bluuebunny/crossref_metadata_2025_split huggingface dataset:
ScaLAPACK's MRRR algorithm
Authors: Vömel Christof 
Published: January 2010

The (sequential) algorithm of Multiple Relatively Robust Representations, MRRR, is a more efficient variant of inverse iteration that does not require reorthogonalization. It solves the eigenproblem of an unreduced symmetric tridiagonal matrix
T
∈

R
n × n

at
O
(
n
2
) cost. The computed normalized eigenvectors are numerically orthogonal in the sense that the dot product between different vectors is
O
(
n
ϵ), where ϵ refers to the relative machine precision.

This article describes the design of ScaLAPACK's parallel MRRR algorithm. One emphasis is on the critical role of the representation tree in achieving both adequate accuracy and parallel scalability. A second point concerns the favorable properties of this code: subset computation, the use of static memory, and scalability.
Unlike ScaLAPACK's Divide & Conquer and QR, MRRR can compute subsets of eigenpairs at reduced cost. And in contrast to inverse iterations which can fail, it is guaranteed to produce a satisfactory answer while maintaining memory scalability.
ParEig, the parallel MRRR algorithm for PLAPACK, uses dynamic memory allocation. This is avoided by our code at marginal additional cost. We also use a different representation tree criterion that allows for more accurate computation of the eigenvectors but can make parallelization more difficult.
From program verification to program synthesis
Authors: Srivastava Saurabh , Gulwani Sumit , Foster Jeffrey S. 
Published: January 2010

This paper describes a novel technique for the synthesis of imperative programs. Automated program synthesis has the potential to make programming and the design of systems easier by allowing programs to be specified at a higher-level than executable code. In our approach, which we call proof-theoretic synthesis, the user provides an input-output functional specification, a description of the atomic operations in the programming language, and a specification of the synthesized program's looping structure, allowed stack space, and bound on usage of certain operations. Our technique synthesizes a program, if there exists one, that meets the input-output specification and uses only the given resources.
The insight behind our approach is to interpret program synthesis as generalized program verification, which allows us to bring verification tools and techniques to program synthesis. Our synthesis algorithm works by creating a program with unknown statements, guards, inductive invariants, and ranking functions. It then generates constraints that relate the unknowns and enforces three kinds of requirements: partial correctness, loop termination, and well-formedness conditions on program guards. We formalize the requirements that program verification tools must meet to solve these constraint and use tools from prior work as our synthesizers.
We demonstrate the feasibility of the proposed approach by synthesizing programs in three different domains: arithmetic, sorting, and dynamic programming. Using verification tools that we previously built in the VS3 project we are able to synthesize programs for complicated arithmetic algorithms including Strassen's matrix multiplication and Bresenham's line drawing; several sorting algorithms; and several dynamic programming algorithms. For these programs, the median time for synthesis is 14 seconds, and the ratio of synthesis to verification time ranges between 1x to 92x (with an median of 7x), illustrating the potential of the approach.
Predicting the effect of climate change on aggregation behaviour in four species of terrestrial isopods
Authors: Derhé Mia , Moss Anna , Edwards David , Carmenta Rachel , Hassall Mark 
Published: January 2010

AbstractClimate warming has changed the spatial distributions and temporal behaviours of several taxa. A key question that remains is how behaviours that alter microclimatic conditions might be used to buffer the effects of climate change. In this study, we focus on the aggregation behaviour of four species of terrestrial isopods, in which groups of individuals clump together to prevent moisture-loss, and use a laboratory protocol to investigate the effects of changes in relative humidity (RH) and temperature on aggregation. We find that three species aggregate more at lower RH and at higher temperatures, and that species that are better adapted to reducing moisture loss aggregate less than do species with fewer such adaptations. These results suggest that behavioural variation can buffer the effects of changes in microclimate. We finish by suggesting that it is critical to determine how such behavioural shifts will affect isopod densities and competitive hierarchies.
Animal tool use: current definitions and an updated comprehensive catalog
Authors: Bentley-Condit Vicki , Smith  
Published: January 2010

AbstractDespite numerous attempts to define animal tool use over the past four decades, the definition remains elusive and the behaviour classification somewhat subjective. Here, we provide a brief review of the definitions of animal tool use and show how those definitions have been modified over time. While some aspects have remained constant (i.e., the distinction between 'true' and 'borderline' tool use), others have been added (i.e., the distinction between 'dynamic' and 'static' behaviours). We present an updated, comprehensive catalog of documented animal tool use that indicates whether the behaviours observed included any 'true' tool use, whether the observations were limited to captive animals, whether tool manufacture has been observed, and whether the observed tool use was limited to only one individual and, thus, 'anecdotal' (i.e., N = 1). Such a catalog has not been attempted since Beck (1980). In addition to being a useful reference for behaviourists, this catalog demonstrates broad tool use and manufacture trends that may be of interest to phylogenists, evolutionary ecologists, and cognitive evolutionists. Tool use and tool manufacture are shown to be widespread across three phyla and seven classes of the animal kingdom. Moreover, there is complete overlap between the Aves and Mammalia orders in terms of the tool use categories (e.g., food extraction, food capture, agonism) arguing against any special abilities of mammals. The majority of tool users, almost 85% of the entries, use tools in only one of the tool use categories. Only members of the Passeriformes and Primates orders have been observed to use tools in four or more of the ten categories. Thus, observed tool use by some members of these two orders (e.g., Corvus, Papio) is qualitatively different from that of all other animal taxa. Finally, although there are similarities between Aves and Mammalia, and Primates and Passeriformes, primate tool use is qualitatively different. Approximately 35% of the entries for this order demonstrate a breadth of tool use (i.e., three or more categories by any one species) compared to other mammals (0%), Aves (2.4%), and the Passeriformes (3.1%). This greater breadth in tool use by some organisms may involve phylogenetic or cognitive differences — or may simply reflect differences in length and intensity of observations. The impact that tool usage may have had on groups' respective ecological niches and, through niche-construction, on their respective evolutionary trajectories remains a subject for future study.
The delictual origin, penal nature and reipersecutory object of the actio damni iniuriae legis Aquiliae
Authors: Sirks Boudewijn 
Published: January 2010

AbstractIt is commonly assumed that the litis aestimatio of the actio legis Aquiliae was a penalty which, in practice, was set at the loss suffered by the victim of the wrong and therefore functioned as compensation. This assumption is based on the nature of the action as founding in a delict and characterised by the Romans as a penal action. It also shares the elements of penal actions. But this is at odds with other texts which treat the action as directed purely at compensation. It is suggested that in order to understand this we have to distinguish between the origin of the penal actions, which is penal and which carries certain common features such as the fundamental impossibility to sue heirs or descendants of the wrongdoer, and their purpose or object. It is possible to distinguish two groups, one aiming at a penalty, the other aiming at compensation. Only in the latter group the action can be exercised against the heir of the wrongdoer and only restrictedly: it is the compensatory aim which allows for this. Further, the lex Aquilia and its chapters are examined whether a compensatory purpose is distinguishable here as well.
'Augustine' versus Jerome: commentaries on Gratian's Decretum, D. 9, c. 6, from Paucapalea to Juan de Torquemada
Authors: Linde J. Cornelia 
Published: January 2010

AbstractIn his Decretum, D. 9, c. 6, Gratian stated the respective value of Hebrew, Greek and Latin manuscripts of the Bible for the emendation of Latin Scripture. This article deals with the commentaries on this passage from the mid-twelfth to the mid-fifteenth century. Due to the misattribution of a statement to Augustine rather than Jerome in the Decretum, and the later introduction of an out-of-context quotation by Jerome, the two Church Fathers seemed to contradict each other on the matter in question. For three centuries, the decretists sought to explain or even reconcile this contradiction in various ways which are traced in this article.
Antwerp commercial legislation in Amsterdam in the 17th century: legal transplant or jumping board?
Authors: De ruysscher Dave 
Published: January 2010

AbstractThe 1582 Antwerp costuymen influenced Amsterdam law during the seventeenth and eighteenth centuries. Although the Antwerp law has often been considered as an applicable law in the Amstel city, its role was more limited. At the end of the sixteenth century and during the first half of the seventeenth century, it was used as a common and subsidiary applicable law for certain mercantile issues. Later on, as the Amsterdam legislator issued ordinances on these themes, this function declined. Yet, references to the Antwerp law book were still common in the eighteenth century, although they were more a consequence of a cultural attraction than of an actual application of the Brabant law book.
Dutch litigation before the Great Council of Mechlin An additional calendar of the 'Appeals from Holland'
Authors: Wijffels Alain 
Published: January 2010

AbstractM. Oosterbosch's additional calendar of documents belonging to the series 'Appeals from Holland' (Brussels, General Archives of the Realm, Collection Great Council of Mechlin) refers to hitherto unknown documents which may encourage fresh thematic research and case-studies on conflicts and litigation which originated mostly from Holland and Zeeland (from the 1460s until the 1580s), and to a lesser extent from Utrecht and (also during later periods) from Gelderland.
Influence of the 26°N RAPID–MOCHA Array and Florida Current Cable Observations on the ECCO–GODAE State Estimate
Authors: Baehr Johanna 
Published: January 2010

Abstract
The incorporation of local temperature and salinity observations from the Rapid Climate Change–Meridional Overturning Circulation and Heatflux Array (RAPID–MOCHA), as well as the cable estimates of volume transport in the Florida Current (FC), is tested in the Estimating the Circulation and Climate of the Ocean–Global Ocean Data Assimilation Experiment (ECCO–GODAE) estimation system for their impact on the estimate of the meridional overturning circulation (MOC) and the meridional heat transport in the Atlantic. An experimental setup covering the first deployment period of RAPID–MOCHA from March 2004 to March 2005 is used to test different strategies for incorporating these datasets. Incorporating both monthly means of the FC data and monthly means of the RAPID–MOCHA temperature and salinity measurements at the eastern and western boundaries of the basin as an observational constraint in a 1-yr experiment results in an adjustment to the reference estimate, which does not include these datasets, of approximately 1 Sv (1 Sv ≡ 106 m3 s−1) in the MOC at 26°N and the adjacent latitudes (approximately ±15°), with a larger northward branch of the MOC above 1000 m, compensated by a larger flow in the southward branch of the MOC between approximately 2000 and 3000 m. The meridional heat transport from 26°N to near 40°N is approximately 0.05 PW larger than in the reference experiment.
SST–North American Hydroclimate Links in AMIP Simulations of the Drought Working Group Models: A Proxy for the Idealized Drought Modeling Experiments
Authors: Ruiz-Barradas Alfredo , Nigam Sumant 
Published: January 2010

Abstract
The present study assesses the potential of the U.S. Climate Variability and Predictability (CLIVAR) Drought Working Group (DWG) models in simulating interannual precipitation variability over North America, especially the Great Plains. It also provides targets for the idealized DWG model experiments investigating drought origin. The century-long Atmospheric Model Intercomparison Project (AMIP) simulations produced by version 3.5 of NCAR’s Community Atmosphere Model (CAM3.5), the Lamont-Doherty Earth Observatory’s Community Climate Model (CCM3), and NASA’s Seasonal-to-Interannual Prediction Project (NSIPP-1) atmospheric models are analyzed; CCM3 and NSIPP-1 models have 16- and 14-ensemble simulations, respectively, while CAM3.5 only has 1.
The standard deviation of summer precipitation is different in AMIP simulations. The maximum over the central United States seen in observations is placed farther to the west in simulations. Over the central plains the models exhibit modest skill in simulating low-frequency precipitation variability, a Palmer drought severity index proxy. The presence of a linear trend increases correlations in the period 1950–99 when compared with those for the whole century. The SST links of the Great Plains drought index have features in common with observations over both the Pacific and Atlantic Oceans.
Interestingly, summer-to-fall precipitation regressions of the warm Trend, cold Pacific, and warm Atlantic modes of annual mean SST variability (used in forcing the DWG idealized model experiments) tend to dry the southwestern, midwestern, and southeastern regions of the United States in the observations and, to a lesser extent, in the simulations.
The similarity of the idealized SST-forced droughts in DWG modeling experiments with AMIP precipitation regressions of the corresponding SST principal components, evident especially in the case of the cold Pacific pattern, suggests that the routinely conducted AMIP simulations could have served as an effective proxy for the more elaborated suite of DWG modeling experiments.
The Use of Euclidean Geometric Distance on RGB Color Space for the Classification of Sky and Cloud Patterns
Authors: Mantelli Neto Sylvio Luiz , von Wangenheim Aldo , Pereira Enio Bueno , Comunello Eros 
Published: January 2010

Abstract
The current work describes the use of multidimensional Euclidean geometric distance (EGD) and Bayesian methods to characterize and classify the sky and cloud patterns present in image pixels. From specific images and using visualization tools, it was noticed that sky and cloud patterns occupy a typical locus on the red–green–blue (RGB) color space. These two patterns were linearly distributed parallel to the RGB cube’s main diagonal at distinct distances. A characterization of the cloud and sky patterns EGD was done by supervision to eliminate errors due to outlier patterns in the analysis. The exploratory data analysis of EGD for sky and cloud patterns showed a Gaussian distribution, allowing generalizations based on the central limit theorem. An intensity scale of brightness is proposed from the Euclidean geometric projection (EGP) on the RGB cube’s main diagonal. An EGD-based classification method was adapted to be properly compared with existing ones found in related literature, because they restrict the examined color-space domain. Elimination of this limitation was considered a sufficient criterion for a classification system that has resource restrictions. The EGD-adapted results showed a correlation of 97.9% for clouds and 98.4% for sky when compared to established classification methods. It was also observed that EGD was able to classify cloud and sky patterns invariant to their brightness attributes and with reduced variability because of the sun zenith angle changes. In addition, it was observed that Mie scattering could be noticed and eliminated (together with the reflector’s dust) as an outlier during the analysis. Although Mie scattering could be classified with additional analysis, this is left as a suggestion for future work.
Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways
Authors: Mano Adi , Tuller Tamir , Béjà Oded , Pinter Ron Y 
Published: January 2010

Abstract

Background
Pathways provide topical descriptions of cellular circuitry. Comparing analogous pathways reveals intricate insights into individual functional differences among species. While previous works in the field performed genomic comparisons and evolutionary studies that were based on specific genes or proteins, whole genomic sequence, or even single pathways, none of them described a genomic system level comparative analysis of metabolic pathways. In order to properly implement such an analysis one should overcome two specific challenges: how to combine the effect of many pathways under a unified framework and how to appropriately analyze co-evolution of pathways.
Here we present a computational approach for solving these two challenges. First, we describe a comprehensive, scalable, information theory based computational pipeline that calculates pathway alignment information and then compiles it in a novel manner that allows further analysis. This approach can be used for building phylogenies and for pointing out specific differences that can then be analyzed in depth. Second, we describe a new approach for comparing the evolution of metabolic pathways. This approach can be used for detecting co-evolutionary relationships between metabolic pathways.

Results
We demonstrate the advantages of our approach by applying our pipeline to data from the MetaCyc repository (which includes a total of 205 organisms and 660 metabolic pathways). Our analysis revealed several surprising biological observations. For example, we show that the different habitats in which Archaea organisms reside are reflected by a pathway based phylogeny. In addition, we discover two striking clusters of metabolic pathways, each cluster includes pathways that have very similar evolution.

Conclusion
We demonstrate that distance measures that are based on the topology and the content of metabolic networks are useful for studying evolution and co-evolution.
Better score function for peptide identification with ETD MS/MS spectra
Authors: Liu Xiaowen , Shan Baozhen , Xin Lei , Ma Bin 
Published: January 2010

Abstract

Background
Tandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics. A good score function for measuring the match quality between a peptide and an MS/MS spectrum is instrumental for the protein identification. Traditionally the to-be-measured peptides are fragmented with the collision induced dissociation (CID) method. More recently, the electron transfer dissociation (ETD) method was introduced and has proven to produce better fragment ion ladders for larger and more basic peptides. However, the existing software programs that analyze ETD MS/MS data are not as advanced as they are for CID.

Results
To take full advantage of ETD data, in this paper we develop a new score function to evaluate the match between a peptide and an ETD MS/MS spectrum. Experiments on real data demonstrated that this newly developed score function significantly improved the de novo sequencing accuracy of the PEAKS software on ETD data.

Conclusion
A new and better score function for ETD MS/MS peptide identification was developed. The method used to develop our ETD score function can be easily reused to train new score functions for other types of MS/MS data.
Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm
Authors: Hsieh Chih-Hung , Chang Darby Tien-Hao , Hsueh Cheng-Hao , Wu Chi-Yeh , Oyang Yen-Jen 
Published: January 2010

Abstract

Background
MicroRNAs (miRNAs) are short non-coding RNA molecules, which play an important role in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs) over the years. Recently, ab initio approaches have attracted more attention because they do not depend on homology information and provide broader applications than comparative approaches. Kernel based classifiers such as support vector machine (SVM) are extensively adopted in these ab initio approaches due to the prediction performance they achieved. On the other hand, logic based classifiers such as decision tree, of which the constructed model is interpretable, have attracted less attention.

Results
This article reports the design of a predictor of pre-miRNAs with a novel kernel based classifier named the generalized Gaussian density estimator (G2DE) based classifier. The G2DE is a kernel based algorithm designed to provide interpretability by utilizing a few but representative kernels for constructing the classification model. The performance of the proposed predictor has been evaluated with 692 human pre-miRNAs and has been compared with two kernel based and two logic based classifiers. The experimental results show that the proposed predictor is capable of achieving prediction performance comparable to those delivered by the prevailing kernel based classification algorithms, while providing the user with an overall picture of the distribution of the data set.

Conclusion
Software predictors that identify pre-miRNAs in genomic sequences have been exploited by biologists to facilitate molecular biology research in recent years. The G2DE employed in this study can deliver prediction accuracy comparable with the state-of-the-art kernel based machine learning algorithms. Furthermore, biologists can obtain valuable insights about the different characteristics of the sequences of pre-miRNAs with the models generated by the G2DE based predictor.