Moment-preserving thresolding: A new approach

Accumulation of APP C-terminal fragments causes endolysosomal dysfunction through the dysregulation of late endosome to lysosome-ER contact sites

Neuronal endosomal and lysosomal abnormalities are among the early changes observed in Alzheimer's disease (AD) before plaques appear. However, it is unclear whether distinct endolysosomal defects are temporally organized and how altered γ-secretase function or amyloid precursor protein (APP) metabolism contribute to these changes. Inhibiting γ-secretase chronically, in mouse embryonic fibroblast and hippocampal neurons, led to a gradual endolysosomal collapse initiated by decreased lysosomal calcium and increased cholesterol, causing downstream defects in endosomal recycling and maturation. This endolysosomal demise is γ-secretase dependent, requires membrane-tethered APP cytoplasmic domains, and is rescued by APP depletion. APP C-terminal fragments (CTFs) localized to late endosome/lysosome-endoplasmic reticulum contacts; an excess of APP-CTFs herein reduced lysosomal Ca2+ refilling from the endoplasmic reticulum, promoting cholesterol accretion. Tonic regulation by APP-CTFs provides a mechanistic explanation for their cellular toxicity: failure to timely degrade APP-CTFs sustains downstream signaling, instigating lysosomal dyshomeostasis, as observed in prodromal AD. This is the opposite of substrates such as Notch, which require intramembrane proteolysis to initiate signaling.

Hyperactivation of MEK1 in cortical glutamatergic neurons results in projection axon deficits and aberrant motor learning

Abnormal extracellular signal-regulated kinase 1/2 (ERK1/2, encoded by Mapk3 and Mapk1, respectively) signaling is linked to multiple neurodevelopmental diseases, especially the RASopathies, which typically exhibit ERK1/2 hyperactivation in neurons and non-neuronal cells. To better understand how excitatory neuron-autonomous ERK1/2 activity regulates forebrain development, we conditionally expressed a hyperactive MEK1 (MAP2K1) mutant, MEK1S217/221E, in cortical excitatory neurons of mice. MEK1S217/221E expression led to persistent hyperactivation of ERK1/2 in cortical axons, but not in soma/nuclei. We noted reduced axonal arborization in multiple target domains in mutant mice and reduced the levels of the activity-dependent protein ARC. These changes did not lead to deficits in voluntary locomotion or accelerating rotarod performance. However, skilled motor learning in a single-pellet retrieval task was significantly diminished in these MEK1S217/221E mutants. Restriction of MEK1S217/221E expression to layer V cortical neurons recapitulated axonal outgrowth deficits but did not affect motor learning. These results suggest that cortical excitatory neuron-autonomous hyperactivation of MEK1 is sufficient to drive deficits in axon outgrowth, which coincide with reduced ARC expression, and deficits in skilled motor learning. Our data indicate that neuron-autonomous decreases in long-range axonal outgrowth may be a key aspect of neuropathogenesis in RASopathies.

Remote sensing and monitoring of water resources: A comparative study of different indices and thresholding methods

Water resources are essential for the ecological system and the development of civilization. Water is imperative factor for health preservation and sustaining various human activities, including industrial production, agriculture, and daily life. Remote sensing provides a cost-effective and practical means to detect and monitor water bodies, offers valuable insights into the impact of climatic events on water structures, especially in coastal lake regions. The research primarily utilizes Landsat-9 OLI-2 satellite images to evaluate the effectiveness of various water indices (WRI, NWI, MNDWI, NDWI) in combination with global automatic thresholding methods (K-Means, Zhenzhou's, Adaptive, Intermodes, Prewitt and Mendelsohn's Minimum, Maximum Entropy, Median, Concavity, Percentile, Intermeans, Kittler and Illingworth's Minimum Error, Tsai's Moments, Otsu's, Huang's fuzzy, Triangle, Mean, IsoData, Li's). The study was carried out on Lake Nazik, Lake Iznik, and Lake Beyşehir, which have unique geographical characteristics, and examined the adaptability and robustness of the selected indices and thresholding methods. MNDWI consistently stands out as a robust index for water extraction, delivering accurate results across different thresholding methods in regions all three lakes. As a result of quite extensive analysis, it is obtained that MNDWI and NDWI are reliable choices for water feature extraction in various lake environments, but the specific index should consider the thresholding method and unique lake characteristics. The Minimum thresholding method stands out as the most effective thresholding technique, demonstrating impressive results across different lakes. Specifically, it achieved an average Peak Signal-to-Noise Ratio (PSNR) of 78.97 and Structural Similarity Index (SSIM) of 99.37 for Lake Nazik, 74.08 PSNR and 98.34 SSIM for Lake Iznik, and 63.96 PSNR and 93.61 SSIM for Lake Beyşehir.

Genetic context modulates aging and degeneration in the murine retina

Background

Age is the principal risk factor for neurodegeneration in both the retina and brain. The retina and brain share many biological properties; thus, insights into retinal aging and degeneration may shed light onto similar processes in the brain. Genetic makeup strongly influences susceptibility to age-related retinal disease. However, studies investigating retinal aging have not sufficiently accounted for genetic diversity. Therefore, examining molecular aging in the retina across different genetic backgrounds will enhance our understanding of human-relevant aging and degeneration in both the retina and brain-potentially improving therapeutic approaches to these debilitating conditions.

Methods

Transcriptomics and proteomics were employed to elucidate retinal aging signatures in nine genetically diverse mouse strains (C57BL/6J, 129S1/SvlmJ, NZO/HlLtJ, WSB/EiJ, CAST/EiJ, PWK/PhK, NOD/ShiLtJ, A/J, and BALB/cJ) across lifespan. These data predicted human disease-relevant changes in WSB and NZO strains. Accordingly, B6, WSB and NZO mice were subjected to human-relevant in vivo examinations at 4, 8, 12, and/or 18M, including: slit lamp, fundus imaging, optical coherence tomography, fluorescein angiography, and pattern/full-field electroretinography. Retinal morphology, vascular structure, and cell counts were assessed ex vivo.

Results

We identified common molecular aging signatures across the nine mouse strains, which included genes associated with photoreceptor function and immune activation. Genetic background strongly modulated these aging signatures. Analysis of cell type-specific marker genes predicted age-related loss of photoreceptors and retinal ganglion cells (RGCs) in WSB and NZO, respectively. Fundus exams revealed retinitis pigmentosa-relevant pigmentary abnormalities in WSB retinas and diabetic retinopathy (DR)-relevant cotton wool spots and exudates in NZO retinas. Profound photoreceptor dysfunction and loss were confirmed in WSB. Molecular analyses indicated changes in photoreceptor-specific proteins prior to loss, suggesting photoreceptor-intrinsic dysfunction in WSB. In addition, age-associated RGC dysfunction, loss, and concomitant microvascular dysfunction was observed in NZO mice. Proteomic analyses revealed an early reduction in protective antioxidant processes, which may underlie increased susceptibility to DR-relevant pathology in NZO.

Conclusions

Genetic context is a strong determinant of retinal aging, and our multi-omics resource can aid in understanding age-related diseases of the eye and brain. Our investigations identified and validated WSB and NZO mice as improved preclinical models relevant to common retinal neurodegenerative diseases.

Optimization of leaf area index measurement method and correction of green plot ratio formula based on regional plant characteristics-a study in Chongqing, China

The quantification of green space green plot ratio (GPR) is mostly based on estimation formulas, and the leaf area index (LAI) estimation values in these estimation formulas have not been well verified by measured LAI values, resulting in errors and uncertainties in GPR quantification results. This study aims to address this gap by measuring the LAI of 113 regional plants in Chongqing, China, following a standardized measurement path for digital hemispherical photography (DHP). The results indicate that the optimal relative exposure value (REV) was - 1 under overcast conditions and - 2 under sunny and cloudy conditions. Among the threshold algorithms for hemispherical images, the Intermodes algorithm in ImageJ was the best. The LAI of regional plants is highest in summer, followed by spring and autumn, and lowest in winter. Tree height (h) and crown width (w) are key factors affecting LAI, but the LAI also varies with plant species. Overall, the LAI of evergreen trees is higher than that of deciduous trees. The LAI of evergreen trees and shrubs with a height shorter than 5 m is the largest, and that of deciduous trees and shrubs with a crown width larger than 8 m is the largest. The study further verified that the existing GPR estimation formula exhibited large errors in Chongqing, while there was a strong correlation (R2 = 0.973) between the GPR estimation value and the measured value. A conversion formula was developed to reduce estimation biases, and the corrected formula is capable of estimating GPR values more accurately when actual LAI measurements are insufficient. Overall, this study verifies the significance of measuring localized LAI values, promotes the understanding of LAI suitability for GPR calculations, and provides an empirical formula for GPR estimation in Chongqing, China.

Evidence for microtubule nucleation at the Golgi in breast cancer cells

Golgi-derived microtubule (MT) arrays are essential to directionally persistent cell migration and vesicle transport. In this study, we have examined MT nucleation sites in two breast cancer cell lines, MDA-MB-231 and MCF-7, with the hypothesis that only the migratory invasive MDA-MB-231 cells exhibit MTs originating from the Golgi. MTs were disassembled and allowed to slightly regrow so individual nucleation sites could then be observed via fluorescently tagged antibodies (α-tubulin, cis-Golgi marker GM130, and EB1-a MT plus-end binding protein) and confocal microscopy. To determine if MT nucleation at the Golgi is more apparent during active migration compared to when cells are stationary, cells were treated with the chemoattractant epidermal growth factor (EGF) and examined for colocalizations between the Golgi, α-tubulin, and γ-tubulin. Images were analyzed qualitatively for color overlap, and quantitatively using Manders Colocalization Coefficients. Differences between groups were tested for significance using one-way analysis of variances and Tukey's post hoc test. Significantly higher colocalization values (coloc) in the highly invasive MDA-MB-231 cells (α-tubulin coloc GM130 = 0.39, GM130 coloc α-tubulin = 0.82, GM130 coloc EB1 = 0.24, and EB1 coloc GM130 = 0.38) compared to the weakly invasive MCF-7 cells (0.15, 0.08, 0.02, and 0.16, respectively) were observed. EGF-treated cells exhibited higher colocalization values than control cells for three of the four protein combinations tested, but EGF-treated MDA-MB-231 cells exhibited significantly higher values (α-tubulin coloc GM130 = 0.20, GM130 coloc α-tubulin = 0.89, and γ-tubulin coloc GM130 = 0.47) than both control groups as well as the EGF-treated MCF-7 cells. Results support the hypothesis that MT nucleation at the Golgi occurs more frequently in the invasive MDA-MB-231 cell line compared to the weakly invasive MCF-7 cells. The presence or absence of Golgi-derived MTs may help to explain the difference in migratory potential commonly exhibited by these two cell lines.

PARSEG: a computationally efficient approach for statistical validation of botanical seeds' images

Human recognition and automated image validation are the most widely used approaches to validate the output of binary segmentation methods but, as the number of pixels in an image easily exceeds several million, they become highly demanding from both practical and computational standpoint. We propose a method, called PARSEG, which stands for PArtitioning, Random Selection, Estimation, and Generalization; being the basic steps within this procedure. Suggested method enables us to perform statistical validation of binary images by selecting the minimum number of pixels from the original image to be used for validation without deteriorating the effectiveness of the validation procedure. It utilizes binary classifiers to accomplish image validation and selects the optimal sample of pixels according to a specific objective function. As a result, the computational complexity of the validation experiment is substantially reduced. The procedure's effectiveness is illustrated by considering images composed of approximately 13 million pixels from the field of seed recognition. PARSEG provides roughly the same precision of the validation process when extended to the entire image, but it utilizes only about 4% of the original number of pixels, thus reducing, by about 90%, the computing time required to validate a binary segmented image.

Vessel density on optical coherence tomography angiography is prognostic for future disease course in intermediate uveitis

As most rare diseases, intermediate uveitis lacks reliable endpoints necessary for randomized clinical trials. Therefore, we investigated longitudinal changes of retinal and choriocapillaris perfusion on optical coherence tomography angiography (OCT-A) in intermediate uveitis and their prognostic value for future best corrected visual acuity (BCVA) and central retinal thickness (CRT). In this retrospective, longitudinal cohort study eyes of patients with intermediate uveitis were imaged by swept-source OCT-A (macula-centered 3 × 3 mm; PLEX Elite 9000, Zeiss) and stratified into clinically stable, worsened and improved based on changes in clinical parameters. Superficial (SRL) and deep retinal layers (DRL) were automatically analyzed for vessel density (VD) and choriocapillaris layer for non-perfused area (CCNPA) using ImageJ. Mixed-effects regression analysis controlling for age, sex, and OCT-A signal strength index (SSI) was used to evaluate the prognostic value of OCT-A parameters. 91 eyes (62 stable, 12 worsened, and 17 improved) were included in the analysis and mean follow-up time was 296 days. Longitudinal changes of VD were different between all three groups (p = 0.002 for SRL and p = 0.017 for DRL). Clinically worsened eyes showed a decrease in VD (- 0.032 ± 0.055 for SRL and - 0.027 ± 0.025 for DRL), whereas clinically improved eyes showed an increase in VD (0.037 ± 0.039 for SRL and 0.001 ± 0.023 for DRL). No difference was found for CCNPA. When controlling for age, sex, and SSI, observed differences held true in clinically worsened eyes for DRL (p = 0.011) and in clinically improved eyes for SRL (p = 0.002). An increase of CCNPA in clinically worsened eyes (p = 0.03) compared to clinically stable and improved eyes was evident. Predictive analysis revealed an association of VD in SRL and DRL at baseline with BCVA at follow-up (p = 0.039 and p = 0.047, respectively) and of VD in SRL at baseline with CRT at follow-up (p = 0.046). Alterations in retinal perfusion on OCT-A in intermediate uveitis are partly reversible and OCT-A VD may serve to predict future BCVA and CRT. Thus, perfusion parameters on OCT-A might aid monitoring and serve as prognostic imaging-biomarker.

Perinatal Western-style diet exposure associated with decreased microglial counts throughout the arcuate nucleus of the hypothalamus in Japanese macaques

Perinatal exposure to a high-fat, high-sugar Western-style diet (WSD) is associated with altered neural circuitry in the melanocortin system. This association may have an underlying inflammatory component, as consumption of a WSD during pregnancy can lead to an elevated inflammatory environment. Our group previously demonstrated that prenatal WSD exposure was associated with increased markers of inflammation in the placenta and fetal hypothalamus in Japanese macaques. In this follow-up study, we sought to determine whether this heightened inflammatory state persisted into the postnatal period, as prenatal exposure to inflammation has been shown to reprogram offspring immune function and long-term neuroinflammation would present a potential means for prolonged disruptions to microglia-mediated neuronal circuit formation. Neuroinflammation was approximated in 1-yr-old offspring by counting resident microglia and peripherally derived macrophages in the region of the hypothalamus examined in the fetal study, the arcuate nucleus (ARC). Microglia and macrophages were immunofluorescently stained with their shared marker, ionized calcium-binding adapter molecule 1 (Iba1), and quantified in 11 regions along the rostral-caudal axis of the ARC. A mixed-effects model revealed main effects of perinatal diet (P = 0.011) and spatial location (P = 0.003) on Iba1-stained cell count. Perinatal WSD exposure was associated with a slight decrease in the number of Iba1-stained cells, and cells were more densely located in the center of the ARC. These findings suggest that the heightened inflammatory state experienced in utero does not persist postnatally. This inflammatory response trajectory could have important implications for understanding how neurodevelopmental disorders progress.NEW & NOTEWORTHY Prenatal Western-style diet exposure is associated with increased microglial activity in utero. However, we found a potentially neuroprotective reduction in microglia count during early postnatal development. This trajectory could inform the timing of disruptions to microglia-mediated neuronal circuit formation. Additionally, this is the first study in juvenile macaques to characterize the distribution of microglia along the rostral-caudal axis of the arcuate nucleus of the hypothalamus. Nearby neuronal populations may be greater targets during inflammatory insults.

3D printed non-uniform anthropomorphic phantoms for quantitative SPECT

BACKGROUND

A 3D printing grid-based method was developed to construct anthropomorphic phantoms with non-uniform activity distributions, to be used for evaluation of quantitative SPECT images. The aims were to characterize the grid-based method and to evaluate its capability to provide realistically shaped phantoms with non-uniform activity distributions.

METHODS

Characterization of the grid structures was performed by printing grid-filled spheres. Evaluation was performed by micro-CT imaging to investigate the printing accuracy and by studying the modulation contrast ([Formula: see text]) in SPECT images for 177Lu and 99mTc as a function of the grid fillable-volume fraction (FVF) determined from weighing. The grid-based technique was applied for the construction of two kidney phantoms and two thyroid phantoms, designed using templates from the XCAT digital phantoms. The kidneys were constructed with a hollow outer container shaped as cortex, an inner grid-based structure representing medulla and a solid section representing pelvis. The thyroids consisted of two lobes printed as grid-based structures, with void hot spots within the lobes. The phantoms were filled with solutions of 177Lu (kidneys) or 99mTc (thyroids) and imaged with SPECT. For verification, Monte Carlo simulations of SPECT imaging were performed for activity distributions corresponding to those of the printed phantoms. Measured and simulated SPECT images were compared qualitatively and quantitatively.

RESULTS

Micro-CT images showed that printing inaccuracies were mainly uniform across the grid. The relationships between the FVF from weighing and [Formula: see text] were found to be linear (r = 0.9995 and r = 0.9993 for 177Lu and 99mTc, respectively). The FVF-deviations from the design were up to 15% for thyroids and 4% for kidneys, mainly related to possibilities of cleaning after printing. Measured and simulated SPECT images of kidneys and thyroids exhibited similar activity distributions and quantitative comparisons agreed well, thus verifying the grid-based method.

CONCLUSIONS

We find the grid-based technique useful for the provision of 3D printed, realistically shaped, phantoms with non-uniform activity distributions, which can be used for evaluation of different quantitative methods in SPECT imaging.

A critical threshold of MCM10 is required to maintain genome stability during differentiation of induced pluripotent stem cells into natural killer cells

Natural killer (NK) cell deficiency (NKD) is a rare disease in which NK cell function is reduced, leaving affected individuals susceptible to repeated viral infections and cancer. Recently, a patient with NKD was identified carrying compound heterozygous variants of MCM10 (minichromosome maintenance protein 10), an essential gene required for DNA replication, that caused a significant decrease in the amount of functional MCM10. NKD in this patient presented as loss of functionally mature late-stage NK cells. To understand how MCM10 deficiency affects NK cell development, we generated MCM10 heterozygous (MCM10+/-) induced pluripotent stem cell (iPSC) lines. Analyses of these cell lines demonstrated that MCM10 was haploinsufficient, similar to results in other human cell lines. Reduced levels of MCM10 in mutant iPSCs was associated with impaired clonogenic survival and increased genomic instability, including micronuclei formation and telomere erosion. The severity of these phenotypes correlated with the extent of MCM10 depletion. Significantly, MCM10+/- iPSCs displayed defects in NK cell differentiation, exhibiting reduced yields of hematopoietic stem cells (HSCs). Although MCM10+/- HSCs were able to give rise to lymphoid progenitors, these did not generate mature NK cells. The lack of mature NK cells coincided with telomere erosion, suggesting that NKD caused by these MCM10 variants arose from the accumulation of genomic instability including degradation of chromosome ends.

Deciphering the mitophagy receptor network identifies a crucial role for OPTN (optineurin) in acute myeloid leukemia

The selective autophagic degradation of mitochondria via mitophagy is essential for preserving mitochondrial homeostasis and, thereby, disease maintenance and progression in acute myeloid leukemia (AML). Mitophagy is orchestrated by a variety of mitophagy receptors whose interplay is not well understood. Here, we established a pairwise multiplexed CRISPR screen targeting mitophagy receptors to elucidate redundancies and gain a deeper understanding of the functional interactome governing mitophagy in AML. We identified OPTN (optineurin) as sole non-redundant mitophagy receptor and characterized its unique role in AML. Knockdown and overexpression experiments demonstrated that OPTN expression is rate-limiting for AML cell proliferation. In a MN1-driven murine transplantation model, loss of OPTN prolonged overall median survival by 7 days (+21%). Mechanistically, we found broadly impaired mitochondrial respiration and function with increased mitochondrial ROS, that most likely caused the proliferation defect. Our results decipher the intertwined network of mitophagy receptors in AML for both ubiquitin-dependent and receptor-mediated mitophagy, identify OPTN as a non-redundant tool to study mitophagy in the context of leukemia and suggest OPTN inhibition as an attractive therapeutic strategy.Abbreviations: AML: acute myeloid leukemia; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; CTRL: control; DFP: deferiprone; GI: genetic interaction; KD: knockdown; KO: knockout; ldMBM, lineage-depleted murine bone marrow; LFC: log2 fold change; LIR: LC3-interacting region; LSC: leukemic stem cell; MAGeCK: Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout; MDIVI-1: mitochondrial division inhibitor 1; MOI: multiplicity of infection; MOM: mitochondrial outer membrane; NAC: N-acetyl-L-cysteine; OA: oligomycin-antimycin A; OCR: oxygen consumption rate; OE: overexpression; OPTN: optineurin; PINK1: PTEN induced putative kinase 1; ROS: reactive oxygen species; SEM: standard error of the mean; TCGA: The Cancer Genome Atlas; TEM: transmission electron microscopy; UBD: ubiquitin-binding domain; WT: wild type.

Finding Nano-Ötzi: Cryo-Electron Tomography Visualization Guided by Learned Segmentation

Cryo-electron tomography (cryo-ET) is a new 3D imaging technique with unprecedented potential for resolving submicron structural details. Existing volume visualization methods, however, are not able to reveal details of interest due to low signal-to-noise ratio. In order to design more powerful transfer functions, we propose leveraging soft segmentation as an explicit component of visualization for noisy volumes. Our technical realization is based on semi-supervised learning, where we combine the advantages of two segmentation algorithms. First, the weak segmentation algorithm provides good results for propagating sparse user-provided labels to other voxels in the same volume and is used to generate dense pseudo-labels. Second, the powerful deep-learning-based segmentation algorithm learns from these pseudo-labels to generalize the segmentation to other unseen volumes, a task that the weak segmentation algorithm fails at completely. The proposed volume visualization uses deep-learning-based segmentation as a component for segmentation-aware transfer function design. Appropriate ramp parameters can be suggested automatically through frequency distribution analysis. Furthermore, our visualization uses gradient-free ambient occlusion shading to further suppress the visual presence of noise, and to give structural detail the desired prominence. The cryo-ET data studied in our technical experiments are based on the highest-quality tilted series of intact SARS-CoV-2 virions. Our technique shows the high impact in target sciences for visual data analysis of very noisy volumes that cannot be visualized with existing techniques.

Self-adaptive moth flame optimizer combined with crossover operator and Fibonacci search strategy for COVID-19 CT image segmentation

The COVID-19 is one of the most significant obstacles that humanity is now facing. The use of computed tomography (CT) images is one method that can be utilized to recognize COVID-19 in early stage. In this study, an upgraded variant of Moth flame optimization algorithm (Es-MFO) is presented by considering a nonlinear self-adaptive parameter and a mathematical principle based on the Fibonacci approach method to achieve a higher level of accuracy in the classification of COVID-19 CT images. The proposed Es-MFO algorithm is evaluated using nineteen different basic benchmark functions, thirty and fifty dimensional IEEE CEC'2017 test functions, and compared the proficiency with a variety of other fundamental optimization techniques as well as MFO variants. Moreover, the suggested Es-MFO algorithm's robustness and durability has been evaluated with tests including the Friedman rank test and the Wilcoxon rank test, as well as a convergence analysis and a diversity analysis. Furthermore, the proposed Es-MFO algorithm resolves three CEC2020 engineering design problems to examine the problem-solving ability of the proposed method. The proposed Es-MFO algorithm is then used to solve the COVID-19 CT image segmentation problem using multi-level thresholding with the help of Otsu's method. Comparison results of the suggested Es-MFO with basic and MFO variants proved the superiority of the newly developed algorithm.

Counteracting gemcitabine+nab-paclitaxel induced dysbiosis in KRAS wild type and KRASG12D mutated pancreatic cancer in vivo model

Pancreatic cancer (PC) has a very low survival rate mainly due to late diagnosis and refractoriness to therapies. The latter also cause adverse effects negatively affecting the patients' quality of life, often requiring dose reduction or discontinuation of scheduled treatments, compromising the chances of cure. We explored the effects of a specific probiotic blend on PC mice xenografted with KRAS wild-type or KRASG12D mutated cell lines alone or together with gemcitabine+nab-paclitaxel treatment to then assess tumor volume and clinical pathological variables. Beside a semi-quantitative histopathological evaluation of murine tumor and large intestine samples, histochemical and immunohistochemical analyses were carried out to evaluate collagen deposition, proliferation index Ki67, immunological microenvironment tumor-associated, DNA damage markers and also mucin production. Blood cellular and biochemical parameters and serum metabolomics were further analyzed. 16S sequencing was performed to analyze the composition of fecal microbiota. Gemcitabine+nab-paclitaxel treatment impaired gut microbial profile in KRAS wild-type and KRASG12D mice. Counteracting gemcitabine+nab-paclitaxel- induced dysbiosis through the administration of probiotics ameliorated chemotherapy side effects and decreased cancer-associated stromatogenesis. Milder intestinal damage and improved blood count were also observed upon probiotics treatment as well as a positive effect on fecal microbiota, yielding an increase in species richness and in short chain fatty acids producing- bacteria. Mice' serum metabolomic profiles revealed significant drops in many amino acids upon probiotics administration in KRAS wild-type mice while in animals transplanted with PANC-1 KRASG12D mutated all treated groups showed a sharp decline in serum levels of bile acids with respect to control mice. These results suggest that counteracting gemcitabine+nab-paclitaxel-induced dysbiosis ameliorates chemotherapy side effects by restoring a favorable microbiota composition. Relieving adverse effects of the chemotherapy through microbiota manipulation could be a desirable strategy in order to improve pancreatic cancer patients' quality of life and to increase the chance of cure.

Examination of embolisms in maple and birch saplings utilising microCT

We demonstrate the application of synchrotron x-ray microtomography (microCT) to non-invasively examine the internal structure of a maple and birch sapling. We show that, through the use of standard image analysis techniques, embolised vessels can be extracted from reconstructed slices of the stem. By combining these thresholded images with connectivity analysis, we map out the embolisms within the sapling in three dimensions and evaluate the size distribution, showing that large embolisms over 0.005 mm³ in volume compose the majority of the saplings' total embolised volume. Finally we evaluate the radial distribution of embolisms, showing that in maple fewer embolisms are present towards the cambium, while birch has a more uniform distribution.

A Quality, Size and Time Assessment of the Binarization of Documents Photographed by Smartphones

Smartphones with an in-built camera are omnipresent today in the life of over eighty percent of the world's population. They are very often used to photograph documents. Document binarization is a key process in many document processing platforms. This paper assesses the quality, file size and time performance of sixty-eight binarization algorithms using five different versions of the input images. The evaluation dataset is composed of deskjet, laser and offset printed documents, photographed using six widely-used mobile devices with the strobe flash off and on, under two different angles and four shots with small variations in the position. Besides that, this paper also pinpoints the algorithms per device that may provide the best visual quality-time, document transcription accuracy-time, and size-time trade-offs. Furthermore, an indication is also given on the "overall winner" that would be the algorithm of choice if one has to use one algorithm for a smartphone-embedded application.

What Binarization Method Is the Best for Amplitude Inline Fresnel Holograms Synthesized for Divergent Beams Using the Direct Search with Random Trajectory Technique?

Fast reconstruction of holographic and diffractive optical elements (DOE) can be implemented by binary digital micromirror devices (DMD). Since micromirrors of the DMD have two positions, the synthesized DOEs must be binary. This work studies the possibility of improving the method of synthesis of amplitude binary inline Fresnel holograms in divergent beams. The method consists of the modified Gerchberg-Saxton algorithm, Otsu binarization and direct search with random trajectory technique. To achieve a better quality of reconstruction, various binarization methods were compared. We performed numerical and optical experiments using the DMD. Holograms of halftone image with size up to 1024 × 1024 pixels were synthesized. It was determined that local and several global threshold methods provide the best quality. Compared to the Otsu binarization used in the original method of the synthesis, the reconstruction quality (MSE and SSIM values) is improved by 46% and the diffraction efficiency is increased by 27%.

Multi-verse Optimizer with Rosenbrock and Diffusion Mechanisms for Multilevel Threshold Image Segmentation from COVID-19 Chest X-Ray Images

Coronavirus Disease 2019 (COVID-19) is the most severe epidemic that is prevalent all over the world. How quickly and accurately identifying COVID-19 is of great significance to controlling the spread speed of the epidemic. Moreover, it is essential to accurately and rapidly identify COVID-19 lesions by analyzing Chest X-ray images. As we all know, image segmentation is a critical stage in image processing and analysis. To achieve better image segmentation results, this paper proposes to improve the multi-verse optimizer algorithm using the Rosenbrock method and diffusion mechanism named RDMVO. Then utilizes RDMVO to calculate the maximum Kapur's entropy for multilevel threshold image segmentation. This image segmentation scheme is called RDMVO-MIS. We ran two sets of experiments to test the performance of RDMVO and RDMVO-MIS. First, RDMVO was compared with other excellent peers on IEEE CEC2017 to test the performance of RDMVO on benchmark functions. Second, the image segmentation experiment was carried out using RDMVO-MIS, and some meta-heuristic algorithms were selected as comparisons. The test image dataset includes Berkeley images and COVID-19 Chest X-ray images. The experimental results verify that RDMVO is highly competitive in benchmark functions and image segmentation experiments compared with other meta-heuristic algorithms.

Do Corticosteroid Receptor mRNA Levels Predict the Expression of Their Target Genes?

The glucocorticoid stress hormones affect brain function via high-affinity mineralocorticoid receptors (MRs) and lower-affinity glucocorticoid receptors (GRs). MR and GR not only differ in affinity for ligands, but also have distinct, sometimes opposite, actions on neuronal excitability and other cellular and higher-order parameters related to cerebral function. GR and MR messenger RNA (mRNA) levels are often used as a proxy for the responsiveness to glucocorticoids, assuming proportionality between mRNA and protein levels. This may be especially relevant for the MR, which because of its high affinity is already largely occupied at low basal (trough) hormone levels. Here we explore how GR and MR mRNA levels are associated with the expression of a shared target gene, glucocorticoid-induced leucine zipper (GILZ, coded by Tsc22d3) with basal and elevated levels of corticosterone in male mice, using in situ hybridization. Depending on the hippocampal subfield and the corticosterone levels, mRNA levels of MR rather than GR mostly correlated with GILZ mRNA in the hippocampus and hypothalamus at the bulk tissue level. At the individual cell level, these correlations were much weaker. Using publicly available single-cell RNA sequencing data, we again observed that MR and GR mRNA levels were only weakly correlated with target gene expression in glutamatergic and GABAergic neurons. We conclude that MR mRNA levels can be limiting for receptor action, but many other cell-specific and region-specific factors ultimately determine corticosteroid receptor action. Altogether, our results argue for caution while interpreting the consequences of changed receptor expression for the response to glucocorticoids.

Point-of-Care Urinalysis with One Drop of Sample Using an Aggregation-Induced Emission Luminogen under the Coffee-Ring Effect

Development of a practical point-of-care test for urinalysis is crucial for early diagnosis and treatment of chronic kidney disease (CKD). However, the classical gold standard detection method depends on sophisticated instruments and complicated procedures, impeding them from being utilized in resource-limited settings and daily screening. Herein, we report a rapid point-of-care device for the simultaneous quantification of microalbuminuria and leukocyte using one drop of urine. A luminogen (TTVP) with an aggregation-induced emission property can selectively activate its near-infrared fluorescence in the presence of albumin and leukocyte via hydrophobic or electrostatic interactions. The fluorescence signals from urine albumin and leukocyte could be well-separated combined with the coffee-ring effect. Using a smartphone-based detection device, simultaneous quantification of urine albumin and leukocyte was successfully achieved, which only took 20 min and required one drop of urine. The performance of this system is also verified with 120 clinical samples, which might serve as a simple, low-cost, and rapid tool for CKD screening and disease monitoring at the point of care.

Phosphatidylserine clustering by the Ebola virus matrix protein is a critical step in viral budding

Phosphatidylserine (PS) is a critical lipid factor in the assembly and spread of numerous lipid-enveloped viruses. Here, we describe the ability of the Ebola virus (EBOV) matrix protein eVP40 to induce clustering of PS and promote viral budding in vitro, as well as the ability of an FDA-approved drug, fendiline, to reduce PS clustering and subsequent virus budding and entry. To gain mechanistic insight into fendiline inhibition of EBOV replication, multiple in vitro assays were run including imaging, viral budding and viral entry assays. Fendiline lowers PS content in mammalian cells and PS in the plasma membrane, where the ability of VP40 to form new virus particles is greatly lower. Further, particles that form from fendiline-treated cells have altered particle morphology and cannot significantly infect/enter cells. These complementary studies reveal the mechanism by which EBOV matrix protein clusters PS to enhance viral assembly, budding, and spread from the host cell while also laying the groundwork for fundamental drug targeting strategies.

Using Paper Texture for Choosing a Suitable Algorithm for Scanned Document Image Binarization

The intrinsic features of documents, such as paper color, texture, aging, translucency, the kind of printing, typing or handwriting, etc., are important with regard to how to process and enhance their image. Image binarization is the process of producing a monochromatic image having its color version as input. It is a key step in the document processing pipeline. The recent Quality-Time Binarization Competitions for documents have shown that no binarization algorithm is good for any kind of document image. This paper uses a sample of the texture of the scanned historical documents as the main document feature to select which of the 63 widely used algorithms, using five different versions of the input images, totaling 315 document image-binarization schemes, provides a reasonable quality-time trade-off.

Genetic Ablation of Nrf2 Exacerbates Neuroinflammation in Ocular Autoimmunity

Experimental autoimmune uveoretinitis (EAU) is an animal model of non-infectious uveitis and is developed by immunization with retinal antigen, interphotoreceptor retinoid-binding protein (IRBP). Nuclear factor erythroid 2- (NF-E2-) related factor 2 (Nrf2) is responsible for regulating antioxidant and inflammatory responses. In this study, we investigated the role of Nrf2 on the development of EAU. Clinical and pathological examination demonstrated that retinal inflammation was exacerbated in Nrf2 knockout (Nrf2 KO) mice compared to wild type (WT) mice, and the expression of inflammatory cytokines (IFN-γ, IL-6, and IL-17) in the retina was significantly elevated in Nrf2 KO mice. GFAP positive cells (astrocytes) and Iba-1 positive cells (microglia cells) in the retina were more numerous in Nrf2 KO mice compared to WT mice. Furthermore, we examined the suppressive effect of the Nrf2 activator CDDO-Im (2-cyano-3,12 dioxooleana-1,9 dien-28-oyl imidazoline) on the development of EAU. The treatment with CDDO-Im significantly reduced the clinical and pathological score of EAU compared to those of vehicle-treated mice. These findings suggest that Nrf2 plays a regulatory role in the pathogenesis of autoimmune uveoretinitis and the activation of the Nrf2 system may have therapeutic potential for protecting vision from autoimmune neuroinflammation.

A synthetic tear protein resolves dry eye through promoting corneal nerve regeneration

Corneal architecture is essential for vision and is greatly perturbed by the absence of tears due to the highly prevalent disorder dry eye. With no regenerative therapies available, pathological alterations of the ocular surface in response to dryness, including persistent epithelial defects and poor wound healing, result in life-long morbidity. Here, using a mouse model of aqueous-deficient dry eye, we reveal that topical application of the synthetic tear protein Lacripep reverses the pathological outcomes of dry eye through restoring the extensive network of corneal nerves that are essential for tear secretion, barrier function, epithelial homeostasis, and wound healing. Intriguingly, the restorative effects of Lacripep occur despite extensive immune cell infiltration, suggesting tissue reinnervation and regeneration can be achieved under chronic inflammatory conditions. In summary, our data highlight Lacripep as a first-in-class regenerative therapy for returning the cornea to a near homeostatic state in individuals who suffer from dry eye.

Currently, there are no regenerative treatments for ocular pathologies due to dry eye. Efraim et al. demonstrate the synthetic tear peptide Lacripep as a regenerative therapy capable of restoring the damaged, dysfunctional ocular surface to a near homeostatic state through promoting nerve regeneration in the presence of chronic inflammation.

Prominin 1 and Notch regulate ciliary length and dynamics in multiciliated cells of the airway epithelium

Differences in ciliary morphology and dynamics among multiciliated cells of the respiratory tract contribute to efficient mucociliary clearance. Nevertheless, little is known about how these phenotypic differences are established. We show that Prominin 1 (Prom1), a transmembrane protein widely used as stem cell marker, is crucial to this process. During airway differentiation, Prom1 becomes restricted to multiciliated cells, where it is expressed at distinct levels along the proximal-distal axis of the airways. Prom1 is induced by Notch in multiciliated cells, and Notch inactivation abolishes this gradient of expression. Prom1 was not required for multicilia formation, but when inactivated resulted in longer cilia that beat at a lower frequency. Disruption of Notch resulted in opposite effects and suggested that Notch fine-tunes Prom1 levels to regulate the multiciliated cell phenotype and generate diversity among these cells. This mechanism could contribute to the innate defense of the lung and help prevent pulmonary disease.

XIST loss impairs mammary stem cell differentiation and increases tumorigenicity through Mediator hyperactivation

X inactivation (XCI) is triggered by upregulation of XIST, which coats the chromosome in cis, promoting formation of a heterochromatic domain (Xi). XIST role beyond initiation of XCI is only beginning to be elucidated. Here, we demonstrate that XIST loss impairs differentiation of human mammary stem cells (MaSCs) and promotes emergence of highly tumorigenic and metastatic carcinomas. On the Xi, XIST deficiency triggers epigenetic changes and reactivation of genes overlapping Polycomb domains, including Mediator subunit MED14. MED14 overdosage results in increased Mediator levels and hyperactivation of the MaSC enhancer landscape and transcriptional program, making differentiation less favorable. We further demonstrate that loss of XIST and Xi transcriptional instability is common among human breast tumors of poor prognosis. We conclude that XIST is a gatekeeper of human mammary epithelium homeostasis, thus unveiling a paradigm in the control of somatic cell identity with potential consequences for our understanding of gender-specific malignancies.

Multi-constraints based deep learning model for automated segmentation and diagnosis of coronary artery disease in X-ray angiographic images

BACKGROUND

The detection of coronary artery disease (CAD) from the X-ray coronary angiography is a crucial process which is hindered by various issues such as presence of noise, insufficient contrast of the input images along with the uncertainties caused by the motion due to respiration and variation of angles of vessels.

METHODS

In this article, an Automated Segmentation and Diagnosis of Coronary Artery Disease (ASCARIS) model is proposed in order to overcome the prevailing challenges in detection of CAD from the X-ray images. Initially, the preprocessing of the input images was carried out by using the modified wiener filter for the removal of both internal and external noise pixels from the images. Then, the enhancement of contrast was carried out by utilizing the optimized maximum principal curvature to preserve the edge information thereby contributing to increasing the segmentation accuracy. Further, the binarization of enhanced images was executed by the means of OTSU thresholding. The segmentation of coronary arteries was performed by implementing the Attention-based Nested U-Net, in which the attention estimator was incorporated to overcome the difficulties caused by intersections and overlapped arteries. The increased segmentation accuracy was achieved by performing angle estimation. Finally, the VGG-16 based architecture was implemented to extract threefold features from the segmented image to perform classification of X-ray images into normal and abnormal classes.

RESULTS

The experimentation of the proposed ASCARIS model was carried out in the MATLAB R2020a simulation tool and the evaluation of the proposed model was compared with several existing approaches in terms of accuracy, sensitivity, specificity, revised contrast to noise ratio, mean square error, dice coefficient, Jaccard similarity, Hausdorff distance, Peak signal-to-noise ratio (PSNR), segmentation accuracy and ROC curve.

DISCUSSION

The results obtained conclude that the proposed model outperforms the existing approaches in all the evaluation metrics thereby achieving optimized classification of CAD. The proposed method removes the large number of background artifacts and obtains a better vascular structure.

The Permeability of Porous Volcanic Rock Through the Brittle-Ductile Transition

The permeability of volcanic rock controls the distribution of pore fluids and pore fluid pressure within a volcanic edifice, and is therefore considered to influence eruptive style and volcano deformation. We measured the porosity and permeability of a porous volcanic rock during deformation in the brittle and ductile regimes. In the brittle regime, permeability decreases by a factor of 2-6 up to the peak stress due the closure of narrow pore throats but, following shear fracture formation, remains approximately constant as strain is accommodated by sliding on the fracture. In the ductile regime, permeability continually decreases, by up to an order of magnitude, as a function of strain. Although compaction in the ductile regime is localized, permeability is not reduced substantially due to the tortuous and diffuse nature of the compaction bands, the geometry of which was also influenced by a pore shape preferred orientation. Although the evolution of the permeability of the studied porous volcanic rock in the brittle and ductile regimes is qualitatively similar to that for porous sedimentary rocks, the porosity sensitivity exponent of permeability in the elastic regime is higher than found previously for porous sedimentary rocks. This exponent decreases during shear-enhanced compaction toward a value theoretically derived for granular media, suggesting that the material is effectively granulating. Indeed, cataclastic pore collapse evolves the microstructure to one that is more granular. Understanding how permeability can evolve in a volcanic edifice will improve the accuracy of models designed to assist volcano monitoring and volcanic hazard mitigation.

Quantification of vascular networks in photoacoustic mesoscopy

Mesoscopic photoacoustic imaging (PAI) enables non-invasive visualisation of tumour vasculature. The visual or semi-quantitative 2D measurements typically applied to mesoscopic PAI data fail to capture the 3D vessel network complexity and lack robust ground truths for assessment of accuracy. Here, we developed a pipeline for quantifying 3D vascular networks captured using mesoscopic PAI and tested the preservation of blood volume and network structure with topological data analysis. Ground truth data of in silico synthetic vasculatures and a string phantom indicated that learning-based segmentation best preserves vessel diameter and blood volume at depth, while rule-based segmentation with vesselness image filtering accurately preserved network structure in superficial vessels. Segmentation of vessels in breast cancer patient-derived xenografts (PDXs) compared favourably to ex vivo immunohistochemistry. Furthermore, our findings underscore the importance of validating segmentation methods when applying mesoscopic PAI as a tool to evaluate vascular networks in vivo.

Characterizing Time-Series Roving Artisanal and Small-Scale Gold Mining Activities in Indonesia Using Sentinel-1 Data

The rapid growth of roving mining camps has negatively influenced their surrounding environment. Although artisanal and small-scale gold mining (ASGM) is a major source of gold production, the mining activities and their activeness are not well revealed owing to their informal, illegal, and unregulated characteristics. This study characterizes the transformations of roving camp-type ASGM (R-C-ASGM) activities in Central of Katingan Regency, Central Kalimantan Province, Indonesia, from 2015 to 2021 using remotely sensed data, such as the time-series Sentinel-1 dataset. The results show that the growth of active R-C-ASGM sites was identified at the center of the Galangan mining region with expansions to the northwest part along the Kalanaman River, especially in 2021. Hence, these approaches identify the transformations of roving mining activities and their active or nonactive status even in tropical regions experiencing frequent heavy traffic rainstorms. They provide significant information on the socioenvironmental risks possibly caused at local and regional levels. Our results also inform the design of timely interventions suited to local conditions for strengthening environmental governance.

NLRP3 Is Involved in Neutrophil Mobilization in Experimental Periodontitis

The NLRP3 inflammasome is overexpressed in gingiva of periodontitis patients but its role remains unclear. In our study, we use a periodontitis mouse model of ligature, impregnated or not with Porphyromonas gingivalis, in WT or NLRP3 KO mice. After 28 days of induction, ligature alone provoked exacerbated periodontal destruction in KO mice, compared to WT mice, with an increase in activated osteoclasts. No difference was observed at 14 days, suggesting that NLRP3 is involved in regulatory pathways that limit periodontitis. In contrast, in the presence of P. gingivalis, this protective effect of NLRP3 was not observed. Overexpression of NLRP3 in connective tissue of WT mice increased the local production of mature IL-1β, together with a dramatic mobilization of neutrophils, bipartitely distributed between the site of periodontitis induction and the alveolar bone crest. P. gingivalis enhanced the targeting of NLRP3-positive neutrophils to the alveolar bone crest, suggesting a role for this subpopulation in bone loss. Conversely, in NLRP3 KO mice, mature IL-1β expression was lower and almost no neutrophils were mobilized. Our study sheds new light on the role of NLRP3 in periodontitis by highlighting the ambiguous role of neutrophils, and P. gingivalis which affects NLRP3 functions.

Investigation of Long-Term Roving Artisanal and Small-Scale Gold Mining Activities Using Time-Series Sentinel-1 and Global Surface Water Datasets

Artisanal and small-scale gold mining (ASGM) is a significant source of gold production globally despite the sector being informal and illegal. The rapid increase in the number of roving mining camps has negatively impacted the surrounding environment; however, the formation and transformation of roving mining camps have not been well studied. This study investigated the long-term trends and significant hotspots of roving camp-type ASGM (R-C-ASGM) in Katingain Regency, Central Kalimantan Province, Indonesia, from 1988 to 2020 using remotely sensed data, including Sentinel-1 time-series, global surface water (GSW), and world landcover datasets. Results show that several active R-C-ASGM sites existed in the Galangan and Kalanaman areas in 2017/2018. According to the GSW dataset, the Galangan area was estimated to be formed earlier, whereas the Kalanaman areas were recently formed and were associated with the Kalanaman river expansion. Notably, the center of Galangan was still a significant R-C-ASGM hotspot. The findings of this study broaden our understanding of R-C-ASGM transformation and identify significant R-C-ASGM hotspots over a long period. This study contributes to the development of timely and appropriate interventions for strengthening environmental governance.

Unsupervised Building Extraction from Multimodal Aerial Data Based on Accurate Vegetation Removal and Image Feature Consistency Constraint

Accurate building extraction from remotely sensed data is difficult to perform automatically because of the complex environments and the complex shapes, colours and textures of buildings. Supervised deep-learning-based methods offer a possible solution to solve this problem. However, these methods generally require many high-quality, manually labelled samples to obtain satisfactory test results, and their production is time and labour intensive. For multimodal data with sufficient information, extracting buildings accurately in as unsupervised a manner as possible. Combining remote sensing images and LiDAR point clouds for unsupervised building extraction is not a new idea, but existing methods often experience two problems: (1) the accuracy of vegetation detection is often not high, which leads to limited building extraction accuracy, and (2) they lack a proper mechanism to further refine the building masks. We propose two methods to address these problems, combining aerial images and aerial LiDAR point clouds. First, we improve two recently developed vegetation detection methods to generate accurate initial building masks. We then refine the building masks based on the image feature consistency constraint, which can replace inaccurate LiDAR-derived boundaries with accurate image-based boundaries, remove the remaining vegetation points and recover some missing building points. Our methods do not require manual parameter tuning or manual data labelling, but still exhibit a competitive performance compared to 29 methods: our methods exhibit accuracies higher than or comparable to 19 state-of-the-art methods (including 8 deep-learning-based methods and 11 unsupervised methods, and 9 of them combine remote sensing images and 3D data), and outperform the top 10 methods (4 of them combine remote sensing images and LiDAR data) evaluated using all three test areas of the Vaihingen dataset on the official website of the ISPRS Test Project on Urban Classification and 3D Building Reconstruction in average area quality. These comparative results verify that our unsupervised methods combining multisource data are very effective.

Molecular determinants and modifiers of Matrin-3 toxicity, condensate dynamics, and droplet morphology

Matrin-3 (MATR3) is a DNA- and RNA-binding protein implicated in amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and distal myopathy. Here, we report the development of a yeast model of MATR3 proteotoxicity and aggregation. MATR3 is toxic and forms dynamic shell-like nuclear condensates in yeast. Disease-associated mutations in MATR3 impair condensate dynamics and disrupt condensate morphology. MATR3 toxicity is largely driven by its RNA-recognitions motifs (RRMs). Further, deletion of one or both RRMs drives coalescence of these condensates. Aberrant phase separation of several different RBPs underpins ALS/FTD, and we have engineered Hsp104 variants to reverse this misfolding. Here, we demonstrate that these same variants also counter MATR3 toxicity. We suggest that these Hsp104 variants which rescue MATR3, TDP-43, and FUS toxicity might be employed against a range of ALS/FTD-associated proteins. We anticipate that our yeast model could be a useful platform to screen for modulators of MATR3 misfolding.

Neuronal-glial communication perturbations in murine SOD1G93A spinal cord

Amyotrophic lateral sclerosis (ALS) is an incurable disease characterized by proteinaceous aggregate accumulation and neuroinflammation culminating in rapidly progressive lower and upper motor neuron death. To interrogate cell-intrinsic and inter-cell type perturbations in ALS, single-nucleus RNA sequencing was performed on the lumbar spinal cord in the murine ALS model SOD1^G93A transgenic and littermate control mice at peri-symptomatic onset stage of disease, age 90 days. This work uncovered perturbed tripartite synapse functions, complement activation and metabolic stress in the affected spinal cord; processes evidenced by cell death and proteolytic stress-associated gene sets. Concomitantly, these pro-damage events in the spinal cord co-existed with dysregulated reparative mechanisms. This work provides a resource of cell-specific niches in the ALS spinal cord and asserts that interwoven dysfunctional neuronal-glial communications mediating neurodegeneration are underway prior to overt disease manifestation and are recapitulated, in part, in the human post-mortem ALS spinal cord.

In this paper, single-nucleus RNA sequencing was performed to provide a resource of cell-specific niches in the murine ALS model spinal cord at peri-symptomatic onset stage of disease. The data suggest that dysfunctional neuronal-glial communication occurs prior to disease onset, which is partially recapitulated in human post-mortem ALS spinal cord tissue.

Lateral Fluid Percussion Injury Causes Sex-Specific Deficits in Anterograde but Not Retrograde Memory

Cognitive impairment is a common symptom after traumatic brain injury (TBI). Memory, in particular, is often disrupted during chronic post-injury recovery. To understand the sex-specific effects of brain injury on retrograde and anterograde memory, we examined paired associate learning (PAL), spatial learning and memory, and fear memory after lateral fluid percussion TBI. We hypothesized that male and female mice would display unique memory deficits after TBI. PAL task acquisition was initiated via touchscreen operant conditioning 22 weeks before sham injury or TBI. Post-injury PAL testing occurred 7 weeks post-injury. Barnes maze and fear conditioning were completed at 14- and 15-weeks post-injury, respectively. Contrary to our expectations, behavioral outcomes were not primarily influenced by TBI. Instead, sex-specific differences were observed in all tasks which exposed task-specific trends in male TBI mice. Male mice took longer to complete the PAL task, but this was not affected by TBI and did not compromise the ability to make a correct choice. Latency to reach the goal box decreased across testing days in Barnes maze, but male TBI mice lagged in improvement compared to all other groups. Use of two learning indices revealed that male TBI mice were deficient in transferring information from 1 day to the next. Finally, acquisition and contextual retention of fear memory were similar between all groups. Cued retention of the tone-shock pairing was influenced by both injury and sex. Male sham mice displayed the strongest cued retention of fear memory, evidenced by increased freezing behavior across the test trial. In contrast, male TBI mice displayed reduced freezing behavior with repetitive tone exposure. An inverse relationship in freezing behavior to tone exposure was detected between female sham and TBI mice, although the difference was not as striking. Together, these studies show that retrograde memory is intact after lateral TBI. However, male mice are more vulnerable to post-injury anterograde memory deficits. These behaviors were not associated with gross pathological change near the site injury or in subcortical brain regions associated with memory formation. Future studies that incorporate pre- and post-injury behavioral analysis will be integral in defining sex-specific memory impairment after TBI.

Assessment of the Usability of SAR and Optical Satellite Data for Monitoring Spatio-Temporal Changes in Surface Water: Bodrog River Case Study

Mapping watercourses and their surroundings through remote sensing methods is a fast, continuous, and effective method and is a crucial tool for capturing change and possibly predicting hazards. Thanks to Synthetic Aperture Radar (SAR) technology and the ability of its backscattered and emitted radiation to penetrate the atmosphere under any conditions, this type of mapping of water surfaces is of particular importance. This paper presents the possibility of using SAR technology for long-term observations of changes in the behaviour of rivers and river systems, combined with optical multispectral images Sentinel-2. Additionally, it aims to demonstrate the suitability of satellite SAR and multispectral data implementation for mapping changes in watercourses, caused not only by their natural development but especially by inundation processes in their catchment area. Appropriate Sentinel-1 image processing evaluation procedures demonstrate that the usage of vertical-vertical (VV) type polarisation configuration is a suitable methodology for documenting water bodies, and a Lee filter is an acceptable tool for radar noise filtering. The extraction process of water surfaces is based on the determination of threshold values using the “Otsu” principle. Subsequently, the comparison of the results is realised by the spectral indices of water—the Normalized Difference Water Index (NDWI), Modified Normalized Difference Water Index (MNDWI), a pair of Automated Water Extraction Index (AWEI) indices, and supervised classification method Maximum Likelihood Classification (MLC). The results are numerical and graphical evaluated. In assessing the accuracy of SAR extraction, the highest values achieved in Overall Accuracy (OA) were a maximum of 98.6%. On average, the lower values were in User Accuracy (UA) with a maximum of 93.1%, where VV polarisation also dominates. However, vertical-horizontal (VH) polarisation dominates in Producer Accuracy (PA) with a maximum of 84.9%.

Predictive selection rule of favourable image processing methods for X-ray micro-computed tomography images of tablets

Adequately processed X-ray micro-computed tomography images of real pharmaceutical formulations provide the possibility to validate in silico tools for the prediction of disintegration and/or dissolution. However, the evaluation of suitable image processing pathways is time consuming. The objective of this study was to prove the transferability of image processing methods and to develop an approach to select probable favourable image processing approaches for data sets with similar properties to accelerate the evaluation process. Therefore, data from a previously performed evaluation of image processing approaches and parameters were used to analyse the robustness of the image processing by statistical resampling and to develop a predictive rule set. The rule set was verified by both one new ratio of API and excipient within and outside of the ratios used to develop the rule. The rule was applied to images of a binary mixture with new compounds with similar determined image properties to prove the transferability of the rule set. It was possible to identify robust image processing pathways with narrow ranges of input parameters. The prediction of the image processing pathways led to high desirabilities which were confirmed by visual verification for ratios within the calibrated range. The transfer to the new binary mixture was successful and confirmed as well.

Comparison of thresholding methods for shoreline extraction from Sentinel-2 and Landsat-8 imagery: Extreme Lake Salda, track of Mars on Earth

Lake Salda's extreme environment is geologically similar to Jezero Crater paleolake on Mars due to the formation of stromatolites and its extremely alkaline and cold water. It is critical to accurately determine the shoreline in the littoral zone where stromatolite formation occurs, in alkaline clean lakes like Salda, which contain traces of life on Mars, and in monitoring the change that occurs with climate and anthropogenic effect. The performance of global automatic thresholding algorithms on shoreline determination from NDWI and mNDWI water indices is compared in this study using Sentinel-2 and Landsat-8 images atmospherically corrected by different algorithms. Satellite images data acquired on August 12, 2020 for Sentinel-2 and August 11, 2020 for Landsat-8 on Lake Salda were used to determining the shoreline. The shoreline data measured in situ concurrently with the Sentinel-2 satellite acquisition was used as reference data. In the accuracy analysis, ground control points created inside and outside the lake at a distance of 1 pixel and 0.5 pixel to the reference shoreline for each satellite image were used. The performance of the optimal threshold values determined by each thresholding algorithm in the water index images was assessed using Kappa coefficient, Overall Accuracy (OA), %OA of Inside (%OA_inside) and %OA of Outside (%OA_outside) statistics metrics. The optimal threshold values vary depending on the image and the atmospheric correction algorithm applied to the image. The NDWI index produces more accurate results in both Sentinel-2 and Landsat-8 satellite images. While atmospheric correction algorithms do not affect the results in Landsat-8 images, the Sen2Cor algorithm outperforms iCOR in Sentinel-2 images. For thresholding algorithms to be used in different water index and satellite images, Intermode, Isodata, IJ_Isodata, Minimum and Otsu algorithms in Landsat-8_LaSRC_NDWI and Landsat-8_iCOR_NDWI images, and Intermode, Minimum and Huang algorithms in Sentinel-2_Sen2Cor_NDWI images produce the best results. Because the Minimum algorithm causes significant gaps in the lake surface, the Huang and Intermode algorithms should be used for Sentinel-2_Sen2Cor_NDWI images. The 0 (zero) threshold value in the water indices images has a high accuracy only in the NDWI water indices generated from the Landsat-8 image.

His domain protein tyrosine phosphatase and Rabaptin-5 couple endo-lysosomal sorting of EGFR with endosomal maturation

His domain protein tyrosine phosphatase (HD-PTP; also known as PTPN23) collaborates with endosomal sorting complexes required for transport (ESCRTs) to sort endosomal cargo into intralumenal vesicles, forming the multivesicular body (MVB). Completion of MVB sorting is accompanied by maturation of the endosome into a late endosome, an event that requires inactivation of the early endosomal GTPase Rab5 (herein referring to generically to all isoforms). Here, we show that HD-PTP links ESCRT function with endosomal maturation. HD-PTP depletion prevents MVB sorting, while also blocking cargo from exiting Rab5-rich endosomes. HD-PTP-depleted cells contain hyperphosphorylated Rabaptin-5 (also known as RABEP1), a cofactor for the Rab5 guanine nucleotide exchange factor Rabex-5 (also known as RABGEF1), although HD-PTP is unlikely to directly dephosphorylate Rabaptin-5. In addition, HD-PTP-depleted cells exhibit Rabaptin-5-dependent hyperactivation of Rab5. HD-PTP binds directly to Rabaptin-5, between its Rabex-5- and Rab5-binding domains. This binding reaction involves the ESCRT-0/ESCRT-III binding site in HD-PTP, which is competed for by an ESCRT-III peptide. Jointly, these findings indicate that HD-PTP may alternatively scaffold ESCRTs and modulate Rabex-5–Rabaptin-5 activity, thereby helping to coordinate the completion of MVB sorting with endosomal maturation.

Summary: Sorting of endocytic cargo to the multivesicular body is accompanied by endosomal maturation. Here, we provide a potential mechanism by which these two processes are linked.

Apoptosis Quantification in Tissue: Development of a Semi-Automatic Protocol and Assessment of Critical Steps of Image Processing

Apoptosis is associated with numerous phenotypical characteristics, and is thus studied with many tools. In this study, we compared two broadly used apoptotic assays: TUNEL and staining with an antibody targeting the activated form of an effector caspase. To compare them, we developed a protocol based on commonly used tools such as image filtering, z-projection, and thresholding. Even though it is commonly used in image-processing protocols, thresholding remains a recurring problem. Here, we analyzed the impact of processing parameters and readout choice on the accuracy of apoptotic signal quantification. Our results show that TUNEL is quite robust, even if image processing parameters may not always allow to detect subtle differences of the apoptotic rate. On the contrary, images from anti-cleaved caspase staining are more sensitive to handle and necessitate being processed more carefully. We then developed an open-source Fiji macro automatizing most steps of the image processing and quantification protocol. It is noteworthy that the field of application of this macro is wider than apoptosis and it can be used to treat and quantify other kind of images.

A New Validation Methodology for In Silico Tools Based on X-ray Computed Tomography Images of Tablets and a Performance Analysis of One Tool

In silico tools which predict the dissolution of pharmaceutical dosage forms using virtual matrices can be validated with virtual matrices based on X-ray micro-computed tomography images of real pharmaceutical formulations. Final processed images of 3 different tablet batches were used to check the performance of the in silico tool F-CAD. The goal of this work was to prove the performance of the software by comparing the predicted dissolution profiles to the experimental ones and to check the feasibility and application of the validation concept for in silico tools. Both virtual matrices based on X-ray micro-computed tomography images and designed by the software itself were used. The resulting dissolution curves were compared regarding their similarity to the experimental curve. The kinetics were analysed with the Higuchi and Korsmeyers-Peppas plot. The whole validation concept as such was feasible and worked well. It was possible to identify prediction errors of the software F-CAD and issues with the virtual tablets designed within the software.

Quantitative 3D microscopy highlights altered von Willebrand factor α-granule storage in patients with von Willebrand disease with distinct pathogenic mechanisms

BACKGROUND

Platelets play a key role in hemostasis through plug formation and secretion of their granule contents at sites of endothelial injury. Defects in von Willebrand factor (VWF), a platelet α-granule protein, are implicated in von Willebrand disease (VWD), and may lead to defective platelet adhesion and/or aggregation. Studying VWF quantity and subcellular localization may help us better understand the pathophysiology of VWD.

OBJECTIVE

Quantitative analysis of the platelet α-granule compartment and VWF storage in healthy individuals and VWD patients.

PATIENTS/METHODS

Structured illumination microscopy (SIM) was used to study VWF content and organization in platelets of healthy individuals and patients with VWD in combination with established techniques.

RESULTS

SIM capably quantified clear morphological and granular changes in platelets stimulated with proteinase-activated receptor 1 (PAR-1) activating peptide and revealed a large intra- and interdonor variability in VWF-positive object numbers within healthy resting platelets, similar to variation in secreted protein acidic and rich in cysteine (SPARC). We subsequently characterized VWD platelets to identify changes in the α-granule compartment of patients with different VWF defects, and were able to stratify two patients with type 3 VWD rising from different pathological mechanisms. We further analyzed VWF storage in α-granules of a patient with homozygous p.C1190R using electron microscopy and found discrepant VWF levels and different degrees of multimerization in platelets of patients with heterozygous p.C1190 in comparison to VWF in plasma.

CONCLUSIONS

Our findings highlight the utility of quantitative imaging approaches in assessing platelet granule content, which may help to better understand VWF storage in α-granules and to gain new insights in the etiology of VWD.