Identifying gene and protein mentions in text using conditional random fields

We present a model for tagging gene and protein mentions from text using the probabilistic sequence tagging framework of conditional random fields (CRFs). Conditional random fields model the probability P(t|o) of a tag sequence given an observation sequence directly, and have previously been employed successfully for other tagging tasks. The mechanics of CRFs and their relationship to maximum entropy are discussed in detail. We employ a diverse feature set containing standard orthographic features combined with expert features in the form of gene and biological term lexicons to achieve a precision of 86.4% and recall of 78.7%. An analysis of the contribution of the various features of the model is provided

Peril, privilege, and queer comforts: the nocturnal performative geographies of expatriate gay men in Dubai

This article investigates the intersection of expatriate experiences, queer men's lives, and nocturnal geographies within the transnational Middle Eastern setting of Dubai, United Arab Emirates (UAE). Although narrowly focused on cisgender men who self-identify as “Western” and “gay,” the study addresses a lack of research about LGBT+ presence among expatriates globally, and poor coverage of queer residents in Gulf cities generally. Using ethnography and in-depth interviews among this segment of men who have come to Dubai to work in relatively privileged professional roles for at least two years, we illuminate the shifting, performative geographies of queer belonging in which these men engage to distinguish spaces that can be embodied in different moments with degrees of comfort and caution. Despite their imperiled position in an officially homophobic territory, these men use their various privileges (economic, social, cultural, and sometimes phenotypic) to counter peril in performing transnational identities that reaffirm their own senses of self (as gay), forge new collectivities (as Western), and distinguish themselves from others deemed suspect (potentially anyone “non-Western”). Findings point to the uneasy dynamics of inclusion/exclusion in this kind of unfixed gay nightlife geography, and the need to study queer expatriates in other world settings, as well as queer lives in Gulf cities more broadly, from a further intersectional perspective: beyond nocturnal geographies, and encompassing the range of queer denizens, not just this relatively privileged subset

The role of transposable elements in the evolution of aluminium resistance in plants.

Abstract Aluminium (Al) toxicity can severely reduce root growth and consequently affect plant development and yield. A mechanism by which many species resist the toxic effects of Al relies on the efflux of organic anions (OAs) from the root apices via OA transporters. Several of the genes encoding these OA transporters contain transposable elements (TEs) in the coding sequences or in flanking regions. Some of the TE-induced mutations impact Al resistance by modifying the level and/or location of gene expression so that OA efflux from the roots is increased. The importance of genomic modifications for improving the adaptation of plants to acid soils has been raised previously, but the growing number of examples linking TEs with these changes requires highlighting. Here, we review the role of TEs in creating genetic modifications that enhance the adaptation of plants to acid soils by increasing the release of OAs from the root apices. We argue that TEs have been an important source of beneficial mutations that have co-opted OA transporter proteins with other functions to perform this role. These changes have occurred relatively recently in the evolution of many species and likely facilitated their expansion into regions with acidic soils

Automatically annotating documents with normalized gene lists

BACKGROUND: Document gene normalization is the problem of creating a list of unique identifiers for genes that are mentioned within a document. Automating this process has many potential applications in both information extraction and database curation systems. Here we present two separate solutions to this problem. The first is primarily based on standard pattern matching and information extraction techniques. The second and more novel solution uses a statistical classifier to recognize valid gene matches from a list of known gene synonyms. RESULTS: We compare the results of the two systems, analyze their merits and argue that the classification based system is preferable for many reasons including performance, simplicity and robustness. Our best systems attain a balanced precision and recall in the range of 74%–92%, depending on the organism

Spanning Tree Methods for Discriminative Training of Dependency Parsers

Untyped dependency parsing can be viewed as the problem of finding maximum spanning trees (MSTs) in directed graphs. Using this representation, the Eisner (1996) parsing algorithm is sufficient for searching the space of projective trees. More importantly, the representation is extended naturally to non-projective parsing using Chu-Liu-Edmonds (Chu and Liu, 1965; Edmonds, 1967) MST algorithm. These efficient parse search methods support large-margin discriminative training methods for learning dependency parsers. We evaluate these methods experimentally on the English and Czech treebanks

Tropical lowland rainforests :rapid recyclers or efficient storers of carbon?

PhD ThesisAmazonian rainforests are important systems that vigorously cycle carbon and water at the global and regional scale. However, despite their importance, dynamics of organic matter cycling in tropical rainforests within the global carbon cycle is poorly understood. New field-based hydrology and geochemistry data is presented from a three-year study (2009-2011) in the pristine rainforest of central Guyana at the northern rim of Amazonia. The study shows that two commonly used satellite- and interpolated-based models to estimate rainfall greatly overestimate and underestimate in the wet and dry season, respectively. This misrepresentation of hydrology at local and regional scales greatly affects our ability to understand and predict the connections and feedbacks between the hydrological and geochemical cycles. River water δ2H and δ18O isotopes from peak wet and dry seasons suggest that the majority of rainfall has a residence time of at least one month, which provides regions of water saturated zones for organic matter (OM) to be preserved in deeper rainforest soils (Δ14C ages of 360-1200 years). In contrast, Δ14C values of surface soils and dissolved organic matter (DOM) in river water recycle within ~60 years or less. Carbon normalised yields of lignin phenols, used as tracers of vascular plant material, are abundant across the terrestrial-aquatic interface. However, lignin appears to accumulate in river bed sediments. Soil leachate experiments confirm that during mobilisation from soil particulates into the dissolved phase, desorption processes change the composition of lignin biomarker ratios. Surface soil δ13C signatures show that the majority of carbon is fixed through the C3 pathway (-26.4 to -32.0‰). However, a strong variability of up to 10‰ in riverine δ13C of dissolved organic carbon suggests that changing δ13C of DOC reflects changing contributions of degraded and fresh organic compounds within the total OM pool. Superimposed on seasonal cycling, short intense rain events cause rapid mobilisation of large amounts of DOC (up to 114 mg/L) that is divided into two main fractions, humic substances and ‘invisible’ DOM, or ‘iDOM’. The latter group is characterised by non UV-absorbing organic compounds of mono- and oligosaccharides, alcohols, aldehydes, ketones and amino sugars. Importantly, iDOM contributes up to 89% to the total river OM pool during peak DOC supplyInter-American Development Bank (ATN/MC-11548-GY, project GY-T1069-Measurement of Climate Change Impacts and Eco-System Services at Iwokrama), NERC (NE/H525254/1) and the Royal Society Wolfson Research Merit Awar

Economic and Social Impacts of Energy Shocks: A General Equilibrium Analysis for Chile

Oil price increases and the restrictions to natural gas imports from Argentina generate multiple effects which ripple throughout the Chilean economy. The magnitude of the aggregate, sectoral and distributive impacts associated with these changes in the energy sector is debated. In this paper, using a static general equilibrium framework, we analyze quantitatively the direct and indirect effects of these international shocks. The results show that the increase in international prices of oil and fuels generates a slightly negative impact on GDP, which is explained by the recessionary effect on consumption. The sectors most adversely affected are the fuel sector, other sectors strongly linked to the energy sectors such as transport and electricity and those geared to the provision of goods and services for final consumption. The main effect on the productive structure is a strengthening of Chile’s traditional comparative advantages based on primary sectors and natural resources. Within the energy sector, coal gains participation in the energy matrix. The impacts on the income of the poorest and its distribution are clearly negative: contractionary and regressive. The former results are magnified when both natural gas supply restrictions and high hydrocarbon prices are considered together.