An Open, Large-Scale, Collaborative Effort to Estimate the Reproducibility of Psychological Science

Reproducibility is a defining feature of science. However, because of strong incentives for innovation and weak incentives for confirmation, direct replication is rarely practiced or published. The Reproducibility Project is an open, large-scale, collaborative effort to systematically examine the rate and predictors of reproducibility in psychological science. So far, 72 volunteer researchers from 41 institutions have organized to openly and transparently replicate studies published in three prominent psychological journals in 2008. Multiple methods will be used to evaluate the findings, calculate an empirical rate of replication, and investigate factors that predict reproducibility. Whatever the result, a better understanding of reproducibility will ultimately improve confidence in scientific methodology and findings

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Magnetic resonance of phase transitions

Magnetic Resonance of Phase Transitions shows how the effects of phase transitions are manifested in the magnetic resonance data. The book discusses the basic concepts of structural phase and magnetic resonance; various types of magnetic resonances and their underlying principles; and the radiofrequency methods of nuclear magnetic resonance. The text also describes quadrupole methods; the microwave technique of electron spin resonance; and the Mössbauer effect. Phase transitions in various systems such as fluids, liquid crystals, and crystals, including paramagnets and ferroelectrics, are als

RexMart: Empowering Analysts to Configure Research Data Marts to Improve End-User Data Exploration

<p>We set out to build a powerful configuration layer for semi-technical analysts and end users on top of relational database technology. This configuration layer empowers data analysts to define data feeds and transformations, data mart schemas, as well as query builder display properties. A data exploration tool that can readily be configured by both analysts and end-users is more likely to meet users’ needs at a lower cost than fully custom software while providing greater data quality and auditability than spreadsheets.</p

Pharmacological treatment of anxiety disorders: Current treatments and future directions

Modern pharmacological treatments for anxiety disorders are safer and more tolerable than they were 30 years ago. Unfortunately, treatment efficacy and duration have not improved in most cases despite a greater understanding of the pathophysiology of anxiety. Moreover, innovative treatments have not reached the market despite billions of research dollars invested in drug development. In reviewing the literature on current treatments, we argue that evidence-based practice would benefit from better research on the causes of incomplete treatment response as well as the comparative efficacy of drug combinations and sequencing. We also survey three approaches to the development of innovative anxiety treatments: the continued development of drugs based on specific neuroreceptors; the pharmacologigcal manipulation of fear-related memory; and the electrical or electromagnetic stimulation of specific brain areas. We highlight directions for future research, as none of these approaches is ready for clinical use. This record was migrated from the OpenDepot repository service in June, 2017 before shutting down

Metadata Improvement Project

The objective of this OSC project is to improve the definition, collection, curation, and use of open scientific metadata. Possible applications include, but are not limited to, semantically enhanced tools for data exploration and meta-analysis

A Novel Approach for Efficient Submission of Research Data to the National Database for Autism Research (NDAR)

<p>Researchers seeking to share their data with coordinating centers such as the National Database for Autism Research (NDAR), face numerous barriers to establishing new connections and maintaining existing ones. We sought to dramatically reduce the time and money required to establish and maintain the interoperability of data between research centers, by establishing a process where manual recoding of data is replaced by data sharing instructions in the form of extraction and transformation scripts. Over the course of seven typical (20-60 subjects, 400-1000 fields each) data submissions to NDAR, the need for duplication, retranscription, or restructuring of the source data was fully eliminated. Separating the extraction and transformation scripts from data files also eradicated the impact of additional data collection on the time required to repeat successful transmissions. Revision controlled management of these scripts also provided a new benefit: traceability of the transformation process itself. Now, point-in-time retrieval of extraction scripts and explanations for modifications to the data sharing interface are possible. This method has proven to be successful and efficient for interfacing research data with NDAR. It presents little-to-no impact to transmitting investigators’ data, ensures high data integrity, trivializes the complexities of repeatedly modifying a growing dataset over time, and introduces traceability to the collaborative process of integrating two collections of data with one another.</p

RexMart: An Open Source Tool for Exploring and Sharing Research Data without Compromising Data Integrity

<p>Behavioral and biomedical researchers value data integrity, data exploration, and data sharing, but traditional research databases have unacceptable trade-offs among these important data management functions. This case study examines the design, development, and evaluation of RexMart, an open-source application designed to optimize data integrity, exploration, and sharing with easily accessible querying tools including the powerful query language HTSQL.</p

An Open Source, Integrated Data Management System for Medical Registries: A Case Study using RexDB (Informatics to Support Clinical Trials)

<p>Disease- and procedure-specific registries are powerful tools for the improvement of long-term patient care. Unfortunately, registries are typically too expensive for smaller practices and organizations to develop and maintain. This case study examines an affordable and scalable alternative, RexDB®, an open-source solution that can integrate institutional (EHR) and primary research data.</p