Large Contiguous Blocks Research Articles

Computing rank‐revealing factorizations of matrices stored out‐of‐core

SummaryThis paper describes efficient algorithms for computing rank‐revealing factorizations of matrices that are too large to fit in main memory (RAM), and must instead be stored on slow external memory devices such as disks (out‐of‐core or out‐of‐memory). Traditional algorithms for computing rank‐revealing factorizations (such as the column pivoted QR factorization and the singular value decomposition) are very communication intensive as they require many vector‐vector and matrix‐vector operations, which become prohibitively expensive when data is not in RAM. Randomization allows to reformulate new methods so that large contiguous blocks of the matrix are processed in bulk. The paper describes two distinct methods. The first is a blocked version of column pivoted Householder QR, organized as a “left‐looking” method to minimize the number of the expensive write operations. The second method results employs a UTV factorization. It is organized as an algorithm‐by‐blocks to overlap computations and I/O operations. As it incorporates power iterations, it is much better at revealing the numerical rank. Numerical experiments on several computers demonstrate that the new algorithms are almost as fast when processing data stored on slow memory devices as traditional algorithms are for data stored in RAM.

A review of Khmer word segmentation and part-of-speech tagging and an experimental study using bidirectional long short-term memory

Large contiguous blocks of unsegmented Khmer words can cause major problems for natural language processing applications such as machine translation, speech synthesis, information extraction, etc. Thus, word segmentation and part-of- speech tagging are two important prior tasks. Since the Khmer language does not always use explicit separators to split words, the definition of words is not a natural concept. Hence, tokenization and part-of-speech tagging of these languages are inseparable because the definition and principle of one task unavoidably affect the other. In this study, different approaches using in Khmer word segmentation and part-of-speech are reviewed and experimental study using a single long short-term memory network is described. Dataset from Asia Language Treebank is used to train and test the model. The preliminary experimental model achieved 95% accuracy rate. However, more testing to evaluate the model and compare it with different models is needed to conduct to select the more higher accuracy model.

Preserving Large Farming Landscapes: The Case of Lancaster County, Pennsylvania

Preserving large farming landscapes is one of the main goals of farmland preservation programs. Other goals include protecting highly productive soils, maintaining and enhancing the local farming economy, and promoting locally produced fresh food. Farmland preservation programs take time, however, because of the hefty funding require­ments and the detailed process of preserving farmland through the acquisition of conservation easements by purchase or donation. The standard measures of dollars spent and farmland acres preserved do not give an accurate picture of the spatial outcomes of preservation and preservation effectiveness. Three other measures better reflect the spatial effectiveness of farmland preservation: acreage and percentage of preserved farm parcels located in agricultural zones, number and acreage of preserved farm parcels in large contiguous blocks, and number and acreage of preserved farm parcels along growth boundaries. Scattered pre­served farms and preserved farms not located in agricultural zones are likely to face more nonfarm development nearby as well as problems with non­farm neighbors. The farmland preservation effort in Lancaster County, Pennsylvania, provides an important case study of the pattern of farmland preservation over time. Other counties and land trusts can employ geographic information systems (GIS) methods in this study to monitor and evalu­ate the progress of their farmland preservation efforts.

Genetic Map Construction and Detection of Genetic Loci Underlying Segregation Distortion in an Intraspecific Cross of Populus deltoides.

Based on a two-way pseudo-testcross strategy, high density and complete coverage linkage maps were constructed for the maternal and paternal parents of an intraspecific F2 pedigree of Populus deltoides. A total of 1,107 testcross markers were obtained, and the mapping population consisted of 376 progeny. Among these markers, 597 were from the mother, and were assigned into 19 linkage groups, spanning a total genetic distance of 1,940.3 cM. The remaining 519 markers were from the father, and were also were mapped into 19 linkage groups, covering 2,496.3 cM. The genome coverage of both maps was estimated as greater than 99.9% at 20 cM per marker, and the numbers of linkage groups of both maps were in accordance with the 19 haploid chromosomes in Populus. Marker segregation distortion was observed in large contiguous blocks on some of the linkage groups. Subsequently, we mapped the segregation distortion loci in this mapping pedigree. Altogether, eight segregation distortion loci with significant logarithm of odds supports were detected. Segregation distortion indicated the uneven transmission of the alternate alleles from the mapping parents. The corresponding genome regions might contain deleterious genes or be associated with hybridization incompatibility. In addition to the detection of segregation distortion loci, the established genetic maps will serve as a basic resource for mapping genetic loci controlling traits of interest in future studies.

EDITOR'S CHOICE: Surrounding habitats mediate the trade‐off between land‐sharing and land‐sparing agriculture in the tropics

Summary Two strategies are often promoted to mitigate the effects of agricultural expansion on biodiversity: one integrates wildlife‐friendly habitats within farmland (land sharing), and the other intensifies farming to allow the offset of natural reserves (land sparing). Their relative merits for biodiversity protection have been subject to much debate, but no previous study has examined whether trade‐offs between the two strategies depend on the proximity of farmed areas to large tracts of natural habitat. We sampled birds and dung beetles across contiguous forests and agricultural landscapes (low‐intensity cattle farming) in a threatened hotspot of endemism: the Colombian Chocó‐Andes. We test the hypothesis that the relative biodiversity benefits of either strategy depend partially on the degree to which farmlands are isolated from large contiguous blocks of forest. We show that distance from forest mediates the occurrence of many species within farmland. For the majority of species, occurrence on farmland depends on both isolation from forest and the proportionate cover of small‐scale wildlife‐friendly habitats within the farm landscape, with both variables having a similar overall magnitude of effect on occurrence probabilities. Simulations suggest that the biodiversity benefits of land sharing decline significantly with increasing distance from forest, but land sparing benefits remain consistent. In farm management units situated close to large contiguous forest (<500 m), land sharing is predicted to provide equal benefits to land sparing, but land sparing becomes increasingly superior in management units situated further from forest (1500 m). The predicted biodiversity benefits of land sparing are similar across all distances, provided that sparing mechanisms genuinely deliver protection for contiguous forest tracts. Synthesis and applications. The persistence of bird and dung beetle communities in low‐intensity pastoral agriculture is strongly linked to the proximity of surrounding contiguous forests. Land‐sharing policies that promote the integration of small‐scale wildlife‐friendly habitats might be of limited benefit without simultaneous measures to protect larger blocks of natural habitat, which could be achieved via land‐sparing practices. Policymakers should carefully consider the extent and distribution of remaining contiguous natural habitats when designing agri‐environment schemes in the tropics.

Optimizing carbon storage and biodiversity protection in tropical agricultural landscapes.

With the rapidly expanding ecological footprint of agriculture, the design of farmed landscapes will play an increasingly important role for both carbon storage and biodiversity protection. Carbon and biodiversity can be enhanced by integrating natural habitats into agricultural lands, but a key question is whether benefits are maximized by including many small features throughout the landscape ('land-sharing' agriculture) or a few large contiguous blocks alongside intensive farmland ('land-sparing' agriculture). In this study, we are the first to integrate carbon storage alongside multi-taxa biodiversity assessments to compare land-sparing and land-sharing frameworks. We do so by sampling carbon stocks and biodiversity (birds and dung beetles) in landscapes containing agriculture and forest within the Colombian Chocó-Andes, a zone of high global conservation priority. We show that woodland fragments embedded within a matrix of cattle pasture hold less carbon per unit area than contiguous primary or advanced secondary forests (>15 years). Farmland sites also support less diverse bird and dung beetle communities than contiguous forests, even when farmland retains high levels of woodland habitat cover. Landscape simulations based on these data suggest that land-sparing strategies would be more beneficial for both carbon storage and biodiversity than land-sharing strategies across a range of production levels. Biodiversity benefits of land-sparing are predicted to be similar whether spared lands protect primary or advanced secondary forests, owing to the close similarity of bird and dung beetle communities between the two forest classes. Land-sparing schemes that encourage the protection and regeneration of natural forest blocks thus provide a synergy between carbon and biodiversity conservation, and represent a promising strategy for reducing the negative impacts of agriculture on tropical ecosystems. However, further studies examining a wider range of ecosystem services will be necessary to fully understand the links between land-allocation strategies and long-term ecosystem service provision.

Aerosol emitters disrupt codling moth, Cydia pomonella, competitively

Isomate(®) CM MIST aerosol emitters (Pacific BioControl Corp, Vancouver, WA) containing 36 g of codlemone, (E,E)-8,10-dodecadien-1-ol, were deployed at various densities in a commercial apple orchard to generate dosage-response profiles in order to elucidate the behavioral mechanism of disruption. Moth captures decreased asymptotically as Isomate(®) CM MIST densities increased. Data fitting to Miller-Gut and Miller-de Lame plots yielded straight lines, with positive and negative slopes respectively. Catch of male moths decreased from 28 trap(-1) in the control to 0.9 trap(-1) at the highest emitter density. Disruption of >90% was realized at emitter densities greater than 5 units ha(-1) . The resulting set of profiles explicitly matched the predictions for competitive rather than non-competitive disruption. Thus, these devices probably disrupt by inducing false-plume following rather than by camouflaging traps and females. The use of 5 MIST units ha(-1) would be necessary to achieve the same level of codling moth control provided by a standard pheromone treatment with passive reservoir dispensers. The need for only a few aerosol emitters, 2.5-5 units ha(-1) , mitigates the cost of labor required to hand-apply hundreds of passive reservoir dispensers; however, a potential weakness in using this technology is that the low deployment density may leave areas of little or no pheromone coverage, where mate finding may occur. This technology is likely to benefit substantially from treatment of large contiguous blocks of crop.

Songbird Responses to Land Preservation Within Southern New England Cluster Subdivisions

Cluster subdivisions were designed to protect open space in response to rapid rates of conventional development. One of the proclaimed benefits of preserving open space within cluster subdivisions is the provision of habitat for native wildlife, but this has rarely been evaluated. This study examined songbird response to the amount of land protected within cluster subdivisions in Rhode Island (USA). We selected 11 sites along a gradient based on the relative amount of land protected within a site (% land under a conservation easement; %CE). We used nonparametric multivariate statistics to compare songbird communities between protected and developed areas within subdivisions and regression analyses to relate bird abundance and community metrics to %CE. Songbird communities differed significantly between protected and developed areas within cluster subdivisions. Songbird richness and diversity both peaked between 73-74 %CE, while densities of forest interior and human intolerant species increased with increasing %CE. Ovenbird, Veery, and Pine Warbler most typified high %CE sites and were found most often in protected areas far from development edges. This study demonstrates that cluster subdivisions need to preserve approximately 70-75% of the original undeveloped parcel of land in order to maximize songbird diversity. A higher percentage should be preserved in large contiguous blocks to further benefit forest interior species. This suggests that proposed regulations that require Rhode Island subdivisions to protect at least 50% of a parcel’s buildable land may not be adequate to enhance bird diversity or preserve species that depend on large contiguous blocks of forest interior habitat.

Opuntia in México: identifying priority areas for conserving biodiversity in a multi-use landscape.

BackgroundMéxico is one of the world's centers of species diversity (richness) for Opuntia cacti. Yet, in spite of their economic and ecological importance, Opuntia species remain poorly studied and protected in México. Many of the species are sparsely but widely distributed across the landscape and are subject to a variety of human uses, so devising implementable conservation plans for them presents formidable difficulties. Multi–criteria analysis can be used to design a spatially coherent conservation area network while permitting sustainable human usage.Methods and FindingsSpecies distribution models were created for 60 Opuntia species using MaxEnt. Targets of representation within conservation area networks were assigned at 100% for the geographically rarest species and 10% for the most common ones. Three different conservation plans were developed to represent the species within these networks using total area, shape, and connectivity as relevant criteria. Multi–criteria analysis and a metaheuristic adaptive tabu search algorithm were used to search for optimal solutions. The plans were built on the existing protected areas of México and prioritized additional areas for management for the persistence of Opuntia species. All plans required around one–third of México's total area to be prioritized for attention for Opuntia conservation, underscoring the implausibility of Opuntia conservation through traditional land reservation. Tabu search turned out to be both computationally tractable and easily implementable for search problems of this kind.Conclusions Opuntia conservation in México require the management of large areas of land for multiple uses. The multi-criteria analyses identified priority areas and organized them in large contiguous blocks that can be effectively managed. A high level of connectivity was established among the prioritized areas resulting in the enhancement of possible modes of plant dispersal as well as only a small number of blocks that would be recommended for conservation management.

Tigers Need Cover: Multi-Scale Occupancy Study of the Big Cat in Sumatran Forest and Plantation Landscapes

The critically endangered Sumatran tiger (Panthera tigris sumatrae Pocock, 1929) is generally known as a forest-dependent animal. With large-scale conversion of forests into plantations, however, it is crucial for restoration efforts to understand to what extent tigers use modified habitats. We investigated tiger-habitat relationships at 2 spatial scales: occupancy across the landscape and habitat use within the home range. Across major landcover types in central Sumatra, we conducted systematic detection, non-detection sign surveys in 47, 17×17 km grid cells. Within each cell, we surveyed 40, 1-km transects and recorded tiger detections and habitat variables in 100 m segments totaling 1,857 km surveyed. We found that tigers strongly preferred forest and used plantations of acacia and oilpalm, far less than their availability. Tiger probability of occupancy covaried positively and strongly with altitude, positively with forest area, and negatively with distance-to-forest centroids. At the fine scale, probability of habitat use by tigers across landcover types covaried positively and strongly with understory cover and altitude, and negatively and strongly with human settlement. Within forest areas, tigers strongly preferred sites that are farther from water bodies, higher in altitude, farther from edge, and closer to centroid of large forest block; and strongly preferred sites with thicker understory cover, lower level of disturbance, higher altitude, and steeper slope. These results indicate that to thrive, tigers depend on the existence of large contiguous forest blocks, and that with adjustments in plantation management, tigers could use mosaics of plantations (as additional roaming zones), riparian forests (as corridors) and smaller forest patches (as stepping stones), potentially maintaining a metapopulation structure in fragmented landscapes. This study highlights the importance of a multi-spatial scale analysis and provides crucial information relevant to restoring tigers and other wildlife in forest and plantation landscapes through improvement in habitat extent, quality, and connectivity.

Strategic targeting of agricultural conservation easements as a growth management tool

Public and private programs have preserved an estimated 730,000 ha of agricultural land in the United States by acquiring agricultural conservation easements (ACEs) that retire a property's development rights. ACEs could be a potent tool for smart growth if strategically targeted. This paper attempts to quantify measures of strategic targeting of ACEs as guidance for planners. Evaluating the placement of 157 ACEs in the San Francisco Bay Area of California produced mixed results. Preservation and development of agricultural land were both consistent with general plans. In contrast, we found little evidence of ACEs being used on a regional scale either to reinforce urban growth boundaries or to coalesce with other open space to form large contiguous blocks of protected areas. We used the TOPSIS method (Technique for Order Preference by Similarity to Ideal Solution) to identify the most strategic agricultural lands, which are quite different from where easements have been established through 2002. We encourage planners to consider strategic targeting of ACEs as a politically acceptable mechanism to complement traditional planning tools to minimize low density sprawl.

Maryland's Green Infrastructure Assessment: Development of a comprehensive approach to land conservation

Like many parts of the US, Maryland is urbanizing rapidly. The scattered pattern of low-density development consumes an excessive amount of land, fragments the landscape, displaces many native species, and disrupts ecosystem functions. Maryland's Green Infrastructure Assessment is a tool developed in the Maryland Department of Natural Resources (DNR) to help identify and rank those areas of greatest statewide ecological importance, as well as those at greatest risk of loss to development. It identifies large contiguous blocks of natural land (hubs), interconnected by natural corridors to allow animal and plant propagule dispersal and migration. Hubs and corridors were ranked within their physiographic region for a variety of ecological and development risk parameters, as well as combinations of these. Prioritization was also done on a finer scale (0.127 ha) for ecological importance and vulnerability to development, allowing a more detailed analysis for site prioritization within the network. The hub and corridor framework identified through the Green Infrastructure Assessment is being used to guide Maryland's ongoing land conservation efforts. At a multi-state scale, the green infrastructure method has been used as the framework for setting landscape ecological priorities within the Chesapeake Bay program. At a regional scale, the method has been used to rank or focus areas for state land conservation programs. Within a local government planning context, the method is now being translated into locally relevant criteria to support county-scale green infrastructure initiatives. Finally, the cell-based ranking method has been incorporated into parcel prioritization that has been used to aid state, local and private land trust conservation decision-making.

VARIABLE RATE NITROGEN APPLICATION IN FLORIDA CITRUS BASED ON ULTRASONICALLY-SENSED TREE SIZE

Most Florida citrus groves are still managed as large contiguous uniform blocks, despite significant variation infruit yield and tree canopy size. Site-specific grove management by variable rate delivery of inputs such as fertilizers on atree size basis could improve horticultural profitability and environmental protection. Tree canopy sizes were measuredreal-time in a typical 17-ha Valencia grove with an automated ultrasonic sensor system equipped with Differential GlobalPositioning System (DGPS). Prescription maps for variable application of nitrogen fertilizer were generated fromultrasonically scanned tree sizes on a single tree basis using ArcView GIS and Midtech Fieldware. Leaf samples from treeswith different canopy sizes, which had been fertilized at a conventional uniform rate of 270 kg N/ha/y, were analyzed fornitrogen concentration. Analysis of 2980 tree spaces in the grove showed a skewed size distribution, with 62% in the 0- to100-m3/tree volume classes and a median volume of 79 m3/tree. The tree volumes ranged from 0 to 240 m3/tree. Regressionanalysis showed that trees with excess leaf nitrogen (>3%) had canopies less than 100 m3. These trees receiving excessnitrogen are likely to have lower fruit yields and quality, and wasted fertilizer nitrates may leach beyond the root zone togroundwater. In order to rectify the excess fertilization of smaller trees, a granular fertilizer spreader with hydraulicallypowered split-chain outputs controlled with a MidTech Legacy 6000 controller was used for variable rate application ofnitrogen in one-half of the grove. A 38% to 40% saving in granular fertilizer cost was achieved for this grove when variableN rates were implemented on a per-tree basis ranging from 135 to 270 kg N/ha/y.

Landscape ecological assessment of the Chesapeake Bay watershed.

The Chesapeake Bay Watershed, located in the Mid-Atlantic Region of the United States, is experiencing rapid habitat loss and fragmentation from sprawling low-density development. The bay itself is heavily stressed by excess sediment and nutrient runoff. Three states, the District of Columbia, and the federal government signed an agreement in 2000 to address these problems. The commitments included an assessment of the watershed's resource lands, and targeting the most valued lands for protection. As part of this task, the Resource Lands Assessment identified an ecological network comprised of large contiguous blocks (hubs) of forests, wetlands, and streams, interconnected by corridors to allow animal and plant propagule dispersal and migration. Hubs were prioritized by ecoregion, by analyzing a variety of ecological parameters, including: rare species presence, rarity and population viability; vegetation and vertebrate richness; habitat area, condition, and diversity; intactness and remoteness; connectivity potential; and the nature of the surrounding landscape. I found that much of the watershed was still fairly intact, although this varied dramatically by ecoregion. Current protection also varied, and an assessment of vulnerability will help focus protection efforts among the most valuable hubs and corridors.

Modeling the effects of forest harvesting on landscape structure and the spatial distribution of cowbird brood parasitism

Timber harvesting affects both composition and structure of the landscape and has important consequences for organisms using forest habitats. A timber harvest allocation model was constructed that allows the input of specific rules to allocate forest stands for clearcutting to generate landscape patterns reflecting the “look and feel” of managed landscapes. Various harvest strategies were simulated on four 237 km2 study areas in Indiana, USA. For each study area, the model was applied to simulate 80 years of management activity. The resulting landscape spatial patterns were quantified using a suite of landscape pattern metrics and plotted as a function of mean harvest size and total area of forest harvested per decade to produce response surfaces. When the mean clearcut size was 1 ha, the area of forest interior remaining on the landscape was dramatically reduced and the amount of forest edge on the landscape increased dramatically. The potential consequences of the patterns produced by the model were assessed for a generalized neotropical migrant forest bird using a GIS model that generates maps showing the spatial distribution of the relative vulnerability of forest birds to brood parasitism by brown-headed cowbirds. The model incorporates the location and relative quality of cowbird feeding sites, and the relation between parasitism rates and distance of forest from edge. The response surface relating mean harvest size and total area harvested to the mean value of vulnerability to cowbird brood parasitism had a shape similar to the response surfaces showing forest edge. The results of our study suggest that it is more difficult to maintain large contiguous blocks of undisturbed forest interior when harvests are small and dispersed, especially when producing high timber volumes is a management goal. The application of the cowbird model to landscapes managed under different strategies could help managers in deciding where harvest activity will produce the least negative impact on breeding forest birds.

Parallel vision algorithms using sparse array representations

Sparse arrays are arrays in which the number of non-zero elements is a small fraction of the total number of array elements. Parallel algorithms are presented using sparse representations for arrays. It is shown that adopting such a representation not only reduces the processor/space requirement, but also provides efficient load balancing at no increase in time complexity. New parallel primitives needed to work with such a representation are defined. Sample algorithms from the areas of image processing and computer vision are presented. Alternative schemes for dealing with arrays containing large contiguous blocks of elements with identical array values are considered. The parallel architecture considered is a strict SIMD hypercube, and the applicability of the results presented to other architectures is described.

Landscape properties of pocosins and associated wetlands

Most pocosins occur on broad, relatively flat interfluves or near estuaries where rising sea level affects their hydrology. Traditionally accepted ecological functions are low when compared on a unit area basis with other wetland types. An understanding of the interaction of pocosins with the atmosphere is fundamental to revealing mechanisms for their formation and their importance in landscape-level biogeochemical processes such as producing and consuming greenhouse gases and receiving and processing acid deposition. At least four interactions between pocosins and estuaries are important at landscape scales: (1) maintaining landscape elevation in the context of rising sea level, (2) representing a platform upon which landward migrating brackish marshes can develop, (3) exporting high concentrations of organic carbon, and (4) influencing the quality of habitat in primary nursery areas for fish and shellfish. Since pocosins have lower rates of cycling for most elements, greater surface area of pocosin is required to provide the same function and life support as floodplain wetlands. Major habitat attributes are (1) the large contiguous blocks of land that they occupy in contrast to the narrow, linear configurations of riverine forests and (2) their location at the uppermost reaches of wetland continua. Because of these attributes, individual impacts to small areas are relatively inconsequential until their cumulative effects begin to encroach upon the landscape-level processes and functions that they display. Fragmentation by drainage ditches and roads and interspersion of agriculture and silviculture expose the organic soils to peat fires and biological oxidation. The historically slow rate of organic matter accretion is reversed to a more rapid process of degradation. Accelerated oxidation and subsidence create a net efflux of carbon to the atmosphere in contrast to the net influx that has been occurring for millennia.