ALBERT

Description: We estimate the contamination risks from the atmospheric dispersion of radionuclides released by severe nuclear power plant accidents using the ECHAM/Modular Earth Submodel System (MESSy) atmospheric chemistry (EMAC) atmospheric chemistry-general circulation model at high resolution (50 km). We present an overview of global risks and also a case study of nuclear power plants that are currently under construction, planned and proposed in the Eastern Mediterranean and Middle East, a region prone to earthquakes. We implemented continuous emissions from each location, making the simplifying assumption that all potential accidents release the same amount of radioactivity. We simulated atmospheric transport and decay, focusing on 137Cs and 131I as proxies for particulate and gaseous radionuclides, respectively. We present risk maps for potential surface layer concentrations, deposition and doses to humans from the inhalation exposure of 131I. The estimated risks exhibit seasonal variability, with the highest surface level concentrations of gaseous radionuclides in the Northern Hemisphere during winter.

Description: The long-lived pioneer species Pericopsis elata is one of the rare tropical timbers on the list of the Convention on International Trade of Endangered Species, supporting the need for accurate and reliable growth data. In one planted and one natural forest in the Democratic Republic of Congo, respectively four and 37 Pericopsis stem disks were collected. The tree-ring series of planted trees were used to confirm annual tree-ring formation. For the natural forest, a tree-ring chronology with 24 stem disks ranged from 1852 up to 2008. This chronology was compared with time-series of local precipitation, resulting in a significant correlation with the second half of the rainy season (September–November). This seasonal precipitation was related with sea surface temperatures of the West Indian Ocean. Higher precipitation during El Niño years corresponded with higher tree-ring indices but differences were not significant. In addition, pointer years were rare and did not have a consistent link with extreme climatic conditions. The existence of annual tree rings encourages further tree-ring analyses of P. elata and other flagship timber species in order to further document climate-growth responses and to provide the long-term framework that is needed for sustainable management planning.

Description: Background: Bacterial wilt caused by Ralstonia solanacearum is a serious soil-borne disease of peanut (Arachis hypogaea L). The molecular basis of peanut response to R. solanacearum remains unknown. To understand the resistance mechanism behind peanut resistance to R. solanacearum, we used RNA-Seq to perform global transcriptome profiling on the roots of peanut resistant (R) and susceptible (S) genotypes under R. solanacearum infection. Results: A total of 4.95 x 108 raw sequence reads were generated and subsequently assembled into 271, 790 unigenes with an average length of 890 bp and a N50 of 1, 665 bp. 179, 641 unigenes could be annotated by public protein databases. The pairwise transcriptome comparsions of time course (6, 12, 24, 48 and 72 h post inoculation) were conducted 1) between inoculated and control samples of each genotype, 2) between inoculated samples of R and S genotypes. The linear dynamics of transcriptome profile was observed between adjacent samples for each genotype, two genotypes shared similar transcriptome pattern at early time points with most significant up regulation at 12 hour, and samples from R genotype at 24 h and S genotype at 48 h showed similar transcriptome pattern, significant differences of transcriptional profile were observed in pairwise comparisons between R and S genotypes. KEGG analysis showed that the primary metabolisms were inhibited in both genotypes and stronger inhibition in R genotype post inoculation. The defense related genes (R gene, LRR-RLK,cell wall genes, etc.) generally showed a genotype-specific down regulation and different expression between both genotypes. Conclusion: This transcriptome profiling provided the largest data set that explores the dynamic in crosstalk between peanut and R. solanacearum. The results suggested that the down-regulation of primary metabolism is contributed to the resistance difference between R and S genotypes. The genotype-specific expression pattern of defense related DEGs also contributed to the resistance difference between R and S genotype. This study will strongly contribute to better understand the molecular interaction between plant and R. solanacearum.

Description: Our aim is to explore general practitioners’ (GPs’) knowledge about EMF, and to assess whether different knowledge structures are related to the GPs’ concern about EMF. Random samples were drawn from lists of GPs in Germany in 2008. Knowledge about EMF was assessed by seven items. A latent class analysis was conducted to identify latent structures in GPs’ knowledge. Further, the GPs’ concern about EMF health risk was measured using a score comprising six items. The association between GPs’ concern about EMF and their knowledge was analysed using multiple linear regression. In total 435 (response rate 23.3%) GPs participated in the study. Four groups were identified by the latent class analysis: 43.1% of the GPs gave mainly correct answers; 23.7% of the GPs answered low frequency EMF questions correctly; 19.2% answered only the questions relating EMF with health risks, and 14.0% answered mostly “don’t know”. There was no association between GPs’ latent knowledge classes or between the number of correct answers given by the GPs and their EMF concern, whereas the number of incorrect answers was associated with EMF concern. Greater EMF concern in subjects with more incorrect answers suggests paying particular attention to misconceptions regarding EMF in risk communication.

Description: This study aims to explore the efficiency of using online education as an intervention measure to prevent occupational hazards in a clinical nursing setting. The subjects were 320 female nursing staff from two hospitals in Taiwan. The questionnaire results indicated that the subjects primarily experienced human factor occupational hazards, as well as psychological and social hazards. Specifically, 73.1% and 69.8% of the subjects suffered from poor sleep quality and low back pain, respectively. After web-based learning, the experimental group had higher post-test scores than the control group in terms of knowledge, attitudes, and practices (KAP). However, there was only a significant difference (p 〈 0.05) in their knowledge about the prevention of occupational hazards. It is suggested that an online discussion may enhance nursing staff’s participation in web-based learning, and further facilitate their comments on negative factors. The findings can highly promote nursing staff’s attitudes and practices toward preventing occupational hazards through web-based learning.

Description: Ambient particulate matters and temperature were reported to have additive effects over the respiratory disease hospital admissions and deaths. The purpose of this study is to discuss the interactive pulmonary toxicities of cold stress and fine particulate matter (PM2.5) exposure by estimating inflammation and oxidative stress responses. 48 Wistar male rats, matched by weight and age, were randomly assigned to six groups, which were treated with cold stress alone (0 °C, 10 °C, and 20 °C (Normal control)) and cold stresses plus PM2.5 exposures respectively. Cold stress alone groups were intratracheal instillation of 0.25 mL normal saline, while cold stress plus PM2.5 exposure groups were intratracheal instillation of 8 mg/0.25 mL PM2.5. These procedures were carried out for three times with an interval of 48 hours for each treatment. All rats were sacrificed after 48 hours of the third treatment. The bronchoalveolar lavage fluid (BALF) was collected for analyzing inflammatory cells and cytokines, and lung homogenate MDA was determined for oxidative stress estimation. Results showed higher level of total cell and neutrophil in the BALF of PM2.5 exposed groups (p 〈 0.05). Negative relationships between cold stress intensity and the level of tumor necrosis factor alpha (TNF-a), C-reactive protein (CRP) interleukin-6 (IL-6) and interleukin-8 (IL-8) in BALF were indicated in PM2.5 exposure groups. Exposure to cold stress alone caused significant increase of inflammatory cytokines and methane dicarboxylic aldehyde (MDA) and decline of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activity only in 0 °C exposure group (p 〈 0.05). The two-way ANOVA found significant interactive effects between PM2.5 exposure and cold stress in the level of neutrophil, IL-6 and IL-8 and SOD activity (p 〈 0.05). These data demonstrated that inflammation and oxidative stress involved in the additive effect of PM2.5 exposure and cold stress on pulmonary toxicity, providing explanation for epidemiological studies on the health effect of ambient PM2.5 and cold stress.

Description: This paper presents a detailed description of an approach designed to investigate the application of the Health Impact Assessment (HIA) framework to assess the potential health impacts of climate change. A HIA framework has been combined with key climate change terminology and concepts. The fundamental premise of this framework is an understanding of the interactions between people, the environment and climate. The diversity and complexity of these interactions can hinder much needed action on the critical health issue of climate change. The objectives of the framework are to improve the methodology for understanding and assessing the risks associated with potential health impacts of climate change, and to provide decision-makers with information that can facilitate the development of effective adaptation plans. While the process presented here provides guidance with respect to this task it is not intended to be prescriptive. As such, aspects of the process can be amended to suit the scope and available resources of each project. A series of working tables has been developed to assist in the collation of evidence throughout the process. The framework has been tested in a number of locations including Western Australia, Solomon Islands, Vanuatu and Nauru.

Description: One of the most uncertain parameters in stepped spillway design is the length (from the crest) of boundary layer development. The normal velocity profiles responding to the steps as bed roughness are investigated in the developing non-aerated flow region. A detailed analysis of the logarithmic vertical velocity profiles on stepped spillways is conducted through experimental data to verify the computational code and numerical experiments to expand the data available. To determine development length, the hydraulic roughness and displacement thickness, along with the shear velocity, are needed. This includes determining displacement height d and surface roughness length z0 and the relationship of d and z0 to the step geometry. The results show that the hydraulic roughness height ks is the primary factor on which d and z0 depend. In different step height, step width, discharge and intake Froude number, the relations d/ks = 0.22–0.27, z0/ks = 0.06–0.1 and d/z0 = 2.2–4 result in a good estimate. Using the computational code and numerical experiments, air inception will occur over stepped spillway flow as long as the Bauer-defined boundary layer thickness is between 0.72 and 0.79.

Description: A regional-level and dimensionless analysis for designing a domestic rainwater harvesting system (DRWHS) was developed. To consider various combinations of water demand, storage capacity, effective roof area, and rainfall in DRWHS design, two dimensionless ratios were used, namely, demand fraction and storage fraction, along with a relationship between the two ratios. Firstly, Northern Taiwan was divided into four sub-regions through cluster analysis based on the average annual 10-day rainfall distribution at rainfall stations and administrative districts. Easy-to-use dimensionless curves between demand fraction and storage fraction were obtained for five rainwater supply reliabilities of the DRWHS for the four sub-regions. Based on the dimensionless curves, a nomogram was constructed for designing DRWHSs at a rainwater supply reliability of 95% in the sub-region I. Storage capacities determined from the dimensionless curves showed a close fit with those determined from simulated values, but were larger than the values estimated from the method presented in the Green Building Evaluation Manual in most situations. The methodology developed herein can be used effectively for the preliminary design of a DRWHS and for overcoming the difficulties faced in designing a DRWHS without rainfall data and with incomplete rainfall data.

Description: Background: Dyslipidemia is a key independent modifiable risk factor for Cardiovascular Disease, which is a leading contributor to morbidity and mortality in most developed and developing countries. This study was designed to investigate the current epidemiological features of dyslipidemia among adults in rural China. Methods: Between January 2013 and August 2013, we conducted a cross-sectional study involving 11,956 subjects with age 〉=35 years in a general Chinese population. Permanent residents of the population were invited to participate in the study and the response rate was at 85.3%. Dyslipidemia was identified based on serum lipids levels following the standards proposed by the National Cholesterol Education Program Adult Treatment Panel III. Multivariate logistic regression analysis was used to evaluate the associated risk factors for dyslipidemia. Results: Within the study population, 16.4% had high TC, 13.8% had low HDL-C, 7.6% had high LDL-C, and 17.3% had high TG concentrations. Prevalence of lipid abnormality (including borderline dyslipidemia and dyslipidemia) was 47.8%, 13.8%, 25.7% and 30.7% for TC, HDL-C, LDL-C and TG, respectively. Detailed analysis indicated that 36.9% of this population had at least one type of dyslipidemia and 64.4% had at least one type of abnormal lipid concentration. Thus, this study observed an alarmingly higher prevalence of lipid abnormality, in a relatively large population, compared to previous studies. Further, we determined that not all of the risk factors studied, including age, gender, hypertension, diabetes mellitus, obesity, smoking, drinking, education level, marital status, and family income, influenced dyslipidemia to the same extent. Conclusions: Our present study, in a population of 11,956 adults in Liaoning Providence, demonstrated a very high prevalence of dyslipidemia, which represented an alarming rise since the publication of our previous study and other similar studies around the world, which report lower levels. We also examined various risk factors for dyslipidemia, many of which are modifiable risk factors for Cardiovascular Disease (CVD), to provide a comprehensive view that will help in designing strategies to slow the rapid spread and promote effective measures to treat dyslipidemia. Our ultimate goal is to prevent the increasing prevalence of lipid abnormality and reduce the burden of CVD in rural China.

Description: Background: Proteins are composed of one or more amino acid chains and exhibit several structure levels. IDPs (intrinsically disordered proteins) represent a class of proteins that do not fold into any particular conformation and exist as dynamic ensembles in their native state. Due to their intrinsic adaptability, IDPs participate in many regulatory biological processes, including parasite immune escape. Using the information from trypanosomatids proteomes, we developed a pipeline for the identification, characterization and analysis of IDPs. The pipeline employs six disorder prediction methodologies and integrates structural and functional annotation information, subcellular location prediction and physicochemical properties. At the core of the IDP pipeline, there is a relational database that describes the protein disorder knowledge in a logically consistent manner. Results: The results obtained from the IDP pipeline showed that Leishmania and Trypanosoma species have approximately 70% and 55% IDPs, respectively. Our results indicate that IDPs in trypanosomatids contain disorder-promoting amino acids and order-promoting amino acids. The functional annotation analysis demonstrated enrichment of selected Gene Ontology terms. A relevant association was observed between the disordered residue numbers within predicted IDPs and their subcellular location, lack of transmembrane domains and lack of predicted function. We validated our computational findings with 2D electrophoresis designed for IDP identification and found that 100% of the identified protein spots were predicted in silico. Conclusions: Because there is no pipeline or database addressing IDPs in trypanosomatids, the pipeline described here represents the first attempt to establish possible correlations between protein function and structural disorder in these eukaryotes. Interestingly, all significant associations detected in the contingency analysis were observed when the protein disorder content reached approximately 40%. The exploratory data analysis allowed us to develop hypotheses regarding the IDPs' association with key biological features of these parasites, including transcription and transcriptional regulation, RNA processing and splicing, and cytoskeleton.

Description: Background: Songbirds (oscine Passeriformes) are among the most diverse and successful vertebrate groups, comprising almost half of all known bird species. Identifying the genomic innovations that might be associated with this success, as well as with characteristic songbird traits such as vocal learning and the brain circuits that underlie this behavior, has proven difficult, in part due to the small number of avian genomes available until recently. Here we performed a comparative analysis of 48 avian genomes to identify genomic features that are unique to songbirds, as well as an initial assessment of function by investigating their tissue distribution and predicted protein domain structure. Results: Using BLAT alignments and gene synteny analysis, we curated a large set of Ensembl gene models that were annotated as novel or duplicated in the most commonly studied songbird, the Zebra finch (Taeniopygia guttata), and then extended this analysis to 47 additional avian and 4 non-avian genomes. We identified 10 novel genes uniquely present in songbird genomes. A refined map of chromosomal synteny disruptions in the Zebra finch genome revealed that the majority of these novel genes localized to regions of genomic instability associated with apparent chromosomal breakpoints. Analyses of in situ hybridization and RNA-seq data revealed that a subset of songbird-unique genes is expressed in the brain and/or other tissues, and that 2 of these (YTHDC2L1 and TMRA) are highly differentially expressed in vocal learning-associated nuclei relative to the rest of the brain. Conclusions: Our study reveals novel genes unique to songbirds, including some that may subserve their unique vocal control system, substantially improves the quality of Zebra finch genome annotations, and contributes to a better understanding of how genomic features may have evolved in conjunction with the emergence of the songbird lineage.

Description: Background: Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. However, ontology development and usage can be hampered by the segregation of knowledge by domain that occurs due to independent development and use of the ontologies. The ability to infer data associated with one ontology to data associated with another ontology would prove useful in expanding information content and scope. We here focus on relating two ontologies: the Gene Ontology (GO), which encodes canonical gene function, and the Mammalian Phenotype Ontology (MP), which describes non-canonical phenotypes, using statistical methods to suggest GO functional annotations from existing MP phenotype annotations. This work is in contrast to previous studies that have focused on inferring gene function from phenotype primarily through lexical or semantic similarity measures. Results: We have designed and tested a set of algorithms that represents a novel methodology to define rules for predicting gene function by examining the emergent structure and relationships between the gene functions and phenotypes rather than inspecting the terms semantically. The algorithms inspect relationships among multiple phenotype terms to deduce if there are cases where they all arise from a single gene function.We apply this methodology to data about genes in the laboratory mouse that are formally represented in the Mouse Genome Informatics (MGI) resource. From the data, 7444 rule instances were generated from five generalized rules, resulting in 4818 unique GO functional predictions for 1796 genes. Conclusions: We show that our method is capable of inferring high-quality functional annotations from curated phenotype data. As well as creating inferred annotations, our method has the potential to allow for the elucidation of unforeseen, biologically significant associations between gene function and phenotypes that would be overlooked by a semantics-based approach. Future work will include the implementation of the described algorithms for a variety of other model organism databases, taking full advantage of the abundance of available high quality curated data.

Description: Background: The transcription factor Nrf2, encoded by the NFE2L2 gene, is an important regulator of the cellular protection against oxidative stress. Parkinson?s disease is a neurodegenerative disease highly associated with oxidative stress. In a previously published study, we reported associations of NFE2L2 haplotypes with risk and age at onset of idiopathic Parkinson?s disease in a Swedish discovery material and a Polish replication material. Here, we have extended the replication study and performed meta-analyses including the Polish material and four new independent European patient-control materials. Furthermore, all SNPs included in the haplotype windows were investigated individually for associations with Parkinson?s disease in meta-analyses including all six materials. Methods: Totally 1038 patients and 1600 control subjects were studied. Based on previous NFE2L2 haplotype associations with Parkinson?s disease, five NFE2L2 tag SNPs were genotyped by allelic discrimination and three functional NFE2L2 promoter SNPs were genotyped by sequencing. The impact of individual SNPs and haplotypes on risk and age at onset of Parkinson?s disease were investigated in each material individually and in meta-analyses of the obtained results. Results: Meta-analyses of NFE2L2 haplotypes showed association of haplotype GAGCAAAA, including the fully functional promoter haplotype AGC, with decreased risk (OR?=?0.8 per allele, p?=?0.012) and delayed onset (+1.1?years per allele, p?=?0.048) of Parkinson?s disease. These results support the previously observed protective effect of this haplotype in the first study. Further, meta-analyses of the SNPs included in the haplotypes revealed four NFE2L2 SNPs associated with age at onset of Parkinson?s disease (rs7557529 G?〉?A, ?1.0?years per allele, p?=?0.042; rs35652124 A?〉?G, ?1.1?years per allele, p?=?0.045; rs2886161 A?〉?G, ?1.2?years per allele, p?=?0.021; rs1806649 G?〉?A, +1.2?years per allele, p?=?0.029). One of these (rs35652124) is a functional SNP located in the NFE2L2 promoter. No individual SNP was associated with risk of Parkinson?s disease. Conclusion: Our results support the hypothesis that variation in the NFE2L2 gene, encoding a central protein in the cellular protection against oxidative stress, may contribute to the pathogenesis of Parkinson?s disease. Functional studies are now needed to explore these results further.

Description: Background: Most PCR-based diagnostics are still considered time- and labor-intensive due to disparate purification, amplification, and detection steps. Advancements in PCR enzymes and buffer chemistry have increased inhibitor tolerance, facilitating PCR directly from crude samples. Obviating the need for DNA purification, while lacking a concentration step, these direct sample methods are particularly apt for human genetic testing. However, direct PCR protocols have traditionally employed thermal cyclers with slow ramp rates and conservative hold times that significantly increase an assay?s time-to-result. For this proof-of-principle study, our objective was to significantly reduce sample preparation and assay time for a PCR-based genetic test, for myotonic dystrophy type 1 (DM1), by pairing an inhibitor-resistant enzyme mix with a rapid thermal cycler to analyze samples directly in whole blood. Methods: DM1 genetic screening was done with an adapted conventional PCR approach that employed the Streck Philisa? Thermal Cycler, the inhibitor-resistant NEBNext? High-Fidelity 2X PCR Master Mix, and agarose gel electrophoresis or an Agilent 2100 Bioanalyzer for detection. The Gene Link? Myotonic Dystrophy Genemer? Kit was used as a reference assay kit to evaluate the rapid assay. Results: In this work, a rapid and direct PCR assay testing 10% whole blood as template has been developed as an exclusionary screening assay for DM1, a triple-repeat genetic disorder. PCR amplification was completed in 15 minutes using 30 cycles, including in situ hot-start/cell lysis. Out of the 40 donors screened, this assay identified 23 (57.5%) as DM1 negative suggesting no need for further testing. These data are 100% concordant with data collected using the commercially available Gene Link Genemer? Kit per the kit-specific PCR protocol. Conclusions: The PCR assay described in this study amplified DM1 short tandem repeats in 15 minutes. By eliminating sample purification and slower conventional PCR protocols, we demonstrated how adaptation of current PCR technology and chemistries can produce a simple-to-use exclusionary screening assay that is independent of up-front sample prep, improving a clinical lab technician?s time-to-result. We envision this direct and rapid methodology could be applied to other conventional PCR-based genetic tests and sample matrices where genomic DNA is targeted for analysis within a given molecular diagnostic platform.

Description: Background: Marburg viruses have been responsible for a number of outbreaks throughout sub-Saharan Africa, as well as a number of laboratory infections. Despite many years of experience with the viruses, little is known about several important epidemiologic parameters relating to the development of Marburg virus disease. The analysis uses pooled data from all Marburg cases between 1967 and 2008 to develop estimates for the incubation period and the clinical onset serial interval (COSI). Methods: Data were obtained from original outbreak investigation forms (n = 406) and from published data (n = 45). Incubation periods were calculated for person-to-person exposure, for laboratory-acquired infections, and for presumed zoonotic exposures. Similar analysis was conducted for COSI, using only cases with unambiguous person-to-person transmission where both the primary and the secondary case patients had well-defined illness onsets. Results: Seventy-six cases were retained for the incubation period analysis. Incubation periods ranged from a minimum of 2 days in the case of two laboratory workers to a maximum of at least 26 days for a person-to-person household transmission. Thirty-eight cases were retained for COSI analysis. The median COSI was 11 days, with an interquartile range of 8 to 15. Conclusions: This study extends the maximum known incubation period of Marburg virus disease to 26 days. The analysis was severely hampered by a lack of completeness in epidemiologic data. It is necessary to prioritize obtaining more accurate epidemiologic data in future outbreaks; greater use of COSI may facilitate an improved understanding of outbreak dynamics in Marburg and other diseases.

Description: Three ideal point-based multi-criteria decision methods (MCDM), i.e., iterative ideal point thresholding (IIPT), compromise programming (CP) and a newly-proposed CP variant, called balanced compromise programming (BCP), were applied to the Tabacay catchment in Ecuador with the aim of finding a distribution of land use types (LUT) that optimizes regional land performance. This performance was expressed in terms of several conflicting on-site ecosystem services (ESS), namely water conservation, soil protection, carbon storage and monetary income. IIPT selects the best performing LUT on a per-land unit basis, that is the assignment of a LUT to a land unit is completely independent with respect to other land units. CP and BCP, on the other hand, aim at optimizing the integrated regional performance. These methods produce a LUT distribution that is as close as possible to the absolute optimal performance that would be achieved when conflict among ESS is not considered. In general, similar results were obtained with CP and BCP. This was not the case when the results produced by these two methods were contrasted with IIPT. For most ESS under consideration, CP and BCP produced balanced results that were closer to the absolute optimal values when compared to IIPT. We conclude from our results that, when optimization of land performance at a regional scale is at stake, CP-derived models emerge as the preferable option over IIPT, especially when balanced solutions are a requirement.

Description: Current understanding of aspen fire ecology in western North America includes the paradoxical characterization that aspen-dominated stands, although often regenerated following fire, are “fire-proof”. We tested this idea by predicting potential fire behavior across a gradient of aspen dominance in northern Utah using the Forest Vegetation Simulator and the Fire and Fuels Extension. The wind speeds necessary for crowning (crown-to-crown fire spread) and torching (surface to crown fire spread) were evaluated to test the hypothesis that predicted fire behavior is influenced by the proportion of aspen in the stand. Results showed a strong effect of species composition on crowning, but only under moderate fire weather, where aspen-dominated stands were unlikely to crown or torch. Although rarely observed in actual fires, conifer-dominated stands were likely to crown but not to torch, an example of “hysteresis” in crown fire behavior. Results support the hypothesis that potential crown fire behavior varies across a gradient of aspen dominance and fire weather, where it was likely under extreme and severe fire weather, and unlikely under moderate and high fire weather. Furthermore, the “fire-proof” nature of aspen stands broke down across the gradient of aspen dominance and fire weather.

Description: Background: Collaborative tools are of great help in conducting projects involving distant workers. Recent web technologies have helped to build such tools for jointly editing office documents and scientific data, yet none are available for handling phylogenies. Though a large number of studies and projects in evolutionary biology and systematics involve collaborations between scientists of different institutes, current tree comparison visualization software and websites are directed toward single-user access. Moreover, tree comparison functionalities are dispersed between different software that mainly focus on high level single tree visualization but to the detriment of basic tree comparison features. Results: The web platform presented here, named CompPhy, intends to fill this gap by allowing collaborative work on phylogenies and by gathering simple advanced tools dedicated to tree comparison. It offers functionalities for tree edition, tree comparison, supertree inference and data management in a collaborative environment. The latter aspect is a specific feature of the platform, allowing people located in different places to work together at the same time on a common project. CompPhy thus proposes shared tree visualization, both synchronous and asynchronous tree manipulation, data exchange/storage, as well as facilities to keep track of the progress of analyses in working sessions. Specific advanced comparison tools are also available, such as consensus and supertree inference, or automated branch swaps of compared trees. As projects can be readily created and shared, CompPhy is also a tool that can be used easily to interact with students in a educational setting, either in the classroom or for assignments. Conclusions: CompPhy is the first web platform devoted to the comparison of phylogenetic trees allowing real-time distant collaboration on a phylogenetic/phylogenomic project. This application can be accessed freely with a recent browser at the following page of the ATGC bioinformatics platform: http://www.atgc-montpellier.fr/compphy/.

Description: Background: Paracoccidioides spp is a fungi genus and the agent of paracoccidioidomycosis. The strategies of infection used by these pathogens involve the expression of proteins related to adaptation to the host, particularly regarding the uptake of micronutrients. This study analyzed the adhesion of Paracoccidioides lutzii during conditions of copper (Cu) and iron (Fe) deprivation, while also evaluating the proteins expressed in conditions of Cu depletion in the presence of four extracellular matrix (ECM) components (laminin, fibronectin and types I and IV collagen). Results: We cultured the P. lutzii in a chemically defined media without Cu and Fe. The fungus was then placed in contact with different ECM components and adhesion was evaluated. A significant increase in binding to all ECM components was observed when the fungus was cultured without Cu; which might be related to some adhesins expression. A proteomic assay was developed and revealed 39 proteins expressed that are involved in processes such as virulence, protein synthesis, metabolism, energy, transcription, transport, stress response and the cell cycle when the fungus was interacting with the ECM components. The up-regulated expression of two important adhesins, enolase and 14-3-3, was observed at the fungal cell wall during the interaction with the ECM components, indicating the role of these proteins in the Paracoccidioides?host interaction. Conclusions: This study is important for determining prospective proteins that may be involved in the interaction of Paracoccidioides with a host. Understanding the adaptive response to different growth conditions, elucidating the processes of adhesion and cell invasion, and identifying the proteins that are differentially expressed during the fungus-host interaction may help elucidate mechanisms used for survival and growth of Paracoccidioides in various human tissues.

Description: Background: Integrated Ocean Drilling Program Expedition 338 was the second scientific expedition with D/V Chikyu during which riser drilling was conducted as part of the Nankai Trough Seismogenic Zone Experiment. Riser drilling enabled sampling and real-time monitoring of drilling mud gas with an onboard scientific drilling mud gas monitoring system (?SciGas?). A second, independent system was provided by Geoservices, a commercial mud logging service. Both systems allowed the determination of (non-) hydrocarbon gas, while the SciGas system also monitored the methane carbon isotope ratio (?13CCH4). The hydrocarbon gas composition was predominated by methane (〉 1 %), while ethane and propane were up to two orders of magnitude lower. ?13CCH4 values suggested an onset of thermogenic gas not earlier than 1600 meter below seafloor. This study aims on evaluating the onboard data and subsequent geological interpretations by conducting shorebased analyses of drilling mud gas samples. Results: During shipboard monitoring of drilling mud gas the SciGas and Geoservices systems recorded up to 8.64% and 16.4% methane, respectively. Ethane and propane concentrations reached up to 0.03 and 0.013%, respectively, in the SciGas system, but 0.09% and 0.23% in the Geoservices data. Shorebased analyses of discrete samples by gas chromatography showed a gas composition with ~0.01 to 1.04% methane, 2 ? 18 ppmv ethane, and 2 ? 4 ppmv propane. Quadruple mass spectrometry yielded similar results for methane (0.04 to 4.98%). With ?D values between -171? and -164?, the stable hydrogen isotopic composition of methane showed little downhole variability. Conclusions: Although the two independent mud gas monitoring systems and shorebased analysis of discrete gas sample yielded different absolute concentrations they all agree well with respect to downhole variations of hydrocarbon gases. The data point to predominantly biogenic methane sources but suggest some contribution from thermogenic sources at depth, probably due to mixing. In situ thermogenic gas production at depths shallower 2000 mbsf is unlikely based on in situ temperature estimations between 81?C and 85?C and a cumulative time-temperature index of 0.23. In conclusion, the onboard SciGas data acquisition helps to provide a preliminary, qualitative evaluation of the gas composition, the in situ temperature and the possibility of gas migration.

Description: In this study we evaluate the capabilities of three satellite sensors for assessing water composition and bottom depth in Lake Garda, Italy. A consistent physics-based processing chain was applied to Moderate Resolution Imaging Spectroradiometer (MODIS), Landsat-8 Operational Land Imager (OLI) and RapidEye. Images gathered on 10 June 2014 were corrected for the atmospheric effects with the 6SV code. The computed remote sensing reflectance (Rrs) from MODIS and OLI were converted into water quality parameters by adopting a spectral inversion procedure based on a bio-optical model calibrated with optical properties of the lake. The same spectral inversion procedure was applied to RapidEye and to OLI data to map bottom depth. In situ measurements of Rrs and of concentrations of water quality parameters collected in five locations were used to evaluate the models. The bottom depth maps from OLI and RapidEye showed similar gradients up to 7 m (r = 0.72). The results indicate that: (1) the spatial and radiometric resolutions of OLI enabled mapping water constituents and bottom properties; (2) MODIS was appropriate for assessing water quality in the pelagic areas at a coarser spatial resolution; and (3) RapidEye had the capability to retrieve bottom depth at high spatial resolution. Future work should evaluate the performance of the three sensors in different bio-optical conditions.

Description: From a holistic view, this paper addresses a perspective of coordinated development of economy, society, and environment for regional sustainability assessment. Firstly, a comprehensive indicator system for co-evaluating the level of economic, social, and environmental subsystems is presented based on a holistic understanding of regional sustainability. Then, a coordinated development index model focusing on the level of coordination among the subsystems as well as their comprehensive development level is established. Furthermore, an empirical study of all the provinces and municipalities is conducted by collecting the panel data from 2004 to 2010. The result shows that: (1) the coordinated developments of the most developed and the most underdeveloped regions stay stable while the regions with medium development level possess more fluctuant trends during the study years; (2) regional disparities are indicated according to the grading of CDI (the coordinated development index), which are further analyzed to be related to the local economic development patterns; (3) the conditions and causes of economic, social, and environmental development in real situations under different grades of CDI are discussed through detailed case studies of typical regions, which indicate specific suggestions of sustainable development for regions in the same pattern.

Description: As the largest solid waste (SW) generator in the world, China is facing serious pollution issues induced by increasing quantities of SW. The sustainability assessment of SW management is very important for designing relevant policy for further improving the overall efficiency of solid waste management (SWM). By focusing on industrial solid waste (ISW) and municipal solid waste (MSW), the paper investigated the sustainability performance of SWM by applying decoupling analysis, and further identified the main drivers of SW change in China by adopting Logarithmic Mean Divisia Index (LMDI) model. The results indicate that China has made a great achievement in SWM which was specifically expressed as the increase of ISW utilized amount and harmless disposal ratio of MSW, decrease of industrial solid waste discharged (ISWD), and absolute decoupling of ISWD from economic growth as well. However, China has a long way to go to achieve the goal of sustainable management of SW. The weak decoupling, even expansive negative decoupling of ISW generation and MSW disposal suggests that China needs timely technology innovation and rational institutional arrangement to reduce SW intensity from the source and promote classification and recycling. The factors of investment efficiency and technology are the main determinants of the decrease in SW, inversely, economic growth has increased SW discharge. The effects of investment intensity showed a volatile trend over time but eventually decreased SW discharged. Moreover, the factors of population and industrial structure slightly increased SW.

Description: This paper aims to construct conservation laws for a Benjamin–Bona–Mahony equation with variable coefficients, which is a third-order partial differential equation. This equation does not have a Lagrangian and so we transform it to a fourth-order partial differential equation, which has a Lagrangian. The Noether approach is then employed to construct the conservation laws. It so happens that the derived conserved quantities fail to satisfy the divergence criterion and so one needs to make adjustments to the derived conserved quantities in order to satisfy the divergence condition. The conservation laws are then expressed in the original variable. Finally, a conservation law is used to obtain exact solution of a special case of the Benjamin–Bona–Mahony equation.

Description: The sensorimotor system (SMS) plays an important role in sports and in every day movement. Several tools for assessment and training have been designed. Many of them are directed to specific populations, and have major shortcomings due to the training effect or safety. The aim of the present study was to design and assess a dynamic sensorimotor test and training device that can be adjusted for all levels of performance. The novel pneumatic-driven mechatronic device can guide the trainee, allow independent movements or disrupt the individual with unpredicted perturbations while standing on a platform. The test-reliability was evaluated using intraclass correlation coefficient (ICC). Subjects were required to balance their center of pressure (COP) in a target circle (TITC). The time in TITC and the COP error (COPe) were recorded for analysis. The results of 22 males and 14 females (23.7 ± 2.6 years) showed good to excellent test–retest reliability. The newly designed Active Balance System (ABS) was then compared with the Biodex Balance System SD® (BBS). The results of 15 females, 14 males (23.4 ± 1.6 years) showed modest correlation in static and acceptable correlation in dynamic conditions, suggesting that ABS could be a reliable and comparable tool for dynamic balance assessments.

Description: Climate change will increase the frequency and magnitude of extreme weather events and create risks that will impact health care facilities. Health care facilities will need to assess climate change risks and adopt adaptive management strategies to be resilient, but guidance tools are lacking. In this study, a toolkit was developed for health care facility officials to assess the resiliency of their facility to climate change impacts. A mixed methods approach was used to develop climate change resiliency indicators to inform the development of the toolkit. The toolkit consists of a checklist for officials who work in areas of emergency management, facilities management and health care services and supply chain management, a facilitator’s guide for administering the checklist, and a resource guidebook to inform adaptation. Six health care facilities representing three provinces in Canada piloted the checklist. Senior level officials with expertise in the aforementioned areas were invited to review the checklist, provide feedback during qualitative interviews and review the final toolkit at a stakeholder workshop. The toolkit helps health care facility officials identify gaps in climate change preparedness, direct allocation of adaptation resources and inform strategic planning to increase resiliency to climate change.

Description: The World Health Organization defines social determinants of health as “complex, integrated, and overlapping social structures and economic systems” that are responsible for most health inequities. Similar to the individual-level risk factors such as behavioral and biological risk factors that influence disease, we consider social determinants of health such as the distribution of income, wealth, influence and power as risk factors for risk of disease. We operationally define health inequity in a disease within a population due to a risk factor that is unfair and avoidable as the difference between the disease outcome with and without the risk factor in the population. We derive expressions for difference in health inequity between two populations due to a risk factor that is unfair and avoidable for a given disease. The difference in heath inequity between two population groups due to a risk factor increases with increasing difference in relative risks and the difference in prevalence of the risk factor in the two populations. The difference in health inequity could be larger than the difference in health outcomes between the two populations in some situations. Compared to health disparities which are typically measured and monitored using absolute or relative disparities of health outcomes, the methods presented in this manuscript provide a different, yet complementary, picture because they parse out the contributions of unfair and avoidable risk factors.

Description: Background: Recent studies have demonstrated a relationship between fructose consumption and risk of developing metabolic syndrome. Mechanisms by which dietary fructose mediates metabolic changes are poorly understood. This study compared the effects of fructose, glucose and sucrose consumption on post-postprandial lipemia and low grade inflammation measured as hs-CRP. Methods: This was a randomized, single blinded, cross-over trial involving healthy subjects (n = 14). After an overnight fast, participants were given one of 3 different isocaloric drinks, containing 50 g of either fructose or glucose or sucrose dissolved in water. Blood samples were collected at baseline, 30, 60 and 120 minutes post intervention for the analysis of blood lipids, glucose, insulin and high sensitivity C-reactive protein (hs-CRP). Results: Glucose and sucrose supplementation initially resulted in a significant increase in glucose and insulin levels compared to fructose supplementation and returned to near baseline values within 2 hours. Change in plasma cholesterol, LDL and HDL-cholesterol (measured as area under curve, AUC) was significantly higher when participants consumed fructose compared with glucose or sucrose (P 〈 0.05). AUC for plasma triglyceride levels however remained unchanged regardless of the dietary intervention. Change in AUC for hs-CRP was also significantly higher in subjects consuming fructose compared with those consuming glucose (P 〈 0.05), but not sucrose (P = 0.07). Conclusion: This study demonstrates that fructose as a sole source of energy modulates plasma lipids and hsCRP levels in healthy individuals. The significance of increase in HDL-cholesterol with a concurrent increase in LDL-cholesterol and elevated hs-CRP levels remains to be delineated when considering health effects of feeding fructose-rich diets.Registration number for clinical trials: ACTRN12614000431628

Description: Background: Comparable to commercial expensive high-fat diets, cholesterol-cholate-butterfat (CCB) diet has also been used to induce hyperlipidemia in rats. Our objective was to explore its influence on multiple organs. Consequence of fasting was also analysed. Methods: Rats in groups 1 and 2 received normal diet (ND) whereas groups 3 and 4 received CCB-diet. Food was withdrawn daily for two hours from groups 2 (ND-F) and 4 (CCB-F). Blood was collected at fourth and sixth week for biochemical estimation; Morris water maze was done in the sixth week for learning ability and memory; after which aortae were isolated for vascular reactivity. Results: Apart from hyperlipidemia, CCB also induced hyperglycemia with marked increase in hepatic enzymes: gamma-glutamyl transferase (GGT), alanine and aspartate aminotransferase (ALT and AST); and vascular biomarkers: uric acid (UA), phosphorus and alkaline phosphatase (ALP). Isolated aortae, pre-contracted with phenylephrine, were less responsive to acetylcholine indicating endothelial dysfunction - serum nitric oxide (NO) production was limited with subsequent inhibition of endothelial NO synthase. CCB diet also compromised learning ability. CCB-coupled fasting potentiated hyperlipidemia but prevented memory-loss. Conclusion: We introduce CCB-diet for multi-organ dysfunction in rats, and propose its use for research on cardiovascular diseases and associated manifestations involving immense interplay of integrated pathways.

Description: In this research, structural-functional integrated cement-based materials were prepared by employing cement paste and a microencapsulated phase change material (MPCM) manufactured using urea-formaldehyde resin as the shell and paraffin as the core material. The encapsulation ratio of the MPCM could reach up to 91.21 wt%. Thermal energy storage cement pastes (TESCPs) incorporated with different MPCM contents (5%, 10%, 15%, 20% and 25% by weight of cement) were developed, and their thermal and mechanical properties were studied. The results showed that the total energy storage capacity of the hardened cement specimens with MPCM increased by up to 3.9-times compared with that of the control cement paste. The thermal conductivity at different temperature levels (35–36 °C, 55–56 °C and 72–74 °C) decreased with the increase of MPCM content, and the decrease was the highest when the temperature level was 55–56 °C. Moreover, the compressive strength, flexural strength and density of hardened cement paste decreased with the increase in MPCM content linearly. Among the evaluated properties, the compressive strength of TESCPs had a larger and faster degradation with the increase of MPCM content.

Description: Background: Asthma is an inflammatory disease of the airways, but in clinical practice inflammation is rarely monitored. The aim of this study was to assess the level of airway inflammation in steroid naive adult and pediatric patients with intermittent asthma over one year. Methods: 54 children and 50 adults with intermittent asthma (GINA step 1) were included. On up to 6 visits lung function, airway hyperresponsiveness to methacholine (PC20FEV1), sputum eosinophils and exhaled nitric oxide (FeNO) were assessed. Results: 36 pediatric and 34 adult patients were able to produce at least three adequate sputum samples over the study period and were included into the analysis.In 8 children (22%) the percentage of sputum eosinophils was always below 2.5%. A higher level of eosinophils (〉2.5%) was found on at least one visit in 16 (44%) and always 〉2.5% in 12 children (33%). In the adult group the respective numbers were 14 patients (41%) with always low (

Description: Background: Tests for the evolutionary conservation of associations between genes coding for transcription factors (TFs) and other genes have been limited to a few model organisms due to the lack of experimental information of functional associations in other organisms. We aimed at surmounting this limitation by using the most co-occurring gene pairs as proxies for the most conserved functional interactions available for each gene in a genome. We then used genes predicted to code for TFs to compare their most conserved interactions against the most conserved interactions for the rest of the genes within each prokaryotic genome available. Results: We plotted profiles of phylogenetic profiles, p-cubic, to compare the maximally scoring interactions of TFs against those of other genes. In most prokaryotes, genes coding for TFs showed lower co-occurrences when compared to other genes suggesting that transcriptional regulation evolves quickly in most, if not all prokaryotes. We also show that genes coding for TFs tend to have lower Codon Adaptation Indexes compared to other genes further suggesting quick gene exchange and rewiring of transcriptional regulation across prokaryotes.Keywordstranscription factors; interactome; evolvability; comparative genomics; phylogenetic profiles; regulatory interactions

Description: Land surface temperature (LST) retrieval is a key issue in infrared quantitative remote sensing. In this paper, a split window algorithm is proposed to estimate LST with daytime data in two mid-infrared channels (channel 66 (3.746~4.084 μm) and channel 68 (4.418~4.785 μm)) from Airborne Hyperspectral Scanner (AHS). The estimation is conducted after eliminating reflected direct solar radiance with the aid of water vapor content (WVC), the view zenith angle (VZA), and the solar zenith angle (SZA). The results demonstrate that the LST can be well estimated with a root mean square error (RMSE) less than 1.0 K. Furthermore, an error analysis for the proposed method is also performed in terms of the uncertainty of LSE and WVC, as well as the Noise Equivalent Difference Temperature (NEΔT). The results show that the LST errors caused by a LSE uncertainty of 0.01, a NEΔT of 0.33 K, and a WVC uncertainty of 10% are 0.4~2.8 K, 0.6 K, and 0.2 K, respectively. Finally, the proposed method is applied to the AHS data of 4 July 2008. The results show that the differences between the estimated and the ground measured LST for water, bare soil and vegetation areas are approximately 0.7 K, 0.9 K and 2.3K, respectively.

Description: Enhanced geothermal systems (EGS) extract heat from underground hot dry rock (HDR) by first fracturing the HDR and then circulating a geofluid (typically water) into it and bringing the heated geofluid to a power plant to generate electricity. This study focuses on analysis, examination, and comparison of leading geothermal power plant configurations with a geofluid temperature from 200 to 800 °C, and also analyzes the embodied energy of EGS surface power plants. The power generation analysis is focused on flash type cycles for using subcritical geofluid (〈374 °C) and expansion type cycles for using supercritical geofluid (>374 °C). Key findings of this study include: (i) double-flash plants have 24.3%–29.0% higher geofluid effectiveness than single-flash ones, and 3%–10% lower specific embodied energy; (ii) the expansion type plants have geofluid effectiveness > 750 kJ/kg, significantly higher than flash type plants (geofluid effectiveness 〈 300 kJ/kg) and the specific embodied energy is lower; (iii) to increase the turbine outlet vapor fraction from 0.75 to 0.90, we include superheating by geofluid but that reduces the geofluid effectiveness by 28.3%; (iv) for geofluid temperatures above 650 °C, double-expansion plants have a 2% higher geofluid effectiveness and 5%–8% lower specific embodied energy than single-expansion ones.

Description: A new method of depositing tin dioxide nanofibers in order to develop chemical sensors is presented. It involves an electrospinning process with in-plane electrostatic focusing over micromechanized substrates. It is a fast and reproducible method. After an annealing process, which can be performed by the substrate heaters, it is observed that the fibers are intertwined forming porous networks that are randomly distributed on the substrate. The fiber diameters oscillate from 100 nm to 200 nm and fiber lengths reach several tens of microns. Each fiber has a polycrystalline structure with multiple nano-grains. The sensors have been tested for the detection of acetone and hydrogen peroxide (precursors of the explosive triacetone triperoxide, TATP) in air in the ppm range. High and fast responses to these gases have been obtained.

Description: IntroductionExposure to elevated seawater PCO2 limits the thermal tolerance of crustaceans but the underlying mechanisms have not been comprehensively explored. Larval stages of crustaceans are even more sensitive to environmental hypercapnia and possess narrower thermal windows than adults. Results: In a mechanistic approach, we analysed the impact of high seawater CO2 on parameters at different levels of biological organization, from the molecular to the whole animal level. At the whole animal level we measured oxygen consumption, heart rate and activity during acute warming in zoea and megalopa larvae of the spider crab Hyas araneus exposed to different levels of seawater PCO2. Furthermore, the expression of genes responsible for acid?base regulation and mitochondrial energy metabolism, and cellular responses to thermal stress (e.g. the heat shock response) was analysed before and after larvae were heat shocked by rapidly raising the seawater temperature from 10?C rearing temperature to 20?C. Zoea larvae showed a high heat tolerance, which decreased at elevated seawater PCO2, while the already low heat tolerance of megalopa larvae was not limited further by hypercapnic exposure. There was a combined effect of elevated seawater CO2 and heat shock in zoea larvae causing elevated transcript levels of heat shock proteins. In all three larval stages, hypercapnic exposure elicited an up-regulation of genes involved in oxidative phosphorylation, which was, however, not accompanied by increased energetic demands. Conclusion: The combined effect of seawater CO2 and heat shock on the gene expression of heat shock proteins reflects the downward shift in thermal limits seen on the whole animal level and indicates an associated capacity to elicit passive thermal tolerance. The up-regulation of genes involved in oxidative phosphorylation might compensate for enzyme activities being lowered through bicarbonate inhibition and maintain larval standard metabolic rates at high seawater CO2 levels. The present study underlines the necessity to align transcriptomic data with physiological responses when addressing mechanisms affected by an interaction of elevated seawater PCO2 and temperature extremes.

Description: The effects of aflatoxin B1 (AFB1) exposure and sodium selenite supplementation on cell apoptosis of jejunum in broilers were studied. A total of 240 one-day-old male AA broilers were randomly assigned four dietary treatments containing 0 mg/kg of AFB1 (control), 0.3 mg/kg AFB1 (AFB1), 0.4 mg/kg supplement Se (+ Se) and 0.3 mg/kg AFB1 + 0.4 mg/kg supplement Se (AFB1 + Se), respectively. Compared with the control broilers, the number of apoptotic cells, the expression of Bax and Caspase-3 mRNA were significantly increased, while the expression of Bcl-2 mRNA and the Bcl-2/Bax ratio were significantly decreased in AFB1 broilers. The number of apoptotic cells and the expression of Caspase-3 mRNA in AFB1 + Se broilers were significantly higher than those in the control broilers, but significantly lower than those in AFB1 broilers. There were no significant changes in the expression of Bax mRNA between AFB1 + Se and control broilers; the expression of Bcl-2 mRNA and the Bcl-2/Bax ratio in AFB1 + Se broilers were significantly lower than those in the control broilers, but significantly higher than those in AFB1 broilers. In conclusion, 0.3 mg/kg AFB1 in the diet can increase cell apoptosis, decrease Bcl-2 mRNA expression, and increase of Bax and Caspase-3 mRNA expression in broiler’s jejunum. However, supplementation of dietary sodium selenite at the concentration of 0.4 mg/kg Se may ameliorate AFB1-induced apoptosis by increasing Bcl-2 mRNA expression, and decreasing Bax and Caspase-3 mRNA expression.

Description: In this study, an electroactive polymer (EAP), poly(2,5-bis(N-methyl-N-hexylamino)phenylene vinylene) (BAM-PPV) was investigated as a potential alternative surface pretreatment for hexavalent chromium (Cr(VI))-based aerospace coatings. BAM-PPV was tested as a pretreatment coating on an aerospace aluminum alloy (AA2024-T3) substrate in combination with a non-Cr(VI) epoxy primer and a polyurethane Advanced Performance Coating (APC) topcoat. This testing was undertaken to determine BAM-PPV’s adhesion, corrosion-inhibition, compatibility and survivability in laboratory testing and during outdoor field-testing. BAM-PPV showed excellent adhesion and acceptable corrosion performance in laboratory testing. The BAM-PPV aerospace coating system (BAM-PPV, non-Cr(VI) epoxy primer and polyurethane APC topcoat) was field tested for one year on the rear hatch door of the United States Air Force C-5 cargo plane. After one year of field testing there was no evidence of delamination or corrosion of the BAM-PPV aerospace coating system.

Description: The effect of chemical treatment of hemp hurds slices in three solutions (EDTA (Ethylenediaminetetraacetic acid), NaOH and Ca(OH)2) on the properties of natural material was discussed in this paper. Changes in the morphology, chemical composition and structure as well as thermal stability of hemp hurds before and after their modification were investigated by using FTIR (Fourier transform infrared spectroscopy), XRD (X-ray powder diffraction analysis) and TG (thermogravimetry)/DSC (differential scanning calorimetry). Size exclusion chromatography (SEC) measurements were used for determination of degree of cellulose polymerization of hemp hurd samples. Chemical modification is related to the partial removal of non-cellulosic components of lignin, hemicellulose and pectin as well as waxes from the surface of hemp hurd slices. Another effect of the chemical treatment applied is connected with increasing the crystallinity index of cellulose determined by FTIR and XRD methods. Decrease in degree of cellulose polymerization and polydispersity index in chemically modified hemp hurds compared to the original sample was observed. Increase in thermal stability of treated hemp hurd was found. The most significant changes were observed in alkaline treated hemp hurds by NaOH.

Description: Light Detection and Ranging (LiDAR) is an active sensor that can effectively acquire a large number of three-dimensional (3-D) points. LiDAR systems can be equipped on different platforms for different applications, but to integrate the data, point cloud registration is needed to improve geometric consistency. The registration of airborne and terrestrial mobile LiDAR is a challenging task because the point densities and scanning directions differ. We proposed a scheme for the registration of airborne and terrestrial mobile LiDAR using the least squares 3-D surface registration technique to minimize the surfaces between two datasets. To analyze the effect of point density in registration, the simulation data simulated different conditions and estimated the theoretical errors. The test data were the point clouds of the airborne LiDAR system (ALS) and the mobile LiDAR system (MLS), which were acquired by Optech ALTM 3070 and Lynx, respectively. The resulting simulation analysis indicated that the accuracy of registration improved as the density increased. For the test dataset, the registration error of mobile LiDAR between different trajectories improved from 40 cm to 4 cm, and the registration error between ALS and MLS improved from 84 cm to 4 cm. These results indicate that the proposed methods can obtain 5 cm accuracy between ALS and MLS.

Description: Nighttime satellite imagery from the Defense Meteorological Satellite Programs’ Operational Linescan System (DMSP OLS) is being used for myriad applications including population mapping, characterizing economic activity, disaggregate estimation of CO2 emissions, wildfire monitoring, and more. Here we present a method for in situ radiance calibration of the DMSP OLS using a ground based light source as an active target. We found that the wattage of light used by our active target strongly correlates with the signal measured by the DMSP OLS. This approach can be used to enhance our ability to make intertemporal and intersatellite comparisons of DMSP OLS imagery. We recommend exploring the possibility of establishing a permanent active target for the calibration of nocturnal imaging systems.

Description: Background: Identification of individual components in complex mixtures is an important and sometimes daunting task in several research areas like metabolomics and natural product studies. NMR spectroscopy is an excellent technique for analysis of mixtures of organic compounds and gives a detailed chemical fingerprint of most individual components above the detection limit. For the identification of individual metabolites in metabolomics, correlation or covariance between peaks in 1H NMR spectra has previously been successfully employed. Similar correlation of 2D 1H-13C Heteronuclear Single Quantum Correlation spectra was recently applied to investigate the structure of heparine. In this paper, we demonstrate how a similar approach can be used to identify metabolites in human biofluids (post-prostatic palpation urine). Results: From 50 1H-13C Heteronuclear Single Quantum Correlation spectra, 23 correlation plots resembling pure metabolites were constructed. The identities of these metabolites were confirmed by comparing the correlation plots with reported NMR data, mostly from the Human Metabolome Database. Conclusions: Correlation plots prepared by statistically correlating 1H-13C Heteronuclear Single Quantum Correlation spectra from human biofluids provide unambiguous identification of metabolites. The correlation plots highlight cross-peaks belonging to each individual compound, not limited by long-range magnetization transfer as conventional NMR experiments.

Description: Background: Alternative Splicing (AS) as a post-transcription regulation mechanism is an important application of RNA-seq studies in eukaryotes. A number of software and computational methods have been developed for detecting AS. Most of the methods, however, are designed and tested on animal data, such as human and mouse. Plants genes differ from those of animals in many ways, e.g., the average intron size and preferred AS types. These differences may require different computational approaches and raise questions about their effectiveness on plant data. The goal of this paper is to benchmark existing computational differential splicing (or transcription) detection methods so that biologists can choose the most suitable tools to accomplish their goals. Results: This study compares the eight popular public available software packages for differential splicing analysis using both simulated and real Arabidopsis thaliana RNA-seq data. All software are freely available. The study examines the effect of varying AS ratio, read depth, dispersion pattern, AS types, sample sizes and the influence of annotation. Using a real data, the study looks at the consistences between the packages and verifies a subset of the detected AS events using PCR studies. Conclusions: No single method performs the best in all situations. The accuracy of annotation has a major impact on which method should be chosen for AS analysis. DEXSeq performs well in the simulated data when the AS signal is relative strong and annotation is accurate. Cufflinks achieve a better tradeoff between precision and recall and turns out to be the best one when incomplete annotation is provided. Some methods perform inconsistently for different AS types. Complex AS events that combine several simple AS events impose problems for most methods, especially for MATS. MATS stands out in the analysis of real RNA-seq data when all the AS events being evaluated are simple AS events.

Description: Background: Colonial reef-building corals have evolved a broad spectrum of colony morphologies based on coordinated asexual reproduction of polyps on a secreted calcium carbonate skeleton. Though cnidarians have been shown to possess and use similar developmental genes to bilaterians during larval development and polyp formation, little is known about genetic regulation of colony morphology in hard corals. We used RNA-seq to evaluate transcriptomic differences between functionally distinct regions of the coral (apical branch tips and branch bases) in two species of Caribbean Acropora, the staghorn coral, A. cervicornis, and the elkhorn coral, A. palmata. Results: Transcriptome-wide gene profiles differed significantly between different parts of the coral colony as well as between species. Genes showing differential expression between branch tips and bases were involved in developmental signaling pathways, such as Wnt, Notch, and BMP, as well as pH regulation, ion transport, extracellular matrix production and other processes. Differences both within colonies and between species identify a relatively small number of genes that may contribute to the distinct "staghorn" versus "elkhorn" morphologies of these two sister species. Conclusions: The large number of differentially expressed genes supports a strong division of labor between coral branch tips and branch bases. Genes involved in growth of mature Acropora colonies include the classical signaling pathways associated with development of cnidarian larvae and polyps as well as morphological determination in higher metazoans.

Description: Background: In addition to gene identification and annotation, repetitive sequence analysis has become an integral part of genome sequencing projects. Identification of repeats is important not only because it improves gene prediction, but also because of the role that repetitive sequences play in determining the structure and evolution of genes and genomes. Several methods using different repeat-finding strategies are available for whole-genome repeat sequence analysis. Four independent approaches were used to identify and characterize the repetitive fraction of the Mycosphaerella graminicola (synonym Zymoseptoria tritici) genome. This ascomycete fungus is a wheat pathogen and its finished genome comprises 21 chromosomes, eight of which can be lost with no obvious effects on fitness so are dispensable. Results: Using a combination of four repeat-finding methods, at least 17% of the M. graminicola genome was estimated to be repetitive. Class I transposable elements, that amplify via an RNA intermediate, account for about 70% of the total repetitive content in the M. graminicola genome. The dispensable chromosomes had a higher percentage of repetitive elements as compared to the core chromosomes. Distribution of repeats across the chromosomes also varied, with at least six chromosomes showing a non-random distribution of repetitive elements. Repeat families showed transition mutations and a CpA [erase to the left] TpA dinucleotide bias, indicating the presence of a repeat-induced point mutation (RIP)-like mechanism in M. graminicola. One gene family and two repeat families specific to subtelomeres also were identified in the M. graminicola genome. A total of 78 putative clusters of nested elements was found in the M. graminicola genome. Several genes with putative roles in pathogenicity were found associated with these nested repeat clusters. This analysis of the transposable element content in the finished M. graminicola genome resulted in a thorough and highly curated database of repetitive sequences. Conclusions: This comprehensive analysis will serve as a scaffold to address additional biological questions regarding the origin and fate of transposable elements in fungi. Future analyses of the distribution of repetitive sequences in M. graminicola also will be able to provide insights into the association of repeats with genes and their potential role in gene and genome evolution.

Description: Background: Plant NBS-LRR pathogen-resistance genes tend to be found in clusters, which have been shown to be hot spots of genome variability, particularly in the form of presence/absence gene variation. In melon, half of the 81 predicted NBS-LRR genes group in nine clusters, and a 1 Mb region on linkage group V contains the highest density of R-genes and the highest concentration of PAV polymorphisms found in the melon genome. This region has been shown to contain the locus of Vat, an agronomically important gene that confers resistance to aphids. However, the presence of duplications makes the sequencing of R-gene clusters and their subsequent annotation difficult, usually resulting in multi-gapped sequences with higher than average errors. Results: A 1-Mb long sequence that contains the largest NBS-LRR gene cluster found in the melon genome was improved using a strategy that combines Illumina paired-end sequence mapping and PCR-based gap closing. Unknown sequence was decreased by 70% while about 3,000 SNPs and small indels were corrected. As a result, the annotations of 18 of a total of 23 NBS-LRR genes found in this region were modified, including additional coding sequence, due to gap closing and various amino acid changes. Manual annotation resulted in the correction of several splicing boundaries, and genes previously annotated as independent ORFs were fused in common transcription units. A phylogeny analysis of the R-genes and their comparison with syntenic sequences in other cucurbits point to a pattern of local gene amplifications since the diversification of cucurbits from other families, and through speciation within the family. A candidate Vat gene is proposed based on the sequence similarity between a reported Vat gene from a Korean melon cultivar and a sequence fragment previously absent in the unrefined sequence. Conclusions: A sequence refinement strategy allowed substantial improvement of a 1 Mb fragment of the melon genome and the re-annotation of the largest cluster of NBS-LRR gene homologues found in melon. Analysis of the cluster revealed that new resistance genes have been essentially produced by sequence duplication in adjacent genome locations since the divergence of cucurbits from other close families, and through the process of speciation within the family. With this sequence refinement, a candidate Vat gene was also identified using sequence previously unavailable, which demonstrates the advantages of genome assembly refinements when analyzing complex regions such as those containing clusters of highly similar genes.

Description: Background: MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes such as growth, development and stress responses. Chilling is a common abiotic stress that seriously affects plants growth and development. Recently, chilling-responsive miRNAs have been detected in several plant species. However, little is known about the miRNAs in the model plant tomato. 'LA1777' (Solanum habrochaites) has been shown to survive chilling stress due to its various characteristics. Results: Here, two small RNA libraries and two degradome libraries were produced from chilling-treated (CT) and non-chilling-treated (NT) leaves of S. habrochaites seedlings. Following high-throughput sequencing and filtering, 161 conserved and 236 novel miRNAs were identified in the two libraries. Of these miRNAs, 192 increased in the response to chilling stress while 205 decreased. Furthermore, the target genes of the miRNAs were predicted using a degradome sequencing approach. It was found that 62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Additionally, nine miRNAs and six target genes were validated by quantitative real-time PCR (qRT-PCR). Target gene functional analysis showed that most target genes played positive roles in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzyme and genes involved in cell wall formation. Conclusions: Tomato is an important model plant for basic biological research. In this study, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, and the target genes were analyzed by degradome sequencing. The work helps identify chilling-responsive miRNAs in tomato and increases the number of identified miRNAs involved in chilling stress. Furthermore, the work provides a foundation for further study of the regulation of miRNAs in the plant response to chilling stress.

Description: For near real-time water applications, the Moderate Resolution Imaging Spectroradiometers (MODIS) on Terra and Aqua are currently the only satellite instruments that can provide well-calibrated top-of-atmosphere (TOA) radiance data over the global aquatic environments. However, TOA radiance data in the MODIS ocean bands over turbid atmosphere in east China often saturate, leaving only four land bands to use. In this study, an approach based on Empirical Orthogonal Function (EOF) analysis has been developed and validated to estimate chlorophyll a concentrations (Chla, μg/L) in surface waters of Taihu Lake, the third largest freshwater lake in China. The EOF approach analyzed the spectral variance of normalized Rayleigh-corrected reflectance (Rrc) data at 469, 555, 645, and 859 nm, and subsequently related that variance to Chla using 28 concurrent MODIS and field measurements. This empirical algorithm was then validated using another 30 independent concurrent MODIS and field measurements. Image analysis and radiative transfer simulations indicated that the algorithm appeared to be tolerant to aerosol perturbations, with unbiased RMS uncertainties of 〈80% for Chla ranging between 3 and 100 μg/L. Application of the algorithm to a total of 853 MODIS images between 2000 and 2013 under cloud-free conditions revealed spatial distribution patterns and seasonal changes that are consistent to previous findings based on floating algae mats. The current study can provide additional quantitative estimates of Chla that can be assimilated in an existing forecast model, which showed improved performance over the use of a previous Chla algorithm. However, the empirical nature, relatively large uncertainties, and limited number of spectral bands all point to the need of further improvement in data availability and accuracy with future satellite sensors.

Description: MEMS Inertial Measurement Units are available at low cost and can replace expensive units in mobile mapping platforms which need direct georeferencing. This is done through the integration with GNSS measurements in order to achieve a continuous positioning solution and to obtain orientation angles. This paper presents the results of the assessment of the accuracy of a system that integrates GNSS and a MEMS IMU in a terrestrial platform. We describe the methodology used and the tests realized where the accuracy of the positions and orientation parameters were assessed using an independent photogrammetric technique employing cameras that integrate the mobile mapping system developed by the authors. Results for the accuracy of attitude angles and coordinates show that accuracies better than a decimeter in positions, and under a degree in angles, can be achieved even considering that the terrestrial platform is operating in less than favorable environments.

Description: This paper proposes an automated system for monitoring mobility patterns using a network of very low resolution visual sensors (30 30 pixels). The use of very low resolution sensors reduces privacy concern, cost, computation requirement and power consumption. The core of our proposed system is a robust people tracker that uses low resolution videos provided by the visual sensor network. The distributed processing architecture of our tracking system allows all image processing tasks to be done on the digital signal controller in each visual sensor. In this paper, we experimentally show that reliable tracking of people is possible using very low resolution imagery. We also compare the performance of our tracker against a state-of-the-art tracking method and show that our method outperforms. Moreover, the mobility statistics of tracks such as total distance traveled and average speed derived from trajectories are compared with those derived from ground truth given by Ultra-Wide Band sensors. The results of this comparison show that the trajectories from our system are accurate enough to obtain useful mobility statistics.

Description: Magnetic sensing technology offers an attractive alternative for in vivo tracking with much better performance than RF and ultrasound technologies. In this paper, an efficient in vivo magnetic tracking system is presented. The proposed system is intended to localize an endoscopic capsule which delivers biomarkers around specific locations of the gastrointestinal (GI) tract. For efficiently localizing a magnetic marker inside the capsule, a mathematical model has been developed for the magnetic field around a cylindrical magnet and used with a localization algorithm that provides minimum error and fast computation. The proposed tracking system has much reduced complexity compared to the ones reported in the literature to date. Laboratory tests and in vivo animal trials have demonstrated the suitability of the proposed system for tracking a magnetic marker with expected accuracy.

Description: Terra Preta Sanitation (TPS) plays a key role in sustainable sanitation (SuSan) and in the sustainable management of resources such as water, energy, soil (agriculture), liquid and solid organic waste streams as well as in the development of sustainable urban environment and infrastructure systems. This paper discusses the advantages of, and requirements for, SuSan systems, focusing on TPS. Case studies showing the stepwise extension and re-development of conventional sanitation systems (CSS) using TPS technologies and system approaches are presented and discussed. Decentralized TPS systems integrated in sustainable urban resource management were implemented in the German cities of Hamburg and Berlin. The compilation of best practice examples and findings using the newest TPS systems illustrates the immense potential of this approach for the transformation from conventional to SuSan systems. For this purpose, the potential savings of drinking water resources and the recycling potential of nutrient components are quantified. The results strongly suggest the need to encourage the development and application of innovative decentralized sanitation technologies, urban infrastructures, and resource management systems that have TP as a key component.

Description: Native chilies (Capsicum spp.) are currently underutilized in Bolivia, one of this crop’s centers of diversity. Fewer local farmers cultivate native chilies annually due to low market demand. Increasing its private use value can lead to the in-situ conservation of this crop. The objective of the paper is to evaluate the market acceptability of three native chili products: (a) chili marmalade; (b) chili cooking paste; and (c) pickled chilies. Multi-product Becker-DeGroot-Marschak experimental auctions and hedonic tests were conducted with 337 participants in La Paz and Santa Cruz. Data were analyzed using seemingly unrelated regressions. Results suggest that consumers are willing to pay price premiums of about 25–50 percent. Biodiversity conservation and improvements in farmers’ quality of life statements would not have influence on first purchase decisions but rather on repurchase decisions and therefore on consumers’ product loyalty. This in turn could lead to sustainable agro-biodiversity conservation, centered on consumers’ purchase of these products over time.

Description: This study proposes a new concept, green organisational ambidexterity, that integrates green exploration learning and green exploitation learning simultaneously. Besides, this study argues that the antecedents of green organisational ambidexterity are green shared vision and green absorptive capacity and its consequents are green radical innovation performance and green incremental innovation performance. The results demonstrate that green exploration learning partially mediates the positive relationships between green radical innovation performance and its two antecedents—green shared vision and green absorptive capacity. In addition, this study indicates that green exploitation learning partially mediates the positive relationships between green incremental innovation performance and its two antecedents—green shared vision and green absorptive capacity. Hence, firms have to increase their green shared vision, green absorptive capacity, and green organisational ambidexterity to raise their green radical innovation performance and green incremental innovation performance.

Description: This paper presents a sensor fusion system of cameras and a 2D laser sensorfor large-scale 3D reconstruction. The proposed system is designed to capture data on afast-moving ground vehicle. The system consists of six cameras and one 2D laser sensor,and they are synchronized by a hardware trigger. Reconstruction of 3D structures is doneby estimating frame-by-frame motion and accumulating vertical laser scans, as in previousworks. However, our approach does not assume near 2D motion, but estimates free motion(including absolute scale) in 3D space using both laser data and image features. In orderto avoid the degeneration associated with typical three-point algorithms, we present a newalgorithm that selects 3D points from two frames captured by multiple cameras. The problemof error accumulation is solved by loop closing, not by GPS. The experimental resultsshow that the estimated path is successfully overlaid on the satellite images, such that thereconstruction result is very accurate.

Description: The proliferation of mobile smart devices has led to a rapid increase of location-based services, many of which are amassing large datasets of user trajectory information. Unfortunately, current trajectory information is not yet sufficiently rich to support classification of user transportation modes. In this paper, we propose a method that employs both the Global Positioning System and accelerometer data from smart devices to classify user outdoor transportation modes. The classified modes include walking, bicycling, and motorized transport, in addition to the motionless (stationary) state, for which we provide new depth analysis. In our classification, stationary mode has two sub-modes: stay (remaining in the same place for a prolonged time period; e.g., in a parked vehicle) and wait (remaining at a location for a short period; e.g., waiting at a red traffic light). These two sub-modes present different semantics for data mining applications. We use support vector machines with parameters that are optimized for pattern recognition. In addition, we employ ant colony optimization to reduce the dimension of features and analyze their relative importance. The resulting classification system achieves an accuracy rate of 96.31% when applied to a dataset obtained from 18 mobile users.

Description: For many years, ultrasound has provided clinicians with an affordable and effective imaging tool for applications ranging from cardiology to obstetrics. Development of microbubble contrast agents over the past several decades has enabled ultrasound to distinguish between blood flow and surrounding tissue. Current clinical practices using microbubble contrast agents rely heavily on user training to evaluate degree of localized perfusion. Advances in separating the signals produced from contrast agents versus surrounding tissue backscatter provide unique opportunities for specialized sensors designed to image microbubbles with higher signal to noise and resolution than previously possible. In this review article, we describe the background principles and recent developments of ultrasound transducer technology for receiving signals produced by contrast agents while rejecting signals arising from soft tissue. This approach relies on transmitting at a low-frequency and receiving microbubble harmonic signals at frequencies many times higher than the transmitted frequency. Design and fabrication of dual-frequency transducers and the extension of recent developments in transducer technology for dual-frequency harmonic imaging are discussed.

Description: In this paper, a new low complexity and lossless image compression system for capsule endoscopy (CE) is presented. The compressor consists of a low-cost YEF color space converter and variable-length predictive with a combination of Golomb-Rice and unary encoding. All these components have been heavily optimized for low-power and low-cost and lossless in nature. As a result, the entire compression system does not incur any loss of image information. Unlike transform based algorithms, the compressor can be interfaced with commercial image sensors which send pixel data in raster-scan fashion that eliminates the need of having large buffer memory. The compression algorithm is capable to work with white light imaging (WLI) and narrow band imaging (NBI) with average compression ratio of 78% and 84% respectively. Finally, a complete capsule endoscopy system is developed on a single, low-power, 65-nm field programmable gate arrays (FPGA) chip. The prototype is developed using circular PCBs having a diameter of 16 mm. Several in-vivo and ex-vivo trials using pig's intestine have been conducted using the prototype to validate the performance of the proposed lossless compression algorithm. The results show that, compared with all other existing works, the proposed algorithm offers a solution to wireless capsule endoscopy with lossless and yet acceptable level of compression.

Description: A reflection fiber inclinometer is proposed and experimentally demonstrated based on two linearly polarized (LP) modes coupling. The configuration consists of a section of polarization-maintaining fiber (PMF) containing a fiber Bragg grating (FBG) splicing with single mode fiber (SMF). Bending the PMF in the upstream of FBG can induce an additional birefringence of PMF, which results in the intensity changes of two LP modes owing to orthogonal polarization coupling. The experimental results represent that the device shows different bending responses at the angle range from 0° to 40°and from 64° to 88°, respectively. Moreover, the temperature change just shifts the wavelengths of LP modes reflected and does not influence their intensities, which effectively avoid the temperature cross-sensitivity and make it a good candidate for measuring inclinometer and temperature simultaneously.

Description: Background: Over the course of its intraerythrocytic developmental cycle (IDC), the malaria parasite Plasmodium falciparum tightly orchestrates the rise and fall of transcript levels for hundreds of genes. Considerable debate has focused on the relative importance of transcriptional versus post-transcriptional processes in the regulation of transcript levels. Enzymatically active forms of RNAPII in other organisms have been associated with phosphorylation on the serines at positions 2 and 5 of the heptad repeats within the C-terminal domain (CTD) of RNAPII. We reasoned that insight into the contribution of transcriptional mechanisms to gene expression in P. falciparum could be obtained by comparing the presence of enzymatically active forms of RNAPII at multiple genes with the abundance of their associated transcripts. Results: We exploited the phosphorylation state of the CTD to detect enzymatically active forms of RNAPII at most P. falciparum genes across the IDC. We raised highly specific monoclonal antibodies against three forms of the parasite CTD, namely unphosphorylated, Ser5-P and Ser2/5-P, and used these in ChIP-on-chip type experiments to map the genome-wide occupancy of RNAPII. Our data reveal that the IDC is divided into early and late phases of RNAPII occupancy evident from simple bi-phasic RNAPII binding profiles. By comparison to mRNA abundance, we identified sub-sets of genes with high occupancy by enzymatically active forms of RNAPII and relatively low transcript levels and vice versa. We further show that the presence of active and repressive histone modifications correlates with RNAPII occupancy over the IDC. Conclusions: The simple early/late occupancy by RNAPII cannot account for the complex dynamics of mRNA accumulation over the IDC, suggesting a major role for mechanisms acting downstream of RNAPII occupancy in the control of gene expression in this parasite.

Description: Background: Through a review of three cases, the etiopathogenetic, clinical-diagnostic, and therapeutic aspects of ectopic thyroid tissue are herein discussed to highlight the main presentations of this polymorphous disease.Case presentations: The first case involved an ectopic thyroid gland in the lingual area in a 45-year-old Caucasian woman who presented with dysphagia and midline swelling at the base of the tongue. The second case involved a 22-year-old Caucasian woman with a submandibular mass comprising ectopic thyroid tissue. The third case involved a 33-year-old Caucasian man with a typical thyroglossal duct cyst characterized by the presence of thyroid tissue upon histological analysis. Conclusion: Surgery seems to be the most appropriate treatment for patients with ectopic thyroid tissue showing clinical signs of upper airway obstruction or when the lesion shows signs of infection or malignant degeneration. When a site of ectopic thyroid tissue is the only such site in the body, removal of this tissue will usually lead to hypothyroidism that requires medical thyroid hormone replacement.

Description: Background: Otolaryngologists encounter cases of various foreign bodies in the oral and pharyngeal regions. One commonly found foreign body is a fish bone, ingested in most cases by carelessness or an accident. These foreign materials are removed by endoscopy or through a simple procedure. However, hypopharyngeal damage is rarely caused by a foreign body in the pharynx following the swallowing of a toothbrush.Case presentationA 44-year-old Asian male visited the emergency room with chief complaints of intraoral pain and dysphagia that had started on the same day. The patient had paranoid-type schizophrenia that began 10 years ago; he had been hospitalized and was being treated at another clinic, and was transferred to the emergency room by the medical staff after swallowing a toothbrush. We successfully removed a toothbrush located within the pharynx of a patient with a history of a psychologic disorder via surgery and conservative treatment. Conclusion: The case with this patient, and a rapid diagnosis as well as treatment is imperative. The presence and state of a foreign body must be determined through a careful physical examination and imaging, followed by the immediate removal of the foreign body, all while keeping in mind the possibility of accompanying damage to nearby tissues.

Description: Background: PGxClean is a new web application that performs quality control analyses for data produced by the Affymetrix DMET chip or other candidate gene technologies. Importantly, the software does not assume that variants are biallelic single-nucleotide polymorphisms, but can be used on the variety of variant characteristics included on the DMET chip. Once quality control analyses has been completed, the associated PGxClean-Viz web application performs principal component analyses and provides tools for characterizing and visualizing population structure.FindingsThe PGxClean web application accepts genotype data from the Affymetrix DMET chip or the PLINK PED format with genotypes annotated as (A,C,G,T or 1,2,3,4). Options for removing missing data and calculating genotype and allele frequencies are offered. Data can be subdivided by cohort characteristics, such as family ID, sex, phenotype, or case-control status. Once the data has been processed through the PGxClean web application, the output files can be entered into the PGxClean-Viz web application for performing principal component analysis to visualize population substructure. Conclusions: The PGxClean software provides rapid quality-control processing, data analysis, and data visualization for the Affymetrix DMET chip or other candidate gene technologies while improving on common analysis platforms by not assuming that variants are biallelic. The web application is available at www.pgxclean.com.

Description: Biological invasions of aquatic systems disrupt ecological communities, and cause major changes in diversity and ecosystem function. The Laurentian Great Lakes of North America have been dramatically altered by such invasions, especially zebra (Dreissena polymorpha) and quagga (D. rostriformis bugensis) mussels. Responses to mussel invasions have included increased water clarity, and decreased chlorophyll and phytoplankton abundance. Although not all systems have responded similarly, in general, mussels have changed nutrient dynamics and physical habitat conditions. Therefore examination of different impacts can help us further understand mechanisms that underlie ecosystem responses to biological invasions. To aid our understanding of ecosystem impacts, we sampled established locations along a well-studied trophic gradient in Green Bay, Lake Michigan, after the 1993 zebra mussel invasion. A strong trophic gradient remained during the period sampled after the mussel invasion (2000–2012). However, mean summer chlorophyll increased and other measures of phytoplankton biomass (microscope and electronic cell counting) did not change significantly. Multivariate analyses of phytoplankton community structure demonstrate a significant community shift after the invasion. Cyanobacteria increased in dominance, with Microcystis becoming the major summer taxon in lower Green Bay. Diatom diversity and abundance also increased and Chlorophyta became rare. Phytoplankton responses along the trophic gradient of Green Bay to zebra mussel invasion highlight the importance of mussel effects on nutrient dynamics and phytoplankton diversity and function.

Description: This paper proposes a polygeneration system based on a multi-input chemical looping combustion system, which generates methanol and electricity, through the use of natural gas and coal. In this system, the chemical looping hydrogen (CLH) production system and the coal-based methanol production system are integrated. A high quality fuel, natural gas, is used to improve the conversion ratio of coal. The Gibbs energy of the two kinds of fuels is fully used. Benefitting from the chemical looping process, 27% CO2 can be captured without energy penalty. With the same outputs of methanol and electricity, the energy savings ratio of the new system is about 12%. Based on the exergy analyses, it is disclosed that the integration of synthetic utilization of natural gas and coal plays a significant role in reducing the exergy destruction of the new system. The promising results obtained in this paper may lead to a clean coal technology that will utilize natural gas and coal more efficiently and economically.

Description: Background: Heat shock transcriptional factors (Hsfs) play important roles in the processes of biotic and abiotic stresses as well as in plant development. Cotton (Gossypium hirsutum, 2n = 4x = (AD)2 = 52) is an important crop for natural fiber production. Due to continuous high temperature and intermittent drought, heat stress is becoming a handicap to improve cotton yield and lint quality. Recently, the related wild diploid species Gossypium raimondii genome (2n = 2x = (D5)2 = 26) has been fully sequenced. In order to analyze the functions of different Hsfs at the genome-wide level, detailed characterization and analysis of the Hsf gene family in G. hirsutum is indispensable. Results: EST assembly and genome-wide analyses were applied to clone and identify heat shock transcription factor (Hsf) genes in Upland cotton (GhHsf). Forty GhHsf genes were cloned, identified and classified into three main classes (A, B and C) according to the characteristics of their domains. Analysis of gene duplications showed that GhHsfs have occurred more frequently than reported in plant genomes such as Arabidopsis and Populus. Quantitative real-time PCR (qRT-PCR) showed that all GhHsf transcripts are expressed in most cotton plant tissues including roots, stems, leaves and developing fibers, and abundantly in developing ovules. Three expression patterns were confirmed in GhHsfs when cotton plants were exposed to high temperature for 1 h. GhHsf39 exhibited the most immediate response to heat shock. Comparative analysis of Hsfs expression differences between the wild-type and fiberless mutant suggested that Hsfs are involved in fiber development. Conclusions: Comparative genome analysis showed that Upland cotton D-subgenome contains 40 Hsf members, and that the whole genome of Upland cotton contains more than 80 Hsf genes due to genome duplication. The expression patterns in different tissues in response to heat shock showed that GhHsfs are important for heat stress as well as fiber development. These results provide an improved understanding of the roles of the Hsf gene family during stress responses and fiber development.

Description: IntroductionFood availability is an important environmental cue for animals for deciding how much to invest in reproduction, and it ultimately affects population size. The importance of food limitation has been extensively studied in terrestrial vertebrate populations, especially in birds, by experimentally manipulating food supply. However, the factors explaining variation in reproductive decisions in response to food supplementation remain unclear. By performing meta-analyses, we aim to quantify the extent to which supplementary feeding affects several reproductive parameters in birds, and identify the key factors (life-history traits, behavioural factors, environmental factors, and experimental design) that can induce variation in laying date, clutch size and breeding success (i.e., number of fledglings produced) in response to food supplementation. Results: Food supplementation produced variable but mostly positive effects across reproductive parameters in a total of 201 experiments from 82 independent studies. The outcomes of the food effect were modulated by environmental factors, e.g., laying dates advanced more towards low latitudes, and food supplementation appeared not to produce any obvious effect on bird reproduction when the background level of food abundance in the environment was high. Moreover, the increase in clutch size following food addition was more pronounced in birds that cache food, as compared to birds that do not. Supplementation timing was identified as a major cause of variation in breeding success responses. We also document the absence of a detectable food effect on clutch size and breeding success when the target species had poor access to the feed due to competitive interactions with other animals. Conclusions: Our findings indicate that, from the pool of bird species and environments reviewed, extra food is allocated to immediate reproduction in most cases. Our results also support the view that bird species have evolved different life-history strategies to cope with environmental variability in food supply. However, we encourage more research at low latitudes to gain knowledge on how resource allocation in birds changes along a latitudinal gradient. Our results also emphasize the importance of developing experimental designs that minimise competition for the supplemented food and the risk of reproductive bottle-necks due to inappropriate supplementation timings.

Description: Many city governments choose to supply more developable land and transportation infrastructure with the hope of attracting people and businesses to their cities. However, like those in Taiwan, major cities worldwide suffer from traffic congestion. This study applies the system thinking logic of the causal loops diagram (CLD) model in the System Dynamics (SD) approach to analyze the issue of traffic congestion and other issues related to roads and land development in Taiwan’s cities. Comparing the characteristics of development trends with yearbook data for 2002 to 2013 for all of Taiwan’s cities, this study explores the developing phenomenon of unlimited city sprawl and identifies the cause and effect relationships in the characteristics of development trends in traffic congestion, high-density population aggregation in cities, land development, and green land disappearance resulting from city sprawl. This study provides conclusions for Taiwan’s cities’ sustainability and development (S&D). When developing S&D policies, during decision making processes concerning city planning and land use management, governments should think with a holistic view of carrying capacity with the assistance of system thinking to clarify the prejudices in favor of the unlimited developing phenomena resulting from city sprawl.

Description: This study assessed the feasibility of community-based comprehensive intervention on Type 2 diabetes mellitus (T2DM) on a large population in China. An intervention study was conducted on 7200 T2DM patients within one year and consisted of six lectures on health issues, and four times face-to-face lifestyle counseling delivered by general health practitioners, at local primary health centers (PHCs). A “knowledge, attitude and practice” (KAP) survey and fasting plasma glucose (FPG) measurement were conducted at baseline and after the intervention, respectively. A total of 6586 T2DM patients completed the intervention. After one year intervention, patients’ KAP level improved significantly (p 〈 0.001) and the average FPG has decreased from 8.53 mmol/L (standard deviation: 2.84) to 7.11 mmol/L (standard deviation: 1.34) (p 〈 0.001). Patients in rural areas and with lower education level showed higher FPG and poorer KAP level both before and after the intervention. In conclusion, community-based comprehensive intervention for T2DM is feasible on a large population. Improving and repeating the comprehensive strategy is greatly recommended in order to sustain the impact, especially in rural areas and for patients with lower education levels.

Description: Building change detection is useful for land management, disaster assessment, illegal building identification, urban growth monitoring, and geographic information database updating. This study proposes an automatic method that applies object-based analysis to multi-temporal point cloud data to detect building changes. The aim of this building change detection method is to identify areas that have changed and to obtain from-to information. In this method, the data are first preprocessed to generate two sets of digital surface models (DSMs), digital elevation models, and normalized DSMs from registered old and new point cloud data. Thereafter, on the basis of differential DSM, candidates for changed building objects are identified from the points in the smooth areas by using a connected component analysis technique. The random sample consensus fitting algorithm is then used to distinguish the true changed buildings from trees. The changed building objects are classified as “newly built”, “taller”, “demolished” or “lower” by using rule-based analysis. Finally, a test data set consisting of many buildings of different types in an 8.5 km2 area is selected for the experiment. In the test data set, the method correctly detects 97.8% of buildings larger than 50 m2. The accuracy of the method is 91.2%. Furthermore, to decrease the workload of subsequent manual checking of the result, the confidence index for each changed object is computed on the basis of object features.

Description: In this study, we test and demonstrate the utility of disturbance and recovery information derived from annual Landsat time series to predict current forest vertical structure (as compared to the more common approaches, that consider a sample of airborne Lidar and single-date Landsat derived variables). Mean Canopy Height (MCH) was estimated separately using single date, time series, and the combination of single date and time series variables in multiple regression and random forest (RF) models. The combination of single date and time series variables, which integrate disturbance history over the entire time series, overall provided better MCH prediction than using either of the two sets of variables separately. In general, the RF models resulted in improved performance in all estimates over those using multiple regression. The lowest validation error was obtained using Landsat time series variables in a RF model (R2 = 0.75 and RMSE = 2.81 m). Combining single date and time series data was more effective when the RF model was used (opposed to multiple regression). The RMSE for RF mean canopy height prediction was reduced by 13.5% when combining the two sets of variables as compared to the 3.6% RMSE decline presented by multiple regression. This study demonstrates the value of airborne Lidar and long term Landsat observations to generate estimates of forest canopy height using the random forest algorithm.

Description: Rice is the most important food security crop in Asia. Information on its seasonal extent forms part of the national accounting of many Asian countries. Synthetic Aperture Radar (SAR) imagery is highly suitable for detecting lowland rice, especially in tropical and subtropical regions, where pervasive cloud cover in the rainy seasons precludes the use of optical imagery. Here, we present a simple, robust, rule-based classification for mapping rice area with regularly acquired, multi-temporal, X-band, HH-polarized SAR imagery and site-specific parameters for classification. The rules for rice detection are based on the well-studied temporal signature of rice from SAR backscatter and its relationship with crop stages. We also present a procedure for estimating the parameters based on “temporal feature descriptors” that concisely characterize the key information in the rice signatures in monitored field locations within each site. We demonstrate the robustness of the approach on a very large dataset. A total of 127 images across 13 footprints in six countries in Asia were obtained between October 2012, and April 2014, covering 4.78 m ha. More than 1900 in-season site visits were conducted across 228 monitoring locations in the footprints for classification purposes, and more than 1300 field observations were made for accuracy assessment. Some 1.6 m ha of rice were mapped with classification accuracies from 85% to 95% based on the parameters that were closely related to the observed temporal feature descriptors derived for each site. The 13 sites capture much of the diversity in water management, crop establishment and maturity in South and Southeast Asia. The study demonstrates the feasibility of rice detection at the national scale using multi-temporal SAR imagery with robust classification methods and parameters that are based on the knowledge of the temporal dynamics of the rice crop. We highlight the need for the development of an open-access library of temporal signatures, further investigation into temporal feature descriptors and better ancillary data to reduce the risk of misclassification with surfaces that have temporal backscatter dynamics similar to those of rice. We conclude with observations on the need to define appropriate SAR acquisition plans to support policies and decisions related to food security.

Description: The amount of liquid water in snow characterizes the wetness of a snowpack. Its temporal evolution plays an important role for wet-snow avalanche prediction, as well as the onset of meltwater release and water availability estimations within a river basin. However, it is still a challenge and a not yet satisfyingly solved issue to measure the liquid water content (LWC) in snow with conventional in situ and remote sensing techniques. We propose a new approach based on the attenuation of microwave radiation in the L-band emitted by the satellites of the Global Positioning System (GPS). For this purpose, we performed a continuous low-cost GPS measurement experiment at the Weissfluhjoch test site in Switzerland, during the snow melt period in 2013. As a measure of signal strength, we analyzed the carrier-to-noise power density ratio (C/N0) and developed a procedure to normalize these data. The bulk volumetric LWC was determined based on assumptions for attenuation, reflection and refraction of radiation in wet snow. The onset of melt, as well as daily melt-freeze cycles were clearly detected. The temporal evolution of the LWC was closely related to the meteorological and snow-hydrological data. Due to its non-destructive setup, its cost-efficiency and global availability, this approach has the potential to be implemented in distributed sensor networks for avalanche prediction or basin-wide melt onset measurements.

Description: On-site analysis is an efficient approach to facilitate analysis at the location of the system under investigation as it can result in more accurate, more precise and quickly available analytical data. In our work, a novel self-made thermal desorption based interface was fabricated to couple solid-phase microextraction with ion mobility spectrometry for on-site water analysis. The portable interface can be connected with the front-end of an ion mobility spectrometer directly without other modifications. The analytical performance was evaluated via the extraction of chemical warfare agents and simulants in water samples. Several parameters including ionic strength and extraction time have been investigated in detail. The application of the developed method afforded satisfactory recoveries ranging from 72.9% to 114.4% when applied to the analysis of real water samples.

Description: We consider the problem of localising an unknown number of land mines usingconcentration information provided by a wireless sensor network. A number of vapoursensors/detectors, deployed in the region of interest, are able to detect the concentrationof the explosive vapours, emanating from buried land mines. The collected data iscommunicated to a fusion centre. Using a model for the transport of the explosive chemicalsin the air, we determine the unknown number of sources using a Principal ComponentAnalysis (PCA)-based technique. We also formulate the inverse problem of determiningthe positions and emission rates of the land mines using concentration measurementsprovided by the wireless sensor network. We present a solution for this problem basedon a probabilistic Bayesian technique using a Markov chain Monte Carlo sampling scheme,and we compare it to the least squares optimisation approach. Experiments conducted onsimulated data show the effectiveness of the proposed approach.

Description: A smart-card-based user authentication scheme for wireless sensor networks (in short, a SUA-WSN scheme) is designed to restrict access to the sensor data only to users who are in possession of both a smart card and the corresponding password. While a significant number of SUA-WSN schemes have been suggested in recent years, their intended security properties lack formal definitions and proofs in a widely-accepted model. One consequence is that SUA-WSN schemes insecure against various attacks have proliferated. In this paper, we devise a security model for the analysis of SUA-WSN schemes by extending the widely-accepted model of Bellare, Pointcheval and Rogaway (2000). Our model provides formal definitions of authenticated key exchange and user anonymity while capturing side-channel attacks, as well as other common attacks. We also propose a new SUA-WSN scheme based on elliptic curve cryptography (ECC), and prove its security properties in our extended model. To the best of our knowledge, our proposed scheme is the first SUA-WSN scheme that provably achieves both authenticated key exchange and user anonymity. Our scheme is also computationally competitive with other ECC-based (non-provably secure) schemes.

Description: Optical mouse chips—equipped with adequate lenses—can serve as small, light, precise, fast, and cheap motion sensors monitoring optic flow induced by self motion of an agent in a contrasted environment. We present a device that extracts self motion parameters exclusively from flow in eight mouse sensors. Four pairs of sensors with opposite azimuth are mounted on a sensor head, each individual sensor looking down with \(-\)45\(^{\circ}\) elevation. The head is mounted on a carriage and is moved at constant height above a textured planar ground. The calibration procedure and tests on the precision of self motion estimates are reported.