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Summary: Understanding the genetic basis of how plants defend against pathogens is important to monitor and maintain resilient tree populations. Swiss needle cast (SNC) and Rhabdocline needle cast (RNC) epidemics are responsible for major damage of forest ecosystems in North America.Here we investigate the genetic architecture of tolerance and resistance to needle cast diseases in Douglas‐fir (Pseudotsuga menziesii) caused by two fungal pathogens: SNC caused by Nothophaeocryptopus gaeumannii, and RNC caused by Rhabdocline pseudotsugae.We performed case–control genome‐wide association analyses and found disease resistance and tolerance in Douglas‐fir to be polygenic and under strong selection. We show that stomatal regulation as well as ethylene and jasmonic acid pathways are important for resisting SNC infection, and secondary metabolite pathways play a role in tolerating SNC once the plant is infected. We identify a major transcriptional regulator of plant defense, ERF1, as the top candidate for RNC resistance.Our findings shed light on the highly polygenic architectures underlying fungal disease resistance and tolerance and have important implications for forestry and conservation as the climate changes. [ABSTRACT FROM AUTHOR]

This work describes particle-resolved simulations of a single aluminum particle within a larger layer of particles that is interacting with a strong nitromethane shock. The objective is to observe how varying the particle's volume fraction within a planar particle curtain changes the deformation of the particles as well as the fluid dynamics around them. First the isolated particle limit, when the distance between the neighbors is very large, is simulated; this is followed by simulating a single-layer of particles subjected to a planar shock propagating normal to the layer. Several initial particle volume fractions of the curtain are considered, and the results are compared and discussed. The results show that the presence and proximity of neighboring particles influence the shape and magnitude of the particle's plastic deformation. The presence of neighboring particles also increases the initial average pressure within the particle during shock interaction as well as the average velocity of the particle afterwards. The strength of the reflected shock from the curtain of particles increases in magnitude and becomes more planar as the volume fraction increases due to neighboring particles' individual reflections that coalesce to form a singular planar shock. The results obtained provide valuable insight into the microscale physics of shock interaction with an array of deformable particles. [ABSTRACT FROM AUTHOR]

Nontuberculous mycobacteria represent an uncommon but important cause of infection of the musculoskeletal system. Such infections require aggressive medical and surgical treatment, and cases are often complicated by delayed diagnosis. We retrospectively reviewed all 14 nonspinal cases of nontuberculous mycobacterial musculoskeletal infections treated over 6 years by orthopedic surgeons at a university-affiliated tertiary referral center. All patients required multiple antimicrobial agents along with aggressive surgical treatment; 13 of 14 patients ultimately achieved cure. Four patients required amputation to control the infection. Half these patients were immunosuppressed by medications or other medical illness when they sought care at the referral center. Six cases involved joint prostheses; all ultimately required hardware removal and placement of an antimicrobial spacer for eradication of infection. Our findings highlight the importance of vigilance for nontuberculous mycobacterial musculoskeletal infection, particularly in patients who are immunosuppressed or have a history of musculoskeletal surgery. [ABSTRACT FROM AUTHOR]

Many important explosives and energetics applications involve multiphase formulations employing dispersed particles. While considerable progress has been made toward developing mathematical models and computational methodologies for these flows, significant challenges remain. In this work, we apply a mathematical model for compressible multiphase flows with dispersed particles to existing shock and explosive dispersal problems from the literature. The model is cast in an Eulerian framework, treats all phases as compressible, is hyperbolic, and satisfies the second law of thermodynamics. It directly applies the continuous-phase pressure gradient as a forcing function for particle acceleration and thereby retains relaxed characteristics for the dispersed particle phase that remove the constituent material sound velocity from the eigenvalues. This is consistent with the expected characteristics of dispersed particle phases and can significantly improve the stable time-step size for explicit methods. The model is applied to test cases involving the shock and explosive dispersal of solid particles and compared to data from the literature. Computed results compare well with experimental measurements, providing confidence in the model and computational methods applied. [ABSTRACT FROM AUTHOR]

A paradox in monoclonal antibody (mAb) therapy is that despite the well-documented tolerogenic properties of deaggregated IgG, most therapeutic IgG mAb induce anti-mAb responses. To analyze CD4 T cell reactions against IgG in various physical states, we developed an adoptive transfer model using CD4+ T cells specific for a Vκ region-derived peptide in the hapten-specific IgG mAb 36–71. We found that heat-aggregated or immune complexes (IC) of mAb 36–71 elicited anti-idiotypic (anti-Id) antibodies, while the deaggregated form was tolerogenic. All 3 forms of mAb 36–71 induced proliferation of cognate CD4+ T cells, but the aggregated and immune complex forms drove more division cycles and induced T follicular helper cells (TFH) development more effectively than did the deaggregated form. These responses occurred despite no adjuvant and no or only trace levels of endotoxin in the preparations. Physical analyses revealed large differences in micron- and nanometer-sized particles between the aggregated and IC forms. These differences may be functionally relevant, as CD4+ T cell proliferation to aggregated, but not IC mAb 36–71, was nearly ablated upon peritoneal injection of B cell-depleting antibody. Our results imply that, in addition to denatured aggregates, immune complexes formed in vivo between therapeutic mAb and their intended targets can be immunogenic. [ABSTRACT FROM AUTHOR]

Bedrock fracture systems facilitate weathering, allowing fresh mineral surfaces to interact with corrosive waters and biota from Earth's surface, while simultaneously promoting drainage of chemically equilibrated fluids. We show that topographic perturbations to regional stress fields explain bedrock fracture distributions, as revealed by seismic velocity and electrical resistivity surveys from three landscapes. The base of the fracture-rich zone mirrors surface topography where the ratio of horizontal compressive tectonic stresses to near-surface gravitational stresses is relatively large, and it parallels the surface topography where the ratio is relatively small. Three-dimensional stress calculations predict these results, suggesting that tectonic stresses interact with topography to influence bedrock disaggregation, groundwater flow, chemical weathering, and the depth of the "critical zone" in which many biogeochemical processes occur. [ABSTRACT FROM AUTHOR]

The success of conifers over much of the world's terrestrial surface is largely attributable to their tolerance to cold stress (i.e., cold hardiness). Due to an increase in climate variability, climate change may reduce conifer cold hardiness, which in turn could impact ecosystem functioning and productivity in conifer-dominated forests. The expression of cold hardiness is a product of environmental cues (E), genetic differentiation (G), and their interaction (G × E), although few studies have considered all components together. To better understand and manage for the impacts of climate change on conifer cold hardiness, we conducted a common garden experiment replicated in three test environments (cool, moderate, and warm) using 35 populations of coast Douglas-fir ( Pseudotsuga menziesii var. menziesii) to test the hypotheses: (i) cool-temperature cues in fall are necessary to trigger cold hardening, (ii) there is large genetic variation among populations in cold hardiness that can be predicted from seed-source climate variables, (iii) observed differences among populations in cold hardiness in situ are dependent on effective environmental cues, and (iv) movement of seed sources from warmer to cooler climates will increase risk to cold injury. During fall 2012, we visually assessed cold damage of bud, needle, and stem tissues following artificial freeze tests. Cool-temperature cues (e.g., degree hours below 2 °C) at the test sites were associated with cold hardening, which were minimal at the moderate test site owing to mild fall temperatures. Populations differed 3-fold in cold hardiness, with winter minimum temperatures and fall frost dates as strong seed-source climate predictors of cold hardiness, and with summer temperatures and aridity as secondary predictors. Seed-source movement resulted in only modest increases in cold damage. Our findings indicate that increased fall temperatures delay cold hardening, warmer/drier summers confer a degree of cold hardiness, and seed-source movement from warmer to cooler climates may be a viable option for adapting coniferous forest to future climate. [ABSTRACT FROM AUTHOR]

Invertebrates dominate many terrestrial ecosystems in terms of biomass, and they also structure ecosystems through their roles as pollinators, detritivores, primary consumers, predators and prey. Invasive rodents (rats and mice) are known to have detrimental effects on many island invertebrates, although these effects are seldom quantified or ecologically understood. Here we provide evidence of the effects of invasive rats ( Rattus spp.) on island invertebrate populations using a large-scale natural experiment. We investigated the effects of invasive rats on Falkland camel crickets ( Parudenus spp.) in the Falkland Islands (South Atlantic) by comparing an index of camel cricket relative abundance between 18 rat-infested islands, six rat-eradicated islands and 13 naturally rat-free islands (in total, 37 islands). Our study provided two key results. First, camel crickets were up to an order of magnitude more abundant on rat-free islands than on rat-infested or rat-eradicated islands. This difference was larger in native tussac grass Poa flabellata than in other vegetation types. Second, camel cricket populations recovered after rat eradication, because the relative abundance of camel crickets on rat-eradicated islands was intermediate between those of naturally rat-free and rat-infested islands, and among rat-eradicated islands relative abundance was lowest where rats had been cleared most recently. Our results demonstrate severe suppression of a superabundant and large-bodied island endemic invertebrate by invasive rodents, and its prompt recovery after rodent eradication. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the expression of biomarkers of implantation, glycodelin A (GdA), osteopontin (OPN), lysophosphatidic acid receptor 3 (LPA3), and HOXA10, in eutopic endometrium of women with and without endometriosis.Design: Prospective observational study.Setting: Clinical research center.Patient(s): Twenty-four women with endometriosis and 23 healthy volunteers of similar age.Intervention(s): Secretory phase endometrial biopsy.Main Outcome Measure(s): Expression of immunohistochemical staining intensity and localization of GdA, OPN, LPA3, and HOXA10 in eutopic endometrium.Result(s): Endometrial GdA expression was significantly reduced in patients after cycle day 22. The endometrium from women with endometriosis also showed decreased expression of OPN in the late secretory phase and LPA3 and HOXA10 expression in the midsecretory and late secretory phases.Conclusion(s): The decreased expression of these four biomarkers of implantation may indicate impaired endometrial receptivity in patients with endometriosis, providing one explanation for the subfertility observed even in women with few pelvic implants. Because many of these markers are P dependent, these findings suggest the possibility of reduced endometrial P action in this population. [ABSTRACT FROM AUTHOR]

1. Maternal effects describe how mothers influence offspring life histories. In many taxa, maternal effects arise by differential resource allocation to young, often identified by variation in propagule size, and which affects individual traits and population dynamics. 2. Using a laboratory model system, the soil mite Sancassania berlesei, we show that, controlling for egg size, older mothers lay eggs that hatch later, develop more slowly, and mature at larger body sizes. 3. Such differences in life histories lead to marked population dynamical effects lasting for multiple generations, as evidenced by an experiment initiated with similarly sized eggs that came from young or old mothers. Differences in maturation from the initial cohort led to differences in population structure and life history that propagated the initial differences over time. 4. Maternal-age effects, which are not related to gross provisioning of the egg and are therefore phenotypically cryptic, can have profound implications for population dynamics, especially if environmental variation can affect the age structure of the adult population. [ABSTRACT FROM AUTHOR]

We present a new instrument, Hoxotope, for the in situ measurement of H2O and its heavy deuterium isotopologue (HDO) in the upper troposphere and lower stratosphere aboard the NASA WB-57. Sensitive measurements of δD are accomplished through the vacuum UV photolysis of water followed by laser-induced fluorescence detection of the resultant OH and OD photofragments. The photolysis laser-induced fluorescence technique can obtain S/N>20 for 1 ppbv HDO and S/N>30 for 5 ppmv H2O for 10 s data, providing the sensitivity required for δD measurements in the tropopause region. The technique responds rapidly to changing water concentrations due to its inherently small sampling volume, augmented by steps taken to minimize water uptake on instrument plumbing. Data from the summer 2005 Aura Validation Experiment Water Isotope Intercomparison Flights (AVE-WIIF) out of Houston, TX show agreement for H2O between Hoxotope and the Harvard water vapor instrument and for HDO between Hoxotope and the Harvard ICOS water isotope instrument, to within stated instrument uncertainties. The successful intercomparison validates Hoxotope as a credible source of δD data in the upper troposphere and lower stratosphere. [ABSTRACT FROM AUTHOR]

Climates are expected to warm considerably over the next century, resulting in expectations that plant populations will not be adapted to future climates. We estimated the risk of maladaptation of current populations of coastal Douglas-fir ( Pseudotsuga menziesii var. menziesii) to future climates as the proportion of nonoverlap between two normal distributions where the means and genetic variances of current and future populations are determined from genecological models derived from seedling common garden studies. The risk of maladaptation was large for most traits when compared with the risk associated with current transfers within seed zones, particularly for the more drastic climate change scenario. For example, the proportion of nonoverlap for a composite trait representing bud set, emergence, growth, and root : shoot ratio was as high as 0.90. We recommend augmenting within-population variation by mixing local populations with some proportion of populations from lower elevations and further south. Populations expected to be adapted to climates a century from now come from locations as far down in elevation as 450–1130 m and as far south in latitude as 1.8–4.9°. [ABSTRACT FROM AUTHOR]

Genetic variation in fall cold damage in coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. menziesii) was measured by exposing excised branches of seedlings from 666 source locations grown in a common garden to freezing temperatures in a programmable freezer. Considerable variation was found among populations in fall cold hardiness of stems, needles, and buds compared with bud burst, bud set, and biomass growth after 2 years. Variation in fall cold hardiness was strongly correlated (r = 0.67) with cold-season temperatures of the source environment. Large population differences corresponding with environmental gradients are evidence that natural selection has been important in determining genetic variation in fall cold hardiness, much more so than in traits of bud burst (a surrogate for spring cold hardiness), bud set, and growth. Seed movement guidelines and breeding zones may be more restrictive when considering genetic variation in fall cold hardiness compared with growth, phenology, or spring cold hardiness. A regional stratification system based on ecoregions with latitudinal and elevational divisions, and roughly corresponding with breeding zones used in Oregon and Washington, appeared to be adequate for minimizing population differences within regions for growth and phenology, but perhaps not fall cold hardiness. Although cold hardiness varied among populations, within-population and within-region variation is sufficiently large that responses to natural or artificial selection may be readily achieved. [ABSTRACT FROM AUTHOR]

The phenology of diameter-growth cessation in trees will likely play a key role in mediating species and ecosystem responses to climate change. A common expectation is that warming will delay cessation, but the environmental and genetic influences on this process are poorly understood. We modeled the effects of temperature, photoperiod, and seed-source climate on diameter-growth-cessation timing in coast Douglas-fir (an ecologically and economically vital tree) using high-frequency growth measurements across broad environmental gradients for a range of genotypes from different seed sources. Our model suggests that cool temperatures or short photoperiods can induce cessation in autumn. At cool locations (high latitude and elevation), cessation seems to be induced primarily by low temperatures in early autumn (under relatively long photoperiods), so warming will likely delay cessation and extend the growing season. But at warm locations (low latitude or elevation), cessation seems to be induced primarily by short photoperiods later in autumn, so warming will likely lead to only slight extensions of the growing season, reflecting photoperiod limitations on phenological shifts. Trees from seed sources experiencing frequent frosts in autumn or early winter tended to cease growth earlier in the autumn, potentially as an adaptation to avoid frost. Thus, gene flow into populations in warm locations with little frost will likely have limited potential to delay mean cessation dates because these populations already cease growth relatively late. In addition, data from an abnormal heat wave suggested that very high temperatures during long photoperiods in early summer might also induce cessation. Climate change could make these conditions more common in warm locations, leading to much earlier cessation. Thus, photoperiod cues, patterns of genetic variation, and summer heat waves could limit the capacity of coast Douglas-fir to extend its growing season in response to climate change in the warm parts of its range. [ABSTRACT FROM AUTHOR]

Oral cavity squamous cell carcinomas (OCSCC) carry high mortality and treatment morbidity. Unlike other mucosal subsites of the head and neck where definitive radiation can cure most cases, RT of gross disease in OCSCC is often ineffective. Thus, there is a need to better understand patient factors that influence response to RT in OCSCC. One such factor influencing response to treatment is the microbiome of the oral cavity and gut. Prior work has shown that the intestinal microbiome shapes systemic immunity and dictates responses to chemotherapy, immunotherapy and RT. Therefore, we hypothesized that the bacterial microbiome is an essential component mediating the response to RT in a murine model of OCSCC. Mouse oral squamous cell carcinoma (MOC1 and MOC2) cells were injected subcutaneously into C57BL/6 mice. Once tumors were palpable, the mice were treated with a broad-spectrum antibiotic (Abx) cocktail of ampicillin, cilastatin, imipenem and vancomycin to deplete intestinal bacteria. At tumor volumes of ∼200 mm3, tumors were focally irradiated (8 Gy single fraction) using the X-RAD SmART+ platform with image guidance. Tumor volumes were compared using repeated measures two-way ANOVA, and survival curves were analyzed using the log-rank test. We use 16S microbiome sequencing, high-dimensional flow cytometry and single-cell RNA sequencing to identify and phenotypically characterize immune cells in the tumor microenvironment for irradiated tumors in the presence and absence of the bacterial microbiome. In the immune-sensitive OCSCC model (MOC1), treatment with Abx prior to RT decreased the efficacy of RT as shown by faster tumor growth (P<0.01) and worse survival (P<0.05) in mice. In the immune-insensitive OCSCC model (MOC2), treatment with Abx prior to RT did not influence tumor growth or survival. MOC1 tumors exhibited more RT-elicited anti-tumor immunity following RT compared to MOC2, which was abrogated with the addition of Abx. The bacterial microbiome regulates anti-tumor responses following RT in OCSCC tumors that are immune responsive, but not in those that are immune insensitive. Therefore, strategies targeting the microbiome rely on understanding the complex interplay between the microbiome, tumor and the immune system. [ABSTRACT FROM AUTHOR]

Background: With increasing interest in animal social networks, field biologists have started exploring the use of advanced tracking technologies for mapping social encounters in free-ranging subjects. Proximity logging, which involves the use of animal-borne tags with the capacity for two-way communication, has attracted particular attention in recent years. While the basic rationale of proximity logging is straightforward, systems generate very large datasets which pose considerable challenges in terms of processing and visualisation. Technical aspects of data handling are crucial for the success of proximity-logging studies, yet are only rarely reported in full detail. Here, we describe the procedures we employed for mining the data generated by a recent deployment of a novel proximity-logging system, "Encounternet", to study social-network dynamics in tool-using New Caledonian crows. Results: Our field deployment of an Encounternet system produced some 240,000 encounter logs for 33 crows over a 19-day study period. Using this dataset, we illustrate a range of procedures, including: examination of tag reciprocity (i.e. whether both tags participating in an encounter detected the encounter and, if so, whether their records differed); filtering of data according to a predetermined signal-strength criterion (to enable analyses that focus on encounters within a particular distance range); amalgamation of temporally clustered encounter logs (to remove data artefacts and to enable robust analysis of biological patterns); and visualisation of dynamic network data as timeline plots (which can be used, among other things, to visualise the simulated diffusion of information). Conclusions: Researchers wishing to study animal social networks with proximity-logging systems should be aware of the complexities involved. Successful data analysis requires not only a sound understanding of hardware and software operation, but also bioinformatics expertise. Our paper aims to facilitate future projects by explaining in detail some of the subtleties that are easily overlooked in irst-pass analyses, but are key for reaching valid biological conclusions. We hope that this work will prove useful to other researchers, especially when read in conjunction with three recently published companion papers that report aspects of system calibration and key results. [ABSTRACT FROM AUTHOR]

Models to predict budburst and other phenological events in plants are needed to forecast how climate change may impact ecosystems and for the development of mitigation strategies. Differences among genotypes are important to predicting phenological events in species that show strong clinal variation in adaptive traits. We present a model that incorporates the effects of temperature and differences among genotypes to predict the timing of budburst of coast Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco). The main components of the model are (i) functions to calculate the accumulation of chilling units (CU) and forcing units (FU) during dormancy and (ii) a function defining the combinations of CU and FU needed for budburst (the possibility line). The possibility line was fit to data from 59 populations subjected to eight different winter environments. Differences among populations were incorporated into the possibility line using population coefficients that vary the FU required for budburst. Correlations among the population coefficients and variables describing local environments supported the hypothesis that genetic variation in budburst is largely an adaptation to summer drought. The new model can be used to test potential seed transfers as a strategy to mitigate some of the effects of climate change. On a besoin de modèles capables de prédire le débourrement ainsi que d'autres événements d'ordre phénologique chez les plantes pour prévoir les effets néfastes des changements climatiques sur les écosystèmes et pour élaborer des stratégies visant à atténuer ces effets. Les différences génotypiques sont importantes pour prédire les événements d'ordre phénologique chez les espèces dont les traits adaptatifs sont soumis à une forte variation clinale. Nous présentons un modèle qui intègre les effets de la température et les différences entre les génotypes pour prédire le moment du débourrement chez le douglas de Menzies typique (Pseudotsuga menziesii var. menziesii (Mirb.) Franco). Les principaux éléments du modèle sont (i) des fonctions pour calculer l'accumulation des unités de froid et des unités de forçage durant la période de dormance et (ii) une fonction qui définit les combinaisons d'unités de froid et de forçage nécessaires pour le débourrement (ligne des possibilités). La ligne des possibilités a été ajustée aux données de 59 populations soumises à huit sortes de conditions hivernales différentes. Les différences entre les populations ont été intégrées dans la ligne des possibilités sous forme de coefficients de population qui font varier les unités de forçage requises pour le débourrement. Les corrélations entre les coefficients de population et les variables qui décrivent les conditions environnementales locales supportent l'hypothèse selon laquelle la variation génétique associée au débourrement est en grande partie une adaptation à la sécheresse estivale. Le nouveau modèle peut être utilisé pour tester les transferts potentiels de graines en tant que stratégie pour minimiser certains des effets des changements climatiques. [ABSTRACT FROM AUTHOR]

Provides some insights into the history of seed zone development in forest trees with emphasis on the Pacific Northwest. Transfer guidelines for native plants; Seed movement guidelines for restoration activities; Forestry; Forest and plant restoration.

We developed a gap analysis approach to evaluate whether the genetic resources conserved in situ in protected areas are adequate for conifers in western Oregon and Washington (U.S.A.). We developed geographic information system layers that detail the location of protected areas and the distribution and abundance of each tree species (noble fir [Abies procera Rehd.] and Douglas-fir [Pseudotsuga menzeisii Mirb.]). Distribution and abundance were inferred from available spatial data showing modeled potential and actual vegetation. We stratified the distribution of each species into units for genetic analysis using seed and breeding zones and ecoregions. Most strata contained at least 5000 reproductive-age individuals in protected areas, indicating that genetic resources were well protected in situ throughout most of the study region. Strict in situ protection was limited, however, for noble fir in the Willapa Hills of southwestern Washington. An in situ genetic resource gap arguably occurred for Douglas-fir in the southern Puget lowlands, but this gap was filled by extensive ex situ genetic resources from the same region. The gap analysis method was an effective tool for evaluating the genetic resources of forest trees across a large region. [ABSTRACT FROM AUTHOR]

Under climate change, the reduction of frost risk, onset of warm temperatures and depletion of soil moisture are all likely to occur earlier in the year in many temperate regions. The resilience of tree species will depend on their ability to track these changes in climate with shifts in phenology that lead to earlier growth initiation in the spring. Exposure to warm temperatures ('forcing') typically triggers growth initiation, but many trees also require exposure to cool temperatures ('chilling') while dormant to readily initiate growth in the spring. If warming increases forcing and decreases chilling, climate change could maintain, advance or delay growth initiation phenology relative to the onset of favorable conditions. We modeled the timing of height- and diameter-growth initiation in coast Douglas-fir (an ecologically and economically vital tree in western North America) to determine whether changes in phenology are likely to track changes in climate using data from field-based and controlled-environment studies, which included conditions warmer than those currently experienced in the tree's range. For high latitude and elevation portions of the tree's range, our models predicted that warming will lead to earlier growth initiation and allow trees to track changes in the onset of the warm but still moist conditions that favor growth, generally without substantially greater exposure to frost. In contrast, toward lower latitude and elevation range limits, the models predicted that warming will lead to delayed growth initiation relative to changes in climate due to reduced chilling, with trees failing to capture favorable conditions in the earlier parts of the spring. This maladaptive response to climate change was more prevalent for diameter-growth initiation than height-growth initiation. The decoupling of growth initiation with the onset of favorable climatic conditions could reduce the resilience of coast Douglas-fir to climate change at the warm edges of its distribution. [ABSTRACT FROM AUTHOR]

Seed transfer zones ensure that germplasm selected for restoration is suitable and sustainable in diverse environments. In this study, seed zones were developed for mountain brome (Bromus carinatus Hook. & Arn.) in the Blue Mountains of northeastern Oregon and adjoining Washington. Plants from 148 Blue Mountain seed source locations were evaluated in common-garden studies at two contrasting test sites. Data on phenology, morphology, and production were collected over two growing seasons. Plant traits varied significantly and were frequently correlated with annual precipitation and annual maximum temperature at seed source locations (P < 0.05). Plants from warmer locations generally had higher dry matter production, longer leaves, wider crowns, denser foliage, and greater plant height than those from cooler locations. Regression models of environmental variables with the first two principal components (PC 1 and PC 2) explained 46% and 40% of the total variation, respectively. Maps of PC 1 and PC 2 generally corresponded to elevation, temperature, and precipitation gradients. The regression models developed from PC 1 and PC 2 and environmental variables were used to map seed transfer zones. These maps will be useful in selecting mountain brome seed sources for habitat restoration in the Blue Mountains. [ABSTRACT FROM AUTHOR]

Adaptation to cold is one of the greatest challenges to forest trees. This process is highly synchronized with environmental cues relating to photoperiod and temperature. Here, we use a candidate gene-based approach to search for genetic associations between 384 single-nucleotide polymorphism (SNP) markers from 117 candidate genes and 21 cold-hardiness related traits. A general linear model approach, including population structure estimates as covariates, was implemented for each marker-trait pair. We discovered 30 highly significant genetic associations [false discovery rate (FDR) Q < 0.101 across 12 candidate genes and 10 of the 21 traits. We also detected a set of 7 markers that had elevated levels of differentiation between sampling sites situated across the Cascade crest in northeastern Washington. Marker effects were small (r2 < 0.05) and within the range of those published previously for forest trees. The derived SNP allele, as measured by a comparison to a recently diverged sister species, typically affected the phenotype in away consistent with cold hardiness. The majority of markerswere characterized as having largely nonadditive modes of gene action, especially underdominance in the case of cold-tolerance related phenotypes. We place these results in the context of trade-offs between the abilities to grow longer and to avoid fall cold damage, as well as putative epigenetic effects. These associations provide insight into the genetic components of complex traits in coastal Douglas fir, as well as highlight the need for landscape genetic approaches to the detection of adaptive genetic diversity. [ABSTRACT FROM AUTHOR]

We describe here the Harvard integrated cavity output spectroscopy (ICOS) isotope instrument, a mid-IR infrared spectrometer using ICOS to make in situ measurements of the primary isotopologues of water vapor (H2O, HDO, and H218O) in the upper troposphere and lower stratosphere (UTLS). The long path length provided by ICOS provides the sensitivity and accuracy necessary to measure these or other trace atmospheric species at concentrations in the ppbv range. The Harvard ICOS isotope instrument has been integrated onto NASA’s WB-57 high-altitude research aircraft and to date has flown successfully in four field campaigns from winter 2004–2005 to the present. Off-axis alignment and a fully passive cavity ensure maximum robustness against the vibrationally hostile aircraft environment. The very simple instrument design permitted by off-axis ICOS is also helpful in minimizing contamination necessary for accurate measurements in the dry UTLS region. The instrument is calibrated in the laboratory via two separate water addition systems and crosscalibrated against other instruments. Calibrations have established an accuracy of 5% for all species. The instrument has demonstrated measurement precision of 0.14 ppmv, 0.10 ppbv, and 0.16 ppbv in 4 s averages for H2O, HDO, and H218O, respectively. At a water vapor mixing ratio of 5 ppmv the isotopologue ratio precision is 50‰ and 30‰ for δD and δ18O, respectively. [ABSTRACT FROM AUTHOR]

Purpose/objective(s): Current pathologic lymph node (LN) staging for head and neck squamous cell carcinomas (HNSCC) is based on LN size, laterality, and presence of extracapsular extension. However, some retrospective registry and single institution studies have suggested that the number of positive (+) LNs is the dominant nodal factor driving survival in HNSCC. Given the limitations of these datasets, it is unclear whether number of +LNs increases mortality through increased locoregional recurrence (LRR), distant metastases (DM), or both. In this study, we evaluate the prognostic value of number of +LNs in HNSCC using an international cohort of patients enrolled on three prospective randomized controlled trials (RCTs).Materials/methods: Secondary analysis was performed of RTOG 9501, RTOG 0234, and EORTC 22931, 3 prospective RCTs of patients undergoing surgery followed by post-operative radiation (RT) with or without systemic therapy. Univariate and multivariable models with restricted cubic splines were constructed to evaluate the association between number of +LNs and overall survival (OS), disease-free survival (DFS), LRR, and DM. Competing risks analysis was used for LRR and DM. Non-linear restricted cubic splines were used to model the relationship between +LN number and outcomes.Results: Overall, 947 patients were included in this secondary analysis. OS independently decreased with increasing number of +LNs without plateau, which was most pronounced up to a change point of 5 +LNs (hazard ratio [HR], 1.19 per LN; 95% confidence interval [CI], 1.10-1.29; P < 0.001). Mortality risk continued to increase after 5 +LNs, but more slowly (HR per LN, 1.03; 95% CI, 1.01-1.05; P < 0.001). Similarly, DFS decreased sharply up to 5 LNs (HR per LN, 1.19; 95% CI, 1.1-1.29; P < 0.001), and more gradually beyond this (HR per LN, 1.03; 95% CI, 1.01-1.05; P < 0.001). DM displayed similar behavior to OS and DFS, with risk increasing sharply with each +LN up to 5 (HR per LN, 1.14; 95% CI, 1.01-1.28; P = 0.04), and more slowly beyond this (HR per LN, 1.05; 95% CI, 1.02-1.07; P = 0.002). By contrast, although LRR increased sharply up to 5 +LNs (HR per LN, 1.25; 95% CI, 1.11-1.39, P < 0.001), risk plateaued beyond this (HR per LN, 1.00; 95% CI, 0.967-1.04; P = 0.91). There were marked differences in 5-year OS (54% vs 42%, P < 0.001), DFS (47% vs 27%, P < 0.001), LRR (22% vs 32%, P = 0.003), and DM (22% vs 38%, P < 0.001) when comparing patients with ≤5 and > 5 +LNs, respectively.Conclusion: Number of +LNs was validated as an independent factor associated with worse OS and DFS without plateau in a secondary analysis of 3 RCTs of patients with HNSCC undergoing surgery and post-operative RT. For patients with ≤5 +LNs, increased mortality was driven by both increased LRR and DM risk. However, beyond 5 +LNs, additional mortality increases were driven entirely by increasing DM. These changing patterns of recurrence as a function of quantitative nodal burden can help inform future clinical trials attempted to improve outcomes through treatment intensification. [ABSTRACT FROM AUTHOR]