Publications by authors named "Qi Tian"

286 Publications

Verifying the Feasibility of Implementing Semantic Interoperability in Different Countries Based on the OpenEHR Approach: Comparative Study of Acute Coronary Syndrome Registries.

JMIR Med Inform 2021 Oct 19;9(10):e31288. Epub 2021 Oct 19.

College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China.

Background: The semantic interoperability of health care information has been a critical challenge in medical informatics and has influenced the integration, sharing, analysis, and use of medical big data. International standard organizations have developed standards, approaches, and models to improve and implement semantic interoperability. The openEHR approach-one of the standout semantic interoperability approaches-has been implemented worldwide to improve semantic interoperability based on reused archetypes.

Objective: This study aimed to verify the feasibility of implementing semantic interoperability in different countries by comparing the openEHR-based information models of 2 acute coronary syndrome (ACS) registries from China and New Zealand.

Methods: A semantic archetype comparison method was proposed to determine the semantics reuse degree of reused archetypes in 2 ACS-related clinical registries from 2 countries. This method involved (1) determining the scope of reused archetypes; (2) identifying corresponding data items within corresponding archetypes; (3) comparing the semantics of corresponding data items; and (4) calculating the number of mappings in corresponding data items and analyzing results.

Results: Among the related archetypes in the two ACS-related, openEHR-based clinical registries from China and New Zealand, there were 8 pairs of reusable archetypes, which included 89 pairs of corresponding data items and 120 noncorresponding data items. Of the 89 corresponding data item pairs, 87 pairs (98%) were mappable and therefore supported semantic interoperability, and 71 pairs (80%) were labeled as "direct mapping" data items. Of the 120 noncorresponding data items, 114 (95%) data items were generated via archetype evolution, and 6 (5%) data items were generated via archetype localization.

Conclusions: The results of the semantic comparison between the two ACS-related clinical registries prove the feasibility of establishing the semantic interoperability of health care data from different countries based on the openEHR approach. Archetype reuse provides data on the degree to which semantic interoperability exists when using the openEHR approach. Although the openEHR community has effectively promoted archetype reuse and semantic interoperability by providing archetype modeling methods, tools, model repositories, and archetype design patterns, the uncontrolled evolution of archetypes and inconsistent localization have resulted in major challenges for achieving higher levels of semantic interoperability.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2196/31288DOI Listing
October 2021

Individual exposure to ambient PM and hospital admissions for COPD in 110 hospitals: a case-crossover study in Guangzhou, China.

Environ Sci Pollut Res Int 2021 Sep 21. Epub 2021 Sep 21.

National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Department of Biostatistics, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.

Few studies have evaluated the short-term association between hospital admissions and individual exposure to ambient particulate matter (PM). Particularly, no studies focused on hospital admissions for chronic obstructive pulmonary disease (COPD) at the individual level. We assessed the short-term effects of PM on hospitalization admissions for COPD in Guangzhou, China, during 2014-2015, based on satellite-derived estimates of ambient PM concentrations at a 1-km resolution near the residential address as individual-level exposure for each patient. Around 40,002 patients with COPD admitted to 110 hospitals were included in this study. A time-stratified case-crossover design with conditional logistic regression models was applied to assess the effects of PM based on a 1-km grid data of aerosol optical depth provided by the National Aeronautics and Space Administration on hospital admissions for COPD. Further, we performed stratified analyses by individual demographic characteristics and season of hospital admission. Around 10 μg/m increase in individual-level PM was associated with an increase of 1.6% (95% confidence interval [CI]: 0.6%, 2.7%) in hospitalization for COPD at a lag of 0-5 days. The impact of PM on hospitalization for COPD was greater significantly in males and patients admitted in summer. Our study strengthened the evidence for the adverse effect of PM based on satellite-based individual-level exposure data.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11356-021-16539-xDOI Listing
September 2021

Manipulation of TAD reorganization by chemical-dependent genome linking.

STAR Protoc 2021 Sep 8;2(3):100799. Epub 2021 Sep 8.

RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China.

Reorganization of topologically associated domain (TAD) is considered to be a novel mechanism for cell fate transitions. Here, we present a protocol to manipulate TAD via abscisic acid (ABA)-dependent genome linking. We use this protocol to merge two adjacent TADs and evaluate the influence on cell fate transitions. The advantages are that the manipulation does not change the genome and is reversible by withdrawing ABA. The major challenge is how to select linking loci for efficient TAD reorganization. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.xpro.2021.100799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8433250PMC
September 2021

A molecular mechanism investigation of the transdermal/topical absorption classification system on the basis of drug skin permeation and skin retention.

Int J Pharm 2021 Oct 8;608:121082. Epub 2021 Sep 8.

School of Pharmacy, Shenyang Pharmaceutical University, No. 26 Huatuo Road, High & New Technology Development Zone, Benxi 117004, China. Electronic address:

A transdermal/topical absorption classification system for the characterization of the systemic or local delivery of drugs is the theoretical basis for the design and evaluation of transdermal/topical formulations. A classification system was established on the basis of the in vitro and in vivo skin permeation/retention behaviors of 12 model drugs. Drug skin penetration/retention exhibited a significant correlation with physicochemical parameters (log K, molecular weight, polar surface area, and polarizability). Four representative model drugs were selected to clarify the molecular mechanisms of drug skin permeation/retention behaviors. The excellent lipid-disrupting effect and enhanced partitioning exhibited by propranolol (high permeation-high retention) and zolmitriptan (high permeation-low retention) via the formation of moderate H-bonds with skin lipids were proven by ATR-FTIR (Δν > 2 cm), Raman spectra (ΔLPP, SPP > 0.2 nm), and X-ray scattering (lipid crystallization) and were supported by C NMR results. The low lipid miscibility of zolmitriptan (ΔH = 126.92 J/g) caused the low skin retention of this drug. High polarizabiltiy (α = 38.5 × 10 cm) and low H-bond forming capability (E = 0 kcal/mol) restricted terbinafine (low permeation-high retention) in terms of partitioning (k = 0.09). Diclofenac (low permeation-low retention) stabilized skin lipids through the formation of strong H-bonds and exhibited excessive drug-lipid miscibility (ΔH = -128.73 J/g), thus restricting its skin absorption. This classification system reflects the most essential drug skin absorption characteristics and provides a theoretical basis for the design of transdermal/topical formulations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ijpharm.2021.121082DOI Listing
October 2021

Multiscale Spatio-Temporal Graph Neural Networks for 3D Skeleton-Based Motion Prediction.

IEEE Trans Image Process 2021 14;30:7760-7775. Epub 2021 Sep 14.

We propose a multiscale spatio-temporal graph neural network (MST-GNN) to predict the future 3D skeleton-based human poses in an action-category-agnostic manner. The core of MST-GNN is a multiscale spatio-temporal graph that explicitly models the relations in motions at various spatial and temporal scales. Different from many previous hierarchical structures, our multiscale spatio-temporal graph is built in a data-adaptive fashion, which captures nonphysical, yet motion-based relations. The key module of MST-GNN is a multiscale spatio-temporal graph computational unit (MST-GCU) based on the trainable graph structure. MST-GCU embeds underlying features at individual scales and then fuses features across scales to obtain a comprehensive representation. The overall architecture of MST-GNN follows an encoder-decoder framework, where the encoder consists of a sequence of MST-GCUs to learn the spatial and temporal features of motions, and the decoder uses a graph-based attention gate recurrent unit (GA-GRU) to generate future poses. Extensive experiments are conducted to show that the proposed MST-GNN outperforms state-of-the-art methods in both short and long-term motion prediction on the datasets of Human 3.6M, CMU Mocap and 3DPW, where MST-GNN outperforms previous works by 5.33% and 3.67% of mean angle errors in average for short-term and long-term prediction on Human 3.6M, and by 11.84% and 4.71% of mean angle errors for short-term and long-term prediction on CMU Mocap, and by 1.13% of mean angle errors on 3DPW in average, respectively. We further investigate the learned multiscale graphs for interpretability.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TIP.2021.3108708DOI Listing
September 2021

Conversational Image Search.

IEEE Trans Image Process 2021 10;30:7732-7743. Epub 2021 Sep 10.

Conversational image search, a revolutionary search mode, is able to interactively induce the user response to clarify their intents step by step. Several efforts have been dedicated to the conversation part, namely automatically asking the right question at the right time for user preference elicitation, while few studies focus on the image search part given the well-prepared conversational query. In this paper, we work towards conversational image search, which is much difficult compared to the traditional image search task, due to the following challenges: 1) understanding complex user intents from a multimodal conversational query; 2) utilizing multiform knowledge associated images from a memory network; and 3) enhancing the image representation with distilled knowledge. To address these problems, in this paper, we present a novel contextuaL imAge seaRch sCHeme (LARCH for short), consisting of three components. In the first component, we design a multimodal hierarchical graph-based neural network, which learns the conversational query embedding for better user intent understanding. As to the second one, we devise a multi-form knowledge embedding memory network to unify heterogeneous knowledge structures into a homogeneous base that greatly facilitates relevant knowledge retrieval. In the third component, we learn the knowledge-enhanced image representation via a novel gated neural network, which selects the useful knowledge from retrieved relevant one. Extensive experiments have shown that our LARCH yields significant performance over an extended benchmark dataset. As a side contribution, we have released the data, codes, and parameter settings to facilitate other researchers in the conversational image search community.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TIP.2021.3108724DOI Listing
September 2021

Use of Surfacer, an inside-out device, in tandem with HeRO graft for creation of vascular access: Case report of three patients with 18-months follow up.

J Vasc Access 2021 Aug 31:11297298211041434. Epub 2021 Aug 31.

Department of General Surgery (Vascular Surgery), Sengkang General Hospital, Singapore.

The Surfacer Inside-Out Access Catheter System (Surfacer) is a novel approach to restore access in total central vein occlusion (TCVO). We report a series of three cases, with mean 18-months follow up, in our institution where this technique was safely and effectively used in tandem with Hemodialysis Reliable Outflow (HeRO) graft for creation of upper limb vascular access in patients with TCVO. Although there have been reports describing the simultaneous combination of Surfacer and HeRO graft, to our knowledge, this is the first time where the outcomes with 18-months mean follow-up are reported. All three patients had failed prior conventional attempts at TCVO crossing and had exhausted most conventional upper limb vascular access methods. The above technique yielded a 100% technical success rate with mean operative time of 140 min. Cannulation rate was 100% with all undergoing successful early cannulation by post-operative day 3. Mean primary patency of 199 days was achieved. Average intervention rate of 1.2 a year was required to maintain patency. The Surfacer device used together with HeRO graft is a feasible technique to avoid femoral catheter in patients where conventional attempts to cross the TCVO have failed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1177/11297298211041434DOI Listing
August 2021

Corrigendum to "Hippo/YAP signaling pathway mitigates blood-brain barrier disruption after cerebral ischemia/reperfusion injury" [Behav. Brain Res. 356 (2019) 8-17].

Behav Brain Res 2022 Jan 20;416:113531. Epub 2021 Aug 20.

Department of Anesthesiology and Critical Care Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. Electronic address:

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbr.2021.113531DOI Listing
January 2022

The autism risk gene CNTN4 modulates dendritic spine formation.

Hum Mol Genet 2021 Aug 20. Epub 2021 Aug 20.

Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.

Contactin 4 (CNTN4) is a crucial synaptic adhesion protein that belongs to the contactin superfamily. Evidence from both human genetics and mouse models suggests that synapse formation and structural deficits strongly correlate with neurodevelopmental disorders, including autism. In addition, several lines of evidence suggest that CNTN4 is associated with the risk of autism. However, the biological functions of CNTN4 in neural development and disease pathogenesis are poorly understood. In this study, we investigated whether and how CNTN4 is autonomously involved in the development of dendrites and dendritic spines in cortical neurons. Disruption of Cntn4 decreased the number of excitatory synapses, which led to a reduction in neural activity. Truncated proteins lacking the signal peptide, FnIII domains, or GPI domain lacked the ability to regulate dendritic spine formation, indicating that CNTN4 regulates dendritic spine density through a mechanism dependent on FnIII domains. Importantly, we revealed that autism-related variants lacked the ability to regulate spine density and neural activity. In conclusion, our study suggests that CNTN4 is essential for promoting dendrite growth and dendritic spine formation and that disruptive variants of CNTN4 interfere with abnormal synapse formation and may increase the risk of autism.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/hmg/ddab233DOI Listing
August 2021

Dual-Functional Graphene Oxide-Based Photothermal Materials with Aligned Channels and Oleophobicity for Efficient Solar Steam Generation.

Langmuir 2021 Aug 9;37(33):10191-10199. Epub 2021 Aug 9.

Key Laboratory of Environment-Friendly Composite Materials of the State Ethnic Affairs Commission, College of Chemical Engineering, Northwest Minzu University, Lanzhou, Gansu 730030, P. R. China.

Desalination by solar steam generation (SSG) has emerged as one of the most efficient approaches to address the issue of global water shortage. In this work, novel graphene oxide (GO)-based solar steam generators (GO-SSGs) with aligned channels were prepared by directional freezing and simple carbonization of a hydrogel composed of GO and poly(vinyl alcohol) (PVA). Benefitting from their excellent light absorption (light absorption efficiency exceeds 94%), better thermal insulation (thermal conductivity, 0.259 W/(m K)), and suitable porous structure, which facilitates rapid water transportation, the GO-SSGs show superior SSG performance with a high solar energy conversion efficiency of up to 92% achieved under an irradiation of 1.0 kW/m. Interestingly, uniquely aligned channels endow them with good salt-rejection performance; the solar energy conversion efficiency of GO-SSGs in 20 wt % NaCl, KCl, and MgCl brine can reach more than 85%. To improve their antifouling performance, a chemically hydrophilic and oleophobic modification was conducted, making it possible to run SSG even in oily wastewater; for instance, a solar energy conversion efficiency of 84% was obtained in an aqueous solution containing 10 wt % -hexadecane. Compared with the existing photothermal materials, these materials show advantages of simple manufacture, high SSG efficiency, superior salt tolerance, and antifouling performance, which make them promising candidates as a kind of new high-performance photothermal materials for desalination even in oily wastewater, thus further expanding the scope of their practical SSG application.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.langmuir.1c01647DOI Listing
August 2021

The Pro-Gly or Hyp-Gly Containing Peptides from Absorbates of Fish Skin Collagen Hydrolysates Inhibit Platelet Aggregation and Target PY Receptor by Molecular Docking.

Foods 2021 Jul 5;10(7). Epub 2021 Jul 5.

College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.

Previous studies found that the collagen hydrolysates of fish skin have antiplatelet activity, but this component remained unknown. In this study, eleven peptides were isolated and identified in the absorbates of Alcalase-hydrolysates and Protamex-hydrolysates of skin collagen of by reverse-phase C18 column and HPLC-MS/MS. Nine of them contained a Pro-Gly (PG) or Hyp-Gly (OG) sequence and significantly inhibited ADP-induced platelet aggregation in vitro, which suggested that the PG(OG) sequence is the core sequence of collagen peptides with antiplatelet activity. Among them, OGSA has the strongest inhibiting activities against ADP-induced platelet aggregation in vitro (IC = 0.63 mM), and OGSA inhibited the thrombus formation in rats at a dose of 200 μM/kg.bw with no risk of bleeding. The molecular docking results implied that the OG-containing peptides might target the PY receptor and form hydrogen bonds with the key sites Cys97, Ser101, and Lys179. As the sequence PG(OG) is abundant in the collagen amino acid sequence of the collagen hydrolysates of might have great potential for being developed as dietary supplements to prevent cardiovascular diseases in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/foods10071553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8303285PMC
July 2021

COVID-19 pandemic related long-term chronic stress on the prevalence of depression and anxiety in the general population.

BMC Psychiatry 2021 07 28;21(1):380. Epub 2021 Jul 28.

Department of Stress Medicine, Faculty of Psychology, Navy Medical University, 800 Xiangyin Road, Shanghai, China.

Background: The COVID-19 pandemic has lasted for more than 1 year, causing far-reaching and unprecedented changes in almost all aspects of society. This study aimed to evaluate the long-term consequences of the COVID-19 pandemic on depression and anxiety, and explore the factors associated with it.

Methods: A cross-sectional study using an online survey was conducted to assess mental health problems from February 2 to February 9, 2021 by using patient health questionnaire-9 (PHQ-9) and generalized anxiety disorder-7 (GAD-7). The insomnia severity index (ISI), demographic data and COVID-19 related variables were measured by a self-designed questionnaire. The factors associated with depressive and anxiety symptoms were identified by Pearson chi-square test and binary logistic regression analysis.

Results: In the study that 1171 participants enrolled, the overall prevalence of depressive and anxiety symptoms among general people was 22.6 and 21.4% respectively in the present study. Living alone was a potential risk factor for depressive symptoms, while regular exercises was a potential protective factor. The prevalence of depressive and anxiety symptoms was significantly associated with the severity of insomnia symptoms and the negative feelings about pandemic.

Conclusion: COVID-19 pandemic- related chronic stress has brought about profound impacts on long-term mental health in the general population. The level of insomnia and a negative attitude towards the pandemic are significantly correlated with unfavorable mental health. However, we failed to found a significant association of age and gender with the mental health symptoms, although they were recognized as well-established risk factors during the outbreak by some other studies. This discrepancy may be because the acute and chronic effects of the pandemic are influenced by different factors, which reminds that more attention should be paid to the intrinsic psychological factors and physical reactions towards COVID-19.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12888-021-03385-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8316891PMC
July 2021

Development and Validation of a Ferroptosis-Related Gene Signature for Overall Survival Prediction in Lung Adenocarcinoma.

Front Cell Dev Biol 2021 7;9:684259. Epub 2021 Jul 7.

Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.

Ferroptosis is an iron-dependent programmed cell death process. Recent studies have found that ferroptosis inducers hold promising potential in the treatment of lung adenocarcinoma (LUAD). However, the comprehensive analysis about the prognostic value of ferroptosis-related genes in LUAD remains to be elucidated. The RNA sequencing data and corresponding clinical information were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A total of 259 ferroptosis-related genes were extracted from FerrDb website. The ferroptosis-related prognostic signature was developed by least absolute shrinkage and selection operator (LASSO) Cox regression analysis in TCGA LUAD cohort, and then validated by 5 independent GEO cohorts. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were performed to identify the difference in biological processes and functions between different risk groups. The expression levels of core prognostic genes were then verified in LUAD samples by immunohistochemistry (IHC) and erastin-treated LUAD cell lines by real-time polymerase chain reaction (PCR). The potential roles of GPX2 and DDIT4 as ferroptosis drivers in LUAD cell line were further confirmed by experiments. A total of 20 intersecting genes between 70 ferroptosis-related DEGs and 45 potential prognostic genes were obtained for LASSO Cox regression analysis. The ferroptosis-related prognostic signature was developed by 7 core prognostic DEGs, and stratified LUAD patients into two risk groups. Kaplan-Meier analysis showed that the overall survival (OS) of LUAD patients in the high-risk group was significantly worse than that of the low-risk group. External validation of 5 independent GEO cohorts further confirmed that the ferroptosis-related prognostic signature was an ideal biomarker for predicting the survival of LUAD patients. Significant enrichment of fatty acid metabolism and cell cycle-related pathways were found in different risk groups. The expression patterns of 7 core prognostic genes in LUAD and adjacent normal lung tissues were validated by IHC, which was almost consistent with the results from public database. Furthermore, the changes related to cell cycle and ferroptosis after erastin treatment were also validated in LUAD cell lines. In addition, silencing GPX2 or DDIT4 could partially reverse the erastin-induced ferroptosis. In summary, the ferroptosis-related prognostic signature based on 7 core prognostic DEGs indicated superior predictive performance of LUAD patients. Targeting ferroptosis holds potential to be a therapeutic alternative for LUAD.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcell.2021.684259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8294813PMC
July 2021

SLC39A5 dysfunction impairs extracellular matrix synthesis in high myopia pathogenesis.

J Cell Mol Med 2021 Sep 24;25(17):8432-8441. Epub 2021 Jul 24.

Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.

High myopia is one of the leading causes of visual impairment worldwide with high heritability. We have previously identified the genetic contribution of SLC39A5 to nonsyndromic high myopia and demonstrated that disease-related mutations of SLC39A5 dysregulate the TGF-β pathway. In this study, the mechanisms underlying SLC39A5 involvement in the pathogenesis of high myopia are determined. We observed the morphogenesis and migration abnormalities of the SLC39A5 knockout (KO) human embryonic kidney cells (HEK293) and found a significant injury of ECM constituents. RNA-seq and qRT-PCR revealed the transcription decrease in COL1A1, COL2A1, COL4A1, FN1 and LAMA1 in the KO cells. Further, we demonstrated that TGF-β signalling, the regulator of ECM, was inhibited in SLC39A5 depletion situation, wherein the activation of receptor Smads (R-Smads) via phosphorylation was greatly blocked. SLC39A5 re-expression reversed the phenotype of TGF-β signalling and ECM synthesis in the KO cells. The fact that TGF-β signalling was zinc-regulated and that SLC39A5 was identified as a zinc transporter urged us to check the involvement of intracellular zinc in TGF-β signalling impairment. Finally, we determined that insufficient zinc chelation destabilized Smad proteins, which naturally inhibited TGF-β signalling. Overall, the SLC39A5 depletion-induced zinc deficiency destabilized Smad proteins, which inhibited the TGF-β signalling and downstream ECM synthesis, thus contributing to the pathogenesis of high myopia. This discovery provides a deep insight into myopic development.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/jcmm.16803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8419198PMC
September 2021

Development and validation of an immune gene set-based prognostic signature in cutaneous melanoma.

Future Oncol 2021 Nov 22;17(31):4115-4129. Epub 2021 Jul 22.

Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.

We aimed to fully understand the landscape of the skin cutaneous melanoma (SKCM) microenvironment and develop an immune prognostic signature that can predict the prognosis for SKCM patients. RNA sequencing data and clinical information were downloaded from the Cancer Genome Atlas and Gene Expression Omnibus databases. The immune-prognostic signature was constructed by LASSO Cox regression analysis. We calculated the relative abundance of 29 immune-related gene sets based on the mRNA expression profiles of 314 SKCM patients in the Cancer Genome Atlas training set. Hierarchical clustering was performed to classify SKCM patients into three clusters: immunity-high, -medium and -low. The values of our prognostic model in predicting disease progression, metastasis and immunotherapeutic responses were also validated. In conclusion, the prognostic model demonstrated a powerful ability to distinguish and predict SKCM patients' prognosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2217/fon-2021-0104DOI Listing
November 2021

Spreads to the Large Intestine Lumen via Multiple Pathways.

Infect Immun 2021 Sep 19;89(10):e0025421. Epub 2021 Jul 19.

Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.

in the genital tract is known to spread via the blood circulation system to the large intestine lumen to achieve long-lasting colonization. However, the precise pathways by which genital accesses the large intestine lumen remain unclear. The spleen was recently reported to be critical for chlamydial spreading. In the current study, it was found that following intravaginal inoculation with , mice with and without splenectomy both yielded infectious on rectal swabs, indicating that the spleen is not essential for genital to spread to the gastrointestinal tract. This conclusion was validated by the observation that intravenously inoculated was also detected on the rectal swabs of mice regardless of splenectomy. Careful comparison of the tissue distribution of live chlamydial organisms following intravenous inoculation revealed redundant pathways by which can reach the large intestine lumen. The intravenously inoculated was predominantly recruited to the spleen within 12 h and then detected in the stomach lumen by 24 h, in the intestinal lumen by 48 h, and on rectal swabs by 72 h. These observations suggest a potential spleen-to-stomach pathway for hematogenous to reach the large intestine lumen. This conclusion was supported by the observation made in mice under coprophagy-free condition. However, in the absence of spleen, hematogenous was predominantly recruited to the liver and then simultaneously detected in the intestinal tissue and lumen, suggesting a potential liver-to-intestine pathway for to reach the large intestine lumen. Thus, genital/hematogenous may reach the large intestine lumen via multiple redundant pathways.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/IAI.00254-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8445164PMC
September 2021

BiSPL: Bidirectional Self-Paced Learning for Recognition From Web Data.

IEEE Trans Image Process 2021 19;30:6512-6527. Epub 2021 Jul 19.

Deep learning (DL) is inherently subject to the requirement of a large amount of well-labeled data, which is expensive and time-consuming to obtain manually. In order to broaden the reach of DL, leveraging free web data becomes an attractive strategy to alleviate the issue of data scarcity. However, directly utilizing collected web data to train a deep model is ineffective because of the mixed noisy data. To address such problems, we develop a novel bidirectional self-paced learning (BiSPL) framework which reduces the effect of noise by learning from web data in a meaningful order. Technically, the BiSPL framework consists of two essential steps. Relying on distances defined between web samples and labeled source samples, first, the web samples with short distances are sampled and combined to form a new training set. Second, based on the new training set, both easy and hard samples are initially employed to train deep models for higher stability, and hard samples are gradually dropped to reduce the noise as the training progresses. By iteratively alternating such steps, deep models converge to a better solution. We mainly focus on the fine-grained visual classification (FGVC) tasks because their corresponding datasets are generally small and therefore face a more significant data scarcity problem. Experiments conducted on six public FGVC tasks demonstrate that our proposed method outperforms the state-of-the-art approaches. Especially, BiSPL suffices to achieve the highest stable performance when the scale of the well-labeled training set decreases dramatically.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TIP.2021.3094744DOI Listing
July 2021

Gastrointestinal Chlamydia-Induced CD8 T Cells Promote Chlamydial Pathogenicity in the Female Upper Genital Tract.

Infect Immun 2021 Sep 6;89(10):e0020521. Epub 2021 Jul 6.

Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA.

Chlamydia is known to both ascend to the upper genital tract and spread to the gastrointestinal tract following intravaginal inoculation. Gastrointestinal Chlamydia was recently reported to promote chlamydial pathogenicity in the genital tract since mice intravaginally inoculated with an attenuated Chlamydia strain, which alone failed to develop pathology in the genital tract, were restored to develop hydrosalpinx by intragastric coinoculation with wild-type Chlamydia. Gastrointestinal Chlamydia promoted hydrosalpinx via an indirect mechanism since Chlamydia in the gut did not directly spread to the genital tract lumen. In the current study, we further investigated the role of CD8 T cells in the promotion of hydrosalpinx by gastrointestinal Chlamydia. First, we confirmed that intragastric coinoculation with wild-type Chlamydia promoted hydrosalpinx in mice that were inoculated with an attenuated Chlamydia strain in the genital tract 1 week earlier. Second, the promotion of hydrosalpinx by intragastrically coinoculated Chlamydia was blocked by depleting CD8 T cells. Third, adoptive transfer of gastrointestinal Chlamydia-induced CD8 T cells was sufficient for promoting hydrosalpinx in mice that were intravaginally inoculated with an attenuated Chlamydia strain. These observations have demonstrated that CD8 T cells induced by gastrointestinal Chlamydia are both necessary and sufficient for promoting hydrosalpinx in the genital tract. The study has laid a foundation for further revealing the mechanisms by which Chlamydia-induced T lymphocyte responses (as a 2nd hit) promote hydrosalpinx in mice with genital Chlamydia-triggered tubal injury (as a 1st hit), a continuing effort in testing the two-hit hypothesis as a chlamydial pathogenic mechanism.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/IAI.00205-21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8445165PMC
September 2021

A Novel Ferroptosis-Related Gene Signature for Overall Survival Prediction in Patients With Breast Cancer.

Front Cell Dev Biol 2021 17;9:670184. Epub 2021 Jun 17.

Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.

Introduction: Breast cancer is the most common malignant tumor in women worldwide. However, advanced multidisciplinary therapy cannot rescue the mortality of high-risk breast cancer metastasis. Ferroptosis is a newly discovered form of regulating cell death that related to cancer treatment, especially in eradicating aggressive malignancies that are resistant to traditional therapies. However, the prognostic value of ferroptosis-related gene in breast cancer remains unknown.

Materials And Methods: In this study, a total of 1,057 breast cancer RNA expression data with clinical and follow-up information were downloaded from the TCGA cohort, multivariate Cox regression was used to construct the 11-gene prognostic ferroptosis-related gene signature. The breast cancer patients from the GEO cohort were used for validation. The expression levels of core prognostic genes were also verified in erastin-treated breast cancer cell lines by real-time polymerase chain action (PCR).

Results And Discussion: Our results showed that 78% ferroptosis-related genes were differentially expressed between breast cancer tumor tissue and adjacent non-tumorous tissues, including 29 of them which were significantly correlated with OS in the univariate Cox regression analysis. Patients were divided into high-risk group and low-risk group by the 11-gene signature. Patients with high-risk scores had a higher probability of death earlier than the low-risk group both in the TCGA construction cohort and in the GEO validation cohort (all < 0.001). Meanwhile, the risk score was proved to be an independent predictor for OS in both univariate and multivariate Cox regression analyses (HR > 1, < 0.01). The predictive efficacy of the prognostic signature for OS was further verified by the time-dependent ROC curves. Moreover, we also enriched many immune-related biological processes in later functional analysis; the immune status showed a statistical difference between the two risk groups. In addition, the differences in expression levels of 11 core prognostic genes were examined in ferroptosis inducer-treated breast cancer cell lines.

Conclusion: In conclusion, a novel ferroptosis-related gene model can be used for prognostic prediction in breast cancer. New ferroptosis-related genes may be used for breast cancer targeting therapy in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcell.2021.670184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8247647PMC
June 2021

A Real-Time Global Inference Network for One-Stage Referring Expression Comprehension.

IEEE Trans Neural Netw Learn Syst 2021 Jul 1;PP. Epub 2021 Jul 1.

Referring expression comprehension (REC) is an emerging research topic in computer vision, which refers to the detection of a target region in an image given a test description. Most existing REC methods follow a multistage pipeline, which is computationally expensive and greatly limits the applications of REC. In this article, we propose a one-stage model toward real-time REC, termed real-time global inference network (RealGIN). RealGIN addresses the issues of expression diversity and complexity of REC with two innovative designs: adaptive feature selection (AFS) and Global Attentive ReAsoNing (GARAN). Expression diversity concerns varying expression content, which includes information such as colors, attributes, locations, and fine-grained categories. To address this issue, AFS adaptively fuses features of different semantic levels to tackle the changes in expression content. In contrast, expression complexity concerns the complex relational conditions in expressions that are used to identify the referent. To this end, GARAN uses the textual feature as a pivot to collect expression-aware visual information from all regions and then diffuses this information back to each region, which provides sufficient context for modeling the relational conditions in expressions. On five benchmark datasets, i.e., RefCOCO, RefCOCO+, RefCOCOg, ReferIT, and Flickr30k, the proposed RealGIN outperforms most existing methods and achieves very competitive performances against the most advanced one, i.e., MAttNet. More importantly, under the same hardware, RealGIN can boost the processing speed by 10-20 times over the existing methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TNNLS.2021.3090426DOI Listing
July 2021

Multi-Scale Structure-Aware Network for Weakly Supervised Temporal Action Detection.

IEEE Trans Image Process 2021 24;30:5848-5861. Epub 2021 Jun 24.

Weakly supervised temporal action detection has better scalability and practicability than fully supervised action detection in reality deployment. However, it is difficult to learn a robust model without temporal action boundary annotations. In this paper, we propose an en-to-end Multi-Scale Structure-Aware Network (MSA-Net) for weakly supervised temporal action detection by exploring both the global structure information of a video and the local structure information of actions. The proposed SA-Net enjoys several merits. First, to localize actions with different durations, each video is encoded into feature representations with different temporal scales. Second, based on the multi-scale feature representation, the proposed model has designed two effective structure modeling mechanisms including global structure modeling and local structure modeling, which can effectively learn discriminative structure aware representations for robust and complete action detection. To the best of our knowledge, this is the first work to fully explore the global and local structure information in a unified deep model for weakly supervised action detection. And extensive experimental results on two benchmark datasets demonstrate that the proposed MSA-Net performs favorably against state-of-the-art methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TIP.2021.3089361DOI Listing
June 2021

Position-Aware Participation-Contributed Temporal Dynamic Model for Group Activity Recognition.

IEEE Trans Neural Netw Learn Syst 2021 Jun 17;PP. Epub 2021 Jun 17.

Group activity recognition (GAR) aiming at understanding the behavior of a group of people in a video clip has received increasing attention recently. Nevertheless, most of the existing solutions ignore that not all the persons contribute to the group activity of the scene equally. That is to say, the contribution from different individual behaviors to group activity is different; meanwhile, the contribution from people with different spatial positions is also different. To this end, we propose a novel Position-aware Participation-Contributed Temporal Dynamic Model (P²CTDM), in which two types of the key actor are constructed and learned. Specifically, we focus on the behaviors of key actors, who maintain steady motions (long moving time, called long motions) or display remarkable motions (but closely related to other people and the group activity, called flash motions) at a certain moment. For capturing long motions, we rank individual motions according to their intensity measured by stacking optical flows. For capturing flash motions that are closely related to other people, we design a position-aware interaction module (PIM) that simultaneously considers the feature similarity and position information. Beyond that, for capturing flash motions that are highly related to the group activity, we also present an aggregation long short-term memory (Agg-LSTM) to fuse the outputs from PIM by time-varying trainable attention factors. Four widely used benchmarks are adopted to evaluate the performance of the proposed P²CTDM compared to the state of the art.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TNNLS.2021.3085567DOI Listing
June 2021

Filter Sketch for Network Pruning.

IEEE Trans Neural Netw Learn Syst 2021 Jun 14;PP. Epub 2021 Jun 14.

We propose a novel network pruning approach by information preserving of pretrained network weights (filters). Network pruning with the information preserving is formulated as a matrix sketch problem, which is efficiently solved by the off-the-shelf frequent direction method. Our approach, referred to as FilterSketch, encodes the second-order information of pretrained weights, which enables the representation capacity of pruned networks to be recovered with a simple fine-tuning procedure. FilterSketch requires neither training from scratch nor data-driven iterative optimization, leading to a several-orders-of-magnitude reduction of time cost in the optimization of pruning. Experiments on CIFAR-10 show that FilterSketch reduces 63.3% of floating-point operations (FLOPs) and prunes 59.9% of network parameters with negligible accuracy cost for ResNet-110. On ILSVRC-2012, it reduces 45.5% of FLOPs and removes 43.0% of parameters with only 0.69% accuracy drop for ResNet-50. Our code and pruned models can be found at https://github.com/lmbxmu/FilterSketch.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1109/TNNLS.2021.3084206DOI Listing
June 2021

A Frameshift Variant in the SEMA6B Gene Causes Global Developmental Delay and Febrile Seizures.

Neurosci Bull 2021 Sep 10;37(9):1357-1360. Epub 2021 Jun 10.

Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, 410008, China.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12264-021-00717-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8423932PMC
September 2021

First Report of Nondeletional Hb H Disease Caused by an α2-Globin Gene Mutation: : c.184A>T.

Hemoglobin 2021 May 26;45(3):210-211. Epub 2021 May 26.

Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong Province, People's Republic of China.

We report a rare mutation, : c.184A>T on the α2-globin gene, detected in a Chinese proband who presented with Hb H disease and a mild anemia. This frameshift mutation results in a premature termination of translation at position 61 of the α2-globin gene. Carriers of this mutation showed a borderline microcytic hypochromia. Our study indicates the importance of screening nondeletional α-thalassemia (α-thal) in areas with a particularly high prevalence of thalassemia such as in Southern China, especially for couples with one partner carrying an α-thal deletion.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/03630269.2021.1930553DOI Listing
May 2021

Effective treatments for FGF12-related early-onset epileptic encephalopathies patients.

Brain Dev 2021 Sep 19;43(8):851-856. Epub 2021 May 19.

Department of Medical Genetics, Maternal, Child Health Hospital of Hunan Province, Changsha Hunan 410008, China; National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China. Electronic address:

Background: FGF12 (FHF1) gene encodes voltage-gated sodium channel (Nav)-binding protein fibroblast growth factor homologous factor 1, which could cause seizures by regulating voltage dependence of Nav fast inactivation and neuron excitability. The most common pathogenic variant FGF12 c.341G > A related early-onset epileptic encephalopathies (EOEE) was characterized by intractable seizures and developmental disabilities.

Results: Using whole exome sequencing, a de novo hotspot variant c.341G > A (NM_021032.4) of FGF12 was identified in three unrelated EOEE probands. All probands were seizure free after a combination treatment of valproic acid (VPA) and topiramate (TPM). The motor and cognitive skills in two probands were improved due to the early and effective treatment. In order to compare the effectiveness of different treatment strategies for the disease, a review of treatments for FGF12-related epilepsy was made.

Conclusion: We reported three FGF12 c.341G > A related EOEE patients responded well to a combination antiepileptic therapy of VPA and TPM. The current study is the first to describe the combination therapy of VPA and TPM in FGF12 c.341G > A related EOEE patients. This study may contribute to future medication consultation for intractable epilepsy with FGF12 hotspot variants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.braindev.2021.04.010DOI Listing
September 2021

Biodegradation of alicyclic amines by a newly isolated hypersaline tolerant strain Paenarthrobacter sp. TYUT067.

Water Sci Technol 2021 May;83(9):2160-2168

College of Civil Engineering, Taiyuan University of Technology, Taiyuan, Shanxi 030024, China.

Alicyclic amines are widely used in several types of industries, and considerable attention has been devoted to possible environmental pollution by alicyclic amines in hypersaline industrial wastewater. In this study, a new hypersaline tolerant bacterial TYUT067 capable of growing in liquid basal salt medium with cyclohexylamine (CHAM) as the sole carbon source and energy source, was isolated from soil, and discovered with highly efficient CHAM degrading ability. The strain TYUT067 was identified as Paenarthrobacter sp. based on 16S rDNA gene sequence, and its degradation characteristic was examined. The results revealed that the isolated TYUT067 could grow well under pH range of 6.5-10.0, temperature from 20 °C to 30 °C. For degradation of 60 mM of cyclohexylamine, 100% degradation could be finished within 120 h. The TYUT067 could degrade 10 mM CHAM under hypersaline conditions (3-5% NaCl, w/v), revealed the hypersaline tolerance of TYUT067. Different type of amines was also tested with TYUT067, the degradations of >90% were achieved toward several alicyclic amines. The current results suggested that TYUT067 was a potential species could be efficiently used for the degradation of alicyclic amines and might be applicable to a hypersaline wastewater treatment system for the removal of alicyclic amines.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2166/wst.2021.130DOI Listing
May 2021

Decision aids for prenatal testing: A systematic review and meta-analysis.

J Adv Nurs 2021 Oct 3;77(10):3964-3979. Epub 2021 May 3.

School of Nursing, Jilin University, Changchun, Jilin Province, China.

Aims: To analyse the effect of decision aids (DAs) used by pregnant women on prenatal testing decisions.

Design: Systematic review and meta-analysis.

Data Resources: We searched Embase, PubMed, Web of Science and the Cochrane Central Library ending October 2020.

Review Methods: Papers were selected for analysis in accordance with the PRISMA guidelines. The meta-analysis was carried out using Review Manager 5.3 software. The quality of the studies was assessed using the risk of bias tool recommended by the Cochrane Handbook. The result is knowledge, decision conflict, anxiety and other secondary outcomes.

Results: A total of 18 studies were included in the systematic review and meta-analysis. Comprehensive analysis showed that DAs could significantly improve knowledge and decision-making satisfaction, reduce decision conflict, increase the proportion of women who make informed choice and had no influence on anxiety and decision regret.

Conclusions: This article systematically reviewed the positive effect of DAs on the decision-making of pregnant women facing prenatal testing. In the future, nurses should be encouraged to develop DAs in accordance with strict standards and apply them to pregnant women of different backgrounds.

Impact: There is a growing consensus that health care should be patient-centred, and the values and preferences of pregnant women who undergo prenatal testing need to be incorporated into the clinical decision-making process. This review reports that the use of DAs can increase pregnant women's chances of participating in prenatal testing decisions and may improve the quality of their decision-making. It also provides information on the role and practice of nurses in promoting evidence-based prenatal testing for DAs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/jan.14875DOI Listing
October 2021

Case Report: Compound Heterozygous Variants in Identified in a Chinese Infant With Molybdenum Cofactor Deficiency.

Front Genet 2021 8;12:651878. Epub 2021 Apr 8.

Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.

The molybdenum cofactor (Moco) deficiency in humans results in the inactivity of molybdenum-dependent enzymes and is caused by pathogenic variants in (), (), and (). These genes along with () are involved in Moco biosynthesis and providing cofactors to Moco-dependent enzymes. Until now, there was no study to confirm that is a causative gene of Moco deficiency. Detailed clinical information was collected in the pedigree. The Whole-exome sequencing (WES) accompanied with Sanger sequencing validation were performed. We described the clinical presentations of an infant, born to a non-consanguineous healthy family, diagnosed as having variants caused Moco deficiency and showing typical features of Moco deficiency including severe neurologic symptoms and cystic encephalomalacia in the brain MRI, resulting in neonatal death. Compound heterozygous variants in the gene were identified by WES. Positive sulfite and decreased levels of uric acid in plasma and urine were detected. To our knowledge, this is the first case of variants causing Moco deficiency. Our study may contribute to genetic diagnosis of Moco deficiency and future genetic counseling.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2021.651878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060434PMC
April 2021

Parental mosaicism in de novo neurodevelopmental diseases.

Am J Med Genet A 2021 07 14;185(7):2119-2125. Epub 2021 Apr 14.

Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, China.

Neurodevelopmental diseases are increasingly recognized to be caused by "de novo" variants with the expanding use of next-generation sequencing. The apparent de novo variants may actually be low-level hereditary parental mosaic variants, which could increase the recurrence risk of disease by >50% and is thought to be an underappreciated cause of neurodevelopmental diseases. Our study aimed to investigate the frequency of parental mosaicism in "de novo" neurodevelopmental diseases. A total of 237 patients (and parents) with neurodevelopmental diseases carrying apparent de novo pathogenic or likely pathogenic variants were recruited consecutively. Deep next-generation sequencing was performed on parental samples to identify parental mosaicism. Fourteen parental disease-causing mosaicism variants (3.0%) in 11 genes were detected with alternate allele frequency (AAF) 0.22%-34%. Three parents showed milder clinical phenotypes than their offspring with relatively high AAF (23.33%, 25%, 34% separately). One recurrent variant was identified prenatally. A review of cohort study on parental mosaicism in neurodevelopmental diseases was performed. Our study highlights that identifying the parental mosaic disease-causing variants especially the low-level mosaicism will contribute to improving the accuracy of genetic counseling and prenatal diagnosis for reproductive risks.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ajmg.a.62174DOI Listing
July 2021
-->