Applying collective motion models to study discordant individual behaviours within a school of fish.

Computational models of collective motion successfully reproduce the most common behaviours of a school of fish, using only a few elementary interactions between individuals. However, their ability to also reproduce individual behaviours that are discordant from those of the group has not yet been adequately investigated. In this paper, a self-propelled particle model using three interaction zones is considered in relation to the counter-rotation of an individual: a phenomenon observable in real schools of fish milling in a torus, when an individual moves in the same torus but in the opposite direction for a certain period of time. This study shows that the interactions of repulsion, orientation and attraction between individuals moving at constant speed in a three-dimensional space, with asynchronous updating, can generate temporary counter-rotations. The analysis of such events sheds light on the mechanisms that start the counter-rotation and those that end it. Although the contribution of the repulsion interaction is often significant to start and terminate the counter-rotation, it does not prove to be decisive. Indeed, it is observed that even when interactions between individuals are limited to attraction alone, temporary counter-rotations of individuals occur, provided the fish density along the circumference is not uniform. Some of these conclusions, deduced from the simulations performed, are visually consistent with what is observed in some underwater video recordings of milling schools of fish.

Where Do We Stand in Regularization for Life Science Studies?

More and more biologists and bioinformaticians turn to machine learning to analyze large amounts of data. In this context, it is crucial to understand which is the most suitable data analysis pipeline for achieving reliable results. This process may be challenging, due to a variety of factors, the most crucial ones being the data type and the general goal of the analysis (e.g., explorative or predictive). Life science data sets require further consideration as they often contain measures with a low signal-to-noise ratio, high-dimensional observations, and relatively few samples. In this complex setting, regularization, which can be defined as the introduction of additional information to solve an ill-posed problem, is the tool of choice to obtain robust models. Different regularization practices may be used depending both on characteristics of the data and of the question asked, and different choices may lead to different results. In this article, we provide a comprehensive description of the impact and importance of regularization techniques in life science studies. In particular, we provide an intuition of what regularization is and of the different ways it can be implemented and exploited. We propose four general life sciences problems in which regularization is fundamental and should be exploited for robustness. For each of these large families of problems, we enumerate different techniques as well as examples and case studies. Lastly, we provide a unified view of how to approach each data type with various regularization techniques.

Atherosclerotic saccular aneurysm of the extracranial internal carotid artery: Surgical repair.

INTRODUCTION AND IMPORTANCE: Extracranial carotid aneurysms (ECCAs) are relatively uncommon. Most of these lesions are due to atherosclerosis, trauma, infection, radiotherapy, previous surgery or iatrogenic event. Severe complications include rupture, dysphagia, respiratory symptoms and brain embolization. CASE PRESENTATION: We report a case of a large saccular aneurysm of the extracranial internal carotid artery (EICA) in a 83-year old asymptomatic woman without any apparent causative history. The patient underwent a successful repair of the aneurysm by aneurysmectomy and primary end-to-end anastomosis between the proximal and distal portion of the remaining vessel with continuity restored without tension. CLINICAL DISCUSSION: ECCAs are rare with few cases reported in the most recent literature. There is little knowledge of their natural history and management. Both surgical and endovascular as well as medical treatments have been recommended depending on disease-location and comorbidities. CONCLUSION: Although treatment should be individualized time by time by evaluating patient's characteristics, the surgical repair could be a safe and effective solution to treat distal EICAs, especially for symptomatic and true growing lesions. The presentation, the diagnostic evaluation, and the successful surgical treatment are discussed.

Wideband 2-D sparse array optimization combined with multiline reception for real-time 3-D medical ultrasound.

Three-dimensional (3-D) ultrasound medical imaging provides advantages over a traditional 2-D visualization method. However, the use of a 2-D array to acquire 3-D images may result in a transducer composed of thousands of elements and a large amount of data in the front-end, making it impractical to implement high volume rate imaging and individually control all elements with the scanner. This paper proposes an original approach, valid for wideband operations centered on the design center frequency, to maintain a limited number of active elements and firing events, while preserving high resolution and volume rate. A 7 MHz 2-D array is composed of two circular concentric subparts. In the inner footprint the elements are distributed following a regular grid, while in the outer subpart a sparse non-grid solution is adopted. The inner circular dense array is composed of 256 elements with a pitch of 0.5λ. The overall footprint, delimited by the outer subpart, is equivalent to a 256-element array with a pitch of 1.5λ. All the elements of the inner subpart are activated in transmission. Following an optimization procedure, both subparts, including a subset of the elements placed in the inner footprint (i.e., sparse on-the-grid array) and the elements spread over the outer subpart (i.e., sparse off-the-grid array) are used to receive. A total number of 256 elements, defined by the sum of elements distributed in the inner and outer subparts, is fixed in reception. The proposed approach implies a multiline reception strategy, where for each transmission 3 × 3 firing events occur in reception. The sparse receive array is optimized by using a simulated annealing optimization. An original cost function is designed specifically to achieve successful results in wideband conditions. The receive array is optimized in order to obtain consistent results for different signal bandwidths of the excitation pulse. For all the desired bandwidths, the optimized array will provide the recovery of the lower lateral resolution of the transmission phase and, at the same time, a significant reduction of the undesired side lobe raised in the 3-D two-way beam pattern. The 3-D two-way beam pattern analysis reveals that the proposed solution is able to guarantee a lateral resolution of 1.35 mm at a focus depth of 25 mm for the three fractional signal bandwidths of interest (i.e., 30%, 50% and 70%) considered in the optimization process. The undesired side lobes are successfully suppressed especially when, as a consequence of the multiline strategy, non-coincident steering angles are used in transmission and reception. Moreover, thanks to the firing scheme adopted, a high-volume rate of 63 volumes per second may be achieved at the focus depth. The volume rate decreases to 32 volumes per second at twice the focal depth. Phantom image simulations show that the proposed method maintains a satisfactory and almost uniform image quality in terms of resolution and contrast for all the signal bandwidths of interest.

Oxygen Delivery Therapy with EPIFLO Reduces Wound Hyperperfusion in Patients with Chronic Leg Ulcers: A Laser Speckle Contrast Analysis.

BACKGROUND: Today transdermal continuous oxygen therapy (TCOT) is used in wound care to promote healing by improving local hypoxia and preventing infection, and it has been described to reduce local inflammation over 1 month of administration. The present study aims to investigate the effects of this treatment on wound microcirculation through laser speckle contrast analysis (LASCA). METHODS: 20 adult patients (mean age: 76 ± 11.5 years) were prospectively enrolled. Inclusion criteria were presence of venous or mixed lower limb ulcers from three or more months without dimension reduction and without indication to surgery and weekly treatment by our outpatient clinic with silver dressings. Subjects underwent 1 month of TCOT (EPIFLO®) in addition to foam dressing. The primary endpoint was the comparison of ulcer and healthy skin perfusion through LASCA, performed before and after the treatment period. Secondary considered endpoints were wound area, wound area severity index and PUSH Tools 3.0 ulcer severity scales, and pain assessment (Numerical Rating Scale [NRS]). RESULTS: Before treatment, the wound area was significantly more perfused than healthy skin (+45%; P = 0.005). At the end of the study, this difference was not significant anymore (+20.5%; P = 0.11). Ulcer perfusion decreased (-12.5%, P = 0.047), whereas healthy skin perfusion did not vary significantly. A reduction of the wound dimension (median difference: 2 cm; P = 0.009) and pain (median difference: 2 NRS point; P < 0.001) after therapy were assessed. CONCLUSIONS: LASCA shows that 1 month of TCOT can help reduce hyperperfusion of ulcer bed in patients with chronic lower limb ulcers, strengthening the hypothesis that this treatment effectively contrasts inflammation. This could correlate with the area and pain reduction assessed; however, the absence of a control group in this study does not allow a generalization of this hypothesis. Larger, controlled trials are needed to properly assess the relationship between TCOT effects on wound microenvironment and effective healing process.

Day surgery versus Outpatient setting for endovenous laser ablation treatment. A prospective cohort study.

OBJECTIVES: The traditional surgical approach to the treatment of the superficial venous insufficiency requires at least 12 h of post-operative monitoring and this often means the necessity of an overnight hospitalization. The introduction of new, less invasive techniques (i.e endovenous laser ablation) reduces the hospitalization stay in a Day Surgery setting. However, the increasing skills of the operators and the patient's selection, allows to propose endovenous laser ablation in an Outpatient setting. The aim of this study is to evaluate the activity of a single high-volume center. METHOD: We enrolled 112 consecutive patients with great sapehous vein insufficiency and indication to endothermal laser ablation, 57 operations (51%) were performed in Day Surgery setting and 55 (49%) in Outpatient setting according to endovascular laser ablation's criteria. Past medical history, CEAP classification, VCSS score, type of symptoms and intervention's data were collected. Post-operative results (success and complications rates, patient's functional and aesthetic satisfaction) were evaluated at 7 and 30 days after intervention. A QoL questionnaire (CIVIQ) was submitted to the patients 30 days after surgery. RESULTS: We did not observe a statistically significant difference between the two groups concerning treatment results and complications onset. The QoL assessment did not differed significantly, except for over 65-year old patients undergoing outpatient treatment that showed a better QoL compared to those undergoing the same treatment in Day Surgery (p 0.05). CONCLUSIONS: The endothermal laser ablation technique allows a safe, comfortable and faster management of the venous disease in Outpatient setting. This would further reduce the costs of the treatment while preserving the functional and aesthetic results and the low complication rate of the Day Surgery setting.

Audio Tracking in Noisy Environments by Acoustic Map and Spectral Signature.

A novel method is proposed for generic target tracking by audio measurements from a microphone array. To cope with noisy environments characterized by persistent and high energy interfering sources, a classification map (CM) based on spectral signatures is calculated by means of a machine learning algorithm. Next, the CM is combined with the acoustic map, describing the spatial distribution of sound energy, in order to obtain a cleaned joint map in which contributions from the disturbing sources are removed. A likelihood function is derived from this map and fed to a particle filter yielding the target location estimation on the acoustic image. The method is tested on two real environments, addressing both speaker and vehicle tracking. The comparison with a couple of trackers, relying on the acoustic map only, shows a sharp improvement in performance, paving the way to the application of audio tracking in real challenging environments.

Magnetic resonance and ultrasound contrast imaging of polymer-shelled microbubbles loaded with iron oxide nanoparticles.

Dual-mode contrast agents (CAs) have great potential for improving diagnostics. However, the effectiveness of CAs is strictly related to both the solution adopted to merge the two agents into a single probe unit, and the ratio between the two agents. In this study, two dual-mode CAs for simultaneous magnetic resonance imaging (MRI) and ultrasound imaging (UI) were assessed. For this purpose, different densities of superparamagnetic iron oxide nanoparticles (SPIONs) were anchored to the external surface of polymer-shelled microbubbles (MBs) or were physically entrapped into the shell. In vitro static and dynamic experiments were carried out with a limited concentration of modified MBs (106 bubbles ml-1) by avoiding destruction during UI (performed at a peak pressure lower than 320 kPa) and by using a low-field MRI system (with a magnetic flux density equal to 0.25 T). Under these conditions, different imaging techniques, set-up parameters and SPION densities were used to achieve satisfactory detection of the CAs by using both UI and MRI. However, when the SPION density was increased, the MRI contrast improved, whereas the UI contrast worsened due to the reduced elasticity of the MB shell. For both UI and MRI, MBs with externally anchored SPIONs provided better performance than MBs with SPIONs entrapped into the shell. In particular, a SPION density of 29% with respect to the mass of the MBs was successfully tested.

Fault Diagnosis Strategies for SOFC-Based Power Generation Plants.

The success of distributed power generation by plants based on solid oxide fuel cells (SOFCs) is hindered by reliability problems that can be mitigated through an effective fault detection and isolation (FDI) system. However, the numerous operating conditions under which such plants can operate and the random size of the possible faults make identifying damaged plant components starting from the physical variables measured in the plant very difficult. In this context, we assess two classical FDI strategies (model-based with fault signature matrix and data-driven with statistical classification) and the combination of them. For this assessment, a quantitative model of the SOFC-based plant, which is able to simulate regular and faulty conditions, is used. Moreover, a hybrid approach based on the random forest (RF) classification method is introduced to address the discrimination of regular and faulty situations due to its practical advantages. Working with a common dataset, the FDI performances obtained using the aforementioned strategies, with different sets of monitored variables, are observed and compared. We conclude that the hybrid FDI strategy, realized by combining a model-based scheme with a statistical classifier, outperforms the other strategies. In addition, the inclusion of two physical variables that should be measured inside the SOFCs can significantly improve the FDI performance, despite the actual difficulty in performing such measurements.

In vivo quantification of ultrasound targeted microbubbles to enhance cancer assessment.

Contrast-enhanced ultrasound with targeted microbubble contrast agents is an emerging technique for imaging biological processes at the molecular level. The accumulation of targeted microbubbles at tissue sites overexpressing specific molecular markers increases the backscattered signal for noninvasive evaluations of diseases. The aim of this preliminary study was to combine molecular imaging with an in vivo contrast agent quantification to support the early diagnosis of the pathology and to enhance the assessment of neoplastic tissues. Tumor growth was induced by subcutaneous injection of prostate cancer cells in four rats. Microbubbles targeted to tissue factor (TF) were administered. A vascularized region located in proximity to the tumor and centered around the focus depth was analyzed in each animal. The backscattered signals (i.e. the radio-frequency data) were acquired during two different perfusion conditions to evaluate the contribution of attached microbubbles. After image generation by means of a multi-pulse contrast-enhanced technique, a nonlinear regression method based on the support vector machine was employed to estimate the contrast agent concentrations in cubic voxels (1-mm side length). The number of attached microbubbles per mm(3) was estimated based on a multi-dimensional vector of features extracted from the processed radio-frequency signals. A significant correlation (p < 0.05) between the size of the tumors and the estimated microbubble concentration was found, thus opening the possibility for combining molecular imaging and contrast agent concentration mapping to refine pathology evaluation. Copyright © 2016 John Wiley & Sons, Ltd.

Serum Procalcitonin as a Valuable Diagnostic Tool in the Early Detection of Infectious Complications after Open Abdominal Aortic Repair.

BACKGROUND: Aortic aneurysm repair is a resolutive and effective surgical operation, which can be associated with severe postoperative complications. Procalcitonin (PCT) in clinical practice could play a role in early diagnosis and monitoring of therapy for complications, especially infections, making for timely and more effective interventions. Our aim was to investigate whether PCT could be a predictive marker in early diagnosis of infectious complications after open abdominal aortic surgery. METHODS: Eighty-three consecutive patients who underwent elective open aortic repair at our institution were enrolled. Blood samples were taken before surgery, and each day over the 7-day postoperative period, and measurement of serum PCT, C-reactive protein (CRP), and leukocytes levels were carried out. Data regarding clinical progress, instrumental examinations, and blood chemistry were prospectively collected. RESULTS: Postoperative infectious complications occurred in 24 patients. Within 30 days, 1 death occurred. In the study sample, we found a significant difference in PCT curves of patients with and without infectious complications, especially on third postoperative day (POD; P = 0.004). On analysis of the area under the curve (AUC curve), PCT was shown to be a fair predictor in distinguishing cases with infectious complications (AUC, 0.765 on third POD; CI, 0.638-0.877). Conversely, other inflammatory markers commonly used (leucocytes and CRP) had similar trends in patients with and without postoperative infections. CONCLUSIONS: On the basis of the results collected in this pilot study, despite some limitations, PCT could be considered a better marker of infectious complications after open abdominal aortic repair, when compared with other routinely used parameters.

Increasing efficacy of endovascular recanalization with covered stent graft for TransAtlantic Inter-Society Consensus II D aortoiliac complex occlusion.

OBJECTIVE: We compared the outcomes and the durability of endovascular recanalization (EVR) with the Viabahn (W. L. Gore and Associates, Flagstaff, Ariz) covered stent graft vs traditional aortobifemoral or aortofemoral bypass grafting for complex aortoiliac occlusions. METHODS: Between 2008 and 2014, 11 unilateral iliac occlusions and 11 aortobiiliac occlusions were treated by EVR. Also collected were data from the last 21 consecutive patients treated in the same period by aortofemoral (n = 6) or aortobifemoral (n = 15) bypass grafting. In accordance with the TransAtlantic Inter-Society Consensus II (TASC II) document, only patients with type D lesions were considered. Kaplan-Meier estimates for patency were calculated, and Cox proportional hazard modeling was performed. RESULTS: The difference in risk factors between the groups was not significant. General anesthesia was required in 100% of the surgical group, and local or locoregional anesthesia was used for EVR. Suprarenal aortic cross-clamping was required in nine of the open surgical procedures (41%). A brachial percutaneous approach was performed in all patients undergoing EVR, and technical success was 100% in both groups. All of the attempts at EVR were successful. At the 2-year follow-up, primary patency did not differ significantly between the endovascular (91%) and surgical (95%) groups. This was seen in the univariate model (hazard ratio [HR], 0.27; 95% confidence interval [CI], 0.02-2.95; P = .28) and in the multivariate model (HR, 0.77; 95% CI, 0.06-10.07; P = .84) for group (HR, 0.58; 95% CI, 0.04-7.72; P = .68), age (HR, 0.89; 95% CI, 0.73-1.08; P = .24), symptoms (HR, 1.98; 95% CI, 0.42-9.46; P = .39), and occlusion (HR, 3.22; 95% CI, 0.51-20.35; P = .21). The average hospital length of stay was shorter for patients treated with ERV than for those treated with open surgery (3.9 ± 2.2 vs 5.8 ± 3.1 days, respectively; P = .03). The complication rate was 4% for EVR vs 18% in the surgical group (P = .32). CONCLUSIONS: At 2 years of follow-up, the results of endoluminal bypass grafting with the Viabahn stent to treat complex aortoiliac disease are promising. Longer-term results are needed to fully evaluate the potential benefits and longer-term patency.

U Stent-Graft Technique as a Treatment for Homolateral Metachronous Common Iliac and Internal Iliac Arteries Aneurysms after Open Surgery.

We report a case of a metachronous common iliac artery and the internal iliac artery (IIA) aneurysm developed 8 years after an aortobi-femoral bypass for treatment of abdominal aortic aneurysm associated at chronic occlusion of the right iliac axis. To exclude the metachronous aneurysm on the left iliac axis and to maintain the pelvic circulation, an external to IIA endografts were positioned ("U stent-graft technique"). At 6-month follow-up, the computed tomography scan showed patency of the endografts, of the bypass and of the IIA, without endoleak, or other adverse events.

Maximum Constrained Directivity of Oversteered End-Fire Sensor Arrays.

For linear arrays with fixed steering and an inter-element spacing smaller than one half of the wavelength, end-fire steering of a data-independent beamformer offers better directivity than broadside steering. The introduction of a lower bound on the white noise gain ensures the necessary robustness against random array errors and sensor mismatches. However, the optimum broadside performance can be obtained using a simple processing architecture, whereas the optimum end-fire performance requires a more complicated system (because complex weight coefficients are needed). In this paper, we reconsider the oversteering technique as a possible way to simplify the processing architecture of equally spaced end-fire arrays. We propose a method for computing the amount of oversteering and the related real-valued weight vector that allows the constrained directivity to be maximized for a given inter-element spacing. Moreover, we verify that the maximized oversteering performance is very close to the optimum end-fire performance. We conclude that optimized oversteering is a viable method for designing end-fire arrays that have better constrained directivity than broadside arrays but with a similar implementation complexity. A numerical simulation is used to perform a statistical analysis, which confirms that the maximized oversteering performance is robust against sensor mismatches.

Acoustic characterization and contrast imaging of microbubbles encapsulated by polymeric shells coated or filled with magnetic nanoparticles.

The combination of superparamagnetic iron oxide nanoparticles with polymeric air-filled microbubbles is used to produce two types of multimodal contrast agents to enhance medical ultrasound and magnetic resonance imaging. The nanoparticles are either covalently linked to the shell or physically entrapped into the shell. In this paper, the characterization of the acoustic properties (backscattered power, fracturing pressure, attenuation and dispersion of the ultrasonic wave) and ultrasound imaging of the two types of magnetic microbubbles are presented. In vitro B-mode images are generated using a medical ultrasound scanner by applying a nonconventional signal processing technique that is suitable to detect polymeric bubbles and based on the combination of multipulse excitation and chirp coding. Even if both types of microbubbles can be considered to be effective ultrasound contrast agents, the different structure of the shell loaded with nanoparticles has a pronounced effect on the echogenicity and the detection sensitivity of the imaging technique. The best results are obtained using microbubbles that are externally coated with nanoparticles. A backscattered power of 20 dB was achieved at lower concentration, and an increment of 8 dB in the contrast-to-tissue ratio was observed with respect to the more rigid microbubbles with particles entrapped into the shell.

Ultrasound assessment of polymer-shelled magnetic microbubbles used as dual contrast agents.

This letter describes an ultrasound imaging assessment of novel contrast agents that are detectable by both medical ultrasound and magnetic resonance imaging. Such agents are created by including superparamagnetic particles in polymer-shelled microbubbles through two different approaches. The reduced echogenicity and nonlinearity of the microbubbles are observed, depending on the strategy used to include the particles and the resulting density. The best results are obtained using imaging techniques that exploit the third-order nonlinear term, which is especially true when the microbubbles are excited by means of chirp pulses.

The synthesis of robust broadband beamformers for equally-spaced linear arrays.

Broadband beamforming applied to superdirective arrays is known to be highly sensitive to transducers characteristics errors. Recently, an effective method to synthesize a robust, broadband, data-independent, filter-and-sum beamformer, which considers the probability distributions of errors, has been proposed. It considers an array with arbitrary lay-out and provides a spatial directivity pattern close to the desired one. Unfortunately, the evaluation of the cost function requires a computational load and an amount of memory that increases very quickly with the transducers and the filter coefficients. As the synthesis process requires an iterative minimization, it may become unacceptably long. In this paper, an alternative procedure for evaluating the same cost function is presented, drastically reducing such problems and without introducing any approximation. The only additional constraint is on the antenna which must be an equally-spaced linear array. This procedure makes it much easier to apply the above-mentioned synthesis method to a wide panorama of practical situations.

Chirp zeta transform beamforming for three-dimensional acoustic imaging.

This letter considers the possibility of the generation of three-dimensional acoustic images with a limited computational load by considering the extension of Chirp zeta transform beam forming to the case of planar array and near-field conditions. This extension, with a few innovative solutions, allows for a dramatic reduction in the number of on-line operations over traditional time-domain beamforming.

On the shaping of the main lobe in wide-band arrays.

This paper describes a method to obtain a wide-band beam pattern whose main lobe has the desired shape and, at the same time, the level of the side lobes is acceptable. The aim is to reproduce a main lobe profile as close as possible to the desired one through the synthesis of the array-weighting window. A typical goal is to obtain, in wide-band conditions, a flat-top shaped beam similar to the ones produced by specific narrow-band windows. To achieve this result, an optimization process based on simulated annealing is developed and applied under different operating conditions, including two wide-band beam pattern definitions and different values of the fractional bandwidth. Although the shape of the resulting main lobe is not as good as the one obtained in narrow-band conditions (the reasons for this drawback are given), it is shown that the adoption of windows synthesized by the proposed method is more suitable than the direct application of narrow-band windows in wide-band conditions. In addition to providing better performances, it is shown that the windows synthesized by the proposed method also result in greater robustness to random perturbations of weight values, which are unavoidable in real systems.

On the stability of wideband beam patterns with respect to weighting and envelope fluctuations.

This paper presents a study on the worsening caused by a random perturbation of the weighting window (modeling, in this way, the uncertainty on the channel sensitivity), or by an alteration of the shape of the transmitted pulse, for a wideband array. In the stability evaluation, main-lobe width and signal to noise ratio evaluated at different dB levels of the beam pattern play the role of quality parameters. Two different profiles of the weighting window have been used for this analysis: a typical raised cosine, and a window optimized by a Simulated Annealing procedure. Also for the pulse envelope, two distinct shapes have been chosen: perfectly Gaussian and experimentally measured. The analysis of the obtained results provides useful hints about the amount and the kind of the beam pattern worsening, when realistic fluctuations occur. Moreover, the results show that the weighting windows provided by the simulated annealing procedure are particularly robust to such fluctuations.