Curated benchmark dataset for ultrasound based breast lesion analysis.

A new detailed dataset of breast ultrasound scans (BrEaST) containing images of benign and malignant lesions as well as normal tissue examples, is presented. The dataset consists of 256 breast scans collected from 256 patients. Each scan was manually annotated and labeled by a radiologist experienced in breast ultrasound examination. In particular, each tumor was identified in the image using a freehand annotation and labeled according to BIRADS features and lexicon. The histopathological classification of the tumor was also provided for patients who underwent a biopsy. The BrEaST dataset is the first breast ultrasound dataset containing patient-level labels, image-level annotations, and tumor-level labels with all cases confirmed by follow-up care or core needle biopsy result. To enable research into breast disease detection, tumor segmentation and classification, the BrEaST dataset is made publicly available with the CC-BY 4.0 license.

Cognitive Impairment and Anxiety Are Prevalent in Kidney Transplant Recipients.

INTRODUCTION: Cognitive impairment (CI) is common in end-stage kidney disease (ESKD), including kidney transplant recipients. Patients with cognitive problems may find it difficult to comply with medical recommendations after kidney transplantation (KT), which can be the cause of many complications, poorer prognosis, and increased hospitalization rates after transplantation. Additionally, some patients after KT may experience depression and anxiety, which are prevalent comorbidities in patients with ESKD. METHODS: In this single-center, cross-sectional study, we included 56 consecutive adult patients after KT. Cognitive function was assessed using the Addenbrooke Cognitive Test III (ACE III). In addition, all patients were screened for depression and anxiety using the Hospital Anxiety and Depression Scale (HADS). The impact of immunosuppressive therapy and other disease-related variables on cognitive function was also assessed. RESULTS: A total of 56 KT patients, with a mean age of 50.3 ± 11.7 years, transplanted ≤35 months ago were included in the study. The prevalence of CI was 30%. Compared with cognitively unimpaired patients, patients with CI scored significantly lower in all cognitive domains. Furthermore, better cognitive functioning after KT was significantly associated with more years of schooling. We found no significant correlation between CI and age at assessment, duration of dialysis before KT, creatinine levels, creatinine clearance, uric acid levels, hemoglobin levels, comorbid cardiovascular diseases, and immunosuppressive therapy. In addition, the prevalence of depression and anxiety in screening tests was 12.5% and 27%, respectively, and patients receiving higher daily dose of prednisone had higher HADS scores on both the depression and anxiety subscales (not statistically significant). DISCUSSION: Cognitive disorders are a relevant issue in kidney transplant recipients. There might be many factors, both before and after KT, that have a negative impact on cognition. Therefore, further research is needed to increase knowledge about the course and profile of cognitive function after KT.

Patterns of Cognitive Impairment in Hemodialysis Patients and Related Factors including Depression and Anxiety.

INTRODUCTION: Hemodialysis patients are at higher risk of developing cognitive impairment, but the pattern of affected cognitive domains is still undetermined. Little is also known about the symptoms of depression and anxiety in hemodialysis patients. METHODS: In this cross-sectional study, we included 74 consecutive adult patients undergoing hemodialysis. Cognitive functions were assessed using the Addenbrooke Cognitive Test III. In addition, all patients were screened for symptoms of depression and anxiety using the Hospital Anxiety and Depression Scale. RESULTS: The mean age of hemodialysis patients was 65.69 ± 14 years. Among the patients, there were 27% and 31% of patients with mild cognitive impairment and suspected dementia, respectively. In the group of patients with suspected dementia, all cognitive functions had significantly lower values compared to these functions in incognitively unimpaired and mild cognitive impairment patients. The most impaired domain was verbal fluency, which reflects impairments in executive function. Depression and anxiety symptoms were observed in 28% and 22% of patients, respectively. Patients with anxiety symptoms had higher levels of endogenous creatinine, parathyroid hormone, and hemoglobin, as well as decreased creatinine clearance, being younger and less educated. No factors contributing to the occurrence of depressive symptoms were found. CONCLUSION: Cognitive dysfunction is a significant problem in hemodialysis patients. Our study showed that the prevalence of cognitive impairment and depression and anxiety symptoms in hemodialysis patients was high. The domain of executive functions was most affected. Furthermore, creatinine, parathyroid hormone, hemoglobin levels, creatinine clearance, and education affected the anxiety scale score.

Derivation of acoustical streaming equations for nonlinear and dispersive fluids.

The equations of streaming generated by an acoustic mod propagating in a nonlinear dispersive medium (exhibiting absorption and dispersion of phase sound speed) are derived with an arbitrarily shaped incident acoustical field assumed. This field may be periodic or non-periodic. A general dispersion model represented by a convolution operator taking into account relaxation effects was taken into account. Making the assumption of a periodic acoustic field from the general streaming equation. The quasi-stationary flow is driven by a force given by the average value of the dispersion operator with respect to the velocity and acoustic pressure fields. In the spectral representation, it is given by the weighted spectral power density distribution of the acoustic field. The weight of the distribution is the dispersion coefficient - the eigenvalue of the dispersion operator. A new result also reveals the effect of the refractive index deviation on the driving force of streaming. The possibility of generalizing the description of streaming in the simplest case of a non-Newtonian fluid was analyzed. The Reiner-Revlin model of a simple liquid was assumed. It was also noted that the streaming model in the Maxwell liquid is analytically solvable. It was found that asymptotic states of streaming in this model and the Navier-Stokes model are identical. The derivations use new methods different from those used so far. They are based on the separation of nonlinear modes in the momentum transport equation and on the properties of the Gauss-Weierstrass function for the Fick diffusion operator. So far, the method of successive approximations has been used. The consistency of the obtained equations with the assumptions was checked. The obtained formulas generalize the known descriptions of the form of forces driving streaming and extend their application to the case of nonlinear propagation.

Prevalence of Cognitive Impairment in Peritoneal Dialysis Patients and Associated Factors.

BACKGROUND: Cognitive impairment (CI) in patients with chronic kidney disease, including those treated with renal replacement therapy, is a growing problem worldwide. OBJECTIVES: The study aimed to assess the prevalence of CI and associated factors in patients undergoing peritoneal dialysis (PD). METHODS: In this cross-sectional study, 18 consecutive patients with PD therapy and 15 controls were evaluated for CI using the Addenbrooke's Cognitive Examination III (ACE III) test. RESULTS: The prevalence of CI was 33% in patients and 27% in the control group and was not statistically significant. A higher prevalence of CI was found in subjects aged ≥65 years old than in those <65 years old (p = 0.02), but only in the control group. The prevalence of CI in PD patients over and under 65 years of age did not differ statistically significantly (p = 0.12). Memory and verbal fluency were the most affected cognitive domain in PD patients with CI (p = 0.00, p = 0.04, respectively). There was a significant correlation between higher educated PD patients and the ACE III test results. The duration of dialysis did not affect the results of the cognitive screening test. CONCLUSIONS: CI is a growing problem in the course of chronic kidney disease and dialysis therapy. It seems that cognitive problems may occur in patients undergoing PD at a younger age than in the general population with particularly affected memory and verbal fluency. Higher educated patients score better on the cognitive screening test.

Analysis of estimation of optical properties of sub superficial structures in multi layered tissue model using distribution function method.

BACKGROUND AND OBJECTIVE: This paper is focused on the analysis of a method of estimation of the absorption and scattering coefficients of nonhomogeneous two layered structures in time resolved near infrared spectroscopy using method based on cumulative distributions of time of flight of photons. METHODS: The research is based on the analysis of the superposition of cumulative distributions of time of flight of photons. This approach allows for detailed analysis of small variations in characteristics of time of flight of photons caused by an electromagnetic propagation in highly scattering non-homogeneous media. The method presented, based on the variation of statistical minimum distance estimation, is compared to the method of standard curve fitting. It is analyzed by fitting the results obtained from Monte-Carlo simulations of light propagation in the turbid medium to the data from the simulated measurements. RESULTS: The analysis is carried out for a vast range of optical properties of two layered medium in reflectance geometry. CONCLUSIONS: The method allows the estimation of the optical parameters despite the noise in the measured signal, with higher accuracy and generally with smaller number of error function evaluations.

Grating lobes suppression by adding virtual receiving subaperture in synthetic aperture imaging.

A method of suppression of grating lobes is presented, analyzed, and verified. The method is based on creating a Virtual Receiving Subaperture (VRS) by adding virtual transducer elements not existing in the physical layout of the receiver. The VRS channels are filled with data based on signals from real channels. The analytical model of the synthetic aperture imaging system's impulse response is presented to describe the properties of the VRS. The model shows a reduction of the receiving grating lobes' amplitude (with a comparison to the main lobe's amplitude) by a magnitude equal to the number of receiving transducer elements. It is shown that effective properties of the entire system with a VRS are similar to a system with a pitch in the receiving aperture that is twice as small. The numerical calculations of the impulse response show a doubling of the signal to noise ratio, which results in a reduction of the receiving grating lobes. For experimental validation, the generalized Plane Wave Imaging with and without the VRS is compared with a basic synthetic transmit aperture (STA) imaging. The experiment confirmed that the use of a VRS allows for visualization of the objects in a medium in which they are not imaged without a VRS or are visualized with a lower contrast. The reduction of grating lobes attained using the proposed method is at the level of 15dB in the visualization of the superficial cyst.

Performance assessment of time-domain optical brain imagers, part 2: nEUROPt protocol.

The nEUROPt protocol is one of two new protocols developed within the European project nEUROPt to characterize the performances of time-domain systems for optical imaging of the brain. It was applied in joint measurement campaigns to compare the various instruments and to assess the impact of technical improvements. This protocol addresses the characteristic of optical brain imaging to detect, localize, and quantify absorption changes in the brain. It was implemented with two types of inhomogeneous liquid phantoms based on Intralipid and India ink with well-defined optical properties. First, small black inclusions were used to mimic localized changes of the absorption coefficient. The position of the inclusions was varied in depth and lateral direction to investigate contrast and spatial resolution. Second, two-layered liquid phantoms with variable absorption coefficients were employed to study the quantification of layer-wide changes and, in particular, to determine depth selectivity, i.e., the ratio of sensitivities for deep and superficial absorption changes. We introduce the tests of the nEUROPt protocol and present examples of results obtained with different instruments and methods of data analysis. This protocol could be a useful step toward performance tests for future standards in diffuse optical imaging.

Multiwavelength time-resolved detection of fluorescence during the inflow of indocyanine green into the adult's brain.

Optical technique based on diffuse reflectance measurement combined with indocyanine green (ICG) bolus tracking is extensively tested as a method for clinical assessment of brain perfusion in adults at the bedside. Methodology of multiwavelength and time-resolved detection of fluorescence light excited in the ICG is presented and advantages of measurements at multiple wavelengths are discussed. Measurements were carried out: 1. on a physical homogeneous phantom to study the concentration dependence of the fluorescence signal, 2. on the phantom to simulate the dynamic inflow of ICG at different depths, and 3. in vivo on surface of the human head. Pattern of inflow and washout of ICG in the head of healthy volunteers after intravenous injection of the dye was observed for the first time with time-resolved instrumentation at multiple emission wavelengths. The multiwavelength detection of fluorescence signal confirms that at longer emission wavelengths, probability of reabsorption of the fluorescence light by the dye itself is reduced. Considering different light penetration depths at different wavelengths, and the pronounced reabsorption at longer wavelengths, the time-resolved multiwavelength technique may be useful in signal decomposition, leading to evaluation of extra- and intracerebral components of the measured signals.

Time-resolved detection of fluorescent light during inflow of ICG to the brain-a methodological study.

It was reported that time-resolved reflectance measurements carried out during inflow and washout of an optical contrast agent may provide information on the blood supply to the brain cortex of human adults. It was also shown that a measurement of fluorescence excited in the dye circulating in the brain is feasible. Unfortunately, patterns of time-resolved fluorescence signals observed during in vivo measurements are difficult to interpret. The aim of this study was to analyze the influence of several factors on the fluorescence signals measured during in vivo experiments. A laboratory instrument for recording the distributions of arrival of fluorescence photons was constructed and optimized for measurements on humans. Monte Carlo simulations and laboratory measurements on liquid phantoms as well as in vivo measurements on healthy volunteers were carried out. An influence of source-detector separation, position of the source-detector pair on the head, as well as a dose of the injected indocyanine green (ICG) on the fluorescence signals were studied in detail. It was shown that even for a small dose of ICG (0.025 mg kg(-1)) the time-resolved signals can be successfully detected on the surface of the head. Strong influence of the studied factors on the fluorescence signals was observed. It was also noted that the changes in moments of distributions of arrival times of fluorescence photons depend on the anatomical structure of the tissues located between the source and the detector.

Wavelength-resolved measurements of fluorescence lifetime of indocyanine green.

We study fluorescence lifetime of indocyanine green (ICG) using femtosecond laser and sensitive detection based on time-correlated single-photon counting. A time-resolved multichannel spectral system is constructed and applied for determination of the fluorescence lifetime of the ICG in different solvents. Emission properties of ICG in water, milk, and 1% intralipid solution are investigated. Fluorescence of the fluorophore of different concentrations (in a range of 1.7-160 µM) dissolved in different solutions is excited by femtosecond pulses generated with the use of Ti:Sa laser tuned within the range of 740-790 nm. It is observed that fluorescence lifetime of ICG in water is 0.166 ± 0.02 ns and does not depend on excitation and emission wavelengths. We also show that for the diffusely scattering solvents (milk and intralipid), the lifetime may depend on the dye concentration (especially for large concentrations of ICG). This effect should be taken into account when analyzing changes in the mean time of arrival of fluorescence photons excited in ICG dissolved in such optically turbid media.

Optical system based on time-gated, intensified charge-coupled device camera for brain imaging studies.

An imaging system for brain oxygenation based on a time-gated, intensified charge-coupled device camera was developed. It allows one to image diffusely reflected light from an investigated medium at defined time windows delayed with respect to the laser pulse. Applying a fast optomechanical switch to deliver the light at a wavelength of 780 nm to nine source fibers allowed one to acquire images in times as short as 4 s. Thus, the system can be applied in in vivo studies. The system was validated in phantom experiments, in which absorbing inclusions were localized at different depths and different lateral positions. Then, the decrease in absorption of the brain tissue related to increase in oxygenation was visualized in the motor cortex area during finger tapping by a healthy volunteer.

Estimation of speed distribution of particles moving in an optically turbid medium using decomposition of a laser-Doppler spectrum.

In this paper we present validation of laser-Doppler spectrum decomposition procedure in estimation of speed distribution of particles. Decomposition method is based on assumption that measured laser-Doppler spectrum can be approximated by linear combination of Doppler shift probability distributions calculated for different speeds of particles and anisotropy of light scattering in the medium. The Doppler shift probability distributions were calculated using Monte-Carlo simulations for Henyey-Greenstein scattering phase function. This decomposition method allows to obtain distribution of speeds of moving particles in the medium, not only average speed as it was possible in laser-Doppler perfusion monitors. Recently we reported that the method was positively verified on spectra generated for different speed distributions using Monte Carlo simulations. In this study we present results of application of the decomposition procedure in analysis of laser-Doppler spectra obtained in physical phantom experiments. A diluted solution of milk was pumped through a tube with different speeds. The dependence of the obtained distributions of speed of moving particles on the speed of flow was observed. Laser-Doppler spectra obtained during in-vivo experiment were also successfully decomposed. A healthy volunteer was investigated and the spectra of laser-Doppler signal during postocclusive hyperemia test were recorded and analyzed. We conclude that the spectrum decomposition procedure can be successfully applied in analysis of the measured laser-Doppler spectra and the amount of information provided by laser-Doppler technique can be significantly increased.

Time-resolved optical imager for assessment of cerebral oxygenation.

A time-resolved optical instrument allowing for noninvasive assessment of cerebral oxygenation is presented. The instrument is equipped with picosecond diode lasers, fast photodetectors, and time-correlated single photon counting electronics. This technology enables depth-resolved estimation of changes in absorption and, in consequence, assessment of changes in hemoglobin concentrations in the brain cortex. Changes in oxyhemoglobin (HbO(2)) and deoxyhemoglobin (Hb) can be evaluated selectively in extra- and intracerebral tissue compartments using the moments of distributions of times of flight of photons measured at two wavelengths in the near-infrared region. The combination of the data acquired from multiple sources and detectors located on the surface of the head with the depth-resolved analysis, based on the moments, enables imaging of cortex oxygenation. Results of the tests on physical phantoms as well as in vivo validation of the instrument during the motor stimulation experiment are presented.

Optimization of the Monte Carlo code for modeling of photon migration in tissue.

The Monte Carlo method is frequently used to simulate light transport in turbid media because of its simplicity and flexibility, allowing to analyze complicated geometrical structures. Monte Carlo simulations are, however, time consuming because of the necessity to track the paths of individual photons. The time consuming computation is mainly associated with the calculation of the logarithmic and trigonometric functions as well as the generation of pseudo-random numbers. In this paper, the Monte Carlo algorithm was developed and optimized, by approximation of the logarithmic and trigonometric functions. The approximations were based on polynomial and rational functions, and the errors of these approximations are less than 1% of the values of the original functions. The proposed algorithm was verified by simulations of the time-resolved reflectance at several source-detector separations. The results of the calculation using the approximated algorithm were compared with those of the Monte Carlo simulations obtained with an exact computation of the logarithm and trigonometric functions as well as with the solution of the diffusion equation. The errors of the moments of the simulated distributions of times of flight of photons (total number of photons, mean time of flight and variance) are less than 2% for a range of optical properties, typical of living tissues. The proposed approximated algorithm allows to speed up the Monte Carlo simulations by a factor of 4. The developed code can be used on parallel machines, allowing for further acceleration.