Reconsideration and Reflection on Spinal Disorders Through the Study of Intervertebral Discs in Patients with Lumbar Spondylolisthesis.

OBJECTIVE: This study analyzed and explored the relationship between isthmic spondylolisthesis and disc degeneration by comparing the degree of disc degeneration in patients with isthmic spondylolisthesis, lumbar disc herniation, and asymptomatic healthy individuals. METHODS: This study included a total of 138 cases, consisting of L5-S1 single segment lesion patients and a normal lumbar spine population. The cases were divided into 3 groups based on the type of disease: fifty eight cases in the isthmic spondylolisthesis (IS) group, 50 cases in the lumbar disc herniation (LDH) group, and 30 cases in the normal lumbar vertebrae (NLV) group. RESULTS: The research findings indicate that the proportion of intervertebral disc degeneration in the LDH group is significantly higher than that in the IS group and NLV group (65.3% vs. 33.3% vs. 25.8%, P < 0.05). The Pfirrmann grades of lumbar intervertebral discs (L1-L4) in the LDH group are significantly higher than those in the IS group and NLV group (P < 0.05), and the intervertebral height index (IHI) (L1-L4) of lumbar vertebrae in the LDH group is significantly lower than that in the IS group and NLV group (P < 0.05). CONCLUSIONS: The results showed that the degree of intervertebral disc degeneration in patients with isthmic spondylolisthesis was lighter than that in patients with LDH, and even similar to that in healthy individuals. The occurrence of IS may have slowed down the degeneration of nonaffected segment intervertebral discs through certain factors.

STAM-binding Protein-like 1 Promotes Growth and Migration of Colorectal Cancer by NF-κB Pathway.

BACKGROUND: STAM-binding protein-like 1 (STAMBPL1) functions as a deubiquitinase to cleave Lys63 ubiquitin linkage, and is associated with cancer dissemination and progression. The role of STAMBPL1 in colorectal cancer (CRC) remains unclear. METHODS: STAMBPL1 expression was determined by western blot and qRT-PCR. Cell proliferation was detected by colony formation and MTT assays, and apoptosis was assessed by flow cytometry. The metastasis was evaluated by transwell and wound healing assays. An animal xenograft experiment was used to investigate the effect of STAMBPL1 on tumor growth. RESULTS: The expression of STAMBPL1 was elevated in CRC cells. Knockdown of STAMBPL1 reduced cell viability of CRC and suppressed the proliferation, invasion, and migration. Apoptosis of CRC was induced by silence of STAMBPL1. Tumor growth of CRC was also suppressed by the silence of STAMBPL1. Knockdown of STAMBPL1 increased IκB and decreased phosphorylation of IκB to reduce p65 phosphorylation. CONCLUSION: Knockdown of STAMBPL1 inhibited cell growth and metastasis of CRC through inactivation of the NF-κB pathway.

Osthole inhibits malignant phenotypes and induces ferroptosis in KRAS-mutant colorectal cancer cells via suppressing AMPK/Akt signaling.

PURPOSE: Ferroptosis is a form of cell death driven by iron-dependent lipid peroxidation. Intriguingly, KRAS-mutant cancers are particularly vulnerable to ferroptosis. Osthole is a natural coumarin extracted from Cnidium spp. and other Apiaceous plants. In the present study, we explored the antitumor potential of osthole in KRAS-mutant colorectal cancer (CRC) cells. METHODS: Cell viability assay, EdU incorporation assay, flow cytometry, tumor xenograft model, western blot, immunochemistry staining, immunofluorescence, transcriptome RNA sequencing and quantitative reverse transcription-PCR were performed to evaluate the influence of osthole treatment on KRAS-mutant CRC cells. RESULTS: We found that osthole treatment suppressed proliferation and tumor growth of KRAS-mutant CRC cell lines HCT116 and SW480. Moreover, osthole treatment increased ROS production and induced ferroptosis. Osthole treatment also promoted autophagy, but inhibition of autophagy by ATG7 knockdown or 3-MA showed no influence on osthole-induced ferroptosis. In comparison, osthole increased lysosomal activation, and co-treatment with lysosome inhibitor Baf-A1 attenuated osthole-induced ferroptosis. Besides, osthole treatment reduced the phosphorylation of AMPK, Akt and mTOR in HCT116 and SW480 cells, while restored AMPK signaling by AMPK agonist AICAR partially abrogated ferroptosis induced by osthole treatment. Finally, co-treatment with osthole increased the cytotoxicity of cetuximab in KRAS-mutant CRC cells in vitro and in vivo. CONCLUSION: Our results suggested that the natural product osthole exerted its anticancer effects in KRAS-mutant CRC cells via inducing ferroptosis, and this was partially through inhibiting AMPK/Akt/mTOR signaling. Our results may expand our current knowledge for the use of osthole as an anticancer agent.

Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data.

BACKGROUND: Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging Schema.org could benefit biomedical research resource providers, but it can be challenging to apply Schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize Schema.org or other biomedical schema projects. RESULTS: Our browser-based tool includes features which can help address many of the barriers towards Schema.org-compliance such as: The ability to easily browse for relevant Schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schema-a large multi-class schema for harmonizing various COVID-19 related resources. CONCLUSIONS: We have created a browser-based tool to empower biomedical research resource providers to leverage Schema.org classes to make their research outputs more FAIR.

MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes.

Gene definitions and identifiers can be painful to manage-more so when trying to include gene function annotations as this can be highly context-dependent. Creating groups of genes or gene sets can help provide such context, but it compounds the issue as each gene within the gene set can map to multiple identifiers and have annotations derived from multiple sources. We developed MyGeneset.info to provide an API for integrated annotations for gene sets suitable for use in analytical pipelines or web servers. Leveraging our previous work with MyGene.info (a server that provides gene-centric annotations and identifiers), MyGeneset.info addresses the challenge of managing gene sets from multiple resources. With our API, users readily have read-only access to gene sets imported from commonly-used resources such as Wikipathways, CTD, Reactome, SMPDB, MSigDB, GO, and DO. In addition to supporting the access and reuse of approximately 180k gene sets from humans, common model organisms (mice, yeast, etc.), and less-common ones (e.g. black cottonwood tree), MyGeneset.info supports user-created gene sets, providing an important means for making gene sets more FAIR. User-created gene sets can serve as a way to store and manage collections for analysis or easy dissemination through a consistent API.

Development of Indirect Competitive ELISA and Colloidal Gold Immunochromatographic Strip for Endosulfan Detection Based on a Monoclonal Antibody.

Endosulfan, as an effective broad-spectrum insecticide, has been banned in agricultural areas because of the potential harmful effects on human health. This study aimed to develop an indirect competitive enzyme-linked immunosorbent assay (ic-ELISA) and colloidal gold immunochromatographic (ICA) strip based on a prepared monoclonal antibody (mAb) for quantitative and qualitative detection of endosulfan. A new mAb with high sensitivity and affinity was designed and screened. The ic-ELISA showed a 50% inhibition concentration (IC50) value of 5.16 ng/mL for endosulfan. Under optimum conditions, the limit of detection (LOD) was determined to be 1.14 ng/mL. The average recoveries of endosulfan in spiked pear and apple samples ranged from 91.48-113.45% and 92.39-106.12% with an average coefficient of variation (CV) of less than 7%, respectively. The analysis of colloidal gold ICA strip could be completed within 15 min by naked eye and the visual limit of detection (vLOD) was both 40 ng/mL in pear and apple samples. In conclusion, both developed immunological methods were suitable and reliable for the on-site detection of endosulfan in real samples at trace levels.

Neogenin suppresses tumor progression and metastasis via inhibiting Merlin/YAP signaling.

From in situ growth to invasive dissemination is the most lethal attribute of various tumor types. This transition is majorly mediated by the dynamic interplay between two cancer hallmarks, EMT and cell cycle. In this study, we applied nonlinear association analysis in 33 cancer types and found that most signaling receptors simultaneously associating with EMT and cell cycle are potential tumor suppressors. Here we find that a top co-associated receptor, Neogenin (NEO1), inhibits colorectal cancer (CRC) and Glioma in situ growth and metastasis by forming a complex with Merlin (NF2), and subsequent simultaneous promoting the phosphorylation of YAP. Furthermore, Neogenin protein level is associated with good prognosis and correlates with Merlin status in CRC and Glioma. Collectively, our results define Neogenin as a tumor suppressor in CRC and Glioma that acts by restricting oncogenic signaling by the Merlin-YAP pathway, and suggest Neogenin as a candidate therapeutic agent for CRC and Glioma.

Developing a standardized but extendable framework to increase the findability of infectious disease datasets.

Biomedical datasets are increasing in size, stored in many repositories, and face challenges in FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices to promote transparency, encourage reproducibility, and accelerate research advances through data reuse. To improve FAIRness of our datasets and computational tools, we evaluated metadata standards across established biomedical data repositories. The vast majority do not adhere to a single standard, such as Schema.org, which is widely-adopted by generalist repositories. Consequently, datasets in these repositories are not findable in aggregation projects like Google Dataset Search. We alleviated this gap by creating a reusable metadata schema based on Schema.org and catalogued nearly 400 datasets and computational tools we collected. The approach is easily reusable to create schemas interoperable with community standards, but customized to a particular context. Our approach enabled data discovery, increased the reusability of datasets from a large research consortium, and accelerated research. Lastly, we discuss ongoing challenges with FAIRness beyond discoverability.

Transcriptome Analysis and Functional Characterization Reveal That Peclg Gene Contributes to the Virulence of Penicillium expansum on Apple Fruits.

Penicillium expansum is the causal agent of blue mold decay on apple fruits and is also known to be the major producer of patulin, a mycotoxin that represents serious hazard to human health. Several mechanisms have been suggested to explain the pathogenesis of P. expansum in host plants. Secreted effector proteins are vital for the pathogenicity of many fungal pathogens through manipulating their hosts for efficient colonization. In this study, we performed a RNA-Seq analysis followed by computational prediction of effector proteins from P. expansum during infection of the host apple fruits, and a total of 212 and 268 candidate effector protein genes were identified at 6 and 9 h after inoculation (hai), respectively. One of the candidate effector protein genes was identified as a concanavalin A-like lectin/glucanase (Peclg), which was dramatically induced during the pathogen-host interaction. Targeted knockout of Peclg resulted in significant reduction in conidial production and germination relative to the wild type. Further studies showed that in addition to salt stress, the mutant was much more sensitive to SDS and Congo red, suggesting a defect in cell wall integrity. Pathogenicity assays revealed that the ΔPeclg mutant showed significant decrease in virulence and infectious growth on apple fruits. All these results suggest that Peclg is required for fungal growth, stress response, and the virulence of P. expansum.

Outbreak.info Research Library: a standardized, searchable platform to discover and explore COVID-19 resources.

Outbreak.info Research Library is a standardized, searchable interface of coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) publications, clinical trials, datasets, protocols and other resources, built with a reusable framework. We developed a rigorous schema to enforce consistency across different sources and resource types and linked related resources. Researchers can quickly search the latest research across data repositories, regardless of resource type or repository location, via a search interface, public application programming interface (API) and R package.

Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.

In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales.

Effect of infrared irradiation combined with mannitol and kinesiology tape on postoperative swelling and pain in patients with a periarticular ankle fracture.

Objectives: To explore the effect of infrared irradiation combined with mannitol and Kinesiology tape on postoperative swelling and pain in patients with a periarticular ankle fracture. Methods: The research subjects of this study were 88 patients with periarticular ankle fracture treated by surgery in the Department of Orthopedics of Baoding No.1 Central Hospital from October, 2019 to May, 2021. They were randomly divided into the observation group and the control group based on the random number table method, with 44 cases in each group. All patients were treated after the operation. Patients in the control group were treated with conventional drugs; while those in the observation group were provided with infrared irradiation combined with mannitol and Kinesiology tape. Further comparison was conducted on the degree of swelling, pain and satisfaction after treatment at three, five and seven days after operation. Results: At three, five and seven days after operation, the cross-section diameter of the injured limb was significantly smaller in the observation group than that in the control group, and the difference was statistically significant (p<0. 05). The degree of pain in both groups was significantly lower at three, five and seven days after operation than that before treatment; moreover, the degree of pain in the observation group was significantly lower than that in the control group, and the difference was statistically significant (p<0. 05). Besides, the comparison of posttreatment satisfaction in both groups after treatment revealed that the total satisfaction of patients in the observation group (97.73%) was higher than that in the control group (79.55%), with a statistically significant difference (p<0.05). Conclusion: Infrared irradiation combined with mannitol and Kinesiology tape can effectively alleviate postoperative swelling and pain of patients with a periarticular ankle fracture.

Health-promoting properties of barley: A review of nutrient and nutraceutical composition, functionality, bioprocessing, and health benefits.

Barley is one of the world's oldest cereal crops forming an important component of many traditional diets. Barley is rich in a variety of bioactive phytochemicals with potentially health-promoting effects. However, its beneficial nutritional attributes are not being fully realized because of the limited number of foods it is currently utilized in. It is therefore crucial for the food industry to produce novel barley-based foods that are healthy and cater to customers' tastes. This article reviews the nutritional and functional characteristics of barley, with an emphasis on its ability to improve glucose/lipid metabolism. Then, recent trends in barley product development are discussed. Finally, current limitations and future research directions in glucolipid modulation mechanisms and barley bioprocessing are discussed.

Enhanced ultrasound-guided versus non-enhanced ultrasound-guided percutaneous needle biopsy in tissue cellularity of lung malignancies: a propensity score matched study.

Background: Though ultrasound-guided percutaneous lung needle biopsy (US-PLNB) is a first-line small biopsy method for peripheral lung lesions, quality of cellularity in specimens obtained via US-PLNB is uncertain. This study investigated the accuracy, sensitivity, and cellularity of US-PLNB. It examined the ability of contrast-enhanced ultrasound (CEUS) to improve the effectiveness of US-PLNB. Methods: We retrospectively analyzed all data of patients with subpleural lung lesions who underwent US-PLNB. The cellularity of US-PLNB from malignant lesions included the tumor cell number and proportion. The definition of high-quality cellularity (HQC) was concurrently achieving a tumor cell number ≥400 and a proportion ≥20%. The sensitivity, the actual numbers of tumor cell number/proportion, and the rate of HQC were calculated and compared between the CEUS and non-enhanced US groups after propensity score matching (PSM) with subgroup analyses by lesion size (small lesion ≤30 mm and large lesion >30 mm). Results: A total of 345 patients undergoing 345 US-PLNBs were evaluated, with 3.7±1.1 of punctures on average. There were 201 malignant and 144 benign lesions with a mean size of 43.8±24.1 mm. Among the 201 malignant lesions, 124 cases underwent CEUS and 77 underwent non-enhanced US. The quantity of tumor cells, the proportion of tumor cells, and the rate of HQC in 201 cases of US-PLNB from malignant lesions were 2,862.1±2,288.0, 44.6%±24.5%, and 82.1% [95% confidence interval (CI): 76.6% to 87.1%], respectively. The quantity of tumor cells, the proportion of tumor cells, and rate of HQC were significantly higher in the CEUS group than that in the non-enhanced US group, both in the analysis of overall malignant lesions and in large malignant lesions (all P<0.05). Conclusions: The US-PLNB has high sensitivity and thereby obtains HQC samples for subpleural lung malignant lesions. The CEUS helps improve the rate of HQC and tissue cellularity of lung malignancies.

Diagnostic ability and its influenced factors of ultrasound-guided percutaneous pleural needle biopsy diagnosis for malignant pleural mesothelioma.

Background: Malignant pleural mesothelioma (MPM) is a highly invasive malignant tumor. Ultrasound guidance has the advantages of real-time, convenience and nonradiative. We sought to identify diagnostic value and its influenced factors of ultrasound-guided percutaneous pleural needle biopsy (US-PPNB) for MPM. Methods: Patients who underwent US-PPNB between March 2014 and March 2020 and were finally diagnosed with MPM were retrospectively analyzed. We retrospectively analyzed the US-PPNBs pathological results of all patients clinically confirmed as MPM, and divided US-PPNBs into correctly and incorrectly diagnosed groups. Patient, thoracic, and biopsy variables that affected diagnostic accuracy were assessed. All variables significant on univariate analyses were subjected to multivariate logistic regression to identify significant predictors of diagnostic accuracy. We derived cutoffs for all significant continuous variables and used the Mantel-Haenszel test to determine whether the diagnostic accuracy of US-PPNB for MPM increased with pleural thickness. Results: In total, 49 patients with clinically confirmed MPM underwent US-PPNB; 37 diagnoses were correct and 12 were incorrect (accuracy = 75.5%). The pleura was significantly thicker in the correctly diagnosed group (p < 0.001). The pleural thickness cutoff was 4.15 mm and diagnostic accuracy increased with pleural thickness grade (p for trend <0.05). The diagnostic accuracy was significantly higher when 16-G rather than 18-G biopsy needles were used (p < 0.05). Multivariate logistic regression showed that pleural thickness (odds ratio: 17.2, 95% confidence interval: 2.8-104.1, p = 0.002) and needle size (odds ratio: 6.8, 95% confidence interval: 1.0-44.5, p = 0.044) independently predicted diagnostic accuracy. Conclusion: US-PPNB afforded high MPM diagnostic accuracy, and pleural thickness and needle size significantly impacted accuracy.

Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data.

Background: Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging schema.org could benefit biomedical research resource providers, but it can be challenging to apply schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize schema.org or other biomedical schema projects. Results: Our browser-based tool includes features which can help address many of the barriers towards schema.org -compliance such as: The ability to easily browse for relevant schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schemaâ€"a large multi-class schema for harmonizing various COVID-19 related resources. Conclusions: We have created a browser-based tool to empower biomedical research resource providers to leverage schema.org classes to make their research outputs more FAIR.

Development of a colloidal gold immunochromatographic strip for the rapid detection of pefloxacin in grass carp with a novel pretreatment method.

A rapid colloidal gold immunochromatography assay (GICA) for the detection of pefloxacin (PEF) was established and optimized. The anti-PEF monoclonal antibody (mAb) was used to target PEF as a colloidal gold-mAb conjugate. The mAb belonged to the IgG2b subtype, lambda light chain, the affinity constant (Ka) was 5.21 × 109 L·mol-1, and its half maximal inhibitory concentration (IC50) was 0.23 ng·mL-1. No obvious cross-reactivity (CR) was observed with other common fluoroquinolone antibiotics, including ciprofloxacin (CIP), norfloxacin (NOR), lomefloxacin (LOM) and ofloxacin (OFL). The visual limit of detection (vLOD) of the optimized GICA was 2 ng·g-1 under the conventional pretreatment method, and the assay was completed in 15 min. Liquid chromatography tandem-mass spectrometry (LC-MS/MS) was employed to confirm the performance of the strip. In addition, a novel pretreatment was established and compared with conventional pretreatment. Without the removal of organic solvents, the novel pretreatment method reduced the sample pretreatment time (more than 10 min). The vLOD of the optimized GICA was also 2 ng·g-1 when applying the novel pretreatment method. In conclusion, the proposed PEF-GICA could detect samples containing PEF rapidly and accurately, and the novel pretreatment method saved the time of sample pretreatment and improved the efficiency of detection.

Outbreak.info Research Library: A standardized, searchable platform to discover and explore COVID-19 resources.

To combat the ongoing COVID-19 pandemic, scientists have been conducting research at breakneck speeds, producing over 52,000 peer-reviewed articles within the first year. To address the challenge in tracking the vast amount of new research located in separate repositories, we developed outbreak.info Research Library, a standardized, searchable interface of COVID-19 and SARS-CoV-2 resources. Unifying metadata from sixteen repositories, we assembled a collection of over 350,000 publications, clinical trials, datasets, protocols, and other resources as of October 2022. We used a rigorous schema to enforce consistency across different sources and resource types and linked related resources. Researchers can quickly search the latest research across data repositories, regardless of resource type or repository location, via a search interface, public API, and R package. Finally, we discuss the challenges inherent in combining metadata from scattered and heterogeneous resources and provide recommendations to streamline this process to aid scientific research.