The Normal College News, February 22, 1918

BACKGROUND: Knowledge graphs can represent the contents of biomedical literature and databases as subject-predicate-object triples, thereby enabling comprehensive analyses that identify e.g. relationships between diseases. Some diseases are often diagnosed in patients in specific temporal sequences, which are referred to as disease trajectories. Here, we determine whether a sequence of two diseases forms a trajectory by leveraging the predicate information from paths between (disease) proteins in a knowledge graph. Furthermore, we determine the added value of directional information of predicates for this task. To do so, we create four feature sets, based on two methods for representing indirect paths, and both with and without directional information of predicates (i.e., which protein is considered subject and which object). The added value of the directional information of predicates is quantified by comparing the classification performance of the feature sets that include or exclude it. RESULTS: Our method achieved a maximum area under the ROC curve of 89.8% and 74.5% when evaluated with two different reference sets. Use of directional information of predicates significantly improved performance by 6.5 and 2.0 percentage points respectively. CONCLUSIONS: Our work demonstrates that predicates between proteins can be used to identify disease trajectories. U

D-term inflation in non-minimal supergravity

D-term inflation is one of the most interesting and versatile models of inflation. It is possible to implement naturally D-term inflation within high energy physics, as for example SUSY GUTs, SUGRA, or string theories. D-term inflation avoids the $\eta$-problem, while in its standard form it always ends with the formation of cosmic strings. Given the recent three-year WMAP data on the cosmic microwave background temperature anisotropies, we examine whether D-term inflation can be successfully implemented in non-minimal supergravity theories. We show that for all our choices of K\"ahler potential, there exists a parameter space for which the predictions of D-term inflation are in agreement with the measurements. The cosmic string contribution on the measured temperature anisotropies is always dominant, unless the superpotential coupling constant is fine tuned; a result already obtained for D-term inflation within minimal supergravity. In conclusion, cosmic strings and their r\^ole in the angular power spectrum cannot be easily hidden by just considering a non-flat K\"ahler geometry.Comment: 29 pages, 9 figures; minor changes to match publihed versio

High Scale Physics Connection to LHC Data

The existing data appears to provide hints of an underlying high scale theory. These arise from the gauge coupling unification, from the smallness of the neutrino masses, and via a non-vanishing muon anomaly. An overview of high scale models is given with a view to possible tests at the Large Hadron Collider. Specifically we discuss here some generic approaches to deciphering their signatures. We also consider an out of the box possibility of a four generation model where the fourth generation is a mirror generation rather than a sequential generation. Such a scenario can lead to some remarkably distinct signatures at the LHC.Comment: 23 pages, no figures. Based on invited lectures at the 46th Course at the International School of Subnuclear Physics- Erice -Sicily: 29 August -7 September, 200

Discovering information from an integrated graph database

The information explosion in science has become a different problem, not the sheer amount per se, but the multiplicity and heterogeneity of massive sets of data sources. Relations mined from these heterogeneous sources, namely texts, database records, and ontologies have been mapped to Resource Description Framework (RDF) triples in an integrated database. The subject and object resources are expressed as references to concepts in a biomedical ontology consisting of the Unified Medical Language System (UMLS), UniProt and EntrezGene and for the predicate resource to a predicate thesaurus. All RDF triples have been stored in a graph database, including provenance. For evaluation we used an actual formal PRISMA literature study identifying 61 cerebral spinal fluid biomarkers and 200 blood biomarkers for migraine. These biomarkers sets could be retrieved with weighted mean average precision values of 0.32 and 0.59, respectively, and can be used as a first reference for further refinements

Anni 2.0: a multipurpose text-mining tool for the life sciences

Anni 2.0 provides an ontology-based interface to MEDLINE

Observing Brane Inflation

Linking the slow-roll scenario and the Dirac-Born-Infeld scenario of ultra-relativistic roll (where, thanks to the warp factor, the inflaton moves slowly even with an ultra-relativistic Lorentz factor), we find that the KKLMMT D3/anti-D3 brane inflation is robust, that is, enough e-folds of inflation is quite generic in the parameter space of the model. We show that the intermediate regime of relativistic roll can be quite interesting observationally. Introducing appropriate inflationary parameters, we explore the parameter space and give the constraints and predictions for the cosmological observables in this scenario. Among other properties, this scenario allows the saturation of the present observational bound of either the tensor/scalar ratio r (in the intermediate regime) or the non-Gaussianity f_NL (in the ultra-relativistic regime), but not both.Comment: 31 pages, 12 figures; typo correcte

Drug-induced atrial fibrillation

Atrial fibrillation (AF) is the most common sustained rhythm disorder observed in clinical practice and predominantly associated with cardiovascular disorders such as coronary heart disease and hypertension. However, several classes of drugs may induce AF in patients without apparent heart disease or may precipitate the onset of AF in patients with preexisting heart disease. We reviewed the literature on drug-induced AF, using the PubMed/Medline and Micromedex databases and lateral references. Successively, we discuss the potential role in the onset of AF of cardiovascular drugs, respiratory system drugs, cytostatics, central nervous system drugs, genitourinary system drugs, and some miscellaneous agents. Drug-induced AF may play a role in only a minority of the patients presenting with AF. Nevertheless, it is important to recognize drugs or other agents as a potential cause, especially in the elderly, because increasing age is associated with multiple drug use and a high incidence of AF. This may contribute to timely diagnosis and management of drug-induced AF

Rewriting and suppressing UMLS terms for improved biomedical term identification

<p>Abstract</p> <p>Background</p> <p>Identification of terms is essential for biomedical text mining.. We concentrate here on the use of vocabularies for term identification, specifically the Unified Medical Language System (UMLS). To make the UMLS more suitable for biomedical text mining we implemented and evaluated nine term rewrite and eight term suppression rules. The rules rely on UMLS properties that have been identified in previous work by others, together with an additional set of new properties discovered by our group during our work with the UMLS. Our work complements the earlier work in that we measure the impact on the number of terms identified by the different rules on a MEDLINE corpus. The number of uniquely identified terms and their frequency in MEDLINE were computed before and after applying the rules. The 50 most frequently found terms together with a sample of 100 randomly selected terms were evaluated for every rule.</p> <p>Results</p> <p>Five of the nine rewrite rules were found to generate additional synonyms and spelling variants that correctly corresponded to the meaning of the original terms and seven out of the eight suppression rules were found to suppress only undesired terms. Using the five rewrite rules that passed our evaluation, we were able to identify 1,117,772 new occurrences of 14,784 rewritten terms in MEDLINE. Without the rewriting, we recognized 651,268 terms belonging to 397,414 concepts; with rewriting, we recognized 666,053 terms belonging to 410,823 concepts, which is an increase of 2.8% in the number of terms and an increase of 3.4% in the number of concepts recognized. Using the seven suppression rules, a total of 257,118 undesired terms were suppressed in the UMLS, notably decreasing its size. 7,397 terms were suppressed in the corpus.</p> <p>Conclusions</p> <p>We recommend applying the five rewrite rules and seven suppression rules that passed our evaluation when the UMLS is to be used for biomedical term identification in MEDLINE. A software tool to apply these rules to the UMLS is freely available at <url>http://biosemantics.org/casper</url>.</p

Характеристика экономических отношений на финансовом рынке Украины

Розглянуто проблеми, особливості функціонування та взаємодії учасників фінансового ринку України. Обґрунтовано наявність внутрішніх фінансових джерел формування ресурсного потенціалу вітчизняних банків, доведено їх пріоритетність для країни порівняно із зовнішніми джерелами. Окреслено причини, що зумовлюють дефіцит ресурсного потенціалу в банківській системі України. Ключові слова: заощадження, нагромадження, банки, економічне зростання, посередники, фінансовий ринок, ресурси, трансформація, інвестиційний потенціал.Рассмотрены проблемы, особенности функционирования и взаимодействия участников финансового рынка Украины. Обосновано наличие внутренних финансовых источников формирования ресурсного потенциала отечественных банков, доказана их приоритетность для страны по сравнению с внешними источниками. Очерчены причины, которые предопределяют дефицит ресурсного потенциала в банковской системе Украины. Ключевые слова: сбережения, накопления, банки, экономический рост, посредники, финансовый рынок, ресурсы, трансформация, инвестиционный потенциал.The present paper examines topical problems related to the specific aspects of economic relations in the financial market of Ukraine. The relevance and selection of the theme stem from the fact that financial market as a specific organization form of cash flows takes a leading place in the economic mechanism of market economy. Agents of this market are engaged in a whole range of complex economic relations which in their turn play a key role in securing a dynamic and sustainable economic growth of a country. Development of the financial market and creation of adequate flexible and adaptive economic relations between its players are critical for Ukraine. This is explained by specific aspects of the economic system formation and reforming, which are related to undergoing an intersystem transformation stage. The indicated circumstances predetermined the goal and objectives of the study pursued, which come to examination of economic relations in the financial market of Ukraine, identification of the interaction specificity of various financial intermediaries in the accumulation process of idle cash and its transformation into the investment capital of national economy. Based on the results of the analysis conducted, it is established that unlike countries with developed financial systems, where the majority of institutional participants of the capital market are proportionally developed, it is the banking sector that dominates in Ukraine and has a determinant role in financing the economic development of the state. The availability of domestic financial resources for forming the resource potential of banks is substantiated, and their priority versus external resources for Ukraine is proved. The comparison of gross savings and gross capital formation allowed identifying certain problems as to transformation of the former into investment resources in Ukraine. The paper outlines some causes of a poor resource potential of national banking institutions. Keywords: savings, accumulation, banks, economic growth, intermediaries, financial market, resources, transformation, investment potential

Hunting long-lived gluinos at the Pierre Auger Observatory

Eventual signals of split sypersymmetry in cosmic ray physics are analyzed in detail. The study focusses particularly on quasi-stable colorless R-hadrons originating through confinement of long-lived gluinos (with quarks, anti-quarks, and gluons) produced in pp collisions at astrophysical sources. Because of parton density requirements, the gluino has a momentum which is considerable smaller than the energy of the primary proton, and so production of heavy (mass ~ 500 GeV) R-hadrons requires powerful cosmic ray engines able to accelerate particles up to extreme energies, somewhat above 10^{13.6} GeV. Using a realistic Monte Carlo simulation with the AIRES engine, we study the main characteristics of the air showers triggered when one of these exotic hadrons impinges on a stationary nucleon of the Earth atmosphere. We show that R-hadron air showers present clear differences with respect to those initiated by standard particles. We use this shower characteristics to construct observables which may be used to distinguish long-lived gluinos at the Pierre Auger Observatory.Comment: 13 pages revtex, 9 eps figures. A ps version with high resolution figures is available at http://www.hep.physics.neu.edu/staff/doqui/rhadron_highres.p