Syntactic Topic Models

The syntactic topic model (STM) is a Bayesian nonparametric model of language that discovers latent distributions of words (topics) that are both semantically and syntactically coherent. The STM models dependency parsed corpora where sentences are grouped into documents. It assumes that each word is drawn from a latent topic chosen by combining document-level features and the local syntactic context. Each document has a distribution over latent topics, as in topic models, which provides the semantic consistency. Each element in the dependency parse tree also has a distribution over the topics of its children, as in latent-state syntax models, which provides the syntactic consistency. These distributions are convolved so that the topic of each word is likely under both its document and syntactic context. We derive a fast posterior inference algorithm based on variational methods. We report qualitative and quantitative studies on both synthetic data and hand-parsed documents. We show that the STM is a more predictive model of language than current models based only on syntax or only on topics

Differential and Joint Effects of Metformin and Statins on Overall Survival of Elderly Patients with Pancreatic Adenocarcinoma: A Large Population-Based Study.

Background: Published evidence indicates that individual use of metformin and statin is associated with reduced cancer mortality. However, their differential and joint effects on pancreatic cancer survival are inconclusive.Methods: We identified a large population-based cohort of 12,572 patients ages 65 years or older with primary pancreatic ductal adenocarcinoma (PDAC) diagnosed between 2008 and 2011 from the Surveillance, Epidemiology, and End Results (SEER)-Medicare-linked database. Exposure to metformin and statins was ascertained from Medicare Prescription Drug Event files. Cox proportional hazards models with time-varying covariates adjusted for propensity scores were used to assess the association while controlling for potential confounders.Results: Of 12,572 PDAC patients, 950 (7.56%) had used metformin alone, 4,506 (35.84%) had used statin alone, and 2,445 (19.45%) were dual users. Statin use was significantly associated with improved overall survival [HR, 0.94; 95% confidence interval (CI), 0.90-0.98], and survival was more pronounced in postdiagnosis statin users (HR, 0.69; 95% CI, 0.56-0.86). Metformin use was not significantly associated with overall survival (HR, 1.01; 95% CI, 0.94-1.09). No beneficial effect was observed for dual users (HR, 1.00; 95% CI, 0.95-1.05).Conclusions: Our findings suggest potential benefits of statins on improving survival among elderly PDAC patients; further prospective studies are warranted to corroborate the putative benefit of statin therapy in pancreatic cancer.Impact: Although more studies are needed to confirm our findings, our data add to the body of evidence on potential anticancer effects of statins. Cancer Epidemiol Biomarkers Prev; 26(8); 1225-32. ©2017 AACR

Measuring discursive influence across scholarship

Assessing scholarly influence is critical for understanding the collective system of scholarship and the history of academic inquiry. Influence is multifaceted, and citations reveal only part of it. Citation counts exhibit preferential attachment and follow a rigid “news cycle” that can miss sustained and indirect forms of influence. Building on dynamic topic models that track distributional shifts in discourse over time, we introduce a variant that incorporates features, such as authorship, affiliation, and publication venue, to assess how these contexts interact with content to shape future scholarship. We perform in-depth analyses on collections of physics research (500,000 abstracts; 102 years) and scholarship generally (JSTOR repository: 2 million full-text articles; 130 years). Our measure of document influence helps predict citations and shows how outcomes, such as winning a Nobel Prize or affiliation with a highly ranked institution, boost influence. Analysis of citations alongside discursive influence reveals that citations tend to credit authors who persist in their fields over time and discount credit for works that are influential over many topics or are “ahead of their time.” In this way, our measures provide a way to acknowledge diverse contributions that take longer and travel farther to achieve scholarly appreciation, enabling us to correct citation biases and enhance sensitivity to the full spectrum of scholarly impact

Scalable Cross-lingual Document Similarity through Language-specific Concept Hierarchies

With the ongoing growth in number of digital articles in a wider set of languages and the expanding use of different languages, we need annotation methods that enable browsing multi-lingual corpora. Multilingual probabilistic topic models have recently emerged as a group of semi-supervised machine learning models that can be used to perform thematic explorations on collections of texts in multiple languages. However, these approaches require theme-aligned training data to create a language-independent space. This constraint limits the amount of scenarios that this technique can offer solutions to train and makes it difficult to scale up to situations where a huge collection of multi-lingual documents are required during the training phase. This paper presents an unsupervised document similarity algorithm that does not require parallel or comparable corpora, or any other type of translation resource. The algorithm annotates topics automatically created from documents in a single language with cross-lingual labels and describes documents by hierarchies of multi-lingual concepts from independently-trained models. Experiments performed on the English, Spanish and French editions of JCR-Acquis corpora reveal promising results on classifying and sorting documents by similar content.Comment: Accepted at the 10th International Conference on Knowledge Capture (K-CAP 2019

A reverse pathway? Actual and perceived skill proficiency and physical activity

Purpose: Motor skills are considered a prerequisite to physical activity, yet the relationship may be reciprocal and perceived sports competence might mediate associations.Methods: In 2006/2007, 215 adolescents completed motor skill proficiency (Get Skilled Get Active), perceived sport competence (Physical Self-Perception Profile) and physical activity assessments (Adolescent Physical Activity Recall Questionnaire) as part of the Physical Activity and Skills Study. Using AMOS (Version 7.0), reciprocal relationships were examined between motor skill (object control and locomotor) and moderate to vigorous physical activity (MVPA). Both models were then run in different versions to understand the role of perceived sports competence as a potential mediator. Results: Mean age was 16.4 yr (SD = 0.6), 51.6% (111/215) were females. A reciprocal relationship between object control and MVPA and a one-way relationship from MVPA to locomotor skill was found. When perceived sports competence was examined as a mediator, the best-fitting model versions explained 16% (R&sup2; = 0.16)MVPA variation, and 30% object control (R&sup2; = 0.30), and 12% locomotor skill variation (R&sup2; = 0.12) (reverse relationship). Perceived sports competence partially mediates the relationship between object control proficiency and physical activity for both directions and fully mediates the relationship between physical activity and locomotor skill; but only when locomotor skill is the outcome.Conclusions: If the relationship between object control skill and physical activity is viewed as a &lsquo;&lsquo;positive feedback loop,&rsquo;&rsquo; skill development and increasing physical activity should simultaneously be targeted in physical activity interventions. Increasing perceived sport competence should also be an intervention focus.<br /

Stability of mRNA/DNA and DNA/DNA Duplexes Affects mRNA Transcription

Nucleic acids, due to their structural and chemical properties, can form double-stranded secondary structures that assist the transfer of genetic information and can modulate gene expression. However, the nucleotide sequence alone is insufficient in explaining phenomena like intron-exon recognition during RNA processing. This raises the question whether nucleic acids are endowed with other attributes that can contribute to their biological functions. In this work, we present a calculation of thermodynamic stability of DNA/DNA and mRNA/DNA duplexes across the genomes of four species in the genus Saccharomyces by nearest-neighbor method. The results show that coding regions are more thermodynamically stable than introns, 3′-untranslated regions and intergenic sequences. Furthermore, open reading frames have more stable sense mRNA/DNA duplexes than the potential antisense duplexes, a property that can aid gene discovery. The lower stability of the DNA/DNA and mRNA/DNA duplexes of 3′-untranslated regions and the higher stability of genes correlates with increased mRNA level. These results suggest that the thermodynamic stability of DNA/DNA and mRNA/DNA duplexes affects mRNA transcription

Soil: the great connector of our lives now and beyond COVID-19

Humanity depends on the existence of healthy soils, both for the production of food and for ensuring a healthy, biodiverse environment, among other functions. COVID-19 is threatening food availability in many places of the world due to the disruption of food chains, lack of workforce, closed borders and national lockdowns. As a consequence, more emphasis is being placed on local food production, which may lead to more intensive cultivation of vulnerable areas and to soil degradation. In order to increase the resilience of populations facing this pandemic and future global crises, transitioning to a paradigm that relies more heavily on local food production on soils that are carefully tended and protected through sustainable management is necessary. To reach this goal, the Intergovernmental Technical Panel on Soils (ITPS) of the Food and Agriculture Organization of the United Nations (FAO) recommends five active strategies: improved access to land, sound land use planning, sustainable soil management, enhanced research, and investments in education and extension

Measurements of fiducial and differential cross sections for Higgs boson production in the diphoton decay channel at s√=8 TeV with ATLAS

Measurements of fiducial and differential cross sections are presented for Higgs boson production in proton-proton collisions at a centre-of-mass energy of s√=8 TeV. The analysis is performed in the H → γγ decay channel using 20.3 fb−1 of data recorded by the ATLAS experiment at the CERN Large Hadron Collider. The signal is extracted using a fit to the diphoton invariant mass spectrum assuming that the width of the resonance is much smaller than the experimental resolution. The signal yields are corrected for the effects of detector inefficiency and resolution. The pp → H → γγ fiducial cross section is measured to be 43.2 ±9.4(stat.) − 2.9 + 3.2 (syst.) ±1.2(lumi)fb for a Higgs boson of mass 125.4GeV decaying to two isolated photons that have transverse momentum greater than 35% and 25% of the diphoton invariant mass and each with absolute pseudorapidity less than 2.37. Four additional fiducial cross sections and two cross-section limits are presented in phase space regions that test the theoretical modelling of different Higgs boson production mechanisms, or are sensitive to physics beyond the Standard Model. Differential cross sections are also presented, as a function of variables related to the diphoton kinematics and the jet activity produced in the Higgs boson events. The observed spectra are statistically limited but broadly in line with the theoretical expectations