Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles

<p>Abstract</p> <p>Background</p> <p>The hierarchical clustering tree (HCT) with a dendrogram <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> and the singular value decomposition (SVD) with a dimension-reduced representative map <abbrgrp><abbr bid="B2">2</abbr></abbrgrp> are popular methods for two-way sorting the gene-by-array matrix map employed in gene expression profiling. While HCT dendrograms tend to optimize local coherent clustering patterns, SVD leading eigenvectors usually identify better global grouping and transitional structures.</p> <p>Results</p> <p>This study proposes a flipping mechanism for a conventional agglomerative HCT using a rank-two ellipse (R2E, an improved SVD algorithm for sorting purpose) seriation by Chen <abbrgrp><abbr bid="B3">3</abbr></abbrgrp> as an external reference. While HCTs always produce permutations with good local behaviour, the rank-two ellipse seriation gives the best global grouping patterns and smooth transitional trends. The resulting algorithm automatically integrates the desirable properties of each method so that users have access to a clustering and visualization environment for gene expression profiles that preserves coherent local clusters and identifies global grouping trends.</p> <p>Conclusion</p> <p>We demonstrate, through four examples, that the proposed method not only possesses better numerical and statistical properties, it also provides more meaningful biomedical insights than other sorting algorithms. We suggest that sorted proximity matrices for genes and arrays, in addition to the gene-by-array expression matrix, can greatly aid in the search for comprehensive understanding of gene expression structures. Software for the proposed methods can be obtained at <url>http://gap.stat.sinica.edu.tw/Software/GAP</url>.</p

To Enhance the Fire Resistance Performance of High-Speed Steel Roller Door with Water Film System

The structure of high-speed roller door with water film has improved in this study. The flameproof water film system is equipped with a water circulating device to reduce the water consumption of water film system. The water film is generated at the roller box of the high-speed roller door in this study. The heating test is done with the full-scale heating furnace. Both cases of the water film on unexposed surface and water film on exposed surface passed the fire resistance test based on ISO 834, proving that the high-speed roller door with water film system has 120A fire resistance period. The main findings indicate that the water film on exposed surface shows that as the amount of water film evaporated by high temperature inside the furnace must be greater than the evaporation capacity of water film on unexposed surface, the required water supply is 660 L more than the water film on unexposed surface

Does higher demand for medicinal plants lead to more harvest? Evidence from the dual trade of Nardostachy jatamansi and Fritillaria cirrhosa and Tibetan people’s harvesting behavior

IntroductionAs the demand for herbal medicines is surging worldwide, regions of medicinal plants are vulnerable to large-scale and unsustainable exploitation for commercial trade and use. Yet, we still lack the understanding about the relationship between indigenous people harvesting and trade practices of medicinal plants and their influencing factors for possible intervention measures.MethodsHere, we combined qualitative and quantitative methods to survey traders (N = 20) and local harvesters (N = 923) from nine Tibetan townships in Hongyuan county, Sichuan Province, on the eastern Qinghai-Tibetan plateau in China. Specifically, we elucidated the local value chain of medicinal plants trade and harvest of Nardostachy jatamansi and Fritillaria cirrhosa, and explored the factors influencing harvester’s willingness to harvest these plants. Furthermore, we empirically tested the constructs of the COM-B model (Capability, Opportunity, Motivation -Behavior) in predicting the sustainable harvesting behavior of medicinal plants.Results and DiscussionOur results revealed that the trade characteristics of N. jatamansi and F. cirrhosa were contrasting, and the sustainability of the former species was largely dependent on the latter one. Importantly, the traders’ practices were affected by the supply, while the harvesters’ willingness to harvest were mainly influenced by harvest incomes, past harvesting experience, and grassland tenure. Finally, though motivation was not directly affecting harvesting behavior, the harvesters’ ecological worldview indirectly affected their harvesting behavior, particularly through the mediation of the level of compliance of village rules and customs. Overall, our results provided crucial insights for the conservation and sustainable management of the valuable wild medicinal plants

Applying a co-design approach with key stakeholders to design interventions to reduce illegal wildlife consumption

1. Co-design, an approach that seeks to incorporate the experiences and perspectives of different stakeholders, is increasingly being used to develop audience-oriented behaviour change interventions. 2. The complexity of wildlife consumption behaviour makes the co-design approach an important potential tool for the design of conservation interventions that aim to reduce illegal wildlife trade. Yet, little is known about how to adapt and apply the co-design approach to the wildlife trade sector. 3. Here, we applied a co-design approach to develop interventions aimed at reducing illegal animal-based medicine consumption in China. We conducted three workshops with key stakeholders: consumers of animal-based medicines, pharmacy workers who sell them and traditional Chinese medicine (TCM) doctors who prescribe them. We then developed a theory of change to ensure the relevance of the co-designed intervention prototypes. 4. Our co-design process identified five main pathways of interventions, including two inclusive solutions that may have been previously overlooked in behaviour change work in this context. These were an intervention to promote the appropriate use of TCM and one to increase consumers' capacity to identify the legality of products. Our prototype interventions also enhanced existing views related to the role of medical practitioners in health-risk communication. 5. We used our co-design process and reflections on its application to this specific market to provide guidelines for future conservation program planning in the broader wildlife trade context. Some intervention prototypes produced during co-design may need wider stakeholder involvement to increase their feasibility for implementation. 6. We show that the co-design process can integrate multiple stakeholders' perspectives in the ideation stage, and has the potential to produce inclusive intervention designs that could drive innovation in conservation efforts to reduce illegal consumption of a range of wild species

Kimura’s disease: A clinicopathological study of 23 cases

IntroductionKimura’s disease (KD) is an uncommon lymphoproliferative fibroinflammatory disorder. Patients present with head and neck subcutaneous nodules with or without lymphadenopathy. Peripheral blood eosinophilia and elevated serum immunoglobulin E (IgE) levels are typical. This study was designed to delineate the clinicopathological features, pattern of care, and disease course of 23 Taiwanese patients with KD.MethodsWe retrospectively analyzed the clinical data of 23 consecutive cases (16 male and 7 female; age at diagnosis: 12–77 years) of KD diagnosed at our institution from 2015 to 2020.ResultsThe median time from presentation to diagnosis was 1 month. Twenty-one patients presented with unilateral or bilateral head and neck masses. The remaining two presented with right flank and right arm lesions, respectively. Peripheral blood eosinophilia was observed in nine, and elevated IgE levels were observed in four. All were diagnosed using either excisional or core-needle biopsy. Seven patients underwent fine needle aspiration without a diagnostic yield. Salivary gland and lymph node involvement was observed in three and seven patients, respectively. Most lesions showed tissue eosinophilia (100%) and florid follicular hyperplasia (78.26%). Three cases had histological KD-IgG4-RD overlap and three had comorbid IgG4-RD were recognized. Thirteen patients underwent surgical resection, one received adjuvant therapy, and two received prednisolone monotherapy.ConclusionKD should be considered in patients with subcutaneous masses, eosinophilia, and elevated IgE levels. Biopsy remains the gold standard of diagnosis. Increased recruitment of IgG4+ plasma cells is a common feature. Consideration of IgG4-RD in all KD patients may be prudent

Do Bird Assemblages Predict Susceptibility by E-Waste Pollution? A Comparative Study Based on Species- and Guild-Dependent Responses in China Agroecosystems

Indirect effects of electronic waste (e-waste) have been proposed as a causal factor in the decline of bird populations, but analyses of the severity impacts on community assembly are currently lacking. To explore how population abundance/species diversity are influenced, and which functional traits are important in determining e-waste susceptibility, here we surveyed breeding and overwintering birds with a hierarchically nested sampling design, and used linear mixed models to analyze changes in bird assemblages along an exposure gradient in South China. Total bird abundance and species diversity decreased with e-waste severity (exposed < surrounding < reference), reflecting the decreasing discharge and consequent side effects. Twenty-five breeding species exclusively used natural farmland, and nine species decreased significantly in relative abundance at e-waste polluted sites. A high pairwise similarity between exposed and surrounding sites indicates a diffuse effect of pollutants on the species assembly at local scale. We show that sensitivity to e-waste severity varies substantially across functional guild, with the prevalence of woodland insectivorous and grassland specialists declining, while some open farmland generalists such as arboreal frugivores, and terrestrial granivores were also rare. By contrast, the response of waterbirds, omnivorous and non-breeding visitors seem to be tolerable to a wide range of pollution so far. These findings underscore that improper e-waste dismantling results in a severe decline of bird diversity, and the different bird assemblages on polluted and natural farmlands imply species- and guild-dependent susceptibility with functional traits. Moreover, a better understanding of the impact of e-waste with different pollution levels, combined multiple pollutants, and in a food-web context on bird is required in future

Lasing on nonlinear localized waves in curved geometry

The use of geometrical constraints opens many new perspectives in photonics and in fundamental studies of nonlinear waves. By implementing surface structures in vertical cavity surface emitting lasers as manifolds for curved space, we experimentally study the impacts of geometrical constraints on nonlinear wave localization. We observe localized waves pinned to the maximal curvature in an elliptical-ring, and confirm the reduction in the localization length of waves by measuring near and far field patterns, as well as the corresponding dispersion relation. Theoretically, analyses based on a dissipative model with a parabola curve give good agreement remarkably to experimental measurement on the transition from delocalized to localized waves. The introduction of curved geometry allows to control and design lasing modes in the nonlinear regime.Comment: 6 pages, 6 figure

Characterisation of alkaline treatment and fiber content on the physical, thermal and mechanical properties of ground coffee waste/oxo-biodegradable HDPE Biocomposites

Effect of alkali treatment on ground coffee waste/oxo-biodegradable HDPE (GCW/oxoHDPE) composites was evaluated using 5%, 10%, 15% and 20% volume fraction of GCW. The composites were characterize using structurally (fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM)), thermally (thermogravimetry analysis (TGA) and differential scanning calorimetry (DSC)), mechanically (tensile and impact test), and water absorption. FTIR spectrum indicated the eradication of lipids, hemicellulose, lignin and impurities after the treatments the lead to an improvement of the filler/matrix interface adhesion. This is confirmed by SEM results. Degree of crystallinity index was increased by 5% after the treatment. Thermal stability for both untreated and treated GCW composites were alike. Optimum tensile result achieved when using 10% volume fraction with enhancement of 25% for tensile strength and 24% for tensile modulus compared to untreated. Specific tensile strength and modulus had improved as the composite has lower density. The highest impact properties was achieved when using 15% volume fraction that lead to an improvement of 6%. Treated GCW composited show a better water resistance with 57% improvement compared to untreated. This light weight and ecofriendly biocomposite has the potential in packaging, internal automotive parts, lightweight furniture and other composite engineering applications