Semi-supervised prediction of protein interaction sentences exploiting semantically encoded metrics

Protein-protein interaction (PPI) identification is an integral component of many biomedical research and database curation tools. Automation of this task through classification is one of the key goals of text mining (TM). However, labelled PPI corpora required to train classifiers are generally small. In order to overcome this sparsity in the training data, we propose a novel method of integrating corpora that do not contain relevance judgements. Our approach uses a semantic language model to gather word similarity from a large unlabelled corpus. This additional information is integrated into the sentence classification process using kernel transformations and has a re-weighting effect on the training features that leads to an 8% improvement in F-score over the baseline results. Furthermore, we discover that some words which are generally considered indicative of interactions are actually neutralised by this process

Comparison of nutrient management recommendations and soil health indicators in southern Idaho

Advanced soil tests are being developed to help improve the estimation of plant available nutrients in order to better match fertilizer additions with plant needs as well as provide a measure of soil health, in some instances. The Soil Health Tool (SHT) has been developed with both goals in mind, yet it has not been tested for use in semi-arid regions such as southern Idaho. In the present study, we compared the use of the SHT for making fertilizer recommendations vs. using the standard regional method as well as evaluated the SHT soil health score (SHS) relative to crop yields and quality. The SHT was designed to analyze samples for 0-15 cm depth and regional guidelines call for deeper soil sampling (0-30 cm or 0-60 cm). In order to determine N fertilizer applications, use of the tool without accounting for depth, would recommend greater N application (~138 kg/ha) than the current regional methodology. However, it does appear that by accounting for depth in the SHT can provide similar available N estimates for the top 30 cm of soil. While N mineralization was not well predicted utilizing the method included in the SHT or from the regional methodology, the average estimated available N for these soils (47 kg/ha) was similar to the N mineralization value used in the current regional methodology (50 kg/ha). The P fertilizer recommendations were more similar between the two methodologies with the SHT recommending, on average 4.7 kg/ha less P than the regional method. The lower P recommendation are likely due to a lack of accounting for the effects of high calcium carbonate levels on the P availability from fertilizers in this region. The SHS was highly correlated with measures of soil C but was not positively correlated to crop yield. In some instances, increasing SHS resulted in decreases in crop quality as the addition of manure increased soil C but also created other potential problems such as high salt contents and release of late season N. With modification to more accurately represent irrigation conditions and including sampling to greater soil depths, this test may be tailored to better estimate soil nutrient status and provide better fertilizer recommendations for the region

Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

Thorough analysis of input physics in CESAM and CLES codes

This contribution is not about the quality of the agreement between stellar models computed by CESAM and CLES codes, but more interesting, on what ESTA-Task~1 run has taught us about these codes and about the input physics they use. We also quantify the effects of different implementations of the same physics on the seismic properties of the stellar models, that in fact is the main aim of ESTA experiments.Comment: 11 pages, 12 fig. Accepted for publication in ApSS CoRoT/ESTA Volu

ASTEC -- the Aarhus STellar Evolution Code

The Aarhus code is the result of a long development, starting in 1974, and still ongoing. A novel feature is the integration of the computation of adiabatic oscillations for specified models as part of the code. It offers substantial flexibility in terms of microphysics and has been carefully tested for the computation of solar models. However, considerable development is still required in the treatment of nuclear reactions, diffusion and convective mixing.Comment: Astrophys. Space Sci, in the pres

Macdonald Polynomials from Sklyanin Algebras: A Conceptual Basis for the pp-Adics-Quantum Group Connection

We establish a previously conjectured connection between $p$-adics and quantum groups. We find in Sklyanin's two parameter elliptic quantum algebra and its generalizations, the conceptual basis for the Macdonald polynomials, which ``interpolate'' between the zonal spherical functions of related real and $p$\--adic symmetric spaces. The elliptic quantum algebras underlie the $Z_n$\--Baxter models. We show that in the n \air \infty limit, the Jost function for the scattering of {\em first} level excitations in the $Z_n$\--Baxter model coincides with the Harish\--Chandra\--like $c$\--function constructed from the Macdonald polynomials associated to the root system $A_1$. The partition function of the $Z_2$\--Baxter model itself is also expressed in terms of this Macdonald\--Harish\--Chandra\ $c$\--function, albeit in a less simple way. We relate the two parameters $q$ and $t$ of the Macdonald polynomials to the anisotropy and modular parameters of the Baxter model. In particular the $p$\--adic ``regimes'' in the Macdonald polynomials correspond to a discrete sequence of XXZ models. We also discuss the possibility of ``$q$\--deforming'' Euler products.Comment: 25 page

Recent Advances in Modeling Stellar Interiors

Advances in stellar interior modeling are being driven by new data from large-scale surveys and high-precision photometric and spectroscopic observations. Here we focus on single stars in normal evolutionary phases; we will not discuss the many advances in modeling star formation, interacting binaries, supernovae, or neutron stars. We review briefly: 1) updates to input physics of stellar models; 2) progress in two and three-dimensional evolution and hydrodynamic models; 3) insights from oscillation data used to infer stellar interior structure and validate model predictions (asteroseismology). We close by highlighting a few outstanding problems, e.g., the driving mechanisms for hybrid gamma Dor/delta Sct star pulsations, the cause of giant eruptions seen in luminous blue variables such as eta Car and P Cyg, and the solar abundance problem.Comment: Proceedings for invited talk at conference High Energy Density Laboratory Astrophysics 2010, Caltech, March 2010, submitted for special issue of Astrophysics and Space Science; 7 pages; 5 figure

Comprehensive analysis of epigenetic clocks reveals associations between disproportionate biological ageing and hippocampal volume

The concept of age acceleration, the difference between biological age and chronological age, is of growing interest, particularly with respect to age-related disorders, such as Alzheimer’s Disease (AD). Whilst studies have reported associations with AD risk and related phenotypes, there remains a lack of consensus on these associations. Here we aimed to comprehensively investigate the relationship between five recognised measures of age acceleration, based on DNA methylation patterns (DNAm age), and cross-sectional and longitudinal cognition and AD-related neuroimaging phenotypes (volumetric MRI and Amyloid-β PET) in the Australian Imaging, Biomarkers and Lifestyle (AIBL) and the Alzheimer’s Disease Neuroimaging Initiative (ADNI). Significant associations were observed between age acceleration using the Hannum epigenetic clock and cross-sectional hippocampal volume in AIBL and replicated in ADNI. In AIBL, several other findings were observed cross-sectionally, including a significant association between hippocampal volume and the Hannum and Phenoage epigenetic clocks. Further, significant associations were also observed between hippocampal volume and the Zhang and Phenoage epigenetic clocks within Amyloid-β positive individuals. However, these were not validated within the ADNI cohort. No associations between age acceleration and other Alzheimer’s disease-related phenotypes, including measures of cognition or brain Amyloid-β burden, were observed, and there was no association with longitudinal change in any phenotype. This study presents a link between age acceleration, as determined using DNA methylation, and hippocampal volume that was statistically significant across two highly characterised cohorts. The results presented in this study contribute to a growing literature that supports the role of epigenetic modifications in ageing and AD-related phenotypes

Risk profiles and one-year outcomes of patients with newly diagnosed atrial fibrillation in India: Insights from the GARFIELD-AF Registry.

BACKGROUND: The Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF) is an ongoing prospective noninterventional registry, which is providing important information on the baseline characteristics, treatment patterns, and 1-year outcomes in patients with newly diagnosed non-valvular atrial fibrillation (NVAF). This report describes data from Indian patients recruited in this registry. METHODS AND RESULTS: A total of 52,014 patients with newly diagnosed AF were enrolled globally; of these, 1388 patients were recruited from 26 sites within India (2012-2016). In India, the mean age was 65.8 years at diagnosis of NVAF. Hypertension was the most prevalent risk factor for AF, present in 68.5% of patients from India and in 76.3% of patients globally (P < 0.001). Diabetes and coronary artery disease (CAD) were prevalent in 36.2% and 28.1% of patients as compared with global prevalence of 22.2% and 21.6%, respectively (P < 0.001 for both). Antiplatelet therapy was the most common antithrombotic treatment in India. With increasing stroke risk, however, patients were more likely to receive oral anticoagulant therapy [mainly vitamin K antagonist (VKA)], but average international normalized ratio (INR) was lower among Indian patients [median INR value 1.6 (interquartile range {IQR}: 1.3-2.3) versus 2.3 (IQR 1.8-2.8) (P < 0.001)]. Compared with other countries, patients from India had markedly higher rates of all-cause mortality [7.68 per 100 person-years (95% confidence interval 6.32-9.35) vs 4.34 (4.16-4.53), P < 0.0001], while rates of stroke/systemic embolism and major bleeding were lower after 1 year of follow-up. CONCLUSION: Compared to previously published registries from India, the GARFIELD-AF registry describes clinical profiles and outcomes in Indian patients with AF of a different etiology. The registry data show that compared to the rest of the world, Indian AF patients are younger in age and have more diabetes and CAD. Patients with a higher stroke risk are more likely to receive anticoagulation therapy with VKA but are underdosed compared with the global average in the GARFIELD-AF. CLINICAL TRIAL REGISTRATION-URL: http://www.clinicaltrials.gov. Unique identifier: NCT01090362