A promoter-level mammalian expression atlas

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

Project Energise: Using participatory approaches and real time computer prompts to reduce occupational sitting and increase work time physical activity in office workers

Objectives This efficacy study assessed the added impact real time computer prompts had on a participatory approach to reduce occupational sedentary exposure and increase physical activity. Design Quasi-experimental. Methods 57 Australian office workers (mean [SD]; age = 47 [11] years; BMI = 28 [5] kg/m2; 46 men) generated a menu of 20 occupational ‘sit less and move more’ strategies through participatory workshops, and were then tasked with implementing strategies for five months (July–November 2014). During implementation, a sub-sample of workers (n = 24) used a chair sensor/software package (Sitting Pad) that gave real time prompts to interrupt desk sitting. Baseline and intervention sedentary behaviour and physical activity (GENEActiv accelerometer; mean work time percentages), and minutes spent sitting at desks (Sitting Pad; mean total time and longest bout) were compared between non-prompt and prompt workers using a two-way ANOVA. Results Workers spent close to three quarters of their work time sedentary, mostly sitting at desks (mean [SD]; total desk sitting time = 371 [71] min/day; longest bout spent desk sitting = 104 [43] min/day). Intervention effects were four times greater in workers who used real time computer prompts (8% decrease in work time sedentary behaviour and increase in light intensity physical activity; p < 0.01). Respective mean differences between baseline and intervention total time spent sitting at desks, and the longest bout spent desk sitting, were 23 and 32 min/day lower in prompt than in non-prompt workers (p < 0.01). Conclusions In this sample of office workers, real time computer prompts facilitated the impact of a participatory approach on reductions in occupational sedentary exposure, and increases in physical activity.

Comprehending adverbs of doubt and certainty in health communication: A multidimensional scaling approach

This research explored the feasibility of using multidimensional scaling (MDS) analysis in novel combination with other techniques to study comprehension of epistemic adverbs expressing doubt and certainty (e.g., evidently, obviously, probably) as they relate to health communication in clinical settings. In Study 1, Australian English speakers performed a dissimilarity-rating task with sentence pairs containing the target stimuli, presented as "doctors' opinions". Ratings were analyzed using a combination of cultural consensus analysis (factor analysis across participants), weighted-data classical-MDS, and cluster analysis. Analyses revealed strong within-community consistency for a 3-dimensional semantic space solution that took into account individual differences, strong statistical acceptability of the MDS results in terms of stress and explained variance, and semantic configurations that were interpretable in terms of linguistic analyses of the target adverbs. The results confirmed the feasibility of using MDS in this context. Study 2 replicated the results with Canadian English speakers on the same task. Semantic analyses and stress decomposition analysis were performed on the Australian and Canadian data sets, revealing similarities and differences between the two groups. Overall, the results support using MDS to study comprehension of words critical for health communication, including in future studies, for example, second language speaking patients and/or practitioners. More broadly, the results indicate that the techniques described should be promising for comprehension studies in many communicative domains, in both clinical settings and beyond, and including those targeting other aspects of language and focusing on comparisons across different speech communities.

Impact of a new mandatory reporting law on reporting and identification of child sexual abuse: A seven year time trend analysis

Child sexual abuse is widespread and difficult to detect. To enhance case identification, many societies have enacted mandatory reporting laws requiring designated professionals, most often police, teachers, doctors and nurses, to report suspected cases to government child welfare agencies. Little research has explored the effects of introducing a reporting law on the number of reports made, and the outcomes of those reports. This study explored the impact of a new legislative mandatory reporting duty for child sexual abuse in the State of Western Australia over seven years. We analysed data about numbers and outcomes of reports by mandated reporters, for periods before the law (2006-08) and after the law (2009-12). Results indicate that the number of reports by mandated reporters of suspected child sexual abuse increased by a factor of 3.7, from an annual mean of 662 in the three year pre-law period to 2448 in the four year post-law period. The increase in the first two post-law years was contextually and statistically significant. Report numbers stabilised in 2010-12, at one report per 210 children. The number of investigated reports increased threefold, from an annual mean of 451 in the pre-law period to 1363 in the post-law period. Significant decline in the proportion of mandated reports that were investigated in the first two post-law years suggested the new level of reporting and investigative need exceeded what was anticipated. However, a subsequent significant increase restored the pre-law proportion, suggesting systemic adaptive capacity. The number of substantiated investigations doubled, from an annual mean of 160 in the pre-law period to 327 in the post-law period, indicating twice as many sexually abused children were being identified.

Evil Gods and Reckless Saviours : Adaptation and Appropriation in Late Twentieth Century Jesus-Novels

Late twentieth century Jesus-novels search after a completely new picture of Jesus. Novels written for instance by Norman Mailer, José Saramago, Michèle Roberts, Marianne Fredriksson, and Ki Longfellow provide an inversive revision of the canonic Gospels. They read the New Testament in terms of the present age. In their adaptation the story turns often into a critique of the whole Christian history. The investigated contrast-novels end up with an appropriation that is based on prototypical rewriting. They aim at the rehabilitation of Judas, and some of them make Mary Magdalane the key figure of Christianity. Saramago describes God as a blood thirsty tyrant, and Mailer makes God combat with the Devil in a manichean sense as with an equal. Such ideas are familiar both from poststructuralist philosophy and post-metaphysical death-of-God theology. The main result of the intertextual analysis is that these scholars have adopted Nietzschean ideas in their writing. Quite unlike earlier Jesus-novels, these more recent novels present a revision that produces discontinuity with the original source text, the New Testament. The intertextual strategy is based on contradiction. The reader wittnesses contesting and challenging, the authors attack Biblical beliefs and attempt to dissolve Christian doctrines. An attack on Biblical slave morality and violent concept of God deprives Jesus of his Jewish Messianic identity, makes Old Testament law a contradiction of life, calls sacrificial soteriology a violent pattern supporting oppression, and presents God as a cruel monster who enslaves people under his commandments and wishes their death. The new Jesus-figure contests Mosaic Law, despises orthodox Judaism, abandons Jewish customs and even questions Old Testament monotheism. In result, the novels intentionally transfer Jesus out of Judaism. Furthermore, Jewish faith appears in a negative light. Such an intertextual move is not open anti-Semitism but it cannot avoid attacking Jewish worship. Why? One reason that explains these attitudes is that Western culture still carries anti-Judaic attitudes beneath the surface covered with sentiments of equality and tolerance. Despite the evident post-holocaust consciousness present in the novels, they actually adopt an arrogant and ironical refutation of Jewish beliefs and Old Testament faith. In these novels, Jesus is made a complete opposite and antithesis to Judaism. Key words: Jesus-novel, intertextuality, adaptation, slave morality, Nietzsche, theodicy, patriarchy.

“And now to the rest of the trash…” Representations of begging Roma and an ideal society in two Nordic newspapers

Since begging East European Roma became a common view in the streets of larger Nordic cities, vivid discussions about their presence and activities have been carried out in the mass media. This thesis examines the public debates in Finland and Norway through a discursive analysis and comparison of press content from the two countries. The aim of the study is firstly to identify the prominent discourses which construct certain images of the beggars, as well as the elements and internal logics that these discourses are constructed around. But in addition to scrutinizing representations of the Roma, also an opposite perspective is applied. In accordance with the theoretical concept of ‘othering’, debates about ‘them’ are assumed to simultaneously reveal something significant about ‘us’. The second research question is thus what kind of images of the ideal Finnish and Norwegian societies are reflected in the data, and which societal values are salient in these images. The analysis comprises 79 texts printed in the main Finnish and Norwegian quality newspapers; Helsingin Sanomat and Aftenposten. The data consists of news articles, editorials, columns and letters to the editor from a three-month period in the summer of 2010. The analysis was carried out within the theoretical and methodological framework of critical discourse analysis as outlined by Norman Fairclough. A customized nine-step coding scheme was developed in order to reach the most central dimensions of the texts. Seven main discourses were identified; the Deprivation-solidarity, Human rights, Order, Crime, Space and majority reactions, Authority control, and Authority critique discourse. These were grouped into two competing normative stances on what an ideal society looks like; the exclusionary and the inclusionary stance. While the exclusionary stance places the begging Roma within a frame of crime, illegitimate use of public space and threat to the social order, the other advocates an attitude of solidarity and humanitarian values. The analysis points to a dominance of the former, although it is challenged by the latter. The Roma are “individualized” by quoting and/or presenting them by name in a fair part of the Finnish news articles. In Norway, the opposite is true; there the beggars are dominantly presented as anonymous and passive. Overall, the begging Roma are subjected to a double bind as they are faced with simultaneous expectations of activity and passivity. Theories relating to moral panics and ‘the good enemy’ provide for a deepened understanding of the intensity of the debates. Keywords: East European Roma, begging, media, newspapers, Helsingin Sanomat, Aftenposten, critical discourse analysis, Norman Fairclough, othering, ideal society, moral panics, good enemy, double bind, Finland, Norway

Kosmopolitanistisen ilmastoetiikan mahdollisuudet. Diskurssianalyyttinen tulkinta Kööpenhaminan ilmastokokouksesta 2009

Tässä pro gradu –työssä tarkastellaan valtioiden ilmastokonferenssissa pitämissä puheenvuoroissa esiintyviä diskursseja ilmastonmuutoksesta ja siihen liittyvistä oikeudenmukaisuuskysymyksistä. Tutkielmassa etsitään vastauksia ensinnäkin siihen, millä tavoilla valtioiden korkeat edustajat puhuvat ilmastonmuutoksesta ja sen hallinnasta. Toisekseen analysoidaan, tukeutuvatko valtiot puheissa kosmopolitanistisiin käsityksiin ilmasto-oikeudenmukaisuudesta vai hallitseeko niissä kommunitaristinen etiikka. Kosmopolitanistinen etiikka on hallitsevassa asemassa kansainvälisen politiikan filosofiassa, mutta käytännön politiikassa sen ajatellaan olevan kommunitarististen lähestymistapojen varjossa. Tämän työn yhtenä lähtökohtana on ajatus siitä, että kansainvälinen ilmastopolitiikka on ilmastonmuutokseen liittyvän syvän keskinäisriippuvuuden ja yhteistyön välttämättömyyden vuoksi erityisen otollinen politiikan ala kosmopolitanistiselle ajattelulle. Tavoitteena on tutkia, näkyykö tämä valtioiden puhetavoissa. Tutkielman aineistona on 64 Kööpenhaminan ilmastokokouksessa joulukuussa 2009 pidettyä puhetta, jotka ovat otos konferenssissa puhuneiden 192 valtion puheenvuoroista. Puheet on valittu kokouksen lopussa pidetystä kolmen päivän mittaisesta ”korkean tason osiosta”, jossa ministerit ja valtioiden päämiehet pitivät niin kutsuttuja kansallisia lausuntoja. Aineisto on valittu sillä perusteella, että näihin puheisiin tiivistyy kunkin valtion ilmastopoliittisen ajattelun ydin. Aineistoa teemoitellaan ensin erilaisten keskeisten aiheiden kartoittamiseksi. Tämän jälkeen sitä analysoidaan tarkemmin kriittisen diskurssianalyysin keinoin Norman Fairclough’n esittelemillä menetelmillä. Aineistosta nostetaan esiin kuusi erilaista diskurssia ilmastonmuutoksesta ja sen edellyttämästä politii-kasta. Näitä ovat: ”rikkaiden syyllisyys”, ”talousjärjestelmän kritiikki”, ”oikeus kehittyä”, ”vastuulliset rikkaat”, ”vihreä kasvu” ja ”samalla planeetalla”. Kunkin diskurssin keskeisiä piirteitä ja teemoja esitellään ensin yleisellä tasolla, minkä jälkeen analysoidaan tarkemmin kustakin yhtä puhetta, jossa kyseinen diskurssi on erityisen vahvasti läsnä. Diskurssit ovat erilaisia tulokulmia ilmastoeettisiin kysymyksiin, ja kiinnostuksen kohteena oleva kosmopolitanistinen ajattelu on niissä läsnä erilaisissa asteissa. Vahvimmin kosmopolitanistinen etiikka tulee esiin ”samalla planeetalla” –diskurssissa, joka hallit-see erityisesti monien pienten saarivaltioiden puheita. Sen sijaan eniten kommunitaristisia äänenpainoja on ”oikeus kehittyä” –diskurssissa, joka on vaikutusvaltainen suuressa joukossa kehitysmaiden puheita. Yleisesti kosmopolitanistinen ajattelu tulee lievemmissä muodoissaan aineistossa laajasti esiin, mutta vahva kaikkien maailman ihmisten yhtäläisiin oikeuksiin ja velvollisuuksiin perustuva argumentointi on harvinaista. Johtopäätöksenä todetaan, että kosmopolitanismi on osa kansainvälisten ilmastoneuvotteluiden hyväksyttyä puhetapaa mutta lähinnä sellaisissa muodoissa, joissa sillä ei ole radikaaleja poliittisia seurauksia.

Mining Land Cover Information Using Multilayer Perceptron and Decision Tree from MODIS Data

Land cover (LC) changes play a major role in global as well as at regional scale patterns of the climate and biogeochemistry of the Earth system. LC information presents critical insights in understanding of Earth surface phenomena, particularly useful when obtained synoptically from remote sensing data. However, for developing countries and those with large geographical extent, regular LC mapping is prohibitive with data from commercial sensors (high cost factor) of limited spatial coverage (low temporal resolution and band swath). In this context, free MODIS data with good spectro-temporal resolution meet the purpose. LC mapping from these data has continuously evolved with advances in classification algorithms. This paper presents a comparative study of two robust data mining techniques, the multilayer perceptron (MLP) and decision tree (DT) on different products of MODIS data corresponding to Kolar district, Karnataka, India. The MODIS classified images when compared at three different spatial scales (at district level, taluk level and pixel level) shows that MLP based classification on minimum noise fraction components on MODIS 36 bands provide the most accurate LC mapping with 86% accuracy, while DT on MODIS 36 bands principal components leads to less accurate classification (69%).

Contrained linear spectral unmixing technique for regional land cover mapping using MODIS data

Over the last few decades, there has been a significant land cover (LC) change across the globe due to the increasing demand of the burgeoning population and urban sprawl. In order to take account of the change, there is a need for accurate and up- to-date LC maps. Mapping and monitoring of LC in India is being carried out at national level using multi-temporal IRS AWiFS data. Multispectral data such as IKONOS, Landsat- TM/ETM+, IRS-1C/D LISS-III/IV, AWiFS and SPOT-5, etc. have adequate spatial resolution (~ 1m to 56m) for LC mapping to generate 1:50,000 maps. However, for developing countries and those with large geographical extent, seasonal LC mapping is prohibitive with data from commercial sensors of limited spatial coverage. Superspectral data from the MODIS sensor are freely available, have better temporal (8 day composites) and spectral information. MODIS pixels typically contain a mixture of various LC types (due to coarse spatial resolution of 250, 500 and 1000 m), especially in more fragmented landscapes. In this context, linear spectral unmixing would be useful for mapping patchy land covers, such as those that characterise much of the Indian subcontinent. This work evaluates the existing unmixing technique for LC mapping using MODIS data, using end- members that are extracted through Pixel Purity Index (PPI), Scatter plot and N-dimensional visualisation. The abundance maps were generated for agriculture, built up, forest, plantations, waste land/others and water bodies. The assessment of the results using ground truth and a LISS-III classified map shows 86% overall accuracy, suggesting the potential for broad-scale applicability of the technique with superspectral data for natural resource planning and inventory applications.

Averting biodiversity collapse in tropical forest protected areas

The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon(1-3). With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses(4-9). As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve `health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.

Scale-dependent relationships between tree species richness and ecosystem function in forests

1. The relationship between species richness and ecosystem function, as measured by productivity or biomass, is of long-standing theoretical and practical interest in ecology. This is especially true for forests, which represent a majority of global biomass, productivity and biodiversity. 2. Here, we conduct an analysis of relationships between tree species richness, biomass and productivity in 25 forest plots of area 8-50ha from across the world. The data were collected using standardized protocols, obviating the need to correct for methodological differences that plague many studies on this topic. 3. We found that at very small spatial grains (0.04ha) species richness was generally positively related to productivity and biomass within plots, with a doubling of species richness corresponding to an average 48% increase in productivity and 53% increase in biomass. At larger spatial grains (0.25ha, 1ha), results were mixed, with negative relationships becoming more common. The results were qualitatively similar but much weaker when we controlled for stem density: at the 0.04ha spatial grain, a doubling of species richness corresponded to a 5% increase in productivity and 7% increase in biomass. Productivity and biomass were themselves almost always positively related at all spatial grains. 4. Synthesis. This is the first cross-site study of the effect of tree species richness on forest biomass and productivity that systematically varies spatial grain within a controlled methodology. The scale-dependent results are consistent with theoretical models in which sampling effects and niche complementarity dominate at small scales, while environmental gradients drive patterns at large scales. Our study shows that the relationship of tree species richness with biomass and productivity changes qualitatively when moving from scales typical of forest surveys (0.04ha) to slightly larger scales (0.25 and 1ha). This needs to be recognized in forest conservation policy and management.

Analysis of the Genome and Transcriptome of Cryptococcus neoformans var. grubii Reveals Complex RNA Expression and Microevolution Leading to Virulence Attenuation

Cryptococcus neoformans is a pathogenic basidiomycetous yeast responsible for more than 600,000 deaths each year. It occurs as two serotypes (A and D) representing two varieties (i.e. grubii and neoformans, respectively). Here, we sequenced the genome and performed an RNA-Seq-based analysis of the C. neoformans var. grubii transcriptome structure. We determined the chromosomal locations, analyzed the sequence/structural features of the centromeres, and identified origins of replication. The genome was annotated based on automated and manual curation. More than 40,000 introns populating more than 99% of the expressed genes were identified. Although most of these introns are located in the coding DNA sequences (CDS), over 2,000 introns in the untranslated regions (UTRs) were also identified. Poly(A)-containing reads were employed to locate the polyadenylation sites of more than 80% of the genes. Examination of the sequences around these sites revealed a new poly(A)-site-associated motif (AUGHAH). In addition, 1,197 miscRNAs were identified. These miscRNAs can be spliced and/or polyadenylated, but do not appear to have obvious coding capacities. Finally, this genome sequence enabled a comparative analysis of strain H99 variants obtained after laboratory passage. The spectrum of mutations identified provides insights into the genetics underlying the micro-evolution of a laboratory strain, and identifies mutations involved in stress responses, mating efficiency, and virulence.