ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Evolution of Preprofessional Pharmacy Curricula

Objectives. To examine changes in preprofessional pharmacy curricular requirements and trends, and determine rationales for and implications of modifications. Methods. Prerequisite curricular requirements compiled between 2006 and 2011 from all doctor of pharmacy (PharmD) programs approved by the Accreditation Council of Pharmacy Education were reviewed to ascertain trends over the past 5 years. An online survey was conducted of 20 programs that required either 3 years of prerequisite courses or a bachelor’s degree, and a random sample of 20 programs that required 2 years of prerequisites. Standardized telephone interviews were then conducted with representatives of 9 programs. Results. In 2006, 4 programs required 3 years of prerequisite courses and none required a bachelor’s degree; by 2011, these increased to 18 programs and 7 programs, respectively. Of 40 programs surveyed, responses were received from 28 (70%), 9 (32%) of which reported having increased the number of prerequisite courses since 2006. Reasons given for changes included desire to raise the level of academic achievement of students entering the PharmD program, desire to increase incoming student maturity, and desire to add clinical sciences and experiential coursework to the pharmacy curriculum. Some colleges and schools experienced a temporary decrease in applicants. Conclusions. The preprofessional curriculum continues to evolve, with many programs increasing the number of course prerequisites. The implications of increasing prerequisites were variable and included a perceived increase in maturity and quality of applicants and, for some schools, a temporary decrease in the number of applicants

Large-scale Star Formation Triggering in the Low-mass Arp 82 System: A Nearby Example of Galaxy Downsizing Based on UV/Optical/Mid-IR Imaging

As part of our Spitzer Spirals, Bridges, and Tails project to help understand the effects of galaxy interactions on star formation, we analyze GALEX ultraviolet, SARA optical, and Spitzer infrared images of the interacting galaxy pair Arp 82 (NGC 2535/6) and compare to a numerical simulation of the interaction. We investigate the multiwavelength properties of several individual star forming complexes (clumps). Using optical and UV colors, EW(Halpha), and population synthesis models we constrain the ages of the clumps and find that the median clump age is about 12 Myr. The clumps have masses ranging from a few times 10^6 to 10^9 solar masses. In general, the clumps in the tidal features have similar ages to those in the spiral region, but are less massive. The 8 micron and 24 micron luminosities are used to estimate the far-infrared luminosities and the star formation rates of the clumps. The total clump star formation rate is 2.0+/-0.8 solar masses per year, while the entire Arp 82 system is forming stars at a rate of 4.9+/-2.0 solar masses per year. We find, for the first time, stars in the HI arc to the southeast of the NGC 2535 disk. Population synthesis models indicate that all of the observed populations have young to intermediate ages. We conclude that although the gas disks and some old stars may have formed early-on, the progenitors are late-type or low surface brightness and the evolution of these galaxies was halted until the recent encounter.Comment: Accepted for publication in the AJ, 22 Figures, 5 Table

Evaluating Workplace Mandates with Flows versus Stocks: An Application to California Paid Family Leave

Abstract. Employer mandates often have small effects on wages and employment. Such effects should be most evident using data on employment transitions and wages among new hires. Quarterly Workforce Indicators (QWI) provides county by quarter by demographic group data on the number and earnings of new hires, separations, and recalls (extended leaves). The QWI is used to examine the effects of California’s 2004 paid family leave (CPFL) program, comparing outcomes for young women in California to those for other workers within and outside of California. CPFL had little effect on earnings for young women, but increased separations, hiring, and worker mobility. JEL codes: J32 (nonwage labor costs), J38 (public policy

A Case of Acute Disseminated Encephalomyelitis in a MIddle-Aged Adult

BACKGROUND Acute disseminated encephalomyelitis (ADEM) is a monophasic inflammatory demyelinating disorder of the white matter that is often preceded by viral infection or recent vaccination. Encephalopathy and focal neurological deficits usually manifest one to three weeks after a prodromal illness with neurologic decline progressing rapidly over days to weeks. Approximately 25% of patients will develop multiple sclerosis (MS) within five years of initial presentation of ADEM but the majority of individuals do not progress beyond three months.4 ADEM is most commonly seen in children and young adults, where prognosis is favorable, but very few cases have been reported of middle-aged or elderly patients. The clinical course of these patients as compared to younger patients with ADEM is unclear. Here we present a case of ADEM in a middle-aged adult that recovered well after treatment with high-dose corticosteroids. Pages: 15-17

Who Gives a Trump? Evidence of Framing Effects in Tax Policy

We use a framed survey to measure how associating the name “Trump” with the Tax Cuts and Jobs Act (TCJA) affects people’s satisfaction of said Act. Our research included 72 participant clients from a Volunteer Income Tax Assistants (VITA) program, who were asked to provide baseline data regarding political affiliation and attitudes prior to having tax returns completed. We find that using the name “Trump” with people who self-identify as Republican results in more satisfaction with the Act, whereas, for people with who do not self-identify as Republican, association with the name “Trump” does not precipitate stronger or weaker satisfaction with the Act

Mdivi-1, a mitochondrial fission inhibitor, modulates T helper cells and suppresses the development of experimental autoimmune encephalomyelitis.

BACKGROUND: Unrestrained activation of Th1 and Th17 cells is associated with the pathogenesis of multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). While inactivation of dynamin-related protein 1 (Drp1), a GTPase that regulates mitochondrial fission, can reduce EAE severity by protecting myelin from demyelination, its effect on immune responses in EAE has not yet been studied. METHODS: We investigated the effect of Mdivi-1, a small molecule inhibitor of Drp1, on EAE. Clinical scores, inflammation, demyelination and Drp1 activation in the central nervous system (CNS), and T cell responses in both CNS and periphery were determined. RESULTS: Mdivi-1 effectively suppressed EAE severity by reducing demyelination and cellular infiltration in the CNS. Mdivi-1 treatment decreased the phosphorylation of Drp1 (ser616) on CD4+ T cells, reduced the numbers of Th1 and Th17 cells, and increased Foxp3+ regulatory T cells in the CNS. Moreover, Mdivi-1 treatment effectively inhibited IFN-γ+, IL-17+, and GM-CSF+ CD4+ T cells, while it induced CD4+ Foxp3+ regulatory T cells in splenocytes by flow cytometry. CONCLUSIONS: Together, our results demonstrate that Mdivi-1 has therapeutic potential in EAE by modulating the balance between Th1/Th17 and regulatory T cells

Development of Halofluorochromic Polymer Nanoassemblies for the Potential Detection of Liver Metastatic Colorectal Cancer Tumors Using Experimental and Computational Approaches

Purpose—To develop polymer nanoassemblies (PNAs) modified with halofluorochromic dyes to allow for the detection of liver metastatic colorectal cancer (CRC) to improve therapeutic outcomes. Methods—We combine experimental and computational approaches to evaluate macroscopic and microscopic PNA distributions in patient-derived xenograft primary and orthotropic liver metastatic CRC tumors. Halofluorochromic and non-halofluorochromic PNAs (hfPNAs and n-hfPNAs) were prepared from poly(ethylene glycol), fluorescent dyes (Nile blue, Alexa546, and IR820), and hydrophobic groups (palmitate), all of which were covalently tethered to a cationic polymer scaffold [poly(ethylene imine) or poly(lysine)] forming particles with an average diameter \u3c 30 nm. Results—Dye-conjugated PNAs showed no aggregation under opsonizing conditions for 24 h and displayed low tissue diffusion and cellular uptake. Both hfPNAs and n-hfPNAs accumulated in primary and liver metastatic CRC tumors within 12 h post intravenous injection. In comparison to n-hfPNAs, hfPNAs fluoresced strongly only in the acidic tumor microenvironment (pH \u3c 7.0) and distinguished small metastatic CRC tumors from healthy liver stroma. Computational simulations revealed that PNAs would steadily accumulate mainly in acidic (hypoxic) interstitium of metastatic tumors, independently of the vascularization degree of the tissue surrounding the lesions. Conclusion—The combined experimental and computational data confirms that hfPNAs detecting acidic tumor tissue can be used to identify small liver metastatic CRC tumors with improved accuracy

Benchmarked performance charts using principal components analysis to improve the effectiveness of feedback for audit data in HIV care

Abstract Background Feedback tools for clinical audit data that compare site-specific results to average performance over all sites can be useful for quality improvement. Proposed tools should be simple and clearly benchmark the site’s performance, so that a relevant action plan can be directly implemented to improve patient care services. We aimed to develop such a tool in order to feedback data to UK HIV clinics participating in the 2015 British HIV Association (BHIVA) audit assessing compliance with the 2011 guidelines for routine investigation and monitoring of adult HIV-1- infected individuals. Methods HIV clinic sites were asked to provide data on a random sample of 50–100 adult patients attending for HIV care during 2014 and/or 2015 by completing a self-audit spreadsheet. Outcomes audited included the proportion of patients with recorded resistance testing, viral load monitoring, adherence assessment, medications, hepatitis testing, vaccination management, risk assessments, and sexual health screening. For each outcome we benchmarked the proportion for a specific site against the average performance. We produced performance charts for each site using boxplots for the outcomes. We also used the mean and differences from the mean performance to produce a dashboard for each site. We used principal components analysis to group correlated outcomes and simplify the dashboard. Results The 106 sites included in the study provided information on a total of 7768 patients. Outcomes capturing monitoring of treatment of HIV-infection showed high performance across the sites, whereas testing for hepatitis, and risk assessment for cardiovascular disease and smoking, management of flu vaccination, sexual health screening, and cervical cytology for women were very variable across sites. The principal components analysis reduced the original 12 outcomes to four factors that represented HIV care, hepatitis testing, other screening tests, and resistance testing. These provided simplified measures of adherence to guidelines which were presented as a 4 bar dashboard of performance. Conclusion Our dashboard performance charts provide easily digestible visual summaries of locally relevant audit data that are benchmarked against the overall mean and can be used to improve feedback to HIV services. Feedback from clinicians indicated that they found these charts acceptable and useful