Teaching computational reproducibility for neuroimaging

We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on which the techniques are based. The lectures are often paired with practical workshops in which students run imaging analyses using the graphical interface of specific neuroimaging software packages. Our experience suggests that this combination leaves the student with a superficial understanding of the underlying ideas, and an informal, inefficient, and inaccurate approach to analysis. To address these problems, we based our course around a substantial open-ended group project. This allowed us to teach: (a) computational tools to ensure computationally reproducible work, such as the Unix command line, structured code, version control, automated testing, and code review and (b) a clear understanding of the statistical techniques used for a basic analysis of a single run in an MRI scanner. The emphasis we put on the group project showed the importance of standard computational tools for accuracy, efficiency, and collaboration. The projects were broadly successful in engaging students in working reproducibly on real scientific questions. We propose that a course on this model should be the foundation for future programs in neuroimaging. We believe it will also serve as a model for teaching efficient and reproducible research in other fields of computational science

Learning from open source software projects to improve scientific review

Peer-reviewed publications are the primary mechanism for sharing scientific results. The current peer-review process is, however, fraught with many problems that undermine the pace, validity, and credibility of science. We highlight five salient problems: (1) reviewers are expected to have comprehensive expertise; (2) reviewers do not have sufficient access to methods and materials to evaluate a study; (3) reviewers are neither identified nor acknowledged; (4) there is no measure of the quality of a review; and (5) reviews take a lot of time, and once submitted cannot evolve. We propose that these problems can be resolved by making the following changes to the review process. Distributing reviews to many reviewers would allow each reviewer to focus on portions of the article that reflect the reviewer's specialty or area of interest and place less of a burden on any one reviewer. Providing reviewers materials and methods to perform comprehensive evaluation would facilitate transparency, greater scrutiny, and replication of results. Acknowledging reviewers makes it possible to quantitatively assess reviewer contributions, which could be used to establish the impact of the reviewer in the scientific community. Quantifying review quality could help establish the importance of individual reviews and reviewers as well as the submitted article. Finally, we recommend expediting post-publication reviews and allowing for the dialog to continue and flourish in a dynamic and interactive manner. We argue that these solutions can be implemented by adapting existing features from open-source software management and social networking technologies. We propose a model of an open, interactive review system that quantifies the significance of articles, the quality of reviews, and the reputation of reviewers

Angular dependence of the radiation power of a Josephson STAR-emitter

We calculate the angular dependence of the power of stimulated terahertz amplified radiation (STAR) emitted from a $dc$ voltage applied across a stack of intrinsic Josephson junctions. During coherent emission, we assume a spatially uniform $ac$ Josephson current density in the stack acts as a surface electric current density antenna source, and the cavity features of the stack are contained in a magnetic surface current density source. A superconducting substrate acts as a perfect magnetic conductor with $H_{||,ac}=0$ on its surface. The combined results agree very well with recent experimental observations. Existing Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ crystals atop perfect electric conductors could have Josephson STAR-emitter power in excess of 5 mW, acceptable for many device applications.Comment: 3 pages 3 figure

Towards a sensitive search for variation of the fine structure constant using radio-frequency E1 transitions in atomic dysprosium

It has been proposed that the radio-frequency electric-dipole (E1) transition between two nearly degenerate opposite-parity states in atomic dysprosium should be highly sensitive to possible temporal variation of the fine structure constant ($\alpha$) [V. A. Dzuba, V. V. Flambaum, and J. K. Webb, Phys. Rev. A {\bf 59}, 230 (1999)]. We analyze here an experimental realization of the proposed search in progress in our laboratory, which involves monitoring the E1 transition frequency over a period of time using direct frequency counting techniques. We estimate that a statistical sensitivity of |\adota| \sim 10^{-18}/yr may be achieved and discuss possible systematic effects that may limit such a measurement.Comment: 8 pages, 7 figure

Pain management in the neonatal piglet during routine management procedures. Part 2:Grading the quality of evidence and the strength of recommendations

Piglets reared in swine production in the USA undergo painful procedures that include castration, tail docking, teeth clipping, and identification with ear notching or tagging. These procedures are usually performed without pain mitigation. The objective of this project was to develop recommendations for pain mitigation in 1- to 28-day-old piglets undergoing these procedures. The National Pork Board funded project to develop recommendations for pain mitigation in piglets. Recommendation development followed a defined multi-step process that included an evidence summary and estimates of the efficacies of interventions. The results of a systematic review of the interventions were reported in a companion paper. This manuscript describes the recommendation development process and the final recommendations. Recommendations were developed for three interventions (CO2/O2 general anesthesia, non-steroidal anti-inflammatory drugs (NSAIDs), and lidocaine) for use during castration. The ability to make strong recommendations was limited by low-quality evidence and strong certainty about variation in stakeholder values and preferences. The panel strongly recommended against the use of a CO2/O2 general anesthesia mixture, weakly recommended for the use of NSAIDs and weakly recommended against the use of lidocaine for pain mitigation during castration of 1- to 28-day-old piglets

Case study: Treatment of oral and locomotory stereotypic behaviors in a mature sow

A 32-month-old female 225-kg nonpregnant cross-bred Newsham sow presented a 6-week history of stereotypic behaviors when housed in a laboratory research facility. A behavioral examination over 12 daylight hours revealed 3 main stereotypic motor patterns, namely (1) oral-nasal gate manipulation defined as placement of the snout between the bars of the pen gate with repetitive, forceful up and down movement; (2) head weaving defined as repetitive lateral head and snout movement toward the pen gates while rocking back and forth on her forequarters with hooves remaining on ground at all times; and (3) body weaving defined as repetitive shifting of body weight from one side to the other with front hooves lifting alternately off the ground. The sow performed the oral-nasal gate manipulation and head and body weaving 4.0%, 12.4%, and 6.8% of her total baseline time budget, respectively. The presumptive diagnosis was oral-nasal and locomotory stereotypies. Three treatments were used to mitigate the duration and frequency of these stereotypic behaviors. Treatment 1—Social treatment (change social stimuli by providing visual and nose-to-nose contact with different neighboring sows); Treatment 2—Forage treatment (change foraging substrates by providing peat moss as a rooting substrate); and Treatment 3—Space treatment (change pen configuration by increasing space). The sow performed the oral-nasal gate manipulation and head and body weaving 0%, 0.4%, and 0.1% of her total time budget, respectively; social treatment: the sow performed the oral-nasal gate manipulation and head and body weaving 0.9%, 15.3%, and 11.3% of her total time budget, respectively; and forage treatment: the sow performed the oral-nasal gate manipulation and head and body weaving 0.5%, 28.0%, and 15.5% of her total time budget, respectively. This study is one of the first reports to evaluate the treatment of established stereotypies in a mature sow. Results suggest the promise of environmental enrichment as an effective treatment strategy. Further research is needed to evaluate the persistence of these behavioral changes and relative importance of different environmental manipulations provided