1,324 research outputs found
Unsupervised augmentation optimization for few-shot medical image segmentation
The augmentation parameters matter to few-shot semantic segmentation since
they directly affect the training outcome by feeding the networks with varying
perturbated samples. However, searching optimal augmentation parameters for
few-shot segmentation models without annotations is a challenge that current
methods fail to address. In this paper, we first propose a framework to
determine the ``optimal'' parameters without human annotations by solving a
distribution-matching problem between the intra-instance and intra-class
similarity distribution, with the intra-instance similarity describing the
similarity between the original sample of a particular anatomy and its
augmented ones and the intra-class similarity representing the similarity
between the selected sample and the others in the same class. Extensive
experiments demonstrate the superiority of our optimized augmentation in
boosting few-shot segmentation models. We greatly improve the top competing
method by 1.27\% and 1.11\% on Abd-MRI and Abd-CT datasets, respectively, and
even achieve a significant improvement for SSL-ALP on the left kidney by 3.39\%
on the Abd-CT dataset
FairAdaBN: Mitigating unfairness with adaptive batch normalization and its application to dermatological disease classification
Deep learning is becoming increasingly ubiquitous in medical research and
applications while involving sensitive information and even critical diagnosis
decisions. Researchers observe a significant performance disparity among
subgroups with different demographic attributes, which is called model
unfairness, and put lots of effort into carefully designing elegant
architectures to address unfairness, which poses heavy training burden, brings
poor generalization, and reveals the trade-off between model performance and
fairness. To tackle these issues, we propose FairAdaBN by making batch
normalization adaptive to sensitive attribute. This simple but effective design
can be adopted to several classification backbones that are originally unaware
of fairness. Additionally, we derive a novel loss function that restrains
statistical parity between subgroups on mini-batches, encouraging the model to
converge with considerable fairness. In order to evaluate the trade-off between
model performance and fairness, we propose a new metric, named
Fairness-Accuracy Trade-off Efficiency (FATE), to compute normalized fairness
improvement over accuracy drop. Experiments on two dermatological datasets show
that our proposed method outperforms other methods on fairness criteria and
FATE.Comment: Accepted by MICCAI 202
Seroprevalence of Toxoplasma gondii infection in dairy goats in Shaanxi Province, Northwestern China
<p>Abstract</p> <p>Background</p> <p><it>Toxoplasma gondii </it>is an important zoonotic pathogen causing significant human and animal health problems. Infection in dairy goats not only results in significant reproductive losses, but also represents an important source of human infection due to consumption of infected meat and milk. In the present study we report for the first time seroprevalence of <it>T. gondii </it>infection in Guanzhong and Saanen dairy goats in Shaanxi province, Northwestern China.</p> <p>Results</p> <p>Sera from 751 dairy goats from 9 farms in 6 counties were examined for <it>T. gondii </it>antibodies with an indirect haemagglutination (IHA) test. Antibodies to <it>T. gondii </it>were detected in 106 (14.1%) serum samples, with antibody titres ranging from 1:64 to 1:1024. Seropositive goats were found in all 9 farms and seroprevalences in Guanzhong (16.3%, 75/461) and Saanen (10.7%, 31/290) dairy goats were not statistically significantly different. All the factors (sex, age and location) reported in the present study affected prevalence of infection, and seroprevalence increased with age, suggesting postnatal acquisition of <it>T. gondii </it>infection.</p> <p>Conclusions</p> <p>The results of the present survey indicate that infection by <it>T. gondii </it>is widely prevalent in dairy goats in Shaanxi province, Northwestern China, and this has implications for prevention and control of toxoplasmosis in this province.</p
Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology
Podocytes, specialized epithelial cells that envelop the glomerular
capillaries, play a pivotal role in maintaining renal health. The current
description and quantification of features on pathology slides are limited,
prompting the need for innovative solutions to comprehensively assess diverse
phenotypic attributes within Whole Slide Images (WSIs). In particular,
understanding the morphological characteristics of podocytes, terminally
differentiated glomerular epithelial cells, is crucial for studying glomerular
injury. This paper introduces the Spatial Pathomics Toolkit (SPT) and applies
it to podocyte pathomics. The SPT consists of three main components: (1)
instance object segmentation, enabling precise identification of podocyte
nuclei; (2) pathomics feature generation, extracting a comprehensive array of
quantitative features from the identified nuclei; and (3) robust statistical
analyses, facilitating a comprehensive exploration of spatial relationships
between morphological and spatial transcriptomics features.The SPT successfully
extracted and analyzed morphological and textural features from podocyte
nuclei, revealing a multitude of podocyte morphomic features through
statistical analysis. Additionally, we demonstrated the SPT's ability to
unravel spatial information inherent to podocyte distribution, shedding light
on spatial patterns associated with glomerular injury. By disseminating the
SPT, our goal is to provide the research community with a powerful and
user-friendly resource that advances cellular spatial pathomics in renal
pathology. The implementation and its complete source code of the toolkit are
made openly accessible at https://github.com/hrlblab/spatial_pathomics
Identification, Characterization, and Effects of Xenopus laevis PNAS-4 Gene on Embryonic Development
Apoptosis plays an important role in embryonic development. PNAS-4 has been demonstrated to induce apoptosis in several cancer cells. In this study, we cloned Xenopus laevis PNAS-4 (xPNAS-4), which is homologous to the human PNAS-4 gene. Bioinformatics analysis for PNAS-4 indicated that xPNAS-4 shared 87.6% identity with human PNAS-4 and 85.5% with mouse PNAS-4. The phylogenetic tree of PNAS-4 protein was also summarized. An analysis of cellular localization using an EGFP-fused protein demonstrated that xPNAS-4 was localized in the perinuclear region of the cytoplasm. RT-PCR analysis revealed that xPNAS-4, as a maternally expressed gene, was present in all stages of early embryo development. Whole-mount in situ hybridization showed that xPNAS-4 was mainly expressed in ectoderm and mesoderm. Furthermore, microinjection of xPNAS-4 mRNA in vivo caused developmental defects manifesting as a small eye phenotype in the Xenopous embryos, and as a small eye or one-eye phenotype in developing zebrafish embryos. In addition, embryos microinjected with xPNAS-4 antisense morpholino oligonucleotides (MOs) exhibited a failure of head development and shortened axis
Franck-Condon Effect in Central Spin System
We study the quantum transitions of a central spin surrounded by a
collective-spin environment. It is found that the influence of the
environmental spins on the absorption spectrum of the central spin can be
explained with the analog of the Franck-Condon (FC) effect in conventional
electron-phonon interaction system. Here, the collective spins of the
environment behave as the vibrational mode, which makes the electron to be
transitioned mainly with the so-called "vertical transitions" in the
conventional FC effect. The "vertical transition" for the central spin in the
spin environment manifests as, the certain collective spin states of the
environment is favored, which corresponds to the minimal change in the average
of the total spin angular momentum.Comment: 8 pages, 8 figure
Dysregulation of hepatic microRNA expression in C57BL/6 mice affected by excretory-secretory products of Fasciola gigantica
The excretory-secretory products released by the liver fluke Fasciola gigantica (FgESPs) play important roles in regulating the host immune response during the infection. Identification of hepatic miRNAs altered by FgESPs may improve our understanding of the pathogenesis of F. gigantica infection. In this study, we investigated the alterations in the hepatic microRNAs (miRNAs) in mice treated with FgESPs using high-throughput small RNA (sRNA) sequencing and bioinformatics analysis. The expression of seven miRNAs was confirmed by quantitative stem-loop reverse transcription quantitative PCR (qRT-PCR). A total of 1,313 miRNAs were identified in the liver of mice, and the differentially expressed (DE) miRNAs varied across the time lapsed post exposure to FgESPs. We identified 67, 154 and 53 dysregulated miRNAs at 1, 4 and 12 weeks post-exposure, respectively. 5 miRNAs (miR-126a-3p, miR-150-5p, miR-155-5p, miR-181a-5p and miR-362-3p) were commonly dysregulated at the three time points. We also found that most of the DE miRNAs were induced by FgESPs in the mouse liver after 4 weeks of exposure. These were subjected to Gene Ontology (GO) enrichment analysis, which showed that the predicted targets of the hepatic DE miRNAs of mice 4 weeks of FgESPs injection were enriched in GO terms, including cell membrane, ion binding, cellular communication, organelle and DNA damage. KEGG analysis indicated that the predicted targets of the most downregulated miRNAs were involved in 15 neural activity-related pathways, 6 digestion-related pathways, 20 immune response-related pathways and 17 cancer-related pathways. These data provide new insights into how FgESPs can dysregulate hepatic miRNAs, which play important roles in modulating several aspects of F. gigantica pathogenesis
Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging
The segment anything model (SAM) was released as a foundation model for image
segmentation. The promptable segmentation model was trained by over 1 billion
masks on 11M licensed and privacy-respecting images. The model supports
zero-shot image segmentation with various segmentation prompts (e.g., points,
boxes, masks). It makes the SAM attractive for medical image analysis,
especially for digital pathology where the training data are rare. In this
study, we evaluate the zero-shot segmentation performance of SAM model on
representative segmentation tasks on whole slide imaging (WSI), including (1)
tumor segmentation, (2) non-tumor tissue segmentation, (3) cell nuclei
segmentation. Core Results: The results suggest that the zero-shot SAM model
achieves remarkable segmentation performance for large connected objects.
However, it does not consistently achieve satisfying performance for dense
instance object segmentation, even with 20 prompts (clicks/boxes) on each
image. We also summarized the identified limitations for digital pathology: (1)
image resolution, (2) multiple scales, (3) prompt selection, and (4) model
fine-tuning. In the future, the few-shot fine-tuning with images from
downstream pathological segmentation tasks might help the model to achieve
better performance in dense object segmentation
Lycium barbarum Polysaccharides Attenuate Cisplatin-Induced Hair Cell Loss in Rat Cochlear Organotypic Cultures
The aim of the present study was to investigate the effects of Lycium barbarum polysaccharides (LBP) on cisplatin-induced hair cell damage in the organ of Corti explant. The neonatal (P2–3) rat organ of Corti explant was exposed to cisplatin (20 μM; 48 h) with or without LBP pretreatment (150 and 600 μg/mL; 24 h). Hair cell loss was indicated by FITC-labeled phalloidin staining. The level of reactive oxygen species (ROS) and alteration of mitochondrial membrane potential (ΔΨm) in hair cells were analyzed using fluorescent probes 2′,7′-dichlorofluorescein diacetate and JC-1, respectively. The results showed that LBP significantly attenuated hair cell loss (p < 0.01). Hair cells pretreated with LBP showed significant reduction in ROS production and the decline of ΔΨm compared with cisplatin alone group (p < 0.01), indicating the protective effect of LBP on cisplatin-induced hair cell loss. Taken together, these results indicate that LBP was effective in attenuating cisplatin-induced hair cell loss by reducing the production of ROS and maintaining mitochondrial ΔΨm
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