SciCombinator

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Concept: Type system

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SUMMARY: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast, customisable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search, and a library of “widgets” performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. AVAILABILITY: Freely available from http://www.intermine.org under the LGPL license. CONTACT: g.micklem@gen.cam.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Concepts: Bioinformatics, Statistics, Model organism, Data, Programming language, Data management, Type system, Biological data

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BACKGROUND: Although programming in a type-safe and referentiallytransparent style offers several advantages over working withmutable data structures and side effects, this style of programminghas not seen much use in chemistry-related software. Since functionalprogramming languages were designed with referential transparency in mind,these languages offer a lot of support when writing immutable data structuresand side-effects free code. We therefore started implementingour own toolkit based on the above programming paradigms in a modern,versatile programming language. RESULTS: We present our initial results with functionalprogramming in chemistry by first describing an immutable data structurefor molecular graphs together with a couple of simplealgorithms to calculate basic molecular propertiesbefore writing a complete SMILES parser in accordance with theOpenSMILES specification. Along the way we show how to dealwith input validation, error handling, bulk operations, and parallelizationin a purely functional way. At the end we also analyze and improve our algorithmsand data structures in terms of performance and compare itto existing toolkits both object-oriented and purely functional.All code was written inScala, a modern multi-paradigm programming language with a strongsupport for functional programming and a highly sophisticated type system. CONCLUSIONS: We have successfully made the first importantsteps towards a purely functional chemistry toolkit. The data structuresand algorithms presented in this article perform well while at the sametime they can be safely used in parallelized applications, such as computeraided drug design experiments, withoutfurther adjustments. This stands in contrast to existing object-orientedtoolkits where thread safety of data structures and algorithms isa deliberate design decision that can be hard to implement.Finally, the level of type-safety achieved by \emph{Scala}highly increased the reliability of our codeas well as the productivity of the programmers involved in this project.

Concepts: Programming language, Functional programming, Type system, C Sharp, Programming paradigm, Referential transparency, Purely functional, Haskell

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ABSTRACT Two studies examined the effect of applicants' smiling on hireability. In a pre-test study, participants were asked to rate the expected behavior for four types of applicants. Newspaper reporter applicants were expected to be more serious than applicants for other jobs. In Study 1, participants were randomly assigned to be an applicant or interviewer for a newspaper reporting job. Smiling was negatively related to hiring, and smiling mediated the relation between applicants' motivation to make a good impression and hiring. Hiring was maximized when applicants smiled less in the middle of the interview relative to the start and end. In Study 2, participants watched Study 1 clips and were randomly assigned to believe the applicants were applying to one of four jobs. Participants rated more suitability when applicants smiled less, especially for jobs associated with a serious demeanor. This research shows that job type is an important moderator of the impact of smiling on hiring.

Concepts: Interview, TheStart, Type, Smile, Type system, Reporter, Reporting

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OBJECT This study directly compares the number and severity of subconcussive head impacts sustained during helmet-only practices, shell practices, full-pad practices, and competitive games in a National Collegiate Athletic Association (NCAA) Division I-A football team. The goal of the study was to determine whether subconcussive head impact in collegiate athletes varies with practice type, which is currently unregulated by the NCAA. METHODS Over an entire season, a cohort of 20 collegiate football players wore impact-sensing mastoid patches that measured the linear and rotational acceleration of all head impacts during a total of 890 athletic exposures. Data were analyzed to compare the number of head impacts, head impact burden, and average impact severity during helmet-only, shell, and full-pad practices, and games. RESULTS Helmet-only, shell, and full-pad practices and games all significantly differed from each other (p ≤ 0.05) in the mean number of impacts for each event, with the number of impacts being greatest for games, then full-pad practices, then shell practices, and then helmet-only practices. The cumulative distributions for both linear and rotational acceleration differed between all event types (p < 0.01), with the acceleration distribution being similarly greatest for games, then full-pad practices, then shell practices, and then helmet-only practices. For both linear and rotational acceleration, helmet-only practices had a lower average impact severity when compared with other event types (p < 0.001). However, the average impact severity did not differ between any comparisons of shell and full-pad practices, and games. CONCLUSIONS Helmet-only, shell, and full-pad practices, and games result in distinct head impact profiles per event, with each succeeding event type receiving more impacts than the one before. Both the number of head impacts and cumulative impact burden during practice are categorically less than in games. In practice events, the number and cumulative burden of head impacts per event increases with the amount of equipment worn. The average severity of individual impacts is relatively consistent across event types, with the exception of helmet-only practices. The number of hits experienced during each event type is the main driver of event type differences in impact burden per athletic exposure, rather than the average severity of impacts that occur during the event. These findings suggest that regulation of practice equipment could be a fair and effective way to substantially reduce subconcussive head impact in thousands of collegiate football players.

Concepts: Mode, Arithmetic mean, Mean, Geometric mean, College football, American football, Type system, Interquartile mean

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1) Provide a critical analysis of the contemporary published research pertaining to complementary, alternative, and other non-Complete Decongestive Therapies (CDT) for treatment of lymphedema (LE); and 2) Provide practical applications of that evidence to improve care of patients with or at risk for LE. TYPE: This study meets the defining criteria as a systematic search and review since it includes varied study types. All studies that met the inclusion criteria were evaluated for weight of evidence and value.

Concepts: Medicine, Critical thinking, Therapy, Study skills, Cultural studies, Lymphedema, Type, Type system

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Purpose: Recently, vascular endostapling systems were developed to achieve better sealing at the proximal neck of the aneurysm and to prevent endograft migration. The purpose of this study was to provide a systematic review about the current state and possible options of vascular endostapling systems. Results: No randomized controlled trials were published. The results showed that the use of an endostaple system considerably reduced the rates of endoleaks type 1a and endograft migration. Regarding the use of endostaples in different types of endografts, only a few results were available. Conclusion: The results are not conclusive. With endostaple systems, patients with difficult anatomic features and high risk can potentially be treated. These systems might reduce the high reintervention rates after endovascular aneurysm repair. Controlled randomized trials with larger number of patients are warranted with endostapling use in primary endograft implantation and for use in reintervention for late endoleaks or endograft migrations.

Concepts: Evidence-based medicine, Systematic review, Randomized controlled trial, Human migration, Abdominal aortic aneurysm, Type, Type system

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Here we report occurrence of six different morphotypes of ascaridoid type larvae from 28 species of fish collected from New Caledonian waters. The larvae were morphologically identified as Anisakis type I, Hysterothylacium type VI and new larval types XIII and XIV, Raphidascaris larval type and Terranova larval type II. Representatives of each morphotype were subjected to the amplification of the second internal transcribed spacers (ITS-2) of ribosomal DNA (rDNA) and those sequences were compared with ITS-2 sequences of other ascaridoid nematodes previously deposited in GenBank. ITS-2 sequences of Anisakis larval type I were identical to those of A. typica. ITS-2 sequences of Hysterothylacium larval type VI in the present study were identical to those previously found in Eastern Australian waters. No match was found for ITS-2 sequences of Hysterothylacium larval types XIII and XIV; therefore, the specific identities of these larval types remain unclear. ITS-2 sequences of Raphidascaris larval type were identical to those of R. trichiuri, which have previously been reported in Taiwanese waters. Terranova larval type II in the present study had identical ITS-2 sequences with Terranova larval types reported from Australian waters, however, the specific identity is unknown. This taxonomic work is essential if further research on these zoonotic parasites is to be effective. This includes investigations into such aspects as life cycle studies, impacts on human health and risk assessment for their transmission to humans.

Concepts: Present, Parasites, Larva, Fish, Annelid, Type, Type system, Caledonia

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In the last decade, new types of “bystander effect” have been suggested by multiple research groups and have been challenged by others. In this study, we explored a new type of bystander effect, which has been defined in previous studies as the enhancement of the survival of high-dose targeted cells due to the penumbra-dose exposed neighbor cells. Intensity modulated radiation therapy, which is the most widely used treatment modality, generates local regions of gradient doses between targeted and shielded cells throughout the treatment volume; therefore, we were urged to ascertain whether the new type of effect is real and to suggest a revised treatment planning.

Concepts: Radiation therapy, Cultural studies, Suggestion, Radiation oncology, Social psychology, Type, Type system, Bystander effect

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Technological advances enable the cost-effective acquisition of Multi-Modal Data Sets (MMDS) composed of measurements for multiple, high-dimensional data types obtained from a common set of bio-samples. The joint analysis of the data matrices associated with the different data types of a MMDS should provide a more focused view of the biology underlying complex diseases such as cancer that would not be apparent from the analysis of a single data type alone. As multi-modal data rapidly accumulate in research laboratories and public databases such as The Cancer Genome Atlas (TCGA), the translation of such data into clinically actionable knowledge has been slowed by the lack of computational tools capable of analyzing MMDSs. Here, we describe the Joint Analysis of Many Matrices by ITeration (JAMMIT) algorithm that jointly analyzes the data matrices of a MMDS using sparse matrix approximations of rank-1.

Concepts: Cancer, Sparse matrix, Computational complexity theory, Type theory, Type system, The Cancer Genome Atlas, Data types, Data type

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Today’s science increasingly requires effective ways to find and access existing datasets that are distributed across a range of repositories. For researchers in the life sciences, discoverability of datasets may soon become as essential as identifying the latest publications via PubMed. Through an international collaborative effort funded by the National Institutes of Health (NIH)’s Big Data to Knowledge (BD2K) initiative, we have designed and implemented the DAta Tag Suite (DATS) model to support the DataMed data discovery index. DataMed’s goal is to be for data what PubMed has been for the scientific literature. Akin to the Journal Article Tag Suite (JATS) used in PubMed, the DATS model enables submission of metadata on datasets to DataMed. DATS has a core set of elements, which are generic and applicable to any type of dataset, and an extended set that can accommodate more specialized data types. DATS is a platform-independent model also available as an annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex.

Concepts: Mathematics, Academic publishing, Science, Data set, Java, National Institutes of Health, Type system, Yahoo!