varunr14/newsummary huggingface dataset:
Genome wide association studies and other genetic analyses have identified a large number of genes and variants implicating a variety of disease etiological mechanisms . It is imperative for the study of human diseases to put these genetic findings into a coherent functional context . Here we use system biology tools to examine disease connections of five master genes for CD4 T cell subtypes . We compiled a list of genes functionally interacting with the master genes then we surveyed the disease connections either by experimental evidence or by genetic association . Embryonic lethal genes are over represented in master genes and their interacting genes . Transcription factors are significantly enriched among genes interacting with the master genes . Predicted haploinsufficiency is a feature of most these genes . Disease connected genes are enriched in this list of genes 42 of these genes have a disease connection according to Online Mendelian Inheritance in Man and 74 are associated with some diseases or phenotype in a Genome Wide Association Study . Seemingly not all of the diseases connected to genes surveyed were immune related which may indicate pleiotropic functions of the master regulator genes and associated genes . 


Summary: CD4 T cell subtype master genes and their connected genes are more likely to be associated with a disease or a phenotype. Genes connected to the CD4 T cell subtype master genes are more likely to be transcription factors. CD4 T cell subtype master genes and their connected genes are more likely to be haploinsufficient. CD4 T cell subtype master genes and their connected genes are more likely to be embryonic lethal gene essential genes .
Efficient identification of patient intervention comparison and outcome components in medical articles is helpful in evidence based medicine . The purpose of this study is to clarify whether first sentences of these components are good enough to train naive Bayes classifiers for sentence level PICO element detection . We extracted 19 854 structured abstracts of randomized controlled trials with any P I O label from PubMed for naive Bayes classifiers training . Performances of classifiers trained by first sentences of each section and those trained by all sentences were compared using all sentences by ten fold cross validation . The results measured by recall precision and F measures show that there are no significant differences in performance between CF and CA for detection of O element . However CA perform better for I elements in terms of recall and F measures . For P elements CF have higher precision but lower recall . CF are not always better than CA in sentence level PICO element detection . Their performance varies in detecting different elements . 


Summary: Two sets of naive Bayes classifiers were developed for PICO detection. We trained one set with first sentences and the other with all sentences. The first sentence classifier performs slightly better for patient P elements. The all sentence classifier performs better for intervention I elements. The performances are about the same for outcome O elements.
In a reconfigurable system the response to contextual or internal change may trigger reconfiguration events which on their turn activate scripts that change the system s architecture at runtime . To be safe however such reconfigurations are expected to obey the fundamental principles originally specified by its architect . This paper introduces an approach to ensure that such principles are observed along reconfigurations by verifying them against concrete specifications in a suitable logic . Architectures reconfiguration scripts and principles are specified in Archery an architectural description language with formal semantics . Principles are encoded as constraints which become formulas of a two layer graded hybrid logic where the upper layer restricts reconfigurations and the lower layer constrains the resulting configurations . Constraints are verified by translating them into logic formulas which are interpreted over models derived from Archery specifications of architectures and reconfigurations . Suitable notions of bisimulation and refinement to which the architect may resort to compare configurations are given and their relationship with modal validity is discussed . 


Summary: Describes approach to ensure fundamental principles of a system in reconfigurations. Specifies principles as constraints in an architectural description language. Translates constraints into a two layer graded hybrid logic. Derives interpretation models from specifications of architectures and reconfigurations. Provides equivalence and refinement notions to compare reconfigurations.
Given a set of symmetric antisymmetric filter vectors containing only regular multiresolution filters the method we present in this article can establish a balanced multiresolution scheme for images allowing their balanced decomposition and subsequent perfect reconstruction without the use of any extraordinary boundary filters . We define balanced multiresolution such that it allows balanced decomposition i.e . decomposition of a high resolution image into a low resolution image and corresponding details of equal size . Such a balanced decomposition makes on demand reconstruction of regions of interest efficient in both computational load and implementation aspects . We find this balanced decomposition and perfect reconstruction based on an appropriate combination of symmetric antisymmetric extensions near the image and detail boundaries . In our method exploiting such extensions correlates to performing sample split operations . Our general approach is demonstrated for some commonly used symmetric antisymmetric multiresolution filters . We also show the application of such a balanced multiresolution scheme in real time focus context visualization . 


Summary: Devised balanced multiresolution BMR schemes allow balanced decomposition. Constructed balanced wavelet transform BWT allows perfect reconstruction. BWT provides efficient access to previously extracted details on demand. We eliminate the need for using extraordinary boundary filters. BMR schemes use symmetric antisymmetric extensions at image and detail boundaries.
Purpose Despite years of effort and millions of dollars spent to create unified electronic communicable disease reporting systems the goal remains elusive . A major barrier has been a lack of understanding by system designers of communicable disease work and the public health workers who perform this work . This study reports on the application of user centered design representations traditionally used for improving interface design to translate the complex CD work identified through ethnographic studies to guide designers and developers of CD systems . The purpose of this work is to better understand public health practitioners and their information workflow with respect to CD monitoring and control at a local health agency and to develop evidence based design representations that model this CD work to inform the design of future disease surveillance systems . Methods We performed extensive onsite semi structured interviews targeted work shadowing and a focus group to characterize local health agency CD workflow . Informed by principles of design ethnography and user centered design we created persona scenarios and user stories to accurately represent the user to system designers . Results We sought to convey to designers the key findings from ethnographic studies public health CD work is mobile and episodic in contrast to current CD reporting systems which are stationary and fixed health agency efforts are focused on CD investigation and response rather than reporting and current CD information systems must conform to public health workflow to ensure their usefulness . In an effort to illustrate our findings to designers we developed three contemporary design support representations persona scenario and user story . Conclusions Through application of user centered design principles we were able to create design representations that illustrate complex public health communicable disease workflow and key user characteristics to inform the design of CD information systems for public health . 


Summary: We modeled communicable disease CD workflow at health department using user centered design. Public health CD work is mobile and episodic yet CD reporting systems are stationary and fixed. Health department efforts are focused on CD investigation and response rather than reporting. Current CD information systems do not conform to PH workflow thus affecting their usefulness. Personas scenarios and user stories provide evidence based representations for designers.
Polymorphic programming languages have been adapted for constructing distributed access control systems where a program represents a proof of eligibility according to a given policy . As a security requirement it is typically stated that the programs of such languages should satisfy noninterference . However this property has not been defined and proven semantically . In this paper we first propose a semantics based on Henkin models for a predicative polymorphic access control language based on lambda calculus . A formal semantic definition of noninterference is then proposed through logical relations . We prove a type soundness theorem which states that any well typed program of our language meets the noninterference property defined in this paper . In this way it is guaranteed that access requests from an entity do not interfere with those from unrelated or more trusted entities . 


Summary: A denotational semantics based on Henkin models is given for a predicative polymorphic calculus of access control. Noninterference as a basic semantic notion of security is semantically defined. It is proven that the language is type sound in the sense that every welltyped program of the language satisfies noninterference.
We propose a language independent symbolic execution framework for languages endowed with a formal operational semantics based on term rewriting . Starting from a given definition of a language a new language definition is generated with the same syntax as the original one but whose semantical rules are transformed in order to rewrite over logical formulas denoting possibly infinite sets of program states . Then the symbolic execution of concrete programs is by definition the execution of the same programs with the symbolic semantics . We prove that the symbolic execution thus defined has the properties naturally expected from it . A prototype implementation of our approach was developed in the framework . We demonstrate the tool s genericity by instantiating it on several languages and illustrate it on the reachability analysis and model checking of several programs . 


Summary: We propose a language independent symbolic execution framework for languages. The proposed language independent approach is based on language transformations. We prove that the expected formal properties of symbolic execution. We present a prototype and we use it on several languages.
In this paper we present an efficient approach for parameterizing a genus zero triangular mesh onto the sphere with an optimal radius in an as rigid as possible manner which is an extension of planar ARAP parametrization approach to spherical domain . We analyze the smooth and discrete ARAP energy and formulate our spherical parametrization energy from the discrete ARAP energy . The solution is non trivial as the energy involves a large system of non linear equations with additional spherical constraints . To this end we propose a two step iterative algorithm . In the first step we adopt a local global iterative scheme to calculate the parametrization coordinates . In the second step we optimize a best approximate sphere on which parametrization triangles can be embedded in a rigidity preserving manner . Our algorithm is simple robust and efficient . Experimental results show that our approach provides almost isometric spherical parametrizations with lowest rigidity distortion over state of the art approaches . 


Summary: We develop model of spherical parameterization in a rigidity preserving manner. We analyze ARAP energy from smooth description to its corresponding discrete case. We propose a iterative algorithm to efficiently solve the non linear model.
Intrinsic shape matching has become the standard approach for pose invariant correspondence estimation among deformable shapes . Most existing approaches assume global consistency . While global isometric matching is well understood only a few heuristic solutions are known for partial matching . Partial matching is particularly important for robustness to topological noise which is a common problem in real world scanner data . We introduce a new approach to partial isometric matching based on the observation that isometries are fully determined by local information a map of a single point and its tangent space fixes an isometry . We develop a new representation for partial isometric maps based on equivalence classes of correspondences between pairs of points and their tangent spaces . We apply our approach to register partial point clouds and compare it to the state of the art methods where we obtain significant improvements over global methods for real world data and stronger guarantees than previous partial matching algorithms . 


Summary: We characterize partial isometries of shapes by single point maps up to first order. A novel matching algorithm for partial intrinsic matching. We use redundancy in our representation for approximate partial iso metric matching. Robustness to strong topological noise geometric noise and missing data.
In this paper we discuss the design and development of TRAK an ontology that formally models information relevant for the rehabilitation of knee conditions . TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic studies so that the most effective treatment components can be identified new interventions developed and the quality of future randomized control trials improved to incorporate a control intervention that is well defined and reflects clinical practice . TRAK follows design principles recommended by the Open Biomedical Ontologies Foundry . TRAK uses the Basic Formal Ontology as the upper level ontology and refers to other relevant ontologies such as Information Artifact Ontology Ontology for General Medical Science and Phenotype And Trait Ontology . TRAK is orthogonal to other bio ontologies and represents domain specific knowledge about treatments and modalities used in rehabilitation of knee conditions . Definitions of typical exercises used as treatment modalities are supported with appropriate illustrations which can be viewed in the OBO Edit ontology editor . The vast majority of other classes in TRAK are cross referenced to the Unified Medical Language System to facilitate future integration with other terminological sources . TRAK is implemented in OBO a format widely used by the OBO community . TRAK is available for download from http www.cs.cf.ac.uk trak . In addition its public release can be accessed through BioPortal where it can be browsed searched and visualized . 


Summary: TRAK ontology models domain specific knowledge about the rehabilitation of knee conditions. TRAK provides terminology definitions and graphical illustrations of knee treatments. TRAK supports shared understanding of standard care in knee rehabilitation. TRAK provides the framework that can be used to collect data for epidemiologic studies of knee conditions. TRAK can support randomized control with a control intervention that is well defined and reflects clinical practice.
In this paper we compose six different Python and Prolog VMs into 4 pairwise compositions one using C interpreters one running on the JVM one using meta tracing interpreters and one using a C interpreter and a meta tracing interpreter . We show that programs that cross the language barrier frequently execute faster in a meta tracing composition and that meta tracing imposes a significantly lower overhead on composed programs relative to mono language programs . 


Summary: We present a viable Python Prolog composition and show four different implementations each using a different composition style. We present the first experiment designed to help understand the effects of different composition styles upon performance. We thoroughly analyse and discuss the results of the experiment breaking down the impact that each composition style has on performance.
The actor model is a message passing concurrency model that avoids deadlocks and low level data races by construction . This facilitates concurrent programming especially in the context of complex interactive applications where modularity security and fault tolerance are required . The tradeoff is that the actor model sacrifices expressiveness and safety guarantees with respect to parallel access to shared state . In this paper we present domains as a set of novel language abstractions for safely encapsulating and sharing state within the actor model . We introduce four types of domains namely immutable isolated observable and shared domains that each is tailored to a certain access pattern on that shared state . The domains are characterized with an operational semantics . For each we discuss how the actor model s safety guarantees are upheld even in the presence of conceptually shared state . Furthermore the proposed language abstractions are evaluated with a case study in Scala comparing them to other synchronization mechanisms to demonstrate their benefits in deadlock freedom parallel reads and enforced isolation . 


Summary: The domain model is an extension to the communicating event loop actor model. The domain model retains the safety and liveness properties of the actor model. We provide an operational semantics and validation of the domain model.
The Trapezoid Step Functions domain is introduced in order to approximate continuous functions by a finite sequence of trapezoids adopting linear functions to abstract the upper and the lower bounds of a continuous variable in each time slot . The lattice structure of TSF is studied showing how to build and compute a sound abstraction of a given continuous function . Experimental results underline the effectiveness of the approach in terms of both precision and efficiency with respect to the domain of Interval Valued Step Functions . 


Summary: The domain of Trapezoid Step Functions is introduced for the static analysis on continuous functions values. The domain is a proper refinement of the Interval Valued Step Function Domain. A constructive abstraction procedure is provided that deals with floating point precision issues.
Objective To report on the results of a review concerning the use of mobile phones for health with older adults . Methods PubMed and CINAHL were searched for articles using older adults and mobile phones along with related terms and synonyms between 1965 and June 2012 . Identified articles were filtered by the following inclusion criteria original research project utilizing a mobile phone as an intervention involve target adults 60years of age or older and have an aim emphasizing the mobile phone s use in health . Results Twenty one different articles were found and categorized into ten different clinical domains including diabetes activities of daily life and dementia care among others . The largest group of articles focused on diabetes care followed by COPD Alzheimer s dementia Care and osteoarthritis . Areas of interest studied included feasibility acceptability and effectiveness . While there were many different clinical domains the majority of studies were pilot studies that needed more work to establish a stronger base of evidence . Conclusions Current work in using mobile phones for older adult use are spread across a variety of clinical domains . While this work is promising current studies are generally smaller feasibility studies and thus future work is needed to establish more generalizable stronger base of evidence for effectiveness of these interventions . 


Summary: We review the use of mobile phones for health applied to older adults. The field emerging field contains many feasibility studies with smaller samples. A variety of clinical domains are appropriate for mobile phone interventions. Future work should address generalizability and establish a stronger evidence base.
Although biomedical information available in articles and patents is increasing exponentially we continue to rely on the same information retrieval methods and use very few keywords to search millions of documents . We are developing a fundamentally different approach for finding much more precise and complete information with a single query using predicates instead of keywords for both query and document representation . Predicates are triples that are more complex datastructures than keywords and contain more structured information . To make optimal use of them we developed a new predicate based vector space model and query document similarity function with adjusted tf idf and boost function . Using a test bed of 107 367 PubMed abstracts we evaluated the first essential function retrieving information . Cancer researchers provided 20 realistic queries for which the top 15 abstracts were retrieved using a predicate based and keyword based approach . Each abstract was evaluated double blind by cancer researchers on a 0 5 point scale to calculate precision and relevance . Precision was significantly higher for the predicate based than for the keyword based approach . Relevance was almost doubled with the predicate based approach 2.1 versus 1.6 without rank order adjustment and 1.34 versus 0.98 with rank order adjustment for predicate versus keyword based approach respectively . Predicates can support more precise searching than keywords laying the foundation for rich and sophisticated information search . 


Summary: Predicates called triples contain more structured information than keywords. We propose a new predicate based search engine approach for biomedical texts. We develop a new vector space model and query document similarity function. It achieves higher precision and relevance score than traditional keyword approach. Predicates can support more precise information search than keywords.