Revealing ensemble state transition patterns in multi-electrode neuronal recordings using hidden Markov models

In order to harness the computational capacity of dissociated cultured neuronal networks, it is necessary to understand neuronal dynamics and connectivity on a mesoscopic scale. To this end, this paper uncovers dynamic spatiotemporal patterns emerging from electrically stimulated neuronal cultures using hidden Markov models (HMMs) to characterize multi-channel spike trains as a progression of patterns of underlying states of neuronal activity. However, experimentation aimed at optimal choice of parameters for such models is essential and results are reported in detail. Results derived from ensemble neuronal data revealed highly repeatable patterns of state transitions in the order of milliseconds in response to probing stimuli

Methods for Capturing, Marking, and Estimating Survival of Northern Bobwhite Chicks (Poster Abstract)

Lack of techniques to capture, mark, and observe chicks from hatch to fall has hindered our ability to understand this critical life stage of northern bobwhite (Colinus virginianus) and other galliforms. We present 2 methods for capturing wild, free-ranging northern bobwhite chicks associated with a radiomarked adult and demonstrate application of capture-recapture estimators. Both capture techniques involve monitoring radiomarked adults, locating nests, determining date of hatch, and then locating roosting adults with broods prior to sunrise during the pre-flight period (1–12 days post-hatch). The first technique involves erecting a temporary circular fence around the roosting radio-marked bird and brood, securing the edges with dirt, and systematically clearing all vegetation and ground debris until chicks are captured. The second technique involves placing a temporary fence in a ‘‘V’’ formation with a small mesh funnel trap placed at the apex. Birds are then ‘‘corralled’’ into the funnel trap. We used both methods during the breeding seasons of 1997–99. Overall, we captured 762 chicks from 137 broods. Of 131 capture attempts using the ring method, 18.3% (n = 24) were complete failures, 13.7% (n = 18) resulted in partial capture, whereas 68% (n = 89) resulted in complete capture. Using the funnel method, 22.2% (n = 2) of attempts were complete failures, 22.2% (n = 2) resulted in partial captures, and 55.6% (n = 5) resulted in complete brood capture. Captured chicks can be permanently and uniquely marked using monel patagial wing bands. We demonstrate application of capture-recapture models in program MARK to estimate chick survival from hatch to recruitment in the fall population (Oct 1)

Shoot yield drives phosphorus use efficiency in Brassica oleracea and correlates with root architecture traits

The environmental and financial costs of using inorganic phosphate fertilizers to maintain crop yield and quality are high. Breeding crops that acquire and use phosphorus (P) more efficiently could reduce these costs. The variation in shoot P concentration (shoot-P) and various measures of P use efficiency (PUE) were quantified among 355 Brassica oleracea L. accessions, 74 current commercial cultivars, and 90 doubled haploid (DH) mapping lines from a reference genetic mapping population. Accessions were grown at two or more external P concentrations in glasshouse experiments; commercial and DH accessions were also grown in replicated field experiments. Within the substantial species-wide diversity observed for shoot-P and various measures of PUE in B. oleracea, current commercial cultivars have greater PUE than would be expected by chance. This may be a consequence of breeding for increased yield, which is a significant component of most measures of PUE, or early establishment. Root development and architecture correlate with PUE; in particular, lateral root number, length, and growth rate. Significant quantitative trait loci associated with shoot-P and PUE occur on chromosomes C3 and C7. These data provide information to initiate breeding programmes to improve PUE in B. oleracea

Experimental application to a water delivery canal of a distributed MPC with stability constraints

In this work, a novel distributed MPC algorithm, denoted D-SIORHC, is applied to upstream local control of a pilot water delivery canal. The D-SIORHC algorithm is based on MPC control agents that incorporate stability constraints and communicate only with their adjacent neighbors in order to achieve a coordinated action. Experimental results that show the effect of the parameters configuring the local controllers are presented

Farm diversification strategies, dietary diversity and farm size: results from a cross-country sample in South and Southeast Asia

South and Southeast Asia host almost half of the world's undernourished people. Food and agricultural systems in these regions are highly dependent on the production and consumption of staple cereals such as rice, maize and wheat. More diverse farming systems can potentially improve rural people's nutrition, while reducing the environmental impact of agriculture. Yet, it remains uncertain whether farm diversification is always the most suitable and viable strategy for all types of smallholder farms. We use generalised linear regression models to analyse the farm diversification strategies of 4772 rural households in Cambodia, India, Lao PDR and Vietnam. Our analysis is twofold and focuses first on drivers of farm diversification, and second, on the impacts of farm diversification and other livelihood strategies on dietary diversity. We find that (1) farm diversification is significantly influenced by environmental and climate variables, including rainfall patterns, as well as household and farm characteristics such as farm size and education level; and (2) farm diversification, market orientation and off-farm income generation are all strategies that can improve household and individual dietary diversity. However, their relative effects resulted influenced by farm size. Specifically, the positive effect of farm diversification on dietary diversity was larger for smaller farms, while it decreased for farms of larger size that may improve their diet more by increasing their engagement in off-farm activities and markets. These findings highlight that characteristics such as farm size can represent substantial determinants in production and consumption decisions, suggesting the importance of understanding and considering the type of farm and the situational context of analysis when targeting interventions for improving smallholder farm livelihoods

Dysmorphometrics: the modelling of morphological abnormalities

<p>Abstract</p> <p>Background</p> <p>The study of typical morphological variations using quantitative, morphometric descriptors has always interested biologists in general. However, unusual examples of form, such as abnormalities are often encountered in biomedical sciences. Despite the long history of morphometrics, the means to identify and quantify such unusual form differences remains limited.</p> <p>Methods</p> <p>A theoretical concept, called dysmorphometrics, is introduced augmenting current geometric morphometrics with a focus on identifying and modelling form abnormalities. Dysmorphometrics applies the paradigm of detecting form differences as outliers compared to an appropriate norm. To achieve this, the likelihood formulation of landmark superimpositions is extended with outlier processes explicitly introducing a latent variable coding for abnormalities. A tractable solution to this augmented superimposition problem is obtained using Expectation-Maximization. The topography of detected abnormalities is encoded in a dysmorphogram.</p> <p>Results</p> <p>We demonstrate the use of dysmorphometrics to measure abrupt changes in time, asymmetry and discordancy in a set of human faces presenting with facial abnormalities.</p> <p>Conclusion</p> <p>The results clearly illustrate the unique power to reveal unusual form differences given only normative data with clear applications in both biomedical practice & research.</p

Accelerating root system phenotyping of seedlings through a computer-assisted processing pipeline

Background: There are numerous systems and techniques to measure the growth of plant roots. However, phenotyping large numbers of plant roots for breeding and genetic analyses remains challenging. One major difficulty is to achieve high throughput and resolution at a reasonable cost per plant sample. Here we describe a cost-effective root phenotyping pipeline, on which we perform time and accuracy benchmarking to identify bottlenecks in such pipelines and strategies for their acceleration. Results: Our root phenotyping pipeline was assembled with custom software and low cost material and equipment. Results show that sample preparation and handling of samples during screening are the most time consuming task in root phenotyping. Algorithms can be used to speed up the extraction of root traits from image data, but when applied to large numbers of images, there is a trade-off between time of processing the data and errors contained in the database. Conclusions: Scaling-up root phenotyping to large numbers of genotypes will require not only automation of sample preparation and sample handling, but also efficient algorithms for error detection for more reliable replacement of manual interventions

Six RNA Viruses and Forty-One Hosts: Viral Small RNAs and Modulation of Small RNA Repertoires in Vertebrate and Invertebrate Systems

We have used multiplexed high-throughput sequencing to characterize changes in small RNA populations that occur during viral infection in animal cells. Small RNA-based mechanisms such as RNA interference (RNAi) have been shown in plant and invertebrate systems to play a key role in host responses to viral infection. Although homologs of the key RNAi effector pathways are present in mammalian cells, and can launch an RNAi-mediated degradation of experimentally targeted mRNAs, any role for such responses in mammalian host-virus interactions remains to be characterized. Six different viruses were examined in 41 experimentally susceptible and resistant host systems. We identified virus-derived small RNAs (vsRNAs) from all six viruses, with total abundance varying from “vanishingly rare” (less than 0.1% of cellular small RNA) to highly abundant (comparable to abundant micro-RNAs “miRNAs”). In addition to the appearance of vsRNAs during infection, we saw a number of specific changes in host miRNA profiles. For several infection models investigated in more detail, the RNAi and Interferon pathways modulated the abundance of vsRNAs. We also found evidence for populations of vsRNAs that exist as duplexed siRNAs with zero to three nucleotide 3′ overhangs. Using populations of cells carrying a Hepatitis C replicon, we observed strand-selective loading of siRNAs onto Argonaute complexes. These experiments define vsRNAs as one possible component of the interplay between animal viruses and their hosts

The status of the world's land and marine mammals: diversity, threat, and knowledge

Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action