Pick the Best Pre-trained Model: Towards Transferability Estimation for Medical Image Segmentation

Transfer learning is a critical technique in training deep neural networks for the challenging medical image segmentation task that requires enormous resources. With the abundance of medical image data, many research institutions release models trained on various datasets that can form a huge pool of candidate source models to choose from. Hence, it's vital to estimate the source models' transferability (i.e., the ability to generalize across different downstream tasks) for proper and efficient model reuse. To make up for its deficiency when applying transfer learning to medical image segmentation, in this paper, we therefore propose a new Transferability Estimation (TE) method. We first analyze the drawbacks of using the existing TE algorithms for medical image segmentation and then design a source-free TE framework that considers both class consistency and feature variety for better estimation. Extensive experiments show that our method surpasses all current algorithms for transferability estimation in medical image segmentation. Code is available at https://github.com/EndoluminalSurgicalVision-IMR/CCFVComment: MICCAI2023(Early Accepted

Tissue distribution and excretion of the five components of Portulaca oleracea L. extract in rat assessed by UHPLC

The aim of the present study was to investigate the tissue distribution and excretion of five components of Portulaca oleracea L. extract (POE) in rat following oral administration. A rapid, sensitive and specific ultra-high performance liquid chromatography (UHPLC) method with puerarin as the internal standard was used for the quantitative analysis of five components of POE, including caffeic acid (CA), p-coumaric acid (p-CA), ferulic acid (FA), quercitrin (QUER) and hesperidin (HP) in rat tissues including the liver, intestine, stomach, muscle, heart, lung, brain, kidney and spleen, urine and feces. The results show that onlyp-CA and FA were found in nearly all tissues with low cumulative ratios, and CA was higher in the intestine and stomach with a slightly higher cumulative ratio in the urine and feces after 24 h. HP and QUER were found at low levels in the tissues with low cumulative ratios.O objetivo do presente estudo foi investigar a distribuição tecidual e excreção de cinco componentes de extrato Portulaca oleracea L. (POE) em ratos após administração oral. Um método analítico rápido, sensível e específico para quantificação de cinco componentes de POE (ácido cafeico (CA), ácidop-cumárico (p-CA), ácido ferúlico (FA), quercitrina (QUER) e hesperidina (HP)) por cromatografia líquida de ultra eficiência (UHPLC), empregando puerarina como padrão interno de referência. Os compostos foram quantificados em diferentes tecidos dos animais, sendo eles fígado, intestino, estômago, músculo, coração, pulmão, cérebro, rim e baço, urina e fezes. Os resultados mostraram que apenas p-CA e FA foram encontradas em todos os tecidos com baixas taxas cumulativas e CA apresentou níveis mais altos no intestino e estômago com a taxa cumulativa um pouco mais elevada na urina e nas fezes após 24 h. HP e QUER apresentaram baixas concentrações nos tecidos com baixas taxas cumulativas

The Neuroprotective Effects of Brazilian Green Propolis on Neurodegenerative Damage in Human Neuronal SH-SY5Y Cells

Oxidative stress and synapse dysfunction are the major neurodegenerative damage correlated to cognitive impairment in Alzheimer’s disease (AD). We have found that Brazilian green propolis (propolis) improves the cognitive functions of mild cognitive impairment patients living at high altitude; however, mechanism underlying the effects of propolis is unknown. In the present study, we investigated the effects of propolis on oxidative stress, expression of brain-derived neurotrophic factor (BDNF), and activity-regulated cytoskeleton-associated protein (Arc), the critical factors of synapse efficacy, using human neuroblastoma SH-SY5Y cells. Pretreatment with propolis significantly ameliorated the hydrogen peroxide- (H2O2-) induced cytotoxicity in SH-SY5Y cells. Furthermore, propolis significantly reduced the H2O2-generated reactive oxygen species (ROS) derived from mitochondria and 8-oxo-2′-deoxyguanosine (8-oxo-dG, the DNA oxidative damage marker) but significantly reversed the fibrillar β-amyloid and IL-1β-impaired BDNF-induced Arc expression in SH-SY5Y cells. Furthermore, propolis significantly upregulated BDNF mRNA expression in time- and dose-dependent manners. In addition, propolis induced Arc mRNA and protein expression via phosphoinositide-3 kinase (PI3K). These observations strongly suggest that propolis protects from the neurodegenerative damage in neurons through the properties of various antioxidants. The present study provides a potential molecular mechanism of Brazilian green propolis in prevention of cognitive impairment in AD as well as aging

The application of additive manufacturing technology in pelvic surgery: A bibliometrics analysis

With the development of material science, additive manufacturing technology has been employed for pelvic surgery, addressing the challenges, such as the complex structure of the pelvis, difficulty in exposing the operative area, and poor visibility, of the traditional pelvic surgery. However, only limited studies have been done to review the research hotspots and trends of the additive manufacturing technology applied for pelvic surgery. In this study, we comprehensively analyzed the literatures related to additive manufacturing technology in pelvic surgery by a bibliometrics analysis and found that additive manufacturing technology is widely used in several aspects of preoperative diagnosis, preoperative planning, intraoperative navigation, and personalized implants for pelvic surgery. Firstly, we searched and screened 856 publications from the Web of Science Core Collection (WoSCC) with TS = (3D printing OR 3D printed OR three-dimensional printing OR additive manufacturing OR rapid prototyping) AND TS = (pelvis OR sacrum OR ilium OR pubis OR ischium OR ischia OR acetabulum OR hip) as the search strategy. Then, 565 of these were eliminated by evaluating the titles and abstracts, leaving 291 pieces of research literature whose relevant information was visually displayed using VOSviewer. Furthermore, 10 publications with high citations were selected by reading all publications extensively for carefully evaluating their Titles, Purposes, Results, Limitations, Journal of affiliation, and Citations. Our results of bibliometric analysis demonstrated that additive manufacturing technology is increasingly applied in pelvic surgery, providing readers with a valuable reference for fully comprehending the research hotspots and trends in the application of additive manufacturing technology in pelvic surgery

Cathepsin B Regulates Collagen Expression by Fibroblasts via Prolonging TLR2/NF- κ

Fibroblasts are essential for tissue repair due to producing collagens, and lysosomal proteinase cathepsin B (CatB) is involved in promoting chronic inflammation. We herein report that CatB regulates the expression of collagens III and IV by fibroblasts in response to a TLR2 agonist, lipopolysaccharide from Porphyromonas gingivalis (P.g. LPS). In cultured human BJ fibroblasts, mRNA expression of CatB was significantly increased, while that of collagens III and IV was significantly decreased at 24 h after challenge with P.g. LPS (1 μg/mL). The P.g. LPS-decreased collagen expression was completely inhibited by CA-074Me, the specific inhibitor of CatB. Surprisingly, expression of collagens III and IV was significantly increased in the primary fibroblasts from CatB-deficient mice after challenge with P.g. LPS. The increase of CatB was accompanied with an increase of 8-hydroxy-2′-deoxyguanosine (8-OHdG) and a decrease of IκBα. Furthermore, the P.g. LPS-increased 8-OHdG and decreased IκBα were restored by CA-074Me. Moreover, 87% of CatB and 86% of 8-OHdG were colocalized with gingival fibroblasts of chronic periodontitis patients. The findings indicate the critical role of CatB in regulating the expression of collagens III and IV by fibroblasts via prolonging TLR2/NF-κB activation and oxidative stress. CatB-specific inhibitors may therefore improve chronic inflammation-delayed tissue repair

Determination and prediction of the digestible and metabolizable energy contents of corn germ meal in growing pigs

Objective This experiment was conducted to determine the chemical composition, digestible energy (DE) and metabolizable energy (ME) contents of corn germ meals (CGM) and to develop equations to predict the corresponding energy contents based on the chemical characteristics of individual CGM. Methods Sixty-six barrows (initial body weight = 51.3±4.6 kg) were allotted to 11 diets including a basal diet and 10 CGM test diets in a completely randomized design. In the test diets, CGM was included in replacement of 30% of the energy-providing ingredients in the basal diet, resulting in a final inclusion rate of 29.1%. Each diet was fed to 6 barrows housed in individual metabolism crates for a 7-d acclimation period followed by a 5-d total but separate collection of feces and urine. Results Considerable variation was observed in acid-hydrolyzed ether extract, ether extract, ash, calcium (Ca) and total phosphorus contents among the CGM samples. On dry matter (DM) basis, the DE and ME contents of the CGM ranged from 10.22 to 15.83 MJ/kg and from 9.94 to 15.43 MJ/kg, respectively. The acid detergent fiber (ADF) contents were negatively correlated with the DE and ME contents of CGM samples. The best-fit prediction equations for the DE and ME values (MJ/kg DM) of the 10 CGM were: DE = 26.85–0.28 insoluble dietary fiber (%)–17.79 Ca (%); ME = 21.05–0.43 ADF (%)–11.40 Ca (%). Conclusion The chemical compositions of CGM vary depending on sources, particularly in ether extract and Ca. The DE and ME values of CGM can be predicted based on their chemical composition in growing pigs

Integrating transcriptomics and metabolomics to analyze the mechanism of hypertension-induced hippocampal injury

ObjectiveHypertension is a public health challenge worldwide due to its high prevalence and multiple complications. Hypertension-induced damage to the hippocampus leads to behavioral changes and various brain diseases. Despite the multifaceted effects of hypertension on the hippocampus, the mechanisms underlying hippocampal lesions are still unclear.MethodsThe 32-week-old spontaneously hypertensive rats (SHR) and Wistar-Kyoto (WKY) rats were selected as the study subjects. Behavioral experiments such as an open field test (OFT), an elevated plus maze (EPM) test, and the Morris water maze (MWM) test were performed to show the behavioral characteristics of the rats. A comprehensive transcriptomic and metabolomic analysis was performed to understand the changes in the hippocampus at the metabolic and genetic levels.ResultsBehavioral tests showed that, compared to WKY rats, SHR showed not only reduced memory capacity but more hyperactive and impulsive behavior. In addition, transcriptomic analysis screened for 103 differentially expressed genes. Metabolomic analysis screened 56 metabolites with significant differences, including various amino acids and their related metabolites.ConclusionComprehensive analysis showed that hypertension-induced hippocampal lesions are closely associated with differential metabolites and differential genes detected in this study. The results provide a basis for analyzing the mechanisms of hypertension-induced hippocampal damage

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts