SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

Summary: The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations are either designed as monolithic protein database searching tools or are embedded into other tools. To facilitate easy integration of the fast Single Instruction Multiple Data (SIMD) SW algorithm into third party software, we wrote a C/C++ library, which extends Farrars Striped SW (SSW) to return alignment information in addition to the optimal SW score. Availability: SSW is available both as a C/C++ software library, as well as a stand alone alignment tool wrapping the librarys functionality at https://github.com/mengyao/Complete- Striped-Smith-Waterman-Library Contact: [email protected]: 3 pages, 2 figure

Auswirkung von Politikmaßnahmen auf das Innovationsgeschehen im Bereich der Mikro-Kraft-Wärme-Kopplung

Der Einsatz von Kraft-Wärme-Kopplung (KWK), also die gekoppelte Erzeugung von Strom und Wärme, wird in Deutschland durch eine Reihe von Gesetzes-maßnahmen gefördert. Seit einigen Jahren ist jedoch kein weiterer Anstieg des Anteils von KWK an der Stromerzeugung mehr zu beobachten. Auch entwickelt sich der Markt für Mikro-KWK-Anlagen, also Anlagen, die zum Einsatz in Ein- und Zweifamilienhäusern geeignet sind, bislang nur zögerlich. Aus diesen Gründen wird in der vorliegenden Arbeit eine qualitative Einschätzung der Auswirkungen von Politikmaßnahmen auf das Innovationsgeschehen im Mikro-Kraft-Wärme-Kopplungs-Bereich vorgenommen. Hierfür wurde eine Expertenbefragung unter fünf Produktmanagern. In der Expertenbefragung werden drei Hauptfragestellungen untersucht, die sich mit der Innovationsaktivität der Unternehmen, der Einordnung der Bedeutung verschiedener Politikmaßnahmen sowie den Erwartungen der Teilnehmer an die zukünftigen Entwicklungen der Technologie und ihrer Rahmenbedingun-gen befassen. Das Ergebnis der Befragung ist, dass die Teilnehmer die positive Wirkung der direkten Fördermaßnahmen auf die Diffusion der Technologie zu weiten Teilen aufgehoben sehen durch technische und administrative Hürden im Bereich der Anschlussbedingungen sowie der Abrechnung des Betriebs der Anlagen. Trotz der direkten Förderung der Technologie hat somit der regulatori-sche Rahmen einen negativen Einfluss auf die Technologieentwicklung. von Unternehmen aus der Branche durchgeführt. Als Handlungsempfehlungen für eine effizientere Gestaltung der politischen Rahmenbedingungen für die Technologie ergibt sich die Forderung nach Konsistenz und langfristiger Verlässlichkeit von Politikmaßnahmen. Die teilnehmenden Hersteller geben an, dass sie langfristig die Unabhängigkeit von direkten Fördermaßnahmen anstreben, so dass der Fokus für weitere Politikmaßnahmen auf den regulatorischen Rahmenbedingungen und dem Abbau der technischen und administrativen Hürden liegen sollte. --

Network-analysis-guided synthesis of weisaconitine D and liljestrandinine.

General strategies for the chemical synthesis of organic compounds, especially of architecturally complex natural products, are not easily identified. Here we present a method to establish a strategy for such syntheses, which uses network analysis. This approach has led to the identification of a versatile synthetic intermediate that facilitated syntheses of the diterpenoid alkaloids weisaconitine D and liljestrandinine, and the core of gomandonine. We also developed a web-based graphing program that allows network analysis to be easily performed on molecules with complex frameworks. The diterpenoid alkaloids comprise some of the most architecturally complex and functional-group-dense secondary metabolites isolated. Consequently, they present a substantial challenge for chemical synthesis. The synthesis approach described here is a notable departure from other single-target-focused strategies adopted for the syntheses of related structures. Specifically, it affords not only the targeted natural products, but also intermediates and derivatives in the three families of diterpenoid alkaloids (C-18, C-19 and C-20), and so provides a unified synthetic strategy for these natural products. This work validates the utility of network analysis as a starting point for identifying strategies for the syntheses of architecturally complex secondary metabolites

A longitudinal study of differences in staff assaults by responses to residents in a forensic hospital

Title from PDF of title page (University of Missouri--Columbia, viewed on Feb. 15, 2010).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Dissertation advisor: Dr. Martha Markward.Vita.Ph. D. University of Missouri--Columbia 2009.This study examined psychiatric hospital staff interaction behaviors that have been found to increase the risk of client assault. Observers utilizing the Staff-Resident Interaction Chronograph instrument collected data related to interactions between hospital staff and clients on six social learning wards in a Midwestern forensic psychiatric hospital over a ten year period. Limit setting, activity demand, and denial of requests have been identified in the literature as staff behaviors that increase risk of assault by clients. Utilizing independent samples t-tests, this study compared rates of engagement in these types of interactions between assaulted staff members and non-assaulted staff members to determine if there are significant differences between the two groups. Results show that staff members who engage in limit setting, activity demand, and denial of request are assaulted more frequently than those who don't. This study addresses the need for utilization of a reliable and valid instrument to determine if staff member responses to client behaviors increases risk of client assault.Includes bibliographical reference

Reducing Road Transport Carbon Emissions: Options for Government Policy

Worldwide, carbon emissions from fossil fuel use in the transport sector are increasing faster than carbon emissions from any other sector. The transport modes responsible for most of this carbon emission growth are car travel, road freight and air transport (IPCC 2001). New Zealand statistics reflect this trend and show that New Zealand transport sector carbon emissions grew by 42% between 1990 and 2001 (MfE 2006). The growth in New Zealand transport sector carbon emissions is linked to growth in road transport use, which is projected to increase further in the near future (WRC 1999; NZGovt 2002; WCC 2004; WCC 2006). However, carbon emissions (including those from road transport) are playing an increasing role in climate forcing and global climate change (IPCC 2001), and road transport use is increasingly recognised as a contributing factor in a number of local environmental and social challenges (NZGovt 2002; Ray 2006)

Age-dependent motor dysfunction due to neuron-specific disruption of stress-activated protein kinase MKK7.

c-Jun N-terminal kinase (JNK) is a member of the mitogen-activated protein kinase family and controls various physiological processes including apoptosis. A specific upstream activator of JNKs is the mitogen-activated protein kinase kinase 7 (MKK7). It has been reported that MKK7-JNK signaling plays an important regulatory role in neural development, however, post-developmental functions in the nervous system have not been elucidated. In this study, we generated neuron-specific Mkk7 knockout mice (MKK7 cKO), which impaired constitutive activation of JNK in the nervous system. MKK7 cKO mice displayed impaired circadian behavioral rhythms and decreased locomotor activity. MKK7 cKO mice at 8 months showed motor dysfunctions such as weakness of hind-limb and gait abnormality in an age-dependent manner. Axonal degeneration in the spinal cord and muscle atrophy were also observed, along with accumulation of the axonal transport proteins JNK-interacting protein 1 and amyloid beta precursor protein in the brains and spinal cords of MKK7 cKO mice. Thus, the MKK7-JNK signaling pathway plays important roles in regulating circadian rhythms and neuronal maintenance in the adult nervous system

MARTA: Magyarországi Részletes Talajfizikai Adatbázis létrehozása és alkalmazása a talaj vízgazdálkodásának jellemzésére szélsőséges időjárási körülmények között = MARTA: Development and use of a database of hydrophysical properties of Hungarian soils to characterize the soil water management under extreme weather conditions

A pályázat keretében létrehozott MARTHA (Magyarországi Részletes Talajfizikai és Hidrológiai Adatbázis) adatbázis a hazai talajfizikai laboratóriumokban mért talajfizikai és vízgazdálkodási mérési eredmények (és a hozzájuk kapcsolódó talajtani alapadatok) egységes rendszerbe szervezett gyűjteménye. Reprezentativitása kiterjed az ország egész területére. Alapot nyújt országos és területi pedotranszfer függvények előállítására éppúgy, mint a talajtérképi információk alapján történő csoportbecslési módszerek kidolgozására. A jelenlegi MARTHA ver 2.0 adatbázis mintegy 4000 talajszelvény 15 000 talajrétegének adatait tartalmazza. | The Hungarian Detailed Soil Hydrophysical Database, called MARTHA ver2.0 was developed to collect laboratory test results of physical properties, water management characteristics and basic soil properties. Datasets of the database cover the whole area of Hungary and are organized according to a uniform metadata model and presented in a harmonized manner. The MARTHA database provides a basis for the development of pedotransfer functions for regional or country scale applications. It can be also used for the development of group estimate methods based on soil map information. The current version (v2.0) of the MARTHA databases holds data of some 15000 soil layers from approximately 4000 soil profiles