CEDR: Contextualized Embeddings for Document Ranking

Although considerable attention has been given to neural ranking architectures recently, far less attention has been paid to the term representations that are used as input to these models. In this work, we investigate how two pretrained contextualized language modes (ELMo and BERT) can be utilized for ad-hoc document ranking. Through experiments on TREC benchmarks, we find that several existing neural ranking architectures can benefit from the additional context provided by contextualized language models. Furthermore, we propose a joint approach that incorporates BERT's classification vector into existing neural models and show that it outperforms state-of-the-art ad-hoc ranking baselines. We call this joint approach CEDR (Contextualized Embeddings for Document Ranking). We also address practical challenges in using these models for ranking, including the maximum input length imposed by BERT and runtime performance impacts of contextualized language models

Emission estimates of HCFCs and HFCs in California from the 2010 CalNex study

The CalNex 2010 (California Research at the Nexus of Air Quality and Climate Change) study was designed to evaluate the chemical composition of air masses over key source regions in California. During May to June 2010, air samples were collected on board a National Oceanic and Atmospheric Administration (NOAA) WP-3D aircraft over the South Coast Air Basin of California (SoCAB) and the Central Valley (CV). This paper analyzes six effective greenhouse gases - chlorodifluoromethane (HCFC-22), 1,1-dichloro-1-fluoroethane (HCFC-141b), 1-chloro-1,1-difluoroethane (HCFC-142b), 2-chloro-1,1,1,2-tetrafluoroethane (HCFC-124), 1,1,1,2- tetrafluoroethane (HFC-134a), and 1,1-difluoroethane (HFC-152a) - providing the most comprehensive characterization of chlorofluorocarbon (CFC) replacement compound emissions in California. Concentrations of measured HCFCs and HFCs are enhanced greatly throughout the SoCAB and CV, with highest levels observed in the SoCAB: 310 ± 92 pptv for HCFC-22, 30.7 ± 18.6 pptv for HCFC-141b, 22.9 ± 2.0 pptv for HCFC-142b, 4.86 ± 2.56 pptv for HCFC-124, 109 ± 46.4 pptv for HFC-134a, and 91.2 ± 63.9 pptv for HFC-152a. Annual emission rates are estimated for all six compounds in the SoCAB using the measured halocarbon to carbon monoxide (CO) mixing ratios and CO emissions inventories. Emission rates of 3.05 ± 0.70 Gg for HCFC-22, 0.27 ± 0.07 Gg for HCFC-141b, 0.06 ± 0.01 Gg for HCFC-142b, 0.11 ± 0.03 Gg for HCFC-124, 1.89 ± 0.43 Gg for HFC-134a, and 1.94 ± 0.45 Gg for HFC-152b for the year 2010 are calculated for the SoCAB. These emissions are extrapolated from the SoCAB region to the state of California using population data. Results from this study provide a baseline emission rate that will help future studies determine if HCFC and HFC mitigation strategies are successful. Key PointsHCFC and HFC emissions are calculated for the year 2010 for the SoCABEmissions are extrapolated to the state of CaliforniaEmissions are calculated using CalNex field measurements © 2013. American Geophysical Union. All Rights Reserved

Plxnd1 Expression in Thymocytes Regulates Their Intrathymic Migration While That in Thymic Endothelium Impacts Medullary Topology

An important role for plexinD1 in thymic development is inferred from studies of germline Plxnd1 knockout (KO) mice where mislocalized CD69+ thymocytes as well as ectopic thymic subcapsular medullary structures were observed. Given embryonic lethality of the Plxnd1−/− genotype, fetal liver transplantation was employed in these prior analyses. Such embryonic hematopoietic reconstitution may have transferred Plxnd1 KO endothelial and/or epithelial stem cells in addition to Plxnd1 KO lymphoid progenitors, thereby contributing to that phenotype. Here we use Plxnd1flox/flox mice crossed to pLck-Cre, pKeratin14-Cre, or pTek-Cre transgenic animals to create cell-type specific conditional knockout (CKO) lines involving thymocytes (D1ThyCKO), thymic epithelium (D1EpCKO), and thymic endothelium (D1EnCKO), respectively. These CKOs allowed us to directly assess the role of plexinD1 in each lineage. Loss of plexinD1 expression on double positive (DP) thymocytes leads to their aberrant migration and cortical retention after TCR-mediated positive selection. In contrast, ectopic medulla formation is a consequence of loss of plexinD1 expression on endothelial cells, in turn linked to dysregulation of thymic angiogenesis. D1EpCKO thymi manifest neither abnormality. Collectively, our findings underscore the non-redundant roles for plexinD1 on thymocytes and endothelium, including the dynamic nature of medulla formation resulting from crosstalk between these thymic cellular components

Bayesian modeling of recombination events in bacterial populations

Background: We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currently available methods for recombination detection capable of probabilistic characterization of uncertainty have a limited applicability in practice as the number of strains in a data set increases. Results: We introduce a Bayesian spatial structural model representing the continuum of origins over sites within the observed sequences, including a probabilistic characterization of uncertainty related to the origin of any particular site. To enable a statistically accurate and practically feasible approach to the analysis of large-scale data sets representing a single genus, we have developed a novel software tool (BRAT, Bayesian Recombination Tracker) implementing the model and the corresponding learning algorithm, which is capable of identifying the posterior optimal structure and to estimate the marginal posterior probabilities of putative origins over the sites. Conclusion: A multitude of challenging simulation scenarios and an analysis of real data from seven housekeeping genes of 120 strains of genus Burkholderia are used to illustrate the possibilities offered by our approach. The software is freely available for download at URL http://web.abo.fi/fak/ mnf//mate/jc/software/brat.html

Adsorption in non interconnected pores open at one or at both ends: A reconsideration of the origin of the hysteresis phenomenon

We report on an experimental study of adsorption isotherme of nitrogen onto porous silicon with non interconnected pores open at one or at both ends in order to check for the first time the old (1938) but always current idea based on Cohan's description which suggests that the adsorption of gaz should occur reversibly in the first case and irreversibly in the second one. Hysteresis loops, the shape of which is usually associated to interconnections in porous media, are observed whether the pores are open at one or at both ends in contradiction with Cohan's model.Comment: 5 pages, 4 EPS figure

Impact de l'introduction des légumineuses dans les systèmes de culture sur les émissions de protoxyde d'azote

Dans un objectif d'atténuation du réchauffement climatique, la mise en place de systèmes de culture plus autonomes vis - à - vis des engrais minéraux devient incontournable pour réduire les émissions de gaz à effet de serre (GES) tout en diminuant le coût de la fertilisation. L'insertion de légumineuses dans ces systèmes semble être un levier prometteur pour y parvenir. Les économies d'azote permises par différents modes d'introduction de légumineuses et leur impact sur les émissions de GES ont été estimés et évalués en quantifiant au préalable les flux d'azote dans les systèmes avec ou sans légumineuses à partir de données issues de dispositifs expérimentaux préexistants, disponibles dans la bibliographie ou acquises dans de nouveaux essais. L'introduction de légumineuses présente régulièrement un impact positif sur la réduction de l'emploi des engrais azotés. Le risque d'augmentation de la lixiviation du nitrate dépend de leur mode d'introduction et de leur place dans les rotations. Enfin, les émissions mesurées en cul tures principales de légumineuses sont généralement très significativement réduites en comparaison des cultures fertilisées, cependant la dégradation des résidus des légumineuses (en culture ou en couverts) peut générer des émissions de N 2 O corrélées à leur impact sur les flux d'azote, variable selon les conditions pédoclimatiques. Ces résultats devraient permettre d'élaborer des recommandations pour mieux prendre en compte les légumineuses dans la conception de systèmes de culture plus autonomes vis - à - vis des engrais azotés de synthèse et moins émetteurs de N 2 0

Surprises in the Orbital Magnetic Moment and g-Factor of the Dynamic Jahn-Teller Ion C_{60}^-

We calculate the magnetic susceptibility and g-factor of the isolated C_{60}^- ion at zero temperature, with a proper treatment of the dynamical Jahn-Teller effect, and of the associated orbital angular momentum, Ham-reduced gyromagnetic ratio, and molecular spin-orbit coupling. A number of surprises emerge. First, the predicted molecular spin-orbit splitting is two orders of magnitude smaller than in the bare carbon atom, due to the large radius of curvature of the molecule. Second, this reduced spin-orbit splitting is comparable to Zeeman energies, for instance, in X-band EPR at 3.39KGauss, and a field dependence of the g-factor is predicted. Third, the orbital gyromagnetic factor is strongly reduced by vibron coupling, and so therefore are the effective weak-field g-factors of all low-lying states. In particular, the ground-state doublet of C_{60}^- is predicted to show a negative g-factor of \sim -0.1.Comment: 19 pages RevTex, 2 postscript figures include

Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology