bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coevolutionary Computation
Authors: Paredis Jan 
Published: April 2010

This article proposes a general framework for the use of coevolution to boost the performance of genetic search. It combines coevolution with yet another biologically inspired technique, called lifetime fitness evaluation (LTFE). Two unrelated problems—neural net learning and constraint satisfaction—are used to illustrate the approach. Both problems use predator-prey interactions to boost the search. In contrast with traditional “single population” genetic algorithms (GAs), two populations constantly interact and coevolve. However, the same algorithm can also be used with different types of coevolutionary interactions. As an example, the symbiotic coevolution of solutions and genetic representations is shown to provide an elegant solution to the problem of finding a suitable genetic representation. The approach presented here greatly profits from the partial and continuous nature of LTFE. Noise tolerance is one advantage. Even more important, LTFE is ideally suited to deal with coupled fitness landscapes typical for coevolution.
Determinants of Multiple Semantic Priming: A Meta-analysis and Spike Frequency Adaptive Model of a Cortical Network
Authors: Lavigne Frédéric , Dumercy Laurent , Darmon Nelly 
Published: April 2010

Abstract
Recall and language comprehension while processing sequences of words involves multiple semantic priming between several related and/or unrelated words. Accounting for multiple and interacting priming effects in terms of underlying neuronal structure and dynamics is a challenge for current models of semantic priming. Further elaboration of current models requires a quantifiable and reliable account of the simplest case of multiple priming resulting from two primes on a target. The meta-analytic approach offers a better understanding of the experimental data from studies on multiple priming regarding the additivity pattern of priming. The meta-analysis points to the effects of prime–target stimuli onset asynchronies on the pattern of underadditivity, overadditivity, or strict additivity of converging activation from multiple primes. The modeling approach is then constrained by results of the meta-analysis. We propose a model of a cortical network embedding spike frequency adaptation, which allows frequency and time-dependent modulation of neural activity. Model results give a comprehensive understanding of the meta-analysis results in terms of dynamics of neuron populations. They also give predictions regarding how stimuli intensities, association strength, and spike frequency adaptation influence multiple priming effects.
Encoding Social Interactions: The Neural Correlates of True and False Memories
Authors: Straube Benjamin , Green Antonia , Chatterjee Anjan , Kircher Tilo 
Published: April 2010

Abstract
In social situations, we encounter information transferred in firsthand (egocentric) and secondhand (allocentric) communication contexts. However, the mechanism by which an individual distinguishes whether a past interaction occurred in an egocentric versus allocentric situation is poorly understood. This study examined the neural bases for encoding memories of social interactions through experimentally manipulating the communication context. During fMRI data acquisition, participants watched video clips of an actor speaking and gesturing directly toward them (egocentric context) or toward an unseen third person (allocentric context). After scanning, a recognition task gauged participants' ability to recognize the sentences they had just seen and to recall the context in which the sentences had been spoken. We found no differences between the recognition of sentences spoken in egocentric and allocentric contexts. However, when asked about the communication context (“Had the actor directly spoken to you?”), participants tended to believe falsely that the actor had directly spoken to them during allocentric conditions. Greater activity in the hippocampus was related to correct context memory, whereas the ventral ACC was activated for subsequent inaccurate context memory. For the interaction between encoding context and context memory, we observed increased activation for egocentric remembered items in the bilateral and medial frontal cortex, the BG, and the left parietal and temporal lobe. Our data indicate that memories of social interactions are biased to be remembered egocentrically. Self-referential encoding processes reflected in increased frontal activation and decreased hippocampal activation might be the basis of correct item but false context memory of social interactions.
The Literate Brain: The Relationship between Spelling and Reading
Authors: Rapp Brenda , Lipka Kate 
Published: April 2010

AbstractWe report the results of an fMRI investigation of the neural bases of written language comprehension (reading) and production (spelling). Both tasks were examined in the same individuals, allowing greater precision in establishing the relationship between the neural underpinnings of these two cognitive functions. Also examined was the relationship between written language substrates and those involved in face and object (house) processing. The results reveal that reading and spelling share specific left hemisphere substrates in the mid-fusiform gyrus and in the inferior frontal gyrus/junction. Furthermore, the results indicate that the left mid-fusiform substrates are specifically involved in lexical orthographic processing. We also find that written language and face processing exhibit largely complementary activation patterns in both the fusiform and the inferior frontal/junction areas, with left and right lateralization, respectively. In sum, these results provide perhaps the strongest evidence to date of components that are shared by written language comprehension (reading) and production (spelling), and they further our understanding of the role of literacy within the larger repertoire of cognitive operations and their neural substrates.
Right Hemisphere Dominance in Visual Statistical Learning
Authors: Roser Matthew E. , Fiser József , Aslin Richard N. , Gazzaniga Michael S. 
Published: April 2010

Abstract
Several studies report a right hemisphere advantage for visuospatial integration and a left hemisphere advantage for inferring conceptual knowledge from patterns of covariation. The present study examined hemispheric asymmetry in the implicit learning of new visual feature combinations. A split-brain patient and normal control participants viewed multishape scenes presented in either the right or the left visual fields. Unbeknownst to the participants, the scenes were composed from a random combination of fixed pairs of shapes. Subsequent testing found that control participants could discriminate fixed-pair shapes from randomly combined shapes when presented in either visual field. The split-brain patient performed at chance except when both the practice and the test displays were presented in the left visual field (right hemisphere). These results suggest that the statistical learning of new visual features is dominated by visuospatial processing in the right hemisphere and provide a prediction about how fMRI activation patterns might change during unsupervised statistical learning.
Sharing Cases: The Observationes in Early Modern Medicine
Authors: Pomata Gianna 
Published: May 2010

AbstractThis paper examines the rise of an epistemic genre, the Observationes, a new form of medical writing that emerged in Renaissance humanistic medicine. The Observationes (collections of case-histories) originated in the second half of the sixteenth century, grew rapidly over the course of the seventeenth, and had become a primary form of medical writing by the eighteenth century. The genre developed initially as a form of self-advertisement by court and town physicians, who stressed success in practice, over and above academic learning, as a core element of their professional identity. This unprecedented emphasis on practice as a source of knowledge remained a key feature of the Observationes in its subsequent development. As the genre evolved, the original emphasis on therapeutic success gave way to a new focus on the descriptive knowledge of disease through detailed observation. The authorial identity projected by the writers of Observationes was increasingly that of the learned and experienced observer, bent on comparing notes and sharing his cases with the fellow members of the res publica medica. This paper charts the development of the genre, examining how its growth contributed to the new epistemological value of observation in the age of the Scientific Revolution.
The Sikh Foundations of Ayurveda
Authors: Aggarwal Neil Krishan 
Published: May 2010

AbstractThis paper explores how Sikh scriptures establish a unique claim to Ayurvedic knowledge. After considering Ayurvedic creation myths in the classical Sanskrit canon, passages from Sikh liturgical texts are presented to show how Ayurveda is refashioned to meet the exigencies of Sikh theology. The Sikh texts are then analysed through their relationship with general Puranic literatures and the historical context of Hindu-Sikh relations. Finally, the Indian government’s current propagation of Ayurveda is scrutinised to demonstrate its affiliation with one particular religion to the possible exclusion of others. The Sikh example provides a glimpse into local cultures of Ayurveda before the professionalisation and standardisation of Ayurvedic practice in India’s post-independence period and may serve as a model for understanding other traditions.
Yang Chongrui and the First National Midwifery School: Childbirth Reform in Early Twentieth-Century China
Authors: Johnson Tina Phillips 
Published: May 2010

AbstractThis paper examines the First National Midwifery School (FNMS) and its connexions with the Rockefeller Foundation and the Nationalist government. During the Nationalist era (1927‐37), western medical personnel and Chinese intellectuals attempted to modernise China by reforming childbirth as part of a new public health system. As most of the biomedical personnel in China were trained in the United States, it may be expected that midwifery reform would have followed the same path as in the West, with physicians displacing midwives. On the contrary, in China we see a blending of Chinese cultural and social needs with western public health methods to create a system that has survived in China to this day. The FNMS acted as a liaison between East and West, between private philanthropic organisations and the government. The most significant player in this field, Dr Yang Chongrui, played a vital role in professionalizing the new occupation of the modern Chinese midwife. Yang’s vision to train midwives to reduce the high maternal and infant mortality rates was one of the most important public health efforts in China during this time. In the process, women were targeted both as actors in China’s nation-building strategies and as reproducers of China’s citizenry.
Socio-Economic Dimensions of Tibetan Medicine in the Tibet Autonomous Region, China
Authors: Hofer Theresia 
Published: May 2010

AbstractThis article investigates some of the socio-economic dimensions of contemporary Tibetan medical practices in the rural areas of the Tibet Autonomous Region (TAR), China. The article is divided into two parts. Part One, printed in the last issue of the journal, deals with traditional medical practitioners and their medical practices within the governmental health care system in the TAR. It sheds light on the workings and the effects that the commodification of the official health care system have had on its Tibetan medical practitioners, most of whom now work as hybrid practitioners and incorporate Chinesestyle biomedicine into their practice. I argue that several historical, social and political factors have brought about unequal access and availability of Tibetan medicine as compared to Chinese style biomedical care in the rural areas. Special attention is given to the role of the reintroduction of the Cooperative Medical Services (CMS) scheme in the sidelining of Tibetan medical practices in the rural areas. Part Two describes the work of private Tibetan medical practitioners and explores some of the social dynamics and ethical dilemmas that have arisen for them due to the commodification of the official system and the reintroduction of the CMS. Both parts focus on the situation in the Tsang or Shigatse region of the western and central TAR, hence enabling there to be useful comparisons with medical practices in the capital Lhasa, where most of the anthropological literature has focused on so far. Both contributions are based on extensive anthropological fieldwork in Lhasa and the Tsang region of Tibet.
Determinants of community-acquired pneumonia in children and young adults in primary care
Authors: Teepe J. , Grigoryan L. , Verheij T. J. M. 
Published: May 2010

Most studies on determinants of community-acquired pneumonia (CAP) in primary care have focused primarily on the elderly. Using a case–control study in four Dutch healthcare centres, determinants of CAP among children and young adults were identified.Cases included 156 young adults (aged 16–40 yrs) and 107 children (aged 0–15 yrs) diagnosed with CAP during 1999–2008. For each case, three controls were selected from the same age group. Separate logistic regression analyses were used to identify determinants in young adults and children.Lower age, asthma and previous upper respiratory tract infections (URTIs) were independently associated with CAP in children. Increasing age, asthma, three or more children at home, current smoking and three or more previous URTIs were independent determinants of CAP in young adults.The present study has three remarkable findings: 1) increasing age was an independent determinant of CAP in young adults; 2) having young children increased the risk of the development of CAP in young adults; and 3) the number of previous URTIs was independently associated with CAP in both children and young adults, possibly due to higher infection susceptibility. Further studies are required in order to better understand the aetiology of CAP and permit better diagnosis and treatment of this serious condition.
Fine-tuning structural RNA alignments in the twilight zone
Authors: Bremges Andreas , Schirmer Stefanie , Giegerich Robert 
Published: April 2010

Abstract

Background
A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably.

Results
Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices.

Conclusions
Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.
From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences
Authors: Lane Jérôme , Duroux Patrice , Lefranc Marie-Paule 
Published: April 2010

Abstract

Background
The antigen receptors, immunoglobulins (IG) and T cell receptors (TR), are specific molecular components of the adaptive immune response of vertebrates. Their genes are organized in the genome in several loci (7 in humans) that comprise different gene types: variable (V), diversity (D), joining (J) and constant (C) genes. Synthesis of the IG and TR proteins requires rearrangements of V and J, or V, D and J genes at the DNA level, followed by the splicing at the RNA level of the rearranged V-J and V-D-J genes to C genes. Owing to the particularities of IG and TR gene structures related to these molecular mechanisms, conventional bioinformatic software and tools are not adapted to the identification and description of IG and TR genes in large genomic sequences. In order to answer that need, IMGT®, the international ImMunoGeneTics information system®, has developed IMGT/LIGMotif, a tool for IG and TR gene annotation. This tool is based on standardized rules defined in IMGT-ONTOLOGY, the first ontology in immunogenetics and immunoinformatics.

Results
IMGT/LIGMotif currently annotates human and mouse IG and TR loci in large genomic sequences. The annotation includes gene identification and orientation on DNA strand, description of the V, D and J genes by assigning IMGT® labels, gene functionality, and finally, gene delimitation and cluster assembly. IMGT/LIGMotif analyses sequences up to 2.5 megabase pairs and can analyse them in batch files.

Conclusions
IMGT/LIGMotif is currently used by the IMGT® biocurators to annotate, in a first step, IG and TR genomic sequences of human and mouse in new haplotypes and those of closely related species, nonhuman primates and rat, respectively. In a next step, and following enrichment of its reference databases, IMGT/LIGMotif will be used to annotate IG and TR of more distantly related vertebrate species. IMGT/LIGMotif is available at http://www.imgt.org/ligmotif/.
A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing
Authors: Shimada Makoto K , Hayakawa Yosuke , Takeda Jun-ichi , Gojobori Takashi , Imanishi Tadashi 
Published: April 2010

Abstract

Background
Alternative splicing (AS) is a key molecular process that endows biological functions with diversity and complexity. Generally, functional redundancy leads to the generation of new functions through relaxation of selective pressure in evolution, as exemplified by duplicated genes. It is also known that alternatively spliced exons (ASEs) are subject to relaxed selective pressure. Within consensus sequences at the splice junctions, the most conserved sites are dinucleotides at both ends of introns (splice dinucleotides). However, a small number of single nucleotide polymorphisms (SNPs) occur at splice dinucleotides. An intriguing question relating to the evolution of AS diversity is whether mutations at splice dinucleotides are maintained as polymorphisms and produce diversity in splice patterns within the human population. We therefore surveyed validated SNPs in the database dbSNP located at splice dinucleotides of all human genes that are defined by the H-Invitational Database.

Results
We found 212 validated SNPs at splice dinucleotides (sdSNPs); these were confirmed to be consistent with the GT-AG rule at either allele. Moreover, 53 of them were observed to neighbor ASEs (AE dinucleotides). No significant differences were observed between sdSNPs at AE dinucleotides and those at constitutive exons (CE dinucleotides) in SNP properties including average heterozygosity, SNP density, ratio of predicted alleles consistent with the GT-AG rule, and scores of splice sites formed with the predicted allele. We also found that the proportion of non-conserved exons was higher for exons with sdSNPs than for other exons.

Conclusions
sdSNPs are found at CE dinucleotides in addition to those at AE dinucleotides, suggesting two possibilities. First, sdSNPs at CE dinucleotides may be robust against sdSNPs because of unknown mechanisms. Second, similar to sdSNPs at AE dinucleotides, those at CE dinucleotides cause differences in AS patterns because of the arbitrariness in the classification of exons into alternative and constitutive type that varies according to the dataset. Taking into account the absence of differences in sdSNP properties between those at AE and CE dinucleotides, the increased proportion of non-conserved exons found in exons flanked by sdSNPs suggests the hypothesis that sdSNPs are maintained at the splice dinucleotides of newly generated exons at which negative selection pressure is relaxed.
Functional bias in molecular evolution rate of Arabidopsis thaliana
Authors: Warren Andrew S , Anandakrishnan Ramu , Zhang Liqing 
Published: May 2010

Abstract

Background
Characteristics derived from mutation and other mechanisms that are advantageous for survival are often preserved during evolution by natural selection. Some genes are conserved in many organisms because they are responsible for fundamental biological function, others are conserved for their unique functional characteristics. Therefore one would expect the rate of molecular evolution for individual genes to be dependent on their biological function. Whether this expectation holds for genes duplicated by whole genome duplication is not known.

Results
We empirically demonstrate here, using duplicated genes generated from the Arabidopsis thaliana α-duplication event, that the rate of molecular evolution of genes duplicated in this event depend on biological function. Using functional clustering based on gene ontology annotation of gene pairs, we show that some duplicated genes, such as defense response genes, are under weaker purifying selection or under stronger diversifying selection than other duplicated genes, such as protein translation genes, as measured by the ratio of nonsynonymous to synonymous divergence (dN/dS).

Conclusions
These results provide empirical evidence indicating that molecular evolution rate for genes duplicated in whole genome duplication, as measured by dN/dS, may depend on biological function, which we characterize using gene ontology annotation. Furthermore, the general approach used here provides a framework for comparative analysis of molecular evolution rate for genes based on their biological function.