Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnostic Accuracy of Deep Learning and Radiomics in Lung Cancer Staging: A Systematic Review and Meta-Analysis

Background Artificial intelligence has far surpassed previous related technologies in image recognition and is increasingly used in medical image analysis. We aimed to explore the diagnostic accuracy of the models based on deep learning or radiomics for lung cancer staging. Methods Studies were systematically reviewed using literature searches from PubMed, EMBASE, Web of Science, and Wanfang Database, according to PRISMA guidelines. Studies about the diagnostic accuracy of radiomics and deep learning, including the identifications of lung cancer, tumor types, malignant lung nodules and lymph node metastase, were included. After identifying the articles, the methodological quality was assessed using the QUADAS-2 checklist. We extracted the characteristic of each study; the sensitivity, specificity, and AUROC for lung cancer diagnosis were summarized for subgroup analysis. Results The systematic review identified 19 eligible studies, of which 14 used radiomics models and 5 used deep learning models. The pooled AUROC of 7 studies to determine whether patients had lung cancer was 0.83 (95% CI 0.78–0.88). The pooled AUROC of 9 studies to determine whether patients had NSCLC was 0.78 (95% CI 0.73–0.83). The pooled AUROC of the 6 studies that determined patients had malignant lung nodules was 0.79 (95% CI 0.77–0.82). The pooled AUROC of the other 6 studies that determined whether patients had lymph node metastases was 0.74 (95% CI 0.66–0.82). Conclusion The models based on deep learning or radiomics have the potential to improve diagnostic accuracy for lung cancer staging. Systematic Review Registration https://inplasy.com/inplasy-2022-3-0167/, identifier: INPLASY202230167.
ERα and ERβ Homodimers in the Same Cellular Context Regulate Distinct Transcriptomes and Functions

The two estrogen receptors ERα and ERβ are nuclear receptors that bind estrogen (E2) and function as ligand-inducible transcription factors. They are homologues and can form dimers with each other and bind to the same estrogen-response element motifs in the DNA. ERα drives breast cancer growth whereas ERβ has been reported to be anti-proliferative. However, they are rarely expressed in the same cells, and it is not fully investigated to which extent their functions are different because of inherent differences or because of different cellular context. To dissect their similarities and differences, we here generated a novel estrogen-dependent cell model where ERα homodimers can be directly compared to ERβ homodimers within the identical cellular context. By using CRISPR-cas9 to delete ERα in breast cancer MCF7 cells with Tet-Off-inducible ERβ expression, we generated MCF7 cells that express ERβ but not ERα. MCF7 (ERβ only) cells exhibited regulation of estrogen-responsive targets in a ligand-dependent manner. We demonstrated that either ER was required for MCF7 proliferation, but while E2 increased proliferation via ERα, it reduced proliferation through a G2/M arrest via ERβ. The two ERs also impacted migration differently. In absence of ligand, ERβ increased migration, but upon E2 treatment, ERβ reduced migration. E2 via ERα, on the other hand, had no significant impact on migration. RNA sequencing revealed that E2 regulated a transcriptome of around 800 genes via each receptor, but over half were specific for either ERα or ERβ (417 and 503 genes, respectively). Functional gene ontology enrichment analysis reinforced that E2 regulated cell proliferation in opposite directions depending on the ER, and that ERβ specifically impacted extracellular matrix organization. We corroborated that ERβ bound to cis-regulatory chromatin of its unique proposed migration-related direct targets ANXA9 and TFAP2C. In conclusion, we demonstrate that within the same cellular context, the two ERs regulate cell proliferation in the opposite manner, impact migration differently, and each receptor also regulates a distinct set of target genes in response to E2. The developed cell model provides a novel and valuable resource to further complement the mechanistic understanding of the two different ER isoforms.
Wheelchair Tai Chi Ball Exercise for Improving Neuromuscular Functions of Older Adults With Disability

The purposes of this perspective article were to summarize Wheelchair or Seated Tai Chi studies related to neuromuscular functions of older adults with disability; to describe the development of Wheelchair Tai Chi Ball (WTCB) exercise — a concept to combine mind-body exercise with strength training; and to propose a new Telehealth WTCB exercise for improving neuromuscular functions of old adults with spinal cord injury (SCI) and disability. With reference to neuromuscular functions, WTC intervention may have positive effects on simple reaction time, range of motion at the shoulder and trunk, static and dynamic sitting balance, handgrip strength, vagal activity, and sympathetic activity among older adults with disability. The developed WTCB intervention is a feasible and safe exercise which combines the mind-body exercise and strength conditioning into one exercise which possesses aerobic, stretching and strength trainings and may facilitate neuromuscular functions of older adults with disability. The proposed Telehealth WTCB 12 forms (TWTCB12) exercise with a “Moving Shadow” method in the telehealth may enable the learner to superimpose learner’s image on an expert’s demonstrating model to enhance the learning and practice effects. Since wheelchair users will learn and practice TWTCB12 movements in a seated position or sitting on a wheelchair the “Moving shadow” method on Zoom would provide an ideal telehealth learning and practice environment for the wheelchair users to learn and practice TWTCB12 exercise from home more feasible and user friendly.
Ubiquity and Diversity of Cold Adapted Denitrifying Bacteria Isolated From Diverse Antarctic Ecosystems

Nitrogen cycle has been poorly investigated in Antarctic ecosystems. In particular, how extreme conditions of low temperature, dryness, and high radiation select the microorganisms involved in the cycle is not yet understood. Denitrification is an important step in the nitrogen cycle in which nitrate is reduced stepwise to the gases NO, N2O, and N2. Denitrification is carried out by a wide group of microorganisms spread in the phylogenetic tree. The aim of this work was to isolate and characterize denitrifying bacteria present in different cold environments from Antarctica. Bacterial isolates were obtained from lake, meltwater, sea, glacier ice, ornithogenic soil, and penguin feces samples from King George Island, Fildes peninsula in the Antarctic. Samples were taken during the deicing season in five sampling campaigns. From all the samples we were able to isolate denitrifying strains. A total of 199 bacterial isolates with the capacity to grow in anaerobic mineral media reducing nitrate at 4°C were obtained. The characterization of the isolates by 16S rRNA gene sequence analysis showed a high predominance of the genus Pseudomonas, followed by Janthinobacterium, Flavobacterium, Psychrobacter, and Yersinia. Other minor genera detected were Cryobacterium, Iodobacter, Kaistella, and Carnobacterium. The capacity to denitrify was not previously described for most of the bacteria related to our isolates and in many of them denitrifying genes were not present suggesting the presence of new genes in this extreme environment. Our work demonstrates the ubiquity of denitrification in the Maritime Antarctica and gives important information linking denitrification at cold temperature with taxa in an unequivocal way.
Bibliometric Analysis of 100 Most-Cited Articles in Delirium

Delirium is a cognitive disorder with complex etiology, which brings a great burden to social health care. Articles with high citation frequency can provide important information about the current research situation in a certain field. Web of Science was used to search the 100 most-cited articles and we extracted key information, such as the authors, countries/regions, institutions, journals, and study types of these articles. CiteSpace was used to visually analyze the keywords. Our bibliometric analysis shows that the attention in this field continues to rise. Authors from the United States published the most articles and Inouye SK is the most influential author in the field. The journals that published these articles have high impact factors. Cohort studies are the main cited articles in this field, and there are a large number of systematic reviews or meta-analyses of cohort studies. Risk factors for delirium, psychometric evaluation, hospital care, and various clinical study design are still the focus of research. In short, we summarized the 100 most-cited articles in the field of delirium to identify the current status and global trends. These results enable researchers to understand the quality and trend of research in the field of delirium and make better use of the classical literature.
DYRK1a Inhibitor Mediated Rescue of Drosophila Models of Alzheimer’s Disease-Down Syndrome Phenotypes

Alzheimer’s disease (AD) is the most common neurodegenerative disease which is becoming increasingly prevalent due to ageing populations resulting in huge social, economic, and health costs to the community. Despite the pathological processing of genes such as Amyloid Precursor Protein (APP) into Amyloid-β and Microtubule Associated Protein Tau (MAPT) gene, into hyperphosphorylated Tau tangles being known for decades, there remains no treatments to halt disease progression. One population with increased risk of AD are people with Down syndrome (DS), who have a 90% lifetime incidence of AD, due to trisomy of human chromosome 21 (HSA21) resulting in three copies of APP and other AD-associated genes, such as DYRK1A (Dual specificity tyrosine-phosphorylation-regulated kinase 1A) overexpression. This suggests that blocking DYRK1A might have therapeutic potential. However, it is still not clear to what extent DYRK1A overexpression by itself leads to AD-like phenotypes and how these compare to Tau and Amyloid-β mediated pathology. Likewise, it is still not known how effective a DYRK1A antagonist may be at preventing or improving any Tau, Amyloid-β and DYRK1a mediated phenotype. To address these outstanding questions, we characterised Drosophila models with targeted overexpression of human Tau, human Amyloid-β or the fly orthologue of DYRK1A, called minibrain (mnb). We found targeted overexpression of these AD-associated genes caused degeneration of photoreceptor neurons, shortened lifespan, as well as causing loss of locomotor performance, sleep, and memory. Treatment with the experimental DYRK1A inhibitor PST-001 decreased pathological phosphorylation of human Tau [at serine (S) 262]. PST-001 reduced degeneration caused by human Tau, Amyloid-β or mnb lengthening lifespan as well as improving locomotion, sleep and memory loss caused by expression of these AD and DS genes. This demonstrated PST-001 effectiveness as a potential new therapeutic targeting AD and DS pathology.
Novel Photo- and Thermo-Responsive Nanocomposite Hydrogels Based on Functionalized rGO and Modified SIS/Chitosan Polymers for Localized Treatment of Malignant Cutaneous Melanoma

Melanoma is an aggressive type of skin cancer that accounts for over 75% of skin cancer deaths despite comprising less than 5% of all skin cancers. Despite promising improvements in surgical approaches for melanoma resection, the survival of undetectable microtumor residues has remained a concern. As a result, hyperthermia- and drug-based therapies have grown as attractive techniques to target and treat cancer. In this work, we aim to develop a stimuli-responsive hydrogel based on chitosan methacrylate (ChiMA), porcine small intestine submucosa methacrylate (SISMA), and doxorubicin-functionalized reduced graphene oxide (rGO-DOX) that eliminates microtumor residues from surgically resected melanoma through the coupled effect of NIR light-induced photothermal therapy and heat-induced doxorubicin release. Furthermore, we developed an in silico model to optimize heat and mass transport and evaluate the proposed chemo/photothermal therapy in vitro over melanoma cell cultures.
Effect of ultrasonic degradation on the physicochemical property and bioactivity of polysaccharide produced by Chaetomium globosum CGMCC 6882

Similar to the enzymatic process, there might also be an active fragment in polysaccharides, how to obtain is important for investigating the bioactivity and pharmacological mechanism of polysaccharides. Presently, a Gynostemma pentaphyllum endophytic fungus Chaetomium globosum CGMCC 6882 polysaccharide [Genistein Combined Polysaccharide (GCP)] was degraded by ultrasonic treatment, two polysaccharide fragments of GCP-F1 and GCP-F2 were obtained. Physicochemical results showed that GCP-F1 and GCP-F2 had the same monosaccharide composition of arabinose, galactose, glucose, xylose, mannose, and glucuronic acid as compared to GCP with slightly different molar ratios. However, weight-average molecular weights of GCP-F1 and GCP-F2 decreased from 8.093 × 104 Da (GCP) to 3.158 × 104 Da and 1.027 × 104 Da, respectively. In vitro scavenging assays illustrated that GCP-F1 and GCP-F2 had higher antioxidant activity against 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical, superoxide anions, and hydroxyl radical than GCP, the order was GCP < GCP-F1 < GCP-F2. Meanwhile, antibacterial tests showed that ultrasonic degradation increased the antibacterial activity of GCP-F1 as compared to GCP, but GCP-F2 almost lost its antibacterial activity with further ultrasound treatment. Changes in the antioxidant and antibacterial activities of GCP-F1 and GCP-F2 might be related to the variation of their molecular weights.
Advances in UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) Covalent Inhibition

Peptidoglycan is a cross-linked polymer responsible for maintaining the bacterial cell wall integrity and morphology in Gram-negative and Gram-positive bacteria. The peptidoglycan pathway consists of the enzymatic reactions held in three steps: cytoplasmic, membrane-associated, and periplasmic. The Mur enzymes (MurA-MurF) are involved in a cytoplasmic stage. The UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) enzyme is responsible for transferring the enolpyruvate group from phosphoenolpyruvate (PEP) to UDP-N-acetylglucosamine (UNAG) to form UDP-N-acetylglucosamine enolpyruvate (EP-UNAG). Fosfomycin is a natural product analogous to PEP that acts on the MurA target enzyme via binding covalently to the key cysteine residue in the active site. Similar to fosfomycin, other MurA covalent inhibitors have been described with a warhead in their structure that forms a covalent bond with the molecular target. In MurA, the nucleophilic thiolate of Cys115 is pointed as the main group involved in the warhead binding. Thus, in this minireview, we briefly describe the main recent advances in the design of MurA covalent inhibitors.
Toward improving control performance of myoelectric arm prosthesis by adding wrist position feedback

Wearing a myoelectric prosthesis is a basic way for limb amputees to restore their lost limb functions in the activities of daily living (ADLs). However, it is estimated that around 40% of amputees refuse the prosthesis. One of the primary reasons would be that the current prostheses lack appropriate sensory feedback. Currently, the amputees only depend on their visual feedback (Vis-FB) when using their arm prostheses. It would be difficult for them to accurately control the wrist position, which is vital for flexible manipulation in ADLs. This manuscript designed a myoelectric arm prosthesis with wrist position feedback (WP-FB). To study the effect level of position feedback on prosthetic control, two tests were performed. The vibrotactile perception range test aims to analyze the perception sensitivity of the vibration in humans and obtain the optimal perception range utilized in the sensory feedback test. The sensory feedback test analyzes the effectiveness of the position feedback by comparing three feedback methods of Vis-FB, WP-FB, and a combination of Vis-FB and WP-FB (VP-FB). These tests were conducted by asking six able-bodied subjects to perform 20 movement combinations of five target positions. The WP-FB was transiently activated with five vibrating motors embedded in an armband to stimulate the arm stump when the prosthetic wrist rotates to the target positions. Our experimental results showed that when WP-FB was added to the prosthetic control, the absolute angular error (AAE) of the prosthetic wrist declined from 4.50° to 1.08° while the success rate 3 (SR3) increased from 0.34 to 0.84, respectively. This study demonstrates the importance of WP-FB to the effective control of the arm prosthesis.
Network analysis combined with pharmacological evaluation strategy to reveal the mechanism of Tibetan medicine Wuwei Shexiang pills in treating rheumatoid arthritis

Tibetan medicine is an important part of traditional Chinese medicine and a significant representative of ethnic medicine in China. Tibetan medicine is gradually recognized by the world for its unique curative effects. Wuwei Shexiang pills (WPW) has been widely used to treat “Zhenbu” disease (Also known as rheumatoid arthritis) in Tibetan medicine, however, its potential bioactive ingredients and mechanism for RA treatment remain unclear. In this study, we used a combination of gas chromatography-mass spectrometry (GC-MS), ultra-performance liquid chromatography coupled with quadrupole time-of-fight mass spectrometry (UPLC-Q-TOF/MS), network analysis and experimental validation to elucidate the potential pharmacodynamic substances and mechanisms of WPW in the treatment of rheumatoid arthritis (RA). The results showed that songoramine, cheilanthifoline, saussureanine C, acoric acid, arjunolic acid, peraksine, ellagic acid, arjungenin and other 11 components may be the main activities of WPW in the treatment of RA. PIK3CA, AKT, MAPK, IL-6, TNF, MMP1, MMP3, and CDK1 are considered as core targets. PI3K-AKT, MAPK, apoptosis, cell cycle, and other signaling pathways may be the key pathways for WPW to play a role in the treatment of RA. Furthermore, we validated the underlying molecular mechanism of WPW predicted by network analysis and demonstrated its possible mechanism through in vivo animal experiments. It was found that WPW could significantly improve the degree of paw swelling, and reduce ankle joint diameter and arthritis index. Further histomorphological analysis showed that WPW could reduce the degree of synovial tissue inflammation and ankle joint cartilage damage. Meanwhile, WPW could down-regulate the levels of IL-6, IL-1β, and IL-17, and increase the levels of IL-10 and IL-4 in the serum of AA rats. TUNEL staining confirmed that WPW could significantly promote the apoptosis of synovial cells. Moreover, the immunohistochemical results showed that WPW decreased the expression of PI3K, AKT, MAPK, MMP1, MMP3, CDK1, and Bcl-2, as well as increased the expression of Bax protein. In conclusion, we successfully combined GC-MS, UPLC-Q-TOF/MS, network analysis, and experimental validation strategies to elucidate the inhibition of inflammation by WPW in AA model rats via PI3K/AKT, MAPK, cell cycle and apoptotic pathways process. This not only provides new evidence for the study of potential pharmacodynamic substances and the mechanism of WPW in the treatment of RA, but also provides ideas for the study of other Tibetan medicine compound preparations.
Comparing DESI-MSI and MALDI-MSI Mediated Spatial Metabolomics and Their Applications in Cancer Studies

Metabolic heterogeneity of cancer contributes significantly to its poor treatment outcomes and prognosis. As a result, studies continue to focus on identifying new biomarkers and metabolic vulnerabilities, both of which depend on the understanding of altered metabolism in cancer. In the recent decades, the rise of mass spectrometry imaging (MSI) enables the in situ detection of large numbers of small molecules in tissues. Therefore, researchers look to using MSI-mediated spatial metabolomics to further study the altered metabolites in cancer patients. In this review, we examined the two most commonly used spatial metabolomics techniques, MALDI-MSI and DESI-MSI, and some recent highlights of their applications in cancer studies. We also described AFADESI-MSI as a recent variation from the DESI-MSI and compare it with the two major techniques. Specifically, we discussed spatial metabolomics results in four types of heterogeneous malignancies, including breast cancer, esophageal cancer, glioblastoma and lung cancer. Multiple studies have effectively classified cancer tissue subtypes using altered metabolites information. In addition, distribution trends of key metabolites such as fatty acids, high-energy phosphate compounds, and antioxidants were identified. Therefore, while the visualization of finer distribution details requires further improvement of MSI techniques, past studies have suggested spatial metabolomics to be a promising direction to study the complexity of cancer pathophysiology.
The Role of Fc Gamma Receptors in Antibody-Mediated Rejection of Kidney Transplants

For the past decades, complement activation and complement-mediated destruction of allograft cells were considered to play a central role in anti-HLA antibody-mediated rejection (AMR) of kidney transplants. However, also complement-independent mechanisms are relevant in the downstream immune activation induced by donor-specific antibodies, such as Fc-gamma receptor (FcγR)-mediated direct cellular activation. This article reviews the literature regarding FcγR involvement in AMR, and the potential contribution of FcγR gene polymorphisms to the risk for antibody mediated rejection of kidney transplants. There is large heterogeneity between the studies, both in the definition of the clinical phenotypes and in the technical aspects. The study populations were generally quite small, except for two larger study cohorts, which obviates drawing firm conclusions regarding the associations between AMR and specific FcγR polymorphisms. Although FcγR are central in the pathophysiology of AMR, it remains difficult to identify genetic risk factors for AMR in the recipient’s genome, independent of clinical risk factors, independent of the donor-recipient genetic mismatch, and in the presence of powerful immunosuppressive agents. There is a need for larger, multi-center studies with standardised methods and endpoints to identify potentially relevant FcγR gene polymorphisms that represent an increased risk for AMR after kidney transplantation.