A “Neighborhood” Approach for Using Remotely Sensed Data to Post-Process Species Distribution Models for Conservation Assessments

Species distribution models can be used to predict environmental suitability, estimate changes in species’ geographic ranges, and support conservation assessments. Masking suitability maps built from these models to remove areas currently lacking appropriate vegetation can refine predictions and aid conservation applications. However, the uncertainty around coordinates (even for recent records) can exceed the fine resolution of the additional data. Here, I present a novel yet simple methodological approach to reflect this reality of coordinate uncertainty of occurrence records and mismatch between climatic and habitat data resolution. I implement it for a forest-dwelling species currently considered threatened by the IUCN (Handleyomys chapmani). After building a Maxent species distribution model indicating climatically suitable areas, I determined deforestation tolerance thresholds (the lowest value of forest cover where the species has been observed recently) using two methods based on matching recent records with forest-cover data for the corresponding year: 1) extracting the exact pixel value where a record fell; and 2) using an aggregate measure of that and surrounding pixels (the “neighborhood” more likely within the radius of actual sampling that yielded the record). I applied the respective thresholds to mask the suitability prediction for H. chapmani, identifying areas of inferred habitat loss due to insufficient forest cover. For each method, from the post-processed map and records of the species, I calculated extent of occurrence (EOO) and area of occupancy (AOO), two metrics used by the IUCN for threat level categorization. The post-processing method had little effect on EOO estimates due to loss mostly within the range and not along the spatial margins, but for each method there was a vast difference when calculating EOO from occurrences versus from masked suitability maps. For AOO, the neighborhood method reduced the estimated values somewhat compared with the exact method, highlighting patchy loss throughout the range. However, the localized deforestation evident at a regional extent at the fine resolution of the forest-cover data largely disappeared when projecting to the 2 km x 2 km grid standardized by the IUCN. Overall, the values for EOO and AOO calculated here suggest removing the species from the threatened category, since the most plausible ones for each metric were above the respective thresholds (and substantially higher than those in the current IUCN account). The neighborhood method and associated code provided here may prove useful for many species, particularly those having occurrence records with high coordinate uncertainty in regions of low spatial autocorrelation of the environment, where small georeferencing errors can lead to great differences in habitat information. This research also highlights the importance of obtaining accurate georeferences (corresponding to the habitat sampled) when collecting field data and more generally of using habitat-refined distribution maps for conservation assessments

Young Adults with Cleft Lip and Palate: Personal Perspectives of Transition of Care

Children with cleft lip/palate receive team care which typically ends at eighteen. Young adults then need to transition into an adult-centered model of care. A paucity of literature exists regarding their perspective on transition of care experience. This research explores the experiences of young adults with CLP regarding their transition of care process, within the person-centered ICF framework

RELIABILITY AND ACCURACY OF A STANDARDIZED SHALLOW WATER RUNNING TEST TO DETERMINE CARDIORESPIRATORY FITNESS

A standardized fitness assessment is critical for the development of an individualized exercise prescription. Although the benefits of aquatic exercise have been well established, there remains the need for a standardized nonswimming protocol to accurately assess cardiorespiratory fitness (CRF) in shallow water. The present investigation was designed to assess (a) the reliability of a standardized shallow water run (SWR) test of CRF and (b) the accuracy of a standardized SWR compared with a land-based treadmill (LTM)test. Twenty-three healthy women (20 6 3 years), with body mass index (23.5 6 3 kg$m22), performed 2 shallow water peak oxygen consumption (V_ O2peak) running tests (SWRa and SWRb), and 1 V_ O2max LTM. Intraclass correlation coefficients indicated moderately strong reliability for V_ O2peak (ml$kg21$min21) (r = 0.73, p , 0.01), HR peak (b$min21) (r = 0.82; p , 0.01), and O2pulse (V_ O2 [ml$kg21$min21]$HR [b$min21]) (r = 0.77, p , 0.01). Using paired t-tests and Pearson’s correlations, SWR V_ O2peak and HR peak were significantly lower than during LTM (p # 0.05) and showed moderate correlations of 0.60 and 0.58 (p , 0.001) to LTM. O2pulse was similar (p . 0.05) for the SWR and LTM tests with a moderate correlation of 0.63. A standardized SWR test asa measure of CRF is a reliable, and to some degree, valid alternative to conventional protocols and may be used by strength and conditioning professionals to measure program outcomes and monitor training progress. Furthermore, this protocol provides a water-based option for CRF assessment among healthy women and offers insight toward the development of an effective protocol that can accommodate individuals with limited mobility, or those seeking less musculoskeletal impact from traditional land-based types of training

Hydrologic and isotopic modeling of Alpine Lake Waiau, Mauna Kea, Hawai'i

Analysis of hydrologic, meteorologic, and isotopic data collected over 3 yr quantifies and explains the enormous variability and isotopic enrichment (δ18O = +16.9, δD = +50.0) of alpine Lake Waiau, a culturally and ecologically significant perched lake near the summit of Mauna Kea, Hawai'i. Further, a simple one-dimensional hydrologic model was developed that couples standard water budget modeling with modeling of δD and δ18O isotopic composition to provide daily predictions of lake volume and chemistry. Data analysis and modeling show that winter storms are the primary source of water for the lake, adding a distinctively light isotopic signature appropriate for high-altitude precipitation. Evaporation at the windy, dry summit is the primary loss mechanism for most of the year, greatly enriching the lake in heavy isotopes

2015 AAPP Monograph Series: African American Professors Program

The African American Professors Program (AAPP) at the University of South Carolina is proud to publish its fourteenth edition of this annual monograph series. AAPP recognizes the significance of offering its scholars a venue on which to engage actively in research and to publish their refereed papers. Parallel with the publication of their refereed manuscripts is the opportunity to gain visibility among scholars throughout institutions in national and international settings. Scholars who have contributed papers for this monograph are acknowledged for embracing the value of including this responsibility within their academic milieu. Writing across disciplines adds to the intellectual diversity of these manuscripts. From neophytes to quite experienced individuals, the chapters have been researched and comprehensively written. Founded in 1997 through the Department of Educational Leadership and Policies in the College of Education, AAPP was designed to address the under-representation of African American professors on college and university campuses. Its mission is to expand the pool of these professors in critical academic and research areas. Sponsored by the University of South Carolina, the W.K. Kellogg Foundation, and the South Carolina General Assembly, the program recruits doctoral students for disciplines in which African Americans currently are underrepresented among faculty in higher education. The continuation of this monograph series is seen as responding to a window of opportunity to be sensitive to an academic expectation of graduates as they pursue career placement and, at the same time, to allow for the dissemination of products of scholarship to a broader community. The importance of this monograph series has been voiced by one of our 2002 AAPP graduates, Dr. Shundele LaTjuan Dogan, formerly an Administrative Fellow at Harvard University, a Program Officer for the Southern Education Foundation, and a Program Officer for the Arthur M. Blank Foundation in Atlanta, Georgia. She is currently a Corporate Citizenship and Corporate Affairs Manager for IBM-International Business Machines in Atlanta, Georgia and has written the Foreword for the 2014 monograph. Dr. Dogan wrote: One thing in particular that I want to thank you for is having the African American Professors Program scholars publish articles for the monograph. I have to admit that writing the articles seemed like extra work at the time. However, in my recent interview process, organizations have asked me for samples of my writing. Including an article from a published monograph helped to make my portfolio much more impressive. You were \u27right on target\u27 in having us do the monograph series. (AAPP 2003 Monograph, p. xi) The African American Professors Program continues its tradition as a promoter of scholarship in higher education as evidenced through the inspiration from this group of interdisciplinary manuscripts. As we embark on a new phase of development by initiating the renaming of our program, the Carolina Diversity Professors Program, we are grateful for your continued interest and support of the work of the scholars. In conclusion, I hope that you will envision these published papers as serving as an invaluable contribution to your own professional and career development. John McFadden, Ph.D. The Benjamin Elijah Mays Distinguished Professor Emeritus Director, African American Professors Program University of South Carolinahttps://scholarcommons.sc.edu/mcfadden_monographs/1002/thumbnail.jp

changeRangeR: An R package for reproducible biodiversity change metrics from species distribution estimates

Conservation planning and decision-making rely on evaluations of biodiversity status and threats that are based upon species' distribution estimates. However, gaps exist regarding automated tools to delineate species' current ranges from distribution estimates and use those estimates to calculate both species- and community-level biodiversity metrics. Here, we introduce changeRangeR, an R package that facilitates workflows to reproducibly transform estimates of species' distributions into metrics relevant for conservation. For example, by combining predictions from species distribution models (SDMs) with other maps of environmental data (e.g., suitable forest cover), researchers can characterize the proportion of a species' range that is under protection, metrics used under the IUCN Criteria A and B guidelines (Area of Occupancy and Extent of Occurrence), and other more general metrics such as taxonomic and phylogenetic diversity and endemism. Further, changeRangeR facilitates temporal comparisons among biodiversity metrics to inform efforts toward complementarity and consideration of future scenarios in conservation decisions. changeRangeR also provides tools to determine the effects of modeling decisions through sensitivity tests. Transparent and repeatable workflows for calculating biodiversity change metrics from SDMs such as those provided by changeRangeR are essential to inform conservation decision-making efforts and represent key extensions for SDM methodology and associated metadata documentation.journal articl

Barriers and facilitators to diabetes screening and prevention after a pregnancy complicated by gestational diabetes

OBJECTIVE: Gestational diabetes mellitus (GDM) is increasing in the United States, with higher rates among minoritized racial and ethnic populations and lower income populations. GDM increases risk for type 2 diabetes (T2DM), and postpartum diabetes screening and prevention are imperative. This qualitative study examines barriers and facilitators to postpartum T2DM screening and prevention among non-privately insured individuals with a history of GDM in a state prior to Medicaid expansion. METHODS: Thirty-six non-privately insured women with a history of GDM completed semi-structured interviews. Four focus groups and seven interviews were conducted with 30 nurse practitioners, physicians, physician assistants, nurses and registered dietitians from Federally Qualified Health Centers in St. Louis, MO. Interviews and focus groups were audio-recorded and transcribed. Data were analyzed using an integrative thematic analysis informed by the socio-ecological model. RESULTS: Barriers and facilitators to T2DM screening and prevention occur across multiple environments (society, healthcare system, interpersonal, and individual). Societal barriers include insurance issues, unemployment, and lack of transportation, childcare, safe housing, and healthy food access, while facilitators include government sponsored programs and community organizations. Healthcare system barriers include care fragmentation, scheduling policies and time constraints while facilitators include care coordination, pregnancy support groups, and education materials. Interpersonal barriers include negative care experiences, cultural differences, communication challenges, competing priorities, and lack of a social support network, while facilitators include family and friend support and positive care experiences. Individual barriers include health complications and unhealthy food and exercise patterns, while facilitators include child wellbeing, empowered attitudes and healthy food and exercise patterns. CONCLUSIONS: The socioecological model highlights the societal and systemic determinants that encompass individual and interpersonal factors affecting postpartum T2DM screening and prevention. This framework can inform multi-level interventions to increase postpartum T2DM screening and prevention in this high-risk population, including policy changes to alleviate higher-level barriers

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Since 2012, the United States of America has experienced a biennial spike in pediatric acute flaccid myelitis (AFM)1-6. Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF)2. CSF from children with AFM (n = 42) and other pediatric neurologic disease controls (n = 58) were investigated for intrathecal antiviral antibodies, using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). Metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n = 20 cases) was also performed, both unbiased sequencing and with targeted enrichment for EVs. Using VirScan, the viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n = 29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n = 22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology frequently identified high levels of CSF EV-specific antibodies in AFM compared with controls, providing further evidence for a causal role of non-polio EVs in AFM

Dimensionality and dynamics in the behavior of C. elegans

A major challenge in analyzing animal behavior is to discover some underlying simplicity in complex motor actions. Here we show that the space of shapes adopted by the nematode C. elegans is surprisingly low dimensional, with just four dimensions accounting for 95% of the shape variance, and we partially reconstruct "equations of motion" for the dynamics in this space. These dynamics have multiple attractors, and we find that the worm visits these in a rapid and almost completely deterministic response to weak thermal stimuli. Stimulus-dependent correlations among the different modes suggest that one can generate more reliable behaviors by synchronizing stimuli to the state of the worm in shape space. We confirm this prediction, effectively "steering" the worm in real time.Comment: 9 pages, 6 figures, minor correction