Search Results (1,895)

Human pluripotent stem cells (hPSCs) attract tremendous attention due to their unique properties. Manual extraction of trajectories of cell colonies in experimental image time series is labor intensive and subjective, thus the aim of the work was to develop a computer semi-automated protocol for colony tracking. The developed procedure consists of three major stages, namely, image registration, object detection and tracking. Registration using discrete Fourier transform and tracking based on the solution of a linear assignment problem was implemented as console programs in the Python 3 programming language using a variety of packages. Object detection was implemented as a multistep procedure in the ProStack in-house software package. The procedure consists of more than 40 elementary operations that include setting of several biologically relevant parameters, image segmentation and performing of quantitative measurements. The developed procedure was applied to the dataset containing bright-field images from time-lapse recording of the human embryonic cell line H9. The detection step took about 6 hours for one image time series with a resolution of 2560 by 2160; about 1 min was required for image registration and trajectories extraction. The developed procedure was effective in detecting and analyzing the time series of images with “good” and “bad” phenotypes. The differences between phenotypes in the distance in pixels between the starting and finishing positions of trajectories, in the path length along the trajectory, and the mean instant speed and mean instant angle of the trajectories were identified as statistically significant by Mann–Whitney and Student’s tests. The measured area and perimeter of the detected colonies differed, on average, for different phenotypes throughout the entire time period under consideration. This result confirms previous findings obtained by analyzing static images. Full article

Blepharostoma is one of the most ancient extant liverwort genera, within which the genetic diversity is quite high, whereas the morphological diversity, owing to the supposed stasis, is quite low. Unusually large plants of this genus were collected in North Vietnam and are described here as new-to-science species via an integrative approach. The two studied specimens do not reveal variability in the sequenced ITS1-2 nrDNA and trnL-F cpDNA loci, are clearly separated from other species by the level of genetic distances, and maintain a stable position on the reconstructed phylogenetic trees. This species is characterized, in addition to the large overall size of the plants, by larger leaf segment cells and a mixed character of oil bodies (i.e., small homogeneous and larger finely papillose ones within one cell). A description of the new taxon; its diagnostic characteristics; photographs; and discussions regarding its ecology, morphological similarities, and potential distribution are provided. Full article

Near-infrared autofluorescence (NIA) is a non-invasive retinal imaging technique used to examine the retinal pigment epithelium (RPE) based on the autofluorescence of melanin. Melanin has several functions within RPE cells. It serves as a protective antioxidative factor and is involved in the phagocytosis of photoreceptor outer segments. Disorders affecting the photoreceptor–RPE complex result in alterations of RPE cells which are detectable by alterations of NIA. NIA allows us to detect early alterations in various chorioretinal disorders, frequently before they are ophthalmoscopically visible and often prior to alterations in lipofuscin-associated fundus autofluorescence (FAF) or optical coherence tomography (OCT). Although NIA and FAF relate to disorders affecting the RPE, the findings for both imaging methods differ and the area involved has been demonstrated to be larger in NIA compared to FAF in several disorders, especially inherited retinal dystrophies (IRDs), indicating that NIA detects earlier alterations compared to FAF. Foveal alterations can be much more easily detected using NIA compared to FAF. A reduced subfoveal NIA intensity is the earliest sign of autosomal dominant Best disease, when FAF and OCT are still normal. In other IRDs, a preserved subfoveal NIA intensity is associated with good visual acuity. So far, the current knowledge on NIA in IRD has been presented in multiple separate publications but has not been summarized in an overview. This review presents the current knowledge on NIA in IRD and demonstrates NIA biomarkers. Full article

Segmentation of nuclei in histology images is key in analyzing and quantifying morphology changes of nuclei features and tissue structures. Conventional diagnosis, segmenting, and detection methods have relied heavily on the manual-visual inspection of histology images. These methods are only effective on clearly visible cancerous lesions on histology images thus limited in their performance due to the complexity of tissue structures in histology images. Hence, early detection of breast cancer is key for treatment and profits from Computer-Aided-Diagnostic (CAD) systems introduced to efficiently and automatically segment and detect nuclei cells in pathology. This paper proposes, an automatic watershed segmentation method of cancerous lesions in unsupervised human breast histology images. Firstly, this approach pre-processes data through various augmentation methods to increase the size of dataset images, then a stain normalization technique is applied to these augmented images to isolate nuclei features from tissue structures. Secondly, data enhancement techniques namely; erosion, dilation, and distance transform are used to highlight foreground and background pixels while removing unwanted regions from the highlighted nuclei objects on the image. Consequently, the connected components method groups these highlighted pixel components with similar intensity values and, assigns them to their relevant labeled component binary mask. Once all binary masked groups have been determined, a deep-learning recurrent neural network from the Keras architecture uses this information to automatically segment nuclei objects with cancerous lesions and their edges on the image via watershed filling. This segmentation method is evaluated on an unsupervised, augmented human breast cancer histology dataset of 11,151 images. This proposed method produced a significant evaluation result of $98\%$ F1-accuracy score. Full article

Gastrointestinal complications of diabetes are often overlooked, despite affecting up to 75% of patients. This study innovatively explores local glutathione levels and morphometric changes in the gut of Goto–Kakizaki (GK) rats, a type 2 diabetes animal model. Segments of the intestine, cecum, and colon were collected for histopathological analysis and glutathione quantification. A significant increase in the total thickness of the intestinal wall of GK rats was observed, particularly in the duodenum (1089.02 ± 39.19 vs. 864.19 ± 37.17 µm), ileum (726.29 ± 24.75 vs. 498.76 ± 16.86 µm), cecum (642.24 ± 34.15 vs. 500.97 ± 28.81 µm), and distal colon (1211.81 ± 51.32 vs. 831.71 ± 53.2 µm). Additionally, diabetic rats exhibited thickening of the muscular layers in all segments, except for the duodenum, which was also the only portion where the number of smooth muscle cells did not decrease. Moreover, myenteric neuronal density was lower in GK rats, suggesting neurological loss. Total glutathione levels were lower in all intestinal segments of diabetic rats (except duodenum), and the reduced/oxidized glutathione ratio (GSH/GSSG) was significantly decreased in GK rats, indicating increased oxidative stress. These findings strongly indicate that GK rats undergo significant intestinal remodeling, notable shifts in neuronal populations, and heightened oxidative stress—factors that likely contribute to the functional gastrointestinal alterations seen in diabetic patients. Full article

Background/Objectives: Teosinte branched1/Cycloidea/Proliferating cell nuclear antigen factors (TCPs) are plant-specific transcription factors involved in leaf development, flowering, branching, hormone signaling, and stress responses. Prunus a key temperate fruit tree with ornamental spring blooms, still lacks comprehensive TCP gene studies across many species. Methods: We identified 154 TCP genes in eight Prunus species: 19 in Prunus tenella var. tenella, 19 in P. amygdalus, 17 in P. armeniaca ‘Rojo Pasion’, 19 in P. mira, 20 in P. jamasakura var. jamasakura, 19 in P. fruticosa, 19 in P. mume var. tortuosa, and 22 in P. × yedoensis ‘Somei-yoshino’. These genes were classified into PCF, CIN, and CYC/TB1 groups. We examined segmental duplication, conserved motifs, and cis-acting elements. Expression patterns of 12 TCPs in P. tenella var. tenella were tested under low-temperature stress (25 °C, 5 °C, −5 °C, and −10 °C), and PtTCP9’s subcellular localization was determined. Results: TCP genes within the same groups showed similar motifs and cis-acting elements. Cold stress analysis identified multiple low-temperature-responsive elements in gene promoters. Four genes (PtTCP2, PtTCP6, PtTCP14, and PtTCP16) increased expression under cold stress, while six genes (PtTCP1, PtTCP5, PtTCP8, PtTCP9, PtTCP17, and PtTCP19) decreased. PtTCP9 was localized to the nucleus. Conclusions: This was the first genome-wide study of the TCP gene family in these eight Prunus species, providing valuable insights into the characteristics and functions of TCP genes within this important genus. Full article

Giant cell arteritis (GCA) is an autoimmune/autoinflammatory disease affecting large vessels in patients over 50 years old. The disease presents as an acute inflammatory response with two phenotypes, cranial GCA and large-vessel vasculitis (LV)-GCA, involving the thoracic aorta and its branches. 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET-CT) is among the imaging techniques contributing to diagnosing patients with systemic disease. However, its association with soluble inflammatory markers is still elusive. This proof-of-concept study aims to identify novel soluble serum biomarkers in PET/CT-positive patients with LV-GCA and associate them with active (0 months) and inactive disease (6 months following treatment), in sequential samples. The most-diseased-segment target-to-background ratio (TBR_MDS) was calculated for 13 LV-GCA patients, while 14 cranial GCA and 14 Polymyalgia Rheumatica patients with negative initial PET/CT scans served as disease controls. Serum macrophage-related cytokines were evaluated by cytometric bead array (CBA). Finally, previously published NMR/metabolomics data acquired from the same blood sampling were analyzed along with PET/CT findings. TBR_MDS was significantly increased in active versus inactive disease (3.32 vs. 2.65, p = 0.006). The analysis identified nine serum metabolites as more sensitive to change from the active to inactive state. Among them, choline levels were exclusively altered in the LV-GCA group but not in the disease controls. Cytokine levels were not associated with PET/CT activity. Combining CRP, ESR, and TBR_MDS with choline levels, a composite index was generated to distinguish active and inactive LV-GCA (20.4 vs. 11.62, p = 0.001). These preliminary results could pave the way for more extensive studies integrating serum metabolomic parameters with PET/CT imaging data to extract sensitive composite disease indexes useful for everyday clinical practice. Full article

Background: This study assessed the prognostic value of tumor burden in bone marrow (BM) and total disease (TD), as depicted on 18F-FDG PET/CT in 140 DLBCL patients, for complete remission after first-line systemic treatment (iCR) and 3- and 5-year overall survival (OS3 and OS5). Methods: Baseline 18F-FDG PET/CT scans of 140 DLBCL patients were segmented to quantify metabolic tumor volume (MTV), total lesion glycolysis (TLG), and SUVmax in BMI, findings elsewhere (XL), and TD. Results: Bone marrow involvement (BMI) presented in 35 (25%) patients. Median follow-up time was 47 months; 79 patients (56%) achieved iCR. iCR was significantly associated with TD MTV, XL MTV, BM PET positivity, and International Prognostic Index (IPI). OS3 was significantly worse with TD MTV, XL MTV, IPI, and age. OS5 was significantly associated with IPI, but not with MTVs and TLGs. Univariate factors predicting OS3 were XL MTV (hazard ratio [HR] = 1.29), BMI SUVmax (HR = 0.56), and IPI (HR = 1.92). By multivariate analysis, higher IPI (HR = 2.26) and BMI SUVmax (HR = 0.91) were significant independent predictors for OS3. BMI SUVmax resulted in a negative coefficient and hence indicated a protective effect. Conclusions: Baseline 18F-FDG PET/CT MTV is significantly associated with survival. BMI identified on 18F-FDG PET/CT allows appropriate treatment that may improve survival. Full article

Background/Objectives: T-cell lymphomas are often histologically indistinguishable from benign T-cell infiltrates, and diagnosis typically relies on slow, complex, and expensive multiplexed PCR reactions, requiring significant training and experience to interpret them. We aimed to raise highly specific antibodies against the two alternatively used and very similar T-cell receptor beta constant regions, TCRbeta1 and TCRbeta2, encoded by the TRBC1 and TRBC2 gene segments, respectively. We sought to demonstrate the feasibility of detecting TCRbeta1 and TCRbeta2 immunohistochemically in routine clinical (formalin-fixed, paraffin-embedded (FFPE)) tissue sections as a novel diagnostic strategy for T-cell lymphomas. Methods: Recombinant rabbit antibodies were validated using Western blotting and FFPE immunostaining of T-cell leukemia lines. The immunostaining of FFPE tissue containing benign and lymphomatous T-cell populations was undertaken, with corroboration by BaseScope^TM high-sensitivity in situ hybridization and quantitative real-time PCR (Q-PCR). An additional Q-PCR literature review and analysis of publicly available RNAseq data was used to determine the TCRbeta2/TCRbeta1 ratio cut-off to separate benign and malignant T-cell populations. Results: Our TCRbeta1/TCRbeta2 antibody pair gave highly specific FFPE tissue staining. All benign samples analyzed (immunohistochemically, by BaseScope^TM, by Q-PCR, and by RNAseq data analysis) had TCRbeta1/TCRbeta2 or TRBC1/TRBC2 ranges well within the previously published flow cytometric benign range (TCRbeta2/TCRbeta1 = 0.18:1–5.7:1), while samples of T-cell lymphoma did not. One out of thirteen (7.7%) lymphoma samples showed some detectable TCRbeta1/TCRbeta2 protein co-expression, and 4 out of 13 (30.8%) T-cell lymphomas showed a TRBC1/TRBC2 transcript co-expression using BaseScope^TM. Conclusions: Analyzing T-cell monotypia immunohistochemically, analogous to B-cell monotypia (kappa: lambda ratio for B-cell and plasma cell neoplasms), could make the diagnosis of T-cell lymphomas cheaper, quicker, and more accurate. Larger studies are needed to validate our antibodies for clinical use. Full article

The aim of this study was to evaluate the mechanical effect of ovariectomy, diet, and tooth extraction on the bone structure of the mandible of Wistar rats. Mandibles from 40 female Wistar rats were used, divided into rats with ovariectomy surgery or surgical simulation. Half of the rats had the right upper incisor extracted and a soft diet was introduced for half of the animals for 30 days. After euthanasia, microtomography of the mandibles was performed for bone segmentation to construct three-dimensional models. Each mandible was subjected to a three-point bending test. The simulation by finite element method was configured according to the protocol for positioning the part on the support and force action by the load cell defined in the mechanical tests. Stress dissipation was described qualitatively on a color scale distributed in ranges of stress values. All models showed a higher concentration of stresses in the regions of force action and in the support regions, with differences in stress values and locations. Diet and dental condition interfered in the distribution of stresses, with the lateral surface of the mandible being more influenced by diet and the medial surface of the mandible by diet and dental condition. Full article

The cell wall is a crucial feature that allows ancestral streptophyte green algae to colonize land. Expansin, an extracellular protein that mediates cell wall loosening in a pH-dependent manner, could be a powerful tool for studying cell wall evolution. However, the evolutionary trajectory of the expansin family remains largely unknown. Here, we conducted a comprehensive identification of 2461 expansins across 64 sequenced species, ranging from aquatic algae to terrestrial plants. Expansins originated in chlorophyte algae and may have conferred the ability to loosen cell walls. The four expansin subfamilies originated independently: α-expansin appeared first, followed by β-expansin, and then expansin-like A and expansin-like B, reflecting the evolutionary complexity of plant expansins. Whole genome duplication/segmental duplication and tandem duplication events greatly contributed to expanding the expansin family. Despite notable changes in sequence characteristics, the intron distribution pattern remained relatively conserved among different subfamilies. Phylogenetic analysis divided all the expansins into five clades, with genes from the same subfamily tending to cluster together. Transcriptome data from 16 species across ten lineages and qRT-PCR analysis revealed varying expression patterns of expansin genes, suggesting functional conservation and diversification during evolution. This study enhances our understanding of the evolutionary conservation and dynamics of the expansin family in plants, providing insight into their roles as cell wall-loosening factors. Full article

A novel tailless X-type flapping-wing micro air vehicle with two pairs of independent drive wings is designed and fabricated in this paper. Due to the complexity and unsteady of the flapping wing mechanism, the geometric and kinematic parameters of flapping wings significantly influence the aerodynamic characteristics of the bio-inspired flying robot. The wings of the vehicle are vector-controlled independently on both sides, enhancing the maneuverability and robustness of the system. Unique flight control strategy enables the aircraft to have multiple flight modes such as fast forward flight, sharp turn and hovering. The aerodynamics of the prototype is analyzed via the lattice Boltzmann method of computational fluid dynamics. The chordwise flexible deformation of the wing is implemented via designing a segmented rigid model. The clap-and-peel mechanism to improve the aerodynamic lift is revealed, and two air jets in one cycle are shown. Moreover, the dynamics experiment for the novel vehicle is implemented to investigate the kinematic parameters that affect the generation of thrust and maneuver moment via a 6-axis load cell. Optimized parameters of the flapping wing motion and structure are obtained to improve flight dynamics. Finally, the prototype realizes controllable take-off and flight from the ground. Full article

The reduction in the power cost of air supply systems has emerged as a critical challenge in the development of polymer electrolyte membrane fuel cells. This study proposes the use of dual-lead rotors to improve the performance of twin-screw expanders for the purpose of boosting expanders’ recovery power and consequently lowering the power cost of the air supply subsystem, which is hardly investigated in previous publications. For this purpose, a mathematical model is built to assess the potential of improving the expander performance by means of the dual-lead rotors. And the influence of lead and length of the high-pressure rotor segment and overall rotor length are analyzed. The results demonstrate that the smaller lead and larger length of the high-pressure rotor segment result in better geometric characteristics and thus thermodynamic performance. For example, case #4 with dual-lead rotors exhibits a larger rotating angle at the suction end and a larger suction area than those of constant-lead rotors by 43° and 100%, respectively, which further lower the suction pressure loss. Compared with constant-lead rotors, the maximum increments in the mass flowrate and indicated power are observed as 45% and 25.4%, respectively. However, the dual-lead rotors could not effectively contribute to an increase in the isentropic indicated efficiency of twin-screw expanders due to the severe leakage, and hence, it becomes crucial to address the leakage issues in twin-screw expanders. Full article

T cell receptor beta (TRB) sequences were recovered from the Cancer Genome Atlas Uveal Melanoma blood exome files. Intrinsic disorder scores for amino acid (AA) sequences of the entire TRB variable region were obtained and evaluated as potentially representative of overall survival (OS) distinctions, i.e., for cases representing the upper and lower 50th percentiles for intrinsic disorder scores. Analyses using four intrinsic disorder assessment tools indicated that a lower intrinsic disorder of the blood-sourced TRB variable regions, including continuous AA sequences of the V-gene segment, the complementarity-determining region-3, and the J-gene segment, was associated with a better OS probability (with log-rank p-values ranging from 0.002 to 0.014). We further determined that intrinsic disorder assessments could be used for OS stratification for a second, immunologically cold cancer: MYCN amplified neuroblastoma. Thus, intrinsic disorder assessments of blood-sourced, full TRB variable regions may provide a novel patient stratification approach for patients with immunologically cold cancers. Full article

Background: The invasion of glioblastoma cells beyond the visible tumor margin depicted by conventional neuroimaging is believed to mediate recurrence and predict poor survival. Radiomic biomarkers that are associated with the direction and extent of tumor infiltration are, however, non-existent. Methods: Patients from a single center with newly diagnosed glioblastoma (n = 7) underwent preoperative Q-space magnetic resonance imaging (QSI; 3T, 64 gradient directions, b = 1000 s/mm²) between 2018 and 2019. Tumors were manually segmented, and patterns of inter-voxel coherence spatially intersecting each segmentation were generated to represent tumor-associated tractography. One patient additionally underwent regional biopsy of diffusion tract- versus non-tract-associated tissue during tumor resection for RNA sequencing. Imaging data from this cohort were compared with a historical cohort of n = 66 glioblastoma patients who underwent similar QSI scans. Associations of tractography-derived metrics with survival were assessed using t-tests, linear regression, and Kaplan–Meier statistics. Patient-derived glioblastoma xenograft (PDX) mice generated with the sub-hippocampal injection of human-derived glioblastoma stem cells (GSCs) were scanned under high-field conditions (QSI, 7T, 512 gradient directions), and tumor-associated tractography was compared with the 3D microscopic reconstruction of immunostained GSCs. Results: In the principal enrollment cohort of patients with glioblastoma, all cases displayed tractography patterns with tumor-intersecting tract bundles extending into brain parenchyma, a phenotype which was reproduced in PDX mice as well as in a larger comparison cohort of glioblastoma patients (n = 66), when applying similar methods. Reconstructed spatial patterns of GSCs in PDX mice closely mirrored tumor-associated tractography. On a Kaplan–Meier survival analysis of n = 66 patients, the calculated intra-tumoral mean diffusivity predicted the overall survival (p = 0.037), as did tractography-associated features including mean tract length (p = 0.039) and mean projecting tract length (p = 0.022). The RNA sequencing of human tissue samples (n = 13 tumor samples from a single patient) revealed the overexpression of transcripts which regulate cell motility in tract-associated samples. Conclusions: QSI discriminates tumor-specific patterns of inter-voxel coherence believed to represent white matter pathways which may be susceptible to glioblastoma invasion. These findings may lay the groundwork for future work on therapeutic targeting, patient stratification, and prognosis in glioblastoma. Full article