Fungal diversity and abundance and nitrogen accumulation during forest succession.

General EcologySuccession following a disturbance event can radically alter a forest’s ecosystem. Although many aspects of the community are affected, we chose to analyze the effect succession has on nitrogen levels and fungal diversity and functional groups. We looked at three plots that had each been burned once to study this relationship. At the three sites, we analyzed soil for percent nitrogen levels and did a survey of mushroom species composition, specifically focusing on the functional groups of fungi, mycorrhizal and wood-decomposers. We determined Shannon diversity indices for all the species across the three plots and ran a Chi-squared test to see if the proportion of each functional group was the same throughout the sites. Our soil data showed no significant difference in mean percent nitrogen levels across the three plots. Furthermore, there was no meaningful difference in species diversity, but there was a significant difference in the proportion of functional groups based on the burn year. Although our results were insignificant, other research has indicated that nitrogen levels peak at intermediate stages when organic leaf litter is high, but coarse woody debris is low. Furthermore, we concluded that early successional stages are associated with low fungal species diversity due to low leaf litter and availability of dead wood. Finally, we determined that younger forests have proportionately higher levels of mycorrhizal fungi than wood-decomposers due to the lack of coarse woody debris on which decomposers can live. Having such knowledge about nutrient availability and fungal succession is important for forest management, particularly for understanding the short and long-term consequences a prescribed burn can have on the ecosystem.http://deepblue.lib.umich.edu/bitstream/2027.42/110211/1/Singer_Emma_2014.pd

Utilizing a Culturally Relevant Ecology Curriculum to Help Students see Intersections between their Scientific and Cultural Identities

The purpose of this capstone was to create a two-week long ecology unit for high school biology students rooted in culturally relevant practices. The project sought to answer the question “How can utilizing a culturally relevant ecology curriculum help students see intersections between their scientific and cultural identities?” Data shows that people of color and women are underrepresented within the sciences. Disengagement and lack of interest in the sciences begins in middle and high school, suggesting students feel the material is irrelevant or disconnected from their lives. To address this gap, this project utilized a culturally relevant lens to create an ecology curriculum. Research showed that culturally relevant pedagogy increased student engagement with and retention of science concepts. The created curriculum draws on students’ pools of knowledge and integrates historical and cultural data into the practice of science. Students engage in a variety of learning activities including laboratory experiments, inquiry based activities, and reflective journaling. This project acts as a model for educators looking to engage in culturally relevant practices within the sciences as a mechanism to increase student engagement

Space Producers: An Analysis of Equitably Produced Bike Space

This paper sets out to understand the dynamics of bicycle space production in Philadelphia. To understand the implications of a bike infrastructure as produced space in a city, I analyze specific spaces in Philadelphia through Lefebvre’s tripartite view of the production of space. These spaces – the Vine Street Expressway, Baltimore Avenue, and the 58th Street Greenway – reveal the dominance of perceived space, which often lacks representation from those who use the space day-to-day. Perceived space is found to be heavily influenced by environmental, health, and safety concerns, while leaving out a consideration to equity in the production of bike infrastructure. Greater consideration must be granted to the lived experience of spaces to equitable influence Through an analysis of how these spaces are conceived, perceived, and lived, and how these separate productions of space align, I seek to understand the role Philadelphia’s inhabitants have in the production of their space. And, consequently, what right they have to their city

A mixed methods study of change processes enabling effective transition to team-based care

Team-based care is considered central to achieving value in primary care, yet results of large-scale primary care transformation initiatives have been mixed. We explore how underlying change processes influence the effectiveness of transition to team-based care. We studied 12 academically-affiliated primary care practices participating in a learning collaborative, using longitudinal staff survey data to measure progress toward team-based care and qualitative interviews with practice staff to understand practice transformation. Transformation efforts focused on team formation and capacity building for quality improvement. Using thematic analysis, we explored types of change processes undertaken and the relationship between change processes and effective team-based care. We identified three prototypical approaches to change: pursuing functional and cultural change processes, functional only, and cultural only. Practice sites prioritizing both change processes formed the most effective teams: simultaneous functional and cultural change spurred a mutually-reinforcing virtuous cycle. We describe implications for research, practice and policyThis research was supported by a grant from the Harvard Medical School Center for Primary Care and CRICO [362121]. MAK was supported by a Harvard Business School doctoral fellowship. ELA was supported by funding from a Wellcome Trust Senior Investigator Award [WT097899M]

Optimizing patient partnership in primary care improvement: A qualitative study

BACKGROUND: The need to expand and better engage patients in primary care improvement persists. PURPOSE: Recognizing a continuum of forms of engagement, this study focused on identifying lessons for optimizing patient partnerships, wherein engagement is characterized by shared decision-making and practice improvement co-design. METHODOLOGY: 23 semi-structured interviews with providers and patients involved in improvement efforts in seven U.S. primary care practices in the Academic Innovations Collaborative (AIC). The AIC aimed to implement primary care improvement, emphasizing patient engagement in the process. Data were analyzed thematically. RESULTS: Sites varied in their achievement of patient partnerships, encountering material, technical, and sociocultural obstacles. Time was a challenge for all sites, as was engaging a diversity of patients. Technical training on improvement processes and shared learning ‘on the job’ were important. External, organizational and individual-level resources helped overcome sociocultural challenges: the AIC drove provider buy-in; a team-based improvement approach helped shift relationships from providers and recipients towards teammates; and individual qualities and behaviors that flattened hierarchies and strengthened interpersonal relationships further enhanced ‘teamness’. A key factor influencing progress towards transformative partnerships was a strong shared learning journey, characterized by: frequent interactions; proximity to improvement decision-making; learning together from the ‘lived experience’ of practice improvement. Teams came to value not only patients’ knowledge, but changes wrought by working collaboratively over time. CONCLUSION: Establishing practice improvement partnerships remains challenging, but partnering with patients on improvement journeys offers distinctive gains for high quality patient-centered care. PRACTICE IMPLICATIONS: Engaging diverse patient partners requires significant disruption to organizational norms and routines, and the trend toward team-based primary care offers a fertile context for patient partnerships. Material, technical and sociocultural resources should be evaluated not only for whether they overcome specific challenges, but also for how they enhance the shared learning journey.This research was supported by a grant from the Harvard Medical School Center for Primary Care and CRICO [362121]. Emma-Louise Aveling’s contribution was supported by funding from a Wellcome Trust Senior Investigator Award (WT097899M)

GLUE: a flexible software system for virus sequence data

Background: Virus genome sequences, generated in ever-higher volumes, can provide new scientific insights and inform our responses to epidemics and outbreaks. To facilitate interpretation, such data must be organised and processed within scalable computing resources that encapsulate virology expertise. GLUE (Genes Linked by Underlying Evolution) is a data-centric bioinformatics environment for building such resources. The GLUE core data schema organises sequence data along evolutionary lines, capturing not only nucleotide data but associated items such as alignments, genotype definitions, genome annotations and motifs. Its flexible design emphasises applicability to different viruses and to diverse needs within research, clinical or public health contexts. Results: HCV-GLUE is a case study GLUE resource for hepatitis C virus (HCV). It includes an interactive public web application providing sequence analysis in the form of a maximum-likelihood-based genotyping method, antiviral resistance detection and graphical sequence visualisation. HCV sequence data from GenBank is categorised and stored in a large-scale sequence alignment which is accessible via web-based queries. Whereas this web resource provides a range of basic functionality, the underlying GLUE project can also be downloaded and extended by bioinformaticians addressing more advanced questions. Conclusion: GLUE can be used to rapidly develop virus sequence data resources with public health, research and clinical applications. This streamlined approach, with its focus on reuse, will help realise the full value of virus sequence data

Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination?

Following the development of highly effective direct acting antiviral (DAA) compounds for the treatment of the hepatitis C virus (HCV), WHO has set out plans for disease eradication by 2030. Many barriers must be surmounted before this can be achieved, including buy-in from governments and policy makers, reduced drug costs, and improved infrastructure for the pathway from diagnosis to treatment. A comprehensive set of guidelines was produced by WHO in 2014, updated in 2016, and they are due to be revised later this year

Factors Influencing Team Behaviors in Surgery: A Qualitative Study to Inform Teamwork Interventions.

BACKGROUND: Surgical excellence demands teamwork. Poor team behaviors negatively affect team performance and are associated with adverse events and worse outcomes. Interventions to improve surgical teamwork focusing on frontline team members' nontechnical skills have proliferated but shown mixed results. Literature on teamwork in organizations suggests that team behaviors are also contingent on psychosocial, cultural, and organizational factors. This study examined factors influencing surgical team behaviors to inform more contextually sensitive and effective approaches to optimizing surgical teamwork. METHODS: This qualitative study of cardiac surgical teams in a large United States teaching hospital included 34 semistructured interviews. Thematic network analysis was used to examine perceptions of ideal teamwork and factors influencing team behaviors in the operating room. RESULTS: Perceptions of ideal teamwork were largely shared, but team members held discrepant views of which team and leadership behaviors enhanced or undermined teamwork. Other factors affecting team behaviors were related to the local organizational culture, including management of staff behavior, variable case demands, and team members' technical competence, and fitness of organizational structures and processes to support teamwork. These factors affected perceptions of what constituted optimal interpersonal and team behaviors in the operating room. CONCLUSIONS: Team behaviors are contextually contingent and organizationally determined, and beliefs about optimal behaviors are not necessarily shared. Interventions to optimize surgical teamwork require establishing consensus regarding best practice, ability to adapt as circumstances require, and organizational commitment to addressing contextual factors that affect teams

Suspect and nontarget screening approaches to identify organic contaminant records in lake sediments

Sediment cores provide a valuable record of historical contamination, but so far, new analytical techniques such as high-resolution mass spectrometry (HRMS) have not yet been applied to extend target screening to the detection of unknown contaminants for this complex matrix. Here, a combination of target, suspect, and nontarget screening using liquid chromatography (LC)-HRMS/MS was performed on extracts from sediment cores obtained from Lake Greifensee and Lake Lugano located in the north and south of Switzerland, respectively. A suspect list was compiled from consumption data and refined using the expected method coverage and a combination of automated and manual filters on the resulting measured data. Nontarget identification efforts were focused on masses with Cl and Br isotope information available that exhibited mass defects outside the sample matrix, to reduce the effect of analytical interferences. In silico methods combining the software MOLGEN-MS/MS and MetFrag were used for direct elucidation, with additional consideration of retention time/partitioning information and the number of references for a given substance. The combination of all available information resulted in the successful identification of three suspect (chlorophene, flufenamic acid, lufenuron) and two nontarget compounds (hexachlorophene, flucofuron), confirmed with reference standards, as well as the tentative identification of two chlorophene congeners (dichlorophene, bromochlorophene) that exhibited similar time trends through the sediment cores. This study demonstrates that complementary application of target, suspect, and nontarget screening can deliver valuable information despite the matrix complexity and provide records of historical contamination in two Swiss lakes with previously unreported compounds