Modelling Pinus pinea forest management to attain natural regeneration under present and future climatic scenarios

Natural regeneration-based silviculture has been increasingly regarded as a reliable option in sustainable forest management. However, successful natural regeneration is not always easy to achieve. Recently, new concerns have arisen because of changing future climate. To date, regeneration models have proved helpful in decision-making concerning natural regeneration. The implementation of such models into optimization routines is a promising approach in providing forest managers with accurate tools for forest planning. In the present study, we present a stochastic multistage regeneration model for Pinus pinea L. managed woodlands in Central Spain, where regeneration has been historically unsuccessful. The model is able to quantify recruitment under different silviculture alternatives and varying climatic scenarios, with further application to optimize management scheduling. The regeneration process in the species showed high between-year variation, with all subprocesses (seed production, dispersal, germination, predation, and seedling survival) having the potential to become bottlenecks. However, model simulations demonstrate that current intensive management is responsible for regeneration failure in the long term. Specifically, stand densities at rotation age are too low to guarantee adequate dispersal, the optimal density of seed-producing trees being around 150 stems·ha−1. In addition, rotation length needs to be extended up to 120 years to benefit from the higher seed production of older trees. Stochastic optimization confirms these results. Regeneration does not appear to worsen under climate change conditions; the species exhibiting resilience worthy of broader consideration in Mediterranean silviculture.

Characteristic temperatures of folding of a small peptide

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the folding of a small peptide is a multistage process associated with two characteristic temperatures, the collapse temperature Tθ and the folding temperature Tƒ. Our results give supporting evidence for the energy landscape picture and funnel concept. These ideas were previously developed in the context of studies of simplified protein models, and here are checked in an all-atom Monte Carlo simulation.

A complete genome screen for genes predisposing to severe bipolar disorder in two Costa Rican pedigrees

Bipolar mood disorder (BP) is a debilitating syndrome characterized by episodes of mania and depression. We designed a multistage study to detect all major loci predisposing to severe BP (termed BP-I) in two pedigrees drawn from the Central Valley of Costa Rica, where the population is largely descended from a few founders in the 16th–18th centuries. We considered only individuals with BP-I as affected and screened the genome for linkage with 473 microsatellite markers. We used a model for linkage analysis that incorporated a high phenocopy rate and a conservative estimate of penetrance. Our goal in this study was not to establish definitive linkage but rather to detect all regions possibly harboring major genes for BP-I in these pedigrees. To facilitate this aim, we evaluated the degree to which markers that were informative in our data set provided coverage of each genome region; we estimate that at least 94% of the genome has been covered, at a predesignated threshold determined through prior linkage simulation analyses. We report here the results of our genome screen for BP-I loci and indicate several regions that merit further study, including segments in 18q, 18p, and 11p, in which suggestive lod scores were observed for two or more contiguous markers. Isolated lod scores that exceeded our thresholds in one or both families also occurred on chromosomes 1, 2, 3, 4, 5, 7, 13, 15, 16, and 17. Interesting regions highlighted in this genome screen will be followed up using linkage disequilibrium (LD) methods.

Defects in transforming growth factor-β signaling cooperate with a Ras oncogene to cause rapid aneuploidy and malignant transformation of mouse keratinocytes

Genetic inactivation of the transforming growth factor-β (TGF-β) signaling pathway can accelerate tumor progression in the mouse epidermal model of multistage carcinogenesis. By using an in vitro model of keratinocyte transformation that parallels in vivo malignant conversion to squamous cell carcinoma, we show that v-rasHa transduced primary TGF-β1−/− keratinocytes and keratinocytes expressing a TGF-β type II dominant-negative receptor transgene have significantly higher frequencies of spontaneous transformation than control genotypes. Malignant transformation in the TGF-β1−/− keratinocytes is preceded by aneuploidy and accumulation of chromosomal aberrations. Similarly, transient inactivation of TGF-β signaling with a type II dominant-negative receptor adenovirus causes rapid changes in ploidy. Exogenous TGF-β1 can suppress aneuploidy, chromosome breaks, and malignant transformation of the TGF-β1−/− keratinocytes at concentrations that do not significantly arrest cell proliferation. These results point to genomic instability as a mechanism by which defects in TGF-β signaling could accelerate tumor progression in mouse multistage carcinogenesis.

Parallel detection of violations of color constancy

The perceived colors of reflecting surfaces generally remain stable despite changes in the spectrum of the illuminating light. This color constancy can be measured operationally by asking observers to distinguish illuminant changes on a scene from changes in the reflecting properties of the surfaces comprising it. It is shown here that during fast illuminant changes, simultaneous changes in spectral reflectance of one or more surfaces in an array of other surfaces can be readily detected almost independent of the numbers of surfaces, suggesting a preattentive, spatially parallel process. This process, which is perfect over a spatial window delimited by the anatomical fovea, may form an early input to a multistage analysis of surface color, providing the visual system with information about a rapidly changing world in advance of the generation of a more elaborate and stable perceptual representation.

Chronic estrogen-induced cervical and vaginal squamous carcinogenesis in human papillomavirus type 16 transgenic mice.

High-risk human papillomaviruses (HPVs), including type 16, have been identified as factors in cervical carcinogenesis. However, the presence and expression of the virus per se appear to be insufficient for carcinogenesis. Rather, cofactors most likely are necessary in addition to viral gene expression to initiate neoplasia. One candidate cofactor is prolonged exposure to sex hormones. To examine the possible effects of estrogen on HPV-associated neoplasia, we treated transgenic mice expressing the oncogenes of HPV16 under control of the human keratin-14 promoter (K14-HPV16 transgenic mice) and nontransgenic control mice with slow release pellets of 17beta-estradiol. Squamous carcinomas developed in a multistage pathway exclusively in the vagina and cervix of K14-HPV16 transgenic mice. Estrogen-induced carcinogenesis was accompanied by an incremental increase in the incidence and distribution of proliferating cells solely within the cervical and vaginal squamous epithelium of K14-HPV16 mice. Expression of the HPV transgenes in untreated transgenic mice was detectable only during estrus; estrogen treatment resulted in transgene expression that was persistent but not further upregulated, remaining at low levels at all stages of carcinogenesis. The data demonstrate a novel mechanism of synergistic cooperation between chronic estrogen exposure and the oncogenes of HPV16 that coordinates squamous carcinogenesis in the female reproductive tract of K14-HPV16 transgenic mice.

Antiangiogenic therapy of transgenic mice impairs de novo tumor growth.

Angiogenesis is activated during multistage tumorigenesis prior to the emergence of solid tumors. Using a transgenic mouse model, we have tested the proposition that treatment with angiogenesis inhibitors can inhibit the progression of tumorigenesis after the switch to the angiogenic phenotype. In this model, islet cell carcinomas develop from multifocal, hyperproliferative nodules that show the histological hallmarks of human carcinoma in situ. Mice were treated with a combination of the angiogenesis inhibitor AGM-1470 (TNP-470), the antibiotic minocycline, and interferon alpha/beta. The treatment regimen markedly attenuated tumor growth but did not prevent tumor formation; tumor volume was reduced to 11% and capillary density to 40% of controls. The proliferation index of tumor cells in treated and control mice was similar, whereas the apoptotic index was doubled in treated tumors. This study shows that de novo tumor progression can be restricted solely by antiangiogenic therapy. The results suggest that angiogenesis inhibitors represent a valid component of anticancer strategies aimed at progression from discrete stages of tumorigenesis and demonstrate that transgenic mouse models can be used to evaluate efficacy of candidate antiangiogenic agents.

Illusory contours activate specific regions in human visual cortex: evidence from functional magnetic resonance imaging.

The neural basis for perceptual grouping operations in the human visual system, including the processes which generate illusory contours, is fundamental to understanding human vision. We have employed functional magnetic resonance imaging to investigate these processes noninvasively. Images were acquired on a GE Signa 1.5T scanner equipped for echo planar imaging with an in-plane resolution of 1.5 x 1.5 mm and slice thicknesses of 3.0 or 5.0 mm. Visual stimuli included nonaligned inducers (pacmen) that created no perceptual contours, similar inducers at the corners of a Kanizsa square that created illusory contours, and a real square formed by continuous contours. Multiple contiguous axial slices were acquired during baseline, visual stimulation, and poststimulation periods. Activated regions were identified by a multistage statistical analysis of the activation for each volume element sampled and were compared across conditions. Specific brain regions were activated in extrastriate cortex when the illusory contours were perceived but not during conditions when the illusory contours were absent. These unique regions were found primarily in the right hemisphere for all four subjects and demonstrate that specific brain regions are activated during the kind of perceptual grouping operations involved in illusory contour perception.

Logic-Based Outer Approximation for the Design of Discrete-Continuous Dynamic Systems with Implicit Discontinuities

We address the optimization of discrete-continuous dynamic optimization problems using a disjunctive multistage modeling framework, with implicit discontinuities, which increases the problem complexity since the number of continuous phases and discrete events is not known a-priori. After setting a fixed alternative sequence of modes, we convert the infinite-dimensional continuous mixed-logic dynamic (MLDO) problem into a finite dimensional discretized GDP problem by orthogonal collocation on finite elements. We use the Logic-based Outer Approximation algorithm to fully exploit the structure of the GDP representation of the problem. This modelling framework is illustrated with an optimization problem with implicit discontinuities (diver problem).

Geochemistry of ODP Hole 111-504B basalts (Table 2)

Fifty samples of basalt recovered during ODP Leg 111 from the dikes (Layer 2C) of Hole 504B (1350.0-1562.3 m below seafloor) were analyzed by X-ray-fluorescence techniques. All of the samples are highly depleted in magmaphile elements relative to other mid-ocean ridge basalts, with TiO2 = 0.75-1.24 wt%, Na2O = 1.59-2.22 wt%, Zr = 38-64 ppm, Nb = 0.3-1.5 ppm, and Y = 20-30 ppm (for samples containing 0%-2% phenocrysts), but have ratios of highly incompatible elements similar to normal Type I mid-ocean ridge basalts (e.g., Zr/Nb > 30). Abundances of compatible elements are similar to those of typical mid-ocean ridge basalts, with MgO = 7.2-9.2 wt%, Fe2O3* = 9.3-12.5 wt%, Ni = 55-164 ppm, and Cr = 26-388 ppm. Approximately 2% of the samples recovered from the top part of Hole 504B are similar to normal Type I or Type II ocean floor basalts. However, all of the analyzed Leg 111 samples from Hole 504B are depleted basalts. Aphyric dike rocks from Leg 111 are virtually identical to the depleted aphyric samples recovered from the pillow lavas and dikes in the upper 1075 m of Hole 504B during DSDP Legs 69, 70, and 83, with the exception of elements readily altered by seawater (Sr, Rb, and K). These elements reach a maximum in both abundance and variability in the pillow lavas of the upper 571.5 m of Hole 504B and decline to more constant values in the dike system sampled on Legs 83 and 111, apparently as a result of a decrease in porosity and increase in alteration temperatures relative to the pillow lavas. Based on compositional similarities to the vast majority of the pillows and flows, the dikes sampled on Leg 111 appear to be the feeder system for the pillow lavas in the upper part of Hole 504B. The incompatible-element-depleted compositions of the Costa Rica Rift Zone basalts are consistent with multistage melting of a normal mid-ocean ridge source.

Magnetic properties of igneous rocks recovered at ODP Leg 127 sites

Measurements of natural remanent magnetization (NRM), initial susceptibility (K), anisotropy of magnetic susceptibility, frequency dependent susceptibility (Xfd), and viscous remanent magnetization (VRM) are reported from volcanic rocks recovered during ODP Leg 127 in the Japan Sea. The results indicate a significant difference between the basalts drilled in the Yamato Basin (Site 794 and 797) and in the Japan Basin (Site 795). The Koenigsberger ratios (Q) show very low values in the Yamato Basin attesting that the remanence is not dominant over the induced magnetization. This evidence could explain why no magnetic anomaly pattern has been recognized in this basin. Experiments of VRM acquisition and decay show that both the processes are multistage with the acquisition process proceeding more rapidly and deviates more from a log (t) law than the corresponding decay. The sediments interlayered with the basalts in the acoustic basement of the Yamato Basin show processes of remagnetization related to the emplacement of the dikes. Temperatures of heating between 200° and 250°C were estimated from the different unblocking temperatures of the two components of magnetization.

Mineral, chemical and isotope compositions of clay subfractions from formations of the Srednii Peninsula, Murmansk coast of the Barents Sea

Fine-grained clay subfractions (SFs) with particle size of <0.1, 0.1-0.2, 0.2-0.3, 0.3-0.6, 0.6-2.0, and 2-5 µm separated from claystone of Upper Precambrian Pumanskaya and Poropelonskaya formations on the Srednii Peninsula were studied by transmission electron microscopy, X-ray diffraction, and Rb-Sr methods. All subfractions consist of low-temperature illite and chlorite, and contribution of chlorite decreases with diminishing particle size. The crystallinity index and I002/I001 ratio increase from coarse- to fine-grained SFs. Leaching by ammonium acetate solution and Rb-Sr systematics in combination with mineralogical and morphological data indicate that illite in Upper Proterozoic claystone from the Srednii Peninsula formed during three time intervals: 810-830, 610-620, and about 570 Ma ago. The first generation of this mineral with low Rb/Sr ratio dominates in coarse-grained SFs while the second and third generations with a high Rb/Sr ratio prevail in fine-grained SFs. All of three generations are known in Poropelon claystone, whereas Puman claystone contains only illite of the first and second generations. Geological processes responsible for multistage illite evolution in claystones are discussed.

Submodular Optimization and Data Processing

Thesis (Ph.D.)--University of Washington, 2016-06

Multivariate monitoring of a biological wastewater treatment process: a case study at Melbourne Water's Western Treatment Plant

Biological wastewater treatment is a complex, multivariate process, in which a number of physical and biological processes occur simultaneously. In this study, principal component analysis (PCA) and parallel factor analysis (PARAFAC) were used to profile and characterise Lagoon 115E, a multistage biological lagoon treatment system at Melbourne Water's Western Treatment Plant (WTP) in Melbourne, Australia. In this study, the objective was to increase our understanding of the multivariate processes taking place in the lagoon. The data used in the study span a 7-year period during which samples were collected as often as weekly from the ponds of Lagoon 115E and subjected to analysis. The resulting database, involving 19 chemical and physical variables, was studied using the multivariate data analysis methods PCA and PARAFAC. With these methods, alterations in the state of the wastewater due to intrinsic and extrinsic factors could be discerned. The methods were effective in illustrating and visually representing the complex purification stages and cyclic changes occurring along the lagoon system. The two methods proved complementary, with each having its own beneficial features. (C) 2003 Elsevier B.V. All rights reserved.

Employment restrictions among persons with ICD-10 anxiety disorders: characteristics from a population survey

Disability, employment, and employment restrictions among persons with ICD-10 anxiety disorders were investigated at a population level in comparison to persons without disability or long-term health conditions. Data were provided by the Australian Bureau of Statistics (ABS) collected in a 1998 national survey. Multistage sampling obtained a probability sample of 37,580 individuals in the household component of the survey. Trained lay interviewers using ICD-10 computer-assisted interviews identified household residents with anxiety disorders. Details of employment restrictions are reported and discussed. The four most commonly reported restrictions were: restricted in the type of job (24.0%); need for a support person (23.3%); difficulty changing jobs (18.6%); and restricted in the number of hours (15.4%). The nature and extent of employment restrictions characterizing persons with anxiety disorders indicates a need for strengthened disability and health condition screening at application for Government income support and at gateways to public funded vocational assistance. (c) 2004 Elsevier Inc. All rights reserved.