Assessing spatio-temporal patterns of forest decline across a diverse landscape in the Klamath Mountains using a 28-year Landsat time-series analysis

Rates of tree mortality in California and the Pacific Northwest have greatly increased in recent years, driven largely by pest and pathogen outbreaks as well as the effects of hotter, warmer droughts. While there have been a multitude of regional-scale assessments of mortality and forest decline, landscape-level studies are necessary to better identify forests that are most vulnerable to decline and to anticipate future changes. This need is particularly notable in the remote and little-studied mountains of northwest California, which are renowned for their diverse, heterogeneous vegetation types. A recent observation of elevated levels of Shasta red fir (Abies magnifica var. shastensis) mortality in a central part of this region – the Russian Wilderness – appears to mirror the timing of these larger forest mortality events and has highlighted the need to investigate if recent levels of mortality are historically unusual. The main objectives of my study were to (1) characterize contemporary tree mortality and determine potential drivers of that mortality using field-measured data, (2) integrate both field-measured data and annual LandTrendr data to assess temporal and spatial patterns of the extent and magnitude of forest decline, (3) assess the relationship between topographic and structural attributes with forest decline, and (4) determine whether climate is a potential driver of forest decline. To characterize contemporary tree mortality and determine potential drivers of that mortality, I established 142 field plots in the summer of 2015 measuring tree health and presence of any pests and pathogens on canopy tree species. Next, I used annualized LandTrendr algorithms across a 28-year time period (1986-2014) coupled with a regional forest type map to determine the timing, extent, and magnitude of canopy decline within each forest type. To assess potential drivers of canopy decline and identify specific vulnerabilities to drought, I used PRISM climate data and random forest classification using topographic and stand structure attributes. Plot data showed the highest proportions of mortality occurred in subalpine fir (Abies lasiocarpa, 35.3%) and Shasta red fir (28.6%), with evidence of fir engraver beetle (Scolytus ventralis) and Wien’s dwarf mistletoe (Arceuthobium abietinum subsp. wiensii) on many Shasta red fir individuals (34.7% and 20.4%, respectively). Forest decline was five times higher in the last two years of the time series (2013-2014) than in the previous twenty-six years. The greatest magnitude of decline was found in the red fir and subalpine conifer forest types, findings supported by my field-measured data. Canopy decline was greater at higher elevations, in denser canopies and in stands with larger trees. I did not detect any relationships between annual climate variables and forest decline, possibly due to a discrepancy between the course spatial scale of the climate data and fine-grained scale of forest disturbance, or because only two years exhibited pronounced canopy decline. My study demonstrates effectiveness in characterizing forest decline in a highly diverse landscape using a remote sensing approach and highlights the complexity of climate, pests and pathogens, stand structure, and topography as they relate to tree mortality and forest decline

Development of a new molecular typing method of Salmonella spp. based on SNPs detection

The aim of this study was to develop a new molecular typing method of Salmonella spp. based on the detection of point mutations (Single Nucleotide Polymorphisms or SNPs) in the genome. Several genomic regions (ManB, InvA, pduF) were sequenced in strains isolated from pig, the sequences were aligned and 49 point mutations were identified. A panel of 12 SNPs giving a genotype characteristic of a particular serotype was selected. Until now, thes selected SNPs were unable to distinguish the all strains. Therefore, additional SNPs must be selected

Analytic curves in algebraic varieties over number fields

We establish algebraicity criteria for formal germs of curves in algebraic varieties over number fields and apply them to derive a rationality criterion for formal germs of functions, which extends the classical rationality theorems of Borel-Dwork and P\'olya-Bertrandias valid over the projective line to arbitrary algebraic curves over a number field. The formulation and the proof of these criteria involve some basic notions in Arakelov geometry, combined with complex and rigid analytic geometry (notably, potential theory over complex and $p$-adic curves). We also discuss geometric analogues, pertaining to the algebraic geometry of projective surfaces, of these arithmetic criteria.Comment: 55 pages. To appear in "Algebra, Arithmetic, and Geometry: In Honor of Y.i. Manin", Y. Tschinkel & Yu. Manin editors, Birkh\"auser, 200

Single Strand Annealing Plays a Major Role in RecA-Independent Recombination between Repeated Sequences in the Radioresistant Deinococcus radiodurans Bacterium

© 2015 Ithurbide et al. The bacterium Deinococcus radiodurans is one of the most radioresistant organisms known. It is able to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Our work aims to highlight the genes involved in recombination between 438 bp direct repeats separated by intervening sequences of various lengths ranging from 1,479 bp to 10,500 bp to restore a functional tetA gene in the presence or absence of radiation-induced DNA double strand breaks. The frequency of spontaneous deletion events between the chromosomal direct repeats were the same in recA+ and in ΔrecA, ΔrecF, and ΔrecO bacteria, whereas recombination between chromosomal and plasmid DNA was shown to be strictly dependent on the RecA and RecF proteins. The presence of mutations in one of the repeated sequence reduced, in a MutS-dependent manner, the frequency of the deletion events. The distance between the repeats did not influence the frequencies of deletion events in recA+as well in ΔrecA bacteria. The absence of the UvrD protein stimulated the recombination between the direct repeats whereas the absence of the DdrB protein, previously shown to be involved in DNA double strand break repair through a single strand annealing (SSA) pathway, strongly reduces the frequency of RecA- (and RecO-) independent deletions events. The absence of the DdrB protein also increased the lethal sectoring of cells devoid of RecA or RecO protein. γ-irradiation of recA+cells increased about 10-fold the frequencies of the deletion events, but at a lesser extend in cells devoid of the DdrB protein. Altogether, our results suggest a major role of single strand annealing in DNA repeat deletion events in bacteria devoid of the RecA protein, and also in recA+bacteria exposed to ionizing radiation

Midwest Evaluation of the Adult Functioning of Former Foster Youth

The Midwest Evaluation of the Adult Functioning of Former Foster Youth (Midwest Study) is a prospective study that has been following a sample of young people from Iowa, Wisconsin, and Illinois as they transition out of foster care into adulthood. It is a collaborative effort involving Chapin Hall at the University of Chicago; Partners for Our Children at the University of Washington, Seattle; the University of Wisconsin Survey Center; and the public child welfare agencies in Illinois, Iowa, and Wisconsin.The Midwest Study provides a comprehensive picture of how foster youth are faring during this transition since the Foster Care Independence Act of 1999 became law. Foster youth in Iowa, Wisconsin, and Illinois were eligible to participate in the study if they had entered care before their 16th birthday, were still in care at age 17, and had been removed from home for reasons other than delinquency. Baseline survey data were collected from 732 study participants when they were 17 or 18 years old. Study participants were re-interviewed at ages 19 (n = 603), 21 (n = 591), and 23 or 24 (n = 602). A fifth wave of survey data will be collected when study participants are 25 or 26 years old.Because many of the questions Midwest Study participants were also asked as part of the National Longitudinal Study of Adolescent Health, it is possible to make comparisons between this sample of former foster youth and a nationally representative sample of young people in the general population. These comparisons indicate that young people who have aged out of foster care are faring poorly as a group relative to their peers across a variety of domains.The Midwest Study also presents a unique opportunity to compare the outcomes of young people from one state (i.e., Illinois) that allows foster youth to remain in care until their 21st birthday to the outcomes of young people from two other states (i.e., Iowa and Wisconsin) in which foster youth generally age out when they are 18 years old. The data suggest that extending foster care until age 21 may be associated with better outcomes, at least in some domains

Assessing an Extension Plant Pest Diagnostic Center for Commercial Clients: Satisfaction, Savings, and Success

The descriptive-correlational study reported here sought to assess the effectiveness of the Extension Plant Pest Diagnostic Center (PPDC) for Tennessee\u27s commercial clients. These clients are served through one-on-one consultation regarding their individual plant or household and structural pest problems through submitted samples. The results from a mailed questionnaire showed that the majority of PPDC clients felt that the information was quick enough for their needs. While one-third of the 61 respondents stated that the PPDC recommendations saved them money, only one in 10 estimated the amount of money they saved. Suggestions for future PPDC evaluation studies are discussed

Iterative Approximate Consensus in the presence of Byzantine Link Failures

This paper explores the problem of reaching approximate consensus in synchronous point-to-point networks, where each directed link of the underlying communication graph represents a communication channel between a pair of nodes. We adopt the transient Byzantine link failure model [15, 16], where an omniscient adversary controls a subset of the directed communication links, but the nodes are assumed to be fault-free. Recent work has addressed the problem of reaching approximate consen- sus in incomplete graphs with Byzantine nodes using a restricted class of iterative algorithms that maintain only a small amount of memory across iterations [22, 21, 23, 12]. However, to the best of our knowledge, we are the first to consider approximate consensus in the presence of Byzan- tine links. We extend our past work that provided exact characterization of graphs in which the iterative approximate consensus problem in the presence of Byzantine node failures is solvable [22, 21]. In particular, we prove a tight necessary and sufficient condition on the underlying com- munication graph for the existence of iterative approximate consensus algorithms under transient Byzantine link model. The condition answers (part of) the open problem stated in [16].Comment: arXiv admin note: text overlap with arXiv:1202.609

Monitoring Partially Synchronous Distributed Systems using SMT Solvers

In this paper, we discuss the feasibility of monitoring partially synchronous distributed systems to detect latent bugs, i.e., errors caused by concurrency and race conditions among concurrent processes. We present a monitoring framework where we model both system constraints and latent bugs as Satisfiability Modulo Theories (SMT) formulas, and we detect the presence of latent bugs using an SMT solver. We demonstrate the feasibility of our framework using both synthetic applications where latent bugs occur at any time with random probability and an application involving exclusive access to a shared resource with a subtle timing bug. We illustrate how the time required for verification is affected by parameters such as communication frequency, latency, and clock skew. Our results show that our framework can be used for real-life applications, and because our framework uses SMT solvers, the range of appropriate applications will increase as these solvers become more efficient over time.Comment: Technical Report corresponding to the paper accepted at Runtime Verification (RV) 201

Exacerbated metastatic disease in a mouse mammary tumor model following latent gammaherpesvirus infection

BACKGROUND: Controversy exists as to the ability of human gammaherpesviruses to cause or exacerbate breast cancer disease in patients. The difficulty in conducting definitive human studies can be overcome by investigating developing breast cancer in a mouse model. In this study, we utilized mice latently infected with murine gammaherpesvirus 68 (HV-68) to question whether such a viral burden could exacerbate metastatic breast cancer disease using a mouse mammary tumor model. RESULTS: Mice latently infected with HV-68 had a similar primary tumor burden, but much greater metastatic disease, when compared to mock treated mice given the transplantable tumor, 4 T1. This was true for lung lesions, as well as secondary tumor masses. Increased expression of pan-cytokeratin and VEGF-A in tumors from HV-68 infected mice was consistent with increased metastatic disease in these animals. Surprisingly, no viral particles could be cultured from tumor tissues, and the presence of viral DNA or RNA transcripts could not be detected in primary or secondary tumor tissues. CONCLUSIONS: Latent HV-68 infection had no significant effect on the size of primary 4 T1 mammary tumors, but exacerbated the number of metastatic lung lesions and secondary tumors when compared to mock treated mice. Increased expression of the tumor marker, pan-cytokeratin, and VEGF-A in tumors of mice harboring latent virus was consistent with an exacerbated metastatic disease. Mechanisms responsible for this exacerbation are indirect, since no virus could be detected in cancerous tissues

Geodesic equations and algebro-geometric methods

For an investigation of the physical properties of gravitational fields the observation of massive test particles and light is very useful. The characteristic features of a given space-time may be decoded by studying the complete set of all possible geodesic motions. Such a thorough analysis can be accomplished most effectively by using analytical methods to solve the geodesic equation. In this contribution, the use of elliptic functions and their generalizations for solving the geodesic equation in a wide range of well known space-times, which are part of the general Pleba\'nski-Demia\'nski family of solutions, will be presented. In addition, the definition and calculation of observable effects like the perihelion shift will be presented and further applications of the presented methods will be outlined.Comment: 8 pages, no figures; based on presentation at the conference "Relativity and Gravitation: 100 Years after Einstein in Prague," Prague, 2012. Relativity and Gravitation, volume 157 of Springer Proceedings in Physics, p 91. Springer International Publishing, 201