date records of Taxonomic literature ed. 2.
Trade-offs in a Tempest: Stakeholder Influence on Hurricane Evacuation Decisions
Authors: Dye Karen Chinander , Eggers J. P. , Shapira Zur
Published: February 2014

Stakeholders often control vital resources for decision makers, and this can lead decision makers to take stakeholder opinions into account when making important decisions. This process can be complicated by a number of factors. First, many important decisions involve risk and uncertainty. When the outcome is uncertain, how does a decision maker take the views of stakeholders into account? Second, many decision makers are accountable to multiple different stakeholder groups with different preferences. How do these heterogeneous stakeholder groups affect the process of decision making? More generally, do these stakeholder considerations lead to decisions that are not socially optimal?

We explore these and related questions by focusing on a specific type of high-stakes decision making in a context featuring significant risk and heterogeneous stakeholders—the decision to evacuate a community during the threat of a hurricane hitting land. There is research on weather forecasting techniques and individual evacuation behavior; however, there is no research on the behavior of local officials in making hurricane evacuation decisions. These decisions provide an excellent context for an exploration into the specific processes by which stakeholder considerations may affect the process of decision making.

This study offers a simple model of the process underlying evacuation decision making. The model focuses on how the evacuation threshold is set based on the anticipated costs of Type I versus Type II errors. We then use the model—supplemented with rich qualitative and quantitative data—to offer a series of propositions about the conditions under which nonsocially optimal evacuation decisions may be made. This paper contributes to the literature on decision making by offering a simple model that integrates decision making and stakeholder considerations and by offering specific and novel propositions about this integration.
Synthesis and fundamental HSQC NMR data of monolignol β-glycosides, dihydromonolignol β-glycosides and p-hydroxybenzaldehyde derivative β-glycosides for the analysis of phenyl glycoside type lignin-carbohydrate complexes (LCCs)
Authors: Miyagawa Yasuyuki , Mizukami Takahito , Kamitakahara Hiroshi , Takano Toshiyuki
Published: February 2014

Twelve monolignol (coniferyl alcohol, sinapyl alcohol and p-coumaryl alcohol) β-glycosides (β-glucosides, β-galactosides, β-xylosides and β-mannosides) were synthesised to obtain fundamental NMR data for the analysis of phenyl glycoside type lignin-carbohydrate complexes (LCCs). That is, the 1,2-trans glycosides (the β-glucosides, β-galactosides and β-xylosides) and the 1,2-cis glycosides (the β-mannosides) were synthesized by means of Koenig-Knorr glycosylation and β-selective Mitsunobu glycosylation strategies, respectively. In addition, dihydromonolignol and p-hydroxybenzaldehyde derivative β-glycosides were also prepared from the corresponding monolignol glycosides and their intermediates, respectively. The correlation observed for the C1β-H1β bonds of the sugar moieties in the HSQC spectra of the all β-glycosides varied and were in the range of δ
C/δ
H 96–104/4.7–5.4 ppm. Especially, it was found that the correlations derived from the C1β-H1β bonds of the guaiacyl and p-hydroxyphenyl β-mannosides were close to those derived from the C1α-H1α bonds of the 4-O-methyl-α-D-glucuronic acid moieties described in the literature.
Sequence Profiling of the Saccharomyces cerevisiae Genome Permits Deconvolution of Unique and Multialigned Reads for Variant Detection
Authors: Jubin Claire , Serero Alexandre , Loeillet Sophie , Barillot Emmanuel , Nicolas Alain
Published: February 2014

Advances in high-throughput sequencing (HTS) technologies have accelerated our knowledge of genomes in hundreds of organisms, but the presence of repetitions found in every genome raises challenges to unambiguously map short reads. In particular, short polymorphic reads that are multialigned hinder our capacity to detect mutations. Here, we present two complementary bioinformatics strategies to perform more robust analyses of genome content and sequencing data, validated by use of the Saccharomyces cerevisiae fully sequenced genome. First, we created an annotated HTS profile for the reference genome, based on the production of virtual HTS reads. Using variable read lengths and different numbers of mismatches, we found that 35 nt-reads, with a maximum of 6 mismatches, targets 89.5% of the genome to unique (U) regions. Longer reads consisting of 50−100 nt provided little additional benefits on the U regions extent. Second, to analyze the remaining multialigned (M) regions, we identified the intragenomic single-nucleotide variants and thus defined the unique (MU) and multialigned (MM) subregions, as exemplified for the polymorphic copies of the six flocculation genes and the 50 Ty retrotransposons. As a resource, the coordinates of the U and M regions of the yeast genome have been added to the Saccharomyces Genome Database (www.yeastgenome.org). The benefit of this advanced method of genome annotation was confirmed by our ability to identify acquired single nucleotide polymorphisms in the U and M regions of an experimentally sequenced variant wild-type yeast strain.
unfulfilledInteracting Genes Display Branch-Specific Roles in the Development of Mushroom Body Axons inDrosophila melanogaster
Authors: Bates Karen E , Sung Carl , Hilson Liam , Robinow Steven
Published: February 2014

The mushroom body (MB) of Drosophila melanogaster is an organized collection of interneurons that is required for learning and memory. Each of the three subtypes of MB neurons, γ, α´/β´, and α/β, branch at some point during their development, providing an excellent model in which to study the genetic regulation of axon branching. Given the sequential birth order and the unique patterning of MB neurons, it is likely that specific gene cascades are required for the different guidance events that form the characteristic lobes of the MB. The nuclear receptor UNFULFILLED (UNF), a transcription factor, is required for the differentiation of all MB neurons. We have developed and used a classical genetic suppressor screen that takes advantage of the fact that ectopic expression of unf causes lethality to identify candidate genes that act downstream of UNF. We hypothesized that reducing the copy number of unf-interacting genes will suppress the unf-induced lethality. We have identified 19 candidate genes that when mutated suppress the unf-induced lethality. To test whether candidate genes impact MB development, we performed a secondary phenotypic screen in which the morphologies of the MBs in animals heterozygous for unf and a specific candidate gene were analyzed. Medial MB lobes were thin, missing, or misguided dorsally in five double heterozygote combinations (;unf/+;axin/+, unf/+;Fps85D/+, ;unf/+;Tsc1/+, ;unf/+;Rheb/+, ;unf/+;msn/+). Dorsal MB lobes were missing in ;unf/+;DopR2/+ or misprojecting beyond the termination point in ;unf/+;Sytβ double heterozygotes. These data suggest that unf and unf-interacting genes play specific roles in axon development in a branch-specific manner.
Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis inPodospora anserina
Authors: Grognet Pierre , Bidard Frédérique , Kuchly Claire , Tong Laetitia Chan Ho , Coppin Evelyne , Benkhali Jinane Ait , Couloux Arnaud , Wincker Patrick , Debuchy Robert , Silar Philippe
Published: February 2014

Pseudo-homothallism is a reproductive strategy elected by some fungi producing heterokaryotic sexual spores containing genetically different but sexually compatible nuclei. This lifestyle appears as a compromise between true homothallism (self-fertility with predominant inbreeding) and complete heterothallism (with exclusive outcrossing). However, pseudohomothallic species face the problem of maintaining heterokaryotic mycelia to fully benefit from this lifestyle, as homokaryons are self-sterile. Here, we report on the structure of chromosome 1 in mat+ and mat− isolates of strain S of the pseudohomothallic fungus Podospora anserina. Chromosome 1 contains either one of the mat+ and mat− mating types of P. anserina, which is mostly found in nature as a mat+/mat− heterokaryotic mycelium harboring sexually compatible nuclei. We identified a “mat” region ∼0.8 Mb long, devoid of meiotic recombination and containing the mating-type idiomorphs, which is a candidate to be involved in the maintenance of the heterokaryotic state, since the S mat+ and S mat− strains have different physiology that may enable hybrid-vigor-like phenomena in the heterokaryons. The mat region contains 229 coding sequences. A total of 687 polymorphisms were detected between the S mat+ and S mat− chromosomes. Importantly, the mat region is colinear between both chromosomes, which calls for an original mechanism of recombination inhibition. Microarray analyses revealed that 10% of the P. anserina genes have different transcriptional profiles in S mat+ and S mat−, in line with their different phenotypes. Finally, we show that the heterokaryotic state is faithfully maintained during mycelium growth of P. anserina, yet mat+/mat+ and mat−/mat− heterokaryons are as stable as mat+/mat− ones, evidencing a maintenance of heterokaryosis that does not rely on fitness-enhancing complementation between the S mat+ and S mat− strains.
TargetOrtho: A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets
Authors: Glenwinkel Lori , Wu Di , Minevich Gregory , Hobert Oliver
Published: February 2014

The identification of the regulatory targets of transcription factors is central to our understanding of how transcription factors fulfill their many key roles in development and homeostasis. DNA-binding sites have been uncovered for many transcription factors through a number of experimental approaches, but it has proven difficult to use this binding site information to reliably predict transcription factor target genes in genomic sequence space. Using the nematode Caenorhabditis elegans and other related nematode species as a starting point, we describe here a bioinformatic pipeline that identifies potential transcription factor target genes from genomic sequences. Among the key features of this pipeline is the use of sequence conservation of transcription-factor-binding sites in related species. Rather than using aligned genomic DNA sequences from the genomes of multiple species as a starting point, TargetOrtho scans related genome sequences independently for matches to user-provided transcription-factor-binding motifs, assigns motif matches to adjacent genes, and then determines whether orthologous genes in different species also contain motif matches. We validate TargetOrtho by identifying previously characterized targets of three different types of transcription factors in C. elegans, and we use TargetOrtho to identify novel target genes of the Collier/Olf/EBF transcription factor UNC-3 in C. elegans ventral nerve cord motor neurons. We have also implemented the use of TargetOrtho in Drosophila melanogaster using conservation among five species in the D. melanogaster species subgroup for target gene discovery.
Oat tillering and tiller traits under different nitrogen levels in an eucalyptus agroforestry system in Subtropical Brazil
Authors: Deiss Leonardo , Moraes Anibal de , Pelissari Adelino , Skora Neto Francisco , Oliveira Edilson Batista de , Silva Vanderley Porfírio da
Published: February 2014

In oat production, tillering persistence is the determinant of one important yield component, namely the number of panicles. This process is highly influenced by the inter- and intraspecific interactions of the agroecosystem, which in turn depend on agronomic practices. The hypothesis of this research is that nitrogen does not increase oat tolerance to negative interference from trees, so oat tillering persistence in grain production remains un-modified by nitrogen at distances relative to the eucalyptus tracks, within the alley cropping agroforestry system (ACS). Thus, nitrogen should not be used to increase oat yield potential in these systems. The objective of this study was to determine how the tillering persistence for grain production and oat (Avena sativa L. cv. 'IPR 126') tiller traits were influenced by nitrogen levels (12 and 80kg N ha-1) at five equidistant positions between two adjacent eucalyptus (Eucalyptus dunnii Maiden) double line tracks [20m (4mx3m)] in ACS and traditional no-till agriculture in subtropical Brazil. The experiment was conducted in a split-block randomized block design with four replicates. The goal was to evaluate the oat phytomass, tiller-to-main shoot phytomass ratio, tillers per main shoot, grain yield and tiller-to-main shoot grain yield ratio. The oat tillering persistence for grain production is dependent on different nitrogen levels at distances relative to adjacent eucalyptus tracks and therefore, different nitrogen levels should be used in those areas, to improve oat yield potential inside ACS in subtropical Brazil.
Estimação de parâmetros genéticos de ovinos da raça Santa Inês utilizando modelos uni e bicaracterística
Authors: Carvalho Geane Conceição , Barbosa Leandro Teixeira , Oliveira Tatiana Maia de , Fonseca Fernanda Érica Pereira , Muniz Evandro Neves , Azevedo Hymerson Costa
Published: February 2014

Objetivou-se nesse trabalho, estimar os parâmetros genéticos para características de crescimento em ovinos da raça Santa Inês através do Método da Máxima Verossimilhança Restrita (REML). Os componentes de (co)variâncias e os parâmetros genéticos foram estimados pelo Software MTDFREML (Multiple Trait Derivative-Free Restricted Maximum Likelihood). As características avaliadas em modelos uni e bicaracterística foram: peso ao nascimento (PN) e peso ao desmame (P90). Além dos efeitos fixos de sexo, grupo contemporâneo e tipo de parto, foram utilizados os seguintes efeitos aleatórios: efeito genético aditivo direto, efeito genético aditivo materno e efeito residual. As estimativas de herdabilidade aditiva direta para PN foram 0,20 e 0,21, para os modelos uni e bicaracterística, respectivamente. As estimativas de herdabilidade aditiva direta para P90 foram 0,04 e 0,07, para os modelos uni e bicaracterística, respectivamente. A correlação genética entre PN e P90 foi de 0,11, indicando que ambas as características devem ser trabalhadas simultaneamente.
Respostas ao pastejo ou exclusão podem ser caracterizados por tipos funcionais?
Authors: Castilhos Zélia Maria de Souza , Pillar Valério De Patta
Published: February 2014

O trabalho foi desenvolvido no Centro de Pesquisa de Forrageiras, da FEPAGRO, em São Gabriel, RS, numa área de pastagem natural, de janeiro de 1998 a dezembro de 2000, com o objetivo de definir tipos funcionais para os fatores avaliados. O delineamento experimental utilizado foi um fatorial completamente casualizado em parcela subdividida, com três repetições. Os tratamentos pastejo e exclusão foram alocados nas parcelas principais e os níveis de adubação (com ou sem NPK) nas subparcelas. O pastejo foi realizado por bovinos, equinos e ovinos a partir de janeiro de 1998 e a adubação, anualmente, de fevereiro de 1994 a fevereiro de 1996. A exclusão iniciou em dezembro de 1996. Altura da planta, consistência e superfície ventral da lâmina foliar são atributos que melhor caracterizam os ambientes pastejados e excluídos.
Influence of aluminium inclusions on dielectric properties of three-phase PZT–cement–aluminium composites
Authors: Banerjee Sankha , Cook-Chennault Kimberly A.
Published: February 2014

Novel three-phase piezoelectric composites that comprised lead zirconate titanate (PZT), aluminium and Portland cement were fabricated at a low poling voltage of 0·6 kV/mm and temperature of 160°C. Aluminium and PZT particles were distributed in a Portland cement matrix, and the dielectric constant, tan δ and strain coefficients were experimentally investigated as a function of inclusion volume fraction. The three-phase piezoelectric composites were found to possess higher piezoelectric strain coefficients, d33, than their two-phase counterparts (PZT and Portland cement composites). The highest value of d33observed for the three-phase composite was 8·1 pC/N for volume fractions of 0·7 and 0·2 for PZT and aluminium respectively, which was 164% of the value observed for the two-phase composite, at the same PZT volume fraction. An analytical model was used to predict values for the effective dielectric constant of the three-phase composites, and these values compared reasonably well to the empirical data. An investigation of sample degradation as a function of time was performed. Samples showed the highest degree of reduced dielectric performance occurred within two days of data capture, and minimal subsequent reduction in performance after 300 d. Electrical properties of the composites are influenced by the oxidation of aluminium by the alkaline constituents in the cement matrix, distribution of PZT and aluminium within the matrix, particle agglomeration, inclusion size, contact resistance between particles and air voids. The increased dielectric and piezoelectric strain coefficients, demonstrate that these types of materials may be useful in applications such as structural health monitoring and energy harvesting.
Disentangling the environmental‐heterogeneity–species‐diversity relationship along a gradient of human footprint
Authors: Seiferling Ian , Proulx Raphaël , Wirth Christian
Published: February 2014

Decades of study have attempted to define a generalized environmental‐heterogeneity–biodiversity (EH–BD) relationship, with the traditional MacArthurian niche‐based hypothesis remaining as the dominant reference point; i.e., increasing heterogeneity promotes biodiversity by increasing resource opportunities. However, studies have frequently reported negative or nonsignificant relationships. In a vast majority of them, environmental heterogeneity was defined along a gradient of increasing randomness, toward complete disorder. A new conceptual framework could help to reconcile the array of observed relationships. Using an extensive literature review, we test a conceptual framework proposing that the direction of environmental‐heterogeneity–biodiversity relationships is contingent on the level of human footprint to which an ecosystem is subjected (the anthropocline). The results reveal that highly modified and seminatural ecosystems are characterized by a dominance of positive and negative EH–BD relationships, respectively, whereas natural ecosystems show mixed responses. Out of this novel framework arises the revised perspective that natural ecosystems are typified, not by maximal or minimal, but by intermediate levels of environmental heterogeneity.
Photodynamic Therapy During Supportive Periodontal Care: Clinical, Microbiologic, Immunoinflammatory, and Patient‐Centered Performance in a Split‐Mouth Randomized Clinical Trial
Authors: Kolbe Maria F. , Ribeiro Fernanda V. , Luchesi Vanessa H. , Casarin Renato C. , Sallum Enilson A. , Nociti Francisco H. , Ambrosano Gláucia M.B. , Cirano Fabiano R. , Pimentel Suzana P. , Casati Marcio Z.
Published: February 2014

Background: This study investigates the effect of photodynamic therapy (PDT) as monotherapy during supportive periodontal therapy.

Methods: A split‐mouth, randomized controlled trial was conducted in patients with chronic periodontitis (N = 22) presenting at least three residual pockets (probing depth [PD] ≥5 mm with bleeding on probing [BOP]). The selected sites randomly received the following: 1) PDT; 2) photosensitizer (PS); or 3) scaling and root planing (SRP). At baseline and 3 and 6 months, clinical, microbiologic (real‐time polymerase chain reaction analyses), cytokine pattern (multiplexed bead immunoassay), and patient‐centered (regarding morbidity) evaluations were performed.

Results: All therapies promoted similar improvements in clinical parameters throughout the study (P <0.05), except that BOP was not reduced in the PS protocol (P >0.05). Lower levels of Aggregatibacter actinomycetemcomitans were observed in the PDT and SRP protocols at 3 months when compared with the PS protocol (P <0.05). An inferior frequency detection of Porphyromonas gingivalis was observed in the PDT protocol at 3 and 6 months and in the SRP protocol at 6 months from baseline (P <0.05). In addition, PDT protocol presented inferior frequency of P. gingivalis at 3 months when compared with the other therapies (P <0.05). Only patients in the PDT protocol exhibited augmented levels of anti‐inflammatory interleukin (IL)‐4 and reduced proinflammatory IL‐1β and IL‐6 throughout the study (P <0.05). Intergroup analyses showed reduced IL‐10 and increased interferon‐γ and IL‐1β levels in the PS protocol when compared with the other therapies during follow‐ups (P <0.05). No differences in morbidity were observed between the therapies (P >0.05), although the need for anesthesia was higher in SRP‐treated sites (P <0.05).

Conclusion: PDT as an exclusive therapy may be considered a non‐invasive alternative for treating residual pockets, offering advantages in the modulation of cytokines.
The Pharmacogenetics of Type 2 Diabetes: A Systematic Review
Authors: Maruthur Nisa M. , Gribble Matthew O. , Bennett Wendy L. , Bolen Shari , Wilson Lisa M. , Balakrishnan Poojitha , Sahu Anita , Bass Eric , Kao W.H. Linda , Clark Jeanne M.
Published: February 2014

OBJECTIVE

We performed a systematic review to identify which genetic variants predict response to diabetes medications.

RESEARCH DESIGN AND METHODS

We performed a search of electronic databases (PubMed, EMBASE, and Cochrane Database) and a manual search to identify original, longitudinal studies of the effect of diabetes medications on incident diabetes, HbA1c, fasting glucose, and postprandial glucose in prediabetes or type 2 diabetes by genetic variation. Two investigators reviewed titles, abstracts, and articles independently. Two investigators abstracted data sequentially and evaluated study quality independently. Quality evaluations were based on the Strengthening the Reporting of Genetic Association Studies guidelines and Human Genome Epidemiology Network guidance.

RESULTS

Of 7,279 citations, we included 34 articles (N = 10,407) evaluating metformin (n = 14), sulfonylureas (n = 4), repaglinide (n = 8), pioglitazone (n = 3), rosiglitazone (n = 4), and acarbose (n = 4). Studies were not standalone randomized controlled trials, and most evaluated patients with diabetes. Significant medication–gene interactions for glycemic outcomes included 1) metformin and the SLC22A1, SLC22A2, SLC47A1, PRKAB2, PRKAA2, PRKAA1, and STK11 loci; 2) sulfonylureas and the CYP2C9 and TCF7L2 loci; 3) repaglinide and the KCNJ11, SLC30A8, NEUROD1/BETA2, UCP2, and PAX4 loci; 4) pioglitazone and the PPARG2 and PTPRD loci; 5) rosiglitazone and the KCNQ1 and RBP4 loci; and 5) acarbose and the PPARA, HNF4A, LIPC, and PPARGC1A loci. Data were insufficient for meta-analysis.

CONCLUSIONS

We found evidence of pharmacogenetic interactions for metformin, sulfonylureas, repaglinide, thiazolidinediones, and acarbose consistent with their pharmacokinetics and pharmacodynamics. While high-quality controlled studies with prespecified analyses are still lacking, our results bring the promise of personalized medicine in diabetes one step closer to fruition.
Agritourism in Italy and the Local Impact Referring To Itria Valley. The Organic Firm “Raggio Verde” And Its Ecological Agritourism Project
Authors: Ciervo Margerita
Published: February 2014

The aim of this article, using a paradigmatic approach, is to understand the evolution of agritouristic activity in Italy, to evaluate the possible local impacts referring to Itria Valley and considering the case of study of the organic firm “Raggio Verde” in Cisternino (Brindisi, Italy) with its project of multifunctional initiatives through the creation of an organic ecological agritourism. The thesis supported is that the local impact of the agritouristic activity is different according to the reference’s paradigm (market liberalism or ecological-territorial) and to the agritourism model (with reference to environmental and social relations, and to the dependence’s level from external sources). The methodology is inductive, based on qualitative and quantitative analysis, on indirect, direct and participant observation by a research on the field.
Descriptions of digenean parasites from three snail species, Bithynia fuchsiana (Morelet), Parafossarulus striatulus Benson and Melanoides tuberculata Müller, in North Vietnam
Authors: Besprozvannykh V. , Ngo H. , Ha N. , Hung N. , Rozhkovan K. , Ermolenko A.
Published: February 2014

For first time, 3 species of prosobranchial snails (Bithynia fuchsiana, Parafossarulus striatulus (Bithyniidae) and Melanoides tuberculata (Thiaridae)) from North Vietnam were studied for presence of the parthenitae and cercariae of Trematoda. The morphology of 12 species of larvae belonging to 8 families (Cyathocotylidae, Pleurogenidae, Lecithodendriidae, Paramphistomidae, Heterophyidae, Notocotylidae, Psilostomidae and Echinostomatidae) was described. Data on the life cycles of 3 species (Echinochasmus japonicus, Notocotylus intestinalis and Sphaeridiotrema monorchis) as well as molecular data on 28S rDNA were obtained. There was no intraspecific variability found in any of the sequences examined. The 28S rDNA sequence length determined for N. intestinalis was 1315 bp, while that of S. monorchis was 1292 bp, and that of E. japonicus was 1288 bp.
Application of LSVT BIG Intervention to Address Gait, Balance, Bed Mobility, and Dexterity in People With Parkinson Disease: A Case Series
Authors: Janssens Jorina , Malfroid Klaartje , Nyffeler Thomas , Bohlhalter Stephan , Vanbellingen Tim
Published: February 2014

Background and Purpose

Lee Silverman Voice Treatment Big (LSVT BIG) is characterized by intensive exercising of high-amplitude movements to overcome bradykinesia and hypokinesia in patients with Parkinson disease (PD). The aim of the present case series was to explore possible beneficial effects of LSVT BIG training on gait, balance, bed mobility, and dexterity.

Case Description

Three patients with mild to moderate PD (all male; aged 52, 54, and 70 years; Hoehn & Yahr stages I–III) completed a 4-week LSVT BIG training program (16 individual 1-hour sessions) and an intensive home training program in accordance with the LSVT BIG protocol. Two certified LSVT BIG physical therapists delivered the LSVT BIG training sessions.

Outcomes

The outcome measures for gait and balance included the Functional Gait Assessment (FGA), Functional Reach Test (FRT), Timed “Up & Go” Test (TUG), Freezing of Gait Questionnaire (FOGQ), and motor score on part III of the Unified Parkinson's Disease Rating Scale (UPDRS III). Bed mobility was addressed using the Lindop Parkinson's Disease Mobility Assessment (LPA). The Nine-Hole Peg Test (9HPT) was used to measure dexterity. The 3 patients performed better on balance and gait assessments, as indicated by increased scores on the FRT and FGA (all 3 patients) and decreased scores on the TUG, FOGQ, and UPDRS III, of which scores of the FRT and UPDRS III achieved the minimal detectable change. Furthermore, the patients were quicker in tasks related to bed mobility (LPA). The patients' dexterity skills did not improve for their dominant (right) hand (9HPT).

Discussion

This case series suggests that the LSVT BIG may be beneficial for gait, balance, and bed mobility. Future work is needed to ascertain the effectiveness by means of randomized controlled trials.
Interrater and Intrarater Reliability of Common Clinical Standing Balance Tests for People With Hip Osteoarthritis
Authors: Choi Yik Ming , Dobson Fiona , Martin Joel , Bennell Kim L. , Hinman Rana S.
Published: February 2014

Background

Hip osteoarthritis (OA) is a common musculoskeletal condition affecting older individuals. Clinical balance tests are frequently used to assess standing balance in these people. There is insufficient information regarding the reliability of these tests.

Objective

The aim of this study was to estimate reliability and measurement error of 4 common clinical standing balance tests in people with hip OA.

Design

A prospective study was conducted with repeated measures between 2 independent raters within 1 session and within 1 rater over a 1-week interval.

Methods

Thirty people with hip OA were evaluated. Reliability was estimated for the Four-Square Step Test, Step Test, Functional Reach Test, and Timed Single-Leg Stance Test using intraclass correlation coefficients (ICC [2,1]). Measurement error was expressed as standard error of measurement and minimal detectable change.

Results

The Four-Square Step Test, Step Test, and Timed Single-Leg Stance Test were sufficiently reliable between raters (ICC=.85–.94, lower 1-sided 95% confidence interval [95% CI]=.71–.89), whereas the Step Test (standing on study limb) and Timed Single-Leg Stance Test (standing on nonstudy limb) were sufficiently reliable within a rater over a 1-week interval (ICC=.91, lower 1-sided 95% CI=.80–.83). The Step Test (standing on study limb) and Timed Single-Leg Stance Test (standing on nonstudy limb) achieved optimal levels of reliability (ICC >.90, lower 1-sided 95% CI >.70), with acceptable measurement error (<10%) for clinical outcome measures. The Functional Reach Test was not sufficiently reliable. A ceiling effect was detected for the Timed Single-Leg Stance Test.

Limitations

Reliability was assessed only between 2 raters during a single session and within 1 rater over a 1-week interval, which limits generalizability.

Conclusions

The Step Test (standing on study limb) is recommended as a highly reliable test with acceptable measurement error for assessing standing balance in people with hip OA.
Stability of Serial Range-of-Motion Measurements of the Lower Extremities in Children With Cerebral Palsy: Can We Do Better?
Authors: Darrah Johanna , Wiart Lesley , Gorter Jan Willem , Law Mary
Published: February 2014

Background

Serial joint range-of-motion (ROM) measurements are an important component of assessments for children with cerebral palsy. Most research has studied ROM stability using group data. Examination of longitudinal intraindividual measures may provide more clinically relevant information about measurement variability.

Objective

The aim of this study was to examine the stability of intraindividual longitudinal measurements of hip abduction (ABD), popliteal angle (POP), and ankle dorsiflexion (ADF) ROM measures of children with cerebral palsy.

Design

Secondary data analyses were performed.

Methods

The stability patterns of individual serial measurements of ABD, POP, and ADF from 85 children (mean age=3.8 years, SD=1.4) collected at baseline (T1), 3 months (T2), 6 months (T3), and 9 months (T4) were examined using T1 as the anchor and bandwidths of ±15 degrees (ABD and POP) and ±10 degrees (ADF) as acceptable variability. Frequencies of stability categories (0°–5°, 5.1°–10°, 10.1°–15°, and >15°) were calculated. Patterns of stability across the 4 time periods also were examined. Group means (T1–T4) were compared using repeated-measures analysis of variance.

Results

No significant differences in group means were found except for ABD. Stability patterns revealed that 43.3% to 69.5% of joint measurements were stable with T1 measurements across all 3 subsequent measurements. Stability category frequencies showed that many measurements (ABD=17%, POP=29.9%, and ADF=37.1%) went outside the variability bandwidths even though 39% or more of joint measurements had a change of 5 degrees or less over time.

Limitations

Measurement error and true measurement variability cannot be disentangled. The results cannot be extrapolated to other joint ROMs.

Conclusions

Individual ROM serial measurement exhibits more variability than group data. Range-of-motion data must be interpreted with caution clinically and efforts made to ensure standardization of data collection methods.
Silent reintroduction of wild-type poliovirus to Israel, 2013 – risk communication challenges in an argumentative atmosphere
Authors: Kaliner E , Moran-Gilad J , Grotto I , Somekh E , Kopel E , Gdalevich M , Shimron E , Amikam Y , Leventhal A , Lev B , Gamzu R
Published: February 2014

Israel has been certified as polio-free by the World Health Organization and its routine immunisation schedule consists of inactivated poliovirus vaccine (IPV) only. At the end of May 2013, the Israeli Ministry of Health (MOH) has confirmed the reintroduction of wild-type poliovirus 1 into the country. Documented ongoing human-to-human transmission necessitated a thorough risk assessment followed by a supplemental immunisation campaign using oral polio vaccine (OPV). The unusual situation in which ongoing poliovirus transmission was picked up through an early warning system of sewage monitoring without active polio cases, brought about significant challenges in risk communication. This paper reviews the challenges faced by the MOH and the communication strategy devised, in order to facilitate and optimise the various components of the public health response, particularly vaccination. Lessons learned from our recent experience may inform risk communication approaches in other countries that may face a similar situation as global polio eradication moves towards the 'End game'.
Immunity against poliomyelitis in the Netherlands, assessed in 2006 to 2007: the importance of completing a vaccination series
Authors: van der Maas N A , Mollema L , Berbers G A , van Rooijen D M , van der Avoort H G , Conyn-Van Spaendonck M A E , de Melker H E , van der Klis F R
Published: February 2014

Binary file ES_Abstracts_Final_ECDC.txt matches
The 2010 outbreak of poliomyelitis in Tajikistan: epidemiology and lessons learnt
Authors: Yakovenko M L , Gmyl A P , Ivanova O E , Eremeeva T P , Ivanov A P , Prostova M A , Baykova O Y , Isaeva O V , Lipskaya G Y , Shakaryan A K , Kew O M , Deshpande J M , Agol V I
Published: February 2014

A large outbreak of poliomyelitis, with 463 laboratory-confirmed and 47 polio-compatible cases, took place in 2010 in Tajikistan. Phylogenetic analysis of the viral VP1 gene suggested a single importation of wild poliovirus type 1 from India in late 2009, its further circulation in Tajikistan and expansion into neighbouring countries, namely Kazakhstan, Russia, Turkmenistan and Uzbekistan. Whole-genome sequencing of 14 isolates revealed recombination events with enterovirus C with cross-overs within the P2 region. Viruses with one class of recombinant genomes co-circulated with the parental virus, and representatives of both caused paralytic poliomyelitis. Serological analysis of 327 sera from acute flaccid paralysis cases as well as from patients with other diagnoses and from healthy people demonstrated inadequate immunity against polio in the years preceding the outbreak. Evidence was obtained suggesting that vaccination against poliomyelitis, in rare cases, may not prevent the disease. Factors contributing to the peculiarities of this outbreak are discussed. The outbreak emphasises the necessity of continued vaccination against polio and the need, at least in risk areas, of quality control of this vaccination through well planned serological surveillance.
Molecular epidemiology of silent introduction and sustained transmission of wild poliovirus type 1, Israel, 2013
Authors: Shulman L M , Gavrilin E , Jorba J , Martin J , Burns C C , Manor Y , Moran-Gilad J , Sofer D , Hindiyeh M Y , Gamzu R , Mendelson E , Grotto I , for the Genotype - Phenotype Identification (GPI) group
Published: February 2014

Poliovirus vaccine coverage in Israel is over 90%. The last nine birth cohorts have been vaccinated exclusively with inactivated polio vaccine (IPV). However, between February and July 2013 type 1 wild poliovirus (WPV1) was detected persistently in 10 and intermittently in 8 of 47 environmental surveillance sites in southern and central Israel and in 30 stool samples collected during July from healthy individuals in southern Israel. We report results of sequence and phylogenetic analyses of genes encoding capsid proteins to determine the source and transmission mode of the virus. WPV1 capsid protein 1 nucleotide sequences were most closely related to South Asia (SOAS) cluster R3A polioviruses circulating in Pakistan in 2012 and isolated from Egyptian sewage in December 2012. There was no noticeable geographical clustering within WPV1-positive sites. Uniform codon usage among isolates from Pakistan, Egypt and Israel showed no signs of optimisation or deoptimisation. Bayesian phylogenetic time clock analysis of the entire capsid coding region (2,643 nt) with a 1.1% evolutionary rate indicated that Israeli and Egyptian WPV1-SOAS lineages diverged in September 2012, while Israeli isolates split into two sub-branches after January 2013. This suggests one or more introduction events into Israel with subsequent silent circulation despite high population immunity.