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| 2. |
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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Jin, Ying-Hui, et al.
(författare)
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Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
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Ingår i: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 5. |
- Zhao, Li-Juan, et al.
(författare)
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Lysine demethylase LSD1 delivered via small extracellular vesicles promotes gastric cancer cell stemness
- 2021
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Ingår i: EMBO Reports. - : EMBO. - 1469-221X .- 1469-3178. ; 22:8
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Tidskriftsartikel (refereegranskat)abstract
- Several studies have examined the functions of nucleic acids in small extracellular vesicles (sEVs). However, much less is known about the protein cargos of sEVs and their functions in recipient cells. This study demonstrates the presence of lysine-specific demethylase 1 (LSD1), which is the first identified histone demethylase, in the culture medium of gastric cancer cells. We show that sEVs derived from gastric cancer cells and the plasma of patients with gastric cancer harbor LSD1. The shuttling of LSD1-containing sEVs from donor cells to recipient gastric cancer cells promotes cancer cell stemness by positively regulating the expression of Nanog, OCT4, SOX2, and CD44. Additionally, sEV-delivered LSD1 suppresses oxaliplatin response of recipient cells in vitro and in vivo, whereas LSD1-depleted sEVs do not. Taken together, we demonstrate that LSD1-loaded sEVs can promote stemness and chemoresistance to oxaliplatin. These findings suggest that the LSD1 content of sEV could serve as a biomarker to predict oxaliplatin response in gastric cancer patients.
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| 6. |
- Yu, Wenjin, et al.
(författare)
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Deep Learning-Based Classification of Cancer Cell in Leptomeningeal Metastasis on Cytomorphologic Features of Cerebrospinal Fluid
- 2022
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Ingår i: Frontiers in Oncology. - : Frontiers Media SA. - 2234-943X. ; 12, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Background: It is a critical challenge to diagnose leptomeningeal metastasis (LM), given its technical difficulty and the lack of typical symptoms. The existing gold standard of diagnosing LM is to use positive cerebrospinal fluid (CSF) cytology, which consumes significantly more time to classify cells under a microscope.Objective: This study aims to establish a deep learning model to classify cancer cells in CSF, thus facilitating doctors to achieve an accurate and fast diagnosis of LM in an early stage.Method: The cerebrospinal fluid laboratory of Xijing Hospital provides 53,255 cells from 90 LM patients in the research. We used two deep convolutional neural networks (CNN) models to classify cells in the CSF. A five-way cell classification model (CNN1) consists of lymphocytes, monocytes, neutrophils, erythrocytes, and cancer cells. A four-way cancer cell classification model (CNN2) consists of lung cancer cells, gastric cancer cells, breast cancer cells, and pancreatic cancer cells. Here, the CNN models were constructed by Resnet-inception-V2. We evaluated the performance of the proposed models on two external datasets and compared them with the results from 42 doctors of various levels of experience in the human-machine tests. Furthermore, we develop a computer-aided diagnosis (CAD) software to generate cytology diagnosis reports in the research rapidly.Results: With respect to the validation set, the mean average precision (mAP) of CNN1 is over 95% and that of CNN2 is close to 80%. Hence, the proposed deep learning model effectively classifies cells in CSF to facilitate the screening of cancer cells. In the human-machine tests, the accuracy of CNN1 is similar to the results from experts, with higher accuracy than doctors in other levels. Moreover, the overall accuracy of CNN2 is 10% higher than that of experts, with a time consumption of only one-third of that consumed by an expert. Using the CAD software saves 90% working time of cytologists.Conclusion: A deep learning method has been developed to assist the LM diagnosis with high accuracy and low time consumption effectively. Thanks to labeled data and step-by-step training, our proposed method can successfully classify cancer cells in the CSF to assist LM diagnosis early. In addition, this unique research can predict cancer’s primary source of LM, which relies on cytomorphologic features without immunohistochemistry. Our results show that deep learning can be widely used in medical images to classify cerebrospinal fluid cells. For complex cancer classification tasks, the accuracy of the proposed method is significantly higher than that of specialist doctors, and its performance is better than that of junior doctors and interns. The application of CNNs and CAD software may ultimately aid in expediting the diagnosis and overcoming the shortage of experienced cytologists, thereby facilitating earlier treatment and improving the prognosis of LM.
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| 7. |
- Cao, Lin-Ying, et al.
(författare)
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Structure-dependent activity of polybrominated diphenyl ethers and their hydroxylated metabolites on estrogen related receptor gamma : in vitro and in silico study
- 2018
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 52:15, s. 8894-8902
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Tidskriftsartikel (refereegranskat)abstract
- Estrogen-related receptor gamma (ERR gamma) is an orphan nuclear receptor having functional cross-talk with classical estrogen receptors. Here, we investigated whether ERR gamma is a potential target 8 of polybrominated diphenyl ethers (PBDEs) and their hydroxylated metabolites (OH-PBDEs). By using a fluorescence competitive binding method established in our laboratory, the binding potencies of 30 PBDEs/OH-PBDEs with ERR gamma were determined for the first time. All of the tested OH-PBDEs and some PBDEs bound to ERR gamma with K-d values ranging from 0.13-13.61 mu M. The OH-PBDEs showed much higher binding potency than their parent PBDEs. A quantitative structure-activity relationship (QSAR) model was developed to analyze the chemical binding potencies in relation to their structural and chemical characteristics. The QSAR model indicated that the molecular size, relative ratios of aromatic atoms, and hydrogen bond donors and acceptors were crucial factors for PBDEs/OH-PBDEs binding. By using a reporter gene assay, we found that most of the low-brominated PBDEs/OH-PBDEs exerted agonistic activity toward ERR gamma, while high-brominated PBDEs/OH-PBDEs had no effect on the basal ERR gamma activity. The docking results showed that the low-brominated PBDEs/OH-PBDEs tended to take an agonistic binding mode while the high-brominated ones tended to take an antagonistic binding mode. Overall, our results suggest ERR gamma to be a potential novel target for PBDEs/OH-PBDEs.
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| 8. |
- Chen, Liangliang, et al.
(författare)
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User-Friendly Genetic Conditional Knockout Strategies by CRISPR/Cas9
- 2018
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Ingår i: STEM CELLS INTERNATIONAL. - : HINDAWI LTD. - 1687-966X .- 1687-9678.
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Tidskriftsartikel (refereegranskat)abstract
- Loss-of-function studies are critically important in gene functional analysis of model organisms and cells. However, conditional gene inactivation in diploid cells is difficult to achieve, as it involves laborious vector construction, multifold electroporation, and complicated genotyping. Here, a strategy is presented for generating biallelic conditional gene and DNA regulatory region knockouts in mouse embryonic stem cells by codelivery of CRISPR-Cas9 and short-homology-arm targeting vectors sequentially or simultaneously. Collectively, a simple and rapid method was presented to knock out any DNA element conditionally. This approach will facilitate the functional studies of essential genes and regulatory regions during development.
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| 9. |
- Egelhofer, Thea A, et al.
(författare)
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An assessment of histone-modification antibody quality
- 2011
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Ingår i: Nature Structural & Molecular Biology. - : Springer Science and Business Media LLC. - 1545-9993 .- 1545-9985. ; 18:1, s. 91-93
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Tidskriftsartikel (refereegranskat)abstract
- We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/).
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| 10. |
- Fang, Li Tai, et al.
(författare)
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1151-1160
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Tidskriftsartikel (refereegranskat)abstract
- Tumor-normal paired DNA samples from a breast cancer cell line and a matched lymphoblastoid cell line enable calibration of clinical sequencing pipelines and benchmarking 'tumor-only' or 'matched tumor-normal' analyses. The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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| 11. |
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| 12. |
- Huang, C. Y., et al.
(författare)
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The Cardamine enshiensis genome reveals whole genome duplication and insight into selenium hyperaccumulation and tolerance
- 2021
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Ingår i: Cell Discovery. - : Springer Science and Business Media LLC. - 2056-5968. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- Cardamine enshiensis is a well-known selenium (Se)-hyperaccumulating plant. Se is an essential trace element associated with many health benefits. Despite its critical importance, genomic information of this species is limited. Here, we report a chromosome-level genome assembly of C. enshiensis, which consists of 443.4 Mb in 16 chromosomes with a scaffold N50 of 24 Mb. To elucidate the mechanism of Se tolerance and hyperaccumulation in C. enshiensis, we generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes. The results reveal that flavonoid, glutathione, and lignin biosynthetic pathways may play important roles in protecting C. enshiensis from stress induced by Se. Hi-C analysis of chromatin interaction patterns showed that the chromatin of C. enshiensis is partitioned into A and B compartments, and strong interactions between the two telomeres of each chromosome were correlated with histone modifications, epigenetic markers, DNA methylation, and RNA abundance. Se supplementation could affect the 3D chromatin architecture of C. enshiensis at the compartment level. Genes with compartment changes after Se treatment were involved in selenocompound metabolism, and genes in regions with topologically associated domain insulation participated in cellular responses to Se, Se binding, and flavonoid biosynthesis. This multiomics research provides molecular insight into the mechanism underlying Se tolerance and hyperaccumulation in C. enshiensis.
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| 13. |
- Jaramillo-Jimenez, A, et al.
(författare)
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Prodromal Dementia With Lewy Bodies and Recurrent Panic Attacks as the First Symptom: A Case Report
- 2022
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Ingår i: Frontiers in neurology. - : Frontiers Media SA. - 1664-2295. ; 13, s. 839539-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Psychiatric-onset dementia with Lewy bodies (DLB) might include symptoms of depression, hallucinations, anxiety, and apathy. Here, we report a patient with DLB with recurrent panic attacks as her first symptom 5 years before a biological-based diagnosis of probable DLB. We provide an extended description of the clinical presentation and course from psychiatric-onset DLB to dementia in an 83-year-old woman. This case illustrates the common misdiagnosis of DLB and the delay of having a detailed clinical and biomarker assessment for structured diagnosis. With a detailed description of the clinical presentation of this case, the empirical treatment strategies, and the patient perspectives, we aim to make clinicians aware of panic attacks within the psychiatric-onset DLB.
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| 14. |
- Kim, Jimi, et al.
(författare)
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Formate rescues neural tube defects caused by mutations in Slc25a32
- 2018
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 115:18, s. 4690-4695
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Tidskriftsartikel (refereegranskat)abstract
- Periconceptional folic acid (FA) supplementation significantly reduces the prevalence of neural tube defects (NTDs). Unfortunately, some NTDs are FA resistant, and as such, NTDs remain a global public health concern. Previous studies have identified SLC25A32 as a mitochondrial folate transporter (MFT), which is capable of transferring tetrahydrofolate (THF) from cellular cytoplasm to the mitochondria in vitro. Herein, we show that gene trap inactivation of Slc25a32 (Mft) in mice induces NTDs that are folate (5-methyltetrahydrofolate, 5-mTHF) resistant yet are preventable by formate supplementation. Slc25a32gt/gt embryos die in utero with 100% penetrant cranial NTDs. 5-mTHF supplementation failed to promote normal neural tube closure (NTC) in mutant embryos, while formate supplementation enabled the majority (78%) of knockout embryos to complete NTC. A parallel genetic study in human subjects with NTDs identified biallelic loss of function SLC25A32 variants in a cranial NTD case. These data demonstrate that the loss of functional Slc25a32 results in cranial NTDs in mice and has also been observed in a human NTD patient.
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| 15. |
- Lai, Lizu, et al.
(författare)
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The efficacy of acceptance and commitment therapy for chronic pain : A three-level meta-analysis and a trial sequential analysis of randomized controlled trials
- 2023
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Ingår i: Behaviour Research and Therapy. - : Elsevier. - 0005-7967 .- 1873-622X. ; 165
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Tidskriftsartikel (refereegranskat)abstract
- The current study included randomized controlled trials (RCTs) to assess the benefits of Acceptance and commitment therapy (ACT) for chronic pain. Searches were conducted in Web of Science, PsycINFO, PubMed, Scopus, Cochrane Library, and Embase from inception until September 30, 2022. Thirty-three RCTs, including 2293 participants, were included. Small to medium effect sizes for pain intensity/physical function favoring ACT were found both at post-treatment (pain intensity: g = 0.44; physical function: g = 0.59) and follow-up (pain intensity: g = 0.34; physical function: g = 0.56). The effect sizes on psychological outcomes were significant at post-treatment (depression: g = 0.43; anxiety: g = 0.43; quality of life: g = 0.45) and follow-up (depression: g = 0.43; anxiety: g = 0.35; quality of life: g = 0.43). The results of the trial sequential analyses indicated that pooled estimates were unlikely to be incidental findings, as effects of multiple testing were controlled and power was adequate. Face-to-face ACT yielded significantly larger effects on physical outcomes than internet-delivered ACT. Participants with chronic headache and fibromyalgia showed greater benefit from ACT compared to those with non-specific pain or mixed pain. In addition, the longer the follow-up duration, the smaller the effect sizes for pain intensity/physical function at follow-up. The present meta-analysis suggests sufficient evidence for the significant benefits of ACT for people with chronic pain.
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| 16. |
- Li, Yuchen, et al.
(författare)
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Fabricating an anti-corrosion carbonate coating on Mg-Li alloy by low-temperature plasma
- 2022
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Ingår i: Surface & Coatings Technology. - : Elsevier BV. - 0257-8972 .- 1879-3347. ; 439
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Tidskriftsartikel (refereegranskat)abstract
- Despite the huge demand for ultra-light magnesium-lithium (Mg-Li) alloys, practical applications of Mg-Li alloys are still severely restricted due to their poor corrosion resistance. Here, we report a new method utilizing low-temperature plasma to grow an oxide layer on the Mg-Li alloys in atmospheric condition, which reacts with CO2 and water in the air and consequently transform into a protective coating. The prepared coating has a layered structure consisting of a Mg(OH)(2) inner layer and a Li2CO3 outer layer. The composition distribution can be attributed to the different migration rates between Li+ and Mg2+ during coating formation. The Li2CO3 outer layer is sufficiently compact and very stable, with an ultra-low solubility in water, explaining the superior corrosion resistance of the coating in 3.5% NaCl solution. This simple and eco-friendly surface treatment provides a novel way of fabricating protective coatings on Mg-Li alloys.
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| 17. |
- Li, Ying, et al.
(författare)
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Reduction Kinetics of Cold-Bonded Briquette Prepared from Return Fines of Sinter with Carbon Monoxide and Coke
- 2023
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Ingår i: Steel Research International. - : Wiley. - 1611-3683 .- 1869-344X. ; 94:8
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Tidskriftsartikel (refereegranskat)abstract
- The reduction kinetics of cold-bonded briquette prepared from return fines of sinter is studied. The results reveal that cold-bonded briquettes with coke (CBBC) have a higher reduction velocity index (RVI) value than cold-bonded briquettes without coke (CBB). Interfacial chemical reaction controls the early stages of the CBB reduction process at 900 and 950 °C, followed by both interfacial chemical reaction and internal diffusion. At 1000, 1050, and 1100 °C, the early and final stages of the CBB reduction process are controlled by interfacial chemical reaction and internal diffusion, respectively, while both interfacial chemical reaction and internal diffusion control middle stage. The apparent activation energies of the different stages are 46.20, 56.74, 38.24, and 40.74 kJ mol−1, respectively. The gasification of carbon reaction controls the reduction process of CBBC, and the apparent activation energy is 32.42 kJ mol−1. According to the Friedman method, the apparent activation energy of CBB and CBBC is reasonable. Coke promotes the phase transformation in CBBC. Scanning electron microscopy results show that the CBBC sample is more fully reduced than the CBB sample and that it has smoother corners and edges of the iron-bearing phase or the metallic iron phase than the CBB sample.
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| 18. |
- Ma, Lin Lu, et al.
(författare)
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Coronavirus Disease 2019 Related Clinical Studies : A Cross-Sectional Analysis
- 2020
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Ingår i: Frontiers in Pharmacology. - : Frontiers Media SA. - 1663-9812. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Objective: The quality and rationality of many recently registered clinical studies related to coronavirus disease 2019 (COVID-19) needs to be assessed. Hence, this study aims to evaluate the current status of COVID-19 related registered clinical trial. Methods: We did an electronic search of COVID-19 related clinical studies registered between December 1, 2019 and February 21, 2020 (updated to May 28, 2020) from the ClinicalTrials.gov, and collected registration information, study details, recruitment status, characteristics of the subjects, and relevant information about the trial implementation process. Results: A total of 1,706 studies were included 10.0% of which (n=171) were from France, 943 (55.3%) used an interventional design, and 600 (35.2%) used an observational design. Most of studies (73.6%) aimed to recruit fewer than 500 people. Interferon was the main prevention program, and antiviral drugs were the main treatment program. Hydroxychloroquine and chloroquine (230/943, 24.4%) were widely studied. Some registered clinical trials are incomplete in content, and 37.4% of the 1,706 studies may have had insufficient sample size. Conclusion: The quality of COVID-19 related studies needs to be improved by strengthening the registration process and improving the quality of clinical study protocols so that these clinical studies can provide high-quality clinical evidence related to COVID-19.
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| 19. |
- Ren, Long Jun, et al.
(författare)
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Effect of conventional physiotherapy on pain and muscle stiffness in patients with low back pain assessed by a wireless hand-held tissue ultrasound palpation system (TUPS)
- 2019
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Ingår i: International Journal of Physical Medicine Rehabilitation. - : Omics Publishing Group. - 2329-9096. ; 7:2, s. 1-5
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Tidskriftsartikel (refereegranskat)abstract
- Background: Low back pain (LPB) is a common health problem. While physiotherapy can relieve pain and the muscle stiffness of patients with LBP was shown to be different from healthy people, few studies have investigated the effect of physiotherapy on back muscle stiffness in patients with LBP.Objective: To investigate the effect of a 5-day conventional physiotherapy treatment on muscle stiffness of patients with LBP using a newly developed wireless hand-held ultrasound probe.Methods: A total of ten patients with LBP participated in this study. They received customized conventional physiotherapy containing electrical therapy, traditional Chinese medicine, manipulation and wax therapy. The pain level was evaluated by the visual analogue scale, and the muscle stiffness was measured by a wireless hand-held tissue ultrasound palpation system. The muscle stiffness of left and right sides at L1 and L4 levels and pain level were evaluated in two conditions, including baseline and 5-day post treatments.Results and discussion: After receiving the treatment, the muscle stiffness of all tested low back regions increased significantly (p=0.040). The muscle stiffness at L4 level was significantly higher than that of L1 level (p=0.021). No significant difference of muscle stiffness between left and right sides was found. The correlation between the muscle stiffness and VAS score appeared to decrease after receiving the treatment (R2 changed from 0.3598 to 0.0533).Conclusion: A five-day conventional physiotherapy treatment could relieve the pain level and increase the muscle stiffness of patients with LBP as evaluated by a wireless hand-held ultrasound probe. The stiffness of back muscle at L4 level was significantly higher than that of L1 level in patients with LBP. The treatment may change the correlation between the muscle stiffness and VAS score at low back region.
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| 20. |
- Ren, Luyao, et al.
(författare)
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Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Genomic DNA reference materials are widely recognized as essential for ensuring data quality in omics research. However, relying solely on reference datasets to evaluate the accuracy of variant calling results is incomplete, as they are limited to benchmark regions. Therefore, it is important to develop DNA reference materials that enable the assessment of variant detection performance across the entire genome.RESULTS: We established a DNA reference material suite from four immortalized cell lines derived from a family of parents and monozygotic twins. Comprehensive reference datasets of 4.2 million small variants and 15,000 structural variants were integrated and certified for evaluating the reliability of germline variant calls inside the benchmark regions. Importantly, the genetic built-in-truth of the Quartet family design enables estimation of the precision of variant calls outside the benchmark regions. Using the Quartet reference materials along with study samples, batch effects are objectively monitored and alleviated by training a machine learning model with the Quartet reference datasets to remove potential artifact calls. Moreover, the matched RNA and protein reference materials and datasets from the Quartet project enables cross-omics validation of variant calls from multiomics data.CONCLUSIONS: The Quartet DNA reference materials and reference datasets provide a unique resource for objectively assessing the quality of germline variant calls throughout the whole-genome regions and improving the reliability of large-scale genomic profiling.
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| 21. |
- Sillivan, Stephanie E., et al.
(författare)
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ELK1 Transcription Factor Linked to Dysregulated Striatal Mu Opioid Receptor Signaling Network and OPRM1 Polymorphism in Human Heroin Abusers
- 2013
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Ingår i: Biological Psychiatry. - : Elsevier BV. - 0006-3223 .- 1873-2402. ; 74:7, s. 511-519
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Tidskriftsartikel (refereegranskat)abstract
- Background: Abuse of heroin and prescription opiate medications has grown to disturbing levels. Opioids mediate their effects through mu opioid receptors (MOR), but minimal information exists regarding MOR-related striatal signaling relevant to the human condition. The striatum is a structure central to reward and habitual behavior and neurobiological changes in this region are thought to underlie the pathophysiology of addiction disorders. Methods: We examined molecular mechanisms related to MOR in postmortem human brain striatal specimens from a homogenous European Caucasian population of heroin abusers and control subjects and in an animal model of heroin self-administration. Expression of ets-like kinase 1 (ELK1) was examined in relation to polymorphism of the MOR gene OPRM1 and drug history. Results: A characteristic feature of heroin abusers was decreased expression of MOR and extracellular regulated kinase signaling networks, concomitant with dysregulation of the downstream transcription factor ELK1. Striatal ELK1 in heroin abusers associated with the polymorphism rs2075572 in OPRM1 in a genotype dose-dependent manner and correlated with documented history of heroin use, an effect reproduced in an animal model that emphasizes a direct relationship between repeated heroin exposure and ELK1 dysregulation. A central role of ELK1 was evidenced by an unbiased whole transcriptome microarray that revealed similar to 20% of downregulated genes in human heroin abusers are ELK1 targets. Using chromatin immune precipitation, we confirmed decreased ELK1 promoter occupancy of the target gene Use1. Conclusions: ELK1 is a potential key transcriptional regulatory factor in striatal disturbances associated with heroin abuse and relevant to genetic mutation of OPRM1.
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| 22. |
- Song, Dan-Na, et al.
(författare)
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Luminescent Thermochromic Silver Iodides as Wavelength-Dependent Thermometers
- 2020
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 59:18, s. 13067-13077
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Tidskriftsartikel (refereegranskat)abstract
- Luminescent thermochromic materials with a dramatic shift of emission band under different temperatures are highly desirable in temperature sensing fields. However, the design of the synthesis of such compounds remains a great challenge. In this work, two new luminescent thermochromic silver iodides, (emIm)Ag3I4 (1) and (emIm)Ag2I3 (2) (emIm = 1-ethyl-3-methyl imidazole), have been synthesized under solvothermal conditions. Compound 1 features a [Ag3I4]− anionic layer, while compound 2 possesses an infinite [Ag2I3]− chain structure, both of which are charge balanced by emIm+ cations. Particularly, they display luminescent thermochromism with a significant wavelength shift of emission maximum with temperature change. They represent rare examples of infinite layered or chain silver iodides that show luminescent thermochromism. Furthermore, the results indicate that compounds 1 and 2 are promising wavelength-dependent luminescent thermometers.
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| 23. |
- Tang, Shengwen, et al.
(författare)
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Modeling on the hydration and leaching of eco-friendly magnesium oxychloride cement paste at the micro-scale
- 2019
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Ingår i: Construction and Building Materials. - : Elsevier BV. - 0950-0618. ; 204, s. 684-690
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Tidskriftsartikel (refereegranskat)abstract
- Magnesium oxychloride cement (MOC) has been considered as a kind of eco-friendly cement in view of its significantly low calcination temperature and large capacity of carbon dioxide sequestration, compared with ordinary Portland cement (OPC). In this work, a computer model is established to simulate the hydration and leaching of MOC paste at the micro-scale. The composition of MOC paste in the ultimate hydration is investigated based on the thermodynamic method, and pore structure obtained from the computer simulation is compared with the one from experiments and literature, respectively. The simulated leaching results show that the original solid phase skeleton of MOC paste decomposes into magnesium hydroxide crystals. It is demonstrated that the simulation results are in good agreement with experimental data from literature and the proposed simulation can provide an effective method to reveal the hydration and leaching mechanism of MOC paste.
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| 24. |
- Wang, Xiaojiang, et al.
(författare)
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Electrochemical and Spectroscopic Study of Homo- and Hetero-Dimetallic Phthalocyanines as Catalysts for the Oxygen Reduction Reaction in Acidic Media
- 2018
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Ingår i: ChemElectroChem. - : WILEY-V C H VERLAG GMBH. - 2196-0216. ; 5:22, s. 3478-3485
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Tidskriftsartikel (refereegranskat)abstract
- Metallophthalocyanines (MPc, M=Fe or Co) have been investigated extensively as a typical type of transition metal macrocyclic catalysts for the oxygen reduction reaction (ORR). However, the understanding about ORR catalyzed by binuclear even heterodimetallic phthalocyanines in acidic condition is still not sufficient. Herein we synthesized two homodimetallicphthalocyanine (FePc-PcFe and CoPc-PcCo) and a heterodimetallic phthalocyanine (FePc-PcCo). The electrocatalytic activity of as-synthesized compounds were characterized by cyclic voltammetry (CV) and rotating disk electrode (RDE). Generally, the binuclear metallophthalocyanines show higher activity than their monomeric analogues including FePc and CoPc. Also, the Fe compounds exhibit better catalytic performance than the Co phthalocyanines. However, interestingly the heterodimetallic phthalocyanine FePc-PcCo shows similar half-wave potential and ORR activity with FePc-PcFe, rather than CoPc-PcCo. This may be explained by XPS and XAS, which reveal a similar square-planar structure existed in FePc-PcCo and FePc-PcFe and a non-planar structure in CoPc-PcCo. Furthermore, the increasing of the ORR activity among those five catalysts is well in agreement with the descending LUMO energies in DFT calculations. A lower LUMO energy indicates a favorable adsorption of O-2, which in turn affects the ORR performance.
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| 25. |
- Wang, Ying, et al.
(författare)
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Preliminary exploration of hsa_circ_0032131 levels in peripheral blood as a potential diagnostic biomarker of osteoarthritis
- 2019
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Ingår i: Genetic Testing and Molecular Biomarkers. - : Mary Ann Liebert. - 1945-0265 .- 1945-0257. ; 23:10, s. 717-721
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Tidskriftsartikel (refereegranskat)abstract
- Background: Osteoarthritis (OA) is a common chronic degenerative joint disease characterized by articular cartilage degeneration and synovitis. CircRNAs are increasingly being recognized as functional endogenous RNAs with a stable structure and high tissue specificity. Recent studies have shown that some circRNAs may be involved in the initiation and progression of OA and that there is differential expression of circRNAs in chondrocytes in vitro isolated from patients with OA.Purposes: In this study, we aimed to determine if circRNA levels in the peripheral blood of Chinese Han patients with OA would be diagnostic based on the previous in vitro studies.Methods: We collected peripheral blood samples from 25 patients suffering from OA and 25 healthy controls and measured hsa_circ_0032131_CBC1 RNA levels through quantitative RT-PCR (qRT-PCR). The statistical basis for evaluating the diagnostic value was to calculate the area under the receiver operator characteristic (ROC) curve.Results: The results of the qRT-PCR for hsa_circ_0032131_CBC1 were consistent with those of the microarray analysis. The ROC curve shows that hsa_circ_0032131 holds diagnostic value for OA (0.8455, p < 0.01).Conclusions: Our research indicates that differentially expressed circRNAs may be involved in the development of OA and could be used diagnostically.
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| 26. |
- Wang, Ying, et al.
(författare)
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Screening for differentially expressed circRNA between Kashin–Beck disease and osteoarthritis patients based on circRNA chips
- 2020
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Ingår i: Clinica Chimica Acta. - : Elsevier. - 0009-8981 .- 1873-3492. ; 501, s. 92-101
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Tidskriftsartikel (refereegranskat)abstract
- Objective: This research aims to explore differentially expressed circRNA between OA and KBD and potential diagnostic biomarkers.Methods: Total RNA was extracted from 5 pairs of KBD and OA knee joint cartilage specimens, and the expression of circRNAs was analyzed by Chip Scanning Analysis. The microarray data was verified by quantitative polymerase chain reaction (qRT-PCR). CircRNA-miRNA network was constructed to predict targeting microRNAs of circRNA genes. Peripheral blood samples from 25 KBD patients and 25 OA patients were collected for verification by qRT-PCR. Diagnostic value was evaluated by the area under the receiver operator characteristic (ROC) curve.Results: A total of 1627 circRNAs were differentially expressed between OA and KBD. Five bone and joint disease-related circRNAs were chosen for qRT-PCR validation. The difference in expression profile of hsa_circRNA_0020014 was confirmed by qRT-PCR, and its circRNA-miRNA regulation network was set up. The ROC curve demonstrated that hsa_circ_0020014_CBC1 in peripheral blood could distinguish patients with KBD and OA.Conclusion: The expression profiles of circRNA were significantly different between OA and KBD. hsa_circRNA_0020014 is a potential biomarker for differential diagnosis between these two diseases.
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| 27. |
- Wang, Ying, et al.
(författare)
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Screening for Differentially Expressed Circular RNAs in the Cartilage of Osteoarthritis Patients for Their Diagnostic Value
- 2019
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Ingår i: Genetic Testing and Molecular Biomarkers. - : Mary Ann Liebert. - 1945-0265 .- 1945-0257. ; 23:10, s. 706-716
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Tidskriftsartikel (refereegranskat)abstract
- Background: Osteoarthritis (OA) is the most prevalent osteoarticular disease, which typically involves chronic cartilage degeneration and synovitis. The latest research shows that circular RNAs (circRNAs) play a role in the development of a variety of diseases, including osteoarthrosis.Purposes: The aim of this study was to explore the expression of circRNAs in OA chondrocytes and predict biomarkers for diagnosis.Materials and Methods: The circRNA expression profile was analyzed through use of the Gene Spring software V13.0; differentially expressed circRNAs were screened by comparing OA chondrocytes and normal articular chondrocytes. We validated the microarray data by quantitative real-time polymerase chain reaction analyses of OA chondrocytes and chondrocytes from normal controls. TargetScan software and miRanda software were used to predict networks of circRNA–miRNA interactions in cartilage. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analyses were applied to predict the functions of differentially expressed circRNAs.Results: Overall, 1380 circRNAs were differentially expressed between OA chondrocytes and normal articular chondrocytes (fold-change ≥2, p ≤ 0.05), including 215 that were upregulated and 1165 that were downregulated circRNAs. After analyzing the differentially expressed circRNA genes, the top 20 enriched GO entries and KEGG pathways were annotated. The hsa_circrna_0032131 was identified for further analysis. A circRNA–miRNA network was constructed to represent the 10 most likely target genes associated with the validated circRNA.Conclusions: Our research suggests that some of the differentially expressed circRNAs in OA chondrocytes compared to normal chondrocytes are etiologically associated with the pathological process of OA. It was found that hsa_circRNA_0032131 likely participates in the initiation and progression of OA and has potential as a diagnostic marker.Clinical Relevance: To analyze the difference of circRNA expression profiles between OA and normal controls and explore biomarkers for diagnosis.
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| 28. |
- Xiao, Wenming, et al.
(författare)
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing
- 2021
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Ingår i: Nature Biotechnology. - : Springer Nature. - 1087-0156 .- 1546-1696. ; 39:9, s. 1141-1150
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Tidskriftsartikel (refereegranskat)abstract
- Recommendations are given on optimal read coverage and selection of calling algorithm to maximize the reproducibility of cancer mutation detection in whole-genome or whole-exome sequencing. Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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| 29. |
- Zhou, Qiu-Jie, et al.
(författare)
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Out of chaos : Phylogenomics of Asian Sonerileae
- 2022
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 175
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Tidskriftsartikel (refereegranskat)abstract
- Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with >70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. singlecopy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as well as species trees reconstructed using different tree estimation methods (concatenation/site-based coalescent method/summary method) or different datasets (SCO/genomic/plastome). We explored sources of discordance using multiple approaches and found that the observed discordance in Asian Sonerileae was mainly caused by a combination of biased distribution of missing data, random noise from uninformative genes, incomplete lineage sorting, and hybridization/introgression. Exploration of these sources can enable us to generate hypotheses for future testing, which is the first step towards understanding the evolution of Asian Sonerileae. We also detected high levels of homoplasy for some characters traditionally used in taxonomy, which explains current chaotic generic delimitations. The backbone phylogeny of Asian Sonerileae revealed in this study offers a solid basis for future taxonomic revision at the generic level.
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