Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data.

As the capacity for generating large-scale molecular profiling data continues to grow, the ability to extract meaningful biological knowledge from it remains a limitation. Here, we describe the development of a new fixed repertoire of transcriptional modules, BloodGen3, that is designed to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome data. The construction of this repertoire is based on co-clustering patterns observed across sixteen immunological and physiological states encompassing 985 blood transcriptome profiles. Interpretation is supported by customized resources, including module-level analysis workflows, fingerprint grid plot visualizations, interactive web applications and an extensive annotation framework comprising functional profiling reports and reference transcriptional profiles. Taken together, this well-characterized and well-supported transcriptional module repertoire can be employed for the interpretation and benchmarking of blood transcriptome profiles within and across patient cohorts. Blood transcriptome fingerprints for the 16 reference cohorts can be accessed interactively via: https://drinchai.shinyapps.io/BloodGen3Module/

Noun and verb knowledge in monolingual preschool children across 17 languages: Data from cross-linguistic lexical tasks (LITMUS-CLT)

This article investigates the cross-linguistic comparability of the newly developed lexical assessment tool Cross-linguistic Lexical Tasks (LITMUS-CLT). LITMUS-CLT is a part the Language Impairment Testing in Multilingual Settings (LITMUS) battery (Armon-Lotem, de Jong & Meir, 2015). Here we analyse results on receptive and expressive word knowledge tasks for nouns and verbs across 17 languages from eight different language families: Baltic (Lithuanian), Bantu (isiXhosa), Finnic (Finnish), Germanic (Afrikaans, British English, South African English, German, Luxembourgish, Norwegian, Swedish), Romance (Catalan, Italian), Semitic (Hebrew), Slavic (Polish, Serbian, Slovak) and Turkic (Turkish). The participants were 639 monolingual children aged 3;0-6;11 living in 15 different countries. Differences in vocabulary size were small between 16 of the languages; but isiXhosa-speaking children knew significantly fewer words than speakers of the other languages. There was a robust effect of word class: accuracy was higher for nouns than verbs. Furthermore, comprehension was more advanced than production. Results are discussed in the context of cross-linguistic comparisons of lexical development in monolingual and bilingual populations

Holocene fire activity during low-natural flammability periods reveals scale-dependent cultural human-fire relationships in Europe

Fire is a natural component of global biogeochemical cycles and closely related to changes in human land use. Whereas climate-fuel relationships seem to drive both global and subcontinental fire regimes, human-induced fires are prominent mainly on a local scale. Furthermore, the basic assumption that relates humans and fire regimes in terms of population densities, suggesting that few human-induced fires should occur in periods and areas of low population density, is currently debated. Here, we analyze human-fire relationships throughout the Holocene and discuss how and to what extent human driven fires affected the landscape transformation in the Central European Lowlands (CEL). We present sedimentary charcoal composites on three spatial scales and compare them with climate model output and land cover reconstructions from pollen records. Our findings indicate that widespread natural fires only occurred during the early Holocene. Natural conditions (climate and vegetation) limited the extent of wildfires beginning 8500 cal. BP, and diverging subregional charcoal composites suggest that Mesolithic hunter-gatherers maintained a culturally diverse use of fire. Divergence in regional charcoal composites marks the spread of sedentary cultures in the western and eastern CEL The intensification of human land use during the last millennium drove an increase in fire activity to early-Holocene levels across the CEL Hence, humans have significantly affected natural fire regimes beyond the local scale - even in periods of low population densities - depending on diverse cultural land-use strategies. We find that humans have strongly affected land-cover- and biogeochemical cycles since Mesolithic times

Holocene fires in the central European lowlands and the role of humans

International audienceA major debate concerns the questions of when and to what extent humans affected regional landscapes, especially land cover and associated geomorphological dynamics, significantly beyond natural variability. Fire is both, a natural component of many climate zones and ecosystems around the globe and also closely related to human land cover change. Humans clearly affected natural fire regimes and landscapes in the most recent centuries, acting as prime ignition triggers and later fire suppressors, while Holocene trends in sedimentary charcoal have been mainly associated with climatic factors and partly with Neolithic land cover change. However, little is known since when Paleolithic to Neolithic fire use affected natural landscapes beyond small spatial and temporal scales. Here, we discuss onset and extent of human-driven fires superimposed on natural Holocene landscape transformation for the central European lowlands (CEL), a landscape of low natural flammability and long human history. We present composites of sedimentary charcoal records as new human impact proxies for periods when natural conditions (climate and vegetation) limited wildfires. Together with climate model output and land cover reconstructions from pollen, we find that fire was naturally important only during the early Holocene. The onset of human-driven fires beyond natural fires appeared scale-dependent. Sub-regional fire maxima indicate fire use by Mesolithic hunter-gatherers, already 8,500 years ago. Regionally, fire marks the Neolithisation onset at ∼6,500 years (western CEL) and ∼4,000 years ago (eastern CEL). During the last millennium, farming intensification drove fire up to early Holocene levels across all CEL. Fire activity reduced only in the highly fragmented landscape of northern Germany during the last centuries. As compilations of soil erosion records even mirror Holocene fire trends, we conclude that past human land cover change could have affected sub-regional landscapes more and earlier than previously thought

Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data

International audienceAs the capacity for generating large-scale molecular profiling data continues to grow, the ability to extract meaningful biological knowledge from it remains a limitation. Here, we describe the development of a new fixed repertoire of transcriptional modules, BloodGen3, that is designed to serve as a stable reusable framework for the analysis and interpretation of blood transcriptome data. The construction of this repertoire is based on co-clustering patterns observed across sixteen immunological and physiological states encompassing 985 blood transcriptome profiles. Interpretation is supported by customized resources, including module-level analysis workflows, fingerprint grid plot visualizations, interactive web applications and an extensive annotation framework comprising functional profiling reports and reference transcriptional profiles. Taken together, this well-characterized and well-supported transcriptional module repertoire can be employed for the interpretation and benchmarking of blood transcriptome profiles within and across patient cohorts. Blood transcriptome fingerprints for the 16 reference cohorts can be accessed interactively via: https://drinchai.shinyapps.io/BloodGen3Module/

The Skill-Biased Effects of Exchange Rate Fluctuations

This article examines the linkages between real exchange rate movements and firms' skill demand. Augmenting the model of Campa and Goldberg (2001) with heterogeneous labour, we show that exchange rate movements may affect unskilled workers differently than skilled workers because they change the relative price of imported inputs. Using panel data on Swiss manufacturers covering the period 1998–2012, we find that an appreciation increases high-skilled and reduces low-skilled employment in most firms. We present evidence consistent with our model that the skill-biased effects of exchange rates arise because unskilled labour is more substitutable with imported inputs than skilled labour