Habitat use and reproductive success of waterbirds in the human-dominated landscape of North America’s prairies: Using sparse data to inform management

University of Minnesota Ph.D. dissertation. May 2018. Major: Conservation Biology. Advisor: Todd Arnold. 1 computer file (PDF); xi, 186 pages.Information needed to implement effective management strategies requires an understanding of where, when and how target species use habitats available to them to survive and reproduce. I used new approaches for field data collection and analysis for rare and cryptic species to improve understanding of how anthropogenic and natural habitat characteristics affect the habitat use and reproductive success of grassland waterbirds, to better inform management in North America’s Northern Great Plains. Using historical data on waterfowl age ratios at banding and a database of upland shorebird nest records, I identified spatial and temporal variation in upland nesting waterfowl and shorebird fecundity. Specifically, I found positive relationships between vole population irruptions and metrics of fecundity (age ratios and nest survival) in both upland nesting waterfowl and shorebirds, and that fecundity of both groups was tightly tied to wetland conditions; increases in wetland inundation improved dabbling duck fecundity and Marbled Godwits (Limosa fedoa) experienced higher fecundity in territories with greater wetland cover. Density dependent effects were mixed across species. I used occupancy surveys with behavioral indicators of brood presence to assess whether habitat use by conservation concern upland shorebirds and Northern Pintail (Anas acuta) was altered by oil development in the Bakken oil field, using habitat suitability models to account for natural variation in habitat quality. I found reduced habitat use by breeding pairs and/or broods of all five studied species at sites with higher traffic and that Wilson’s phalarope (Phalaropus tricolor) breeding pairs avoided habitat with higher well density. Using behavior to infer brood presence facilitated identifying effects of traffic on brood habitat use where data would otherwise have been too sparse. Finally, I present a new occupancy survey sampling design that improves estimates for rare species. Management for upland-nesting waterbirds should continue to prioritize maintaining the capacity of less permanent wetland basins to rehydrate and active patch management of grassland. Infrastructure and activity that impacts grassland wildlife should be concentrated within corridors on the landscape while conservation should be concentrated in spaces between development corridors

Local control and possibility of tailored salvage after hypofractionated stereotactic radiotherapy of the cavity after brain metastases resection

Source at https://doi.org/10.1002/cam4.1486.In patients undergoing surgical resection of brain metastases, the risk of local recurrence remains high. Adjuvant whole brain radiation therapy (WBRT) can reduce the risk of local relapse but fails to improve overall survival. At two tertiary care centers in Germany, a retrospective study was performed to evaluate the role of hypofractionated stereotactic radiotherapy (HFSRT) in patients with brain metastases after surgical resection. In particular, need for salvage treatment, for example, WBRT, surgery, or stereotactic radiosurgery (SRS), was evaluated. Both intracranial local (LF) and locoregional (LRF) failures were analyzed. A total of 181 patients were treated with HFSRT of the surgical cavity. In addition to the assessment of local control and distant intracranial control, we analyzed treatment modalities for tumor recurrence including surgical strategies and reirradiation. Imaging follow‐up for the evaluation of LF and LRF was available in 159 of 181 (88%) patients. A total of 100 of 159 (63%) patients showed intracranial progression after HFSRT. A total of 81 of 100 (81%) patients received salvage therapy. Fourteen of 81 patients underwent repeat surgery, and 78 of 81 patients received radiotherapy as a salvage treatment (53% WBRT). Patients with single or few metastases distant from the initial site or with WBRT in the past were retreated by HFSRT (14%) or SRS, 33%. Some patients developed up to four metachronous recurrences, which could be salvaged successfully. Eight (4%) patients experienced radionecrosis. No other severe side effects (CTCAE≥3) were observed. Postoperative HFSRT to the resection cavity resulted in a crude rate for local control of 80.5%. Salvage therapy for intracranial progression was commonly needed, typically at distant sites. Salvage therapy was performed with WBRT, SRS, and surgery or repeated HFSRT of the resection cavity depending on the tumor spread and underlying histology. Prospective studies are warranted to clarify whether or not the sequence of these therapies is important in terms of quality of life, risk of radiation necrosis, and likelihood of neurological cause of death

Gut microbiota alteration in adolescent anorexia nervosa does not normalize with short-term weight restoration

Objective Gut microbiota are linked to metabolic function, body weight regulation, and brain and behavioral changes. Alteration of gut microbiota is repeatedly demonstrated in adults with anorexia nervosa (AN) and transplantation of stool from adult patients with AN reduces weight gain, food consumption and food efficiency in germ-free mice. No similar data are available for adolescents, who might differ from adults due to their shorter duration of illness. Method Nineteen female adolescent patients with AN at admission and after short-term weight recovery were included in a longitudinal study and compared to 20 healthy controls (HC). DNA was extracted from stool samples and subjected to 16S rRNA gene sequencing and analysis. Group comparisons, indicator genera and simper analysis were applied. Taxon abundances at admission was used to predict inpatient treatment duration. Results Alpha diversity is increased in patients with AN after short-term weight recovery, while beta diversity shows clear group differences with HC before and after weight gain. A reduction in Romboutsia and taxa belonging to Enterobacteriaceae at both timepoints and an increase in taxa belonging to Lachnospiraceae at discharge are most indicative of patients. Lachnospiraceae abundance at admission helped to predict shorter inpatient treatment duration. Discussion This pilot study provides first evidence of gut microbiota alterations in adolescent patients with AN that do not normalize with weight gain. If verified in larger studies, the predictive power of taxa belonging to Lachnospiraceae for clinical outcome could complement known predictors at admission, inform clinicians and serve as a target for nutritional interventions

Lower serum levels of IL-1β and IL-6 cytokines in adolescents with anorexia nervosa and their association with gut microbiota in a longitudinal study

Introduction Anorexia nervosa (AN) is an often chronic and debilitating psychiatric disease whose etiology is not completely understood. Recently, a potential role of inflammation has emerged in other psychiatric diseases, such as depression, PTSD and schizophrenia. The first results in adults with AN seemed to confirm a low-grade proinflammatory state until recent studies presented more differential findings. Studying adolescents with a shorter illness duration and fewer confounding factors might help elucidate the role of inflammation in the underlying pathophysiology of AN; however, the few available studies in adolescents remain ambiguous, and no longitudinal data are available in this age range. Results TNF-α serum levels were significantly elevated in patients with AN at admission, while IL-1β and IL-6 levels were lower at admission and discharge than in HC. After treatment, we also found significantly elevated levels of IL-6 Rα compared to HC, while IL-15 did not show significant changes. Exploratory analyses revealed positive associations of cytokine and genus-level changes between admission and discharge for IL-1β (Bacteroides) and IL-15 (Romboutsia), and negative associations for IL-15 (Anaerostipes) and TNF-α (uncultured Lachnospiraceae). Conclusion We confirmed a previous finding of elevated levels of TNF-α also in adolescents with AN; however, the reduced IL-1β and IL-6 levels differed from the mostly increased levels found in adults. A mixed pro- and anti-inflammatory state appears to be present in adolescents, potentially due to their shorter illness duration. The gut microbiota, with its regulatory function on cytokine production, might play a role in mediating these inflammatory processes in AN and could offer targets for new therapeutic approaches

Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: a report of the international immuno‐oncology biomarker working group

The clinical significance of the tumor-immune interaction in breast cancer (BC) has been well established, and tumor-infiltrating lymphocytes (TILs) have emerged as a predictive and prognostic biomarker for patients with triple-negative (estrogen receptor, progesterone receptor, and HER2 negative) breast cancer (TNBC) and HER2-positive breast cancer. How computational assessment of TILs can complement manual TIL-assessment in trial- and daily practices is currently debated and still unclear. Recent efforts to use machine learning (ML) for the automated evaluation of TILs show promising results. We review state-of-the-art approaches and identify pitfalls and challenges by studying the root cause of ML discordances in comparison to manual TILs quantification. We categorize our findings into four main topics; (i) technical slide issues, (ii) ML and image analysis aspects, (iii) data challenges, and (iv) validation issues. The main reason for discordant assessments is the inclusion of false-positive areas or cells identified by performance on certain tissue patterns, or design choices in the computational implementation. To aid the adoption of ML in TILs assessment, we provide an in-depth discussion of ML and image analysis including validation issues that need to be considered before reliable computational reporting of TILs can be incorporated into the trial- and routine clinical management of patients with TNBC

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Occupancy Survey Data and analysis code for shorebird and waterfowl habitat use in NW North Dakota, 2014-2015

See Metadata fileData and R code examine quarter-section site occupancy rates of upland nesting waterbirds relative to oil well density and traffic activity to accompany H. Specht PhD Thesis 2018, University of Minnesota.Ducks Unlimited Canada, the National Science Foundation (Grant #00039202), the University of Minnesota Graduate School and the Bell Museum (UMN) provided support to HS and this project

Data and model code for assessing dabbling duck age ratios and corresponding environmental correlates in the North American Prairies, 1969-2015

These files provide model code and data used to assess temporal variation in fecundity data derived from post-breeding banding age ratio data for North American upland nesting duck species. Details can be found in the included metadata file and in related paper.Fecundity estimates for demographic modeling are difficult to acquire at the regional spatial scales that correspond to climate shifts, land use impacts or habitat management programs, yet are important for evaluating such effects. While waterfowl managers have historically used harvest-based age ratios to assess fecundity at continental scales, widely available age ratios from late-summer banding data present an underutilized opportunity to examine a regional fecundity index with broad temporal replication. We used age ratios from banding data and hierarchical mixed-effect models to examine how fecundity of five North American dabbling duck species was affected by temporal variation in hydrological cycles, intra- and inter-specific density dependence and alternate prey availability, and whether those relationships were consistent across a broad geographic area. The data and code for these analysis are included here

Habitat selection and nest survival in two Great Plains shorebirds

As breeding populations of many grassland bird species decline, assessments of breeding habitat selection and reproductive success can provide useful insight into breeding ecology to support conservation delivery. Here, we demonstrate the use of nest location and survival data collated from 20 data contributors across the Prairie Pothole Region of the United States and Canada over a half century to examine habitat selection and nest survival of Western Willets (Tringa semipalmata inornata) and Marbled Godwits (Limosa fedoa), hereafter "willets" and "godwits." Both willets and godwits selected territories with less variation in vegetation height and topography relative to available locations. Willets selected nest sites that were flatter, closer to wetlands, and had shorter vegetation than Marbled Godwits, while godwits selected territories with greater wetland cover and shorter vegetation. Despite differences in fine-scale habitat selection, willets and godwits experienced similar daily nest survival rates and ecological drivers of nest survival. Nest success for the entire nest exposure period was estimated to be 0.521 (95% credible interval: 0.39-0.65) for willets and 0.562 (95% credible interval: 0.42-0.70) for godwits. Nest survival for both species increased with nest age and distance from the nest to the nearest wetland edge, while nest survival of godwits declined with conspecific breeding density. These relationships, as well as a weaker positive effect of microtine rodent abundance on nest survival, resembled drivers of upland nesting waterfowl reproductive success in the same region, which we attribute to their shared nest predators. Nest survival analyses of our collaborative dataset required substantial consideration of biases emerging from different data collection methods, ultimately reaffirming the importance of nest aging techniques in proper nest fate assignment. Analysis of compiled datasets using emerging analysis methods will continue to grow our understanding of the ecology of data sparse species