Learning Deep Similarity Metric for 3D MR-TRUS Registration

Purpose: The fusion of transrectal ultrasound (TRUS) and magnetic resonance (MR) images for guiding targeted prostate biopsy has significantly improved the biopsy yield of aggressive cancers. A key component of MR-TRUS fusion is image registration. However, it is very challenging to obtain a robust automatic MR-TRUS registration due to the large appearance difference between the two imaging modalities. The work presented in this paper aims to tackle this problem by addressing two challenges: (i) the definition of a suitable similarity metric and (ii) the determination of a suitable optimization strategy. Methods: This work proposes the use of a deep convolutional neural network to learn a similarity metric for MR-TRUS registration. We also use a composite optimization strategy that explores the solution space in order to search for a suitable initialization for the second-order optimization of the learned metric. Further, a multi-pass approach is used in order to smooth the metric for optimization. Results: The learned similarity metric outperforms the classical mutual information and also the state-of-the-art MIND feature based methods. The results indicate that the overall registration framework has a large capture range. The proposed deep similarity metric based approach obtained a mean TRE of 3.86mm (with an initial TRE of 16mm) for this challenging problem. Conclusion: A similarity metric that is learned using a deep neural network can be used to assess the quality of any given image registration and can be used in conjunction with the aforementioned optimization framework to perform automatic registration that is robust to poor initialization.Comment: To appear on IJCAR

CARDIAC AND OPERANT BEHAVIOR RESPONSE OF STARLINGS (Sturnus vulgaris) TO DISTRESS AND ALARM SOUNDS

A variety of auditory stimuli have been used for many years as a means of repelling nuisance birds from problem areas (Boudreau, 1968; Bremond et al., 1968; Frings and Jumber, 1954; Langowski et al., 1969; Nelson and Seubert 1966; Pearson and Corner, 1967; Thompson et al., 1966, 1968a, b). This approach to alleviating bird problems is ap- pealing because wild birds are considered very sensitive to sound stimuli of biological origin, and such stimuli are harmless to both target and nontarget species. The harmless aspect is an important advantage in dealing with wildlife related problems because of the increased public concern about the safety and environmental impact of the use of chemicals to alleviate some types of problems. The major limitation to the use of auditory stimuli to effectively repel birds is that, regardless of the strength of the communication signal, there is a decrement in physiological and behavioral response with repeated stimulation, resulting in habitua- tion and loss of repellent ability. In addition, the effectiveness of sound stimuli is in- fluenced by environmental and behavioral facts such as light intensity and flock behavior (Thompson et al., 1966, 1968a). Because of these limiting factors there is a need to compare the fright producing ability of different auditory stimuli to identify the strongest stimuli for field application. To facilitate this, we developed laboratory methodology to compare repellency strength of prerecorded sound stimuli. The methodology is illustrated in the present starling study by measuring (1) heart rate (HR) as a second order function of telemetered electrocar- diogram (ECG), and (2) keypecking rate (KPR) as an operant response in a switchback experimental design for four treatments. The switchback design was used to minimize error due to between-bird-variation in slope of the habituation curve and also to reduce the number of birds required for sensitive comparisons of stimuli

CARDIAC AND OPERANT BEHAVIOR RESPONSE OF STARLINGS (Sturnus vulgaris) TO DISTRESS AND ALARM SOUNDS

A variety of auditory stimuli have been used for many years as a means of repelling nuisance birds from problem areas (Boudreau, 1968; Bremond et al., 1968; Frings and Jumber, 1954; Langowski et al., 1969; Nelson and Seubert 1966; Pearson and Corner, 1967; Thompson et al., 1966, 1968a, b). This approach to alleviating bird problems is ap- pealing because wild birds are considered very sensitive to sound stimuli of biological origin, and such stimuli are harmless to both target and nontarget species. The harmless aspect is an important advantage in dealing with wildlife related problems because of the increased public concern about the safety and environmental impact of the use of chemicals to alleviate some types of problems. The major limitation to the use of auditory stimuli to effectively repel birds is that, regardless of the strength of the communication signal, there is a decrement in physiological and behavioral response with repeated stimulation, resulting in habitua- tion and loss of repellent ability. In addition, the effectiveness of sound stimuli is in- fluenced by environmental and behavioral facts such as light intensity and flock behavior (Thompson et al., 1966, 1968a). Because of these limiting factors there is a need to compare the fright producing ability of different auditory stimuli to identify the strongest stimuli for field application. To facilitate this, we developed laboratory methodology to compare repellency strength of prerecorded sound stimuli. The methodology is illustrated in the present starling study by measuring (1) heart rate (HR) as a second order function of telemetered electrocar- diogram (ECG), and (2) keypecking rate (KPR) as an operant response in a switchback experimental design for four treatments. The switchback design was used to minimize error due to between-bird-variation in slope of the habituation curve and also to reduce the number of birds required for sensitive comparisons of stimuli

Rainbow Trout Spawning Characteristics and Relation to the Parasite Myxobolus cerebralis in the Missouri River, Montana

The myxosporean parasite Myxobolus cerebralis is responsible for significant declines of rainbow trout (Oncorhynchus mykiss) populations in several western states, including Montana. Despite a high prevalence of the parasite in Montana’s Missouri River, there have been no apparent impacts to the rainbow trout population. This study examined long-term M. cerebralis monitoring data from the Missouri River system below Holter Dam and evaluated rainbow trout spawning characteristics such as migration distance, spawning location, site fidelity and amount of spawning in the Missouri River and tributaries over three years in an attempt to explain why the population has not declined in the presence of M. cerebralis. Over 13 years of monitoring, a mean 5.3 percent of rainbow trout handled during population estimates had clinical signs of M. cerebralis infection. In experiments using sentinel fish 53 percent of the spawning habitat had high severity of M. cerebralis, 38 percent had low to moderate severity, and 9 percent had no infection. Radio telemetry showed spawning locations varied among years and tagged fish lacked spawning site fidelity. The distance that radio-tagged rainbow trout migrated to spawning locations was significantly different among river sections of the study area. Twenty-eight percent of the spawning redds were found in the Missouri River and 72 percent in the tributaries. Relative to previous studies, we found less tributary spawning and an increase in Missouri River spawning, where M. cerebralis infection severity is lower. Our findings suggest that diverse spawning behaviors may contribute to rainbow trout population stability by spreading the risk of M. cerebralis impact over spawning locations that have a broad range of infection severity

Measuring and Building Soil Health

This fact sheet provide facts about soil health and will help land managers understand what soil health is, how to measure it, and how to potentially build it on their soils

Mobilizing the genome of Lepidoptera through novel sequence gains and end creation by non-autonomous Lep1 Helitrons

Transposable elements (TEs) can affect the structure of genomes through their acquisition and transposition of novel DNA sequences. The 134-bp repetitive elements, Lep1, are conserved non-autonomous Helitrons in lepidopteran genomes that have characteristic 5\u27-CT and 3\u27-CTAY nucleotide termini, a 3\u27-terminal hairpin structure, a 5\u27- and 3\u27-subterminal inverted repeat (SIR), and integrations that occur between AT or TT nucleotides. Lep1 Helitrons have acquired and propagated sequences downstream of their 3\u27-CTAY termini that are 57-344-bp in length and have termini composed of a 3\u27-CTRR preceded by a 3\u27-hairpin structure and a region complementary to the 5\u27-SIR (3\u27-SIRb). Features of both the Lep1 Helitron and multiple acquired sequences indicate that secondary structures at the 3\u27-terminus may have a role in rolling circle replication or genome integration mechanisms, and are a prerequisite for novel end creation by Helitron-like TEs. The preferential integration of Lep1 Helitrons in proximity to gene-coding regions results in the creation of genetic novelty that is shown to impact gene structure and function through the introduction of novel exon sequence (exon shuffling). These findings are important in understanding the structural requirements of genomic DNA sequences that are acquired and transposed by Helitron-like TEs

MarkerMiner 1.0: a new application for phylogenetic marker development using angiosperm transcriptomes

Premise of the study: Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. Methods and Results: We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. Conclusions: MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development

The role of orthographic neighbourhood effects in lateralized lexical decision: a replication study and meta-analysis

The effect of orthographic neighbourhood size (N) on lexical decision reaction time differs when words are presented in the left or right visual fields. Evidence suggests a facilitatory N effect (i.e., faster reaction times for words with larger neighbourhoods) in the left visual field. However, the N effect in the right visual field remains controversial: it may have a weaker facilitative role or it may even be inhibitory. In a pre-registered online experiment, we replicated the interaction between N and visual field and provided support for an inhibitory N effect in the right visual field. We subsequently conducted a pre-registered systematic review and meta-analysis to synthesise the available evidence and determine the direction of N effects across visual fields. Based on the evidence, it would seem the effect is inhibitory in the right visual field. Furthermore, the size of the N effect is considerably smaller in the right visual field. Both studies revealed considerable heterogeneity between participants and studies, and we consider the implications of this for future work