Positive Pixels Research Articles

ROLE OF TEXTURE ANALYSIS IN PREDICTING HISTOPATHOLOGICAL OUTCOME IN PATIENTS WITH BRAIN MASSES USING CT AND MRI IMAGING

Objectives: Brain tumors, particularly gliomas, are difficult to differentiate radiologically, whether they are benign or malignant, which usually requires histopathological examination. Texture analysis (TA), a method for quantification of heterogeneity of the tumor, can be used as a tool for this differentiation. This study aims to elucidate possible associations between computed tomography (CT) scan or magnetic resonance imaging TA (MRI TA) of brain tumors and their histopathological diagnosis. Methods: A total of 20 patients with brain tumor were retrospectively studied. A detailed history was taken so that only pre-treatment CT/MRI scans were included to avoid heterogeneity of the sample. Patients from all age groups and sexes were included. Postcontrast images with the largest cross-section of the tumor were processed for TA (using texRAD software). Results: In this study, it was found that for World Health Organisation (WHO) grade I and II brain tumors, mean and mean of positive pixel (MPP) are high and Kurtosis is low when compared with WHO grade III and IV. The strongest differences on unfiltered images were found for mean and MPP (p=0.049) and on medium-level filter for Kurtosis (p=0.049). Conclusion: TA has a great potential to improve the diagnosis and stratification of patients of brain tumors. It can also give information regarding the underlying growth patterns, and hormonal/tumor markers, may add inputs in decisions regarding therapeutic efficacy, follow-up before and after treatment and prognosis, thus helping in the management of the patient. Objectives: Brain tumors, particularly gliomas, are difficult to differentiate radiologically, whether they are benign or malignant, which usually requires histopathological examination. Texture analysis (TA), a method for quantification of heterogeneity of the tumor, can be used as a tool for this differentiation. This study aims to elucidate possible associations between computed tomography (CT) scan or magnetic resonance imaging TA (MRI TA) of brain tumors and their histopathological diagnosis. Methods: A total of 20 patients with brain tumor were retrospectively studied. A detailed history was taken so that only pre-treatment CT/MRI scans were included to avoid heterogeneity of the sample. Patients from all age groups and sexes were included. Postcontrast images with the largest cross-section of the tumor were processed for TA (using texRAD software). Results: In this study, it was found that for World Health Organisation (WHO) grade I and II brain tumors, mean and mean of positive pixel (MPP) are high and Kurtosis is low when compared with WHO grade III and IV. The strongest differences on unfiltered images were found for mean and MPP (p=0.049) and on medium-level filter for Kurtosis (p=0.049). Conclusion: TA has a great potential to improve the diagnosis and stratification of patients of brain tumors. It can also give information regarding the underlying growth patterns, and hormonal/tumor markers, may add inputs in decisions regarding therapeutic efficacy, follow-up before and after treatment and prognosis, thus helping in the management of the patient.

A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus

Unsupervised segmentation in biological and non-biological images is only partially resolved. Segmentation either requires arbitrary thresholds or large teaching datasets. Here, we propose a spatial autocorrelation method based on Local Moran’s I coefficient to differentiate signal, background, and noise in any type of image. The method, originally described for geoinformatics, does not require a predefined intensity threshold or teaching algorithm for image segmentation and allows quantitative comparison of samples obtained in different conditions. It utilizes relative intensity as well as spatial information of neighboring elements to select spatially contiguous groups of pixels. We demonstrate that Moran’s method outperforms threshold-based method in both artificially generated as well as in natural images especially when background noise is substantial. This superior performance can be attributed to the exclusion of false positive pixels resulting from isolated, high intensity pixels in high noise conditions. To test the method’s power in real situation, we used high power confocal images of the somatosensory thalamus immunostained for Kv4.2 and Kv4.3 (A-type) voltage-gated potassium channels in mice. Moran’s method identified high-intensity Kv4.2 and Kv4.3 ion channel clusters in the thalamic neuropil. Spatial distribution of these clusters displayed strong correlation with large sensory axon terminals of subcortical origin. The unique association of the special presynaptic terminals and a postsynaptic voltage-gated ion channel cluster was confirmed with electron microscopy. These data demonstrate that Moran’s method is a rapid, simple image segmentation method optimal for variable and high noise conditions.

A novel image segmentation method based on spatial autocorrelation identifies A-type potassium channel clusters in the thalamus.

Unsupervised segmentation in biological and non-biological images is only partially resolved. Segmentation either requires arbitrary thresholds or large teaching datasets. Here, we propose a spatial autocorrelation method based on Local Moran's I coefficient to differentiate signal, background, and noise in any type of image. The method, originally described for geoinformatics, does not require a predefined intensity threshold or teaching algorithm for image segmentation and allows quantitative comparison of samples obtained in different conditions. It utilizes relative intensity as well as spatial information of neighboring elements to select spatially contiguous groups of pixels. We demonstrate that Moran's method outperforms threshold-based method in both artificially generated as well as in natural images especially when background noise is substantial. This superior performance can be attributed to the exclusion of false positive pixels resulting from isolated, high intensity pixels in high noise conditions. To test the method's power in real situation, we used high power confocal images of the somatosensory thalamus immunostained for Kv4.2 and Kv4.3 (A-type) voltage-gated potassium channels in mice. Moran's method identified high-intensity Kv4.2 and Kv4.3 ion channel clusters in the thalamic neuropil. Spatial distribution of these clusters displayed strong correlation with large sensory axon terminals of subcortical origin. The unique association of the special presynaptic terminals and a postsynaptic voltage-gated ion channel cluster was confirmed with electron microscopy. These data demonstrate that Moran's method is a rapid, simple image segmentation method optimal for variable and high noise conditions.

Interannual variations of normalized difference vegetation index and potential evapotranspiration and their relationship in the Baghdad area

Abstract A monthly correlation between urban vegetation growth and potential evapotranspiration (PET) is needed for better knowledge of controlling water resources and organized irrigation processes. This study aims to explore their relationship within an urban area like Baghdad, using a linear regression model to derive a best-fit line drawn in a scatterplot on a monthly time scale. Based on two different monthly data sources: weather variables (e.g., air temperature, solar radiation, and relative humidity) and Sentinel-2 satellite imagery of 2 years, 2018 and 2021, this study presented the interannual variations of PET and normalized difference vegetation index (NDVI). The choice of these years has a significant feature of climatic differences, which are arid and semi-arid, respectively. PET values were estimated by the Truc method, while the areas of vegetation (represented by NDVI) were calculated using the Geographic Information Sensing program. The results show that the maximum PET in both years was found in the summer months (June and July) with mean values of about 8.8 mm/day, while their minimum mean values of about 1.5 mm/day occurred in winter months (January and December). From the spatial distribution of NDVI, it was found that at positive pixels when NDVI >0.2, vegetation cover in March, April, and December 2018 had large areas with more than 200 km2 in 2018, while they were largest only in May 2021 with 197.8 km2. There was a linear correlation with slope (0.03) and intercept (= 1.8) and a strong correlation, R 2 = 0.72. The practical implications of the findings contribute to enhancing a solid scientific basis for improving agricultural water management, especially under dry conditions.

TYK2 Protein Expression and Its Potential as a Tissue-Based Biomarker for the Diagnosis of Colorectal Cancer.

The aim of this study was to examine the expression of TYK2 in colorectal cancer (CRC) and to determine the potential diagnostic and prognostic significance of this kinase. Digital image analysis was performed to assess immunohistochemical TYK2 reactivity. There were significant differences for all positive pixels between CRC and normal colonic mucosa, with higher TYK2 expression levels observed in surgical margins than in adenocarcinomas (p = 0.0004). Paired t tests showed elevated immunoreactivity for overall TYK2 expression in matched pairs of CRC with adjacent surgical margins (p < 0.0001). Higher percentages of weak (p < 0.0001) and strong pixels (p = 0.0260) were detected in normal colonic mucosa than in cancer tissues. To distinguish cancer from normal intestinal mucosa, the following cutoffs for the TYK2 immune score were found: 29.5% for all cases and 31% for matched pairs. Tumor budding (Bd) was negatively correlated with the percentage of strong pixels for TYK2 (ρ = -0.270, p = 0.0096). The percentage of strong pixels was significantly elevated for the T parameter (p = 0.0428). There was a positive correlation between the number of involved lymph nodes and weak pixels (ρ = 0.239, p = 0.0242). Immunofluorescence staining showed significantly higher signal intensities in colonic mucosa than in CRC. The protein level of TYK2 was significantly higher in controls than in cancer tissues. TEM imaging showed lower levels of TYK2 in cancer than in ulcerative colitis. TYK2 protein expression may bring diagnostic value in patients diagnosed with CRC.

The link between amyloid β and ferroptosis pathway in Alzheimer’s disease progression

Alzheimer’s disease (AD) affects millions of people worldwide and represents the most prevalent form of dementia. Treatment strategies aiming to interfere with the formation of amyloid β (Aβ) plaques and neurofibrillary tangles (NFTs), the two major AD hallmarks, have shown modest or no effect. Recent evidence suggests that ferroptosis, a type of programmed cell death caused by iron accumulation and lipid peroxidation, contributes to AD pathogenesis. The existing link between ferroptosis and AD has been largely based on cell culture and animal studies, while evidence from human brain tissue is limited. Here we evaluate if Aβ is associated with ferroptosis pathways in post-mortem human brain tissue and whether ferroptosis inhibition could attenuate Aβ-related effects in human brain organoids. Performing positive pixel density scoring on immunohistochemically stained post-mortem Brodmann Area 17 sections revealed that the progression of AD pathology was accompanied by decreased expression of nuclear receptor co-activator 4 and glutathione peroxidase 4 in the grey matter. Differentiating between white and grey matter, allowed for a more precise understanding of the disease’s impact on different brain regions. In addition, ferroptosis inhibition prevented Aβ pathology, decreased lipid peroxidation and restored iron storage in human AD iPSCs-derived brain cortical organoids at day 50 of differentiation. Differential gene expression analysis of RNAseq of AD organoids compared to isogenic controls indicated activation of the ferroptotic pathway. This was also supported by results from untargeted proteomic analysis revealing significant changes between AD and isogenic brain organoids. Determining the causality between the development of Aβ plaques and the deregulation of molecular pathways involved in ferroptosis is crucial for developing potential therapeutic interventions.

Evaluation of Minimum-to-Severe Global and Macrovesicular Steatosis in Human Liver Specimens: A Portable Ambient Light-Compatible Spectroscopic Probe.

Hepatic steatosis (HS), particularly macrovesicular steatosis (MaS), influences transplant outcomes. Accurate assessment of MaS is crucial for graft selection. While traditional assessment methods have limitations, non-invasive spectroscopic techniques like Raman and reflectance spectroscopy offer promise. This study aimed to evaluate the efficacy of a portable ambient light-compatible spectroscopic system in assessing global HS and MaS in human liver specimens. A two-stage approach was employed on thawed snap-frozen human liver specimens under ambient room light: biochemical validation involving a comparison of fat content from Raman and reflectance intensities with triglyceride (TG) quantifications and histopathological validation, contrasting Raman-derived fat content with evaluations by an expert pathologist and a "Positive Pixel Count" algorithm. Raman and reflectance intensities were combined to discern significant (≥ 10%) discrepancies in global HS and MaS. The initial set of 16 specimens showed a positive correlation between Raman and reflectance-derived fat content and TG quantifications. The Raman system effectively differentiated minimum-to-severe global and macrovesicular steatosis in the subsequent 66 specimens. A dual-variable prediction algorithm was developed, effectively classifying significant discrepancies (> 10%) between algorithm-estimated global HS and pathologist-estimated MaS. Our study established the viability and reliability of a portable spectroscopic system for non-invasive HS and MaS assessment in human liver specimens. The compatibility with ambient light conditions and the ability to address limitations of previous methods marks a significant advancement in this field. By offering promising differentiation between global HS and MaS, our system introduces an innovative approach to real-time and quantitative donor HS assessments. The proposed method holds the promise of refining donor liver assessment during liver recovery and ultimately enhancingtransplantation outcomes.

Tiber River-Driven Chlorophyll-a and Total Suspended Matter Dynamics and Their Impacts along the Central Tyrrhenian Sea Coast: A Sentinel-2 Approach

Chlorophyll-a (Chl-a) and Total Suspended Matter (TSM) are key health indicators of the coastal ocean and seas. The former is linked to primary productivity, while the latter is associated with water quality; both are influenced by change in climate. Recent studies have highlighted a declining trend in Chl-a levels along the Mediterranean coastal region. River discharge plays an important role in regulating the coastal Chl-a concentration levels. The present research primarily focuses on understanding the significance of Tiber River −driven spatial dynamics of Chl-a and TSM along the central Tyrrhenian Sea coasts. The research also focuses on evaluating the applicability of Sentinel-2 and identifying a suitable method for estimating Chl-a and TSM from Sentinel-2. Neural networks and dark spectrum fitting techniques were applied using multiple algorithms to estimate the dynamic distribution of Chl-a and TSM driven by the Tiber River in the study area. Multiple statistical analyses were performed, and statistically significant relationships were observed. The Case-2 Regional Coast Colour Neural Network (C2RCC-Net) outperformed all other algorithms, with an R2 value of 0.903 for Chl-a and an R2 value of 0.966 for TSM. Furthermore, the present research also identified a positive pixel to pixel spatial correlation between Chl-a and TSM in all four seasons, highlighting the positive impact of Tiber River on maintaining Chl-a levels along the coasts of Tyrrhenian Sea. This stands in contrast with the negative trend seen in the Mediterranean scale.

Functional Optical Coherence Tomography of Rat Cortical Neurovascular Activation during Monopulse Electrical Stimulation with the Microelectrode Array

This paper presents a study to evoke rat cortical functional activities, including hemodynamic and neural tissue signal changes, by monopulse electrical stimulation with a microelectrode array using functional optical coherence tomography (fOCT). Based on the principal component analysis and fuzzy clustering method (PCA-FCM), the hemodynamic response of different size blood vessels in rat cortex are analyzed, showing that the hemodynamic response of the superficial large blood vessels is more concentrated. In the regions of neural tissue where blood vessels are removed, positive significant pixels (the intensity of the pixel for five consecutive frames is greater than the average value plus triple standard deviation) and negative significant pixels (the intensity of the pixel for five consecutive frames is less than the average value minus triple standard deviation) exist, and the averaged intensity signal responds rapidly with an onset time of ~20.8 ms. Furthermore, the hemodynamic response was delayed by ~3.5 s from the neural tissue response. fOCT can provide a label-free, large-scale and depth-resolved map of cortical neurovascular activation, which is a promising technology to monitor cortical small-scale neurovascular activities.

Comparison of two region-of-interest placement methods for histogram analysis of apparent diffusion coefficient maps for glioma grading.

We assessed the value of histogram analysis (HA) of apparent diffusion coefficient (ADC) maps for grading low-grade (LGG) and high-grade (HGG) gliomas. We compared the diagnostic performance of two region-of-interest (ROI) placement methods (ROI 1: the entire tumor; ROI 2: the tumor excluding cystic and necrotic portions). We retrospectively evaluated 54 patients with supratentorial gliomas (18 LGG and 36 HGG). All subjects underwent standard 3T contrast-enhanced magnetic resonance imaging. Histogram parameters of ADC maps calculated with the two segmentation methods comprised mean, median, maxi-mum, minimum, kurtosis, skewness, entropy, standard deviation (sd), mean of positive pixels (mpp), uniformity of positive pixels, and their ratios (r) between lesion and normal white matter. They were compared using the independent t-test, chi-square test, or Mann-Whitney U test. For statistically significant results, receiver operating characteristic curves were constructed, and the optimal cutoff value, sensitivity, and specificity were determined by maximizing Youden's index. The ROI 1 method resulted in significantly higher rADC mean, rADC median, and rADC mpp for LGG than for HGG; these parameters had value for predicting the histological glioma grade with a cutoff (sensitivity, specificity) of 1.88 (77.8%, 61.1%), 2.25 (44.4%, 97.2%), and 1.88 (77.8%, 63.9%), respectively. The ROI 2 method resulted in significantly higher ADC mean, ADC median, ADC mpp, ADC sd, ADC max, rADC median, rADC mpp, rADC mean, rADC sd, and rADC max for LGG than for HGG, while skewness was lower for LGG than for HGG (0.27 [0.98] vs 0.91 [0.81], p = 0.014). In ROI 2, ADC median, ADC mpp, ADC mean, rADC median, rADC mpp, and rADC mean performed well in differentiating glioma grade with cutoffs (sensitivity, specificity) of 1.28 (77.8%, 88.9%), 1.28 (77.8%, 88.9%), 1.25 (77.8%, 91.7%), 1.81 (83.3%, 91.7%), 1.74 (83.3%, 91.7%), and 1.81 (83.3%, 91.7%), respectively. HA parameters had value for grading gliomas. Ex-cluding cystic and necrotic portions of the tumor for measuring HA parameters was preferable to using the entire tumor as the ROI. In this segmentation, rADC median showed the highest performance in predicting histological glioma grade, followed by rADC mpp, rADC mean, ADC median, ADC mpp, and ADC mean.

Microvascular permeability and texture analysis of bone marrow in diabetic rabbits with critical limb ischemia based on dynamic contrast-enhanced magnetic resonance imaging.

Early on in the development of diabetes, skeletal muscles can exhibit microarchitectural changes that can be detected using texture analysis (TA) based on volume transfer constant (Ktrans) maps. Nevertheless, there have been few studies and thus we evaluated microvascular permeability and the TA of the bone marrow in diabetics with critical limb ischemia (CLI). Eighteen male rabbits were randomly assigned equally into an operation group with hindlimb ischemia and diabetes, a sham-operated group with diabetes only, and a control group. Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) was performed on all rabbits at predetermined intervals (1, 5, 10, 15, 20, and 25 days post-surgery). The pharmacokinetic model was used to generate the permeability parameters, while the textural parameters were derived from the Ktrans map. Data analysis methods included the independent sample t-test, Mann-Whitney U test, repeated-measures analysis of variance, and Pearson correlation tests. The Ktrans values reached a minimum on day 1 after ischemia induction, then gradually recovered, but remained lower than those of the sham-operated group. The volume fraction only showed a significant difference between the operation group and the sham-operated group on day 5 post-surgery, but not in the extravascular extracellular space volume fraction at all time points. A significantly reduced Ktrans on day 1, a decreased number of bone trabeculae (Tb.N), and the area of bone trabeculae (Tb.Ar), and an increased microvessel density on day 25 in the operation group compared with the sham-operated group were observed. At each time point, there was a discernible difference between the two groups in the mean value, mean of positive pixels, and sumAverage. The early stages of diabetic bone marrow with CLI can be evaluated by DCE-MRI for microvascular permeability. Texture analysis based on DCE-MRI could act as an imaging discriminator and new radiological analysis tool for critical limb ischemia in diabetes mellitus.

Click-pixel Cognition Fusion Network with Balanced Cut for Interactive Image Segmentation.

Interactive image segmentation (IIS) has been widely used in various fields, such as medicine, industry, etc. However, some core issues, such as pixel imbalance, remain unresolved so far. Different from existing methods based on pre-processing or post-processing, we analyze the cause of pixel imbalance in depth from the two perspectives of pixel number and pixel difficulty. Based on this, a novel and unified Click-pixel Cognition Fusion network with Balanced Cut (CCF-BC) is proposed in this paper. On the one hand, the Click-pixel Cognition Fusion (CCF) module, inspired by the human cognition mechanism, is designed to increase the number of click-related pixels (namely, positive pixels) being correctly segmented, where the click and visual information are fully fused by using a progressive three-tier interaction strategy. On the other hand, a general loss, Balanced Normalized Focal Loss (BNFL), is proposed. Its core is to use a group of control coefficients related to sample gradients and forces the network to pay more attention to positive and hard-to-segment pixels during training. As a result, BNFL always tends to obtain a balanced cut of positive and negative samples in the decision space. Theoretical analysis shows that the commonly used Focal and BCE losses can be regarded as special cases of BNFL. Experiment results of five well-recognized datasets have shown the superiority of the proposed CCF-BC method compared to other state-of-the-art methods. Code will be publicly available at https://github.com/lab206/CCF-BC.

Apparent diffusion coefficient histogram in the differentiation of benign and malignant testicular tumors.

Purpose: This retrospective study assessed the value of histogram parameters of the apparent diffusion coefficient (ADC) map (HA) in differentiating between benign and malignant testicular tumors. We compared the diagnostic performance of two different volume-of-interest (VOI) placement methods: VOI 1, the entire tumor; VOI 2, the tumor excluding its cystic, calcified, hemorrhagic, and necrotic portions. Materials and methods: We retrospectively evaluated 45 patients with testicular tumors examined with scrotal contrast-enhanced magnetic resonance imaging. These patients underwent surgery with the pathological result of seven benign and 39 malignant tumors. We calculated the HA parameters, including mean, median, maximum, minimum, kurtosis, skewness, entropy, standard deviation (SD), mean of positive pixels, and uniformity of positive pixels by the two different VOI segmentation methods. We compared these parameters using the chi-square test, Mann-Whitney U test, and area under the receiver operating characteristic curve (AUC) to determine their optimal cut-off, sensitivity (Se), and specificity (Sp). Result: This study included 45 patients with 46 testicular lesions (seven benign and 39 malignant tumors), one of which had bilateral testicular seminoma. With the VOI 1 method, benign lesions had significantly lower maximum ADC (p = 0.002), ADC skewness (p = 0.017), and ADC variance (p = 0.000) than malignant lesions. In contrast, their minimum ADC was significantly higher ADC (p = 0.000). With the VOI 2 method, the benign lesions had significantly higher ADC SD (p = 0.048) and maximum ADC (p = 0.015) than malignant lesions. In contrast, their minimum ADC was significantly lower (p = 0.000). With the VOI 1 method, maximum ADC, ADC variance, and ADC skewness performed well in differentiating benign and malignant testicular lesions with cut-offs (Se, Sp, AUC) of 1846.000 (74.4%, 100%, 0.883), 39198.387 (79.5%, 85.7%, 0.868), and 0.893 (48.7%, 100%, 0.758). Conclusion: The HA parameters showed value in differentiating benign and malignant testicular neoplasms. The entire tumor VOI placement method was preferable to the VOI placement method excluding cystic, calcified, hemorrhagic, and necrotic portions in measuring HA parameters. Using this VOI segmentation, maximum ADC performed best in discriminating benign and malignant testicular lesions, followed by ADC variance and skewness.

Wave-Like Class Activation Map With Representation Fusion for Weakly-Supervised Semantic Segmentation

The Class Activation Map (CAM) is widely used to generate pseudo-labels for Weakly Supervised Semantic Segmentation (WSSS), while it does not adequately consider the modeling of foreground-independent information, resulting in prone to false positive pixels. In this paper, we propose a Wave-like Class Activation Map (WaveCAM) from the perspective of representation fusion and dynamic aggregation representation to alleviate the above problem. Specifically, our WaveCAM includes the foreground-aware representation modeling that enhances perception of foreground information, and the foreground-independent representation modeling that enhances perception of foreground-independent information, and a representation-adaptive fusion module that fuses the two representations. Both representations are expressed as wave functions with amplitude and phase to dynamically aggregate representations and extract semantic information after initialization, and they are fused through the adaptive fusion module to obtain an output containing rich semantic information. Extensive experiments on PASCAL VOC 2012 dataset and MS COCO 2014 dataset validate that our WaveCAM can easily embed multi-stage WSSS and end-to-end WSSS, achieving the state-of-the-art performance. The release code is available at: <uri xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/Rongtao-Xu/RepresentationLearning/tree/main/WaveCAM-TMM2023</uri> .

Phosphorylated tau in the Down syndrome brain: Age related increases and comparison to late‐onset Alzheimer’s Disease

AbstractBackgroundIndividuals with Down Syndrome (DS) have an increased risk of developing Alzheimer’s Disease (AD) with nearly all individuals exhibiting neuropathological changes in the brain by age 40 years, and with a mean diagnosis of dementia by age ∼55 years. The purpose of this postmortem study was to characterize the age‐associated burden of several tau phosphorylation epitopes, including threonine (pT) 181, 217, and 231 by immunohistochemistry in the frontal cortex. We hypothesized that cerebral pT burden would increase with age in DS but not in controls and be higher in DS with AD neuropathology (DSAD) compared to late‐onset AD (LOAD).MethodWe examined 117 brains from: controls (non‐DS n = 53; ages 1‐91), DS without AD (n = 13; ages 1‐48), DSAD (n = 31; age 43‐68), and LOAD (n = 20; ages 63‐96). Serial sections from the frontal cortex were cut at 30µm and immunostained for phosphorylated tau pT181, pT217 and pT231. Whole slide images were digitized and analyzed by Aperio ImageScope software. The % area for each type of tau was quantified using positive pixel counts. Spearman rank correlations on log‐transformed data were used to test for positive age associations and t‐test was used to compare pT between DSAD and LOAD.ResultIn control cases, there was a positive correlation of age with pT181 (r = 0.47 p&lt;0.001) but not with pT217 or pT231. In DS cases across the lifespan (DS and DSAD combined) displayed a positive correlation of age with pT181 (r = 0.70 p&lt;.001), pT217 (r = 0.70 p&lt;.001), and pT231 (r = 0.42 p = 0.005). DSAD cases had significantly higher pT181, pT217 and pT231 (p&lt;.001) than late‐onset AD and control cases.ConclusionThese results suggest that tau phosphorylation for these epitopes is more positively correlated with age in people with DS than people without DS. Although pT181 increased with age in both cohorts, pT217 and pT231 showed a positive correlation with age in people with DS but not controls. Fluid biomarker studies focused on pTau in longitudinal cohorts of people with DS with subsequent brain donation will help reveal the link between peripheral and central pTau levels.

Alterations of Astrocytic Aquaporin 4 expression and distribution in Down Syndrome with Alzheimer’s Disease onset

AbstractBackgroundAstrocytic Aquaporin 4 (AQP4) is a water channel that is typically expressed in astrocytic endfeet, associated with the blood brain barrier (BBB). This association is thought to facilitate the removal of waste products (e.g. beta amyloid (Aβ)) via the ‘glymphatic system’. With Aβ plaque deposition in Alzheimer’s Disease (AD), AQP4 becomes dysregulated observed as a shift in distribution from astrocytic endfeet to astrocytic processes, resulting in inefficient Aβ removal. Here, AQP4 expression and distribution within astrocytes was characterized via immunohistochemistry in human brain tissue from people with Down Syndrome without AD (DS) and with AD (DSAD). We hypothesized that AQP4 protein level would be higher and distributed along astrocytic processes as opposed to the BBB in DSAD relative to DS.MethodAQP4 was evaluated by immunohistochemistry and quantified using QuPath (% loads, positive pixel count) for both frontal (FC) and occipital cortex (OC) in the following groups: DS (n = 17, age range = 0‐51) and DSAD (n = 20, age range = 46‐70). In addition, AQP4 distribution was classified by a blinded observer who annotated distinct AQP4 positive astrocytic morphologies, listed as follows: In WM, ‘Star,’ ‘Webbed,’ and ‘Stippled,’ and in GM, ‘Bushy,’ ‘Branched,’ ‘Globular,’ ‘Endfoot/Vascular Associated.’ResultWe show that AQP4 protein staining was higher in GM DS with AD neuropathology than in DS without AD neuropathology for both FC and OC (FC p = 0.0007; OC p = 0.0034). In addition, we observed a shift from ‘star’ shaped distribution within DS astrocytes to more ‘webbed’ and ‘stippled’ shapes in DSAD; this was not observed in OC. We found a shift in GM morphologies from ‘bushy’ morphology of AQP4 immunostaining in DS to more ‘Branched and Globular’ shapes in DSAD in OC whereas there is a shift from a ‘Bushy’ morphology in DS to more ‘Endfoot/Vascular Associated’ morphologies in the DSAD FC.ConclusionAQP4 expression is higher in DSAD than DS and appears to show a spectrum of astrocyte morphologies with distinct patterns based upon spatial location (FC/OC and GM/WM). Taken together, AQP4 dysfunction and shift to abnormal spatial location may reduce Aβ clearance through the glymphatic system, leading to enhanced plaque formation in DSAD.

Analysis of the Mitochondrial Density and Longitudinal Distribution in Rat Live-Skeletal Muscle Fibers by Confocal Microscopy.

The mitochondrion is an organelle that can be elongated, fragmented, and renovated according to the metabolic requirements of the cells. The remodeling of the mitochondrial network allows healthy mitochondria to meet cellular demands; however, the loss of this capacity has been related to the development or progression of different pathologies. In skeletal muscle, mitochondrial density and distribution changes are observed in physiological and pathological conditions such as exercise, aging, and obesity, among others. Therefore, the study of the mitochondrial network may provide a better understanding of mechanisms related to those conditions. Here, a protocol for mitochondria imaging of live-skeletal muscle fibers from rats is described. Fibers are manually dissected in a relaxing solution and incubated with a fluorescent live-cell imaging indicator of mitochondria (tetramethylrhodamine ethyl ester, TMRE). The mitochondria signal is recorded by confocal microscopy using the XYZ scan mode to obtain confocal images of the intermyofibrillar mitochondrial (IMF) network. After that, the confocal images are processed by thresholding and binarization. The binarized confocal image accounts for the positive pixels for mitochondria, which are then counted to obtain the mitochondrial density. The mitochondrial network in skeletal muscle is characterized by a high density of IMF population, which has a periodic longitudinal distribution similar to that of T-tubules (TT).The Fast Fourier Transform (FFT) is a standard analysis technique performed to evaluate the distribution of TT that allows finding the distribution frequency and the level of their organization. In this protocol, the implementation of the FFT algorithm is described for the analysis of the longitudinal mitochondrial distribution in skeletal muscle.

Retinal phosphorylated tau correlates with the presence of microglia in Alzheimer’s disease and primary tauopathies.

AbstractBackgroundPhosphorylated tau (p‐tau) is a hallmark of neurodegenerative diseases such as Alzheimer’s disease (AD). We recently showed that p‐tau in the retina was increased in the plexiform layers of the retina in patients with AD and other tauopathies[1]. Microglia, the resident immune cells of the central nervous system, have also been found to be activated in the retina of patients with AD. To obtain more insight in AD related changes in the retina we investigate the correlation between p‐tau and microglia in the retina of patients with AD and non‐AD tauopathies.MethodRetinal tissue samples were obtained from post‐mortem eyes of patients with AD (n = 16), primary tauopathies (n = 7) and non‐demented controls (n = 11). Immunohistochemistry was performed to detect p‐tau Ser202/Thr205 (AT8) and microglia in activated and resting state (IBA‐1). The mean positive pixel count in the inner plexiform layer (IPL) of p‐tau and microglia were analyzed using Qupath.ResultAs previously described[1], we found increased levels of p‐tau Ser202/Thr205 in controls with Braak NFT I‐III, AD and primary tauopathies. In the current study, p‐tau Ser202/Thr205 was correlated to microglia (IBA‐1). We found a positive correlation between p‐tau Ser202/Thr205 and microglia in the inner plexiform layer of the far (rs[46] = 0.29, p &lt; 0.05) and mid periphery of the retina (rs[42] = 0.37, p &lt; 0.05).ConclusionOur findings show a correlation between the presence of p‐tau Ser202/Thr205 and microglia as assessed with IBA‐1 in a cohort of non‐demented controls, AD cases and non‐AD tauopathies. These results suggest that microglia play role in retinal tau pathology, and support the strong connection between microglia activation and tau pathology as observed in the brain. The results of this study may provide new insights into the pathology of AD in the retina and provide opportunities for early detection and monitoring treatment of the disease.1. Phosphorylated tau in the retina correlates with tau pathology in the brain in Alzheimer’s disease and primary tauopathies. Acta Neuropathol, 2023. 145(2): p. 197‐218 https://doi.org/10.1007/s00401-022-02525-1.

Radiomics analysis with three-dimensional and two-dimensional segmentation to predict survival outcomes in pancreatic cancer.

Radiomics can assess prognostic factors in several types of tumors, but considering its prognostic ability in pancreatic cancer has been lacking. To evaluate the performance of two different radiomics software in assessing survival outcomes in pancreatic cancer patients. We retrospectively reviewed pretreatment contrast-enhanced dual-energy computed tomography images from 48 patients with biopsy-confirmed pancreatic ductal adenocarcinoma who later underwent neoadjuvant chemoradiation and surgery. Tumors were segmented using TexRad software for 2-dimensional (2D) analysis and MIM software for 3D analysis, followed by radiomic feature extraction. Cox proportional hazard modeling correlated texture features with overall survival (OS) and progression-free survival (PFS). Cox regression was used to detect differences in OS related to pretreatment tumor size and residual tumor following treatment. The Wilcoxon test was used to show the relationship between tumor volume and the percent of residual tumor. Kaplan-Meier analysis was used to compare survival in patients with different tumor densities in Hounsfield units for both 2D and 3D analysis. 3D analysis showed that higher mean tumor density [hazard ratio (HR) = 0.971, P = 0.041)] and higher median tumor density (HR = 0.970, P = 0.037) correlated with better OS. 2D analysis showed that higher mean tumor density (HR = 0.963, P = 0.014) and higher mean positive pixels (HR = 0.962, P = 0.014) correlated with better OS; higher skewness (HR = 3.067, P = 0.008) and higher kurtosis (HR = 1.176, P = 0.029) correlated with worse OS. Higher entropy correlated with better PFS (HR = 0.056, P = 0.036). Models determined that patients with increased tumor size greater than 1.35 cm were likely to have a higher percentage of residual tumors of over 10%. Several radiomics features can be used as prognostic tools for pancreatic cancer. However, results vary between 2D and 3D analyses. Mean tumor density was the only variable that could reliably predict OS, irrespective of the analysis used.

High-Capacity Reversible Data Hiding in Encrypted Images Based on Pixel Prediction and QuadTree Decomposition

Over the past few years, a considerable number of researchers have shown great interest in reversible data hiding for encrypted images (RDHEI). One popular category among various RDHEI methods is the reserving room before encryption (RRBE) approach, which leverages data redundancy in the original image before encryption to create space for data hiding and to achieve high embedding rates (ERs). This paper introduces an RRBE-based RDHEI method that employs pixel prediction, quadtree decomposition, and bit plane reordering to provide high embedding capacity and error-free reversibility. Initially, the content owner predicts the error image using a prediction method, followed by mapping it to a new error image with positive pixel values and a compressed binary label map is generated for overhead pixels. Subsequently, quadtree decomposition is applied to each bit plane of the mapped prediction error image to identify homogeneous blocks, which are then reordered to create room for data embedding. After generating the encrypted image with the encryption key, the data hider employs the data hiding key to embed the data based on the auxiliary information added to each embeddable bit plane’s beginning. Finally, the receiver is able to retrieve the secret message without any error, decrypt the image, and restore it without any loss or distortion. The experimental results demonstrate that the proposed RDHEI method achieves significantly higher ERs than previous competitors, with an average ER exceeding 3.6 bpp on the BOSSbase and BOWS-2 datasets.