Toward Real-Time Animal Tracking with Integrated Stimulus Control for Automated Conditioning in Aquatic Eco-Neurotoxicology.

Aquatic eco-neurotoxicology is an emerging field that requires new analytical systems to study the effects of pollutants on animal behaviors. This is especially true if we are to gain insights into one of the least studied aspects: the potential perturbations that neurotoxicants can have on cognitive behaviors. The paucity of experimental data is partly caused by a lack of low-cost technologies for the analysis of higher-level neurological functions (e.g., associative learning) in small aquatic organisms. Here, we present a proof-of-concept prototype that utilizes a new real-time animal tracking software for on-the-fly video analysis and closed-loop, external hardware communications to deliver stimuli based on specific behaviors in aquatic organisms, spanning three animal phyla: chordates (fish, frog), platyhelminthes (flatworm), and arthropods (crustacean). The system's open-source software features an intuitive graphical user interface and advanced adaptive threshold-based image segmentation for precise animal detection. We demonstrate the precision of animal tracking across multiple aquatic species with varying modes of locomotion. The presented technology interfaces easily with low-cost and open-source hardware such as the Arduino microcontroller family for closed-loop stimuli control. The new system has potential future applications in eco-neurotoxicology, where it could enable new opportunities for cognitive research in diverse small aquatic model organisms.

Light Field View Synthesis Using the Focal Stack and All-in-Focus Image.

Light field reconstruction and synthesis algorithms are essential for improving the lower spatial resolution for hand-held plenoptic cameras. Previous light field synthesis algorithms produce blurred regions around depth discontinuities, especially for stereo-based algorithms, where no information is available to fill the occluded areas in the light field image. In this paper, we propose a light field synthesis algorithm that uses the focal stack images and the all-in-focus image to synthesize a 9 × 9 sub-aperture view light field image. Our approach uses depth from defocus to estimate a depth map. Then, we use the depth map and the all-in-focus image to synthesize the sub-aperture views, and their corresponding depth maps by mimicking the apparent shifting of the central image according to the depth values. We handle the occluded regions in the synthesized sub-aperture views by filling them with the information recovered from the focal stack images. We also show that, if the depth levels in the image are known, we can synthesize a high-accuracy light field image with just five focal stack images. The accuracy of our approach is compared with three state-of-the-art algorithms: one non-learning and two CNN-based approaches, and the results show that our algorithm outperforms all three in terms of PSNR and SSIM metrics.

A room impulse response database for multizone sound field reproduction (L).

This letter introduces a database of Room Impulse Responses (RIRs) measured in seven different rooms for multizone sound field reproduction research in various acoustic environments. A circular array of 60 loudspeakers was installed in each room, with two microphone arrays placed sequentially in five different zones inside the loudspeaker array. A total of 260 400 RIRs were measured to establish the database. As a demonstration application of the database for multizone sound field reproduction, simulations were performed on the pressure matching and acoustic contrast control methods to investigate how a system optimized with the RIRs measured in one room would perform in other rooms.

Noise-Resilient Depth Estimation for Light Field Images Using Focal Stack and FFT Analysis.

Depth estimation for light field images is essential for applications such as light field image compression, reconstructing perspective views and 3D reconstruction. Previous depth map estimation approaches do not capture sharp transitions around object boundaries due to occlusions, making many of the current approaches unreliable at depth discontinuities. This is especially the case for light field images because the pixels do not exhibit photo-consistency in the presence of occlusions. In this paper, we propose an algorithm to estimate the depth map for light field images using depth from defocus. Our approach uses a small patch size of pixels in each focal stack image for comparing defocus cues, allowing the algorithm to generate sharper depth boundaries. Then, in contrast to existing approaches that use defocus cues for depth estimation, we use frequency domain analysis image similarity checking to generate the depth map. Processing in the frequency domain reduces the individual pixel errors that occur while directly comparing RGB images, making the algorithm more resilient to noise. The algorithm has been evaluated on both a synthetic image dataset and real-world images in the JPEG dataset. Experimental results demonstrate that our proposed algorithm outperforms state-of-the-art depth estimation techniques for light field images, particularly in case of noisy images.

MSBOTS: a multiple small biological organism tracking system robust against non-ideal detection and segmentation conditions.

Accurately tracking a group of small biological organisms using algorithms to obtain their movement trajectories is essential to biomedical and pharmaceutical research. However, object mis-detection, segmentation errors and overlapped individual trajectories are particularly common issues that restrict the development of automatic multiple small organism tracking research. Extending on previous work, this paper presents an accurate and generalised Multiple Small Biological Organism Tracking System (MSBOTS), whose general feasibility is tested on three types of organisms. Evaluated on zebrafish, Artemia and Daphnia video datasets with a wide variety of imaging conditions, the proposed system exhibited decreased overall Multiple Object Tracking Precision (MOTP) errors of up to 77.59%. Moreover, MSBOTS obtained more reliable tracking trajectories with a decreased standard deviation of up to 47.68 pixels compared with the state-of-the-art idTracker system. This paper also presents a behaviour analysis module to study the locomotive characteristics of individual organisms from the obtained tracking trajectories. The developed MSBOTS with the locomotive analysis module and the tested video datasets are made freely available online for public research use.

Spatial decorrelation of wind noise with porous microphone windscreens.

This paper explores the wind noise reduction mechanism of porous microphone windscreens by investigating the spatial correlation of wind noise. First, the spatial structure of the wind noise signal is studied by simulating the magnitude squared coherence of the pressure measured with two microphones at various separation distances, and it is found that the coherence of the two signals decreases with the separation distance and the wind noise is spatially correlated only within a certain distance less than the turbulence wavelength. Then, the wind noise reduction of the porous microphone windscreen is investigated, and the porous windscreen is found to be the most effective in attenuating wind noise in a certain frequency range, where the windscreen diameter is approximately 2 to 4 times the turbulence wavelengths (2 < D0/ξ < 4), regardless of the wind speed and windscreen diameter. The spatial coherence between the wind noise outside and inside a porous microphone windscreen is compared with that without the windscreen, and the coherence is found to decrease significantly when the windscreen diameter is approximately 2 to 4 times the turbulence wavelengths, corresponding to the most effective wind noise reduction frequency range of the windscreen. Experimental results with a fan are presented to support the simulations. It is concluded that the wind noise reduction mechanism of porous microphone windscreens is related to the spatial decorrelation effect on the wind noise signals provided by the porous material and structure.

Mitigating wind noise with a spherical microphone array.

This paper utilizes a rigid spherical microphone array to reduce wind noise. In the experiments conducted, a loudspeaker is used to reproduce the desired sound signal and an axial fan is employed to generate wind noise in an anechoic chamber. The sound signal and wind noise are measured separately with the spherical microphone array and analyzed in the spherical harmonic domain. The wind noise is found to be irregularly distributed in the spherical harmonic domain, distinct from the sound signal which is concentrated in the first few spherical harmonic modes. This difference is utilized to reduce wind noise without degrading the desired sound pressure level (SPL) by use of a low pass filter method in the spherical harmonic domain. Experimental results with both single-tonal and multi-tonal sound signals demonstrate that the proposed method can reduce wind noise by more than 10 dB in the frequency range below 500 Hz. The SPL of the desired sound signal can be extracted from wind noise with an error within 1.0 dB, even when the sound level is 8 dB lower than wind noise.

Wind noise spectra in small Reynolds number turbulent flows.

Wind noise spectra caused by wind from fans in indoor environments have been found to be different from those measured in outdoor atmospheric conditions. Although many models have been developed to predict outdoor wind noise spectra under the assumption of large Reynolds number [Zhao, Cheng, Qiu, Burnett, and Liu (2016). J. Acoust. Soc. Am. 140, 4178-4182, and the references therein], they cannot be applied directly to the indoor situations because the Reynolds number of wind from fans in indoor environments is usually much smaller than that experienced in atmospheric turbulence. This paper proposes a pressure structure function model that combines the energy-containing and dissipation ranges so that the pressure spectrum for small Reynolds number turbulent flows can be calculated. The proposed pressure structure function model is validated with the experimental results in the literature, and then the obtained pressure spectrum is verified with the numerical simulation and experiment results. It is demonstrated that the pressure spectrum obtained from the proposed pressure structure function model can be utilized to estimate wind noise spectra caused by turbulent flows with small Reynolds numbers.

Automatic multiple zebrafish larvae tracking in unconstrained microscopic video conditions.

The accurate tracking of zebrafish larvae movement is fundamental to research in many biomedical, pharmaceutical, and behavioral science applications. However, the locomotive characteristics of zebrafish larvae are significantly different from adult zebrafish, where existing adult zebrafish tracking systems cannot reliably track zebrafish larvae. Further, the far smaller size differentiation between larvae and the container render the detection of water impurities inevitable, which further affects the tracking of zebrafish larvae or require very strict video imaging conditions that typically result in unreliable tracking results for realistic experimental conditions. This paper investigates the adaptation of advanced computer vision segmentation techniques and multiple object tracking algorithms to develop an accurate, efficient and reliable multiple zebrafish larvae tracking system. The proposed system has been tested on a set of single and multiple adult and larvae zebrafish videos in a wide variety of (complex) video conditions, including shadowing, labels, water bubbles and background artifacts. Compared with existing state-of-the-art and commercial multiple organism tracking systems, the proposed system improves the tracking accuracy by up to 31.57% in unconstrained video imaging conditions. To facilitate the evaluation on zebrafish segmentation and tracking research, a dataset with annotated ground truth is also presented. The software is also publicly accessible.

On the wind noise reduction mechanism of porous microphone windscreens.

This paper investigates the wind noise reduction mechanism of porous microphone windscreens. The pressure fluctuations inside the porous windscreens with various viscous and inertial coefficients are studied with numerical simulations. The viscous and inertial coefficients represent the viscous forces resulting from the fluid-solid interaction along the surface of the pores and the inertial forces imposed on the fluid flow by the solid structure of the porous medium, respectively. Simulation results indicate that the wind noise reduction first increases and then decreases with both viscous and inertial coefficients after reaching a maximum. Experimental results conducted on five porous microphone windscreens with porosity from 20 to 60 pores per inch (PPI) show that the 40 PPI windscreen has the highest wind noise reduction performance, and this supports the simulation results. The existence of the optimal values for the viscous and inertial coefficients is explained qualitatively and it is shown that the design of the porous microphone windscreens should take into account both the turbulence suppression inside and the wake generation behind the windscreen to achieve optimal performance.

Hypophosphatemia and recovery of post-hepatectomy liver insufficiency.

BACKGROUND: Hypophosphatemia (HP) is frequent following liver resection, and thought to represent use of phosphate during liver regeneration. We sought to evaluate the association of post-hepatectomy HP with liver insufficiency and recovery. METHODS: Liver resections were retrospectively reviewed from 2009 to 2012 at a single institution. We explored the relationship between HP (defined as serum phosphate ≤0.65 mmol/L), occurrence of initial liver insufficiency (ILI) [bilirubin >50 µmol/L, international normalized ratio (INR) >1.7 within 72 hours of surgery] and in-hospital recovery of ILI. Secondary outcomes included 30-day post-operative major morbidity (Clavien grade 3 and 4 complications), mortality, and re-admission. RESULTS: Among 402 patients, 223 (55.5%) experienced HP and 64 (15.9%) met our definition of ILI, of which 53 (82.8%) recovered. Length of stay, 30-day post-operative major morbidity, mortality, and re-admission were similar between patients with and without HP. Among patients with ILI, 44 (68.8%) experienced HP. Following ILI, patients with HP recovered more often than those with NP (90.9% vs. 65.0%; P=0.03). CONCLUSIONS: In patients who experience post-hepatectomy ILI, HP is associated with improved recovery, potentially indicating more efficient liver regeneration. Further studies should explore the usefulness of post-hepatectomy HP as an early prognostic factor of recovery from ILI.

The impact of red blood cell transfusions on perioperative outcomes in the contemporary era of liver resection.

BACKGROUND: Perioperative red blood cell transfusions (RBCTs) are common in patients undergoing partial hepatectomy. We sought to explore the relationship between RBCTs and posthepatectomy perioperative outcomes in the contemporary surgical era. METHODS: We reviewed all patients undergoing partial hepatectomy from 2003 to 2012. Primary outcome was 30-day major morbidity (MM). We compared patients who did and received perioperative RBCT (defined as from time of operation until 30 days postoperatively. Multivariate analysis was performed to identify factors associated with MM and duration of stay, using logistic and negative binomial regression. RESULTS: Among 712 patients, 16.8% experienced MM, of whom 53.3% received RBCT. Patients who received RBCT experienced MM more commonly (30.8% vs 11.1%; P < .001). On multivariate analysis, the only factors associated with MM were age (relative risk [RR], 1.03; 95% CI, 1.00-1.06), greater operative time (RR, 1.29; 95% CI, 1.11-1.50), and RBCT (RR, 3.57; 95% CI, 1.81-7.04). RBCT was associated independently with a greater duration of stay (RR, 1.47; 95% CI, 1.13-1.91). CONCLUSION: Receipt of RBCT is associated independently with perioperative MM and prolonged hospitalization after partial hepatectomy. These findings further the rationale supporting the need for a strategy of blood management to decrease the use of RBCT after hepatectomy.

Pressure spectra in turbulent flows in the inertial and the dissipation ranges.

Based on existing studies that provide the pressure spectra in turbulent flows from the asymptotic pressure structure function in the inertial range, this paper extends the pressure spectrum to the dissipation range by proposing a pressure structure function model that incorporates both the inertial and dissipation ranges. Existing experiment results were used to validate the proposed pressure structure function model first, and then the obtained pressure spectrum was compared with the simulation and measurement data in the literature and the wind-induced noise measured outdoors. All comparisons demonstrate that the pressure spectrum obtained from the proposed pressure structure function model can be used to estimate the pressure spectra in both the inertial and dissipation ranges in turbulent flows with a sufficiently large Reynolds number.

Is central venous pressure still relevant in the contemporary era of liver resection?

BACKGROUND: Perioperative red blood cell transfusion (RBCT) remains common after liver resection and carries risk of increased morbidity and worse oncologic outcomes. We sought to assess the factors associated with perioperative RBCT after hepatectomy with a focus on intraoperative hemodynamics. METHODS: We performed a retrospective review of our prospective hepatectomy database, supplemented by a review of anesthetic records of all patients undergoing hepatectomy with hemodynamic monitoring (arterial and central venous pressures [CVP]) from 2003-2012. Primary outcome was perioperative RBCT (during and within 30 d after surgery). After descriptive and univariate comparisons, multivariate analysis was conducted to identify factors associated with RBCT. RESULTS: Of 851 hepatectomies, 530 had complete hemodynamic data and 30.2% (161 of 530) received RBCT. Among transfused patients, female gender (P = 0.01), preoperative anemia (P < 0.001), and major liver resection (P = 0.02) were more common. Mean estimated blood loss was 1.1 L higher (2.0 versus 0.9 L; P < 0.001) and operating time was 1.1 h longer (5.8 versus 4.7 h; P < 0.001) in transfused patients. Trends in intraoperative CVP differed significantly based on transfusion status (P = 0.007). Independent factors associated with RBCT included female gender (odds ratio [OR], 2.27; P = 0.01), preoperative anemia (OR, 2.38; P = 0.03), longer operative time (OR, 1.19 per hour; P = 0.03), and higher intraoperative CVP at 1 h during surgery (OR, 1.10 per mm Hg; P = 0.005). CONCLUSIONS: Likelihood of RBCT is independently associated with female gender, preoperative anemia, longer operative time, and higher intraoperative CVP. Focus on management of preoperative anemia, operative efficiency, and low intraoperative CVP is needed to minimize the need for RBCTs.

The impact of portal pedicle clamping on survival from colorectal liver metastases in the contemporary era of liver resection: a matched cohort study.

INTRODUCTION: Portal pedicle clamping (PPC) may impact micro-metastases' growth. This study examined the association between PPC and survival after a hepatectomy for colorectal liver metastases (CRLM). METHODS: A matched cohort study was conducted on hepatectomies for CRLM at a single institution (2003-2012). Cohorts were selected based on PPC use, with 1:1 matching for age, time period and the Clinical Risk Score. Outcomes were overall and recurrence-free survival (OS and RFS). Cox regression was performed to assess the association between PPC and survival. RESULTS: Of 481 hepatectomies, 26.9% used PPC. One hundred and ten pairs of patients were matched in the cohorts. There was no significant difference in OS [hazard ratio (HR) 1.18; 95% confidence interval (CI): 0.76-1.83], with a 5-year OS of 57.8% (95%CI: 52.4-63.2%) with PPC versus 62.3% (95%CI: 57.1-67.5%) without. Five-year RFS did not differ (HR 0.98; 95%CI: 0.71-1.35) with 29.7% (95%CI: 24.9-34.5%) with PPC versus 28.0% (95%CI: 23.2-32.8%) without. When adjusting for extent of resection, transfusion, operative time and surgeon, there was no difference in OS (HR 0.91; 95%CI: 0.52-1.60) or RFS (HR: 0.86; 95%CI: 0.57-1.30). CONCLUSIONS: PPC was not associated with a significant difference in OS or RFS in a hepatectomy for CRLM. PPC remains a safe technique during hepatectomy.

The Impact of Perioperative Red Blood Cell Transfusions on Long-Term Outcomes after Hepatectomy for Colorectal Liver Metastases.

BACKGROUND: Red blood cell transfusions (RBCTs) are associated with cancer recurrence following resection of colorectal cancer. Their impact after colorectal liver metastases (CRLM) resection remains debated. We sought to explore the association between perioperative RBCT and oncologic outcomes following resection of CRLM. METHODS: We reviewed patients undergoing partial hepatectomy for CRLM from 2003 to 2012 at a single institution. Date of death was abstracted from a validated population-based cancer registry. Primary outcome was overall survival (OS). Secondary outcome was recurrence-free survival (RFS). Survivals were estimated using Kaplan-Meier methods and compared with log-rank test based on transfusion status. Cox regression analysis examined the association of RBCT with OS and RFS, while adjusting for age, preoperative chemotherapy, Clinical Risk Score, and period of treatment (2003-2007 vs. 2008-2012). RESULTS: Among 483 patients, 27.5 % received RBCT. Ninety-day postoperative mortality was 4.8 %. At median follow-up of 33 (interquartile range 20.1-54.8) months, 5-year OS was inferior in transfused patients (45.9 vs. 61.0 %; p < 0.0001). Five-year RFS was decreased with RBCT (15.5 vs. 31.6 %; p < 0.0001). The difference persisted when considering only 90-day survivors for 5-year OS (53.1 vs. 61.9 %, p = 0.023) and RFS (15.6 vs. 31.6 %; p < 0.0001). After adjustment for prognostic factors, RBCT was independently associated with decreased OS (hazard ratio 2.24; 95 % confidence interval 1.60-3.15) and RFS (hazard ratio 1.71; 95 % confidence interval 1.28-2.28). CONCLUSIONS: Perioperative RBCT is independently associated with decreased OS and RFS following hepatectomy for CRLM. Interventions to minimize and rationalize the use of RBCT for hepatectomy are warranted to mitigate this detrimental effect on long-term outcomes.

A qualitative study of patient and clinician attitudes regarding surveillance after a resection of pancreatic and peri-ampullary cancer.

BACKGROUND: After surgical resection of pancreatic adenocarcinoma, most patients will develop recurrence within 2 years. Intense follow-up is often recommended; however, its impact on survival is unknown. Patient and clinician attitudes towards follow-up were qualitatively assessed along with the perceived benefits and challenges. METHODS: A semi-structured interview guide was developed. Purposive sampling identified patients who were in active surveillance or had developed recurrence. Clinicians involved in patient care were also interviewed. Interviews were conducted until saturation was reached and themes were derived using standard qualitative methods. RESULTS: A total of 15 patients and seven clinicians were interviewed. Patient themes included a limited understanding of disease prognosis, a desire for reassurance, a desire to know if and when recurrence occurred and minimal difficulties with follow-up. Clinician themes included expectation that patients are aware of the recurrence risk, a desire to provide reassurance, support for intense follow-up and perceived patient challenges in follow-up. Overall, the dominant theme was one of disconnect between patients and clinicians in the understanding of the disease and its prognosis. DISCUSSION: Patients have an intense need for reassurance and obtain this through follow-up appointments with their oncologists. Consequently, they express few difficulties with the process. Clinicians recognize this desire for reassurance. Patients' understanding and expectations contrast starkly with clinicians' perspectives regarding prognosis.