bluuebunny/crossref_metadata_2025 huggingface dataset:
Short-term variability in the sedimentary BIT index of Lake Challa, East Africa over the past 2200 years: validating the precipitation proxy
Authors: Buckles L. K. , Weijers J. W. H. , Verschuren D. , Cocquyt C. , Sinninghe Damsté J. S.
Published: April 2015

Abstract. The branched vs. isoprenoid index of tetraethers (BIT index) in Lake Challa sediments has been applied as a monsoon precipitation proxy on the assumption that the primary source of branched tetraether lipids (brGDGTs) was soil washed in from the lake's catchment. However, water column production has since been identified as the primary source of brGDGTs in Lake Challa, meaning that there is no longer a clear mechanism linking BIT index variation and precipitation. Here we investigate BIT index variation and GDGT concentrations at a decadal resolution over the past 2200 years, in combination with GDGT data from profundal surface sediments and 45 months of sediment-trap deployment. The 2200 year record reveals high-frequency variability in GDGT concentrations, and therefore the BIT index. Also surface sediments collected in January 2010 show a distinct shift in GDGT composition relative to those collected in August 2007. Increased bulk flux of settling particles with high Ti / Al ratios during March–April 2008 reflect an event of high detrital input to Lake Challa, concurrent with intense precipitation at the onset of the principal rain season that year. Although brGDGT distributions in the settling material are initially unaffected, this soil erosion event is succeeded by a large diatom bloom in July–August 2008 and a concurrent increase in GDGT-0 fluxes. Near-zero crenarchaeol fluxes indicate that no thaumarchaeotal bloom developed during the subsequent austral summer season; instead a peak in brGDGT fluxes is observed in December 2008. We suggest that increased nutrient availability, derived from eroded soil washed into the lake, stimulated both diatom productivity and the GDGT-0 producing archaea which help decompose dead diatoms passing through the suboxic zone of the water column. This disadvantaged the Thaumarchaeota that normally prosper during the following austral summer. Instead, a bloom of supposedly heterotrophic brGDGT-producing bacteria occurred. Episodic recurrence of such high soil-erosion events, integrated over multi-decadal and longer timescales and possibly enhanced by other mechanisms generating low BIT index values in dry years, can explain the positive relationship between the sedimentary BIT index and monsoon precipitation at Lake Challa. However, application elsewhere requires ascertaining the local situation of lacustrine brGDGT production and of variables affecting the productivity of Thaumarchaeota.
Metrics for linking emissions of gases and aerosols to global precipitation changes
Authors: Shine K. P. , Allan R. P. , Collins W. J. , Fuglestvedt J. S.
Published: April 2015

Abstract. Recent advances in understanding have made it possible to relate global precipitation changes more directly to emissions of particular gases and aerosols that influence climate. Using these advances, a new index is developed here called the Global Precipitation-change Potential (GPP), which measures the precipitation change per unit mass of emissions. It is recognised that precipitation changes are predicted to be highly variable in size and sign between different regions, and ultimately climate change impacts will be more dependent on these regional changes. Nevertheless, the GPP presents a useful measure of the global-mean role of emissions of individual forcing agents. Results are presented for pulse (GPPP) and sustained (GPPS) emissions for selected long- and short-lived forcing agents (CO2, CH4, N2O, sulphate and black carbon – BC) using illustrative values of required parameters. The GPP can be used as a metric to compare the importance of emissions. This is akin to the global warming potential (GWP) and the global temperature-change potential (GTP) which are used to place emissions on a common scale. The GPP is further down the cause-effect chain from emissions to impacts than the GWP and GTP, and so provides an additional perspective. One key parameter needed for the GPP is the surface–atmosphere partitioning of radiative forcing. Few studies have presented results for this partitioning for different forcings, leading to more uncertainty in quantification of the GPP than the GWP or GTP. Using CO2 as references gas, the pulse and sustained GPP values for the non-CO2 species are larger than the corresponding GTP values, because the CO2 GPP is the sum of two quite strongly opposing terms. For BC emissions, the atmospheric forcing is sufficiently strong that the GPPS is opposite in sign to the GTPS. The choice of CO2 as a reference gas is problematic, especially for the GPPS at time horizons less than about 60 years, because the opposing terms make the CO2 GPPS particularly sensitive to uncertainties in input parameters. The GPP can also be used to evaluate the contribution of different emissions to precipitation change during or after a period of emissions. As an illustration, the precipitation changes resulting from emissions in 2008 (using the GPPP) and emissions sustained at 2008 levels (using the GPPS) are presented. These indicate that for periods of 20 years (after the 2008 emissions) and 50 years (for sustained emissions at 2008 levels) methane is the dominant driver of positive precipitation changes due to those emissions. For sustained emissions, the sum of the effect of the 5 species included here does not become positive until after 50 years, by which time the global surface temperature increase exceeds 1 K.
Modelling of sedimentation processes inside Roseires Reservoir (Sudan)
Authors: Omer A. Y. A. , Ali Y. S. A. , Roelvink J. A. , Dastgheib A. , Paron P. , Crosato A.
Published: April 2015

Abstract. Roseires Reservoir, located on the Blue Nile River in Sudan, is the first trap to the sediments coming from the vast upper river catchment in Ethiopia, which suffers from high erosion and desertification problems. The reservoir has already lost more than one-third of its storage capacity due to sedimentation in the last four decades. Appropriate management of the eroded soils in the upper basin could mitigate this problem. In order to do that, the areas providing the highest sediment volumes to the river have to be identified, since they should have priority with respect to the application of erosion control practices. This requires studying the sedimentation record inside Roseires Reservoir in order to assess when and how much sediment is deposited and to identify its source. This paper deals with the identification of deposition time and soil stratification inside the reservoir, based on historical bathymetric data, numerical modelling and newly acquired soil data. The remoteness of the study area and the extreme climate result in coring campaigns being expensive and difficult. Therefore, these activities need to be optimised and coring locations selected beforehand. This was done by combining bathymetric data and the results of a depth-averaged morphodynamic model recording the vertical stratification in sediment deposits. The model allowed for recognising the areas that are potentially subject to neither net erosion nor bar migration during the lifespan of the reservoir. Verification of these results was carried out by analysing sediment stratification from the data collected during the subsequent field campaign.
Technical Note: Field experiences using UV/VIS sensors for high-resolution monitoring of nitrate in groundwater
Authors: Huebsch M. , Grimmeisen F. , Zemann M. , Fenton O. , Richards K. G. , Jordan P. , Sawarieh A. , Blum P. , Goldscheider N.
Published: April 2015

Abstract. Two different in situ spectrophotometers are compared that were used in the field to determine nitrate-nitrogen (NO3-N) concentrations at two distinct spring discharge sites. One sensor was a double wavelength spectrophotometer (DWS) and the other a multiple wavelength spectrophotometer (MWS). The objective of the study was to review the hardware options, determine ease of calibration, accuracy, influence of additional substances and to assess positive and negative aspects of the two sensors as well as troubleshooting and trade-offs. Both sensors are sufficient to monitor highly time-resolved NO3-N concentrations in emergent groundwater. However, the chosen path length of the sensors had a significant influence on the sensitivity and the range of detectable NO3-N. The accuracy of the calculated NO3-N concentrations of the sensors can be affected if the content of additional substances such as turbidity, organic matter, nitrite or hydrogen carbonate significantly varies after the sensors have been calibrated to a particular water matrix. The MWS offers more possibilities for calibration and error detection but requires more expertise compared with the DWS.
Dynamic synthesis of machine with slider-crank mechanism
Authors: Jomartov A. A. , Joldasbekov S. U. , Drakunov Yu. M.
Published: April 2015

Abstract. In this paper we consider the formulation and solution of the task of a dynamic synthesis machine with an asynchronous electric motor and a slider-crank mechanism. The constant parameters of the slider-crank mechanism (mass and moments of inertia and centers of gravity of links) and the parameters of the electrical motor are defined. The laws of motion of the machine and kinematic parameters of the mechanism are considered as given. We have developed the method of optimal dynamic synthesis of the machine, which consists of an asynchronous electric motor and a slider-crank mechanism. The criterion of optimization of the dynamic synthesis of a machine is the root mean square sum of the moments of driving forces, the forces of resistance and inertia forces which are reduced to the axis of rotation of the crank. The method of optimal dynamic synthesis of a machine can be used in the design of new and the improvement of known mechanisms and machines.
Amalgamation in landslide maps: effects and automatic detection
Authors: Marc O. , Hovius N.
Published: April 2015

Abstract. Inventories of individually delineated landslides are a key to understanding landslide physics and mitigating their impact. They permit assessment of area–frequency distributions and landslide volumes, and testing of statistical correlations between landslides and physical parameters such as topographic gradient or seismic strong motion. Amalgamation, i.e. the mapping of several adjacent landslides as a single polygon, can lead to potentially severe distortion of the statistics of these inventories. This problem can be especially severe in data sets produced by automated mapping. We present five inventories of earthquake-induced landslides mapped with different materials and techniques and affected by varying degrees of amalgamation. Errors on the total landslide volume and power-law exponent of the area–frequency distribution, resulting from amalgamation, may be up to 200 and 50%, respectively. We present an algorithm based on image and digital elevation model (DEM) analysis, for automatic identification of amalgamated polygons. On a set of about 2000 polygons larger than 1000 m2, tracing landslides triggered by the 1994 Northridge earthquake, the algorithm performs well, with only 2.7–3.6% incorrectly amalgamated landslides missed and 3.9–4.8% correct polygons incorrectly identified as amalgams. This algorithm can be used broadly to check landslide inventories and allow faster correction by automating the identification of amalgamation.
Sustainability: Teaching an Interdisciplinary Threshold Concept through Traditional Lecture and Active Learning
Authors: Levintova Ekaterina M , Mueller Daniel W
Published: April 2015

One of the difficulties in teaching global sustainability in the introductory political science classes is the different emphases placed on this concept and the absence of the consensus on where the overall balance between environmental protection, economic development, and social justice should reside. Like many fuzzy concepts with which students struggle, teaching sustainability lends itself to pedagogical examination within the scholarship of threshold concepts. This article investigates students’ understanding of sustainability in the seven semesters when the concept of sustainability was introduced via role-playing simulation and compares it with the similar data from a more recent semester when simulation was supplemented with traditional lecture and classroom exercises. Ultimately, our research question is twofold: (1) How do students define a multi-faceted concept like global sustainability and (2) what is the better way to teach it – active learning only or active learning in combination with traditional instruction?
Certaines des difficultés rencontrées quand on enseigne la durabilité mondiale dans des cours de base de sciences politiques sont les divers accents mis sur ces concepts et l’absence de consensus sur la question de savoir où devrait se situer l’équilibre général entre la protection de l’environnement, le développement économique et la justice sociale. Tout comme c’est le cas avec de nombreux concepts flous qui donnent des difficultés aux étudiants, l’enseignement de la durabilité se prête à un examen pédagogique au sein de la recherche sur les concepts de seuil. Cet article se penche sur la manière dont les étudiants ont compris la durabilité pendant les sept semestres au cours desquels le concept de durabilité a été présenté par le biais de simulation de jeux de rôles et il la compare aux données semblables recueillies lors d’un semestre plus récent au cours duquel la simulation a été supplémentée par des cours magistraux traditionnels et des exercices de classe. En fin de compte, notre question de recherche est double : 1) Comment les étudiants définissent-ils un concept qui présente de nombreuses facettes tel que la durabilité mondiale, et 2) Quelle est la meilleure manière de l’enseigner - exclusivement par un apprentissage actif ou par le biais d’un apprentissage actif combiné à une instruction traditionnelle?
Anxiety and Self-efficacy’s Relationship with Undergraduate Students’ Perceptions of the use of Metacognitive Writing Strategies
Authors: Stewart Graeme , Seifert Tricia Anne , Rolheiser Carol
Published: April 2015

There is growing interest in promoting metacognition among college and university students, as this has been linked with positive student learning outcomes. This study explores the relationship between student writing anxiety and self-efficacy on undergraduate students’ self-reported use of metacognitive writing strategies. Using undergraduate student survey data from a large, research-intensive university in Ontario, Canada, we found reductions in writing anxiety and increased self-efficacy had a statistically significant association with students’ perceptions of using metacognitive writing strategies. These findings have implications for both theory and practice. They demonstrate that writing metacognition is influenced by emotional factors, such as the level of anxiety and the extent of self-beliefs around writing. It also suggests that writing interventions that seek to reduce anxiety and increase undergraduate students’ self-efficacy with respect to writing may positively enhance students’ use of metacognitive writing strategies, and ultimately improve student writing outcomes.
On s’intéresse de plus en plus à promouvoir la métacognition parmi les étudiants des collèges et des universités car ce processus a été lié avec des résultats d’apprentissage positifs. Cette étude explore la relation qui existe entre l’anxiété que les étudiants ressentent devant les travaux d’écriture et l’efficacité personnelle tel que rapporté dans des questionnaires portant sur l’usage de stratégies d’écriture métacognitives remplis par des étudiants de premier cycle. À partir de données de sondages menés auprès d’étudiants de premier cycle d’une grande université d’Ontario, Canada, centrée sur la recherche, nous avons découvert que la réduction de l’anxiété ressentie devant les travaux d’écriture et l’augmentation de l’efficacité personnelle présentaient une association statistiquement significative avec les perceptions des étudiants qui utilisaient des stratégies d’écriture métacognitives. Ces résultats ont des implications à la fois théoriques et pratiques. Ils prouvent que la métacognition en écriture est influencée par des facteurs émotionnels, tels que le degré d’anxiété et la portée des auto-croyances en ce qui concerne les travaux d’écriture. Ils suggèrent également que les interventions d’écriture qui tentent de réduire l’anxiété et d’augmenter l’efficacité personnelle des étudiants en ce qui a trait à l’écriture pourraient améliorer de façon positive l’emploi fait par les étudiants de stratégies d’écriture métacognitives et, en fin de compte, améliorer les résultats des étudiants en matière d’écriture.
The Determinants of Financial Ratio Disclosures and Quality: Evidence from an Emerging market
Authors: Agyei-Mensah Ben k.
Published: April 2015

This study investigated the influence of firm-specific characteristics which include proportion of Non-Executive Directors, ownership concentration, firm size, profitability, debt equity ratio, liquidity and leverage on the extent and quality of financial ratios disclosed by firms listed on the Ghana Stock Exchange.The research was conducted through detailed analysis of the 2012 financial statements of  the listed firms.  Descriptive analysis was performed to provide the background statistics of the variables examined.  This was followed by regression analysis which forms the main data analysis.  The results of the extent of financial ratio disclosure level, mean of 62.78%, indicate that most of the firms listed on the Ghana Stock Exchange did not overwhelmingly disclose such ratios in their annual reports.  The results of the low quality of financial ratio disclosure mean of 6.64% indicate that the disclosures failed woefully to meet the International Accounting Standards Board's qualitative characteristics of relevance, reliability, comparability and understandability.The results of the multiple regression analysis show that leverage and return on investment are associated on a statistically significant level as far as the extent of financial ratio disclosure is concerned. Board ownership concentration and proportion of (independent) non-executive directors, on the other hand were found to be statistically associated with the quality of financial ratio disclosed. There is a significant negative relationship between ownership concentration and the quality of financial ratio disclosure.  This means that under a higher level of ownership concentration less quality financial ratios are disclosed. The findings also show that there is a significant positive relationship between board composition (proportion of non-executive directors) and the quality of financial ratio disclosure.  JEL CLASSIFICATION: G3, M1, M2, M4.
Gaps in Executive and Worker Compensation as an Organizational and Management Challenge
Authors: McFarlane Donovan A.
Published: April 2015

This paper examines the gaps in chief executive officer (CEO) and worker compensation by exploring the vital data of 10 corporations as uncovered in a study by NerdWallet.com on the differences in hourly compensation between CEOs and average hourly workers or employees. The author examines the problem of excessive compensation for CEOs as a major organizational challenge that affects perceptions of fairness by stakeholders, especially employees or workers whose contributions to organizational performance and success are not being adequately rewarded, but instead transferred to CEOs and other executives as companies increase revenues and profits through the sweat and toil of ordinary workers. The author argues that executive compensation should be linked to organizational results and performance, and examines the standards and considerations for determining fair wage and compensation, and from examining vital data on CEO compensation and average worker compensation, explores the implications for organizational change, including consideration of quality work life (QWL) investments. Several recommendations are made for meeting the challenge of excessive CEO compensation to include the following: (1) developing new approaches or methods of compensation that take worker rewards into consideration; (2) limiting CEO or executive compensation relative to established multiple of the average worker’s wage; (3) intervention and petition from governmental and administrative agencies including workers’ rights organizations for change; and (4) more compassionate leadership and management by organizational CEO and executives with increased concern for workers’ well-being. Employee Retention, Employee Satisfaction, Excessive Compensation, Executive Compensation, Fair Wage, Organizational Citizenship Behavior (OCB), Quality Work Life (QWL), Stakeholders.
From state control to network governance of primary education in Tanzania: has local empowerment been attained?
Authors: Masue Orest Sebastian , Swai Idda Lyatonga
Published: April 2015

Abstract Governance networks have recently become popular and apparently indispensable in public administration especially due to the fact that we are operating in the context of complex, fragmented and multi-layered societies. The purpose of this theoretical paper is to (1) delineate the concept of governance in terms of its three distinct modes (state control, market and networks/pluralist modes), (2) show how governance of primary education in Tanzania has changed along these three modes of governance and (3) comment on whether the change in the mode of governance of Primary Education in Tanzania from state control to governance networks has led to empowerment of the people at the grassroots levels. Our observation in this paper is that the move from the state control to network governance mode is too theoretical, and has not sufficiently led to empowerment of people at the grassroots levels in the governance of primary education. Therefore, this paper calls upon the state to willingly change radically from its culture from hierarchical control to authentic local empowerment.
Public Service Improvement: A case study of One Door Service in Lao People Democratic Republic
Authors: Onxayvieng Chantha , Tan Shukui , Darasen Viengsamay , Katiyalath Malasy , Kevreaksmey Pho
Published: April 2015

An analytical framework on One Door Service in this article derived from new public management that takes a coordinated, holistic approach to public service delivery. These service delivery approaches have become a famous and adaptable mode of administrative decentralization of government services in Laos, and gives strategic focus on governance and public administration reform for better service delivery. This article reviews these rationales in the conceptual introduction of One Door Service initiatives in Laos. The ODS has been justified mainly on managerial and governance grounds and viewed by government as a partial successful governance and public administration reform of early stage. The change of it is placed in public service improvement, using the collaborative customer interface model through the four sets of critical assessment challenge on governance, performance management, workforce and information sharing. The analysis assesses the performance by looking at the empirical results and draws on experiences on how One Door Service has been operating and providing services to citizens at the ground. With this knowledge of linkages with the concept of public service improvement in Laos, we can pose the question of whether the One Door Service project has achieved the aims of governance and public administration reform and benefited the majority of citizens. The overall image presented a positive and negative- a positive image is an innovative mode of service delivery which has expanded across the country in terms of establishing, but a negative image is an inadequate step for administrative reform during the design and implementation.
Sources of Information in Adoption of Sustainable Agricultural Practices as Perceived by Farmers in Sindh Province of Pakistan
Authors: Muhammad Ismail Kumbhar  , Har Bakhsh Makhijani  , Shuhabuddin Mughal  , Hameeda Masood Shah  , Naseer Ahmed Abbasi
Published: April 2015

Agriculture is the backbone of Pakistan’s economy in terms of providing food and employment and foreign exchange earnings. It contributes 21.9 percent to the gross domestic product (GDP). The importance of sustainable agriculture practices for the farmers to a large extent depends upon the effective sources of information. It is believed that farmers do not often make visit to the research stations, however, they obtained required knowledge from different sources like mass media, fertilizer agency, fellow farmers, radio, television, extension personnel and contact farmers. It is imperative to communicate sustainable agriculture practices to the farmers through various sources of information. This study used a descriptive research methodology the universe of study consisted of six districts of Sindh province comprising Larkana, Naushehro Feroze, Shaheed Benazirabad, Sanghar, Mirpurkhas and Badin. A sample of 180 farmers was randomly selected for the study. A well structured interview schedule was used to collect information from the small farmers on their personal and socio-economic characteristics and sources of information. The study found that about 36.11% of the respondents were youth having age group (26-35 years), while 66.67% of the respondents were married, however a large percentage (44.44%) maintained a range of small farmers having land 13-25 acres of land and 66.67% of the respondents having their primary education. In addition 66.67% of the respondents having farming experience between 6 to 10 years. The results of the study showed that the most frequently used sources of information about Sustainable Agriculture were Television Broadcast, Neighboring Farmer, Fertilizer and Herbicide Dealer and Seed Dealer, while slightly over half the farmers reported using information about Sustainable Agriculture from Public Extension Agent, Private Extension Agent, Research Workers, Farm Magazine and Publications, Local Newspapers, Relatives and Extension Materials. On the basis of the results and conclusion drawn from the study it is recommended that Government should establish farmers radio and television station for dissemination of the agricultural programs for sustainable agriculture in Sindh province. Sustainable agriculture programs should be broadcast through television and radio programs. Neighbor farmers and fertilizer herbicide dealers should be educated for sustainable agriculture practices.
Arthrodesis of a Distal Interphalangeal Joint in a wild African Buffalo (Syncerus caffer)
Authors: Shakespeare Anthony Scott
Published: April 2015

Intensification of wild ruminants has resulted in more lameness cases that are presented for medical and surgical intervention. Claw problems in these wild and often dangerous animals, although similar to those seen in domestic bovines often require quick decisions and speedy adaptations of generally accepted treatment and procedure protocols. The arthrodesis of the pedal joint in a buffalo cow is one such example.
Hvordan får man forfatterne til at indsætte DOI i deres kildehenvisninger?
Authors: Thestrup Jesper Boserup , Frederiksen Niels Erik
Published: April 2015

For at kunne tildele DOI til et tidsskrifts artikler er tidsskiftet forpligtet til at sikre, at der i litteraturhenvisningerne til de enkelte artikler indgår DOI (hvis referencen har et sådant). Dette kan tidsskriftchefen sikre som led i indleveringsprocessen.
Switching immune signals on and off
Authors: Chu Nam , Cole Philip A
Published: April 2015

Bruton's tyrosine kinase, an enzyme that is important for B cell function, can be activated in a number of ways.
Overview of the Purification of Recombinant Proteins
Authors: Wingfield Paul T.
Published: April 2015

When the first version of this unit was written in 1995, protein purification of recombinant proteins was based on a variety of standard chromatographic methods and approaches, many of which were described and mentioned throughoutCurrent Protocols in Protein Science. In the interim, there has been a shift toward an almost universal usage of the affinity or fusion tag. This may not be the case for biotechnology manufacture where affinity tags can complicate producing proteins under regulatory conditions. Regardless of the protein expression system, questions are asked as to which and how many affinity tags to use, where to attach them in the protein, and whether to engineer a self‐cleavage system or simply leave them on. We will briefly address some of these issues. Also, although this overview focuses onE.coli, protein expression and purification, other commonly used expression systems are mentioned and, apart from cell‐breakage methods, protein purification methods and strategies are essentially the same. © 2015 by John Wiley & Sons, Inc.
Site‐Specific Recombinational Cloning Using Gateway and In‐Fusion Cloning Schemes
Authors: Park Jaehong , Throop Andrea L. , LaBaer Joshua
Published: April 2015

The comprehensive study of protein structure and function, or proteomics, depends on the obtainability of full‐length cDNAs in species‐specific expression vectors and subsequent functional analysis of the expressed protein. Recombinational cloning is a universal cloning technique based on site‐specific recombination that is independent of the insert DNA sequence of interest, which differentiates it from classical restriction enzyme−based cloning methods. Recombinational cloning enables rapid and efficient parallel transfer of DNA inserts into multiple expression systems. This unit summarizes strategies for generating expression‐ready clones using the most popular commercial recombinational cloning technologies, Gateway (Life Technologies) and In‐Fusion (Clontech). © 2015 by John Wiley & Sons, Inc.
Use of Proteasome Inhibitors
Authors: Downey Sondra L. , Florea Bogdan I. , Overkleeft Herman S. , Kisselev Alexei F.
Published: April 2015

Proteasome inhibitors are indispensable research tools in immunology and cell biology. With numerous proteasome inhibitors available commercially, choosing the appropriate compound for a biological experiment may be challenging, especially for a novice. This unit provides an overview of the proteasome inhibitors commonly used in research. It discusses how to select an appropriate highly specific inhibitor, its concentration, and length of exposure for mammalian cell culture experiments. In addition, assays that can be used to confirm proteasome inhibition are discussed. © 2015 by John Wiley & Sons, Inc.
Use of Affymetrix Arrays in the Diagnosis of Gene Copy‐Number Variation
Authors: Zahir Farah R. , Marra Marco A.
Published: April 2015

Diagnosing constitutional pathogenic copy number variants (CNVs) requires detecting submicroscopic segmental chromosomal imbalances. The Affymetrix GeneChip mapping array was one of the initial microarray platforms used to measure duplication and deletion of genetic material in DNA samples. Unlike oligonucleotide microarrays from NimbleGen and Agilent, developed around the same time to infer copy number status for the DNA sequence covered by the probe, the Affymetrix GeneChip system used 25‐mer oligonucleotide probes designed to interrogate SNPs. Thus, it was possible to use the Affymetrix ‘SNP chips’ to both identify SNPs and to identify copy number status. Affymetrix now offers the CytoScan microarray platforms, which are optimized for copy‐number analyses, and provides accompanying software. They also offer several other microarray platforms suitable for copy‐number analyses. Here we discuss the application of the CytoScan high‐density (HD) platform for the detection of genomic imbalance. We provide an overview of the sequence of computational analyses involved in identifying pathogenic CNVs and highlight important parameters for consideration in assessing the pathogenicity of a detected CNV. © 2015 by John Wiley & Sons, Inc.
Probe‐Directed Degradation (PDD) for Flexible Removal of Unwanted cDNA Sequences from RNA‐Seq Libraries
Authors: Archer Stuart K. , Shirokikh Nikolay E. , Preiss Thomas
Published: April 2015

Most applications for RNA‐seq require the depletion of abundant transcripts to gain greater coverage of the underlying transcriptome. The sequences to be targeted for depletion depend on application and species and in many cases may not be supported by commercial depletion kits. This unit describes a method for generating RNA‐seq libraries that incorporates probe‐directed degradation (PDD), which can deplete any unwanted sequence set, with the low‐bias split‐adapter method of library generation (although many other library generation methods are in principle compatible). The overall strategy is suitable for applications requiring customized sequence depletion or where faithful representation of fragment ends and lack of sequence bias is paramount. We provide guidelines to rapidly design specific probes against the target sequence, and a detailed protocol for library generation using the split‐adapter method including several strategies for streamlining the technique and reducing adapter dimer content. © 2015 by John Wiley & Sons, Inc.
Cell Proliferation Method: Click Chemistry Based on BrdU Coupling for Multiplex Antibody Staining
Authors: Cappella Paolo , Gasparri Fabio , Pulici Maurizio , Moll Jürgen
Published: April 2015

Determination of incorporation of the thymidine analog 5‐bromo‐2′‐deoxyuridine (BrdU) into DNA is a widely used method to analyze the cell cycle. However, DNA denaturation is required for BrdU detection with the consequence that most protein epitopes are destroyed and their immunocytochemical detection for multiplex analysis is not possible. A novel assay is presented for identifying cells in active S‐phase that does not require the DNA denaturation step but nevertheless detects BrdU. For this purpose, cells were pulsed for a short time by 5‐ethynyl‐2′‐deoxyuridine (EdU) which is incorporated into DNA. The nucleotide‐exposed ethynyl residue was then derivatized by a copper‐catalyzed cycloaddition reaction (“click chemistry” coupling) using a BrdU azide probe. The resulting DNA‐bound bromouracil moieties were then detected by commercial anti‐BrdU monoclonal antibodies without the need for a denaturation step. This method has been tested using several cell lines and is more sensitive than traditional BrdU and allows multicolor and multiplex analysis in flow cytometry (FCM) and image‐based cytometry. © 2015 by John Wiley & Sons, Inc.
Multiday thermospheric density oscillations associated with variations in solar radiation and geomagnetic activity
Authors: Xu Jiyao , Wang Wenbin , Zhang Shunrong , Liu Xiao , Yuan Wei
Published: April 2015

Thermospheric densities observed by Challenging Minisatellite Payload and Gravity Recovery and Climate Experiment satellites during 2002–2010 and the globally averaged thermospheric densities from 1967 to 2007 have been used to investigate latitudinal, longitudinal, and height dependences of the multiday oscillations of thermospheric densities. The data show that the main multiday oscillations in thermospheric densities are 27, 13.5, 9, and 7 day oscillations. The high‐correlation coefficients between the density oscillations and the F10.7 or Ap index indicate that these oscillations are externally driven. The 27 day density oscillation, being the strongest, is induced by variations in solar radiation, as well as recurrent geomagnetic activity that is the result of corotating interaction regions (CIRs) and high‐speed solar wind streams of coronal hole origin. Density oscillations at periods of 13.5, 9, and 7 days at solar minimum and during the declining phase are stronger than those at solar maximum. These oscillations are mainly associated with recurrent geomagnetic activity due to coronal hole high‐speed streams and CIRs. The multiday, periodic oscillations of thermospheric density exhibit strong latitudinal and longitudinal variations in the geomagnetic coordinate and oscillate synchronously at different heights. Oscillations with zonal wave number 0 oscillate globally, whereas those with nonzero wave numbers are strong at high geomagnetic latitudes, and hemispherically asymmetric. They are stronger in the Southern Hemisphere. The spectral distributions of thermospheric densities at different heights have almost the same latitude and longitude structures, but the spectral magnitudes increase with height.
A prediction model for the global distribution of whistler chorus wave amplitude developed separately for two latitudinal zones
Authors: Kim Jin‐Hee , Lee Dae‐Young , Cho Jung‐Hee , Shin Dae‐Kyu , Kim Kyung‐Chan , Li Wen , Kim Thomas K.
Published: April 2015

Whistler mode chorus waves are considered to play a central role in accelerating and scattering electrons in the outer radiation belt. While in situ measurements are usually limited to the trajectories of a small number of satellites, rigorous theoretical modeling requires a global distribution of chorus wave characteristics. In the present work, by using a large database of chorus wave observations made on the Time History of Events and Macroscale Interactions during Substorms satellites for about 5 years, we develop prediction models for a global distribution of chorus amplitudes. The development is based on two main components: (a) the temporal dependence of average chorus amplitudes determined by correlating with the preceding solar wind and geomagnetic conditions as represented by the interplanetary magnetic field (IMF) Bz and AE index and (b) the determination of spatial distribution pattern of chorus amplitudes, specifically, the profiles in L in all 2 h magnetic local time zones, which are categorized by activity levels of either the IMF Bz or AE index. Two separate models are developed: one based only on the IMF Bz and the other based only on AE. Both models predict chorus amplitudes for two different latitudinal zones separately: |magnetic latitude (MLAT)| < 10°, and |MLAT| = 10°–25°. The model performance is measured by the coefficient of determination R2 and the rank‐order correlation coefficient (ROCC) between the observations and model prediction results. When tested for a new data interval of ~1.5 years, the AE‐based model works slightly better than the IMF Bz‐based model: for the AE‐based model, the mean R2 and ROCC values are ~0.46 and ~0.78 for |MLAT| < 10°, respectively, and ~0.4 and ~0.74 for |MLAT| = 10°–25°, respectively; for the IMF Bz‐based model, the mean R2 and ROCC values are ~0.39 and ~0.74 for |MLAT| < 10°, respectively, and ~0.33 and ~0.70 for |MLAT| = 10°–25°, respectively. We provide all of the model information in the text and supporting information so that the developed chorus models can be used for the existing outer radiation belt electron models.
Very low frequency earthquakes in Cascadia migrate with tremor
Authors: Ghosh Abhijit , Huesca‐Pérez Eduardo , Brodsky Emily , Ito Yoshihiro
Published: April 2015

We find very low frequency earthquakes (VLFEs) in Cascadia under northern Washington during 2011 episodic tremor and slip event. VLFEs are rich in low‐frequency energy (20–50 s) and depleted in higher frequencies (higher than 1 Hz) compared to local earthquakes. Based on a grid search centroid moment tensor inversion, we find that VLFEs are located near the plate interface in the zone where tremor and slow slip are observed. In addition, they migrate along strike with tremor activity. Their moment tensor solutions show double‐couple sources with shallow thrust mechanisms, consistent with shear slip at the plate interface. Their magnitude ranges between Mw 3.3 and 3.7. Seismic moment released by a single VLFE is comparable to the total cumulative moment released by tremor activity during an entire episodic tremor and slip event. The VLFEs contribute more seismic moment to this episodic tremor and slip event than cumulative tremor activity and indicate a higher seismic efficiency of slow earthquakes in Cascadia than previously thought. Spatiotemporal correlation of VLFE and tremor activity suggests that they are the results of the same physical processes governing slow earthquakes.
Nonlocal impacts of the Loop Current on cross‐slope near‐bottom flow in the northeastern Gulf of Mexico
Authors: Nguyen Thanh‐Tam , Morey Steven L. , Dukhovskoy Dmitry S. , Chassignet Eric P.
Published: April 2015

Cross‐slope near‐bottom motions near De Soto Canyon in the northeastern Gulf of Mexico are analyzed from a multidecadal ocean model simulation to characterize upwelling and downwelling, important mechanisms for exchange between the deep ocean and shelf in the vicinity of the 2010 BP Macondo well oil spill. Across the continental slope, large‐scale depression and offshore movement of isopycnals (downwelling) occur more frequently when the Loop Current impinges upon the West Florida Shelf slope farther south. Upwelling and onshore movement of isopycnals occurs with roughly the same likelihood regardless of Loop Current impingement on the slope. The remote influence of Loop Current on the De Soto Canyon region downwelling is a consequence of a high‐pressure anomaly that extends along the continental slope emanating from the location of Loop Current impact.
Potential for larger earthquakes in the East San Francisco Bay Area due to the direct connection between the Hayward and Calaveras Faults
Authors: Chaussard E. , Bürgmann R. , Fattahi H. , Nadeau R. M. , Taira T. , Johnson C. W. , Johanson I.
Published: April 2015

The Hayward and Calaveras Faults, two strike‐slip faults of the San Andreas System located in the East San Francisco Bay Area, are commonly considered independent structures for seismic hazard assessment. We use Interferometric Synthetic Aperture RADAR to show that surface creep on the Hayward Fault continues 15 km farther south than previously known, revealing new potential for rupture and damage south of Fremont. The extended trace of the Hayward Fault, also illuminated by shallow repeating micro‐earthquakes, documents a surface connection with the Calaveras Fault. At depths greater than 3–5 km, repeating micro‐earthquakes located 10 km north of the surface connection highlight the 3‐D wedge geometry of the junction. Our new model of the Hayward and Calaveras Faults argues that they should be treated as a single system with potential for earthquake ruptures generating events with magnitudes greater than 7, posing a higher seismic hazard to the East San Francisco Bay Area than previously considered.
Northern Adriatic meteorological tsunamis: Assessment of their potential through ocean modeling experiments
Authors: Šepić Jadranka , Vilibić Ivica , Fine Isaac
Published: April 2015

Potential for generation of meteotsunami waves via open ocean resonance has been documented for the shallow northern Adriatic, based on a set of barotropic numerical modeling experiments. Model simulations were forced by a bell‐shaped traveling atmospheric (air pressure, wind) disturbance, with shape and propagation parameters chosen in accordance with measurements done during several observed northern Adriatic meteotsunamis. Air pressure disturbances were found to generate much larger meteotsunami waves than wind disturbances, with wind disturbances having a limited influence in the very coastal and shallow areas only. Numerical simulations reveal that the most important factor for generation of large meteotsunami waves is matching between the speed of the atmospheric disturbance and the speed of long‐ocean waves. Already a small (∼10%) deviation from resonant conditions stops the wave growth and dramatically decreases height of predicted waves. A train of atmospheric disturbances can significantly increase maximum wave heights at selected locations at which multiple reflections and superimpositions of meteotsunami waves occur. Sensitivity of model simulations to resonant conditions and limited cross‐propagation width of atmospheric disturbance explain the localization of destructive meteotsunami waves in a limited area during destructive historic events. Mapping of maximum predicted wave heights indicates places with large meteotsunami hazard potential, matching the locations where real events were observed, and may be a useful tool for assessing vulnerability and risks in coastal areas during extreme sea level events.
The Development of Alternative Brake Systems
Authors: Gombert Bernd D.M. , Schautt Martin , Roberts Richard P.
Published: April 2015

Over the past 15 years or so, there has been considerable interest within the automobile industry in dry electrically powered brake systems. This has been driven by a variety of different reasons, including the inherent compatibility with electronic higher level vehicle systems, a desire to remove hydraulic components and so simplify assembly and maintenance, improved passive safety (pedal), more flexibility in pedal design and feel, and simpler tuning of systems by means of software. While there is still no production system on the mass market, the trend toward more electric vehicles will only strengthen the motivation to introduce them.

In this chapter, we explain some of the benefits of dry brake‐by‐wire (BBW) systems in the context of current developments. We then introduce a selection of alternative approaches to the problem, both in terms of brake actuator construction and vehicle concepts. Next, we address the challenges facing any supplier orOEMwho intends to introduce such a system. These help explain why there is still no such system on the market, despite many optimistic forecasts at the turn of the millennium. Some of the issues addressed during the development of the SiemensVDOelectronic wedge brake (EWB) are then briefly discussed. Finally, we summarize the situation in some brief conclusions.
Batteries Indication and Management
Authors: Kortschak Bernhard
Published: April 2015

The aim of this chapter is to present concepts for the indication of the state of traction batteries for hybrid or full electric vehicles, namely the calculation of the state‐of‐charge, state‐of‐health, and state‐of‐function of a battery. With respect to battery management, this chapter discusses the control aspects and the related components, which can be managed directly by the battery controller. In addition, the realization in hardware and software is presented.
Exhaust Emissions
Authors: Matti Maricq M.
Published: April 2015

Emissions regulations present a growing challenge in the design of new vehicles. The necessity to lower pollutants to ultra low levels requires careful tuning of the engine with progressively more elaborate aftertreatment systems. At the same time, engines must be made more efficient and vehicles lighter to meet requirements for reduced greenhouse gas emissions. The brunt of engine calibration and aftertreatment development is conducted with engine and chassis dynamometer systems coupled to sensitive instrumentation that can detect parts per million levels of pollutants in vehicle exhaust. This chapter reviews the current state of the art in this area. It examines the sampling systems used to probe the myriads of constituents present in combustion exhaust. The chemical compounds and particulate matter are analyzed by a wide array of instrumentation. These are increasingly evolving in capability, both in terms of sensitivity and time response. This chapter describes the traditional methods for the detection of hydrocarbons,NOx,CO, andPM. It further details advances inFTIRmethods aimed at detectingNO,NO2,N2O,NH3, non‐methane organics, and other species, and new developments in aerosol instrumentation used for real‐time measurement of particle size distributions and number and mass emissions.