bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a Microfluidic-Based Optical Sensing Device for Label-Free Detection of Circulating Tumor Cells (CTCs) Through Their Lactic Acid Metabolism
Authors: Chiu Tzu-Keng , Lei Kin-Fong , Hsieh Chia-Hsun , Hsiao Hung-Bo , Wang Hung-Ming , Wu Min-Hsien
Published: March 2015

This study reports a microfluidic-based optical sensing device for label-free detection of circulating tumor cells (CTCs), a rare cell species in blood circulation. Based on the metabolic features of cancer cells, live CTCs can be quantified indirectly through their lactic acid production. Compared with the conventional schemes for CTC detection, this label-free approach could prevent the biological bias due to the heterogeneity of the surface antigens on cancer cells. In this study, a microfluidic device was proposed to generate uniform water-in-oil cell-encapsulating micro-droplets, followed by the fluorescence-based optical detection of lactic acid produced within the micro-droplets. To test its feasibility to quantify cancer cells, experiments were carried out. Results showed that the detection signals were proportional to the number of cancer cells within the micro-droplets, whereas such signals were insensitive to the existence and number of leukocytes within. To further demonstrate its feasibility for cancer cell detection, the cancer cells with known cell number in a cell suspension was detected based on the method. Results revealed that there was no significant difference between the detected number and the real number of cancer cells. As a whole, the proposed method opens up a new route to detect live CTCs in a label-free manner.
Broadband and High Sensitive Time-of-Flight Diffraction Ultrasonic Transducers Based on PMNT/Epoxy 1–3 Piezoelectric Composite
Authors: Liu Dongxu , Yue Qingwen , Deng Ji , Lin Di , Li Xiaobing , Di Wenning , Wang Xi'an , Zhao Xiangyong , Luo Haosu
Published: March 2015

5–6 MHz PMNT/epoxy 1–3 composites were prepared by a modified dice-and-fill method. They exhibit excellent properties for ultrasonic transducer applications, such as ultrahigh thickness electromechanical coupling coefficient kt (85.7%), large piezoelectric coefficient d33 (1209 pC/N), and relatively low acoustic impedance Z (1.82 × 107 kg/(m2·s)). Besides, two types of Time-of-Flight Diffraction (TOFD) ultrasonic transducers have been designed, fabricated, and characterized, which have different matching layer schemes with the acoustic impedance of 4.8 and 5.7 × 106 kg/(m2·s), respectively. In the detection on a backwall of 12.7 mm polystyrene, the former exhibits higher detectivity, the relative pulse-echo sensitivity and −6 dB relative bandwidth are −21.93 dB and 102.7%, respectively, while the later exhibits broader bandwidth, the relative pulse-echo sensitivity and −6 dB relative bandwidth are −24.08 dB and 117.3%, respectively. These TOFD ultrasonic transducers based on PMNT/epoxy 1–3 composite exhibit considerably improved performance over the commercial PZT/epoxy 1–3 composite TOFD ultrasonic transducer.
Low Carbon Footprint Routes for Bird Watching
Authors: Fang Wei-Ta , Huang Chin-Wei , Chou Jui-Yu , Cheng Bai-You , Shih Shang-Shu
Published: March 2015

Bird watching is one of many recreational activities popular in ecotourism. Its popularity, therefore, prompts the need for studies on energy conservation. One such environmentally friendly approach toward minimizing bird watching’s ecological impact is ensuring a reduced carbon footprint by using an economic travel itinerary comprising a series of connected routes between tourist attractions that minimizes transit time. This study used a travel-route planning approach using geographic information systems to detect the shortest path, thereby solving the problems associated with time-consuming transport. Based on the results of road network analyses, optimal travel-route planning can be determined. These methods include simulated annealing (SA) and genetic algorithms (GA). We applied two algorithms in our simulation research to detect which one is an appropriate algorithm for running carbon-routing algorithms at the regional scale. SA, which is superior to GA, is considered an excellent approach to search for the optimal path to reduce carbon dioxide and high gasoline fees, thereby controlling travel time by using the shortest travel routes.
Willingness to Pay for Carbon Sequestration and Co-Benefits of Forests in Turkey
Authors: Tolunay Ahmet , Başsüllü Çağlar
Published: March 2015

Scientists express concern about increasing levels of greenhouse gases mainly due to fossil fuel consumption and deforestation. In response to the latter, policy-makers have introduced a range of policy measures to conserve and enhance forest ecosystems for carbon sequestration. The costs for policy measures to maintain ecosystem services can be calculated easily, but especially non-market/non-use benefits of forests are not easy to estimate. Economics can help designing climate change policies by eliciting public preferences on different attributes of climate change and carbon sequestration. This study was prepared for the purpose of identifying per capita consumer/equivalent surplus or maximum willingness to pay and the total economic value in relation to forests to be established in Turkey to reduce air pollution around cities, to prevent the adverse effects of climate change and to sequester carbon. The data for the estimation of maximum willingness to pay, total economic value and co-benefits of forests were collected with a questionnaire form prepared according to the contingent valuation method. Analyses have been conducted by correlation analysis and regression analysis. According to the analyses, per capita consumer/equivalent surplus or maximum willingness to pay to establish a new forest was estimated at US$ 23.52 on average, while total economic value was estimated at US$ 270,443,962.68.
The Cryptophlebia Leucotreta Granulovirus—10 Years of Commercial Field Use
Authors: Moore Sean , Kirkman Wayne , Richards Garth , Stephen Peter
Published: March 2015

In the last 15 years, extensive work on the Cryptophlebia leucotreta granulovirus (CrleGV) has been conducted in South Africa, initially in the laboratory, but subsequently also in the field. This culminated in the registration of the first CrleGV-based biopesticide in 2004 (hence, the 10 years of commercial use in the field) and the second one three years later. Since 2000, more than 50 field trials have been conducted with CrleGV against the false codling moth, Thaumatotibia leucotreta, on citrus in South Africa. In a representative sample of 13 field trials reported over this period, efficacy (measured by reduction in larval infestation of fruit) ranged between 30% and 92%. Efficacy was shown to persist at a level of 70% for up to 17 weeks after application of CrleGV. This only occurred where the virus was applied in blocks rather than to single trees. The addition of molasses substantially and sometimes significantly enhanced efficacy. It was also established that CrleGV should not be applied at less than ~2 × 1013 OBs per ha in order to avoid compromised efficacy. As CrleGV-based products were shown to be at least as effective as chemical alternatives, persistent and compatible with natural enemies, their use is recommended within an integrated program for control of T. leucotreta on citrus and other crops.
Aspects morphologiques du Massif Central guyanais (Geomorphological features of the guianan central massif)
Authors: Petit Michel
Published: March 2015

Abstract. - This short paper, written after recent and unpublished geological works, shows the interest of geomorphological features in the central highlands of Guiana : differencial erosion, hydrographical network, meaning and correlations of the low erosion surfaces, crusts and forms on hillslops, alluvial fills.
Le rôle du vent au cours des derniers millénaires dans le bassin saharien d'Araouane (Mali) (Wind action during the last millenaries in the saharian basin of Araouane - Mali)
Authors: Riser Jean
Published: March 2015

Abstract. - During Holocene the winds have built dunes, ranging from 5 to 7 m high, and dug yardangs from 1 to 2m deep. The present ergs surrounding holo- cenes lake deposits were built in less than 4000 years. In the Araouane basin, the ablation caused by wind over 6500 years has been about 60 cm.
Les mouvements de terrain, facteur géomorphologique d'intérêt régional en Grèce centrale (Ground movements as a geomorphological factor of regional importance in central Greece)
Authors: Bousquet Bernard , Péchoux Pierre-Yves
Published: March 2015

Résumé. - On étudie les séismes en tant que générateurs habituels de mouvements de masse, et donc comme agents ordinaires de la morphogenèse dans certains contextes régionaux séismiques comme la Grèce centrale.
Magnetic properties of self-organized Co dimer nanolines on Si/Ag(110)
Authors: Michez Lisa , Chen Kai , Cheynis Fabien , Leroy Frédéric , Ranguis Alain , Jamgotchian Haik , Hanbücken Margrit , Masson Laurence
Published: March 2015

We demonstrate the kinetically controlled growth of one-dimensional Co nanomagnets with a high lateral order on a nanopatterned Ag(110) surface. First, self-organized Si nanoribbons are formed upon submonolayer condensation of Si on the anisotropic Ag(110) surface. Depending on the growth temperature, individual or regular arrays (with a pitch of 2 nm) of Si nanoribbons can be grown. Next, the Si/Ag(110) system is used as a novel one-dimensional Si template to guide the growth of Co dimer nanolines on top of the Si nanoribbons, taking advantage of the fact that the thermally activated process of Co diffusion into the Si layer is efficiently hindered at 220 K. Magnetic characterization of the Co nanolines using X-ray magnetic circular dichroism reveals that the first atomic Co layer directly adsorbed onto the Si nanoribbons presents a weak magnetic response. However, the second Co layer exhibits an enhanced magnetization, strongly suggesting a ferromagnetic ordering with an in-plane easy axis of magnetization, which is perpendicular to the Co nanolines.
Professional Development Implications of Ebola Virus Disease Education: Part I
Authors: Smith Elaine L. , Kerner Robert L. , Schindler Jaclyn S. , DeVoe Barbara
Published: March 2015

This article is the first in a two-part series that explores how one large, integrated health care system swiftly responded to the emerging threat of Ebola virus disease. In this first article, the context and initial steps in planning staff education and training are outlined.
J Contin Educ Nurs.
2015;46(1):8–9.
Semantic++ Electronic Commerce Architecture and Models in Cloud
Authors: Zhang Guigang , Li Chao , Zhang Yong , Xing Chunxiao , Xue Sixin , Liu Yuenan
Published: March 2015

Electronic commerce is playing a more and more important role in today's commercial activities. In this chapter, the authors propose a kind of new electronic commerce architecture in the cloud and give two kinds of new electronic commerce models. This chapter opens the discussion of why we need to design a new architecture in the cloud environment. Firstly, the authors have a discussion about the semantic++ computing. After the discussion, they give the architecture that can satisfy the requirements in the cloud. This architecture mainly includes five technologies, which are the massive EC data storage technology in the cloud, the massive EC data processing technology in the cloud, the EC security management technology in the cloud, OLAP technology for EC in the cloud, and active EC technology in the cloud. Then, the authors propose two kinds of semantic++ electronic commerce models based on big data. These two models are the new electronic commerce models. The first model is semantic++ electronic commerce Q/A (Questions/Answers) model and another is the active semantic++ electronic commerce model. These two models are all based on big data. Finally, the authors conclude this chapter and give future work.
Evaluation of B2B Pharmaceutical Supply Chain in Australia
Authors: Lin Chad , Jalleh Geoffrey
Published: March 2015

The pharmaceutical industry is one of the most innovative and research-intensive industries in the world. For example, five out of the top global Research and Development (R&D) companies were pharmaceutical companies. However, the industry is lagging behind other industries in adopting Business-to-Business (B2B) and supply chain technologies. With supply chain costs constituting around 25-40% of an organization's operating expenses, it is imperative for senior pharmaceutical executives to minimize this cost. Hence, the main objective of this chapter is to identify key B2B e-commerce management, evaluation, and benefits realization factors and challenges within the Australian pharmaceutical supply chain. The results of this study suggest that pharmaceutical companies not only need to carefully examine their B2B investment management and evaluation practices but also must invest in using appropriate evaluation methodologies for identifying and managing benefits, risks, and costs associated with their investments in B2B and supply chains.
The benthic macro-invertebrate diversity in relation to water quality of a stream habitat at Dediyagala, Sri Lanka
Authors: Madhushankha H.M.T.C. , Asanthi H.B. , Maithreepala R.A.
Published: March 2015

The streams collect sediment and other fine and particulate material from their watersheds and transport them downstream as fluvial material. Macro-benthos is the most important secondary producers in stream ecosystem and their diversity explains the water quality of a stream to a greater extent. The present study determines the water quality and macro-benthos diversity at five sites of the 180m stream stretch at Dediyagala for a period of three months from February to April in 2012. Random samples were collected using a Surber sampler for benthos, and a Ruttner sampler for water samples.

Water discharge was significantly different from headwater (0.0198 m3s-1) to downstream (0.0456 m3s−1).Bottom substrate was non uniform according to Uniformity Coefficient analysis except at two sampling sites of cascade and riffle habitats. There was no significant site specific or time specific variations in water temperature, pH, biochemical oxygen demand (BOD3), total suspended solids (TSS), total dissolved solids (TDS), and orthophosphate concentration. Nitrate concentration, dissolved oxygen (DO) and organic matter content of lithophytes varied significantly among the sampling sites (P
Molecular Evolution of Hypoallergenic Hybrid Proteins for Vaccination against Grass Pollen Allergy
Authors: Linhart Birgit , Focke-Tejkl Margarete , Weber Milena , Narayanan Meena , Neubauer Angela , Mayrhofer Hannes , Blatt Katharina , Lupinek Christian , Valent Peter , Valenta Rudolf
Published: March 2015

More than 10% of the population in Europe and North America suffer from IgE-associated allergy to grass pollen. In this article, we describe the development of a vaccine for grass pollen allergen-specific immunotherapy based on two recombinant hypoallergenic mosaic molecules, designated P and Q, which were constructed out of elements derived from the four major timothy grass pollen allergens: Phl p 1, Phl p 2, Phl p 5, and Phl p 6. Seventeen recombinant mosaic molecules were expressed and purified in Escherichia coli using synthetic genes, characterized regarding biochemical properties, structural fold, and IgE reactivity. We found that depending on the arrangement of allergen fragments, mosaic molecules with strongly varying IgE reactivity were obtained. Based on an extensive screening with sera and basophils from allergic patients, two hypoallergenic mosaic molecules, P and Q, incorporating the primary sequence elements of the four grass pollen allergens were identified. As shown by lymphoproliferation experiments, they contained allergen-specific T cell epitopes required for tolerance induction, and upon immunization of animals induced higher allergen-specific IgG Abs than the wild-type allergens and a registered monophosphoryl lipid A–adjuvanted vaccine based on natural grass pollen allergen extract. Moreover, IgG Abs induced by immunization with P and Q inhibited the binding of patients’ IgE to natural allergens from five grasses better than IgG induced with the wild-type allergens or an extract-based vaccine. Our results suggest that vaccines based on the hypoallergenic grass pollen mosaics can be used for immunotherapy of grass pollen allergy.
FOXO1 Regulates Dendritic Cell Activity through ICAM-1 and CCR7
Authors: Dong Guangyu , Wang Yu , Xiao Wenmei , Pacios Pujado Sandra , Xu Fanxing , Tian Chen , Xiao E , Choi Yongwon , Graves Dana T.
Published: March 2015

The transcription factor FOXO1 regulates cell function and is expressed in dendritic cells (DCs). We investigated the role of FOXO1 in activating DCs to stimulate a lymphocyte response to bacteria. We show that bacteria induce FOXO1 nuclear localization through the MAPK pathway and demonstrate that FOXO1 is needed for DC activation of lymphocytes in vivo. This occurs through FOXO1 regulation of DC phagocytosis, chemotaxis, and DC–lymphocyte binding. FOXO1 induces DC activity by regulating ICAM-1 and CCR7. FOXO1 binds to the CCR7 and ICAM-1 promoters, stimulates CCR7 and ICAM-1 transcriptional activity, and regulates their expression. This is functionally important because transfection of DCs from FOXO1-deleted CD11c.Cre+FOXO1L/L mice with an ICAM-1–expressing plasmid rescues the negative effect of FOXO1 deletion on DC bacterial phagocytosis and chemotaxis. Rescue with both CCR7 and ICAM-1 reverses impaired DC homing to lymph nodes in vivo when FOXO1 is deleted. Moreover, Ab production following injection of bacteria is significantly reduced with lineage-specific FOXO1 ablation. Thus, FOXO1 coordinates upregulation of DC activity through key downstream target genes that are needed for DCs to stimulate T and B lymphocytes and generate an Ab defense to bacteria.
Inhibition of CD40-Induced N-Ras Activation Reduces Leishmania major Infection
Authors: Chakraborty Sushmita , Srivastava Ankita , Jha Mukesh Kumar , Nair Arathi , Pandey Surya Prakash , Srivastava Neetu , Kumari Sangeeta , Singh Shailza , Krishnasastry Musti V. , Saha Bhaskar
Published: March 2015

Leishmania major is a parasite that resides and replicates in macrophages. We previously showed that the parasite enhanced CD40-induced Raf-MEK-ERK signaling but inhibited PI3K-MKK-p38MAPK signaling to proleishmanial effects. As Raf and PI3K have a Ras-binding domain but exert opposite effects on Leishmania infection, we examined whether Ras isoforms had differential roles in Leishmania infection. We observed that L. major enhanced N-Ras and H-Ras expression but inhibited K-Ras expression in macrophages. L. major infection enhanced N-Ras activity but inhibited H-Ras and K-Ras activity. TLR2 short hairpin RNA or anti-TLR2 or anti-lipophosphoglycan Abs reversed the L. major–altered N-Ras and K-Ras expressions. Pam3CSK4, a TLR2 ligand, enhanced N-Ras expression but reduced K-Ras expression, indicating TLR2-regulated Ras expression in L. major infection. Whereas N-Ras silencing reduced L. major infection, K-Ras and H-Ras silencing enhanced the infection both in macrophages in vitro and in C57BL/6 mice. BALB/c-derived macrophages transduced with lentivirally expressed N-Ras short hairpin RNA and pulsed with L. major–expressed MAPK10 enhanced MAPK10-specific Th1-type response. CD40-deficient mice primed with these macrophages had reduced L. major infection, accompanied by higher IFN-γ but less IL-4 production. As N-Ras is activated by Sos, a guanine nucleotide exchange factor, we modeled the N-Ras–Sos interaction and designed two peptides from their interface. Both the cell-permeable peptides reduced L. major infection in BALB/c mice but not in CD40-deficient mice. These data reveal the L. major–enhanced CD40-induced N-Ras activation as a novel immune evasion strategy and the potential for Ras isoform–targeted antileishmanial immunotherapy and immunoprophylaxis.
Profiling of the Three Circulating Monocyte Subpopulations in Human Obesity
Authors: Devêvre Estelle F. , Renovato-Martins Mariana , Clément Karine , Sautès-Fridman Catherine , Cremer Isabelle , Poitou Christine
Published: March 2015

Three subpopulations of circulating monocytes have been described: CD142+CD16− (classical monocytes [CM]), CD142+CD16+ (intermediate monocytes [IM]), and CD14+CD162+ (nonclassical monocytes [NCM]). We previously showed that obesity is associated with an increased proportion of IM and NCM. Our objective is to decipher the migratory and inflammatory functions of each monocyte subset in obesity-related low-grade inflammation. Twenty-six healthy, normal-weight and nondiabetic volunteers (C) and 40 obese nondiabetic (Ob) individuals were included in this study. We explored the gene expression profile of 18 inflammatory genes in each subset of C and Ob subjects and measured protein expression of the upregulated genes. We then tested their functional response to TLR signaling in both groups. We showed an increased expression of CX3CR1 in all monocyte subpopulations and of CCR2 and CCR5 in CM and IM in the Ob group. We found negative correlation between CCR2 and CX3CR1 expressions and high-density lipoprotein-cholesterol, whereas CCR5 expression was positively linked to obesity-related metabolic traits. Production of inflammatory proteins upon bacterial LPS and viral ssRNA stimulation was higher in CM and NCM of the Ob group compared with the C group. Our work highlights an enhanced inflammatory phenotype of monocytes with a higher response to TLR4 and TLR8 stimulations in obesity. Moreover, it suggests an increased migration capacity of CM and IM subpopulations.
Regulation of Pulmonary Graft-versus-Host Disease by IL-26+CD26+CD4 T Lymphocytes
Authors: Ohnuma Kei , Hatano Ryo , Aune Thomas M. , Otsuka Haruna , Iwata Satoshi , Dang Nam H. , Yamada Taketo , Morimoto Chikao
Published: March 2015

Obliterative bronchiolitis is a potentially life-threatening noninfectious pulmonary complication after allogeneic hematopoietic stem cell transplantation and the only pathognomonic manifestation of pulmonary chronic graft-versus-host disease (cGVHD). In the current study, we identified a novel effect of IL-26 on transplant-related obliterative bronchiolitis. Sublethally irradiated NOD/Shi-scidIL2rγnull mice transplanted with human umbilical cord blood (HuCB mice) gradually developed clinical signs of graft-versus-host disease (GVHD) such as loss of weight, ruffled fur, and alopecia. Histologically, lung of HuCB mice exhibited obliterative bronchiolitis with increased collagen deposition and predominant infiltration with human IL-26+CD26+CD4 T cells. Concomitantly, skin manifested fat loss and sclerosis of the reticular dermis in the presence of apoptosis of the basilar keratinocytes, whereas the liver exhibited portal fibrosis and cholestasis. Moreover, although IL-26 is absent from rodents, we showed that IL-26 increased collagen synthesis in fibroblasts and promoted lung fibrosis in a murine GVHD model using IL-26 transgenic mice. In vitro analysis demonstrated a significant increase in IL-26 production by HuCB CD4 T cells following CD26 costimulation, whereas Ig Fc domain fused with the N-terminal of caveolin-1 (Cav-Ig), the ligand for CD26, effectively inhibited production of IL-26. Administration of Cav-Ig before or after onset of GVHD impeded the development of clinical and histologic features of GVHD without interrupting engraftment of donor-derived human cells, with preservation of the graft-versus-leukemia effect. These results therefore provide proof of principle that cGVHD of the lungs is caused in part by IL-26+CD26+CD4 T cells, and that treatment with Cav-Ig could be beneficial for cGVHD prevention and therapy.
Evaluation of Sorption Coefficients for Pyroxasulfone, s-Metolachlor, and Dimethenamid-p
Authors: Westra Eric P. , Shaner Dale L. , Barbarick Ken A. , Khosla Raj
Published: March 2015

Sorption coefficients were evaluated for pyroxasulfone, s-metolachlor, and dimethenamid- p across 25 soil types with different chemical and physical properties to better understand how soil properties influence the binding of pyroxasulfone in different soils. Sorption coefficients were determined using a batch equilibrium method to evaluate relative differences in binding among the three herbicides. Based on water solubility values, we would have expected the relative order of binding to be dimethenamid- p (1450 mg L−1 at 20°C), s-metolachlor (530 mg L−1 at 20°C), and pyroxasulfone (3.49 mg L−1 at 20°C) in order of increasing binding. However, when sorption coefficients were calculated, we observed the order of pyroxasulfone = dimethenamid- p < s-metolachlor in the order of increasing binding. The average Kd(sorption coefficient) values were 1.7, 2.3, and 4.0 L kg−1 for pyroxasulfone, dimethenamid- p, and s-metolachlor, respectively. Although dimethenamid- p has water solubility values that are over 400 times greater than pyroxasulfone, there was no statistical difference in binding between pyroxasulfone and dimethenamid- p. s-Metolachlor binding was statistically greater than both pyroxasulfone and dimethenamid- p. Across all soil chemical and physical properties, sorption coefficients for all three herbicides were highly and statistically correlated to soil organic matter. Sand and silt were also statistically correlated to binding, although these correlations could be explained by the high correlation of organic matter to these properties. Evaluation of sorption coefficients indicates that pyroxasulfone is most prevalent in the soil solution where herbicides are available for plant uptake. Reduced soil binding and greater activity at the target site could contribute to comparable weed control efficacies of pyroxasulfone even when applied at lower use rates compared to either s-metolachlor or dimethenamid- p.
GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials
Authors: Zhao Yingdong , Polley Eric C. , Li Ming-Chung , Lih Chih-Jian , Palmisano Alida , Sims David J. , Rubinstein Lawrence V. , Conley Barbara A. , Chen Alice P. , Williams P. Mickey , Kummar Shivaani , Doroshow James H. , Simon Richard M.
Published: March 2015

We have developed an informatics system, GeneMed, for the National Cancer Institute (NCI) molecular profiling-based assignment of cancer therapy (MPACT) clinical trial (NCT01827384) being conducted in the National Institutes of Health (NIH) Clinical Center. This trial is one of the first to use a randomized design to examine whether assigning treatment based on genomic tumor screening can improve the rate and duration of response in patients with advanced solid tumors. An analytically validated next-generation sequencing (NGS) assay is applied to DNA from patients’ tumors to identify mutations in a panel of genes that are thought likely to affect the utility of targeted therapies available for use in the clinical trial. The patients are randomized to a treatment selected to target a somatic mutation in the tumor or with a control treatment. The GeneMed system streamlines the workflow of the clinical trial and serves as a communications hub among the sequencing lab, the treatment selection team, and clinical personnel. It automates the annotation of the genomic variants identified by sequencing, predicts the functional impact of mutations, identifies the actionable mutations, and facilitates quality control by the molecular characterization lab in the review of variants. The GeneMed system collects baseline information about the patients from the clinic team to determine eligibility for the panel of drugs available. The system performs randomized treatment assignments under the oversight of a supervising treatment selection team and generates a patient report containing detected genomic alterations. NCI is planning to expand the MPACT trial to multiple cancer centers soon. In summary, the GeneMed system has been proven to be an efficient and successful informatics hub for coordinating the reliable application of NGS to precision medicine studies.
HCsnip: An R Package for Semi-Supervised Snipping of the Hierarchical Clustering Tree
Authors: Obulkasim Askar , Van De Wiel Mark A.
Published: March 2015

Hierarchical clustering (HC) is one of the most frequently used methods in computational biology in the analysis of high-dimensional genomics data. Given a data set, HC outputs a binary tree leaves of which are the data points and internal nodes represent clusters of various sizes. Normally, a fixed-height cut on the HC tree is chosen, and each contiguous branch of data points below that height is considered as a separate cluster. However, the fixed-height branch cut may not be ideal in situations where one expects a complicated tree structure with nested clusters. Furthermore, due to lack of utilization of related background information in selecting the cutoff, induced clusters are often difficult to interpret. This paper describes a novel procedure that aims to automatically extract meaningful clusters from the HC tree in a semi-supervised way. The procedure is implemented in the R package HCsnip available from Bioconductor. Rather than cutting the HC tree at a fixed-height, HCsnip probes the various way of snipping, possibly at variable heights, to tease out hidden clusters ensconced deep down in the tree. The cluster extraction process utilizes, along with the data set from which the HC tree is derived, commonly available background information. Consequently, the extracted clusters are highly reproducible and robust against various sources of variations that “haunted” high-dimensional genomics data. Since the clustering process is guided by the background information, clusters are easy to interpret. Unlike existing packages, no constraint is placed on the data type on which clustering is desired. Particularly, the package accepts patient follow-up data for guiding the cluster extraction process. To our knowledge, HCsnip is the first package that is able to decomposes the HC tree into clusters with piecewise snipping under the guidance of patient time-to-event information. Our implementation of the semi-supervised HC tree snipping framework is generic, and can be combined with other algorithms that operate on detected clusters.
Case-Based Retrieval Framework for Gene Expression Data
Authors: Anaissi Ali , Goyal Madhu , Catchpoole Daniel R. , Braytee Ali , Kennedy Paul J.
Published: March 2015

Background

The process of retrieving similar cases in a case-based reasoning system is considered a big challenge for gene expression data sets. The huge number of gene expression values generated by microarray technology leads to complex data sets and similarity measures for high-dimensional data are problematic. Hence, gene expression similarity measurements require numerous machine-learning and data-mining techniques, such as feature selection and dimensionality reduction, to be incorporated into the retrieval process.

Methods

This article proposes a case-based retrieval framework that uses a k-nearest-neighbor classifier with a weighted-feature-based similarity to retrieve previously treated patients based on their gene expression profiles.

Results

The herein-proposed methodology is validated on several data sets: a childhood leukemia data set collected from The Children's Hospital at Westmead, as well as the Colon cancer, the National Cancer Institute (NCI), and the Prostate cancer data sets. Results obtained by the proposed framework in retrieving patients of the data sets who are similar to new patients are as follows: 96% accuracy on the childhood leukemia data set, 95% on the NCI data set, 93% on the Colon cancer data set, and 98% on the Prostate cancer data set.

Conclusion

The designed case-based retrieval framework is an appropriate choice for retrieving previous patients who are similar to a new patient, on the basis of their gene expression data, for better diagnosis and treatment of childhood leukemia. Moreover, this framework can be applied to other gene expression data sets using some or all of its steps.
Differentiation ofCorynespora cassiicolaandCercosporasp. in leaf-spot diseases ofHydrangea macrophyllausing a PCR-mediated method
Authors: Mmbaga M. T. , Kim M.-S. , Mackasmiel L. , Klopfenstein N. B.
Published: March 2015

Mmbaga, M. T., Kim M.-S., Mackasmiel, L. and Klopfenstein, N. B. 2015. Differentiation of Corynespora cassiicola and Cercospora sp. in leaf-spot diseases of Hydrangea macrophylla using a PCR-mediated method. Can. J. Plant Sci. 95: 711–717. Corynespora cassiicola and Cercospora sp. have been identified as the most prevalent and destructive leaf-spot pathogens of garden hydrangea [Hydrangea macrophylla (Thunberg) Seringe] in the southeastern USA, but they are often difficult to accurately detect and distinguish because they often occur together in a disease complex with other pathogenic leaf-spot fungi and produce very similar symptoms. This study was conducted to provide diagnostic PCR primers for detecting and distinguishing Corynespora cassiicola and Cercospora sp. among other leaf-spot pathogens of garden hydrangea. Two primer pairs showed specificity to Corynespora cassiicola and one primer pair showed specificity to Cercospora sp., and these primers did not amplify DNA from any other common fungal pathogens associated with hydrangea leaf-spot diseases. Results from this study show that DNA-based diagnostic primers provide a useful tool for pathogen detection/identification in hydrangea leaf-spot disease, which is an essential step toward understanding disease etiology and developing/applying appropriate disease-management practices in the southeastern USA.
Antioxidant properties of lingonberry (Vaccinium vitis-idaeaL.) leaves within a set of wild clones and cultivars
Authors: Vyas Poorva , Curran Nicholas H. , Igamberdiev Abir U. , Debnath Samir C.
Published: March 2015

Vyas, P., Curran, N. H., Igamberdiev, A. U. and Debnath, S. C. 2015. Antioxidant properties of lingonberry (Vaccinium vitis-idaea L.) leaves within a set of wild clones and cultivars. Can. J. Plant Sci. 95: 663–669. The antioxidant activities and the contents of total soluble phenolics, flavonoids, anthocyanins and proanthocyanidins were studied in wild and cultivated lingonberries (Vaccinium vitis-idaea L.). The antioxidant properties of wild clones were much higher than those of the cultivars. The levels of antioxidant compounds were positively correlated with latitude, altitude, reduced temperature and increased precipitation of the collected sites.
The effect of late fall seeding time on the seed production of Italian ryegrass
Authors: Coulman Bruce , Loeppky Heather , Entz Martin
Published: March 2015

Coulman, B., Loeppky, H. and Entz, M. 2015. The effect of late fall seeding time on the seed production of Italian ryegrass. Can. J. Plant Sci. 95: 641–645. Italian ryegrass (Lolium multiflorum Lam.) is a cool-season grass, which behaves as an annual in the Great Plains region of western Canada and is used as a grazing crop. Italian ryegrass requires vernalization for reproductive development to occur. Late fall (dormant) seedings, which have been used for annual crop species, have often resulted in earlier developing seedlings in the spring and higher yield than spring seedings. For Italian ryegrass, dormant seedings may result in vernalization of early-spring-germinating seedlings, allowing seed production without having to overwinter established plants. The objective of this study was to compare the seed yield and stand establishment of late fall (dormant) and spring seedings of Italian ryegrass at three locations in the Great Plains region of western Canada. Stand establishment was assessed by measuring tiller density in the month of June, and these densities were greater for spring than late fall seedings. Most spring seedings had no reproductive development and, thus, no seed yield; however, most late fall seedings produced seed the following year, indicating that vernalization of early-developing seedlings did occur. There were significant differences in seed yield among the four cultivars tested and among sites. Based on the high variation in seed yield among cultivars and sites and the relatively low yield levels obtained, late fall seedings of Italian ryegrass cannot be recommended in the Great Plains region of western Canada.
Net primary productivity and below-ground crop residue inputs for root crops: Potato (Solanum tuberosum L.) and sugar beet (Beta vulgaris L.)
Authors: Bolinder Martin A. , Kätterer Thomas , Poeplau Christopher , Börjesson Gunnar , Parent Leon E.
Published: March 2015

Bolinder, M. A., Kätterer, T., Poeplau, C., Börjesson, G. and Parent, L. E. 2015. Net primary productivity and below-ground crop residue inputs for root crops: Potato (Solanum tuberosum L.) and sugar beet (Beta vulgaris L.). Can. J. Soil Sci. 95: 87–93. Root crops are significant in agro-ecosystems of temperate climates. However, the amounts of crop residues for these crop types are not well documented and they need to be accounted for in the modeling of soil organic carbon dynamics. Our objective was to review field measurements of root biomass left in the soil as crop residues at harvest for potato and sugar beet. We considered estimates for crop residue inputs as root biomass presented in the literature and some unpublished results. Our analysis showed that compared to, for example, cereals, the contribution of below-ground net primary productivity (NPP) to crop residues is at least two to three times lower for root crops. Indeed, the field measurements indicated that root biomass for topsoils only represents on average 25 to 30 g dry matter (DM) m−2 yr−1. Other estimates, albeit variable and region-specific, tended to be higher. We suggest relative plant DM allocation coefficients for agronomic yield (RP), above-ground biomass (RS) and root biomass (RR) components, expressed as a proportion of total NPP. These coefficients, representative for temperate climates (0.739:0.236:0.025 for potato and 0.626:0.357:0.017 for sugar beet), should be useful in the modeling of agro-ecosystems that include root crops.
Finite Element Simulation of Ballistic Performance of Dissimilar Metallic Plates Welded Joints
Authors: Sureshkumar S. , Sushinder K. , Sudersan S.
Published: March 2015

Studies of ballistic penetration into metal plates and their numerical simulation currently play a vital role in the defence sector. However, no congruent results have been presented so far, especially when it comes to impact on welded plates. Furthermore, these issues are investigated for normal impacts and very few have made an attempt for oblique impacts. Thus the aim of the present work is to conduct numerical simulation using Abaqus/Explicit in order to evaluate the ballistic performance of similar and dissimilar welded plates subjected to various bullet velocities and impact angles. The effect of post weld residual stresses and associated plastic damage on the ballistic performance of similar (Al6061) and dissimilar (Al 6061- SS 304) welded plates is also determined. The energy absorbed by the welded plates for various configurations was determined and the results are critically evaluated.
Prototype Aircraft Sub-Assembly Fabrication using Common Stage Walking Line Assembly Model
Authors: Gopinath L. , Ravishankar S.
Published: March 2015

This paper describes the application of Walking Line Assembly (WLA) in prototype fabrication of yoke sub-assembly and its effectiveness. The technical aspects and challenges involved in development and fabrication of engine mount yoke tube assembly for a civil aircraft are presented. Activities representing reverse engineering process and fabrication of yoke tube are detailed comprehensively. WLA model adopted for this assembly is compared with conventional methods and fixed layouts. Further, WLA model is modified with a common stage set on every process where the expected capability of the task in the shop floor is brought out in consensus with the operational demand and standards. This is achieved with very little disturbance to the existing aircraft fixed line fabrication set up. This model has given encouraging results by expediting the processes and provides an ideal option for building of prototypes in the development stage of an aircraft project.
Investigations on Dissimilar Welded Joints by Magnetic Pulse Method
Authors: Muthukumaran S. , Kudiyarasan S. , Arungalai Vendan S. , Senthil Kumar A.
Published: March 2015

Experimental investigations on magnetic pulse welding of dissimilar materials are carried out in this study. Detailed studies are carried out to assess the mechanical properties, microstructure and interface pattern of lap joint of Aluminium alloy tube and Copper alloy rod by Magnetic Pulse Welding (MPW). The torsion strength values are higher than that of the aluminium tube when the discharge voltage of MPW process is not less than 6 kV. The joint basically comprises of interfaces, non-uniform transition zone and base metals obtained under discharge voltage of 10 kV, the contact angle being 50Â° and radial gap of 1.2-1.4 mm. It is observed from microstructure examinations that high-density dislocations are present in basic metals along the interfaces. The transition zone appears to have higher hardness as compared to the other classified zones based on the metallurgical configurations. The multidirectional micro-cracks and micro-apertures characterise the transition zone of MPW joint. The mutual diffusion of Cu and Al elements occurs in the transition zone, where content of Al element is higher than Cu element besides a narrow region close to the interface of Cu and Al zone. Through this investigation, the suitability of MPW for joining dissimilar conductive materials is established.
Spatiotemporal variability of water vapor investigated using lidar and FTIR vertical soundings above the Zugspitze
Authors: Vogelmann H. , Sussmann R. , Trickl T. , Reichert A.
Published: March 2015

Abstract. Water vapor is the most important greenhouse gas and its spatiotemporal variability strongly exceeds that of all other greenhouse gases. However, this variability has hardly been studied quantitatively so far. We present an analysis of a 5-year period of water vapor measurements in the free troposphere above the Zugspitze (2962 m a.s.l., Germany). Our results are obtained from a combination of measurements of vertically integrated water vapor (IWV), recorded with a solar Fourier transform infrared (FTIR) spectrometer on the summit of the Zugspitze and of water vapor profiles recorded with the nearby differential absorption lidar (DIAL) at the Schneefernerhaus research station. The special geometrical arrangement of one zenith-viewing and one sun-pointing instrument and the temporal resolution of both instruments allow for an investigation of the spatiotemporal variability of IWV on a spatial scale of less than 1 km and on a timescale of less than 1 h. The standard deviation of differences between both instruments σIWV calculated for varied subsets of data serves as a measure of variability. The different subsets are based on various spatial and temporal matching criteria. Within a time interval of 20 min, the spatial variability becomes significant for horizontal distances above 2 km, but only in the warm season (σIWV =0.35 mm). However, it is not sensitive to the horizontal distance during the winter season. The variability of IWV within a time interval of 30 min peaks in July and August (σIWV > 0.55 mm, mean horizontal distance = 2.5 km) and has its minimum around midwinter (σIWV < 0.2 mm, mean distance > 5 km). The temporal variability of IWV is derived by selecting subsets of data from both instruments with optimal volume matching. For a short time interval of 5 min, the variability is 0.05 mm and increases to more than 0.5 mm for a time interval of 15 h. The profile variability of water vapor is determined by analyzing subsets of water vapor profiles recorded by the DIAL within time intervals from 1 to 5 h. For all altitudes, the variability increases with widened time intervals. The lowest relative variability is observed in the lower free troposphere around an altitude of 4.5 km. Above 5 km, the relative variability increases continuously up to the tropopause by about a factor of 3. Analysis of the covariance of the vertical variability reveals an enhanced variability of water vapor in the upper troposphere above 6 km. It is attributed to a more coherent flow of heterogeneous air masses, while the variability at lower altitudes is also driven by local atmospheric dynamics. By studying the short-term variability of vertical water vapor profiles recorded within a day, we come to the conclusion that the contribution of long-range transport and the advection of heterogeneous layer structures may exceed the impact of local convection by 1 order of magnitude even in the altitude range between 3 and 5 km.
Methane emission estimates using chamber and tracer release experiments for a municipal waste water treatment plant
Authors: Yver-Kwok C. E. , Müller D. , Caldow C. , Lebègue B. , Mønster J. G. , Rella C. W. , Scheutz C. , Schmidt M. , Ramonet M. , Warneke T. , Broquet G. , Ciais P.
Published: March 2015

Abstract. This study presents two methods for estimating methane emissions from a waste water treatment plant (WWTP) along with results from a measurement campaign at a WWTP in Valence, France. These methods, chamber measurements and tracer release, rely on Fourier Transform Infrared (FTIR) spectroscopy and Cavity Ring Down Spectroscopy (CRDS) instruments. We show that the tracer release method is suitable to quantify facility- and some process-scale emissions, while the chamber measurements, provide insight into individual process emissions. Uncertainties for the two methods are described and discussed. Applying the methods to CH4 emissions of the WWTP, we confirm that the open basins are not a major source of CH4 on the WWTP (about 10% of the total emissions), but that the pretreatment and sludge treatment are the main emitters. Overall, the waste water treatment plant represents a small part (about 1.5%) of the methane emissions of the city of Valence and its surroundings, which is lower than the national inventories.
GROMOS-C, a novel ground based microwave radiometer for ozone measurement campaigns
Authors: Fernandez S. , Murk A. , Kämpfer N.
Published: March 2015

Abstract. Stratospheric ozone is of major interest as it absorbs most of harmful UV radiation from the sun, allowing life on Earth. Ground based microwave remote sensing is the only method that allows to measure ozone profiles up to the mesopause, 24 h and under different weather conditions with high time resolution. In this paper a novel ground based microwave radiometer is presented. It is called GROMOS-C (GRound based Ozone MOnitoring System for Campaigns), and it has been designed to measure the vertical profile of ozone distribution in the middle atmosphere, by observing ozone emission spectra at a frequency of 110.836 GHz. The instrument is designed in a compact way which makes it transportable and suitable for outdoor use in campaigns, an advantageous feature that is lacking in present day ozone radiometers. It is operated through remote control. GROMOS-C is a total power radiometer which uses a preamplified heterodyne receiver, and a digital Fast Fourier Transform spectrometer for the spectral analysis. Among its main new features stands out the incorporation of different calibration loads, including a noise diode and a new type of blackbody target specifically designed for this instrument, based on Peltier elements. The calibration scheme does not depend on the use of liquid nitrogen, therefore GROMOS-C can be operated at remote places with no maintenance requirements. In addition the instrument can be switched in frequency to observe the CO line at 115 GHz. A description of the main characteristics of GROMOS-C is included in this paper, as well as the results of a first campaign at the High Altitude Research Station in Jungfraujoch (HFSJ), Switzerland. The validation is performed by comparison of the retrieved profiles against equivalent profiles from MLS satellite data, ECMWF model data, as well as our nearby NDACC ozone radiometer measuring at Bern.