Large-scale land acquisitions exacerbate local farmland inequalities in Tanzania.

Land inequality stalls economic development, entrenches poverty, and is associated with environmental degradation. Yet, rigorous assessments of land-use interventions attend to inequality only rarely. A land inequality lens is especially important to understand how recent large-scale land acquisitions (LSLAs) affect smallholder and indigenous communities across as much as 100 million hectares around the world. This paper studies inequalities in land assets, specifically landholdings and farm size, to derive insights into the distributional outcomes of LSLAs. Using a household survey covering four pairs of land acquisition and control sites in Tanzania, we use a quasi-experimental design to characterize changes in land inequality and subsequent impacts on well-being. We find convincing evidence that LSLAs in Tanzania lead to both reduced landholdings and greater farmland inequality among smallholders. Households in proximity to LSLAs are associated with 21.1% (P = 0.02) smaller landholdings while evidence, although insignificant, is suggestive that farm sizes are also declining. Aggregate estimates, however, hide that households in the bottom quartiles of farm size suffer the brunt of landlessness and land loss induced by LSLAs that combine to generate greater farmland inequality. Additional analyses find that land inequality is not offset by improvements in other livelihood dimensions, rather farm size decreases among households near LSLAs are associated with no income improvements, lower wealth, increased poverty, and higher food insecurity. The results demonstrate that without explicit consideration of distributional outcomes, land-use policies can systematically reinforce existing inequalities.

Mean and Variance of Phylogenetic Trees.

We describe the use of the Fréchet mean and variance in the Billera-Holmes-Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Fréchet mean is comparable to other summary methods, and, despite its stickiness property, is more likely to be binary than the majority-rule consensus tree. We show that the Fréchet variance is faster and more precise than commonly used variance measures. The Fréchet mean and variance are more theoretically justified, and more robust, than previous estimates of this type and can be estimated reasonably efficiently, providing a foundation for building more advanced statistical methods and leading to applications such as mean hypothesis testing and outlier detection.

Computational Creativity and Aesthetics with Algorithmic Information Theory.

We build an analysis based on the Algorithmic Information Theory of computational creativity and extend it to revisit computational aesthetics, thereby, improving on the existing efforts of its formulation. We discuss Kolmogorov complexity, models and randomness deficiency (which is a measure of how much a model falls short of capturing the regularities in an artifact) and show that the notions of typicality and novelty of a creative artifact follow naturally from such definitions. Other exciting formalizations of aesthetic measures include logical depth and sophistication with which we can define, respectively, the value and creator's artistry present in a creative work. We then look at some related research that combines information theory and creativity and analyze them with the algorithmic tools that we develop throughout the paper. Finally, we assemble the ideas and their algorithmic counterparts to complete an algorithmic information theoretic recipe for computational creativity and aesthetics.

On the Problem of Small Objects.

We discuss how to assess computationally the aesthetic value of "small" objects, namely those that have short digital descriptions. Such small objects still matter: they include headlines, poems, song lyrics, short musical scripts and other culturally crucial items. Yet, small objects are a confounding case for our recent work adapting ideas from algorithmic information theory (AIT) to the domain of computational creativity, as they cannot be either logically deep or sophisticated following the traditional definitions of AIT. We show how restricting the class of models under analysis can make it the case that we can still separate high-quality small objects from ordinary ones, and discuss the strengths and limitations of our adaptation.

Estimating local biodiversity change: a critique of papers claiming no net loss of local diversity.

Global species extinction rates are orders of magnitude above the background rate documented in the fossil record. However, recent data syntheses have found mixed evidence for patterns of net species loss at local spatial scales. For example, two recent data meta-analyses have found that species richness is decreasing in some locations and is increasing in others. When these trends are combined, these papers argued there has been no net change in species richness, and suggested this pattern is globally representative of biodiversity change at local scales. Here we reanalyze results of these data syntheses and outline why this conclusion is unfounded. First, we show the datasets collated for these syntheses are spatially biased and not representative of the spatial distribution of species richness or the distribution of many primary drivers of biodiversity change. This casts doubt that their results are representative of global patterns. Second, we argue that detecting the trend in local species richness is very difficult with short time series and can lead to biased estimates of change. Reanalyses of the data detected a signal of study duration on biodiversity change, indicating net biodiversity loss is most apparent in studies of longer duration. Third, estimates of species richness change can be biased if species gains during post-disturbance recovery are included without also including species losses that occurred during the disturbance. Net species gains or losses should be assessed with respect to common baselines or reference communities. Ultimately, we need a globally coordinated effort to monitor biodiversity so that we can estimate and attribute human impacts as causes of biodiversity change. A combination of technologies will be needed to produce regularly updated global datasets of local biodiversity change to guide future policy. At this time the conclusion that there is no net change in local species richness is not the consensus state of knowledge.

Multi-scale heterogeneity in vegetation and soil carbon in exurban residential land of southeastern Michigan, USA.

Exurban residential land (one housing unit per 0.2-16.2 ha) is growing in importance as a human-dominated land use. Carbon storage in the soils and vegetation of exurban land is poorly known, as are the effects on C storage of choices made by developers and residents. We studied C storage in exurban yards in southeastern Michigan, USA, across a range of parcel sizes and different types of neighborhoods. We divided each residential parcel into ecological zones (EZ) characterized by vegetation, soil, and human behavior such as mowing, irrigation, and raking. We found a heterogeneous mixture of trees and shrubs, turfgrasses, mulched gardens, old-field vegetation, and impervious surfaces. The most extensive zone type was turfgrass with sparse woody vegetation (mean 26% of parcel area), followed by dense woody vegetation (mean 21% of parcel area). Areas of turfgrass with sparse woody vegetation had trees in larger size classes (> 50 cm dbh) than did areas of dense woody vegetation. Using aerial photointerpretation, we scaled up C storage to neighborhoods. Varying C storage by neighborhood type resulted from differences in impervious area (8-26% of parcel area) and area of dense woody vegetation (11-28%). Averaged and multiplied across areas in differing neighborhood types, exurban residential land contained 5240 ± 865 g C/m2 in vegetation, highly sensitive to large trees, and 13 800 ± 1290 g C/m2 in soils (based on a combined sampling and modeling approach). These contents are greater than for agricultural land in the region, but lower than for mature forest stands. Compared with mature forests, exurban land contained more shrubs and less downed woody debris and it had similar tree size-class distributions up to 40 cm dbh but far fewer trees in larger size classes. If the trees continue to grow, exurban residential land could sequester additional C for decades. Patterns and processes of C storage in exurban residential land were driven by land management practices that affect soil and vegetation, reflecting the choices of designers, developers, and residents. This study provides an example of human-mediated C storage in a coupled human-natural system.

Pollux: platform independent error correction of single and mixed genomes.

BACKGROUND: Second-generation sequencers generate millions of relatively short, but error-prone, reads. These errors make sequence assembly and other downstream projects more challenging. Correcting these errors improves the quality of assemblies and projects which benefit from error-free reads. RESULTS: We have developed a general-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software. CONCLUSIONS: Pollux is highly effective at correcting errors across platforms, and is consistently able to perform as well or better than currently available error correction software. Pollux provides general-purpose error correction and may be used in applications with or without assembly.

An assessment of air pollutant exposure methods in Mexico City, Mexico.

UNLABELLED: Geostatistical interpolation methods to estimate individual exposure to outdoor air pollutants can be used in pregnancy cohorts where personal exposure data are not collected. Our objectives were to a) develop four assessment methods (citywide average (CWA); nearest monitor (NM); inverse distance weighting (IDW); and ordinary Kriging (OK)), and b) compare daily metrics and cross-validations of interpolation models. We obtained 2008 hourly data from Mexico City's outdoor air monitoring network for PM10, PM2.5, O3, CO, NO2, and SO2 and constructed daily exposure metrics for 1,000 simulated individual locations across five populated geographic zones. Descriptive statistics from all methods were calculated for dry and wet seasons, and by zone. We also evaluated IDW and OK methods' ability to predict measured concentrations at monitors using cross validation and a coefficient of variation (COV). All methods were performed using SAS 9.3, except ordinary Kriging which was modeled using R's gstat package. Overall, mean concentrations and standard deviations were similar among the different methods for each pollutant. Correlations between methods were generally high (r=0.77 to 0.99). However, ranges of estimated concentrations determined by NM, IDW, and OK were wider than the ranges for CWA. Root mean square errors for OK were consistently equal to or lower than for the IDW method. OK standard errors varied considerably between pollutants and the computed COVs ranged from 0.46 (least error) for SO2 and PM10 to 3.91 (most error) for PM2.5. OK predicted concentrations measured at the monitors better than IDW and NM. Given the similarity in results for the exposure methods, OK is preferred because this method alone provides predicted standard errors which can be incorporated in statistical models. The daily estimated exposures calculated using these different exposure methods provide flexibility to evaluate multiple windows of exposure during pregnancy, not just trimester or pregnancy-long exposures. IMPLICATIONS: Many studies evaluating associations between outdoor air pollution and adverse pregnancy outcomes rely on outdoor air pollution monitoring data linked to information gathered from large birth registries, and often lack residence location information needed to estimate individual exposure. This study simulated 1,000 residential locations to evaluate four air pollution exposure assessment methods, and describes possible exposure misclassification from using spatial averaging versus geostatistical interpolation models. An implication of this work is that policies to reduce air pollution and exposure among pregnant women based on epidemiologic literature should take into account possible error in estimates of effect when spatial averages alone are evaluated.

Exploring agent-level calculations of risk and returns in relation to observed land-use changes in the US Great Plains, 1870-1940.

Land-use change in the U.S. Great Plains since agricultural settlement in the second half of the nineteenth century has been well documented. While aggregate historical trends are easily tracked, the decision-making of individual farmers is difficult to reconstruct. We use an agent-based model to tell the history of the settlement of the West by simulating farm-level agricultural decision making based on historical data about prices, yields, farming costs, and environmental conditions. The empirical setting for the model is the period between 1875 and 1940 in two townships in Kansas, one in the shortgrass region and the other in the mixed grass region. Annual historical data on yields and prices determine profitability of various land uses and thereby inform decision-making, in conjunction with the farmer's previous experience and randomly assigned levels of risk aversion. Results illustrating the level of agreement between model output and unique and detailed household-level records of historical land use and farm size suggest that economic behavior and natural endowments account for land change processes to some degree, but are incomplete. Discrepancies are examined to identify missing processes through model experiments, in which we adjust input and output prices, crop yields, agent memory, and risk aversion. These analyses demonstrate how agent-based modeling can be a useful laboratory for thinking about social and economic behavior in the past.

Land Transitions in the American Plains: Multilevel Modeling of Drivers of Grassland Conversion (1950 to 2000).

This paper examines drivers of land-cover change in the U.S. Great Plains in the last half of the twentieth century. Its central aim is to evaluate the dynamics of grassland preservation and conversion, across the region, and to identify areas of grassland that were never plowed during the period. The research compares land-cover data from 400 sample areas, selected from and nested within 50 counties, to aggregate data from the agricultural and population censuses. The spatially explicit land-cover data were interpreted from aerial photographs taken at three time points (1950s, 1970s and 2000s). Sample areas were chosen using a stratified random design based on the Public Land Survey grid with in the target counties, in several clusters across the region. We modeled the sequences and magnitudes of changes in the interpreted air photo data in a multi-level panel model that included soil quality and slope of sample areas and agricultural activities and employment reported in the U.S. Censuses of Agriculture and Population. We conclude that land retirement programs and production subsidies have worked at cross purposes, destabilizing micro-level patterns of land use in recent decades, increasing levels of switching between cropland and grassland and reducing the size of remaining areas of native grassland in the U.S. Great Plains.

PANDAseq: paired-end assembler for illumina sequences.

BACKGROUND: Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information. RESULTS: PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods. CONCLUSIONS: PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.

More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs.

BACKGROUND: Identifying recombinations in HIV is important for studying the epidemiology of the virus and aids in the design of potential vaccines and treatments. The previous widely-used tool for this task uses the Viterbi algorithm in a hidden Markov model to model recombinant sequences. RESULTS: We apply a new decoding algorithm for this HMM that improves prediction accuracy. Exactly locating breakpoints is usually impossible, since different subtypes are highly conserved in some sequence regions. Our algorithm identifies these sites up to a certain error tolerance. Our new algorithm is more accurate in predicting the location of recombination breakpoints. Our implementation of the algorithm is available at http://www.cs.uwaterloo.ca/~jmtruszk/jphmm_balls.tar.gz. CONCLUSIONS: By explicitly accounting for uncertainty in breakpoint positions, our algorithm offers more reliable predictions of recombination breakpoints in HIV-1. We also document a new domain of use for our new decoding approach in HMMs.

Geostatistical exploration of spatial variation of summertime temperatures in the Detroit metropolitan region.

BACKGROUND: Because of the warming climate urban temperature patterns have been receiving increased attention. Temperature within urban areas can vary depending on land cover, meteorological and other factors. High resolution satellite data can be used to understand this intra-urban variability, although they have been primarily studied to characterize urban heat islands at a larger spatial scale. OBJECTIVE: This study examined whether satellite-derived impervious surface and meteorological conditions from multiple sites can improve characterization of spatial variability of temperature within an urban area. METHODS: Temperature was measured at 17 outdoor sites throughout the Detroit metropolitan area during the summer of 2008. Kriging and linear regression were applied to daily temperatures and secondary information, including impervious surface and distance-to-water. Performance of models in predicting measured temperatures was evaluated by cross-validation. Variograms derived from several scenarios were compared to determine whether high-resolution impervious surface information could capture fine-scale spatial structure of temperature in the study area. RESULTS: Temperatures measured at the sites were significantly different from each other, and all kriging techniques generally performed better than the two linear regression models. Impervious surface values and distance-to-water generally improved predictions slightly. Restricting models to days with lake breezes and with less cloud cover also somewhat improved the predictions. In addition, incorporating high-resolution impervious surface information into cokriging or universal kriging enhanced the ability to characterize fine-scale spatial structure of temperature. CONCLUSIONS: Meteorological and satellite-derived data can better characterize spatial variability in temperature across a metropolitan region. The data sources and methods we used can be applied in epidemiological studies and public health interventions to protect vulnerable populations from extreme heat events.

Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence.

We have developed a novel method for estimating the parameters of hidden Markov models for gene finding in newly sequenced species. Our approach does not rely on curated training data sets, but instead uses extrinsic evidence (including paired-end ditags that have not been used in gene finding previously) and iterative training. This new method is particularly suitable for annotation of species with large evolutionary distance to the closest annotated species. We have used our approach to produce an initial annotation of more than 16,000 genes in the newly sequenced Schistosoma japonicum draft genome. We established the high quality of our predictions by comparison to full-length cDNAs (withdrawn from the extrinsic evidence) and to CEGMA core genes. We also evaluated the effectiveness of the new training procedure on Caenorhabditis elegans genome. ExonHunter and the newest parametric files for S. japonicum genome are available for download at www.bioinformatics.uwaterloo.ca/downloads/exonhunter.

Carbon emissions from the global land rush and potential mitigation.

Global drivers and carbon emissions associated with large-scale land transactions have been poorly investigated. Here we examine major factors behind such transactions (income, agricultural productivity, availability of arable land and water scarcity) and estimate potential carbon emissions under different levels of deforestation. We find that clearing lands transacted between 2000 and 2016 (36.7 Mha) could have emitted ~2.26 GtC, but constraining land clearing to historical deforestation rates would reduce emissions related to large-scale land transactions to ~0.81 GtC.

Decoding HMMs using the k best paths: algorithms and applications.

BACKGROUND: Traditional algorithms for hidden Markov model decoding seek to maximize either the probability of a state path or the number of positions of a sequence assigned to the correct state. These algorithms provide only a single answer and in practice do not produce good results. RESULTS: We explore an alternative approach, where we efficiently compute the k paths of highest probability to explain a sequence and then either use those paths to explore alternative explanations for a sequence or to combine them into a single explanation. Our procedure uses an online pruning technique to reduce usage of primary memory. CONCLUSION: Out algorithm uses much less memory than naive approach. For membrane proteins, even simple path combination algorithms give good explanations, and if we look at the paths we are combining, we can give a sense of confidence in the explanation as well. For proteins with two topologies, the k best paths can give insight into both correct explanations of a sequence, a feature lacking from traditional algorithms in this domain.

New decoding algorithms for Hidden Markov Models using distance measures on labellings.

BACKGROUND: Existing hidden Markov model decoding algorithms do not focus on approximately identifying the sequence feature boundaries. RESULTS: We give a set of algorithms to compute the conditional probability of all labellings "near" a reference labelling lambda for a sequence y for a variety of definitions of "near". In addition, we give optimization algorithms to find the best labelling for a sequence in the robust sense of having all of its feature boundaries nearly correct. Natural problems in this domain are NP-hard to optimize. For membrane proteins, our algorithms find the approximate topology of such proteins with comparable success to existing programs, while being substantially more accurate in estimating the positions of transmembrane helix boundaries. CONCLUSION: More robust HMM decoding may allow for better analysis of sequence features, in reasonable runtimes.

A tutorial of techniques for improving standard Hidden Markov Model algorithms.

In this tutorial, we discuss two main algorithms for Hidden Markov Models or HMMs: the Viterbi algorithm and the expectation phase of the Baum-Welch algorithm, and we describe ways to improve their naïve implementations. For the Baum-Welch algorithm we first present an implementation of the expectation computations using constant space. We then discuss the classical implementation of this calculation and describe ways to reduce its space usage to logarithmic and O(square root n), with their respective CPU costs. We also note where each respective algorithm can be parallelized. For the Viterbi algorithm, we describe O(square root n) and logarithmic space algorithms which increase CPU use by a factor of two and by a logarithmic factor respectively. We also present two recent heuristics for decreasing space use, which in practice lead to logarithmic space use. Classical version of Viterbi cannot be parallelized by splitting sequence in several subsequences, but we show a parallelization that works if we are willing to pay a significant extra CPU cost. Finally we show a very simple parallelization trick which enables full usage of multiple CPUs/cores under the condition that they share memory.

Availability of recreational resources and physical activity in adults.

OBJECTIVES: Using data from a large cohort of adults aged 45 to 84 years-old, we investigated whether availability of recreational resources is related to physical activity levels. METHODS: Data from a multiethnic sample of 2723 adult residents of New York City, NY; Baltimore, Md; and Forsyth County, NC, were linked to data on locations of recreational resources. We measured the availability (density) of resources within 0.5 (0.8 km), 1, 2, and 5 miles of each participant's residence and used binomial regression to investigate associations of density with physical activity. RESULTS: After adjustment for potential confounders, individuals in the tertile of participants residing in areas with the highest density of resources were more likely to report physical activity during a typical week than were individuals in the lowest tertile. Associations between availability of recreational resources and physical activity levels were not present for the smallest area assessed (0.5 miles) but were present for areas ranging from 1 to 5 miles. These associations were slightly stronger among minority and low-income residents. CONCLUSIONS: Availability of resources may be 1 of several environmental factors that influence individuals' physical activity behaviors.

The use of functional domains to improve transmembrane protein topology prediction.

Transmembrane proteins affect vital cellular functions and pathogenesis, and are a focus of drug design. It is difficult to obtain diffraction quality crystals to study transmembrane protein structure. Computational tools for transmembrane protein topology prediction fill in the gap between the abundance of transmembrane proteins and the scarcity of known membrane protein structures. Their prediction accuracy is still inadequate: TMHMM, the current state-of-the-art method, has less than 52% accuracy in topology prediction on one set of transmembrane proteins of known topology. Based on the observation that there are functional domains that occur preferentially internal or external to the membrane, we have extended the model of TMHMM to incorporate functional domains, using a probabilistic approach originally developed for computational gene finding. Our extension is better than TMHMM in predicting the topology of transmembrane proteins. As prediction of functional domain improves, our system's prediction accuracy will likely improve as well.