CEQE: Contextualized Embeddings for Query Expansion

In this work we leverage recent advances in context-sensitive language models to improve the task of query expansion. Contextualized word representation models, such as ELMo and BERT, are rapidly replacing static embedding models. We propose a new model, Contextualized Embeddings for Query Expansion (CEQE), that utilizes query-focused contextualized embedding vectors. We study the behavior of contextual representations generated for query expansion in ad-hoc document retrieval. We conduct our experiments on probabilistic retrieval models as well as in combination with neural ranking models. We evaluate CEQE on two standard TREC collections: Robust and Deep Learning. We find that CEQE outperforms static embedding-based expansion methods on multiple collections (by up to 18% on Robust and 31% on Deep Learning on average precision) and also improves over proven probabilistic pseudo-relevance feedback (PRF) models. We further find that multiple passes of expansion and reranking result in continued gains in effectiveness with CEQE-based approaches outperforming other approaches. The final model incorporating neural and CEQE-based expansion score achieves gains of up to 5% in P@20 and 2% in AP on Robust over the state-of-the-art transformer-based re-ranking model, Birch

Connecting Binuclear Pd(III) and Mononuclear Pd(IV) Chemistry by Pd–Pd Bond Cleavage

Oxidation of binuclear Pd(II) complexes with PhICl$_2$ or PhI(OAc)$_2$ has previously been shown to afford binuclear Pd(III) complexes featuring a Pd–Pd bond. In contrast, oxidation of binuclear Pd(II) complexes with electrophilic trifluoromethylating (“CF$_3^+$”) reagents has been reported to afford mononuclear Pd(IV) complexes. Herein, we report experimental and computational studies of the oxidation of a binuclear Pd(II) complex with “CF$_3^+$” reagents. These studies suggest that a mononuclear Pd(IV) complex is generated by an oxidation–fragmentation sequence proceeding via fragmentation of an initially formed, formally binuclear Pd(III), intermediate. The observation that binuclear Pd(III) and mononuclear Pd(IV) complexes are accessible in the same reactions offers an opportunity for understanding the role of nuclearity in both oxidation and subsequent C–X bond-forming reactions.Chemistry and Chemical Biolog

Experimental Evidence for Reduced Rodent Diversity Causing Increased Hantavirus Prevalence

Emerging and re-emerging infectious diseases have become a major global environmental problem with important public health, economic, and political consequences. The etiologic agents of most emerging infectious diseases are zoonotic, and anthropogenic environmental changes that affect wildlife communities are increasingly implicated in disease emergence and spread. Although increased disease incidence has been correlated with biodiversity loss for several zoonoses, experimental tests in these systems are lacking. We manipulated small-mammal biodiversity by removing non-reservoir species in replicated field plots in Panama, where zoonotic hantaviruses are endemic. Both infection prevalence of hantaviruses in wild reservoir (rodent) populations and reservoir population density increased where small-mammal species diversity was reduced. Regardless of other variables that affect the prevalence of directly transmitted infections in natural communities, high biodiversity is important in reducing transmission of zoonotic pathogens among wildlife hosts. Our results have wide applications in both conservation biology and infectious disease management

Protein expression of the gp78 E3 ligase predicts poor breast cancer outcome based on race

Women of African ancestry suffer higher rates of breast cancer mortality compared with all other groups in the United States. Though the precise reasons for these disparities remain unclear, many recent studies have implicated a role for differences in tumor biology. Using an epitope-validated antibody against the endoplasmic reticulum-associated E3 ligase, gp78, we show that elevated levels of gp78 in patient breast cancer cells predict poor survival. Moreover, high levels of gp78 are associated with poor outcomes in both ER+ and ER- tumors, and breast cancers expressing elevated amounts of gp78 protein are enriched in gene expression pathways that influence cell cycle, metabolism, receptor-mediated signaling, and cell stress response pathways. In multivariate analysis adjusted for subtype and grade, gp78 protein is an independent predictor of poor outcomes in women of African ancestry. Furthermore, gene expression signatures, derived from patients stratified by gp78 protein expression, are strong predictors of recurrence and pathological complete response in retrospective clinical trial data and share many common features with gene sets previously identified to be overrepresented in breast cancers based on race. These findings implicate a prominent role for gp78 in tumor progression and offer insights into our understanding of racial differences in breast cancer outcomes.Fil: Singhal, Sandeep K.. No especifíca;Fil: Byun, Jung S.. National Institutes of Health; Estados UnidosFil: Yan, Tingfen. National Institutes of Health; Estados UnidosFil: Yancey, Ryan. Columbia University; Estados UnidosFil: Caban, Ambar. Columbia University; Estados UnidosFil: Hernandez, Sara Gil. National Institutes of Health; Estados UnidosFil: Bufford, Sediqua. No especifíca;Fil: Hewitt, Stephen M.. No especifíca;Fil: Winfield, Joy. Columbia University; Estados UnidosFil: Pradhan, Jaya. Columbia University; Estados UnidosFil: Mustkov, Vesco. Columbia University; Estados UnidosFil: McDonald, Jasmine A.. No especifíca;Fil: Pérez Stable, Eliseo J.. National Institutes of Health; Estados UnidosFil: Nápoles, Anna María. National Institutes of Health; Estados UnidosFil: Vohra, Nasreen. No especifíca;Fil: de Siervi, Adriana. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Yates, Clayton. No especifíca;Fil: Davis, Melissa B.. No especifíca;Fil: Yang, Mei. No especifíca;Fil: Tsai, Yien Che. No especifíca;Fil: Weissman, Allan M.. No especifíca;Fil: Gardner, Kevin. Columbia University; Estados Unido

Ecological implications of fine-scale fire patchiness and severity in tropical savannas of northern Australia

Research ArticleUnderstanding fine-scale fire patchiness has significant implications for ecological processes and biodiversity conservation. It can affect local extinction of and recolonisation by relatively immobile fauna and poorly seed-dispersed flora in fire-affected areas. This study assesses fine-scale fire patchiness and severity, and associated implications for biodiversity, in north Australian tropical savanna systems. We used line transects to sample burning patterns of ground layer vegetation in different seasons and vegetation structure types, within the perimeter of 35 fires that occurred between 2009 and 2011. We evaluated two main fire characteristics: patchiness (patch density and mean patch length) and severity (inferred from char and scorch heights, and char and ash proportions). The mean burned area of ground vegetation was 83 % in the early dry season (EDS: May to July) and 93 % in the late dry season (LDS: August to November). LDS fires were less patchy (smaller and fewer unburned patches), and had higher fire severity (higher mean char and scorch heights, and twice the proportion of ash) than EDS fires. Fire patchiness varied among vegetation types, declining under more open canopy structure. The relationship between burned area and fire severity depended on season, being strongly correlated in the EDS and uncorrelated in the LDS. Simulations performed to understand the implications of patchiness on the population dynamics of fire-interval sensitive plant species showed that small amounts of patchiness substantially enhance survival. Our results indicate that the ecological impacts of high frequency fires on firesensitive regional biodiversity elements are likely to be lower than has been predicted from remotely sensed studies that are based on assumptions of homogeneous burninginfo:eu-repo/semantics/publishedVersio

RE: pedagogy – after neutrality

Within the UK and in many parts of the world, official accounts of what it is to make sense of religion are framed within a rhetorics of neutrality in which such study is premised upon the possibility of dispassionate engagement and analysis. This paper, which is largely theoretical in scope, explores both the affordances and the costs of such an approach which has become ‘black boxed’ on account of the work that it achieves. A series of new orientations within the academy that are broadly associated with post-structuralist philosophies, feminist and post-colonial studies, together with insights from Science and Technology Studies, question the plausibility of these claims for neutrality whilst in turn raising a series of new questions and priorities. It therefore becomes necessary to re-think and re-frame what it is to make sense of religious and cultural difference after neutrality. The gathering and co-ordination of new planes of sense-making that are responsive to an emergent series of epistemological, ontological, and ethical orientations are considered. Some of the distinctive pedagogical implications of such an approach that engages material practice, difference and uncertainty are then entertained

Modeling Statistical Properties of Written Text

Written text is one of the fundamental manifestations of human language, and the study of its universal regularities can give clues about how our brains process information and how we, as a society, organize and share it. Among these regularities, only Zipf's law has been explored in depth. Other basic properties, such as the existence of bursts of rare words in specific documents, have only been studied independently of each other and mainly by descriptive models. As a consequence, there is a lack of understanding of linguistic processes as complex emergent phenomena. Beyond Zipf's law for word frequencies, here we focus on burstiness, Heaps' law describing the sublinear growth of vocabulary size with the length of a document, and the topicality of document collections, which encode correlations within and across documents absent in random null models. We introduce and validate a generative model that explains the simultaneous emergence of all these patterns from simple rules. As a result, we find a connection between the bursty nature of rare words and the topical organization of texts and identify dynamic word ranking and memory across documents as key mechanisms explaining the non trivial organization of written text. Our research can have broad implications and practical applications in computer science, cognitive science and linguistics

"A novel in vivo model for the study of human breast cancer metastasis using primary breast tumor-initiating cells from patient biopsies"

<p>Abstract</p> <p>Background</p> <p>The study of breast cancer metastasis depends on the use of established breast cancer cell lines that do not accurately represent the heterogeneity and complexity of human breast tumors. A tumor model was developed using primary breast tumor-initiating cells isolated from patient core biopsies that would more accurately reflect human breast cancer metastasis.</p> <p>Methods</p> <p>Tumorspheres were isolated under serum-free culture conditions from core biopsies collected from five patients with clinical diagnosis of invasive ductal carcinoma (IDC). Isolated tumorspheres were transplanted into the mammary fat pad of NUDE mice to establish tumorigenicity <it>in vivo</it>. Tumors and metastatic lesions were analyzed by hematoxylin and eosin (H+E) staining and immunohistochemistry (IHC).</p> <p>Results</p> <p>Tumorspheres were successfully isolated from all patient core biopsies, independent of the estrogen receptor α (ERα)/progesterone receptor (PR)/Her2/neu status or tumor grade. Each tumorsphere was estimated to contain 50-100 cells. Transplantation of 50 tumorspheres (1-5 × 10³cells) in combination with Matrigel into the mammary fat pad of NUDE mice resulted in small, palpable tumors that were sustained up to 12 months post-injection. Tumors were serially transplanted three times by re-isolation of tumorspheres from the tumors and injection into the mammary fat pad of NUDE mice. At 3 months post-injection, micrometastases to the lung, liver, kidneys, brain and femur were detected by measuring content of human chromosome 17. Visible macrometastases were detected in the lung, liver and kidneys by 6 months post-injection. Primary tumors variably expressed cytokeratins, Her2/neu, cytoplasmic E-cadherin, nuclear β catenin and fibronectin but were negative for ERα and vimentin. In lung and liver metastases, variable redistribution of E-cadherin and β catenin to the membrane of tumor cells was observed. ERα was re-expressed in lung metastatic cells in two of five samples.</p> <p>Conclusions</p> <p>Tumorspheres isolated under defined culture conditions from patient core biopsies were tumorigenic when transplanted into the mammary fat pad of NUDE mice, and metastasized to multiple mouse organs. Micrometastases in mouse organs demonstrated a dormancy period prior to outgrowth of macrometastases. The development of macrometastases with organ-specific phenotypic distinctions provides a superior model for the investigation of organ-specific effects on metastatic cancer cell survival and growth.</p

Identification of rare sequence variation underlying heritable pulmonary arterial hypertension.

Pulmonary arterial hypertension (PAH) is a rare disorder with a poor prognosis. Deleterious variation within components of the transforming growth factor-β pathway, particularly the bone morphogenetic protein type 2 receptor (BMPR2), underlies most heritable forms of PAH. To identify the missing heritability we perform whole-genome sequencing in 1038 PAH index cases and 6385 PAH-negative control subjects. Case-control analyses reveal significant overrepresentation of rare variants in ATP13A3, AQP1 and SOX17, and provide independent validation of a critical role for GDF2 in PAH. We demonstrate familial segregation of mutations in SOX17 and AQP1 with PAH. Mutations in GDF2, encoding a BMPR2 ligand, lead to reduced secretion from transfected cells. In addition, we identify pathogenic mutations in the majority of previously reported PAH genes, and provide evidence for further putative genes. Taken together these findings contribute new insights into the molecular basis of PAH and indicate unexplored pathways for therapeutic intervention