Finite state machine implementation for left ventricle modeling and control.

BACKGROUND: Simulation of a left ventricle has become a critical facet of evaluating therapies and operations that interact with cardiac performance. The ability to simulate a wide range of possible conditions, changes in cardiac performance, and production of nuisances at transition points enables evaluation of precision medicine concepts that are designed to function through this spectrum. Ventricle models have historically been based on biomechanical analysis, with model architectures constituted of continuous states and not conducive to deterministic processing. Producing a finite-state machine governance of a left ventricle model would enable a broad range of applications: physiological controller development, experimental left ventricle control, and high throughput simulations of left ventricle function. METHODS: A method for simulating left ventricular pressure-volume control utilizing a preload, afterload, and contractility sensitive computational model is shown. This approach uses a logic-based conditional finite state machine based on the four pressure-volume phases that describe left ventricular function. This was executed with a physical system hydraulic model using MathWorks' Simulink® and Stateflow tools. RESULTS: The approach developed is capable of simulating changes in preload, afterload, and contractility in time based on a patient's preload analysis. Six pressure-volume loop simulations are presented to include a base-line, preload change only, afterload change only, contractility change only, a clinical control, and heart failure with normal ejection fraction. All simulations produced an error of less than 1 mmHg and 1 mL of the absolute difference between the desired and simulated pressure and volume set points. The acceptable performance of the fixed-timestep architecture in the finite state machine allows for deployment to deterministic systems, such as experimental systems for validation. CONCLUSIONS: The proposed approach allows for personalized data, revealed through an individualized clinical pressure-volume analysis, to be simulated in silico. The computational model architecture enables this control structure to be executed on deterministic systems that govern experimental left ventricles. This provides a mock circulatory system with the ability to investigate the pathophysiology for a specific individual by replicating the exact pressure-volume relationship defined by their left ventricular functionality; as well as perform predictive analysis regarding changes in preload, afterload, and contractility in time.

Development of an adaptive pulmonary simulator for in vitro analysis of patient populations and patient-specific data.

BACKGROUND AND OBJECTIVE: Patient-specific modeling (PSM) is gaining more attention from researchers due to its ability to potentially improve diagnostic capabilities, guide the design of intervention procedures, and optimize clinical management by predicting the outcome of a particular treatment and/or surgical intervention. Due to the hemodynamic diversity of specific patients, an adaptive pulmonary simulator (PS) would be essential for analyzing the possible impact of external factors on the safety, performance, and reliability of a cardiac assist device within a mock circulatory system (MCS). In order to accurately and precisely replicate the conditions within the pulmonary system, a PS should not only account for the ability of the pulmonary system to supply blood flow at specific pressures, but similarly consider systemic outflow dynamics. This would provide an accurate pressure and flow rate return supply back into the left ventricular section of the MCS (i.e. the initial conditions of the left heart). METHODS: Employing an embedded Windkessel model, a control system model was developed utilizing MathWorks' Simulink® Simscape™. Following a verification and validation (V&V) analysis approach, a PI-controlled closed-loop hydraulic system was developed using Simscape™. This physical system modeling tool was used to (1) develop and control the in silico system during verification studies and (2) simulate pulmonary performance for validation of this control architecture. RESULTS: The pulmonary Windkessel model developed is capable of generating the left atrial pressure (LAP) waveform from given pulmonary factors, aortic conditions, and systemic variables. Verification of the adaptive PS's performance and validation of this control architecture support this modeling methodology as an effective means of reproducing pulmonary pressure waveforms and systemic outflow conditions, unique to a particular patient. Adult and geriatric with and without Heart Failure and a Normal Ejection Fraction (HFNEF) are presented. CONCLUSIONS: The adaptability of this modelling approach allows for the simulation of pulmonary conditions without the limitations of a dedicated hardware platform for use in in vitro investigations.

A robust automatic birdsong phrase classification: A template-based approach.

Automatic phrase detection systems of bird sounds are useful in several applications as they reduce the need for manual annotations. However, birdphrase detection is challenging due to limited training data and background noise. Limited data occur because of limited recordings or the existence of rare phrases. Background noise interference occurs because of the intrinsic nature of the recording environment such as wind or other animals. This paper presents a different approach to birdsong phrase classification using template-based techniques suitable even for limited training data and noisy environments. The algorithm utilizes dynamic time-warping (DTW) and prominent (high-energy) time-frequency regions of training spectrograms to derive templates. The performance of the proposed algorithm is compared with the traditional DTW and hidden Markov models (HMMs) methods under several training and test conditions. DTW works well when the data are limited, while HMMs do better when more data are available, yet they both suffer when the background noise is severe. The proposed algorithm outperforms DTW and HMMs in most training and testing conditions, usually with a high margin when the background noise level is high. The innovation of this work is that the proposed algorithm is robust to both limited training data and background noise.

Dynamic time warping and sparse representation classification for birdsong phrase classification using limited training data.

Annotation of phrases in birdsongs can be helpful to behavioral and population studies. To reduce the need for manual annotation, an automated birdsong phrase classification algorithm for limited data is developed. Limited data occur because of limited recordings or the existence of rare phrases. In this paper, classification of up to 81 phrase classes of Cassin's Vireo is performed using one to five training samples per class. The algorithm involves dynamic time warping (DTW) and two passes of sparse representation (SR) classification. DTW improves the similarity between training and test phrases from the same class in the presence of individual bird differences and phrase segmentation inconsistencies. The SR classifier works by finding a sparse linear combination of training feature vectors from all classes that best approximates the test feature vector. When the class decisions from DTW and the first pass SR classification are different, SR classification is repeated using training samples from these two conflicting classes. Compared to DTW, support vector machines, and an SR classifier without DTW, the proposed classifier achieves the highest classification accuracies of 94% and 89% on manually segmented and automatically segmented phrases, respectively, from unseen Cassin's Vireo individuals, using five training samples per class.

Tricuspid annulus: a three-dimensional deconstruction and reconstruction.

BACKGROUND: Before clinical manifestation of regurgitation, the tricuspid annulus dilates and flattens when right ventricular dysfunction is potentially reversible. That makes the case for a prophylactic tricuspid annuloplasty even in the absence of significant tricuspid regurgitation. Owing to the appreciation of the favorable prognostic value of tricuspid annuloplasty, the geometry of the normal tricuspid annulus merits critical analysis. METHODS: Three-dimensional transesophageal echocardiographic data from 26 patients were analyzed using Image Arena (TomTec, Munich, Germany) software. Cartesian coordinate data from tricuspid annuli were exported to MATLAB (Mathworks, Natick, MA) for further processing. Annular metrics related to size, shape, and motion were computed. RESULTS: The tricuspid annulus demonstrated significant changes in area (p<0.01) and perimeter (p<0.03) during the cardiac cycle, with maximum values attained at end diastole. There was significant correlation between two- and three-dimensional area changes, indicating true expansion in the annulus. The anterolateral region of the annulus demonstrated the greatest dynamism (p<0.01), and the anteroseptal region showed the least. The anteroseptal region also displayed the most nonplanarity in the annulus. In addition, vertical translational motion was observed, with a mean distance of 11.3±3.7 mm between end systolic and end diastolic annular centroids. CONCLUSIONS: The tricuspid annulus is a dynamic, multiplanar structure with heterogeneous regional behavior. These characteristics should be taken into account for optimal annuloplasty device design and efficacy.

Structural design principles of complex bird songs: a network-based approach.

Bird songs are acoustic communication signals primarily used in male-male aggression and in male-female attraction. These are often monotonous patterns composed of a few phrases, yet some birds have extremely complex songs with a large phrase repertoire, organized in non-random fashion with discernible patterns. Since structure is typically associated with function, the structures of complex bird songs provide important clues to the evolution of animal communication systems. Here we propose an efficient network-based approach to explore structural design principles of complex bird songs, in which the song networks--transition relationships among different phrases and the related structural measures--are employed. We demonstrate how this approach works with an example using California Thrasher songs, which are sequences of highly varied phrases delivered in succession over several minutes. These songs display two distinct features: a large phrase repertoire with a 'small-world' architecture, in which subsets of phrases are highly grouped and linked with a short average path length; and a balanced transition diversity amongst phrases, in which deterministic and non-deterministic transition patterns are moderately mixed. We explore the robustness of this approach with variations in sample size and the amount of noise. Our approach enables a more quantitative study of global and local structural properties of complex bird songs than has been possible to date.

Mock Circulatory Loop Compliance Chamber Employing a Novel Real-Time Control Process.

The use of compliance chambers in mock circulatory loop construction is the predominant means of simulating arterial compliance. Utilizing mock circulatory loops as bench test methods for cardiac assist technologies necessitates that they must be capable of reproducing the circulatory conditions that would exist physiologically. Of particular interest is the ability to determine instantaneous compliance of the system, and the ability to change the compliance in real-time. This capability enables continuous battery testing of conditions without stopping the flow to change the compliance chamber settings, and the simulation of dynamic changes in arterial compliance. The method tested involves the use of a compliance chamber utilizing a circular natural latex rubber membrane separating the fluid and air portions of the device. Change in system compliance is affected by the airspace pressure, which creates more reaction force at the membrane to the fluid pressure. A pressure sensor in the fluid portion of the chamber and a displacement sensor monitoring membrane center deflection allow for real-time inputs to the control algorithm. A predefined numerical model correlates the displacement sensor data to the volume displacement of the membrane. The control algorithm involves a tuned π loop maintaining the volume distention of the membrane via regulation of the air space pressure. The proportional integral (PI) controller tuning was achieved by creating a computational model of the compliance chamber using Simulink™ Simscape® toolboxes. These toolboxes were used to construct a model of the hydraulic, mechanical, and pneumatic elements in the physical design. Parameter Estimation™ tools and Design Optimization™ methods were employed to determine unknown physical parameters in the system, and tune the process controller used to maintain the compliance setting. It was found that the resulting control architecture was capable of maintaining compliance along a pressure-volume curve and allowed for changes to the compliance set point curve without stopping the pulsatile flow.

Is alarm calling risky? Marmots avoid calling from risky places.

Alarm calling is common in many species. A prevalent assumption is that calling puts the vocalizing individual at increased risk of predation. If calling is indeed costly, we need special explanations for its evolution and maintenance. In some, but not all species, callers vocalize away from safety and thus may be exposed to an increased risk of predation. However, for species that emit bouts with one or a few calls, it is often difficult to identify the caller and find the precise location where a call was produced. We analyzed the spatial dynamics of yellow-bellied marmot (Marmota flaviventris) alarm calling using an acoustic localization system to determine the location from which calls were emitted. Marmots almost always called from positions close to the safety of their burrows, and, if they produced more than one alarm call, tended to end their calling bouts closer to safety than they started them. These results suggest that for this species, potential increased predation risk from alarm calling is greatly mitigated and indeed calling may have limited predation costs.

Acoustic localization of antbirds in a Mexican rainforest using a wireless sensor network.

Acoustic localization is a promising method to passively observe vocal animal species, but remains difficult and time consuming to employ. To reduce the labor intensity and impact of deployment, an acoustic localization system has been developed consisting of battery powered wireless sensor nodes. The system also has the ability to perform an acoustic self-survey, which compares favorably in accuracy to global positioning system survey methods, especially in environments such as forest. The self-survey and localization accuracy of the system was tested in the neotropical rainforest of Chiapas, Mexico. A straight-forward and robust correlation sum localization computation method was utilized and is described in detail. Both free-ranging wild antbird songs and songs played from a speaker were localized with mean errors of 0.199 m and 0.445 m, respectively. Finally, additional tests utilizing only a short segment of each song or a subset of sensor nodes were performed and found to minimally affect localization accuracy. The use of a wireless sensor network for acoustic localization of animal vocalizations offers greater ease and flexibility of deployment than wired microphone arrays without sacrificing accuracy.

Perspectives of people in Mali toward genetically-modified mosquitoes for malaria control.

BACKGROUND: Genetically-modified (GM) mosquitoes have been proposed as part of an integrated vector control strategy for malaria control. Public acceptance is essential prior to field trials, particularly since mosquitoes are a vector of human disease and genetically modified organisms (GMOs) face strong scepticism in developed and developing nations. Despite this, in sub-Saharan Africa, where the GM mosquito effort is primarily directed, very little data is available on perspectives to GMOs. Here, results are presented of a qualitative survey of public attitudes to GM mosquitoes for malaria control in rural and urban areas of Mali, West Africa between the months of October 2008 and June 2009. METHODS: The sample consisted of 80 individuals - 30 living in rural communities, 30 living in urban suburbs of Bamako, and 20 Western-trained and traditional health professionals working in Bamako and Bandiagara. Questions were asked about the cause of malaria, heredity and selective breeding. This led to questions about genetic alterations, and acceptable conditions for a release of pest-resistant GM corn and malaria-refractory GM mosquitoes. Finally, participants were asked about the decision-making process in their community. Interviews were transcribed and responses were categorized according to general themes. RESULTS: Most participants cited mosquitoes as one of several causes of malaria. The concept of the gene was not widely understood; however selective breeding was understood, allowing limited communication of the concept of genetic modification. Participants were open to a release of pest-resistant GM corn, often wanting to conduct a trial themselves. The concept of a trial was reapplied to GM mosquitoes, although less frequently. Participants wanted to see evidence that GM mosquitoes can reduce malaria prevalence without negative consequences for human health and the environment. For several participants, a mosquito control programme was preferred; however a transgenic release that satisfied certain requirements was usually acceptable. CONCLUSIONS: Although there were some dissenters, the majority of participants were pragmatic towards a release of GM mosquitoes. An array of social and cultural issues associated with malaria, mosquitoes and genetic engineering became apparent. If these can be successfully addressed, then social acceptance among the populations surveyed seems promising.

Automated species recognition of antbirds in a Mexican rainforest using hidden Markov models.

Behavioral and ecological studies would benefit from the ability to automatically identify species from acoustic recordings. The work presented in this article explores the ability of hidden Markov models to distinguish songs from five species of antbirds that share the same territory in a rainforest environment in Mexico. When only clean recordings were used, species recognition was nearly perfect, 99.5%. With noisy recordings, performance was lower but generally exceeding 90%. Besides the quality of the recordings, performance has been found to be heavily influenced by a multitude of factors, such as the size of the training set, the feature extraction method used, and number of states in the Markov model. In general, training with noisier data also improved recognition in test recordings, because of an increased ability to generalize. Considerations for improving performance, including beamforming with sensor arrays and design of preprocessing methods particularly suited for bird songs, are discussed. Combining sensor network technology with effective event detection and species identification algorithms will enable observation of species interactions at a spatial and temporal resolution that is simply impossible with current tools. Analysis of animal behavior through real-time tracking of individuals and recording of large amounts of data with embedded devices in remote locations is thus a realistic goal.

A test of the chromosomal theory of ecotypic speciation in Anopheles gambiae.

The role of chromosomal inversions in speciation has long been of interest to evolutionists. Recent quantitative modeling has stimulated reconsideration of previous conceptual models for chromosomal speciation. Anopheles gambiae, the most important vector of human malaria, carries abundant chromosomal inversion polymorphism nonrandomly associated with ecotypes that mate assortatively. Here, we consider the potential role of paracentric inversions in promoting speciation in A. gambiae via "ecotypification," a term that refers to differentiation arising from local adaptation. In particular, we focus on the Bamako form, an ecotype characterized by low inversion polymorphism and fixation of an inversion, 2Rj, that is very rare or absent in all other forms of A. gambiae. The Bamako form has a restricted distribution by the upper Niger River and its tributaries that is associated with a distinctive type of larval habitat, laterite rock pools, hypothesized to be its optimal breeding site. We first present computer simulations to investigate whether the population dynamics of A. gambiae are consistent with chromosomal speciation by ecotypification. The models are parameterized using field observations on the various forms of A. gambiae that exist in Mali, West Africa. We then report on the distribution of larvae of this species collected from rock pools and more characteristic breeding sites nearby. Both the simulations and field observations support the thesis that speciation by ecotypification is occurring, or has occurred, prompting consideration of Bamako as an independent species.

Effect of rice cultivation patterns on malaria vector abundance in rice-growing villages in Mali.

Irrigation for rice cultivation increases the production of Anopheles gambiae, the main vector of malaria in Mali. Mosquito abundance is highly variable across villages and seasons. We examined whether rice cultivation patterns mapped using remotely sensed imagery can account for some of this variance. We collected entomologic data and mapped land use around 18 villages in the two cropping seasons during two years. Land use classification accuracy ranged between 70% and 86%. The area of young rice explained 86% of the inter-village variability in An. gambiae abundance in August before the peak in malaria transmission. Estimating rice in a 900-meter buffer area around the villages resulted in the best correlation with mosquito abundance, larger buffer areas were optimum in the October and dry season models. The quantification of the relationship between An. gambiae abundance and rice cultivation could have management applications that merit further study.

Is vector body size the key to reduced malaria transmission in the irrigated region of Niono, Mali?

Malaria vectors can reach very high densities in villages near irrigated rice fields in Africa, leading to the expectation that malaria should be especially prevalent there. Surprisingly, this is not always the case. In Niono, Mali, villages from nonirrigated areas have higher malaria prevalence than those within the irrigated regions, which suffer from higher mosquito numbers. One hypothesis explaining this observation is that mosquitoes from irrigated fields with high densities are inefficient vectors. This could occur if higher larval densities lead to smaller mosquitoes that suffer elevated mortality. Three predictions of the hypothesis were studied. First, the effect of larval density on larval body size was measured for both Anopheles gambiae Giles and Anopheles funestus Giles. Second, the relationship between larval and adult body size was tested. Third, evidence of an effect of adult size on survivorship in both irrigated and nonirrigated villages during the wet and dry seasons was sought. There was a modest positive relationship between densities of immatures and larval size, and a strong relationship between larval and adult size. Furthermore, adult survivorship was higher in nonirrigated areas. However, there was no effect of size on survivorship between comparable samples from both the irrigated and nonirrigated zones. Although density may have a causal relationship with reduced transmission in the irrigated areas of Niono, it is unlikely to be because higher density leads to smaller body size and lower survivorship.

Water quality and immatures of the M and S forms of Anopheles gambiae s.s. and An. arabiensis in a Malian village.

INTRODUCTION: The associations between the immatures of Anopheles gambiae s.s. (Diptera: Culicidae), its M and S forms, and Anopheles arabiensis among and within larval breeding habitats in Banambani, Mali were investigated under varying conditions of water quality and rainfall. The intent was to elucidate on niche partitioning of these taxa. METHODS: Immatures of An. arabiensis, An. gambiae s.s., and its M and S forms were sampled every alternate day for a month in mid-rainy season from three sampling sites in each of the larval breeding habitats (rock pools, swamp, and puddles). Water quality was characterized by alkalinity, conductivity, dissolved oxygen (D.O.), nitrate, orthophosphate, pH, temperature, total dissolved solids (TDS), and turbidity. A type 3 analysis of the GENMOD model was used to examine the associations between the proportional frequencies of young (first and second instar larvae) and old (third and fourth instar larvae and pupae) or total immatures of species or forms among sampling sites within and among larval breeding habitats during a category of rainfall as influenced by water quality. RESULTS: Of the 4,174 immatures sampled, 1,300 were molecularly identified to species and forms. Significant association between the proportional frequencies of young larvae of An. arabiensis, An. gambiae s.s., its M and S forms was found among sampling sites within habitats but not among larval breeding habitats. The proportional frequencies of young larvae of M and S forms varied daily perhaps due to recruitment, mortality, and dispersal within habitats. Conductivity and TDS had significant effects when the proportional frequencies of young larvae of M and S forms among sampling sites within habitats were significantly associated. Alkalinity, D.O., orthophosphate, pH, nitrate, temperature and turbidity had no effects on niche partitioning of species and forms among sampling sites within habitats. Rainfall did not affect the frequencies of these immatures. CONCLUSION: Conductivity and TDS have significant effects on niche partitioning of young larvae of M and S forms among sampling sites within habitats in Banambani, Mali.

Vector abundance and malaria transmission in rice-growing villages in Mali.

Anophelism without malaria has long been recognized. In large irrigation projects, such as that around Niono, Mali, villages in irrigated areas sometimes have more anopheline vectors of malaria than adjacent nonirrigated villages, but overall malaria prevalence is substantially less. One hypothesized explanation for this is high anopheline densities lead to smaller adults, who do not live so long and hence are less efficient at transmitting the disease. We analyzed serial collections from 18 villages in an irrigated area of Mali, measuring correlations between mosquito densities and survival rates, zoophilic rates, and vectorial capacity over the villages and times. Adult density was inversely related to anthropophily and adult survival and its relationship with vectorial capacity was positive at low mosquito densities, flat at intermediate densities, and negative at high densities. This may partly explain why malaria prevalence is low in irrigated villages with high Anopheles density.

Molecular-dynamics simulations of methane hydrate dissociation.

Nonequilibrium molecular-dynamics simulations have been carried out at 276.65 K and 68 bar for the dissolution of spherical methane hydrate crystallites surrounded by a liquid phase. The liquid was composed of pure water or a water-methane mixture ranging in methane composition from 50% to 100% of the corresponding theoretical maximum for the hydrate and ranged in size from about 1600 to 2200 water molecules. Four different crystallites ranging in size from 115 to 230 water molecules were used in the two-phase systems; the nanocrystals were either empty or had a methane occupation from 80% to 100% of the theoretical maximum. The crystal-liquid systems were prepared in two distinct ways, involving constrained melting of a bulk hydrate system or implantation of the crystallite into a separate liquid phase. The breakup rates were very similar for the four different crystal sizes investigated. The method of system preparation was not found to affect the eventual dissociation rates, despite a lag time of approximately 70 ps associated with relaxation of the liquid interfacial layer in the constrained melting approach. The dissolution rates were not affected substantially by methane occupation of the hydrate phase in the 80%-100% range. In contrast, empty hydrate clusters were found to break up significantly more quickly. Our simulations indicate that the diffusion of methane molecules to the surrounding liquid layer from the crystal surface appears to be the rate-controlling step in hydrate breakup. Increasing the size of the liquid phase was found to reduce the initial delay in breakup. We have compared breakup rates computed using different long-range electrostatic methods. Use of the Ewald, minimum image, and spherical cut-off techniques led to more rapid dissociation relative to the Lekner method.

Survivorship and distribution of immature Anopheles gambiae s.l. (Diptera: Culicidae) in Banambani village, Mali.

We observed the survivorship and distribution of larvae and pupae of Anopheles gambiae s.l. Giles immature stages in three habitats (rock pools, swamp, and puddles) in Banambani village. Mali, West Africa, during the mid-rainy season of 2000. Horizontal life tables were constructed for immatures in the laboratory. Times spent in the various immature stages were determined, and laboratory survival was measured. Vertical life tables were obtained from each habitat. We found large day-to-day variation for age class composition within habitats across days. The swamp samples had small but statistically significant different distributions in some instar stages compared with rock pools and puddles as affected by precipitation history. There were obviously unstable age distributions in the swamp and puddles and to some extent in rock pools. There were more individuals in some later age classes than in earlier ones. The daily survival estimates using an exponential decay model were 0.807 in rock pools, 0.899 in the swamp, 0.818 in puddles, and 0.863 in the overall village. Possible reasons for the departure from stable age distribution were cannibalism, predation and other complex interactions, rainfall effects, sampling bias, and differences in physicochemical properties of the water in the habitats.

Spatial and habitat distribution of Anopheles gambiae and Anopheles arabiensis (Diptera: Culicidae) in Banambani village, Mali.

We studied the larval distribution and composition of Anopheles arabiensis Patton, An. gambiae s.s. Giles, and its forms, among local habitats; and their association with the adults between these habitats in Banambani village, Mali during the mid-rainy seasons of 1997-1999. For species and form identification we used polymerase chain reaction (PCR) and PCR-restriction fragment-length polymorphism (RFLP). Differences among species in the distribution of larvae were observed in 1998, but not in 1997 or 1999, although they were on the borderline of statistical significance. Differences among the M and S molecular forms were statistically significant in 1999 when rainfall was high, but not in the two prior, drier sampling periods. Combining all information into the Fisher multiple comparisons test, there were statistically significant differences between species and molecular forms during the 3-yr study period. Hybrid larvae between the M and S forms were observed (0.57%), the first such observation to our knowledge. In spite of differences among larval distribution, no differences of adult species composition were observed among habitats. Factors that influence the distributions of An. gambiae larval populations are discussed.