bluuebunny/crossref_metadata_2025 huggingface dataset:
Kriminalität und Konjunktur
Authors: Schwarz Herbert
Published: December 2008

The aim of the present treatise is to illustrate the connection between the ever-changing economic situation and the anti-social activity of a group living under a uniform juridical system. In the sphere of anti-social activity which presents so many aspects—numerically summarized in the statistics of morality— the student is confronted with several conflicting theories in causality research. The extremes are repressented by the “indeterminist theory of free will” and the “determinist doctrines of environment and heredity”. Whichever theory is accepted is of decisive importance in considering the principles of the policy of criminal law to be applied and its administration at any given period.

The present investigation does not confine itself in the matter of deduction to one of the above theories. It also avoids the analysis of isolated cases. It endeavours to obtain some insight into the functional and causal relationships between the two classes of phenomena by comparing data provided by mass statistics relating to economic and anti-social life.

After introductory expositions on both the significance and nature of the position of the problems and the method underlying the investigation, the historical part of the study deals with the phenomena of crimes against property and the connection between them and economic conditions in Germany during the years 1882—1936. This period is divided into three sections. The years 1882—1913 cover the period of steady development. The war period (1914—18), owing to lack of statistical data, is only treated summarily. In the post-war section the law reforms begun in 1933 are not taken into account, because they did not yet cover the legislative repression of crimes against property.
Hoofdtrekken der Nederlandsche Arbeidersbeweging in de jaren 1876 tot 1886
Authors: RÜter A. J. C.
Published: December 2008

The present article is the second part of a study on the Dutch working-class movement between 1876 and 1886, (the first part was published in Vol. III of this Review), and deals with the economic crisis and the unemployment problem in the years 1884 to 1886.

The economic position of Holland was very bad at that time. Apart from an agricultural crisis, which set in about 1875, a crisis in commerce and industry, especially in ship-building and other building trades, made itself felt after 1883. The number of unemployed was considerable throughout the country; it was particularly great, however, in the large towns, to which numerous labourers from the rural districts had migrated. The author tries to ascertain the magnitude of this unemployement on the strength of certain figures, which, although incomplete, are important as the first data on the unemployment in Holland in the 19th century. Then follows an investigation into the methods of fighting this unemployment, which brings out that, generally speaking, both the government and the individual municipalities were of the opinion that interference in this matter did not fall within their sphere of action. When the normal church- and municipal dole proved to be insufficient, private persons were expected to provide for the extra wants of the poor. This was indeed the case in Amsterdam, Rotterdam, and various smaller towns in the form of a special dole and the organization of relief work. Unemployment insurance was practically not yet thought of at that time.
Ionospheric storm time dynamics as seen by GPS tomography and in situ spacecraft observations
Authors: Pokhotelov D. , Mitchell C. N. , Spencer P. S. J. , Hairston M. R. , Heelis R. A.
Published: December 2008

During major geomagnetic storms anomalous enhancements of the ionospheric density are seen at high and middle latitudes. A number of physical mechanisms have been invoked to explain these storm time density anomalies including an expansion of high‐latitude electric plasma convection to midlatitudes, thermospheric neutral winds, and changes in the ionospheric composition. However, it remains unclear which mechanism plays the dominant role in the formation of storm time density anomalies, partly because of insufficient coverage of the measurements of global electric convection and thermospheric winds at midlatitudes. This paper describes a novel technique for extracting the storm time E × B convection boundary from in situ measurements of plasma bulk motion obtained by LEO DMSP satellites. The convection boundary estimated from the DMSP data during major magnetic storm of 20 November 2003 has been compared with the global distributions of the ionospheric plasma deduced from characteristics of GPS signals acquired by a ground‐based network of GPS receivers. The tomographic inversion of GPS data using a three‐dimensional time‐dependent inversion technique reveals the spatial and temporal evolution of the storm time density anomaly. Comparison between the tomographic reconstructions of the ionospheric plasma distributions and in situ DMSP measurements of plasma bulk motion suggests that the convective flow expanded low enough in latitude to encompass, in part, the formation of the midlatitude TEC anomaly. Some features of the TEC dynamics observed during the 20 November 2003 storm, however, suggest that mechanisms other than the expanded ionospheric convection (such as thermospheric neutral winds) are also involved in the formation of the midlatitude anomaly.
Wind stress measurements from the QuikSCAT‐SeaWinds scatterometer tandem mission and the impact on an ocean model
Authors: Lee Tong , Wang Ou , Tang Wenqing , Liu W. Timothy
Published: December 2008

We examine diurnal signals captured by the QuikSCAT‐SeaWinds scatterometer tandem mission (April–October 2003) and their impact on ocean model simulation. The diurnal variability captured by twice‐daily scatterometer wind from the tandem mission is substantially larger than that estimated by the National Centers for Environmental Prediction (NCEP) reanalysis product (even with a 6‐hourly interval in the latter). Consequently, the impact of diurnal wind on model sea surface temperature (SST) is significantly larger with scatterometer than with NCEP winds because of stronger vertical mixing caused by the twice‐daily scatterometer wind. This is consistent with previous studies that high‐frequency wind at the ocean's inertial frequencies enhances vertical mixing through resonant inertial oscillations. The weak vertical mixing associated with daily scatterometer winds causes warm bias of SST (relative to that resulting from twice‐daily scatterometer wind) and larger deviation from observations. The warm bias reaches several degrees Celsius in midlatitude oceans during summertime and can accumulate with time. Heat flux correction that attempts to account for the feedback of SST would propagate the error in wind and vertical mixing to heat flux without correcting the error source. Because of this error compensation, caution is needed in the interpretation of SST budget resulting from ocean models and data assimilation outputs based on wind products that do not adequately resolve diurnal variability. Our findings highlight the need to resolve diurnal wind in future scatterometer missions. Our study assumes that wind differences between the two scatterometers are primarily due to the sampling of diurnal cycle at different times. However, potential bias between the two needs further investigations.
Ground‐based infrared retrievals of optical depth, effective radius, and composition of airborne mineral dust above the Sahel
Authors: Turner D. D.
Published: December 2008

Mineral dust aerosol optical depth (AOD) at 11 μm and effective radius are retrieved from ground‐based spectral infrared (8–13 μm) radiance observations collected in Niamey, Niger, in 2006 with the Atmospheric Radiation Measurement (ARM) mobile facility. The algorithm used in this study has the ability to differentiate between two different mineral types, allowing the AOD and effective radius of each mineral to be retrieved as long as the minerals have significant and spectrally different absorption bands in the infrared. Kaolinite, gypsum, and quartz, common minerals found in African deserts, have different infrared absorption features and are used in this work. The mineral combination that yielded the best fit to the observations, after accounting for the increased degrees of freedom in the dual mineral fits, was identified as the “radiatively significant” composition of the dust. The results were analyzed as function of period (premonsoon, early monsoon, late monsoon, and postmonsoon) as well as by back‐trajectory direction. High‐AOD events occurred in all four periods, with more high‐AOD events occurring during the drier premonsoon and postmonsoon periods. Kaolinite is an important component to the dust, with 94% of the retrievals having a significant amount of this mineral. Kaolinite + gypsum was determined to fit the spectral observations the best in nearly two thirds of the observations. Additionally, the amount of gypsum was dependent on the back‐trajectory direction, with a larger fraction of the total AOD due to gypsum when the flow was from east of the Niamey site.
Mineral dust plume evolution over the Atlantic from MISR and MODIS aerosol retrievals
Authors: Kalashnikova Olga V. , Kahn Ralph A.
Published: December 2008

We demonstrate how Multiangle Imaging Spectroradiometer (MISR) and Moderate Resolution Imaging Spectroradiometer (MODIS) space‐based aerosol products provide complementary information, characterizing (1) transported desert dust plume extent over water, (2) aerosol optical thickness (AOT) evolution, and (3) particle size sensitivity and fraction spherical evolution for the thicker parts of these plumes. MODIS provides more extensive coverage, whereas MISR's multiangle retrievals include dust properties and fill in areas where glint precludes MODIS optical depth retrievals, increasing by up to 50% dust plume surface area coverage compared to MODIS‐only observations. These results can be used to improve dust aerosol representations in climate, forecast, and transport models. Extensive comparison of MISR and MODIS AOT retrievals with Aerosol Robotic Network (AERONET) observations in dusty regions show accuracies of about 20%; MISR Angstrom exponent is predominantly less than 1, in reasonably good agreement with AERONET. For four selected North African dust transport events, combined MISR and MODIS observations map systematic changes in retrieved plume surface area, on the basis of AOT contours; these reflect differences in aerosol dispersion and removal rates that must be reproduced by models. Within MISR retrieval uncertainties, Angstrom exponent and AOT fraction spherical are lower in the optically thicker parts of the plume by up to 30% and increase as the plume is transported across the ocean, as would be expected; retrieved single‐scattering albedo values are ∼0.98 for all stages of plume evolution. For the cases studied, AERONET shows similar property patterns at points on either side of the Atlantic and indicates ∼15% decrease in aerosol coarse mode effective radius during transoceanic transport.
Spatial and temporal variations in DOM composition in ecosystems: The importance of long‐term monitoring of optical properties
Authors: Jaffé R. , McKnight D. , Maie N. , Cory R. , McDowell W. H. , Campbell J. L.
Published: December 2008

Source, transformation, and preservation mechanisms of dissolved organic matter (DOM) remain elemental questions in contemporary marine and aquatic sciences and represent a missing link in models of global elemental cycles. Although the chemical character of DOM is central to its fate in the global carbon cycle, DOM characterizations in long‐term ecological research programs are rarely performed. We analyzed the variability in the quality of 134 DOM samples collected from 12 Long Term Ecological Research stations by quantification of organic carbon and nitrogen concentration in addition to analysis of UV‐visible absorbance and fluorescence spectra. The fluorescence spectra were further characterized by parallel factor analysis. There was a large range in both concentration and quality of the DOM, with the dissolved organic carbon (DOC) concentration ranging from less than 1 mgC/L to over 30 mgC/L. The ranges of specific UV absorbance and fluorescence parameters suggested significant variations in DOM composition within a specific study area, on both spatial and temporal scales. There was no correlation between DOC concentration and any DOM quality parameter, illustrating that comparing across biomes, large variations in DOM quality are not necessarily associated with corresponding large ranges in DOC concentrations. The data presented here emphasize that optical properties of DOM can be highly variable and controlled by different physical (e.g., hydrology), chemical (e.g., photoreactivity/redox conditions), and biological (e.g., primary productivity) processes, and as such can have important ecological consequences. This study demonstrates that relatively simple DOM absorbance and/or fluorescence measurements can be incorporated into long‐term ecological research and monitoring programs, resulting in advanced understanding of organic matter dynamics in aquatic ecosystems.
An oligarchic microbial assemblage in the anoxic bottom waters of a volcanic subglacial lake
Authors: Gaidos Eric , Marteinsson Viggo , Thorsteinsson Thorsteinn , Jóhannesson Tomas , Rúnarsson Árni Rafn , Stefansson Andri , Glazer Brian , Lanoil Brian , Skidmore Mark , Han Sukkyun , Miller Mary , Rusch Antje , Foo Wilson
Published: December 2008

In 2006, we sampled the anoxic bottom waters of a volcanic lake beneath the Vatnajökull ice cap (Iceland). The sample contained 5 × 105 cells per ml, and whole-cell fluorescent in situ hybridization (FISH) and PCR with domain-specific probes showed these to be essentially all bacteria, with no detectable archaea. Pyrosequencing of the V6 hypervariable region of the 16S ribosomal RNA gene, Sanger sequencing of a clone library and FISH-based enumeration of four major phylotypes revealed that the assemblage was dominated by a few groups of putative chemotrophic bacteria whose closest cultivated relatives use sulfide, sulfur or hydrogen as electron donors, and oxygen, sulfate or CO2 as electron acceptors. Hundreds of other phylotypes are present at lower abundance in our V6 tag libraries and a rarefaction analysis indicates that sampling did not reach saturation, but FISH data limit the remaining biome to <10–20% of all cells. The composition of this oligarchy can be understood in the context of the chemical disequilibrium created by the mixing of sulfidic lake water and oxygenated glacial meltwater.
Variant c-type cytochromes as probes of the substrate specificity of the E. coli cytochrome c maturation (Ccm) apparatus
Authors: Allen James W. A. , Sawyer Elizabeth B. , Ginger Michael L. , Barker Paul D. , Ferguson Stuart J.
Published: December 2008

c-type cytochromes are normally characterized by covalent attachment of the iron cofactor haem to protein through two thioether bonds between the vinyl groups of the haem and the thiol groups of a CXXCH (Cys–Xaa–Xaa–Cys–His) motif. In cells, the haem attachment is an enzyme-catalysed post-translational modification. We have previously shown that co-expression of a variant of Escherichia coli cytochrome b562 containing a CXXCH haem-binding motif with the E. coli Ccm (cytochrome c maturation) proteins resulted in homogeneous maturation of a correctly formed c-type cytochrome. In contrast, in the absence of the Ccm apparatus, the product holocytochrome was heterogeneous, the main species having haem inverted and attached through only one thioether bond. In the present study we use further variants of cytochrome b562 to investigate the substrate specificity of the E. coli Ccm apparatus. The system can mature c-type cytochromes with CCXXCH, CCXCH, CXCCH and CXXCHC motifs, even though these are not found naturally and the extra cysteine residue might, in principle, disrupt the biogenesis proteins which must interact intricately with disulfide-bond oxidizing and reducing proteins in the E. coli periplasm. The Ccm proteins can also attach haem to motifs of the type CXnCH where n ranges from 2 to 6. For n=3 and 4, the haem attachment was correct and homogeneous, but for higher values of n the holocytochromes displayed oxidative addition of sulfur and/or oxygen atoms associated with the covalent haem-attachment process. The implications of our observations for the haem-attachment reaction, for genome analyses and for the substrate specificity of the Ccm system, are discussed.
A study of the electric quadrupole Raman processes of the superionic crystals Rb3H(SO4)2 and Rb3D(SO4)2 using H1, H2, and R87b NMR
Authors: Lim Ae Ran
Published: December 2008

The line shape and spin-lattice relaxation time T1 of the H1, H2, and R87b nuclei in Rb3H(SO4)2 and Rb3D(SO4)2 single crystals were investigated using NMR spectrometry. The superionic phase transitions described here occur at a temperature of TC=400 K, which is about 50 K lower than the previously reported superionic transition temperature (namely, 448 K). The changes in the resonance lines of the H1 and H2 nuclei at TC=400 K indicate that at this temperature, the orientations of the H((SO4)2−)2 dimers change in such a way that the directions of the two kinds of hydrogen bonds in these crystals become approximately the same. The spin-lattice relaxation rate T1−1 of the R87b nuclei in the two crystals was found to increase with increasing temperature, being proportional to T7. This result is in accordance with the Raman processes for nuclear spin-lattice relaxation. Therefore, the high conductivities of the crystals at high temperature may be associated with both symmetry changes in the H((SO4)2−)2 dimers and motion giving rise to a strong temperature dependence of T1.
Study on the microstructural and overall disorder in hydrogenated amorphous silicon carbon films
Authors: Ambrosone G. , Basa D. K. , Coscia U. , Fathallah M.
Published: December 2008

Hydrogenated amorphous silicon carbon alloy films of different carbon compositions were prepared by plasma enhanced chemical vapor deposition system using silane and methane with helium dilution and were characterized by structural and optical techniques to understand the microstructural and overall disorder in amorphous semiconductors. The study demonstrates that the increase of the microstructural disorder results in an increase in the overall disorder and the local defect density induced by carbon incorporation seems to dominate the overall defect structure of the network.
Extensive analysis of resistance evolution due to electromigration induced degradation
Authors: Doyen L. , Petitprez E. , Waltz P. , Federspiel X. , Arnaud L. , Wouters Y.
Published: December 2008

Electromigration failure kinetic has been studied with resistance evolution versus time of interconnects during degradation. Tests were performed on dual damascene copper lines, issued from the 65 nm technology node, of various widths and lengths. All samples exhibit similar resistance evolution: an initial step, characterized by its height called Rstep, follows a linear kinetic characterized by its slope called Rslope. These two parameters were systematically extracted; Rstep is proportional to the critical volume of a void spanning the whole section of the line, and Rslope to the copper drift velocity. On one hand, the linewidth does not affect these two parameters. On the other hand, Rslope is highly dependent on the line length because of the Blech effect, while Rstep remains constant. Consequently, it was demonstrated that the classical linear function L/TTF=f(jL), where TTF is the time to failure, j is the current density, and L is the line length, used to study the Blech effect in interconnects could be substituted with the linear function RslopeL=f(jL), confirming that Rslope is a suitable parameter to study void growth kinetics. At 300 °C and 2 MA/cm2, a void growth velocity of 1.15×10−8 μm3/s was thus determined on long lines, and an activation energy of 0.95 eV was found. Finally based on the resistance analysis, an explanation is proposed concerning the larger spread observed on the TTF measured on short lines at low current density.
The development of truncated inviscid turbulence and the Fermi–Pasta–Ulam problem
Authors: Ooms G. , Boersma B. J.
Published: December 2008

A study was made of the possible similarity between the development of truncated, inviscid turbulence and the Fermi–Pasta–Ulam (FPU) problem. For the case of a constant time scale, which resembles the FPU problem, a significant increase in the time to achieve equipartition was found when the initial energy was decreased. At first a few modes were generated and only rather late in the spectral development other modes appear and equipartition was established.
Silicon nanocluster-sensitized emission from erbium: The role of stress in the formation of silicon nanoclusters
Authors: Ahmad I. , Temple M. P. , Kallis A. , Wojdak M. , Oton C. J. , Barbier D. , Saleh H. , Kenyon A. J. , Loh W. H.
Published: December 2008

Erbium-doped silicon-rich silicon oxide films deposited by plasma enhanced chemical vapor deposition suffer from compressive stress as deposited, which converts to a large tensile stress on annealing due to the release of hydrogen. Although the cracking that results from this stress can be avoided by patterning the films into ridges, significant stress remains along the ridge axis. Measurements of erbium photoluminescence sensitized by silicon nanoclusters in stressed and relaxed films suggest an important role for internal film stresses in promoting the phase separation of excess silicon into nanoclusters, which has previously been thought of as a thermally driven process.
Field-dependant hopping conduction in silicon nanocrystal films
Authors: Rafiq M. A. , Durrani Z. A. K. , Mizuta H. , Hassan M. M. , Oda S.
Published: December 2008

We investigate the electric field dependence of hopping conduction in 300 nm thick films of ∼8 nm diameter silicon nanocrystals. The hopping conductivity σ follows a ln(σ)∝1/T1/2 dependence with temperature T, explained by a percolation hopping conduction model. At high fields F>∼1×105 V/cm, the hopping conductivity follows a ln(σ)∝F1/2 dependence. This dependence is investigated using the concept of “effective temperature,” introduced originally by Shklovskii for hopping conduction in disordered materials.
Three operation modes of lateral-field-excited piezoelectric devices
Authors: Wang Wenyan , Zhang Chao , Zhang Zhitian , Liu Yan , Feng Guanping
Published: December 2008

Through theoretical calculations and experiments, three operation modes of lateral-field-excited piezoelectric bulk acoustic wave devices, which are referred to as the pure lateral field excitation (LFE), quasi-LFE, and pseudo-LFE modes, are presented. Several 4–6 MHz LFE devices with similar geometry using lithium niobate, lithium tantalate, and AT-cut quartz crystals are fabricated and tested in air and de-ionized water, respectively. The experimental results are in well agreement with the theoretical calculations.
The Geography of Pension Liabilities and Fund Governance in the United States
Authors: Monk Ashby H B
Published: December 2008

If finance is the engine driving economic and geographic change, then pensions are its primary vehicle. On the one hand, pension-plan assets, which approached US$18 trillion in 2005 for OECD countries, are having global impacts on financial markets. On the other hand, pension-plan liabilities, larger than the assets in nominal terms, are also having dramatic impacts on plan sponsors. If assets are not properly managed, pension liabilities can threaten the financial solvency of plan sponsors. Consequently, owing to the enormous and growing financial and political importance of pension plans, I contend that the procedures governing these institutions are of increasing importance for economic geographers. In this paper the effectiveness of the current governance system is tested through a widely subscribed ‘expert survey’. Then, the relationship between pension-fund governance and economic geography is demonstrated through case study. I conclude that the current governance model remains inadequate. Moreover, poor pension-fund governance, in addition to having an economic cost, is shown to have tangible geographic impacts.
A rapid new method for assessing sustainability of ornamental fish by-catch from coral reefs
Authors: Feitosa Caroline Vieira , Ferreira Beatrice Padovani , Elisabeth de Araújo Maria
Published: December 2008

The ornamental fish trade has considerable potential for damaging reef environments. Nearly 120 species are currently harvested in the Brazilian trade and little attention has been paid to the effects of the accidental catch of these species. Records of ornamental fish by-catch and the susceptibility and resilience of species from the major Brazilian families in the aquarium trade were examined to test a method and determine the sustainability of these catches. Each species was assessed based on two groups of criteria: (1) relative vulnerability to capture; and (2) population resilience to mortality due to fishing efforts. Each species was also ranked (1–3) for criteria regarding ecology, biology, catchability, numbers of individuals exported by aquarium companies and mortality index. These criteria were then weighted and each species rank in the two groups of criteria was plotted. Nineteen species from 10 families were recorded. The species least likely to have sustainable catch rates included Holacanthus tricolor, H. ciliaris, Chaetodon striatus and Pomacanthus paru. This approach is a useful alternative for management efforts and the assessment of catch sustainability in newly developed multi-species fisheries with limited available data, which occur in areas of high species richness such as reefs.
Copper effects in the copepod Tigriopus angulatus Lang, 1933: natural broad tolerance allows maintenance of food webs in copper-enriched coastal areas
Authors: Medina M. H. , Morandi B. , Correa J. A.
Published: December 2008

Some coastal areas of northern Chile have received copper mine tailings for more than 60 years. At these areas, the toxic effects of copper have eliminated most intertidal seaweed and macroinvertebrate populations. However, the harpacticoid splashpool copepod Tigriopus angulatus seems unaffected, inhabiting heavily impacted sites. Because this species of copepod makes the energy of photosynthesis available to higher trophic levels, it becomes ecologically relevant to define the range of copper it can tolerate without affecting its population size. This was assessed through the analysis of demographic responses measured in a life-cycle experiment with copepods from a site with no history of heavy metal pollution. Results showed that juvenile survival was the most sensitive endpoint and that the species’ intrinsic rate of natural increase (rm) remains unaffected (without showing a fitness cost associated with tolerance) at copper concentrations within the range measured at these impacted areas. Thus, despite the high levels of dissolved copper measured at those sites, the local population of T. angulatus apparently can persist in exploiting its ecological niche and contributing to the overall ecosystem functioning, highlighting an unforeseen role of this copepod in the maintenance of food webs at the copper-enriched environment of northern Chile.
An atmospheric perspective on North American carbon dioxide exchange: CarbonTracker
Authors: Peters Wouter , Jacobson Andrew R. , Sweeney Colm , Andrews Arlyn E. , Conway Thomas J. , Masarie Kenneth , Miller John B. , Bruhwiler Lori M. P. , Pétron Gabrielle , Hirsch Adam I. , Worthy Douglas E. J. , van der Werf Guido R. , Randerson James T. , Wennberg Paul O. , Krol Maarten C. , Tans Pieter P.
Published: December 2008

We present an estimate of net CO
2
exchange between the terrestrial biosphere and the atmosphere across North America for every week in the period 2000 through 2005. This estimate is derived from a set of 28,000 CO
2
mole fraction observations in the global atmosphere that are fed into a state-of-the-art data assimilation system for CO
2
called CarbonTracker. By design, the surface fluxes produced in CarbonTracker are consistent with the recent history of CO
2
in the atmosphere and provide constraints on the net carbon flux independent from national inventories derived from accounting efforts. We find the North American terrestrial biosphere to have absorbed −0.65 PgC/yr (1 petagram = 10
15
g; negative signs are used for carbon sinks) averaged over the period studied, partly offsetting the estimated 1.85 PgC/yr release by fossil fuel burning and cement manufacturing. Uncertainty on this estimate is derived from a set of sensitivity experiments and places the sink within a range of −0.4 to −1.0 PgC/yr. The estimated sink is located mainly in the deciduous forests along the East Coast (32%) and the boreal coniferous forests (22%). Terrestrial uptake fell to −0.32 PgC/yr during the large-scale drought of 2002, suggesting sensitivity of the contemporary carbon sinks to climate extremes. CarbonTracker results are in excellent agreement with a wide collection of carbon inventories that form the basis of the first North American State of the Carbon Cycle Report (SOCCR), to be released in 2007. All CarbonTracker results are freely available at
http://carbontracker.noaa.gov
.
Analysis of nondegradative protein ubiquitylation with a monoclonal antibody specific for lysine-63-linked polyubiquitin
Authors: Wang Haopeng , Matsuzawa Atsushi , Brown Scott A. , Zhou JingRan , Guy Cliff S. , Tseng Ping-Hui , Forbes Karen , Nicholson Thomas P. , Sheppard Paul W. , Häcker Hans , Karin Michael , Vignali Dario A. A.
Published: December 2008

Modification of proteins by the addition of lysine (K)-63-linked polyubiquitin (polyUb) chains is suggested to play important roles in a variety of cellular events, including DNA repair, signal transduction, and receptor endocytosis. However, identifying such modifications in living cells is complex and cumbersome. We have generated a monoclonal antibody (mAb) that specifically recognizes K63-linked polyUb, but not any other isopeptide-linked (K6, K11, K27, K29, K33, or K48) polyUb or monoubiquitin. We demonstrate the sensitivity and specificity of this K63Ub-specific mAb to detect K63Ub-modified proteins in cell lysates by Western blotting and in cells by immunofluorescence, and K63Ub-modified TRAF6 and MEKK1 in vitro and ex vivo. This unique mAb will facilitate the analysis of K63-linked polyubiquitylation ex vivo and presents a strategy for the generation of similar reagents against other forms of polyUb.
Highly parallel identification of essential genes in cancer cells
Authors: Luo Biao , Cheung Hiu Wing , Subramanian Aravind , Sharifnia Tanaz , Okamoto Michael , Yang Xiaoping , Hinkle Greg , Boehm Jesse S. , Beroukhim Rameen , Weir Barbara A. , Mermel Craig , Barbie David A. , Awad Tarif , Zhou Xiaochuan , Nguyen Tuyen , Piqani Bruno , Li Cheng , Golub Todd R. , Meyerson Matthew , Hacohen Nir , Hahn William C. , Lander Eric S. , Sabatini David M. , Root David E.
Published: December 2008

More complete knowledge of the molecular mechanisms underlying cancer will improve prevention, diagnosis and treatment. Efforts such as The Cancer Genome Atlas are systematically characterizing the structural basis of cancer, by identifying the genomic mutations associated with each cancer type. A powerful complementary approach is to systematically characterize the functional basis of cancer, by identifying the genes essential for growth and related phenotypes in different cancer cells. Such information would be particularly valuable for identifying potential drug targets. Here, we report the development of an efficient, robust approach to perform genome-scale pooled shRNA screens for both positive and negative selection and its application to systematically identify cell essential genes in 12 cancer cell lines. By integrating these functional data with comprehensive genetic analyses of primary human tumors, we identified known and putative oncogenes such as
EGFR
,
KRAS
,
MYC
,
BCR-ABL
,
MYB
,
CRKL
, and
CDK4
that are essential for cancer cell proliferation and also altered in human cancers. We further used this approach to identify genes involved in the response of cancer cells to tumoricidal agents and found 4 genes required for the response of CML cells to imatinib treatment:
PTPN1
,
NF1
,
SMARCB1
, and
SMARCE1
, and 5 regulators of the response to FAS activation, FAS, FADD, CASP8, ARID1A and CBX1. Broad application of this highly parallel genetic screening strategy will not only facilitate the rapid identification of genes that drive the malignant state and its response to therapeutics but will also enable the discovery of genes that participate in any biological process.
Precision and recall estimates for two-hybrid screens
Authors: Huang Hailiang , Bader Joel S.
Published: December 2008

Motivation: Yeast two-hybrid screens are an important method to map pairwise protein interactions. This method can generate spurious interactions (false discoveries), and true interactions can be missed (false negatives). Previously, we reported a capture–recapture estimator for bait-specific precision and recall. Here, we present an improved method that better accounts for heterogeneity in bait-specific error rates.

Result: For yeast, worm and fly screens, we estimate the overall false discovery rates (FDRs) to be 9.9%, 13.2% and 17.0% and the false negative rates (FNRs) to be 51%, 42% and 28%. Bait-specific FDRs and the estimated protein degrees are then used to identify protein categories that yield more (or fewer) false positive interactions and more (or fewer) interaction partners. While membrane proteins have been suggested to have elevated FDRs, the current analysis suggests that intrinsic membrane proteins may actually have reduced FDRs. Hydrophobicity is positively correlated with decreased error rates and fewer interaction partners. These methods will be useful for future two-hybrid screens, which could use ultra-high-throughput sequencing for deeper sampling of interacting bait–prey pairs.

Availability: All software (C source) and datasets are available as supplemental files and at http://www.baderzone.org under the Lesser GPL v. 3 license.

Contact:  joel.bader@jhu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Analyses of Advanced Rice Anther Transcriptomes Reveal Global Tapetum Secretory Functions and Potential Proteins for Lipid Exine Formation
Authors: Huang Ming-Der , Wei Fu-Jin , Wu Cheng-Cheih , Hsing Yue-Ie Caroline , Huang Anthony H.C.
Published: December 2008

The anthers in flowers perform important functions in sexual reproduction. Several recent studies used microarrays to study anther transcriptomes to explore genes controlling anther development. To analyze the secretion and other functions of the tapetum, we produced transcriptomes of anthers of rice (Oryza sativa subsp. japonica) at six progressive developmental stages and pollen with sequencing-by-synthesis technology. The transcriptomes included at least 18,000 unique transcripts, about 25% of which had antisense transcripts. In silico anther-minus-pollen subtraction produced transcripts largely unique to the tapetum; these transcripts include all the reported tapetum-specific transcripts of orthologs in other species. The differential developmental profiles of the transcripts and their antisense transcripts signify extensive regulation of gene expression in the anther, especially the tapetum, during development. The transcriptomes were used to dissect two major cell/biochemical functions of the tapetum. First, we categorized and charted the developmental profiles of all transcripts encoding secretory proteins present in the cellular exterior; these transcripts represent about 12% and 30% of the those transcripts having more than 100 and 1,000 transcripts per million, respectively. Second, we successfully selected from hundreds of transcripts several transcripts encoding potential proteins for lipid exine synthesis during early anther development. These proteins include cytochrome P450, acyltransferases, and lipid transfer proteins in our hypothesized mechanism of exine synthesis in and export from the tapetum. Putative functioning of these proteins in exine formation is consistent with proteins and metabolites detected in the anther locule fluid obtained by micropipetting.
Expansion and Diversification of thePopulusR2R3-MYB Family of Transcription Factors
Authors: Wilkins Olivia , Nahal Hardeep , Foong Justin , Provart Nicholas J. , Campbell Malcolm M.
Published: December 2008

The R2R3-MYB proteins comprise one of the largest families of transcription factors in plants. R2R3-MYB family members regulate plant-specific processes, such as the elaboration of specialized cell types, including xylem, guard cells, trichomes, and root hairs, and the biosynthesis of specialized branches of metabolism, including phenylpropanoid biosynthesis. As such, R2R3-MYB family members are hypothesized to contribute to the emergence of evolutionary innovations that have arisen in specific plant lineages. As a first step in determining the role played by R2R3-MYB family members in the emergence of lineage-specific innovations in the genus Populus, the entire Populus trichocarpa R2R3-MYB family was characterized. The Populus R2R3-MYB complement is much larger than that found in other angiosperms with fully sequenced genomes. Phylogenetic analyses, together with chromosome placement, showed that the expansion of the Populus R2R3-MYB family was not only attributable to whole genome duplication but also involved selective expansion of specific R2R3-MYB clades. Expansion of the Populus R2R3-MYB family prominently involved members with expression patterns that suggested a role in specific components of Populus life history, including wood formation and reproductive development. An expandable compendium of microarray-based expression data (PopGenExpress) and associated Web-based tools were developed to better enable within- and between-species comparisons of Populus R2R3-MYB gene expression. This resource, which includes intuitive graphic visualization of gene expression data across multiple tissues, organs, and treatments, is freely available to, and expandable by, scientists wishing to better understand the genome biology of Populus, an ecologically dominant and economically important forest tree genus.
Multiple-wavelength anomalous dispersion techniques applied to powder data: a probabilistic method for finding the substructureviajoint probability distribution functions
Authors: Altomare Angela , Belviso Benny Danilo , Burla Maria Cristina , Campi Gaetano , Cuocci Corrado , Giacovazzo Carmelo , Gozzo Fabia , Moliterni Anna , Polidori Giampiero , Rizzi Rosanna
Published: December 2008

A new joint probability distribution function method is described to find the anomalous scatterer substructure from powder data. The method requires two wavelengths; the conclusive formulas provide estimates of the substructure structure factor moduli, from which the anomalous scatterer positions can be found by Patterson or direct methods. The theory has been preliminarily applied to two compounds, the first having Pt and the second having Fe as anomalous scatterer. Both substructures were correctly identified.
Gender and non‐medical use of prescription opioids: results from a national US survey*
Authors: Tetrault Jeanette M. , Desai Rani A. , Becker William C. , Fiellin David A. , Concato John , Sullivan Lynn E.
Published: December 2008

Aims  Gender differences exist regarding alcohol and illicit drug use disorders in the United States. Little is known about the gender‐related factors associated with non‐medical use of prescription opioids.

Design  Using data from the 2003 National Survey on Drug Use and Health, we examined risk factors for past‐year non‐medical use of prescription opioids stratified by gender.

Setting  Non‐institutionalized US residences.

Participants  Civilian, non‐institutionalized US citizens aged 12 years and older.

Measurements  Self‐reported alcohol and drug use, focusing specifically on past‐year non‐medical use of prescription opioids.

Findings  Among 55 023 respondents, 4.8% reported past‐year, non‐medical use of prescription opioids. For both women and men, alcohol abuse/dependence and marijuana, hallucinogen, cocaine, non‐medical stimulant and sedative/tranquilizer use were associated with past‐year non‐medical use of prescription opioids. Among women but not men, first use of illicit drugs beginning at 24 years or older [adjusted odds ratios (AOR) 1.90, 95% CI 1.05–3.44], serious mental illness (AOR 1.67, 95% CI 1.29–2.17) and cigarette smoking (AOR 1.33, 95% CI 1.05–1.68) were associated with past‐year non‐medical use of prescription opioids. Among men but not women, past‐year inhalant use (AOR 1.93, 95% CI 1.28–2.92) was associated with the outcome.

Conclusions  For both women and men, illicit drug use is associated with the non‐medical use of prescription opioids. Additionally, certain factors associated with the non‐medical use of prescription opioids are notably gender‐specific. Clinicians should recognize that patients with a history of illicit substance use or misuse of other prescription medications are at increased risk for non‐medical use of prescription opioids, and that gender‐specific factors can help to identify individuals at greatest risk.
The role of spending money and drinking alcohol in adolescent smoking
Authors: Zhang Bo , Cartmill Carrie , Ferrence Roberta
Published: December 2008

Aims  Previous studies have shown inconsistent findings with regard to the association between amount of spending money and adolescent smoking. Drinking alcohol may be a mediator of the association between spending money and adolescent smoking. However, no studies have examined this potential role. The objective of this study was to investigate the association between amount of spending money and adolescent smoking and the potential mediation role of alcohol use in this association.

Design  The 2003 Ontario Student Drug Use Survey of students in grades 7–12.

Measurements  Multivariable logistic, probit and linear regression models were used to investigate the association between amount of spending money and smoking, and the contribution of drinking alcoholic beverages to this relationship.

Findings  Spending money was associated positively with experimental smoking, current smoking and daily consumption of cigarettes (P < 0.01). The analysis adjusted for confounders showed that students with spending money ≥$20/week were significantly more likely to be experimental smokers, students with ≥$30/week were significantly more likely to be current smokers and students with ≥$60/week smoked significantly more cigarettes/day (P ≤ 0.05), compared to students with <$10/week. Alcohol use was an important mediator, responsible for 81% of the association of spending money with experimental smoking, 38% with current smoking and 37% with daily consumption of cigarettes.

Conclusions  Amount of spending money was associated significantly and positively with smoking among adolescents, and alcohol use mediated this association. Integrated tobacco prevention programs may be more effective, and increasing taxes on cigarettes and alcohol would increase price sensitivity among youth and protect against adolescent smoking.
Drinking expectancies and motives: a genetic study of young adult women
Authors: Agrawal Arpana , Dick Danielle M. , Bucholz Kathleen K. , Madden Pamela A. F. , Cooper M. Lynne , Sher Kenneth J. , Heath Andrew C.
Published: December 2008

Background  Constructs such as drinking expectancies (beliefs regarding the effects of alcohol) and motives (drinking alcohol to achieve a valued end) have been shown to be associated with various stages of alcohol use behaviors. However, little is known of the extent to which genetic and environmental influences contribute to individual differences in expectancies and motives.

Methods  Using data from 3656 young adult same‐sex female twins, we examined the association between measures of drinking expectancies and motives and drinking behaviors. Using twin models, we estimated the extent to which genetic, shared and non‐shared environmental factors influenced individual differences in expectancies and motives and also tested whether the extent of the genetic and environmental contributions on expectancies varied across abstainers and users of alcohol.

Results  Expectancies predicted initiation of alcohol use. Both motives and expectancies were associated with frequency and quantity of alcohol consumption and drinks‐to‐intoxication. There was no evidence for heritable influences on expectancies and enhancement motives, with familial similarity for these traits being due to shared environment. Heritable influences on social, coping and conformity motives ranged from 11% to 33%. When expectancies were stratified by alcohol use, significant heritable influences (31–39%) were found for cognitive–behavioral impairment and risk‐taking/negative self‐perception (RT/NSP) in abstainers only, while environmental influences contributed to familial variance for other measures of expectancies in alcohol users.

Conclusions  Environmental influences (both familial and individual‐specific) shape alcohol expectancies, while heritable influences may predispose to motives for drinking. Individual differences in expectancies are moderated by alcohol use, suggesting that sources of individual differences in expectancies may vary in drinkers versus abstainers.
A two‐step wavelet‐based regularization for linear inversion of geophysical data
Authors: Gholami Ali , Siahkoohi Hamid Reza
Published: December 2008

Regularization methods are used to recover a unique and stable solution in ill‐posed geophysical inverse problems. Due to the connection of homogeneous operators that arise in many geophysical inverse problems to the Fourier basis, for these operators classical regularization methods possess some limitations that one may try to circumvent by wavelet techniques.

In this paper, we introduce a two‐step wavelet‐based regularization method that combines classical regularization methods with wavelet transform to solve ill‐posed linear inverse problems in geophysics. The power of the two‐step wavelet‐based regularization for linear inversion is twofold. First, regularization parameter choice is straightforward; it is obtained froma prioriestimate of data variance. Second, in two‐step wavelet‐based regularization the basis can simultaneously diagonalize both the operator and the prior information about the model to be recovered. The latter is performed by wavelet‐vaguelette decomposition using orthogonal symmetric fractional B‐spline wavelets.

In the two‐step wavelet‐based regularization method, at the first step where fully classical tools are used, data is inverted for the Moore‐Penrose solution of the problem, which is subsequently used as a preliminary input model for the second step. Also in this step, a model‐independent estimate of data variance is made using nonparametric estimation and L‐curve analysis. At the second step, wavelet‐based regularization is used to partially recover the smoothness properties of the exact model from the oscillatory preliminary model.

We illustrated the efficiency of the method by applying on a synthetic vertical seismic profiling data. The results indicate that a simple non‐linear operation of weighting and thresholding of wavelet coefficients can consistently outperform classical linear inverse methods.