Integrating GIS and Remote Sensing with Ecosystem Research

In the Phase II Ecosystem Management Research Program in the Ouachita and Ozark National Forests, an interdisciplinary group of scientists are evaluating the effects and trade-offs of partial cutting methods in a replicated stand level study. Information from approximately 2,000 plots is being collected by more than fifty researchers during this five-year project with plans to continue data collection long term. To evaluate the effects of different management strategies and their interactions with forest resources, data must be brought into a common format and made available to all researchers. To this end, a data support system was developed which utilizes Geographic Information System (GIS), Global Positioning Systems (GPS) and remote sensing technologies. Aerial photography, along with digitized layers of stand and greenbelt boundaries, roads and streams, and GPSed silvicultural plot locations form a framework to which data from diverse research areas can be linked. Researchers can not only share information resources, but can graphically visualize and query both spatial and attribute data to reflect forest ecosystem changes under various management strategies. The methodology used to develop and configure this large, relational database into an easily accessible form usable in an interactive GIS program could be transferable to other areas of natural resource management

Conducting Social Cognition Research in IS: A Methodology for Eliciting and Analyzing Social Representations

This paper presents a methodology for socio-cognitive research based on the theory of social representations. Elements of the methodology include:1) data elicitation through free word association; 2) content analysis/coding to identify key concepts in the social representation; 3) analysis of the structure of the representation using analysis of similarity and core/periphery analysis; 4) correspondence analysis to place the concepts on a perceptual space; and 5) interpretation of the social representation. The methodology is demonstrated in use through a study examining early sense-making about electronic health records (EHRs). Analysis of qualitative survey data from 190 students identified 22 concepts forming the social representation. Merits of the methodology are discussed, including its potential value for investigations based on technology frames of reference (TFR), the social construction of technology (SCOT) and organizing visions for IT innovations

Building Legitimacy for IT Innovations: The Case of Computerized Physician Order Entry Systems

Research on IT innovations has largely relied on economic-rationalistic models and focused on individuals or organizations as the unit of analysis. The intent of this paper is to advance an alternative research agenda that explores the institutional underpinnings of IT innovation diffusion at the inter-organizational level. Through a multi-stage research study, we examine the legitimation function of organizing visions for IT innovations and develop a taxonomy of legitimation strategies employed by the proponents of an IT innovation. We first built a preliminary theoretical framework that synthesizes key arguments on legitimacy drawn from the organization theory and IS literatures. Next, we conducted an exploratory case study of institutional entrepreneurship surrounding computerized physician order entry (CPOE) systems. We examined the discursive actions of CPOE vendors by content analyzing 165 press releases issued between 1998 and 2006. We then combined the findings of the literature analysis and the case study to create a taxonomy of discursive strategies for building IT innovation legitimacy. A post-hoc analysis of the case study data reveals a number of interesting patterns in the CPOE vendors’ use of the legitimation strategies and helps us formulate a set of research questions to guide future investigations. The work reported in this paper lays a foundation for a deeper understanding of the role of legitimacy and legitimation in shaping diffusion of IT innovations. It also contributes to the conceptual and methodological elaboration of the organizing vision framework

The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Staudinger, M. D., Goyert, H., Suca, J. J., Coleman, K., Welch, L., Llopiz, J. K., Wiley, D., Altman, I., Applegate, A., Auster, P., Baumann, H., Beaty, J., Boelke, D., Kaufman, L., Loring, P., Moxley, J., Paton, S., Powers, K., Richardson, D., Robbins, J., Runge, J., Smith, B., Spiegel, C., & Steinmetz, H. The role of sand lances (Ammodytes sp.) in the Northwest Atlantic ecosystem: a synthesis of current knowledge with implications for conservation and management. Fish and Fisheries, 00, (2020): 1-34, doi:10.1111/faf.12445.The American sand lance (Ammodytes americanus, Ammodytidae) and the Northern sand lance (A. dubius, Ammodytidae) are small forage fishes that play an important functional role in the Northwest Atlantic Ocean (NWA). The NWA is a highly dynamic ecosystem currently facing increased risks from climate change, fishing and energy development. We need a better understanding of the biology, population dynamics and ecosystem role of Ammodytes to inform relevant management, climate adaptation and conservation efforts. To meet this need, we synthesized available data on the (a) life history, behaviour and distribution; (b) trophic ecology; (c) threats and vulnerabilities; and (d) ecosystem services role of Ammodytes in the NWA. Overall, 72 regional predators including 45 species of fishes, two squids, 16 seabirds and nine marine mammals were found to consume Ammodytes. Priority research needs identified during this effort include basic information on the patterns and drivers in abundance and distribution of Ammodytes, improved assessments of reproductive biology schedules and investigations of regional sensitivity and resilience to climate change, fishing and habitat disturbance. Food web studies are also needed to evaluate trophic linkages and to assess the consequences of inconsistent zooplankton prey and predator fields on energy flow within the NWA ecosystem. Synthesis results represent the first comprehensive assessment of Ammodytes in the NWA and are intended to inform new research and support regional ecosystem‐based management approaches.This manuscript is the result of follow‐up work stemming from a working group formed at a two‐day multidisciplinary and international workshop held at the Parker River National Wildlife Refuge, Massachusetts in May 2017, which convened 55 experts scientists, natural resource managers and conservation practitioners from 15 state, federal, academic and non‐governmental organizations with interest and expertise in Ammodytes ecology. Support for this effort was provided by USFWS, NOAA Stellwagen Bank National Marine Sanctuary, U.S. Department of the Interior, U.S. Geological Survey, Northeast Climate Adaptation Science Center (Award # G16AC00237), an NSF Graduate Research Fellowship to J.J.S., a CINAR Fellow Award to J.K.L. under Cooperative Agreement NA14OAR4320158, NSF award OCE‐1325451 to J.K.L., NSF award OCE‐1459087 to J.A.R, a Regional Sea Grant award to H.B. (RNE16‐CTHCE‐l), a National Marine Sanctuary Foundation award to P.J.A. (18‐08‐B‐196) and grants from the Mudge Foundation. The contents of this paper are the responsibility of the authors and do not necessarily represent the views of the National Oceanographic and Atmospheric Administration, U.S. Fish and Wildlife Service, New England Fishery Management Council and Mid‐Atlantic Fishery Management Council. This manuscript is submitted for publication with the understanding that the United States Government is authorized to reproduce and distribute reprints for Governmental purposes. Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

<p>Abstract</p> <p>Background</p> <p><it>Tetrahymena thermophila</it>, a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic macronucleus (MAC). The recent draft MAC genome assembly revealed low sequence repetitiveness, a result of the epigenetic removal of invasive DNA elements found only in the MIC genome. Such low repetitiveness makes complete closure of the MAC genome a feasible goal, which to achieve would require standard closure methods as well as removal of minor MIC contamination of the MAC genome assembly. Highly accurate preliminary annotation of <it>Tetrahymena</it>'s coding potential was hindered by the lack of both comparative genomic sequence information from close relatives and significant amounts of cDNA evidence, thus limiting the value of the genomic information and also leaving unanswered certain questions, such as the frequency of alternative splicing.</p> <p>Results</p> <p>We addressed the problem of MIC contamination using comparative genomic hybridization with purified MIC and MAC DNA probes against a whole genome oligonucleotide microarray, allowing the identification of 763 genome scaffolds likely to contain MIC-limited DNA sequences. We also employed standard genome closure methods to essentially finish over 60% of the MAC genome. For the improvement of annotation, we have sequenced and analyzed over 60,000 verified EST reads from a variety of cellular growth and development conditions. Using this EST evidence, a combination of automated and manual reannotation efforts led to updates that affect 16% of the current protein-coding gene models. By comparing EST abundance, many genes showing apparent differential expression between these conditions were identified. Rare instances of alternative splicing and uses of the non-standard amino acid selenocysteine were also identified.</p> <p>Conclusion</p> <p>We report here significant progress in genome closure and reannotation of <it>Tetrahymena thermophila</it>. Our experience to date suggests that complete closure of the MAC genome is attainable. Using the new EST evidence, automated and manual curation has resulted in substantial improvements to the over 24,000 gene models, which will be valuable to researchers studying this model organism as well as for comparative genomics purposes.</p

American Society of Clinical Oncology Summit on Addressing Obesity Through Multidisciplinary Provider Collaboration: Key Findings and Recommendations for Action

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139117/1/oby21987.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139117/2/oby21987_am.pd

Comparison of granulocyte colony-stimulating factor (G-CSF)--mobilized peripheral blood progenitor cells and G-CSF--stimulated bone marrow as a source of stem cells in HLA-matched sibling transplantation

AbstractHLA-identical bone marrow or stem cell transplantation from a sibling is the preferred treatment for patients with chronic myelogenous leukemia, bone marrow failure syndromes, relapsed acute leukemia, and specific inborn errors of metabolism. Several groups have shown that granulocyte colony-stimulating factor (G-CSF)--mobilized peripheral blood progenitor cells (PBPCs) obtained from HLA-matched siblings are effective in reconstitution of marrow function after marrow ablative conditioning therapy. To evaluate whether G-CSF treatment before bone marrow harvest leads to enhanced recovery of PBPC counts and recovery from limited graft-versus-host disease (GVHD), we assessed the outcome of a sequential cohort of patients treated identically and then given either G-CSF--mobilized PBPCs or G-CSF--stimulated bone marrow from HLA-identical siblings. We show that the time to neutrophil engraftment is identical in the 2 cohorts, whereas platelet engraftment is earlier with the use of PBPCs. The incidence of acute GVHD was decreased, and that of chronic GVHD significantly decreased, in the group receiving bone marrow. Overall survival was not different between the 2 groups. Thus, G-CSF--stimulated bone marrow offers a source of stem cells that allows for early neutrophil engraftment with a decreased risk of GVHD.Biol Blood Marrow Transplant 2000;6(4A):434-40

Apoptosis signaling proteins as prognostic biomarkers in colorectal cancer: a review.

Colorectal cancer is a leading cause of cancer related mortality in the Western world. In recent years, combination 5-fluorouracil based adjuvant chemotherapy as first line treatment of this disease has led to improved disease free and overall survival. However drug resistance, both innate and acquired, remains an obstacle in the effective treatment of this disease. Apoptotic pathways are frequently altered in both tumor progression and drug resistance; therefore proteins associated with this pathway may have potential as prognostic biomarkers for this disease. Identification of clinical biomarkers that are able to identify patients who are more likely to respond to specific chemotherapy will lead to more personalized, effective, and less toxic therapy. This review focuses on the current status of apoptosis related proteins as biomarkers for colorectal cancer and discusses the possible application of systems approaches in this context

Evolution and Spread of Ebola Virus in Liberia, 2014–2015

The 2013–present Western African Ebola virus disease (EVD) outbreak is the largest ever recorded with >28,000 reported cases. Ebola virus (EBOV) genome sequencing has played an important role throughout this outbreak; however, relatively few sequences have been determined from patients in Liberia, the second worst-affected country. Here, we report 140 EBOV genome sequences from the second wave of the Liberian outbreak and analyze them in combination with 782 previously published sequences from throughout the Western African outbreak. While multiple early introductions of EBOV to Liberia are evident, the majority of Liberian EVD cases are consistent with a single introduction, followed by spread and diversification within the country. Movement of the virus within Liberia was widespread and reintroductions from Liberia served as an important source for the continuation of the already ongoing EVD outbreak in Guinea. Overall, little evidence was found for incremental adaptation of EBOV to the human host.Organismic and Evolutionary Biolog