Segmentation of Heart Ventricles Using Skeletal Representations

The objective of the project is to develop practical algorithms to segment the human heart’s left and right ventricles from isotropic Magnetic Resonance Imaging (MRI). An advanced algorithm that allows for efficient analysis of the ventricles in 3D or 4D would help diagnose and treat numerous cardiac diseases and illnesses. The left ventricle is a convex-like structure whereas the right ventricle has a relatively more abstract shape. The constant blood flow in and out of the ventricles causes them to look different at any given time. Therefore, our data set is in 4D where the fourth dimension is time. Our algorithms take a 3D MRI volume and first reduces it to a 1D skeletal representation with figure-ground separation followed by morphological analysis. We think the skeletal representation is rich enough to keep the important structural information of ventricles while small enough to scale it to the 4D volume efficiently in the future. The first algorithm further reduces the skeleton into a minimum spanning tree and asks a user for an edge that can separate the ventricle from the rest of the structure. The second algorithm first asks the user for two points inside the ventricle: one near the atrium and the other near its tip. These two points define the skeleton of the ventricle and allows the algorithm to differentiate it from the other structures. We designed a user friendly graphical interface for our testing and demonstration. We tested the first algorithm on 4 data sets provided by the Fornwalt Lab at Geisinger Hospital. Each data contains manual annotations of both left and right ventricles at end-systolic and end-diastolic phases. The algorithm was run on a laptop with 1.80 GHz CPU with 8 GB RAM. The average Intersection over Union (IoU) and time was 60% and 1.484 seconds respectively for the left ventricle and 32% and 1.5281 seconds respectively for the right ventricle. We will report the results of the second algorithm at the conference. The target is 80% IoU for both ventricles

Using Long-Short Term Memory Network to Train Machine Composing Baroque Fugue/Canon

The goal of this project is to train a machine to compose Baroque Fugue/Canon by using Long-Short Term Memory architecture (LSTM). LSTM is a type of artificial recursive neural network (RNN), which excels at learning patterns at both long and short time periods. By limiting to particular “styles” of structures and patterns, the problem becomes more tractable. In our study, we focus on the Baroque Fugue/Canons as they are polyphonic music with standard rules and structures to regulate the composing process. A 2-layer bi-directional LSTM network has been designed. With training data of midi files of Fugue/Canon primarily composed by J.S Bach, have been collected from internet and translated into a text file. Length, frequency, intensity and timing will be considered as training features. The checkpoint file with best validation loss will be used to generate output file, and converted back into midi file. The result will be announced at the conference

Size Constancy in Virtual Reality

This project studies human perception of size within a controlled virtual reality environment. When we open our eyes and glance at the surrounding, we see stable scenes that appear absolute. However, many argue that this is a pure illusion as nothing in our visual pathway is stable. Thus, our perceived size of an object may not reflect accurately the extent of the projection onto our retina. We do experience such false perception when we see celestial objects near the horizon. But are such misjudgments ubiquitous in our daily lives? With this in mind, the virtual reality scene has been created with a manipulated environment to provide a false sense of depth perception to the viewer. We want to test if this setting can cause the viewer to see familiar objects inaccurately in both size and distance. More specifically, we want to test if objects in one scene can look both closer and larger than the same objects in the other scene. If we can create such false perception, then we can conclude that misjudgment of angular size is ubiquitous. To bring this set up to life, the gaming software Unity is used to develop the scene, an HTC-Vive is used as the virtual reality goggles, and a computer running Windows 10 and equipped with an Intel Xeon CPU, 64GB RAM, and a GeForce GPU is used as the host. Subjects to participate in this experiment will be 18 or older and will be recruited around Susquehanna University. They will be asked to judge both size and distance of the objects in the virtual scene. The results will be presented at the conference

The Spatial Signature of Biotic Interactions of a Clonal and a Non-clonal Palmetto in a Subtropical Plant Community

Spatial analyses of plant-distribution patterns can provide inferences about intra- and interspecific biotic interactions. Yet, such analyses are rare for clonal plants because effective tools (i.e., molecular markers) needed to map naturally occurring clonal individuals have only become available recently. Clonal plants are unique in that a single genotype has a potential to spatially place new individuals (i.e., ramets) in response to intra- and interspecific biotic interactions. Laboratory and greenhouse studies suggest that some clonal plants can avoid intra-genet, inter-genet, and inter-specific competition via rootplacement patterns. An intriguing and yet to be explored question is whether a spatial signature of such multi-level biotic interactions can be detected in natural plant communities. The facultatively clonal Serenoa repens and non-clonal Sabal etonia are ecologically similar and co-dominant palmettos that sympatrically occur in the Florida peninsula. We used amplified fragment length polymorphisms (AFLPs) to identify Serenoa genets and also to assign field-unidentifiable small individuals as Sabal seedlings, Serenoa seedlings, or Serenoa vegetative sprouts. Then, we conducted univariate and bivariate multi-distance spatial analyses to examine the spatial interactions of Serenoa (n=271) and Sabal (n=137) within a 20x20 m grid at three levels, intragenet, intergenet and interspecific. We found that spatial interactions were not random at all three levels of biotic interactions. Serenoa genets appear to spatially avoid self-competition as well as intergenet competition. Furthermore, Serenoa and Sabal were spatially negatively associated with each other. However, this negative association pattern was also evident in a spatial comparison between non-clonal Serenoa and Sabal, suggesting that Serenoa genets’ spatial avoidance of Sabal through placement of new ramets is not the explanation of the interspecific-level negative spatial pattern. Our results emphasize the importance of investigating spatial signatures of biotic as well as abiotic interactions at multiple levels in understanding spatial distribution patterns of clonal plants in natural plant communities

Extensive clonal spread and extreme longevity in saw palmetto, a foundation clonal plant

The lack of effective tools have hampered our ability to assess the size, growth and ages of clonal plants. With Serenoa repens (saw palmetto) as a model, we introduce a novel analytical framework that integrates DNA fingerprinting and mathematical modelling to simulate growth and estimate ages of clonal plants. We also demonstrate the application of such life-history information of clonal plants to provide insight into management plans. Serenoa is an ecologically important foundation species in many Southeastern United States ecosystems; yet, many land managers consider Serenoa a troublesome invasive plant. Accordingly, management plans have been developed to reduce or eliminate Serenoa with little understanding of its life history. Using Amplified Fragment Length Polymorphisms, we genotyped 263 Serenoa and 134 Sabal etonia (a sympatric non-clonal palmetto) samples collected from a 20 X 20 m study plot in Florida scrub. Sabal samples were used to assign small field-unidentifiable palmettos to Serenoa or Sabal and also as a negative control for clone detection. We then mathematically modelled clonal networks to estimate genet ages. Our results suggest that Serenoa predominantly propagate via vegetative sprouts and 10000-year-old genets may be common, while showing no evidence of clone formation by Sabal. The results of this and our previous studies suggest that: (i) Serenoa has been part of scrub associations for thousands of years, (ii) Serenoa invasion are unlikely and (ii) once Serenoa is eliminated from local communities, its restoration will be difficult. Reevaluation of the current management tools and plans is an urgent task

Disease history and risk of comorbidity in women's life course : a comprehensive analysis of the Japan Nurses’ Health Study baseline survey

Objective: To classify diseases based on age at peak incidence to identify risk factors for later disease in women’s life course. Design: A cross-sectional baseline survey of participants in the Japan Nurses’ Health Study. Setting: A nationwide prospective cohort study on the health of Japanese nurses. The baseline survey was conducted between 2001 and 2007 (n=49 927). Main outcome measures: Age at peak incidence for 20 diseases from a survey of Japanese women was estimated using the Kaplan-Meier method with the Kernel smoothing technique. The incidence rate and peak incidence for diseases whose peak incidence occurred before the age of 45 years or before the perimenopausal period were selected as early-onset diseases. The OR and 95% CI were estimated to examine the risk of comorbidity between early-onset and other diseases. Results: Four early-onset diseases (endometriosis, anaemia, migraine headache and uterine myoma) were significantly correlated with one another. Late-onset diseases significantly associated (OR>2) with early-onset diseases included comorbid endometriosis with ovarian cancer (3.65 (2.16 to 6.19)), endometrial cancer (2.40 (1.14 to 5.04)) and cerebral infarction (2.10 (1.15 to 3.85)); comorbid anaemia with gastric cancer (3.69 (2.68 to 5.08)); comorbid migraine with transient ischaemic attack (3.06 (2.29 to 4.09)), osteoporosis (2.11 (1.71 to 2.62)), cerebral infarction (2.04 (1.26 to 3.30)) and angina pectoris (2.00 (1.49 to 2.67)); and comorbid uterine myoma with colorectal cancer (2.31 (1.48 to 3.61)). Conclusions: While there were significant associations between four early-onset diseases, women with a history of one or more of the early-onset diseases had a higher risk of other diseases later in their life course. Understanding the history of early-onset diseases in women may help reduce the subsequent risk of chronic diseases in later life

Estimation of Completion of Dormancy in Grapevine Bud Based on Cumulative Temperature

　This study was conducted to investigate the relationship between completion of dormancy of grapevine bud and temperature. Canes of ‘Kyoho’ and ‘Pione’ grapevines (Vitis labrusca×V. vinifera) grown in 7 vineyards with different temperature conditions, in Nagano, Northern Okayama, Yamanashi, Okayama, Okayama University, Fukuoka and Miyazaki, were collected at three different chilling exposures, December, January and February. These were then sent to Okayama University all at the same time. Cuttings with one bud were put into growth chambers kept at 25 or 30°C with 14 hours daylength, and budbreak in each cutting was surveyed at two day intervals for 60 days. Cumulative chilling hours (CCH) of exposure to below 7.2°C in each treatment time was largest in Nagano, followed in order by Northern Okayama, Yamanashi, Okayama, Okayama University, Fukuoka and Miyazaki. The CCH in Nagano was 2.5 to 4.8 times larger than in Miyazaki depending on the treatment time. The later the treatment time and the higher the temperature, the fewer were the number of days to first budbreak (NDFB) after treatment, irrespective of cultivar. A similar trend was observed in the number of days to 60% budbreak. In ‘Kyoho’ the NDFB was short in Nagano, Okayama University and Miyazaki, and longer in Okayama, Yamanashi and Fukuoka. In ‘Pione’ the NDFB was short in Fukuoka and Okayama University, and longer in Yamanashi and Okayama. The result was a weak negative correlation observed between CCH and NDFB in 4 of 7 vineyards. However, there was a strong positive correlation between NDFB and cumulative temperature (CT), a summation of temperature and hours of exposure to above 0°C from November 1 to treatment time and hours of exposure to 25 or 30°C from start of treatment to budbreak in each plot, in 6 vineyards excluding Miyazaki. The importance of estimating the completion of dormancy in grapevine bud based on CT is discussed.ブドウの芽の休眠完了と温度との関係を調査するため，温度条件の異なる７園（中信農試，山梨果試，岡山農試，岡山農試北部支場，岡山大学，福岡農試および宮崎）で栽培されている‘巨峰’と‘ピオーネ’から低温遭遇量の異なる３時期（12月，１月，２月）に結果母枝を採取した．直ちに岡山大学に送り，１芽を持つ挿し穂に調整した後，25または30℃のインキュベーター（14時間日長）に入れ，２日間隔で60日間発芽を調査した．処理開始時の7.2℃以下の遭遇量は中信農試で最も多く，次いで岡山農試北部支場，山梨果試，岡山農試，岡山大学，福岡農試，宮崎の順で，中信農試と宮崎では処理時期により2.5～4.8倍の差があった．発芽所要日数は，両品種とも処理時期が遅いほど，また温度が高いほど少なく，60％発芽所要日数もほぼ同様の傾向であった．‘巨峰’の発芽所用日数は中信農試，岡山大学および宮崎で少ない一方，岡山農試，山梨果試および福岡農試で多く，また‘ピオーネ’では福岡農試と岡山大学で少なく，山梨果試と岡山農試で多かった．７園のうち４園で低温遭遇量と発芽所要日数との間に負の相関がみられたが，相関係数は低かった．一方，11月以降処理開始までの０℃以上の温度の積算値と処理開始から発芽までの25または30℃での積算値を合計した積算温度と発芽所要日数との間には１園を除き極めて高い正の相関が認められた．これらの結果を基に，積算温度によるブドウの休眠完了予測の可能性を考察した