A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, genome-genome alignment, and annotation. For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered phylogenies from multiple datasets that were consistent with previous conflicting estimates of the relationships among mammals. SISRS is open source and freely available at https://github.com/rachelss/SISRS.Comment: 12 pages plus36 figures, 1 supplementary table, 3 supplementary figure

Distribution and Ecotypic Variation of the Invasive Annual Barb Goatgrass (\u3cem\u3eAegiolops triuncialis\u3c/em\u3e) on Serpentine Soil

Successful colonization of newly introduced species is driven by a multitude of factors and is highly dependent on the species. It has long been hypothesized that preadaptation and postestablishment natural selection of introduced species can facilitate their invasion; however, to date, limited research has been dedicated to these theories. In addition, although the correlation between establishment of invasive species and disturbance has been noted and widely studied, the susceptibility of undisturbed habitats to invasion remains unclear. In California, serpentine habitats are severe edaphic environments that have been relatively free of anthropogenic disturbance and nonindigenous species invasions. In this study, we documented the occurrence of the nonindigenous barb goatgrass on serpentine and nonserpentine grasslands in the California Northern Interior Coast Range and the western foothills of the Sierra Nevada Mountains and conducted greenhouse and field experiments to assess the species\u27 degree of adaptation to serpentine soils. Reconnaissance of serpentine intrusions and yearly monitoring suggest that barb goatgrass may grow preferentially on serpentine soil, particularly disturbed serpentine sites. In the greenhouse, for most measures of performance, serpentine populations performed better than nonserpentine populations when grown on serpentine soil. Particularly noteworthy was that serpentine populations had higher root-mass ratios than nonserpentine populations when grown on serpentine soil. In contrast to the greenhouse study, field-grown populations from serpentine and nonserpentine sources performed equally well on nonserpentine; alluvial, disturbed serpentine; and shallow, undisturbed serpentine, although the overall species\u27 performance was diminished on severe serpentine soils. Alarmingly, even in the absence of previous exposure to serpentine, barb goatgrass was capable of establishing and spreading into minimally disturbed sites with strong serpentinitic characteristics

Random field Ising systems on a general hierarchical lattice: Rigorous inequalities

Random Ising systems on a general hierarchical lattice with both, random fields and random bonds, are considered. Rigorous inequalities between eigenvalues of the Jacobian renormalization matrix at the pure fixed point are obtained. These inequalities lead to upper bounds on the crossover exponents $\{\phi_i\}$.Comment: LaTeX, 13 pages, figs. 1a,1b,2. To be published in PR

Professional Development for Educational Leaders in the Era of Performance Evaluation Reform

The word “accountability” has become a mantra in public education. Arguably, this one word, and the movement it has produced, has shaped the direction of our field in the past decade more than any other (Harris, 2011). This movement has led to many positive changes including an examination of gaps in student achievement, the types of assessments used in schools, and the strength of the performance evaluation systems for principals and teachers. Many large urban school districts, as well as entire states, have revamped the way public school principals and teachers are evaluated. In fact many, including the State of Tennessee, Dallas Independent School District, Milwaukee Public Schools, Houston Independent School District, and the State of Illinois, have started or will start using some sort of student achievement metric as part of teacher and/or principal performance evaluations. The ideas surrounding using student growth seem simple enough: If student test scores improve, it means the teacher or principal is doing his or her job well and therefore should be rewarded. This seemingly simple idea is in fact quite complex. Many school administrators may not have the background or training to implement growth models as part of performance evaluations (Mitgang, 2012), which could lead to potentially unethical and incorrect implementation of newer forms of accountability such as growth modeling. Such problems have already arisen in a number of districts across the nation (Harris, 2011)

Individualism and entrepreneurship: Does the pattern depend on the social context?

This article argues that cultural and personal values are relevant in the formation of entrepreneurial intentions; as such, the interplay between both value-levels deserves attention. Individualist values such as achievement, pleasure, self-direction and an exciting and stimulating life are related to entrepreneurial intention and activity, at both the cultural and personal levels. From a sample of 2069 adults with a university degree, the results support a double-effect of culture on entrepreneurial intention: the personal values effect (a more individualist culture leads to more members exhibiting higher entrepreneurial intentions) and the outlier effect (those who are more individualist than average in their culture will exhibit a higher entrepreneurial intention). Within the two individualist dimensions considered (self-enhancement and openness to change), the relationship of self-enhancement to entrepreneurial intention is stronger than that of openness to change. The implications of these results are discussed and avenues for future research are proposed

Patient Preferences in Controlling Access to Their Electronic Health Records: a Prospective Cohort Study in Primary Care

Introduction: Previous studies have measured individuals’ willingness to share personal information stored in electronic health records (EHRs) with health care providers, but none has measured preferences among patients when they are allowed to determine the parameters of provider access. Methods: Patients were given the ability to control access by doctors, nurses, and other staff in a primary care clinic to personal information stored in an EHR. Patients could restrict access to all personal data or to specific types of sensitive information, and could restrict access for a specific time period. Patients also completed a survey regarding their understanding of and opinions regarding the process. Results: Of 139 eligible patients who were approached, 105 (75.5 %) were enrolled, and preferences were collected from all 105 (100 %). Sixty patients (57 %) did not restrict access for any providers. Of the 45 patients (43 %) who chose to limit the access of at least one provider, 36 restricted access only to all personal information in the EHR, while nine restricted access of some providers to a subset of the their personal information. Thirty-four (32.3 %) patients blocked access to all personal information by all doctors, nurses, and/or other staff, 26 (24.8 %) blocked access by all doctors and/or nurses, and five (4.8 %) denied access to all doctors, nurses, and staff. Conclusions: A significant minority of patients chose to restrict access by their primary care providers to personal information contained in an EHR, and few chose to restrict access to specific types of information. More research is needed to identify patient goals and understanding of the implications when facing decisions of this sort, and to identify the impact of patient education regarding information contained in EHRs and their use in the clinical care settin

In-vivo photoacoustic microscopy of nanoshell extravasation from solid tumor vasculature

In this study, high resolution backward-mode photoacoustic microscopy (PAM) is used to noninvasively image progressive extravasation and accumulation of nanoshells within a solid tumor in vivo. PAM takes advantage of the strong near-infrared absorption of nanoshells and their extravasation tendency from leaky tumor vasculatures for imaging. Subcutaneous tumors are grown on immunocompetent BALB/c mice. Polyethylene glycol (PEGylated) nanoshells with a peak optical absorption at ∼800nm are intravenously administered. With an 800-nm laser source, a prescan prior to nanoshell injection is taken to determine the background that is free of nanoshell accumulation. After injection, the 3-D nanoshell distribution at the tumor foci is monitored by PAM for 6h. Experimental results show that accumulated nanoshells delineate the tumor position. Nanoshell accumulation is heterogeneous in tumors: more concentrated within the tumor cortex and largely absent from the tumor core. Because nanoshells have been recently demonstrated to enhance thermal therapy of subcutaneous tumors, we anticipate that PAM will be an important aid before, during, and after nanoshell thermal therapy

Public Health Nutrition: page 1 of 10 doi:10.1017/S1368980012000754 Review Article The science on front-of-package food labels

Objective: The US Food and Drug Administration and Institute of Medicine are currently investigating front-of-package (FOP) food labelling systems to provide sciencebased guidance to the food industry. The present paper reviews the literature on FOP labelling and supermarket shelf-labelling systems published or under review by February 2011 to inform current investigations and identify areas of future research. Design: A structured search was undertaken of research studies on consumer use, understanding of, preference for, perception of and behaviours relating to FOP/ shelf labelling published between January 2004 and February 2011. Results: Twenty-eight studies from a structured search met inclusion criteria. Reviewed studies examined consumer preferences, understanding and use of different labelling systems as well as label impact on purchasing patterns and industry product reformulation. Conclusions: The findings indicate that the Multiple Traffic Light system has most consistently helped consumers identify healthier products; however, additional research on different labelling systems ’ abilities to influence consumer behaviour is needed. In May 2010 the White House Childhood Obesity Task Force highlighted the need to ‘empower parents and caregivers to make healthy choices ’ with simple, practical information, including improved front-of-package (FOP) food labels (1). Currently the US Food and Drug Administration (FDA) has undertaken a Front-of-Package Labeling Initiative (2) with the goal of reviewing available evidence on FOP labelling systems to determine whether one approach can be recommended over others. Congress also requested that the Institute of Medicine (IOM) examine this issue and in October 2010 the Committee o

Provider Responses to Patients Controlling Access to their Electronic Health Records: A Prospective Cohort Study in Primary Care

Introduction: Applying Fair Information Practice principles to electronic health records (EHRs) requires allowing patient control over who views their data. Methods: We designed a program that captures patients’ preferences for provider access to an urban health system’s EHR. Patients could allow or restrict providers’ access to all data (diagnoses, medications, test results, reports, etc.) or only highly sensitive data (sexually transmitted infections, HIV/AIDS, drugs/alcohol, mental or reproductive health). Except for information in free-text reports, we redacted EHR data shown to providers according to patients’ preferences. Providers could “Break the Glass” to display redacted information. We prospectively studied this system in one primary care clinic, noting redactions and when users “Broke the Glass,” and surveyed providers about their experiences and opinions. Results: Eight of 9 eligible clinic physicians and all 23 clinic staff participated. All 105 patients who enrolled completed the preference program.. Providers did not know which of their patients were enrolled and nor their preferences for accessing their EHRs. During the six-month prospective study, 92 study patients (88%) returned 261 times during which providers viewed their EHRs 126 times (48%). Providers “broke the glass” 102 times, 92 times for patients not in the study and 10 times for 6 returning study patients, all of whom had restricted EHR access. Providers “broke the glass” for 6 (14%) of 43 returning study patients with redacted data vs. zero among 49 study patients without redactions (p=0.01). Although 54% of providers agreed that patients should have control over who sees their EHR information, 58% believed restricting EHR access could harm provider-patient relationships and 71% felt quality of care would suffer. Conclusions: Patients frequently preferred restricting provider access to their EHRs. Providers infrequently overrode patients’ preferences to view hidden data. Providers believed restricting EHR access would adversely impact patient care. Applying Fair Information Practice principles to EHRs will require balancing patient preferences, providers’ needs, and health care quality.This study was supported in part by grant number 90HT005 from the Office of the National Coordinator for Health Information Technology (ONC) to the Indiana Health Information Technology Corporation. The opinions expressed in this work are the authors’ and do not necessarily reflect the positions of ONC, IHIT, Eskenazi Health, Indiana University, or the Regenstrief Institute, Inc