Motivic analysis and its relevance to raga identification in carnatic music

A raga is a collective melodic expression consisting of motifs. A raga can be identified using motifs which areunique to it. Motifs can be thought of as signature prosodic phrases. Different ragas may be composed of the same setof notes, or even phrases, but the prosody may be completely different. In this paper, an attempt is made to determinethe characteristic motifs that enable identification of a raga and distinguish between them. To determine this, motifs are first manually marked for a set of five popular raga by a professional musician. The motifs are then normalisedwith respect to the tonic. HMMs are trained for each motif using 80% of the data and about 20% are used for testing. The results do indicate that about 80% of the motifs are identified as belonging to a specific raga accurately.

Metrical strength and contradiction in turkish Makam music

In this paper we investigate how note onsets in Turkish Makam music compositions are distributed, and in how far this distribution supports or contradicts the metrical structure of the pieces, the usul. We use MIDI data to derive the distributions in the form of onset histograms, and comparethem with metrical weights that are applied to describe the usul in theory. We compute correlation and syncopation values to estimate the degrees of support and contradiction, respectively. While the concept of syncopation is rarelymentioned in the context of this music, we can gain interesting insight into the structure of a piece using such a measure.We show that metrical contradiction is systematically applied in some metrical structures. We will compare thedifferences between Western music and Turkish Makam music regarding metrical support and contradiction. Such a study can help avoiding pitfalls in later attempts to perform audio processing tasks such as beat tracking or rhythmic similarity measurements.

Mitochondrial dysfunction increases oxidative stress and decreases chronological life span in fission yeast

Background: Oxidative stress is a probable cause of aging and associated diseases. Reactive oxygen species (ROS) originate mainly from endogenous sources, namely the mitochondria. Methodology/Principal Findings: We analyzed the effect of aerobic metabolism on oxidative damage in Schizosaccharomyces pombe by global mapping of those genes that are required for growth on both respiratory-proficient media and hydrogen-peroxide-containing fermentable media. Out of a collection of approximately 2700 haploid yeast deletion mutants, 51 were sensitive to both conditions and 19 of these were related to mitochondrial function. Twelve deletion mutants lacked components of the electron transport chain. The growth defects of these mutants can be alleviated by the addition of antioxidants, which points to intrinsic oxidative stress as the origin of the phenotypes observed. These respiration-deficient mutants display elevated steady-state levels of ROS, probably due to enhanced electron leakage from their defective transport chains, which compromises the viability of chronologically-aged cells. Conclusion/Significance: Individual mitochondrial dysfunctions have often been described as the cause of diseases or aging, and our global characterization emphasizes the primacy of oxidative stress in the etiology of such processes.

Carnatic music: Svara, Gamaka, Motif and Raga identity

Over the last century in Karnatik music, the method ofunderstanding raga has been to break it down into its variouscomponents, svara, scale, gamaka, and phrases. In this paper, an attempt is made to define the abstract concept of raga in its entirety within the aesthetics of Karnatik music considering the various components and their symbiotic relationship. This paper also attempts to prove that theidentity of a raga exists as a whole. Section 2 explains theconcept of a fundamental musical note or svara. Section 3 illustrates the concept of gamaka or inflections. Section 4 delves into the concept of raga in detail and then flows into Section 5 which enunciates the identity of a raga in terms of svara, gamaka, and phraseology. The paper concludes in Section 6, and Section 7 gives the references.

Transferring QTL technology to the pig breeding industry (PigQTech) - a demonstration project

The aim of the project has been to demonstrate how the farm animal breeding industry can utilise gene mapping technology to accelerate genetic improvement. Previous theoretical studies had suggested that the use of marker assisted selection could potentially increase the annual improvement for quantitative traits like backfat with about 10% and for more difficult traits such as meat quality and reproduction by as much as 40-60% compared with existing technology. The work has comprised two major tasks: 1. Commercially relevant populations have been screened for segregation at QTLs identified in experimental populations. The aim has been to establish optimal strategies for QTL detection in commercial pig populations and the extent to which QTLs explaining major phenotypic differences between divergent lines used in experimental studies also explain quantitative variation within commercial lines. The results are important for specifying future strategies for finding economically valuable QTLs. 2. Marker assisted backcrossing has been used to demonstrate how a QTL allele can be introgressed from one breed to another. The work has focused on the major fatness QTL on pig chromosome 4 previously identified in a wild pig/Large White intercross. The end result was not designed to be a commercially viable product in its own right, but the process has validated a number of points of major importance for the exploitation of QTLs in livestock.

Republicanismo, servidumbre y servicio doméstico

En este trabajo se exploran los condicionantes sociológicos e institucionales del mercado del servicio doméstico en Europa. Para ello se trabajó, básicamente, en tres líneas de investigación que aun están en curso. La primera, consiste en una exploración filosófica republicana, histórica y jurídica de la familia y la empresa capitalistas como instituciones que tienen una raigambre histórica común –la antigua domus, donde se desarrollaban todas las actividades productivas y reproductivas y que se caracterizaba constitutivamente por relaciones de dominación entre el propietario de los medios de producción y todos aquéllos que dependían de éste para subsistir-. Bajo el capitalismo, la familia –entendida ya como el hombre, su mujer e hijos legítimos- se constituyó en una institución eminentemente privada y las actividades desarrolladas en su seno quedaron fuera de lo que se consideró trabajo susceptible de reconocimiento económico. En este sentido, la normativa que regula al servicio doméstico como una relación laboral de carácter “especial” es un reflejo de la desvalorización socioeconómica de que ha sido objeto el trabajo reproductivo y la asociación conceptual entre la “improductividad” del ama de casa y la empleada doméstica. En la segunda línea del trabajo se exploraron las variaciones cuantitativas del mercado del servicio doméstico en Europa, cuya trayectoria presenta una forma de U entre la década de 1880 y mediados de la década de 1990. También mediante el análisis de fuentes secundarias de datos se pudieron establecer las profundas diferencias regionales que ha comportado este resurgimiento del empleo en servicios domésticos y su peso dentro de la estructura de empleo de cada sociedad. Por último, en la tercera se indagó la fluctuación histórica y geográfica de la oferta de trabajadoras domésticas en Europa, que pasó de las migraciones internas a las internacionales, coincidiendo con periodos de fuerte desigualdad económica entre las zonas expulsoras y receptoras.

Noves tecnologies per l'estudi de l'arqueologia de Patagònia (Amèrica del Sud)

The goal of this project was the historical study of Patagonia, the southernmost human settled area of the world. Our aim has been the anlysis of those societies to understand how they maintained their socioeconomic system, that is to say, how social reproduction allowed resolving the basic contradiction between production and reproduction, which is characteristic of all hunter-gatherer societies. New computational technologies have allowed a bettwer integration of the big amount and diversity of data needed. We have analyzed the historical evolution of inter-group and intra-group social relationships among nomad patagonian societies. We have compared different social answers in front of the radical change of their immediate reality produced by european colonization. We have exhaustively analyzed the results of archaeological excavations from diferent regions. We have also integrated information from anthropology, ethnohistory and geography. We are developing computing programs to integrate geographical actual data with paleoenvironmental data about the dynamic nature of soil formation, vegetation, hidrography, etc., with information about the history of productive action and how products were distributed among different human groups.

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Aplicació j2ee de venda i reproducció de contingutsaudiovisuals, que no té cap altre ús que el merament educatiu.

El espacio como producto social: variables arqueológicas para un análisis de la organización social en prehistoria

El espacio social es un concepto ambiguo cuyo componente material está determinado por el carácter del componente social, puesto que la organización de los objetos en el espacio y el espacio mismo, responden a las normas sociales del comportamiento humano. Partimos de la premisa que los residuos generados durante el proceso de producción y del consumo tienden a tener una distribución relativamente regular en el espacio físico. La ausencia de la aleatoriedad en la dispersión de estos restos solo significa que habían sido acumulados y depositados como restos de acciones previamente planificadas no-aleatoriamente. En este trabajo planteamos estudiar la organización y la producción del espacio social de una sociedad cazadora-recolectora concreta – la sociedad yámana - a través del análisis de las actividades cotidianas que figuran en las fuentes etnográficas y en el registro arqueológico. Con este fin creamos una metodología de trabajo interdisciplinaria, basada en un enfoque etnoarqueológico, y a través del estudio de las fuentes etnográficas, los trabajos etnoarqueológicos previos y el registro arquelógico concreto, descubrimos cuáles son las posibilidades y limitaciones de este tipo de estudios. Pudimos reconocer la regularidad espacial de los procesos de producción y reproducción social y a resolver algunas preguntas acerca del estudio de la organización social en prehistoria trabajando con los datos etnoarqueológicos obtenidos en los yacimientos Lanashuaia y Túnel VII (Tierra del Fuego, Argentina), analizando el registro extraido y trabajado en varias campañas de excavaciones arqueológicas en ultimos 25 años. El presente trabajo al fondo es un experimento etnoarqueológico estándar: partiendo de la observación etnográfica registramos unas recurrencias específicas entre algunas variables (por ejemplo: mujer/lugar/tipo de trabajo), intentamos extraer las variables definitorias de esas recurrencias, y finalmente las buscamos en el espacio definido arqueológicamente.  

The post-communist fertility puzzle

Fertility has unanimously declined across the entire post-communist region. This study explores the variation in fertility trends over time among these countries and assesses to what degree three explanations are applicable: second demographic transition (SDT), postponement transition (PPT) or reaction to the economic crisis. Moreover, on the basis of SDT and PPT theoretical tenets, as well as descriptive evidence, the economic context is hypothesized to be linked to two processes of fertility decline conversely. The results show that no one theoretical explanation is sufficient to explain the complex fertility declines across the entire post-communist region from 1990 to 2003. In some countries, a great part of the decline in fertility occurred before significant postponement of childbearing began, which indicates that the dramatic decline was due to stopping behavior or postponement of higher order births. Postponement of first births, either through PPT or SDT processes, greatly contributed to fertility decline in a small number of countries. Pooled cross-sectional time-series analyses of age-specific birthrates confirm that these two distinct processes are present and show that the economic crisis explanation has explanatory power for declining birth rates. In contrast, logistic regressions show that the likelihood of postponing childbirth increases with improved economic conditions. These results confirm the importance of taking the economic context into account when discussing explanations for fertility decline. More specifically, the results indicate that the severity and duration of economic crisis, or absence thereof, influenced the extent and manner in which fertility declined.

Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes

BACKGROUND: Selenoproteins are a diverse family of proteins notable for the presence of the 21st amino acid, selenocysteine. Until very recently, all metazoan genomes investigated encoded selenoproteins, and these proteins had therefore been believed to be essential for animal life. Challenging this assumption, recent comparative analyses of insect genomes have revealed that some insect genomes appear to have lost selenoprotein genes. METHODOLOGY/PRINCIPAL FINDINGS: In this paper we investigate in detail the fate of selenoproteins, and that of selenoprotein factors, in all available arthropod genomes. We use a variety of in silico comparative genomics approaches to look for known selenoprotein genes and factors involved in selenoprotein biosynthesis. We have found that five insect species have completely lost the ability to encode selenoproteins and that selenoprotein loss in these species, although so far confined to the Endopterygota infraclass, cannot be attributed to a single evolutionary event, but rather to multiple, independent events. Loss of selenoproteins and selenoprotein factors is usually coupled to the deletion of the entire no-longer functional genomic region, rather than to sequence degradation and consequent pseudogenisation. Such dynamics of gene extinction are consistent with the high rate of genome rearrangements observed in Drosophila. We have also found that, while many selenoprotein factors are concomitantly lost with the selenoproteins, others are present and conserved in all investigated genomes, irrespective of whether they code for selenoproteins or not, suggesting that they are involved in additional, non-selenoprotein related functions. CONCLUSIONS/SIGNIFICANCE: Selenoproteins have been independently lost in several insect species, possibly as a consequence of the relaxation in insects of the selective constraints acting across metazoans to maintain selenoproteins. The dispensability of selenoproteins in insects may be related to the fundamental differences in antioxidant defense between these animals and other metazoans.

GENCODE: producing a reference annotation for ENCODE

Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manualannotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results.Results: The GENCODE gene features are divided into eight different categories of which onlythe first two (known and novel coding sequence) are confidently predicted to be protein-codinggenes. 5’ rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentallyverify the initial annotation. Of the 420 coding loci tested, 229 RACE products have beensequenced. They supported 5’ extensions of 30 loci and new splice variants in 50 loci. In addition,46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15putative transcripts. We assessed the comprehensiveness of the GENCODE annotation byattempting to validate all the predicted exon boundaries outside the GENCODE annotation. Outof 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only twoof them in intergenic regions.Conclusions: In total, 487 loci, of which 434 are coding, have been annotated as part of theGENCODE reference set available from the UCSC browser. Comparison of GENCODEannotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained withinthe two sets, which is a reflection of the high number of alternative splice forms with uniqueexons annotated. Over 50% of coding loci have been experimentally verified by 5’ RACE forEGASP and the GENCODE collaboration is continuing to refine its annotation of 1% humangenome with the aid of experimental validation.

Multiple non-collinear TF-map alignments of promoter regions

Background: The analysis of the promoter sequence of genes with similar expression patterns isa basic tool to annotate common regulatory elements. Multiple sequence alignments are on thebasis of most comparative approaches. The characterization of regulatory regions from coexpressedgenes at the sequence level, however, does not yield satisfactory results in manyoccasions as promoter regions of genes sharing similar expression programs often do not shownucleotide sequence conservation.Results: In a recent approach to circumvent this limitation, we proposed to align the maps ofpredicted transcription factors (referred as TF-maps) instead of the nucleotide sequence of tworelated promoters, taking into account the label of the corresponding factor and the position in theprimary sequence. We have now extended the basic algorithm to permit multiple promotercomparisons using the progressive alignment paradigm. In addition, non-collinear conservationblocks might now be identified in the resulting alignments. We have optimized the parameters ofthe algorithm in a small, but well-characterized collection of human-mouse-chicken-zebrafishorthologous gene promoters.Conclusion: Results in this dataset indicate that TF-map alignments are able to detect high-levelregulatory conservation at the promoter and the 3'UTR gene regions, which cannot be detectedby the typical sequence alignments. Three particular examples are introduced here to illustrate thepower of the multiple TF-map alignments to characterize conserved regulatory elements inabsence of sequence similarity. We consider this kind of approach can be extremely useful in thefuture to annotate potential transcription factor binding sites on sets of co-regulated genes fromhigh-throughput expression experiments.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library

The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, we show that the analysis of random sequence reads (RSRs) instead of 16S is a suitable shortcut to estimate the biodiversity of a bacterial community from metagenomic libraries. We generated 10,010 RSRs from a metagenomic library of microorganisms found in human faecal samples. Then searched them using the program BLASTN against a prokaryotic sequence database to assign a taxon to each RSR. The results were compared with those obtained by screening and analysing the clones containing 16S rDNA sequences in the whole library. We found that the biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA. We also show that RSRs are suitable to compare the biodiversity between different metagenomic libraries. RSRs can thus provide a good estimate of the biodiversity of a metagenomic library and, as an alternative to 16S, this approach is both faster and cheaper.

A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins

Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3′UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism. SBP2 has been so far functionally characterized only in rats and humans. In this work, we report the characterization of the Drosophila melanogaster SBP2 (dSBP2). Despite its shorter length, it retained the same selenoprotein synthesis-promoting capabilities as the mammalian counterpart. However, a major difference resides in the SECIS recognition pattern: while human SBP2 (hSBP2) binds the distinct form 1 and 2 SECIS RNAs with similar affinities, dSBP2 exhibits high affinity toward form 2 only. In addition, we report the identification of a K (lysine)-rich domain in all SBP2s, essential for SECIS and 60S ribosomal subunit binding, differing from the well-characterized L7Ae RNA-binding domain. Swapping only five amino acids between dSBP2 and hSBP2 in the K-rich domain conferred reversed SECIS-binding properties to the proteins, thus unveiling an important sequence for form 1 binding.