Impacts of non-renewable resource extraction on shrubland songbird nest success and abundance

Shrubland songbirds are a highly imperiled guild across much of North America due to wide-scale land use changes and resulting loss of shrubland habitat. Land management practices which produce early-successional habitat, namely field abandonment and clearcut timber harvests, have become increasingly uncommon in the eastern United States, and natural maintenance processes such as fires and floods are often suppressed. The Appalachian region is rich in natural resources; it has historically seen high amounts of surface mining for coal and is currently experiencing prolific development of shale gas. Both of these practices alter local habitats and the landscape, and it is essential to understand their impacts on shrubland songbirds in order to inform conservation efforts for this declining guild. Research for this thesis was composed of three studies during the breeding seasons of 2012-2013 on four shrubland sites in southwestern Pennsylvania and the northern panhandle of West Virginia. This work aimed to fill knowledge gaps in shrubland songbird ecology and responses to extractive land uses. In my second chapter I focus on habitat selection patterns and nesting ecology of one species, the Blue-winged Warbler (Vermivora cyanoptera). This species has not been studied much outside of its antagonistic relationship to the closely related and highly imperiled Golden-winged Warbler (Vermivora chrysoptera). A quantitative habitat selection study for the species has never been done, although knowing habitat requirements is key to effective conservation measures. I found significant differences in vegetative structure between territories and random plots using non-parametric MANOVA, indicating strong patterns of territory selection. Blue-winged Warblers placed territories in later stages of succession relative to the sites as a whole, having more woody structure, taller vegetation, more shrub, sapling, and canopy cover, and were closer to forest edge than random points. My third chapter is a study on the impact of unconventional shale gas development on shrubland songbird nest success, abundance, and community composition. The practice of unconventional gas development is new to the eastern United States and has become controversial due to concern over environmental impacts, but few studies have been done on the potential effects to terrestrial biota, especially in the east. My objective was to fill a specific research gap, the impacts of development on shrubland songbirds in an already-fragmented landscape context, because this is where both shale gas development and shrubland songbirds are more likely to occur. During the 2013 breeding season, I determined the effects of gas development presence at different spatial scales on shrubland songbird nest success and community dynamics and quantified noise and light emissions from developed pads. There were no differences in noise or light emissions between impacted and non-impacted shrublands, or at a developed site with increasing distance from the wellpad. The presence of gas wells and related infrastructure were important influences on Field Sparrow (Spizella pusilla) nest success; survival was reduced close to the wellpad and increased near pipelines and roads. However, nest survival was higher site-wide for the Field Sparrow and other early successional species on the impacted site than on non-impacted shrublands in the region. Nest predators were important in explaining nest survival variation at the site-level. Within the developed site, nest abandonment was a more likely force near wells and a paved road, while predation better explained variation in survival by distance to the pipeline and unpaved access road. Avian communities significantly differed between impacted and non-impacted sites but the differences were not extractable from vegetative differences. Shannon\u27s diversity and species richness did not differ between impacted and non-impacted sites and had no significant trend with increasing distance from the developed well. Although unconventional gas extraction is new to the region, surface mining has historically been a common practice in Appalachia. Once mining has ceased, these areas stay in early succession conditions for extended durations due to poor topsoil quality, providing habitat for early-successional species which endures on the landscape much longer than habitats in abandoned fields or recent clearcuts. Reclamation of surface mines to a vegetated state is mandated by federal law, but questions have been raised on the habitat quality of the resulting areas. Many studies have assessed the use of former surface mines by various species and the success of grassland-nesting songbirds in these habitats, but none have quantitatively compared nest survival and avian community composition between former surface mines and non-mined shrublands. In my fourth chapter, I determined the utility of former surface mines as breeding habitat for shrubland songbirds. I performed site-level comparisons of community composition, species abundances, and nest survival of three focal species to determine if these metrics differed between former surface mines and non-mined shrublands and also between a reclaimed and a non-reclaimed former surface mine. Whether a site was mined or not was an important factor influencing nest success, as was whether a mined site was reclaimed or not. Daily survival rates of nests for all three species were higher on mined sites and higher on the reclaimed former surface mine. Avian communities did not differ between mined and non-mined sites. Community composition on the reclaimed and non-reclaimed former surface mine sites differed, but most species were detected on both. Vegetative conditions on mined sites were broader and encompassed the range of structure at non-mined sites, providing similar habitat for species found at unmined shrublands, plus more. All sites significantly differed in vegetative characteristics. Higher nest survival on mined sites may result from the higher vegetative heterogeneity there. The reclaimed site may have had higher nest survival due to lower rodent and corvid nest predator abundances. This research informs conservation efforts of the declining early-successional songbird guild and answers questions about the impacts of common energy extraction practices on these species. Blue-winged Warblers select conditions of later succession for nesting, which demonstrates that the early-successional sere should not be treated as a homogeneous management unit which spans only a few years after disturbance, but maintained over a range of ages on the landscape. Unconventional gas development in an already-fragmented landscape context may not degrade shrubland songbird habitat as much as it does interior forests, but does impact nest success and results in the displacement of large amounts of habitat. Former surface mines provide productive, lasting habitats for breeding shrubland songbirds that accommodate the early-successional songbird guild comparably to unmined shrublands. Shrubland songbirds can coexist with the ever-expanding extraction of fossil fuels from Appalachia if their habitat requirements are met. These species rely upon ephemeral conditions, and the key to retaining them remains management of the landscape in a dynamic fashion to provide ample habitat

Assessment of the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire for use in patients after neck dissection for head and neck cancer

BackgroundIn this cross‐sectional study, the sensibility, test‐retest reliability, and validity of the Disabilities of the Arm, Shoulder, and Hand (DASH) questionnaire were assessed in patients who underwent neck dissection.MethodsSensibility was assessed with a questionnaire. Test‐retest reliability was performed with completion of the DASH questionnaire 2 weeks after initial completion; validity, by evaluating differences in scores between patients undergoing different types of neck dissections and correlating DASH scores with Neck Dissection Impairment Index (NDII) scores.ResultsThe DASH questionnaire met sensibility criteria. For test‐retest reliability analysis, the intraclass coefficient was 0.91. The DASH questionnaire showed differences between patients who underwent accessory nerve‐sacrifice and nerve‐sparing neck dissection. DASH questionnaire scores strongly correlated with NDII scores (r = ‐0.86).ConclusionAlthough this study provides preliminary data on some psychometric properties of the DASH questionnaire in patients who have undergone a neck dissection, further assessment of responsiveness and other properties are required. © 2014 Wiley Periodicals, Inc. Head Neck 37: 234‐242, 2015Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110617/1/hed23593.pd

Tumor-expressed adrenomedullin accelerates breast cancer bone metastasis

INTRODUCTION: Adrenomedullin (AM) is secreted by breast cancer cells and increased by hypoxia. It is a multifunctional peptide that stimulates angiogenesis and proliferation. The peptide is also a potent paracrine stimulator of osteoblasts and bone formation, suggesting a role in skeletal metastases-a major site of treatment-refractory tumor growth in patients with advanced disease. METHODS: The role of adrenomedullin in bone metastases was tested by stable overexpression in MDA-MB-231 breast cancer cells, which cause osteolytic bone metastases in a standard animal model. Cells with fivefold increased expression of AM were characterized in vitro, inoculated into immunodeficient mice and compared for their ability to form bone metastases versus control subclones. Bone destruction was monitored by X-ray, and tumor burden and osteoclast numbers were determined by quantitative histomorphometry. The effects of AM overexpression on tumor growth and angiogenesis in the mammary fat pad were determined. The effects of AM peptide on osteoclast-like multinucleated cell formation were tested in vitro. A small-molecule AM antagonist was tested for its effects on AM-stimulated ex vivo bone cell cultures and co-cultures with tumor cells, where responses of tumor and bone were distinguished by species-specific real-time PCR. RESULTS: Overexpression of AM mRNA did not alter cell proliferation in vitro, expression of tumor-secreted factors or cell cycle progression. AM-overexpressing cells caused osteolytic bone metastases to develop more rapidly, which was accompanied by decreased survival. In the mammary fat pad, tumors grew more rapidly with unchanged blood vessel formation. Tumor growth in the bone was also more rapid, and osteoclasts were increased. AM peptide potently stimulated bone cultures ex vivo; responses that were blocked by small-molecule adrenomedullin antagonists in the absence of cellular toxicity. Antagonist treatment dramatically suppressed tumor growth in bone and decreased markers of osteoclast activity. CONCLUSIONS: The results identify AM as a target for therapeutic intervention against bone metastases. Adrenomedullin potentiates osteolytic responses in bone to metastatic breast cancer cells. Small-molecule antagonists can effectively block bone-mediated responses to tumor-secreted adrenomedullin, and such agents warrant development for testing in vivo

The Fire and Tree Mortality Database, for Empirical Modeling of Individual Tree Mortality After Fire

Wildland fires have a multitude of ecological effects in forests, woodlands, and savannas across the globe. A major focus of past research has been on tree mortality from fire, as trees provide a vast range of biological services. We assembled a database of individual-tree records from prescribed fires and wildfires in the United States. The Fire and Tree Mortality (FTM) database includes records from 164,293 individual trees with records of fire injury (crown scorch, bole char, etc.), tree diameter, and either mortality or top-kill up to ten years post-fire. Data span 142 species and 62 genera, from 409 fires occurring from 1981-2016. Additional variables such as insect attack are included when available. The FTM database can be used to evaluate individual fire-caused mortality models for pre-fire planning and post-fire decision support, to develop improved models, and to explore general patterns of individual fire-induced tree death. The database can also be used to identify knowledge gaps that could be addressed in future research

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Sensitivity to Gravitational Waves from Compact Binary Coalescences Achieved during LIGO's Fifth and Virgo's First Science Run

We summarize the sensitivity achieved by the LIGO and Virgo gravitational wave detectors for compact binary coalescence (CBC) searches during LIGO's fifth science run and Virgo's first science run. We present noise spectral density curves for each of the four detectors that operated during these science runs which are representative of the typical performance achieved by the detectors for CBC searches. These spectra are intended for release to the public as a summary of detector performance for CBC searches during these science runs.Comment: 12 pages, 5 figure

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin