bluuebunny/crossref_metadata_2025 huggingface dataset:
Could a Woman Say “No” in Biblical Israel? On the Genealogy of Legal Status in Biblical Law and Literature
Authors: Kawashima Robert S.
Published: May 2011

In Genesis 26, one of the so-called wife–sister stories, Abimelech King of Gerar catches Isaac “playing” with the woman he had introduced as his sister, namely, Rebekah his wife. He immediately confronts the trickster, rebuking him for presenting his wife as a single and therefore sexually available woman: “What is this you have done to us? One of the people could easily have lain with your wife, and you would have brought guilt upon us” (Genesis 26:10). Abimelech's remarks ought to give one pause. He apparently suggests that sexual contact with this Hebrew woman is as easy as brushing elbows with a stranger in a crowded street, which is to say, he fails to consider or even acknowledge the possibility that Rebekah might have just said “No!” Furthermore, the narrowly avoided “guilt” he refers to consists not of this woman's rape by some local sexual predator—in which case her secret identity as Isaac's wife would be irrelevant—but of an otherwise innocent man's unwitting violation, consensual or nonconsensual, it matters not, of her treacherously concealed marital obligations. In other words, the underlying legal reasoning here conceives of Rebekah not as an autonomous subject whose rights (i.e., the right to refuse a sexual advance) must be protected, but as an object within the domain of her husband, whose prior claims—namely, to sexual exclusivity—must be respected. Abimelech's at-first puzzling remarks, then, provide us with a glimpse into a wholly foreign legal episteme or discursive formation.
The First Liability Insurance Cartel in America, 1896–1906
Authors: Pandya Sachin S.
Published: May 2011

This article studies the rise and fall of the first liability insurance cartel in the United States. In 1886, insurance companies in America began selling liability insurance for personal injury accidents, primarily to cover business tort liability for employee accidents at work and non-employee injuries occasioned by their business operations. In 1896, the leading liability insurers agreed to fix premium rates and share information on policyholder losses. In 1906, this cartel fell apart.
“The law recognizes racial instinct”: Tucker v. Blease and the Black–White Paradigm in the Jim Crow South
Authors: Wertheimer John W. , Bradshaw Jessica , Cobb Allyson , Addison Harper , Dudley Colhoun E. , Diamant Samuel , Gilbert Andrew , Higgs Jeffrey , Skipper Nicholas
Published: May 2011

On January 24, 1913, the trustees of the Dalcho School, a segregated, all-white public school in Dillon County, South Carolina, summarily dismissed Dudley, Eugene, and Herbert Kirby, ages ten, twelve, and fourteen, respectively. According to testimony offered in a subsequent hearing, the boys had “always properly behaved,” were “good pupils,” and “never …exercise[d] any bad influence in school.” Moreover, the boys’ overwhelmingly white ancestry, in the words of the South Carolina Supreme Court, technically “entitled [them] to be classified as white,” according to state law. Nevertheless, because local whites believed that the Kirbys were “not of pure Caucasian blood,” and that therefore their removal was in the segregated school's best interest, the court, in Tucker v. Blease (1914), upheld their expulsion.
Jus SoliandJus Sanguinisin the Colonies: The Interwar Politics of Race, Culture, and Multiracial Legal Status in British Africa
Authors: Lee Christopher J.
Published: May 2011

In April 1929, an unremarkable man—a local entrepreneur and defendant in a minor lawsuit—entered the High Court of Nyasaland (contemporary Malawi) and made a remarkable gesture. The son of an Indian immigrant and an African woman, Suleman Abdul Karim declared himself a “non-native” and that he should consequently be tried as such. The lawsuit brought against him concerned the ownership of a Ford truck for which he had failed to complete payment. Approximately ten months earlier on June 28, 1928, Ernest Carr of Blantyre, Nyasaland—a local auctioneer and businessman who frequently ran advertisements inThe Nyasaland Timesduring the 1920s—had sold the Ford to Karim with a written agreement that it would be paid for with £30 as a down payment, £20 on July 31, 1928, with the remaining £50 to be paid in monthly installments of £10 starting August 31, 1928. All told, this business transaction was intended to be resolved expeditiously, with its completion by the new year of 1929. However, the minor expectation that this contract had promised was not fulfilled. Two payments were made, an initial one on the day of sale for £30 and a second several months later on November 16, this time for £8. Karim defaulted on the remaining amount. Furthermore, he failed to make an insurance premium payment of £10 to the African Guarantee and Indemnity Co. Ltd., for which Carr was a local agent. Despite these defaults, Karim had not returned the Ford. Consequently, after several more months elapsed, a claim against Karim came before the High Court on April 11, 1929.
Global Constitutionalism and the Objective Purport of the International Legal Order
Authors: VAN MULLIGEN JOHANNES GERALD
Published: May 2011

Global constitutionalists argue that the international legal order can only be meaningfully construed as having an objective, value-based purport. There is, however, something hybrid about the constitutionalist argument, as constitutionalists espouse a normative agenda whilst at the same time setting out to ground their approach in positive international law. It is contended that to avoid both this foundational problem and the charge of utopianism, and as a rejoinder to positivistic arguments for the denial of objective purport, constitutionalists are forced to reason along indirect, transcendental lines. Thus, constitutionalists are to be construed as avouching global values as necessary conditions for making sense of existing international legal practice, rather than merely invoking direct, positivistic evidence and/or mere normative arguments to ground their position. Moreover, it is submitted, first, that global constitutionalists would do better by adopting a less objectivist stance as regards global values, as on the ideal-agent theory of value. Second, it is argued that even though there might be room for so-called constitutionalist ‘mindsets’, these fall short of establishing the objective purport of the international legal order. Third, d'Aspremont's positivistic argument contra objective purport is construed as (also) an argument to the effect that the rules and architecture of the international legal order only warrant the existence of Hobbesian interests as necessary conditions for making sense of it. The constitutionalist case for objective purport, then, hinges on the issue of whether constitutionalism is necessitated by considerations as regards the intelligibility of international legal argument, by explanatory desiderata regarding trends in international law-making, and as a viable response to the problems posed by fragmentation, deformalization, and international legal scepticism.
Waiting for Godot: An Analysis of the Advisory Opinion on Kosovo
Authors: JACOBS DOV , RADI YANNICK
Published: May 2011

The Kosovo Advisory Opinion gave rise to responses that suggest that the Court went too far, or not far enough, depending on one's perspective. In this article, the authors argue that the Court should either have done nothing or gone all the way. By accepting an inadequately drafted question, the Court was necessarily going to give an inadequate answer. This article adopts a strict approach to the legal nature of the question and considers that the ICJ should have declined its competence, not as an exercise of its discretion, but as a preservation of its core judicial function, which does not include primarily the conduct of non-state entities. Going further, the authors suggest that the Court could have rephrased the question and sought to establish the international responsibility of the United Nations, and, ultimately, of Kosovo, which, it is argued, is in fact implicitly recognized by the Court, both politically and legally.
The Kosovo Advisory Opinion Scrutinized
Authors: VIDMAR JURE
Published: May 2011

In the Kosovo Advisory Opinion, the International Court of Justice took the position that Kosovo's unilateral declaration of independence did not violate any applicable rules of international law. This article does not dispute the final finding, but rather critically examines the Court's somewhat controversial reasoning and considers the added value of the opinion for the clarification of legal doctrine in relation to unilateral declarations of independence. An argument is made that the Court's interpretation of the question and the identification of the authors of the declaration had significant implications for the Court's final finding. Yet, the Court cannot be criticized for not answering the question of whether or not Kosovo is a state, whether Kosovo Albanians are beneficiaries of the right of self-determination, or even whether the ‘right to remedial secession’ is applicable. However, the Court may well have implicitly answered that recognition of Kosovo is not illegal.
Equipping Church Leaders for Mission in the Anglican Church of Kenya
Authors: Nkonge Dickson
Published: May 2011

Leadership remains the biggest challenge facing the Church in Africa today. The Anglican Church in Kenya (ACK) was started in 1844, but was it was not until 1888 that the official training of church leaders was commenced with the opening of a Divinity School at Frere Town. Since its inception the ACK has experienced a tremendous growth in membership, growing at the rate of about 6.7 per cent per annum. In spite of this rapid growth, the ACK is in leadership crises due to lack of enough and well-equipped clergy to run it. The Anglican population of about 3,711,890 Christians is served by only about 1555 clergy, translating to clergy per Christians ratio of about 1 : 2400. This affects the Church's mission in that it is impossible for one clergy to effectively provide spiritual care to 2400 Christians. On top of this, the majority of the clergy currently serving in the ACK are not properly trained to match the rapidly changing Kenyan society. About 83 per cent of these clergy have diploma and below theological qualifications. If the ACK has to be successful in its mission in this century, it has to reconsider its training systems.
Design and Fabrication of Magnet Coils
Authors: Jaski M.
Published: May 2011

Users at the Advanced Photon Source (APS) requested a special purpose undulator that required 456 electromagnetic coils. This paper discusses the design and fabrication techniques used at the APS to build these room-temperature coils. The coils are made from insulated square copper conductor and are vacuum impregnated with epoxy.
Subterranean CO2 ventilation and its role in the net ecosystem carbon balance of a karstic shrubland
Authors: Sanchez‐Cañete E. P. , Serrano‐Ortiz P. , Kowalski A. S. , Oyonarte C. , Domingo F.
Published: May 2011

Recent studies of carbonate ecosystems suggest a possible contribution of subterranean ventilation to the net ecosystem carbon balance. However, both the overall importance of such CO2 exchange processes and their drivers remain unknown. Here we analyze several dry‐season episodes of net CO2 emissions to the atmosphere, along with soil and borehole CO2 measurements. Results highlight important events where rapid decreases of underground CO2 molar fractions correlate well with sizeable CO2 release to the atmosphere. Such events, with high friction velocities, are attributed to ventilation processes, and should be accounted for by predictive models of surface CO2 exchange.
Statistics between mainshocks and foreshocks in Italy and Southern California
Authors: Marzocchi Warner , Zhuang Jiancang
Published: May 2011

The most used and accepted models for daily forecasts are based on short‐term space and time earthquake clustering for occurrence rates and on the Gutenberg‐Richter law for the frequency‐magnitude. These models have been demonstrated to produce reliable prospective space‐time‐magnitude forecasts during an aftershock sequence, but their skill in forecasting mainshocks is still under discussion. This paper studies the foreshock statistics of the Italian and Californian seismicity in two ways: i) we compare the foreshock activity observed in real seismic catalogs and in synthetic catalogs derived from a pure Epidemic‐Type Aftershock Sequence (ETAS) model; ii) we analyze the triggering capability of earthquakes using different ETAS parameterizations, in order to check whether large events are triggered in the same way as regular earthquakes. The results indicate that the foreshock activity observed in the real catalogs is compatible with what is expected by the ETAS model. Moreover, we find that the empirical foreshock rates have an intrinsic variability due to limited sampling that may explain most of the differences found so far in different seismic catalogs.
The electric field effects on the binding energies and the nonlinear optical properties of a donor impurity in a spherical quantum dot
Authors: Kırak M. , Yılmaz S. , Şahin M. , Gençaslan M.
Published: May 2011

In this study, we have investigated the influence of an external electric field on the electronic properties of the ground and excited states and studied the linear and the third-order nonlinear optical properties (i.e., absorption coefficients and refractive indices) in a spherical semiconductor quantum dot of a parabolic confinement with an on-center shallow hydrogenic impurity. In the calculations, a variational procedure was employed within the effective-mass approximation. We found that the binding energies of the ground and excited states, the absorption coefficients, and the refractive index changes of 0s-1p and 1p-2d transitions depend on the applied electric field. The results show that the existence of the electric field has great influence on the optical absorption coefficients and the refractive index changes. Also, we have found that the magnitudes of the absorption coefficient and the refractive index change of the spherical quantum dot increase for transitions between higher levels.
Characterizing plasma mirrors near breakdown
Authors: Geissel Matthias , Schollmeier Marius S. , Kimmel Mark W. , Rambo Patrick K. , Schwarz Jens , Atherton Briggs W. , Brambrink Erik
Published: May 2011

Experiments dedicated to the characterization of plasma mirrors with a high energy, single shot short-pulse laser were performed at the 100 TW target area of the Z-Backlighter Facility at Sandia National Laboratories. A suite of beam diagnostics was used to characterize a high energy laser pulse with a large aperture through focus imaging setup. By varying the fluence on the plasma mirror around the plasma ignition threshold, critical performance parameters were determined and a more detailed understanding of the way in which a plasma mirror works could be deduced. It was found, that very subtle variations in the laser near field profile will have strong effects on the reflected pulse if the maximum fluence on the plasma mirror approaches the plasma ignition threshold.
Solutions of D = 2 supersymmetric Yang-Mills quantum mechanics with SU(N) gauge group
Authors: Korcyl Piotr
Published: May 2011

We describe the generalization of the recently derived solutions of D = 2 supersymmetric Yang-Mills quantum mechanics with SU(3) gauge group to the generic case of SU(N) gauge group. We discuss the spectra and eigensolutions in bosonic as well as fermionic sectors.
A versatile pulse programmer for magnetic resonance imaging
Authors: Ning Ruipeng , Yang Guang , Li Gengying
Published: May 2011

Hardware and software solutions for a versatile pulse programmer have been presented. The core of the pulse programmer is an FPGA device that provides flexibility to the design and reduces the number of electronics elements needed. The event of the pulse programmer consists of 16 bits. The main feature of the proposed pulse programmer is that the 16 outputs can be independently delayed. This is important for correcting delays of the RF channels or the gradient channels due to various causes. The proposed pulse programmer is integrated into an MRI scanner, and the correction of the gradient system delay is taken as an example to experimentally demonstrate its performance.
InGaN/GaN disk-in-nanowire white light emitting diodes on (001) silicon
Authors: Guo Wei , Banerjee Animesh , Bhattacharya Pallab , Ooi Boon S.
Published: May 2011

High density (∼1011 cm−2) GaN nanowires and InGaN/GaN disk-in-nanowire heterostructures have been grown on (001) silicon substrates by plasma-assisted molecular beam epitaxy. The nanowires exhibit excellent uniformity in length and diameter and a broad emission is obtained by incorporating InGaN disks of varying composition along the length of the nanowires. Monolithic lighting emitting diodes were fabricated with appropriate n- and p-doping of contact layers. White light emission with chromaticity coordinates of x=0.29 and y=0.37 and a correlated color temperature of 5500–6500 K at an injection current of 50 A/cm2 is measured. The measured external quantum efficiency of the devices do not exhibit any rollover (droop) up to an injection current density of 400 A/cm2.
On the calculation of effective electric field in In0.53Ga0.47As surface channel metal-oxide-semiconductor field-effect-transistors
Authors: Sonnet A. M. , Galatage R. V. , Hurley P. K. , Pelucchi E. , Thomas K. K. , Gocalinska A. , Huang J. , Goel N. , Bersuker G. , Kirk W. P. , Hinkle C. L. , Wallace R. M. , Vogel E. M.
Published: May 2011

The effective electron mobility of In0.53Ga0.47As metal-oxide-semiconductor field-effect-transistors with HfO2 gate oxide was measured over a wide range of channel doping concentration. The back bias dependence of effective electron mobility was used to correctly calculate the vertical effective electric field. The effective electron mobility at moderate to high vertical effective electric field shows universal behavior independent of substrate impurity concentration.
Life history and morphological variation in intraspecific seeder and resprouter populations of two species from rock outcrop vegetation in north-east New South Wales
Authors: Benwell Andrew , McCorkell Bruce
Published: May 2011

The processes underlying differentiation of seeder and resprouter life histories were explored by studying changes in life history and morphological traits in intraspecific seeder and resprouter populations of the grass Entolasia stricta and shrub Keraudrenia hillii var. hillii from adjoining rock pavement and fringing woodland habitats. Population traits were sampled in the field and studied under controlled conditions in a randomised experimental design with two levels of population/habitat (seeder/rock outcrop and resprouter/woodland) and two levels of fertiliser (low and high). Life history traits reflecting rate of growth, relative allocation of resources to reproductive and vegetative growth and timing of events, as well as a selection of simple morphological traits were recorded. Generalised linear model analysis showed that population had a strong, significant effect on the majority of traits examined, particularly those relating to reproductive output. Many traits were also significantly responsive to nutrient, or induced plasticity, and significant interaction terms were very few. The two species exhibited parallel intraspecific changes in life history between habitats and traits recorded under experimental conditions were similar to those observed in the field. The populations from pavement shrubland produced a more compact shoot system, faster early shoot growth (E. stricta), more numerous flowers and more numerous and lighter seeds. In fringing woodland, both species produced a larger shoot system, slower early shoot growth and fewer and larger seeds. Significant intraspecific differences in population traits and correlation of population with habitat type indicated that the intraspecific seeder-resprouter populations of both species were ecotypes selected by habitat factors, most likely associated with the edaphic environment rather than fire regime variables.
Identification of key environmental variables associated with the presence of Toothed Leionema (Leionema bilobum serrulatum) in the Strzelecki Ranges, Victoria, Australia
Authors: Wright Wendy , Zhu Xuan , Okurowski Mateusz
Published: May 2011

Toothed Leionema is one of four subspecies of Leionema bilobum from the Rutaceae family. A dense shrub or small tree, growing to ~4 m high, it is a poorly investigated species which is considered rare in Victoria, Australia. This paper presents the results of a study using Geographical Information Systems and Weights-of-Evidence predictive modelling to assess the importance of seven environmental factors in determining habitat suitability for this species in the Strzelecki Ranges, Victoria. This method is particularly useful in understanding the distribution of rare species, especially where the ecology of the species of interest is not well understood. Of the seven environmental factors considered here, four were found to be important: elevation, aspect, distance to water and distance to plantation (disturbed) areas. The modelling results indicate that areas with elevations between 350 and 550 m and a dominant south-western aspect that are close to plantation areas (within 700 m), and to water (within 1100–1200 m), provide potentially suitable habitat for Toothed Leionema in the region.
Phosphate adsorption at variable charge soil/water interfaces as influenced by ionic strength
Authors: Wang Yong , Jiang Jun , Xu Ren-kou , Tiwari Diwakar
Published: May 2011

The effect of phosphate adsorption on zeta potential of the colloids of variable charge soils and the effect of ionic strength on phosphate adsorption by the soils were investigated using batch experimental method. The presence of phosphate resulted in the decrease in zeta potential and isoelectric point (IEP) of the colloids of the soils, which further suggested that the phosphate was adsorbed specifically by these soils. The effect of phosphate adsorption on zeta potential was correlated with the content of free Fe/Al oxides in the soils; the higher the content of Fe/Al oxides in a soil the greater was the decrease in zeta potential and IEP of the soil colloids. The intersection of phosphate adsorption–pH curves at different ionic strengths (a characteristic pH) was obtained for 2 Oxisols. Above this pH, the adsorption of phosphate increased with increasing ionic strength, whereas below it the reverse trend occurred. The intersect pH was 4.60 for the Oxisol from Guangdong and 4.55 for the Oxisol from Yunnan, which was lower than the values of PZSE (point of zero salt effect) of these soils, but near the PZNC (point of zero net charge) of the soils. The effects of ionic strength and pH on phosphate adsorption by these soils were interpreted with the help of an adsorption model developed previously by Bowden et al. The results of zeta potential suggested that the potential in an adsorption plane became less negative with increasing ionic strength above the soil PZNC and decreased with increasing ionic strength below the soil PZNC. These results support the hypothesis of the adsorption model that the potential in the adsorption plane changed with ionic strength with an opposite trend to the surface charge of these soils. The phosphate adsorption by these soils was related not only to the ionic strength but also to the types of electrolytes present. K+ induced a greater increase in phosphate adsorption than Na+ due to the greater affinity of the soils to K+ than Na+.
Effects of application of poppy waste on spinach yields, soil properties, and soil carbon sequestration in southern Tasmania
Authors: Hardie M. A. , Cotching W. E.
Published: May 2011

Production of fresh market salad and lettuce in southern Tasmania has reduced soil organic carbon levels, resulting in the development of surface crusts, erosion, and poor water infiltration. Options for increasing soil organic carbon under this production system are limited by strict food safety protocols which prohibit the use of composts or ‘animal’-based waste products. Poppy waste was identified as a suitable seed-free, inexpensive source of non-animal-based organic carbon. Trials were established on a Chromosol to evaluate the effects of poppy waste incorporation on soil organic carbon and production of Bocane spinach (Spinach oleracea). Application of 50–200 m3/ha of poppy waste resulted in significant yield loss (up to 57%) of seedlings planted within 8 weeks following waste incorporation. It was speculated that yield loss resulted from nitrogen drawdown; however, soil analyses demonstrated that yield loss resulted from a combination of increased soil pH and soil salinity (EC). The 200 m3/ha treatment increased soil pHwater from 7.2 before application to 8.5 and 7.7, at 4 and 22 weeks after application. Soil EC1 : 5 increased from 0.15 dS/m before application to 0.45 dS/m at 2 weeks after application, before returning to 0.15 dS/m at 22 weeks. Application of poppy waste at 200 m3/ha significantly increased soil organic carbon from 1.24% to 1.57%; however, applications at lower rates were not significant. The carbon sequestration efficiency from poppy waste to soil organic carbon was calculated to be approximately 0.20.
Multivariate and geostatistical analysis of wetland soil salinity in nested areas of the Yellow River Delta
Authors: Yang M. , Liu S. L. , Yang Z. F. , Sun T. , Beazley Robert
Published: May 2011

This study investigated scale dependency of certain soil salinity ions in topsoil horizons in the Yellow River Delta in north-east Shandong province, China. Factorial kriging analysis (FKA) was used to analyse spatial variability of soil salinity ions (Na+, K+, Mg2+, Ca2+, Cl–, SO42–) sampled at 3 nested areas over a geologically contrasting region. Correlation analysis and principal component analysis (PCA) were performed on the logarithmic variables, then multivariate geostatistics was used to investigate scale dependency of soil salinity spatial variability and auto- and cross-variograms exhibited by 3 spatial structures: nugget effect, short-range, and long-range structures. Statistical analysis showed that NaCl was the main salinity type over the 3 nested sample areas. In addition, the variables were random and regional, which implied that a linear model of coregionalisation was feasible for the analysis of their spatial variability. The coefficients of the coregionalisation matrix showed that the short-range structures of auto- and cross-correlation for soil salinity were dominant at the large and middle-sized sample areas, while the long-range structure dominated at the small area. The resulting structural correlation coefficients showed strong correlations between variables changing as a function of spatial scale. These relationships between soil salinity variables at different spatial structures were not acquired by the linear correlation coefficients.
PCA was then performed on the coregionalisation matrices at each sample area to summarise the relationships among variables at different spatial structures. From the synthetic analysis of coregionalisation matrices, correlation matrices, and principal components, we concluded that soil genesis and parent material may act on short-range variation of soil salinity, while climate and topography may influence long-range structure at the large sample area. At the middle-sized sample area, variations were mostly affected by mineral fertilisation at the short-range structure, while human activities such as irrigation and drainage in wetland restorations influenced the soil salinity spatial variability at the long-range scale. Vegetation and groundwater table may also be important factors influencing the spatial variability of soil salinity at different spatial structures at the small sample areas.
Spectroscopic behaviour of 14C-labeled humic acids in a long-term field experiment with three cropping systems
Authors: Tatzber Michael , Stemmer Michael , Spiegel Heide , Katzlberger Christian , Zehetner Franz , Haberhauer Georg , Garcia-Garcia Elena , Gerzabek Martin H.
Published: May 2011

The stabilisation of 14C-labelled farmyard manure was investigated under different cropping systems (crop rotation, monoculture, and bare fallow) in a long-term field experiment established in 1967. Solid-state 13C-NMR of bulk soils yielded a gradient of increasing aromatic properties in the order: straw manure–crop rotation < straw manure–monoculture < straw and farmyard manure–bare fallow. The opposite trend was observed for O-alkyl groups. The farmyard manure–bare fallow treatment was used to investigate changes of humic acids (HAs) with time. The FT-IR bands of aromatics, carbonyl groups, and a band of methyls and benzene rings increased over the 36 years of the experiment, whereas 2 amide bands and a band of sulfone and/or ester groups decreased. Fluorescence spectroscopy verified the increase in aromatic properties with age. Consequently, during soil organic matter stabilisation, HAs showed increasing properties of carbonyl and aromatic groups, whereas amidic groups decreased. The dynamic character of HAs, as shown by 14C, was also reflected by distinct spectroscopic changes over the period of investigation.
Dominant soil orders in Tasmania: distribution and selected properties
Authors: Cotching W. E. , Lynch S. , Kidd D. B.
Published: May 2011

Dermosols (24%) and Organosols (14.8%) are the dominant soil orders in Tasmania, with the mapped occurrence of >985 000 ha of Organosols in Tasmania being the greatest in any Australian State. Tenosols and Rudosols are well represented in all 3 natural resource management (NRM) regions and Kurosols are more prevalent in the NRM North and South Regions. Tasmania has a greater proportion of Ferrosols (8.4%) than the whole of Australia (0.8%) and these soils are some of the most productive in Tasmania with >25 000 ha used for cropping. Hydrosols (3.7%) are probably underestimated. Chromosols (5.3%) and Sodosols (1.6%) are relatively minor soils in Tasmania, occurring predominantly in lower rainfall areas with <800 mm average annual rainfall. Parent material is a strong determinant of soil distribution in Tasmania but many Soil Orders occur on a wide range of parent materials. Brown suborders are predominant in several Soil Orders. A large part of Tasmania (2 658 000 ha) is mapped as being used for conservation, with one-third of this area being mapped as Organosols. The mean surface horizon soil carbon content (4.3%) is relatively high, likely due to Tasmania’s relatively high annual rainfall and cool temperatures. Most Soil Orders have moderately acid surface horizons but soils on calcareous parent materials are neutral to strongly alkaline (Tenosols and Calcarosols). The dataset covers the mainland extent of Tasmania, as well as all large islands around Tasmania’s coastline including King, Flinders, Hunter, Three Hummock, Robbins, Cape Barren, Clarke, and Maria Islands.
Effect of physiographic conditions on the spatial variation of seasonal topsoil moisture in Mediterranean soils
Authors: López-Vicente M. , Navas A. , Machín J.
Published: May 2011

This paper studies the spatial variation of topsoil moisture within different soil types in a medium-size catchment at the Spanish Pre-Pyrenees (Estaña catchment, 2.5 km2) using seasonal data at high spatial resolution. Topsoil moisture was measured with a Delta-T Theta Probe ML2x device to 80 mm soil depth and at seasonal scale during 2005 and 2006. Measured values were related to the soil water content at field capacity to calculate the relative topsoil moisture (θR, %). The highest values of θR were obtained in autumn (53.2%) and the lowest in summer (32.1%), showing a positive correlation with seasonal precipitation and an inverse relationship with seasonal solar radiation (SR). Steep northern slopes presented the highest values of θR in spring, summer, and winter, and topsoil moisture progressively decreased from steep northern slopes to gentle slopes and from gentle slopes to steep southern slopes, defining a topographical trend. Any topographical trend was observed in autumn when values of θR were very high within the whole catchment. No significant correlation was found between values of θR and those of topographic wetness index (TWI) except in summer. Relative topsoil moisture varied greatly for the different soil types, and the highest values were also measured in steep northern slopes in spring, summer, and winter. Correlation between θR and SR was good for the different soil types in winter when SR varied the most for the different physiographic units and the range of values of θR was the highest. No significant correlation was found in autumn for any soil type due to the very low values of solar radiation. Results of this work draw attention to the importance of considering the slope steepness and aspect conditions for a more precise characterisation of moisture-sensitive areas in Mediterranean environments and soils at seasonal scale.
Identifying splits with clear separation: a new class discovery
method for gene expression data
Authors: von Heydebreck Anja , Huber Wolfgang , Poustka Annemarie , Vingron Martin
Published: May 2011

We present a new class discovery method for microarray gene expression data. Based on a collection of gene expression profiles from different tissue samples, the method searches for binary class distinctions in the set of samples that show clear separation in the expression levels of specific subsets of genes. Several mutually independent class distinctions may be found, which is difficult to obtain from most commonly used clustering algorithms. Each class distinction can be biologically interpreted in terms of its supporting genes. The mathematical characterization of the favored class distinctions is based on statistical concepts. By analyzing three data sets from cancer gene expression studies, we demonstrate that our method is able to detect biologically relevant structures, for example cancer subtypes, in an unsupervised fashion.

Contact: heydebre@molgen.mpg.de
Feature selection for DNA methylation based cancer

classification
Authors: Model Fabian , Adorján Péter , Olek Alexander , Piepenbrock Christian
Published: May 2011

Molecular portraits, such as mRNA expression or DNA methylation patterns, have been shown to be strongly correlated with phenotypical parameters. These molecular patterns can be revealed routinely on a genomic scale. However, class prediction based on these patterns is an under-determined problem, due to the extreme high dimensionality of the data compared to the usually small number of available samples. This makes a reduction of the data dimensionality necessary. Here we demonstrate how phenotypic classes can be predicted by combining feature selection and discriminant analysis. By comparing several feature selection methods we show that the right dimension reduction strategy is of crucial importance for the classification performance. The techniques are demonstrated by methylation pattern based discrimination between acute lymphoblastic leukemia and acute myeloid leukemia.

Contact: Fabian.Model@epigenomics.com
Non-symmetric score matrices and the detection of homologous
transmembrane proteins
Authors: Müller Tobias , Rahmann Sven , Rehmsmeier Marc
Published: May 2011

Given a transmembrane protein, we wish to find related ones by a database search. Due to the strongly hydrophobic amino acid composition of transmembrane domains, suboptimal results are obtained when general-purpose scoring matrices such as BLOSUM are used. Recently, a transmembrane-specific score matrix called PHAT was shown to perform much better than BLOSUM. In this article, we derive a transmembrane score matrix family, called SLIM, which has several distinguishing features. In contrast to currently used matrices, SLIM is non-symmetric. The asymmetry arises because different background compositions are assumed for the transmembrane query and the unknown database sequences. We describe the mathematical model behind SLIM in detail and show that SLIM outperforms PHAT both on simulated data and in a realistic setting. Since non-symmetric score matrices are a new concept in database search methods, we discuss some important theoretical and practical issues.

Contact: muelle_t@molgen.mpg.de
Fast optimal leaf ordering for hierarchical clustering
Authors: Bar-Joseph Ziv , Gifford David K. , Jaakkola Tommi S.
Published: May 2011

We present the first practical algorithm for the optimal linear leaf ordering of trees that are generated by hierarchical clustering. Hierarchical clustering has been extensively used to analyze gene expression data, and we show how optimal leaf ordering can reveal biological structure that is not observed with an existing heuristic ordering method. For a tree with n leaves, there are 2n−1 linear orderings consistent with the structure of the tree. Our optimal leaf ordering algorithm runs in time O(n4), and we present further improvements that make the running time of our algorithm practical.

Contact: {zivbj,gifford}@mit.edu; tommi@ai.mit.edu
Improved prediction of the number of residue contacts in
proteins by recurrent neural networks
Authors: Pollastri Gianluca , Baldi Pierre , Fariselli Pietro , Casadio Rita
Published: May 2011

Knowing the number of residue contacts in a protein is crucial for deriving constraints useful in modeling protein folding, protein structure, and/or scoring remote homology searches. Here we use an ensemble of bi-directional recurrent neural network architectures and evolutionary information to improve the state-of-the-art in contact prediction using a large corpus of curated data. The ensemble is used to discriminate between two different states of residue contacts, characterized by a contact number higher or lower than the average value of the residue distribution. The ensemble achieves performances ranging from 70.1% to 73.1% depending on the radius adopted to discriminate contacts (6Âto 12Â). These performances represent gains of 15% to 20% over the base line statistical predictors always assigning an aminoacid to the most numerous state, 3% to 7% better than any previous method. Combination of different radius predictors further improves the performance.

Server: http://promoter.ics.uci.edu/BRNN-PRED/

Contact: pfbaldi@ics.uci.edu

*To whom all correspondence should be addressed.
Rich probabilistic models for gene expression
Authors: Segal Eran , Taskar Ben , Gasch Audrey , Friedman Nir , Koller Daphne
Published: May 2011

Clustering is commonly used for analyzing gene expression data. Despite their successes, clustering methods suffer from a number of limitations. First, these methods reveal similarities that exist over all of the measurements, while obscuring relationships that exist over only a subset of the data. Second, clustering methods cannot readily incorporate additional types of information, such as clinical data or known attributes of genes. To circumvent these shortcomings, we propose the use of a single coherent probabilistic model, that encompasses much of the rich structure in the genomic expression data, while incorporating additional information such as experiment type, putative binding sites, or functional information. We show how this model can be learned from the data, allowing us to discover patterns in the data and dependencies between the gene expression patterns and additional attributes. The learned model reveals context-specific relationships, that exist only over a subset of the experiments in the dataset. We demonstrate the power of our approach on synthetic data and on two real-world gene expression data sets for yeast. For example, we demonstrate a novel functionality that falls naturally out of our framework: predicting the “cluster” of the array resulting from a gene mutation based only on the gene’s expression pattern in the context of other mutations.

Contact: eran@cs.stanford.edu
Separation of samples into their constituents using gene
expression data
Authors: Venet D. , Pecasse F. , Maenhaut C. , Bersini H.
Published: May 2011

Gene expression measurements are a powerful tool in molecular biology, but when applied to heterogeneous samples containing more than one cellular type the results are difficult to interpret. We present here a new approach to this problem allowing to deduce the gene expression profile of the various cellular types contained in a set of samples directly from the measurements taken on the whole sample.

Contact: davenet@ulb.ac.be
Separating real motifs from their artifacts
Authors: Blanchette Mathieu , Sinha Saurabh
Published: May 2011

The typical output of many computational methods to identify binding sites is a long list of motifs containing some real motifs (those most likely to correspond to the actual binding sites) along with a large number of random variations of these. We present a statistical method to separate real motifs from their artifacts. This produces a short list of high quality motifs that is sufficient to explain the over-representation of all motifs in the given sequences. Using synthetic data sets, we show that the output of our method is very accurate. On various sets of upstream sequences in S. cerevisiae , our program identifies several known binding sites, as well as a number of significant novel motifs.

Contact: blanchem@cs.washington.edu; saurabh@cs.washington.edu

‡The two authors contributed equally to the paper.
Probe selection algorithms with applications in the analysis of
microbial communities
Authors: Borneman James , Chrobak Marek , Della Vedova Gianluca , Figueroa Andres , Jiang Tao
Published: May 2011

We propose two efficient heuristics for minimizing the number of oligonucleotide probes needed for analyzing populations of ribosomal RNA gene (rDNA) clones by hybridization experiments on DNA microarrays. Such analyses have applications in the study of microbial communities. Unlike in the classical SBH (sequencing by hybridization) procedure, where multiple probes are on a DNA chip, in our applications we perform a series of experiments, each one consisting of applying a single probe to a DNA microarray containing a large sample of rDNA sequences from the studied population. The overall cost of the analysis is thus roughly proportional to the number of experiments, underscoring the need for minimizing the number of probes. Our algorithms are based on two well-known optimization techniques, i.e. simulated annealing and Lagrangian relaxation, and our preliminary tests demonstrate that both algorithms are able to find satisfactory probe sets for real rDNA data.

Contact: jiang@cs.ucr.edu
An efficient algorithm for finding short approximate non-tandem

repeats
Authors: Adebiyi Ezekiel F. , Jiang Tao , Kaufmann Michael
Published: May 2011

We study the problem of approximate non-tandem repeat †extraction. Given a long subject string S of length N over a finite alphabet Σ and a threshold D, we would like to find all short substrings of S of length P that repeat with at most D differences, i.e., insertions, deletions, and mismatches. We give a careful theoretical characterization of the set of seeds (i.e., some maximal exact repeats) required by the algorithm, and prove a sublinear bound on their expected numbers. Using this result, we present a sub-quadratic algorithm for finding all short (i.e., of length O(log N)) approximate repeats. The running time of our algorithm is O(DN3pow(ε)−1log N), where ε = D/P and pow(ε) is an increasing, concave function that is 0 when ε = 0 and about 0.9 for DNA and protein sequences.

Contact: adebiyi@informatik.uni-tuebingen.de

†Throughout the paper we only consider non-tandem repeats.
GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles
Authors: Friedman Carol , Kra Pauline , Yu Hong , Krauthammer Michael , Rzhetsky Andrey
Published: May 2011

Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.

Contact: friedman.carol@dmi.columbia.edu
Exact genetic linkage computations for general pedigrees
Authors: Fishelson M. , Geiger D.
Published: May 2011

Motivation: Genetic linkage analysis is a useful statistical tool for mapping disease genes and for associating functionality of genes with their location on the chromosome. There is a need for a program that computes multipoint likelihood on general pedigrees with many markers that also deals with two-locus disease models.

Results: In this paper we present algorithms for performing exact multipoint likelihood calculations on general pedigrees with a large number of highly polymorphic markers, taking into account a variety of disease models. We have implemented these algorithms in a new computer program called superlink which outperforms leading linkage software with regards to functionality, speed, memory requirements and extensibility.

Availability: superlink is available at http://bioinfo.cs.technion.ac.il/superlink

Contact: fmaayan@cs.technion.ac.ildang@cs.technion.ac.il

Keywords: Bayesian networks; Fastlink; Genehunter; linkage analysis; Vitesse.
Representing genetic sequence data for pharmacogenomics: an
evolutionary approach using ontological and relational models
Authors: Rubin Daniel L. , Shafa Farhad , Oliver Diane E. , Hewett Micheal , Altman Russ B.
Published: May 2011

Motivation: The information model chosen to store biological data affects the types of queries possible, database performance, and difficulty in updating that information model. Genetic sequence data for pharmacogenetics studies can be complex, and the best information model to use may change over time. As experimental and analytical methods change, and as biological knowledge advances, the data storage requirements and types of queries needed may also change.

Results: We developed a model for genetic sequence and polymorphism data, and used XML Schema to specify the elements and attributes required for this model. We implemented this model as an ontology in a frame-based representation and as a relational model in a database system. We collected genetic data from two pharmacogenetics resequencing studies, and formulated queries useful for analysing these data. We compared the ontology and relational models in terms of query complexity, performance, and difficulty in changing the information model. Our results demonstrate benefits of evolving the schema for storing pharmacogenetics data: ontologies perform well in early design stages as the information model changes rapidly and simplify query formulation, while relational models offer improved query speed once the information model and types of queries needed stabilize.

Availability: Our ontology and relational models are available at http://smi-web.stanford.edu/projects/helix/pubs/ismb02/.

Contact: rubin@smi.stanford.eduruss.altman@stanford.eduhelp@pharmgkb.org

Keywords: ontologies; relational databases; schema; data models; pharmacogenomics.