bluuebunny/crossref_metadata_2025_split huggingface dataset:
Der Beitrag der klinischen Neuropsychologie bei der Begutachtung von Affekttätern
Authors: Lamberti Georg 
Published: September 2009

Die forensische Begutachtung von Affekttätern zur Frage einer eingeschränkten oder aufgehobenen Steuerungsfähigkeit aufgrund einer „tiefgreifenden Bewusstseinsstörung“ war bis zur Grundsatzentscheidung des Bundesgerichtshofes im Jahre 1958 eine Domäne der forensischen Psychiatrie. Angesichts der erheblichen Entwicklung der Neurowissenschaften in den beiden letzten Jahrzehnten kommt aber gerade der klinischen Neuropsychologie bei der Begutachtung von nicht-krankhaften Bewusstseinsstörungen eine enorme Bedeutung zu. Nach der Erörterung der Begriffe wie „Bewusstsein“ bzw. „Bewusstseinsstörung“ und dem Versuch einer mehr neuropsychologisch orientierten Beschreibung der „affektbedingten Bewusstseinsstörung“ wird die Relevanz neuropsychologischer Kompetenz bei der Begutachtung von Affekttätern anhand einer Kasuistik dargestellt. Dabei handelt es sich um einen 56-jährigen Brandstifter, dessen Biographie einerseits geprägt war von Versagungen, Verlusten, Kränkungen und Aufgaben eigener Interessen und dessen Brandstiftung andererseits erklärt werden konnte als erweiterter Suizidversuch einer stark aggressionsgehemmten Persönlichkeit bei langdauernder spezifischer Tatvorgeschichte. Die Analyse der Affektkriterien n. Saß (1993) zeigt bei diesem Fall die Notwendigkeit einer weitergehenden neuropsychologischen Betrachtung des Affektgeschehens, z. B. im Hinblick auf das Kriterium der „Erinnerungsstörung“. Nach der Neubewertung dieses Falles werden auch die kürzlich von Marneros (2007) vorgeschlagenen Beurteilungsmerkmale von Affektdelikten auf neuropsychologischer Basis reflektiert und abschließend Argumente für eine mehr neuropsychologische Kompetenz bei der Beurteilung einer affektbedingten, tiefgreifenden Bewusstseinsstörung aufgeführt.
Systems Biology Graphical Notation: Process Description language Level 1
Authors: Moodie Stuart , Le Novere Nicolas , Sorokin Anatoly , Mi Huaiyu , Schreiber Falk 
Published: September 2009

AbstractStandard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
Saint: a lightweight integration environment for model annotation
Authors: Lister Allyson L. , Pocock Matthew , Taschuk Morgan , Wipat Anil 
Published: September 2009

Abstract
Summary: Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources.
Availability and Implementation: Saint is freely available for use on the web at http://www.cisban.ac.uk/saint. The web application is implemented in Google Web Toolkit and Tomcat, with all major browsers supported. The Java source code is freely available for download at http://saint-annotate.sourceforge.net. The Saint web server requires an installation of libSBML and has been tested on Linux (32-bit Ubuntu 8.10 and 9.04).
Contact: helpdesk@cisban.ac.uk; a.l.lister@ncl.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Bi-correlation clustering algorithm for determining a set of co-regulated genes
Authors: Bhattacharya Anindya , De Rajat K. 
Published: September 2009

Abstract
Motivation: Biclustering has been emerged as a powerful tool for identification of a group of co-expressed genes under a subset of experimental conditions (measurements) present in a gene expression dataset. Several biclustering algorithms have been proposed till date. In this article, we address some of the important shortcomings of these existing biclustering algorithms and propose a new correlation-based biclustering algorithm called bi-correlation clustering algorithm (BCCA).
Results: BCCA has been able to produce a diverse set of biclusters of co-regulated genes over a subset of samples where all the genes in a bicluster have a similar change of expression pattern over the subset of samples. Moreover, the genes in a bicluster have common transcription factor binding sites in the corresponding promoter sequences. The presence of common transcription factors binding sites, in the corresponding promoter sequences, is an evidence that a group of genes in a bicluster are co-regulated. Biclusters determined by BCCA also show highly enriched functional categories. Using different gene expression datasets, we demonstrate strength and superiority of BCCA over some existing biclustering algorithms.
Availability: The software for BCCA has been developed using C and Visual Basic languages, and can be executed on the Microsoft Windows platforms. The software may be downloaded as a zip file from http://www.isical.ac.in/∼rajat. Then it needs to be installed. Two word files (included in the zip file) need to be consulted before installation and execution of the software.
Contact: rajat@isical.ac.in
Supplementary information: Supplementary data are available at Bioinformatics online.
Automated inference of molecular mechanisms of disease from amino acid substitutions
Authors: Li Biao , Krishnan Vidhya G. , Mort Matthew E. , Xin Fuxiao , Kamati Kishore K. , Cooper David N. , Mooney Sean D. , Radivojac Predrag 
Published: September 2009

Abstract
Motivation: Advances in high-throughput genotyping and next generation sequencing have generated a vast amount of human genetic variation data. Single nucleotide substitutions within protein coding regions are of particular importance owing to their potential to give rise to amino acid substitutions that affect protein structure and function which may ultimately lead to a disease state. Over the last decade, a number of computational methods have been developed to predict whether such amino acid substitutions result in an altered phenotype. Although these methods are useful in practice, and accurate for their intended purpose, they are not well suited for providing probabilistic estimates of the underlying disease mechanism.
Results: We have developed a new computational model, MutPred, that is based upon protein sequence, and which models changes of structural features and functional sites between wild-type and mutant sequences. These changes, expressed as probabilities of gain or loss of structure and function, can provide insight into the specific molecular mechanism responsible for the disease state. MutPred also builds on the established SIFT method but offers improved classification accuracy with respect to human disease mutations. Given conservative thresholds on the predicted disruption of molecular function, we propose that MutPred can generate accurate and reliable hypotheses on the molecular basis of disease for ∼11% of known inherited disease-causing mutations. We also note that the proportion of changes of functionally relevant residues in the sets of cancer-associated somatic mutations is higher than for the inherited lesions in the Human Gene Mutation Database which are instead predicted to be characterized by disruptions of protein structure.
Availability: http://mutdb.org/mutpred
Contact: predrag@indiana.edu; smooney@buckinstitute.org
Identifying related journals through log analysis
Authors: Lu Zhiyong , Xie Natalie , Wilbur W. John 
Published: September 2009

Abstract
Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data.
Availability: http://www.ncbi.nlm.nih.gov/IRET/Journals
Contact: luzh@ncbi.nlm.nih.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
Algorithms for optimal protein structure alignment
Authors: Poleksic Aleksandar 
Published: September 2009

Abstract
Motivation: Structural alignment is an important tool for understanding the evolutionary relationships between proteins. However, finding the best pairwise structural alignment is difficult, due to the infinite number of possible superpositions of two structures. Unlike the sequence alignment problem, which has a polynomial time solution, the structural alignment problem has not been even classified as solvable.
Results: We study one of the most widely used measures of protein structural similarity, defined as the number of pairs of residues in two proteins that can be superimposed under a predefined distance cutoff. We prove that, for any two proteins, this measure can be optimized for all but finitely many distance cutoffs. Our method leads to a series of algorithms for optimizing other structure similarity measures, including the measures commonly used in protein structure prediction experiments. We also present a polynomial time algorithm for finding a near-optimal superposition of two proteins. Aside from having a relatively low cost, the algorithm for near-optimal solution returns a superposition of provable quality. In other words, the difference between the score of the returned superposition and the score of an optimal superposition can be explicitly computed and used to determine whether the returned superposition is, in fact, the best superposition.
Contact: poleksic@cs.uni.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Exploring spatial non-stationarity of fisheries survey data using geographically weighted regression (GWR): an example from the Northwest Atlantic
Authors: Windle Matthew J. S. , Rose George A. , Devillers Rodolphe , Fortin Marie-Josée 
Published: September 2009

AbstractWindle, M. J. S., Rose, G. A., Devillers, R., and Fortin, M-J. 2010. Exploring spatial non-stationarity of fisheries survey data using geographically weighted regression (GWR): an example from the Northwest Atlantic. – ICES Journal of Marine Science, 67: 145–154. Analyses of fisheries data have traditionally been performed under the implicit assumption that ecological relationships do not vary within management areas (i.e. assuming spatially stationary processes). We question this assumption using a local modelling technique, geographically weighted regression (GWR), not previously used in fisheries analyses. Outputs of GWR are compared with those of global logistic regression and generalized additive models (GAMs) in predicting the distribution of northern cod off Newfoundland, Canada, based on environmental (temperature and distance from shore) and biological factors (snow crab and northern shrimp) from 2001. Results from the GWR models explained significantly more variability than the global logistic and GAM regressions, as shown by goodness-of-fit tests and a reduction in the spatial autocorrelation of model residuals. GWR results revealed spatial regions in the relationships between cod and explanatory variables and that the significance and direction of these relationships varied locally. A k-means cluster analysis based on GWR t-values was used to delineate distinct zones of species–environment relationships. The advantages and limitations of GWR are discussed in terms of potential application to fisheries ecology.
Plant SMU-1 and SMU-2 Homologues Regulate Pre-mRNA Splicing and Multiple Aspects of Development
Authors: Chung Taijoon , Wang Dongfang , Kim Cheol-Soo , Yadegari Ramin , Larkins Brian A. 
Published: September 2009

AbstractIn eukaryotes, alternative splicing of pre-mRNAs contributes significantly to the proper expression of the genome. However, the functions of many auxiliary spliceosomal proteins are still unknown. Here, we functionally characterized plant homologues of nematode suppressors of mec-8 and unc-52 (smu). We compared transcript profiles of maize (Zea mays) smu2 endosperm with those of wild-type plants and identified pre-mRNA splicing events that depend on the maize SMU2 protein. Consistent with a conserved role of plant SMU-2 homologues, Arabidopsis (Arabidopsis thaliana) smu2 mutants also show altered splicing of similar target pre-mRNAs. The Atsmu2 mutants occasionally show developmental phenotypes, including abnormal cotyledon numbers and higher seed weights. We identified AtSMU1 as one of the SMU2-interacting proteins, and Atsmu1 mutations cause similar developmental phenotypes with higher penetrance than Atsmu2. The AtSMU2 and AtSMU1 proteins are localized to the nucleus and highly prevalent in actively dividing tissues. Taken together, our data indicated that the plant SMU-1 and SMU-2 homologues appear to be involved in splicing of specific pre-mRNAs that affect multiple aspects of development.
Expressing the Diphtheria Toxin A Subunit from theHAP2(GCS1) Promoter Blocks Sperm Maturation and Produces Single Sperm-Like Cells Capable of Fertilization
Authors: Frank Aubrey C. , Johnson Mark A. 
Published: September 2009

AbstractAfter meiosis, the male germline of flowering plants undergoes two mitoses, producing two sperm that are carried within a pollen tube to an ovule. One sperm fuses with the egg to form the zygote and the other fuses with the central cell to form the primary endosperm. The mechanisms that control male germline development and gene expression, and ensure that sperm properly fuse with female gametes are just beginning to be understood. Expression of the potent translation inhibitor, diphtheria toxin A subunit, from the Arabidopsis (Arabidopsis thaliana) HAP2(GCS1) promoter blocked sperm development before the final cell division, resulting in pollen tubes that carried a single sperm-like cell rather than two sperm. These pollen tubes targeted ovules and fertilized either the egg or the central cell, producing seeds with either endosperm or an embryo, but not both. Endosperm-only seeds significantly outnumbered embryo-only seeds, suggesting that single sperm-like cells preferentially fuse with the central cell. These experiments show that de novo translation is required for completion of sperm development, that the HAP2(GCS1) promoter is very tightly controlled, and that disruption of gene expression can result in male germ cells with a bias for gamete fusion.
MedicagoN2-Fixing Symbiosomes Acquire the Endocytic Identity Marker Rab7 but Delay the Acquisition of Vacuolar Identity
Authors: Limpens Erik , Ivanov Sergey , van Esse Wilma , Voets Guido , Fedorova Elena , Bisseling Ton 
Published: September 2009

AbstractRhizobium bacteria form N2-fixing organelles, called symbiosomes, inside the cells of legume root nodules. The bacteria are generally thought to enter the cells via an endocytosis-like process. To examine this, we studied the identity of symbiosomes in relation to the endocytic pathway. We show that in Medicago truncatula, the small GTPases Rab5 and Rab7 are endosomal membrane identity markers, marking different (partly overlapping) endosome populations. Although symbiosome formation is considered to be an endocytosis-like process, symbiosomes do not acquire Rab5 at any stage during their development, nor do they accept the trans-Golgi network identity marker SYP4, presumed to mark early endosomes in plants. By contrast, the endosomal marker Rab7 does occur on symbiosomes from an early stage of development when they have stopped dividing up to the senescence stage. However, the symbiosomes do not acquire vacuolar SNAREs (SYP22 and VTI11) until the onset of their senescence. By contrast, symbiosomes acquire the plasma membrane SNARE SYP132 from the start of symbiosome formation throughout their development. Therefore, symbiosomes appear to be locked in a unique SYP132- and Rab7-positive endosome stage and the delay in acquiring (lytic) vacuolar identity (e.g., vacuolar SNAREs) most likely ensures their survival and maintenance as individual units.
The Arabidopsis Nitrate Transporter NRT1.7, Expressed in Phloem, Is Responsible for Source-to-Sink Remobilization of Nitrate
Authors: Fan Shu-Chun , Lin Choun-Sea , Hsu Po-Kai , Lin Shan-Hua , Tsay Yi-Fang 
Published: September 2009

Abstract
Several quantitative trait locus analyses have suggested that grain yield and nitrogen use efficiency are well correlated with nitrate storage capacity and efficient remobilization. This study of the Arabidopsis thaliana nitrate transporter NRT1.7 provides new insights into nitrate remobilization. Immunoblots, quantitative RT-PCR, β-glucuronidase reporter analysis, and immunolocalization indicated that NRT1.7 is expressed in the phloem of the leaf minor vein and that its expression levels increase coincidentally with the source strength of the leaf. In nrt1.7 mutants, more nitrate was present in the older leaves, less 15NO3 − spotted on old leaves was remobilized into N-demanding tissues, and less nitrate was detected in the phloem exudates of old leaves. These data indicate that NRT1.7 is responsible for phloem loading of nitrate in the source leaf to allow nitrate transport out of older leaves and into younger leaves. Interestingly, nrt1.7 mutants showed growth retardation when external nitrogen was depleted. We conclude that (1) nitrate itself, in addition to organic forms of nitrogen, is remobilized, (2) nitrate remobilization is important to sustain vigorous growth during nitrogen deficiency, and (3) source-to-sink remobilization of nitrate is mediated by phloem.
A Transporter at the Node Responsible for Intervascular Transfer of Silicon in Rice
Authors: Yamaji Naoki , Ma Jian Feng 
Published: September 2009

Abstract
The concentration of essential mineral nutrients in the edible portion of plants such as grains may affect the nutritional value of these foods, while concentrations of toxic minerals in the plant are matter of food safety. Minerals taken up by the roots from soils are normally redirected at plant nodes before they are finally transported into developing seeds. However, the molecular mechanisms involved in this process have not been identified so far. Herein, we report on a transporter (Lsi6) responsible for the redirection of a plant nutrient at the node. Lsi6 is a silicon transporter in rice (Oryza sativa), and its expression in node I below the panicles is greatly enhanced when the panicle is completely emerged. Lsi6 is mainly localized at the xylem transfer cells located at the outer boundary region of the enlarged large vascular bundles in node I. Knockout of Lsi6 decreased Si accumulation in the panicles but increased Si accumulation in the flag leaf. These results suggest that Lsi6 is a transporter involved in intervascular transfer (i.e., transfer of silicon from the large vascular bundles coming from the roots to the diffuse vascular bundles connected to the panicles). These findings will be useful for selectively enhancing the accumulation of essential nutrients and reducing toxic minerals in the edible portion of cereals.
Why Rice yellow mottle virus, a rapidly evolving RNA plant virus, is not efficient at breaking rymv1‐2 resistance
Authors: POULICARD NILS , PINEL‐GALZI AGNES , HEBRARD EUGENIE , FARGETTE DENIS 
Published: September 2009

SUMMARY Rice yellow mottle virus (RYMV) reaches a high virus content in rice, is genetically highly variable and evolves rapidly. Nevertheless, only a small proportion of isolates overcome rymv1‐2 rice resistance by mutations in the VPg (viral protein genome‐linked). The accumulation rates of wild‐type (WT) and resistance‐breaking (RB) genotypes of the E‐ and T‐pathotypes of RYMV, with average and low virulence, respectively, were assessed. By quantitative reverse transcriptase‐polymerase chain reaction, it was shown that: (i) in resistant plants, both WT genotypes reached a level of 105–107 viral copies per milligram of fresh leaf; (ii) the accumulation of RB genotypes was variable, but was always much higher than the WT, with an RB/WT accumulation ratio of up to 106; (iii) in susceptible plants, the RB genotypes were counter‐selected to a similar level. In competition experiments, there was a straightforward exclusion of WT by RB genotypes in resistant hosts. The mutation rate in VPg was more than 1 × 10−3 mutations per site per year. Overall, a steady supply of highly adaptive RB genotypes was expected in resistant plants. However, the use of the few possible mutational pathways to virulence is tightly regulated by pathotype‐specific genetic constraints: codon usage, mutational bias and sign epistasis. In addition, genetic drift may restrict the fixation of RB mutants. Altogether, both genetic and demographic constraints contribute to the low ability of RYMV to break rymv1‐2 resistance.
Differences in woody vegetation are unrelated to use by African elephants (Loxodonta africana) in Mkhuze Game Reserve, South Africa
Authors: White Angela M. , Goodman Peter S. 
Published: September 2009

AbstractThe reintroduction of African elephants into fenced game reserves throughout South Africa has presented managers with several challenges. Although elephants are a natural part of southern African ecosystems, their confinement to fenced protected areas in South Africa has exacerbated their potential to impact their habitats negatively. However, many studies investigating the impact of elephants have failed to control for the effects of other browsers on the vegetative community. In this study, we used location data on an elephant herd to delineate high‐use and low‐use areas. This paired design allowed us to minimize confounding factors that could explain differences in the structure, diversity and utilization of woody species. We found little evidence to suggest elephant‐mediated change in, or selection for, the structure or diversity of woody species; however, our results suggest that elephants may be altering the composition of species by preferentially using areas with higher canopy diversity and by enhancing sapling recruitment. Although stripping of bark was higher in high‐use areas, there was no evidence of differential mortality of tree species. Therefore, in our study area, and over the current time scale, elephants are having a negligible impact on the vegetative community.