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Abstract Background Gut microbiota is significantly influenced by altitude. However, the dynamics of gut microbiota in relation to altitude remains undisclosed. Methods In this study, we investigated the microbiome profile of 610 healthy young men from three different places in China, grouped by altitude, duration of residence, and ethnicity. We conducted widely targeted metabolomic profiling and clinical testing to explore metabolic characteristics. Results Our findings revealed that as the Han individuals migrated from low altitude to high latitude, the gut microbiota gradually converged towards that of the Tibetan populations but reversed upon returning to lower altitude. Across different cohorts, we identified 51 species specifically enriched during acclimatization and 57 species enriched during deacclimatization to high altitude. Notably, Prevotella copri was found to be the most enriched taxon in both Tibetan and Han populations after ascending to high altitude. Furthermore, significant variations in host plasma metabolome and clinical indices at high altitude could be largely explained by changes in gut microbiota composition. Similar to Tibetans, 41 plasma metabolites, such as lactic acid, sphingosine-1-phosphate, taurine, and inositol, were significantly elevated in Han populations after ascending to high altitude. Germ-free animal experiments demonstrated that certain species, such as Escherichia coli and Klebsiella pneumoniae, which exhibited altitude-dependent variations in human populations, might play crucial roles in host purine metabolism. Conclusions This study provides insights into the dynamics of gut microbiota and host plasma metabolome with respect to altitude changes, indicating that their dynamics may have implications for host health at high altitude and contribute to host adaptation. Video Abstract

Abstract Structural variants (SVs), accounting for a larger fraction of the genome than SNPs/InDels, are an important pool of genetic variation, enabling environmental adaptations. Here, we perform long-read sequencing data of 320 Tibetan and Han samples and show that SVs are highly involved in high-altitude adaptation. We expand the landscape of global SVs, apply robust models of selection and population differentiation combining SVs, SNPs and InDels, and use epigenomic analyses to predict enhancers, target genes and biological functions. We reveal diverse Tibetan-specific SVs affecting the regulatory circuitry of biological functions, including the hypoxia response, energy metabolism and pulmonary function. We find a Tibetan-specific deletion disrupts a super-enhancer and downregulates EPAS1 using enhancer reporter, cellular knock-out and DNA pull-down assays. Our study expands the global SV landscape, reveals the role of gene-regulatory circuitry rewiring in human adaptation, and illustrates the diverse functional roles of SVs in human biology.

Abstract Long non-coding RNAs (lncRNAs) have emerged as crucial regulators of cancer progression and are potential biomarkers for diagnosis and treatment. This study investigates the role of RARA Antisense RNA 1 (RARA-AS1) in cancer and its implications for diagnosis and treatment. Various bioinformatics tools were conducted to analyze the expression patterns, immune-related functions, methylation, and gene expression correlations of RARA-AS1, mainly including the comparisons of different subgroups and correlation analyses between RARA-AS1 expression and other factors. Furthermore, we used short hairpin RNA to perform knockdown experiments, investigating the effects of RARA-AS1 on cell proliferation, invasion, and migration in glioblastoma. Our results revealed that RARA-AS1 has distinct expression patterns in different cancers and exhibits notable correlation with prognosis. Additionally, RARA-AS1 is highly correlated with certain immune checkpoints and mismatch repair genes, indicating its potential role in immune infiltration and related immunotherapy. Further analysis identified potential effective drugs for RARA-AS1 and demonstrated its potential RNA binding protein (RBP) mechanism in glioblastoma. Besides, a series of functional experiments indicated inhibiting RARA-AS1 could decrease cell proliferation, invasion, and migration of glioblastoma cell lines. Finally, RARA-AS1 could act as an independent prognostic factor for glioblastoma patients and may serve as a promising therapeutic target. All in all, Our study provides a comprehensive understanding of the functions and implications of RARA-AS1 in pan-cancer, highlighting it as a promising biomarker for survival. It is also an independent risk factor affecting prognosis in glioblastoma and an important factor affecting proliferation and migration in glioblastoma, setting the stage for further mechanistic investigations.

The validation of remotely sensed evapotranspiration (ET) products is important for the development of ET estimation models and the accuracy of the scientific application of the products. In this study, different ET products such as HiTLL, MOD16A2, ETMonitor, and SoGAE were compared using multi-source remote sensing data and ground-based data to evaluate their applicability in the Heihe River Basin (HRB) during 2010–2019. The results of the comparison with the site observations show that ETMonitor provides a more stable and reliable estimation of ET than the other three products. The ET exhibited significant variations over the decade, characterized by a general increase in rates across the HRB. These changes were markedly influenced by variations in land use and topographical features. Specifically, the analysis showed that farmland and forested areas had higher ET rates due to greater vegetation cover and moisture availability, while grasslands and water bodies demonstrated lower ET rates, reflecting their respective land cover characteristics. This study further explored the influence of various factors on ET, including land use changes, NDVI, temperature, and precipitation. It was found that changes in land use, such as increases in agricultural areas or reforestation efforts, directly influenced ET rates. Moreover, meteorological conditions such as temperature and precipitation patterns also played crucial roles, with warmer temperatures and higher precipitation correlating with increased ET. This study highlights the significant impact of land use and climatic factors on spatiotemporal variations in ET within the HRB, underscoring its importance for optimizing water resource management and land use planning in arid regions.

Circular RNA (circRNA) is one of non-coding RNA with specific circular structure, which has been found to be involved in regulating a series of malignant biological behaviors in many malignant tumors. In this study, based on the IDH1 molecular typing of gliomas, we identified a significant downregulation of circRNA (circIQGAP1) expression in IDH1 mutant gliomas by high-throughput sequencing. In 79 tissue samples, we confirmed that circIQGAP1 expression was significantly downregulated in IDH1 mutant gliomas, and that low circIQGAP1 expression was positively associated with better prognosis. Knockdown of circIQGAP1 in glioma cell lines inhibited glioma cell malignancy and conversely overexpression of circIQGAP1 promoted glioma malignancy. circIQGAP1 regulated glioma cell migration, proliferation, invasion and apoptosis through miR-1256/RCAN1/Bax/Bcl-2/Caspase3 and miR-622/RCAN2/Bax/Bcl-2/Caspase3 axes. These results suggest that circIQGAP1 plays an important role in glioma development, promotes tumor growth, and is a potential therapeutic target for glioma.

Abstract Chronic pain has attracted wide interest because it is a major obstacle affecting the quality of life. Consequently, safe, efficient, and low‐addictive drugs are highly desirable. Nanoparticles (NPs) with robust anti‐oxidative stress and anti‐inflammatory properties possess therapeutic possibilities for inflammatory pain. Herein, a bioactive zeolitic imidazolate framework (ZIF)‐8‐capped superoxide dismutase (SOD) and Fe3O4 NPs (SOD&Fe3O4@ZIF‐8, SFZ) is developed to achieve enhanced catalytic, antioxidative activities, and inflammatory environment selectivity, ultimately improving analgesic efficacy. SFZ NPs reduce tert‐butyl hydroperoxide (t‐BOOH)‐induced reactive oxygen species (ROS) overproduction, thereby depressing the oxidative stress and inhibiting the lipopolysaccharide (LPS)‐induced inflammatory response in microglia. After intrathecal injection, SFZ NPs efficiently accumulate at the lumbar enlargement of the spinal cord and significantly relieve complete Freund's adjuvant (CFA)‐induced inflammatory pain in mice. Moreover, the detailed mechanism of inflammatory pain therapy via SFZ NPs is further studied, where SFZ NPs inhibit the activation of the mitogen‐activated protein kinase (MAPK)/p‐65 signaling pathway, leading to reductions in phosphorylated protein levels (p‐65, p‐ERK, p‐JNK, and p‐p38) and inflammatory factors (tumor necrosis factor [TNF]‐α, interleukin [IL]‐6, and IL‐1β), thereby preventing microglia and astrocyte activation for acesodyne. This study provides a new cascade nanoenzyme for antioxidant treatments and explores its potential applications as non‐opioid analgesics.

Potential acute mountain sickness diagnostic, predictive, protective biomarkers are established using plasma proteomic, clinical and symptom phenotype data with machine learning approaches in a longitudinal cohort of 53 individuals.

Abstract Background Established prediction models of Diabetic kidney disease (DKD) are limited to the analysis of clinical research data or general population data and do not consider hospital visits. Construct a 3-year diabetic kidney disease risk prediction model in patients with type 2 diabetes mellitus (T2DM) using machine learning, based on electronic medical records (EMR). Methods Data from 816 patients (585 males) with T2DM and 3 years of follow-up at the PLA General Hospital. 46 medical characteristics that are readily available from EMR were used to develop prediction models based on seven machine learning algorithms (light gradient boosting machine [LightGBM], eXtreme gradient boosting, adaptive boosting, artificial neural network, decision tree, support vector machine, logistic regression). Model performance was evaluated using the area under the receiver operating characteristic curve (AUC). Shapley additive explanation (SHAP) was used to interpret the results of the best performing model. Results The LightGBM model had the highest AUC (0.815, 95% CI 0.747–0.882). Recursive feature elimination with random forest and SHAP plot based on LightGBM showed that older patients with T2DM with high homocysteine (Hcy), poor glycemic control, low serum albumin (ALB), low estimated glomerular filtration rate (eGFR), and high bicarbonate had an increased risk of developing DKD over the next 3 years. Conclusions This study constructed a 3-year DKD risk prediction model in patients with T2DM and normo-albuminuria using machine learning and EMR. The LightGBM model is a tool with potential to facilitate population management strategies for T2DM care in the EMR era.

Introduction: With the outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the interaction between the host and SARS-CoV-2 was widely studied. However, it is unclear whether and how SARS-CoV-2 infection affects lung microflora, which contribute to COVID-19 complications. Methods: Here, we analyzed the metatranscriptomic data of bronchoalveolar lavage fluid (BALF) of 19 COVID-19 patients and 23 healthy controls from 6 independent projects and detailed the active microbiota landscape in both healthy individuals and COVID-19 patients. Results: The infection of SARS-CoV-2 could deeply change the lung microbiota, evidenced by the α-diversity, β-diversity, and species composition analysis based on bacterial microbiota and virome. Pathogens (e.g., Klebsiella oxytoca causing pneumonia as well), immunomodulatory probiotics (e.g., lactic acid bacteria and Faecalibacterium prausnitzii, a butyrate producer), and Tobacco mosaic virus (TMV) were enriched in the COVID-19 group, suggesting a severe microbiota dysbiosis. The significant correlation between Rothia mucilaginosa, TMV, and SARS-CoV-2 revealed drastic inflammatory battles between the host, SARS-CoV-2, and other microbes in the lungs. Notably, TMV only existed in the COVID-19 group, while human respirovirus 3 (HRV 3) only existed in the healthy group. Our study provides insights into the active microbiota in the lungs of COVID-19 patients and would contribute to the understanding of the infection mechanism of SARS-CoV-2 and the treatment of the disease and complications. Conclusion: SARS-COV-2 infection deeply altered the lung microbiota of COVID-19 patients. The enrichment of several other pathogens, immunomodulatory probiotics (lactic acid or butyrate producers), and TMV in the COVID-19 group suggests a complex and active lung microbiota disorder.

At present, China is in an important stage of transition into a global sports power where “outstanding competitive sports talents” are required to play an important role. Therefore, it is of great theoretical and practical significance to conduct in-depth research on domestic “outstanding competitive sports talents” to promote the sustainable development of China's competitive sports and enhance its comprehensive strength. In this study, WCA refers to “world-class athletes,” indicating a group of talents who won medals in international sports events such as the Olympic Games during 2009–2019. In this regard, this study uses statistical and spatial analysis methods to reveal the spatial and temporal characteristics, evolutionary process, and migration mechanism of Chinese WCA. The conclusion shows that: In terms of temporal characteristics, the population numbers in general and among different genders are characterized by a “three peaks and two troughs” pattern. In contrast, the individual temporal pattern is characterized by an “inverted U″ and “inverted V″, with an average age of 23.18 years. In terms of space, a positive correlation is shown on the whole (Moran's I > 0), however, characteristics of geographical proximity and spatial heterogeneity are not prominent, illustrating the spatial form of random distribution with low aggregation which is primarily concentrated in the southeast of China and demonstrates a “northeast-southwest” trend. There are apparent differences between areas of origin and immigration areas: Liaoning and Shandong are the main areas of origin while destination areas are frequently located in the southeast and “People's Liberation Army of China” (PLA for short). Lastly, this paper discusses the causes and influences of the migration groups from three aspects: the migrating talents, the areas of origin and immigration areas, and Chinese sports, revealing the formation and influence mechanisms.

Abstract Congenital hypothyroidism (CH), a common neonatal endocrine disorder, can result in cognitive deficits if delay in diagnose and treatment. Dentate gyrus (DG) is the severely affected subregion of the hippocampus by the CH, where the dentate granule cells (DGCs) reside in. However, how CH impairs the cognitive function via affecting DGCs and the underlying mechanisms are not fully elucidated. In the present study, the CH model of rat pups was successfully established, and the aberrant dendrite growth of the DGCs and the impaired cognitive behaviors were observed in the offspring. Transcriptome analysis of hippocampal tissues following rat CH successfully identified that calcium/calmodulin-dependent protein kinase IV (CaMKIV) was the prominent regulator involved in mediating deficient growth of DGC dendrites. CaMKIV was shown to be dynamically regulated in the DG subregion of the rats following drug-induced CH. Interference of CaMKIV expression in the primary DGCs significantly reduced the spine density of dendrites, while addition of T3 to the primary DGCs isolated from CH pups could facilitate the spine growth of dendrites. Insights into relevant mechanisms revealed that CH-mediated CaMKIV deficiency resulted in the significant decrease of phosphorylated CREB in DGCs, in association with the abnormality of dendrites. Our results have provided a distinct cell type in hippocampus that is affected by CH, which would be beneficial for the treatment of CH-induced cognitive deficiency.

Abstract The novel coronavirus pneumonia (COVID-19) outbreak that emerged in late 2019 has posed a severe threat to human health and social and economic development, and thus has become a major public health crisis affecting the world. The spread of COVID-19 in population and regions is a typical geographical process, which is worth discussing from the geographical perspective. This paper focuses on Shandong province, which has a high incidence, though the first Chinese confirmed case was reported from Hubei province. Based on the data of reported confirmed cases and the detailed information of cases collected manually, we used text analysis, mathematical statistics and spatial analysis to reveal the demographic characteristics of confirmed cases and the spatio-temporal evolution process of the epidemic, and to explore the comprehensive mechanism of epidemic evolution and prevention and control. The results show that: (1) the incidence rate of COVID-19 in Shandong is 0.76/100,000. The majority of confirmed cases are old and middle-aged people who are infected by the intra-province diffusion, followed by young and middle-aged people who are infected outside the province. (2) Up to February 5, the number of daily confirmed cases shows a trend of “rapid increase before slowing down”, among which, the changes of age and gender are closely related to population migration, epidemic characteristics and intervention measures. (3) Affected by the regional economy and population, the spatial distribution of the confirmed cases is obviously unbalanced, with the cluster pattern of “high–low” and “low–high”. (4) The evolution of the migration pattern, affected by the geographical location of Wuhan and Chinese traditional culture, is dominated by “cross-provincial” and “intra-provincial” direct flow, and generally shows the trend of “southwest → northeast”. Finally, combined with the targeted countermeasures of “source-flow-sink”, the comprehensive mechanism of COVID-19 epidemic evolution and prevention and control in Shandong is revealed. External and internal prevention and control measures are also figured out.

Abstract Background Heart rhythm complexity, a measure of heart rate dynamics and a risk predictor in various clinical diseases, has not been systematically studied in patients with end-stage renal disease. The aim of this study is to investigate the heart rhythm complexity and its prognostic value for mortality in end-stage renal disease patients undergoing hemodialysis. Methods To assess heart rhythm complexity and conventional heart rate variability measures, 4-h continuous electrocardiography for a retrospective cohort of 202 ostensibly healthy control subjects and 51 hemodialysis patients with end-stage renal disease were analyzed. Heart rhythm complexity was quantified by the complexity index from the measurement of the multiscale entropy profile. Results During a follow-up of 13 months, 8 people died in the patient group. Values of either traditional heart rate variability measurements or complexity indices were found significantly lower in patients than those in healthy controls. In addition, the complexity indices (Area 1–5, Area 6–15 and Area 6–20) in the mortality group were significantly lower than those in the survival group, while there were no significant differences in traditional heart rate variability parameters between the two groups. In receiver operating characteristic curve analysis, Area 6–20 (AUC = 0.895, p

Scientific and moderate exercise is an effective remedy to boost the immune system and minimize the risk of infection in coronavirus disease 2019 (COVID-19) epidemic period. In this context, social media platforms play an essential role in communicating scientific fitness at home. Based on the integrated analysis of communication, physical geography, and health geography, this article takes short fitness-based videos on TikTok as the research object and comprehensively uses text analysis, mathematical statistics, and spatial analysis to reveal the characteristics of communication elements, fitness preferences, and the spatiotemporal evolution of these short videos, and to explore the communication mechanism and optimization path of short videos. The results show that: (1) the communication information focusing on “fighting against the epidemic and keeping fit at home” is made into short videos by female youth. Through the communication channels mainly composed of texts, pictures, and audio, the communication subjects carry out multilevel interactive communication with the communication objects; (2) fitness preferences are mainly composed of dances, unarmed fitness, and fitness with equipment; (3) from the perspective of time, taking February 20 as the node, the daily number of released short videos shows a trend of “increase before decrease”; from the perspective of space, the distribution is significantly unbalanced across provinces, and the direction is not apparent; and (4) this article explores the communication mechanism and targeted optimization countermeasures of short fitness-based videos on TikTok in China's COVID-19 epidemic period.

Digital microfluidic biochips (DMFBs) are increasingly important and are used for point-of-care, drug discovery, clinical diagnosis, immunoassays, etc. Pin-constrained DMFBs are an important part of digital microfluidic biochips, and they have gained increasing attention from researchers. However, many previous works have focused on the problem of electrode addressing and aimed to minimize the number of control pins in pin-constrained DMFBs. Although the number of control pins can be effectively redistributed through broadcast addressing technology, the chip reliability will be reduced if the signals are shared arbitrarily. Arbitrary signal sharing can lead to a large number of actuations for many idle electrodes, and as a result, a trapping charge or decreasing contact angle problem could occur for some electrodes, reducing the reliability of the chip. To address this problem, the appropriate electrode matching object should be carefully selected, and the influence of these factors on chip reliability should be fully considered. For this purpose, we aimed to fully consider electrode addressing and the reliability of the chip in improving the reliability of DMFBs. This paper proposed a pin addressing method based on a support vector machine (SVM) with the reliability constraint algorithm, which can fully consider the electrode addressing method and the reliability of the chip together. The proposed method achieved an average maximum number of electrode actuations that was 53.8% and 18.2% smaller than those of the baseline algorithm and the graph-based algorithm, respectively. The simulation experiment results showed that the proposed method can efficiently solve reliability problems during the DMFB design process.

The oncogenic fusion protein AML1-ETO has the ability of AML1 to interact with DNA but blocks AML1-dependent transcription. Here the authors report that histone lysine methyltransferase EZH1 interacts with AML1-ETO and methylates AML1-ETO at lysine 43, promoting AML1-ETO transcriptional repression in leukemia.

Oxygen metabolism is closely related to the intestinal homeostasis environment, and the occurrence of many intestinal diseases is as a result of the destruction of oxygen gradients. The hypobaric hypoxic environment of the plateau can cause dysfunction of the intestine for humans, such as inflammation. The compensatory response of the small intestine cells to the harsh environment definitely changes their gene expression. How the small intestine cells response the hypobaric hypoxic environment is still unclear. We studied the rat small intestine under hypobaric hypoxic conditions to explore the transcriptional changes in rats under acute/chronic hypobaric hypoxic conditions. We randomly divided rats into three groups: normal control group (S), acute hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 2 weeks (W2S) and chronic hypobaric hypoxia group, exposing to hypobaric hypoxic condition for 4 weeks (W4S). The RNA sequencing was performed on the small intestine tissues of the three groups of rats. The results of principal component analysis showed that the W4S and W2S groups were quite different from the control group. We identified a total of 636 differentially expressed genes, such as ATP binding cassette, Ace2 and Fabp. KEGG pathway analysis identified several metabolic and digestive pathways, such as PPAR signaling pathway, glycerolipid metabolism, fat metabolism, mineral absorption and vitamin metabolism. Cogena analysis found that up-regulation of digestive and metabolic functions began from the second week of high altitude exposure. Our study highlights the critical role of metabolic and digestive pathways of the intestine in response to the hypobaric hypoxic environment, provides new aspects for the molecular effects of hypobaric hypoxic environment on intestine, and raises further questions about between the lipid metabolism disorders and inflammation.

Abstract Acute myeloid leukemia (AML) is a malignant tumor of the immature myeloid hematopoietic cells in the bone marrow (BM). It is a highly heterogeneous disease, with rising morbidity and mortality in older patients. Although researches over the past decades have improved our understanding of AML, its pathogenesis has not yet been fully elucidated. Long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) are three noncoding RNA (ncRNA) molecules that regulate DNA transcription and translation. With the development of RNA-Seq technology, more and more ncRNAs that are closely related to AML leukemogenesis have been discovered. Numerous studies have found that these ncRNAs play an important role in leukemia cell proliferation, differentiation, and apoptosis. Some may potentially be used as prognostic biomarkers. In this systematic review, we briefly described the characteristics and molecular functions of three groups of ncRNAs, including lncRNAs, miRNAs, and circRNAs, and discussed their relationships with AML in detail.

Abstract Background Phase-rectified signal averaging (PRSA) was often applied to assess the cardiac vagal modulation. Despite its broad use, this method suffers from the confounding effects of anomalous variants of sinus rhythm. This study aimed to improve the original PRSA method in deceleration capacity (DC) quantification. Methods The refined deceleration capacity (DC ref ) was calculated by excluding from non-vagally mediated abnormal variants of sinus rhythms. Holter recordings from 202 healthy subjects and 51 patients with end-stage renal disease (ESRD) have been used for validity. The DC ref was compared to original DC (DC org ) by the area under receiver operating characteristic curve. Results Experimental results demonstrate that the original and refined DCs calculated from 24-h, 2-h, and 30-min Holter recordings are significantly lower in patients with ESRD than those in the healthy group. In receiver operating characteristic curve analysis, the DC ref provides better performance than the DC org in distinguishing between the patients with ESRD and healthy control subjects. Furthermore, the refined PRSA technique enhances the low frequency and attenuates high frequency components for spectral analysis in ESRD patients. Conclusions The DC ref appears to reduce the influence of non-vagally mediated abnormal variants of sinus rhythm and highlighting the pathological influence. DC ref , especially assessed from short-term electrocardiography recordings, may be complementary to existing autonomic function assessment, risk stratification, and efficacy prediction strategies.

R-wave singularity (RWS) measures the intermittence or discontinuousness of R waves. It has been broadly used in QRS (QRS complex of electrocardiogram) detection, electrocardiogram (ECG) beats classification, etc. In this article, we novelly developed RWS to the analysis of QRS morphology as the measurement of ventricular dyssynchrony and tested the hypothesis that RWS could enhance the discrimination between control and acute myocardial infarction (AMI) patients. Holter ECG recordings were obtained from the Telemetric and Holter ECG Warehouse database, among which database Normal was extracted as normal controls (n = 202) and database AMI (n = 93) as typical subjects of autonomic nervous system dysfunction and cardiac electrical dyssynchrony with high risk for cardiac arrhythmias and sudden cardiac death. Experimental results demonstrate that RWS measured by Lipschitz exponent calculated from 5-min Holter recordings was significantly less negative in early AMI and late AMI than that in Normal subjects for overall, elderly, and elderly male groups, which suggested the heterogeneous depolarization of the ventricular myocardium during AMI. Receiver operating characteristic curve analyses show that combined with heart rate variability parameters, Lipschitz exponent provides higher accuracy in distinguishing between the patients with AMI and healthy control subjects for overall, elderly, elderly male, and elderly female groups. In summary, our study demonstrates the significance of using RWS to probe the cardiac electrical dyssynchrony for AMI. Lipschitz exponent may be valuable and complementary for existing cardiac resynchronization therapy and autonomic nervous system assessment.

Attribute reduction is a critical topic in the field of rough set theory. Currently, to further enhance the stability of the derived reduct, various attribute selectors are designed based on the framework of ensemble selectors. Nevertheless, it must be pointed out that some limitations are concealed in these selectors: (1) rely heavily on the distribution of samples; (2) rely heavily on the optimal attribute. To generate the reduct with higher stability, a novel beam-influenced selector (BIS) is designed based on the strategies of random partition and beam. The scientific novelty of our selector can be divided into two aspects: (1) randomly partition samples without considering the distribution of samples; (2) beam-based selections of features can save the selector from the dependency of the optimal attribute. Comprehensive experiments using 16 UCI data sets show the following: (1) the stability of the derived reducts may be significantly enhanced by using our selector; (2) the reducts generated based on the proposed selector can provide competent performance in classification tasks.

BackgroundMatrix metallopeptidase 14 (MMP14) is an important gene in the regulation of T-cell function. However, the correlation between MMP14 expression, prognosis, and immune cell infiltration in diffuse large B-cell lymphoma (DLBCL) remains unclear.MethodsWe investigated the influence of MMP14 on clinical prognosis using data obtained from three Gene Expression Omnibus (GEO) database sets (GSE98588, GSE10846, and GSE4475). The expression of MMP14 was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA). The correlation between MMP14 and immune cell infiltration was investigated using the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and Tumor Immune Estimation Resource (TIMER) tools. In addition, the correlation between MMP14 expression and immune gene markers was analyzed by TIMER and GEPIA.ResultsMMP14 expression positively correlated with favorable progression-free survival (PFS; GSE98588, P = 0.02) and overall survival (OS; GSE98588, P = 0.003; GSE10846, P = 5.517e-05; and GSE4475, P = 9.85e-04). Moreover, MMP14 expression was higher in DLBCL tumors than in normal tissues. Regarding clinical characteristics, high MMP14 expression was found to be correlated with race. MMP14 expression was also correlated with immune cell infiltration and had a remarkable correlation with various immune marker sets. It was found that M0 macrophages were the immune cells most related to survival, decreasing with the increase in Ann Arbor clinical stage. The results especially showed that MMP14 was a prognostic biomarker and related to the macrophages M0.ConclusionThe results suggest that MMP14 is a novel prognostic molecular marker for DLBCL and is related to the immune cell infiltration, especially related to the macrophages M0. Our study provides insights for understanding the potential roles of MMP14 in tumor immunology and its suitability as a prognosis biomarker in DLBCL.

One of the key features of acute myeloid leukemia (AML), a group of very aggressive myeloid malignancies, is their strikingly heterogenous outcomes. Accurate biomarkers are needed to improve prognostic assessment. Glutamate oxaloacetate transaminase 1 (GOT1) is essential for cell proliferation and apoptosis by regulating cell's metabolic dependency on glucose. It is unclear whether the expression level of GOT1 has clinical implications in AML. Therefore, we analyzed the data of 155 AML patients with GOT1 expression information from The Cancer Genome Atlas (TCGA) database. Among them, 84 patients were treated with chemotherapy alone, while 71 received allogeneic hematopoietic stem cell transplantation (allo-HSCT). In both treatment groups, high GOT1 expression was associated with shorter event-free survival (EFS) and overall survival (OS) (all P < 0.05). Multivariate analysis identified several independent risk factors for both EFS and OS in the chemotherapy-only group, including high GOT1 expression, age ≥60 years, white blood cell count ≥15 × 109/L, bone marrow blasts ≥70%, and DNMT3A, RUNX1 or TP53 mutations (all P < 0.05); but in the allo-HSCT group, the only independent risk factor for survival was high GOT1 expression (P < 0.05 for both EFS and OS). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the genes related to GOT1 expression were mainly concentrated in “hematopoietic cell lineage” and “leukocyte transendothelial migration” signaling pathways. Collectively, GOT1 expression may be a useful prognostic indicator in AML, especially in patients who have undergone allo-HSCT.

The aim of the present study was to explore the expression profiles of lncRNAs and mRNAs in glioma patients and to elucidate any potential relationship between lncRNAs and mRNAs in glioma. High-throughput transcriptome sequencing of mRNAs and lncRNAs from six normal tissues and 16 glioma tissues (grade II, six cases; grade III, four cases; and grade IV, six cases) was performed. Series test of cluster (STC) analysis was used to screen significant trending models associated with glioma. Gene co-expression networks were constructed for the differentially expressed lncRNAs and mRNAs, and gene-ontology (GO) and pathway-enrichment analyses were further performed. Quantitative real-time PCR was performed to validate the five most differentially expressed lncRNAs and mRNAs. After filtering the raw sequencing data, we found 578 lncRNAs and 3,216 mRNAs that were significantly dysregulated in glioma (fold change ≥ 2, p < 0.05). Twenty model profiles of lncRNA and 10 model profiles of mRNA were summarized, and three patterns of lncRNAs and two patterns of mRNAs were of clinical significance. Three gene co-expression networks between mRNAs and lncRNAs were built to clarify the relationship between lncRNAs and mRNAs in glioma. GO and pathway analyses indicated that the differentially expressed lncRNAs and mRNAs were enriched in several biological processes and signaling pathways associated with tumorigenesis. Both lncRNAs and mRNAs exhibited dynamic differential expression profiles that indicated their potential roles in different degrees of glioma malignancy. A series of bioinformatics analyses indicated that most of these lncRNAs and mRNAs are involved in important biological processes and pathways associated with the pathogenesis of glioma. These results provide potential directions and valuable resources for future investigations via the comprehensive integration of these lncRNAs and mRNAs.

ABSTRACT The intestinal microbiota is significantly affected by the external environment, but our understanding of the effects of extreme environments such as plateaus is far from adequate. In this study, we systematically analyzed the variation in the intestinal microbiota and 76 blood clinical indexes among 393 healthy adults with different plateau living durations (Han individuals with no plateau living, with plateau living for 4 to 6 days, with plateau living for >3 months, and who returned to the plain for 3 months, as well as plateau-living Tibetans). The results showed that the high-altitude environment rapidly (4 days) and continually (more than 3 months) shaped both the intestinal microbiota and clinical indexes of the Han population. With prolongation of plateau living, the general characteristics of the intestinal microbiota and clinical indexes of the Han population were increasingly similar to those of the Tibetan population. The intestinal microbiota of the Han population that returned to the plain area for 3 months still resembled that of the plateau-living Han population rather than that of the Han population on the plain. Moreover, clinical indexes such as blood glucose were significantly lower in the plateau groups than in the nonplateau groups, while the opposite result was obtained for testosterone. Interestingly, there were Tibetan-specific correlations between glucose levels and Succinivibrio and Sarcina abundance in the intestine. The results of this study suggest that a hypoxic environment could rapidly and lastingly affect both the human intestinal microbiota and blood clinical indexes, providing new insights for the study of plateau adaptability. IMPORTANCE The data presented in the present study demonstrate that the hypoxic plateau environment has a profound impact on the gut microbiota and blood clinical indexes in Han and Tibetan individuals. The plateau-changed signatures of the gut microbiota and blood clinical indexes were not restored to the nonplateau status in the Han cohorts, even when the individuals returned to the plain from the plateau for several months. Our study will improve the understanding of the great impact of hypoxic environments on the gut microbiota and blood clinical indexes as well as the adaptation mechanism and intervention targets for plateau adaptation.

Background. Traditional invasive hemoglobin (Hb) detection led to delayed diagnosis, operational inefficiency, incorrect critical decision making, and uncomfortable patient experience. To facilitate real-time total hemoglobin (tHb) monitoring, a portable prototype of a noninvasive Hb detection system was developed, and the accuracy of Hb predicted based on partial least squares (PLS) as well as backpropagation artificial neural network (BP-ANN) models was validated. Results. The prototype was combined with a signal processing circuit and a spectrophotometric probe containing 8 wavelength LEDs light source and photodiode array. Laboratory invasive Hb (Lab_tHb) and spot check Hb measurements with PLS (SpHb_PLS) and BP (SpHb_BP) methods were obtained simultaneously by hematology analyzer and the designed system. The invasive and noninvasive estimates of the Hb levels were analyzed using Spearman correlation as well as Bland–Altman plot and receiver operating characteristic (ROC) curve analysis. A total of 238 volunteers had attempted laboratory invasive and noninvasive spot check Hb measurements. Mean Lab_tHb, SpHb_PLS, and SpHb_BP were 13.6 ± 1.80 g/dL, 13.5 ± 1.07 g/dL, and 13.6 ± 1.06 g/dL, respectively. Noninvasive SpHb_PLS (r = 0.61, p

Glioblastoma (GBM) is a complicated brain tumor with heterogeneous outcome. Identification of effective biomarkers is an urgent need for the treatment decision-making and precise evaluation of prognosis. Based on a relatively large dataset of genome-wide methylation (138 glioblastoma patients), a joint-score of 111 methyl-probes was found to be of statistical significance for prognostic evaluation. Low joint-score were significantly associated with adverse outcomes (OS: P < 0.001, PFS: P = 0.03). Multivariable analyses adjusted for known risk factors confirmed the low joint-score of 111 methyl-probes as a high risk factor. The prognostic value of the methylated joint-score was further validated in another dataset of glioblastoma patients (OS: P = 0.006). Additionally, variance analysis revealed that aberrant genetic and epigenetic alterations were significantly associated with the joint-score of those methyl-probes. In conclusion, our results supported the joint-score of 111 methyl-probes as a potential prognosticator for the precision treatment of glioblastoma.

Background/Aims: Acute myeloid leukemia (AML) of French-American-British (FAB) subtypes M0 and M1 are both poorly differentiated AML, but their mutational spectrum and molecular characteristics remain unknown. This study aimed to explore the mutational spectrum and prognostic factors of AML-M0 and M1. Methods: Sixty-five AML patients derived from The Cancer Genome Atlas (TCGA) database were enrolled in this study. Whole-genome sequencing was performed to depict the mutational spectrum of each patient. Clinical characteristics at diagnosis, including peripheral blood (PB) white blood cell counts (WBC), blast percentages in PB and bone marrow (BM), FAB subtypes and the frequencies of known recurrent genetic mutations were described. Survival was estimated using the Kaplan-Meier methods and log-rank test. Univariate and multivariate Cox proportional hazard models were constructed for event-free survival (EFS) and overall survival (OS), using a limited backward elimination procedure. Results: Forty-six patients had more than five recurrent genetic mutations. FLT3 had the highest mutation frequency (n=20, 31%), followed by NPM1 (n=18, 28%), DNMT3A (n=16, 25%), IDH1 (n=14, 22%), IDH2 (n=12, 18%), RUNX1 (n=11, 17%) and TET2 (n=7, 11%). Univariate analysis showed that age ≥60 years and TP53 mutations had adverse effect on EFS (P=0.015, P=0.036, respectively) and OS (P=0.003, P=0.004, respectively), WBC count ≥50×109/L and FLT3-ITD negatively affected EFS (P=0.003, P=0.034, respectively), whereas NPM1 mutations had favorable effect on OS (P=0.035) and allogeneic hematopoietic stem cell transplantation (allo-HSCT) on EFS and OS (all P< 0.001). Multivariate analysis suggested that allo-HSCT and NPM1 mutations were independent favorable prognostic factors for EFS and OS (all P< 0.05), WBC count ≥50×109/L was an independent risk factor for EFS (P=0.002) and TP53 mutations for OS (P=0.043). Conclusions: Our study provided new insights into the mutational spectrum and molecular signatures of AML-M0 and M1. We proposed that FLT3-ITD, NPM1 and TP53 be identified as markers for risk stratification of AML-M0 and M1. Patients with AML-M0 and M1 would likely benefit from allo-HSCT.

Abstract DNA methylation patterns are frequently deregulated in t(8;21) acute myeloid leukaemia (AML), but little is known of the mechanisms by which specific gene sets become aberrantly methylated. Here, we found that the promoter DNA methylation signature of t(8;21)+ AML blasts differs from that of t(8;21)− AMLs. This study demonstrated that a novel hypermethylated zinc finger‐containing protein, THAP10, is a target gene and can be epigenetically suppressed by AML1‐ETO at the transcriptional level in t(8;21) AML. Our findings also show that THAP10 is a bona fide target of miR‐383 that can be epigenetically activated by the AML1‐ETO recruiting co‐activator p300. In this study, we demonstrated that epigenetic suppression of THAP10 is the mechanistic link between AML1‐ETO fusion proteins and tyrosine kinase cascades. In addition, we showed that THAP10 is a nuclear protein that inhibits myeloid proliferation and promotes differentiation both in vitro and in vivo. Altogether, our results revealed an unexpected and important epigenetic mini‐circuit of AML1‐ETO/THAP10/miR‐383 in t(8;21) AML, in which epigenetic suppression of THAP10 predicts a poor clinical outcome and represents a novel therapeutic target.

Abstract Ischemic stroke and the following reperfusion, an acute therapeutic intervention, can cause irreversible brain damages. However, the underlying pathological mechanisms are still under investigation. To obtain a comprehensive, real-time view of the cell-autonomous mechanisms involved in ischemic stroke and reperfusion, we applied the next-generation sequencing (NGS) technology to characterize the temporal changes in gene expression profiles using primarily cultured hippocampal neurons under an oxygen-glucose deprivation/reperfusion (OGD/R) condition. We first identified the differentially expressed genes (DEGs) between normal cultured neurons, neurons with OGD, and neurons with OGD followed by reperfusion for 6 h, 12 h, and 18 h, respectively. We then performed bioinformatics analyses, including gene ontological (GO) and pathway analysis and co-expression network analysis to screen for novel key pathways and genes involved in the pathology of OGD/R. After we confirmed the changes of selected key genes in hippocampal cultures with OGD/R, we further validated their expression changes in an in vivo ischemic stroke model (MCAO). Finally, we demonstrated that prevention of the up-regulation of a key gene (Itga5) associated with OGD/R promoted hippocampal neuronal survival. Our research thereby provided novel insights into the molecular mechanisms in ischemic stroke pathophysiology and potential targets for therapeutic intervention after ischemic stroke.

Abstract Background ETS2 is a downstream effector of the RAS/RAF/ERK pathway, which plays a critical role in the development of malignant tumor. However, the clinical impact of ETS2 expression in AML remains unknown. Methods In this study, we evaluated the prognostic significance of ETS2 expression using two relatively large cohorts of AML patients. Results In the first cohort, compared to low expression of ETS2 (ETS2 low), high expression of ETS2 (ETS2 high) showed significant shorter OS, EFS and RFS in the current treatments including the allogeneic HCT group (n = 72) and the chemotherapy group (n = 100). Notably, among ETS2 high patients, those received allogeneic HCT had longer OS, EFS and RFS than those with chemotherapy alone (allogeneic HCT, n = 39 vs. chemotherapy, n = 47), but treatment modules play insignificant role in the survival of ETS2 low patients (allogeneic HCT, n = 33 vs. chemotherapy, n = 53). Moreover, gene/microRNA expression data provides insights into the biological changes associated with varying ETS2 expression levels in AML. The prognostic value of ETS2 was further validated in the second AML cohort (n = 329). Conclusions Our results indicate that ETS2 high is a poor prognostic factor in AML and may guide treatment decisions towards allogeneic HCT.

Fusobacterium nucleatum (F. nucleatum) is a crucial periodontal pathogen and human gingival fibroblasts (GFs) are the first line of defense against oral pathogens. However, the research on potential molecular mechanisms of host defense and effective treatment of F. nucleatum infection in GFs remains scarce. In this study, we undertook a time-series experiment and performed an RNA-seq analysis to explore gene expression profiles during the process of F. nucleatum infection in GFs. Differentially expressed genes (DEGs) could be divided into three coexpression clusters. Functional analysis revealed that the immune-related signaling pathways were more overrepresented at the early stage, while metabolic pathways were mainly enriched at the late stage. We computationally identified several U.S. Food and Drug Administration (FDA)-approved drugs that could protect the F. nucleatum infected GFs via a coexpression-based drug repositioning approach. Biologically, we confirmed that six drugs (etravirine, zalcitabine, wortmannin, calcium D-pantothenate, ellipticine, and tanespimycin) could significantly decrease F. nucleatum-induced reactive oxygen species (ROS) generation and block the Protein Kinase B (PKB/AKT)/mitogen-activated protein kinase signaling pathways. Our study provides more detailed molecular mechanisms of the process by which F. nucleatum infects GFs and illustrates the value of the cogena-based drug repositioning method and the potential therapeutic application of these tested drugs in the treatment of F. nucleatum infection.

Ascent to high altitude feels uncomfortable in part because of a decreased partial pressure of oxygen due to the decrease in barometric pressure. The molecular mechanisms causing injury in liver tissue after exposure to a hypoxic environment are widely unknown. The liver must physiologically and metabolically change to improve tolerance to altitude-induced hypoxia. Since the liver is the largest metabolic organ and regulates many physiological and metabolic processes, it plays an important part in high altitude adaptation. The cellular response to hypoxia results in changes in the gene expression profile. The present study explores these changes in a rat model. To comprehensively investigate the gene expression and physiological changes under hypobaric hypoxia, we used genome-wide transcription profiling. Little is known about the genome-wide transcriptional response to acute and chronic hypobaric hypoxia in the livers of rats. In this study, we carried out RNA-Sequencing (RNA-Seq) of liver tissue from rats in three groups, normal control rats (L), rats exposed to acute hypobaric hypoxia for 2 weeks (W2L) and rats chronically exposed to hypobaric hypoxia for 4 weeks (W4L), to explore the transcriptional profile of acute and chronic mountain sickness in a mammal under a controlled time-course. We identified 497 differentially expressed genes between the three groups. A principal component analysis revealed large differences between the acute and chronic hypobaric hypoxia groups compared with the control group. Several immune-related and metabolic pathways, such as cytokine-cytokine receptor interaction and galactose metabolism, were highly enriched in the KEGG pathway analysis. Similar results were found in the Gene Ontology analysis. Cogena analysis showed that the immune-related pathways were mainly upregulated and enriched in the acute hypobaric hypoxia group.

Attribute reduction is commonly referred to as the key topic in researching rough set. Concerning the strategies for searching reduct, though various heuristics based forward greedy searchings have been developed, most of them were designed for pursuing one and only one characteristic which is closely related to the performance of reduct. Nevertheless, it is frequently expected that a justifiable searching should explicitly involves three main characteristics: (1) the process of obtaining reduct with low time consumption; (2) generate reduct with high stability; (3) acquire reduct with competent classification ability. To fill such gap, a hybrid based searching mechanism is designed, which takes the above characteristics into account. Such a mechanism not only adopts multiple fitness functions to evaluate the candidate attributes, but also queries the distance between attributes for determining whether two or more attributes can be added into the reduct simultaneously. The former may be useful in deriving reduct with higher stability and competent classification ability, and the latter may contribute to the lower time consumption of deriving reduct. By comparing with 5 state-of-the-art algorithms for searching reduct, the experimental results over 20 UCI data sets demonstrate the effectiveness of our new mechanism. This study suggests a new trend of attribute reduction for achieving a balance among various characteristics.

Digital microfluidic biochips (DMFBs) are attractive instruments for obtaining modern molecular biology and chemical measurements. Due to the increasingly complex measurements carried out on a DMFB, such chips are more prone to failure. To compensate for the shortcomings of the module-based DMFB, this paper proposes a routing-based fault repair method. The routing-based synthesis methodology ensures a much higher chip utilization factor by removing the virtual modules on the chip, as well as removing the extra electrodes needed as guard cells. In this paper, the routing problem is identified as a dynamic path-planning problem and mixed path design problem under certain constraints, and an improved Dijkstra and improved particle swarm optimization (ID-IPSO) algorithm is proposed. By introducing a cost function into the Dijkstra algorithm, the path-planning problem under dynamic obstacles is solved, and the problem of mixed path design is solved by redefining the position and velocity vectors of the particle swarm optimization. The ID-IPSO routing-based fault repair method is applied to a multibody fluid detection experiment. The proposed design method has a stronger optimization ability than the greedy algorithm. The algorithm is applied to 8×9, 8×8, and 7×8 fault-free chips. The proposed ID-IPSO routing-based chip design method saves 13.9%, 14.3%, and 14.5% of the experiment completion time compared with the greedy algorithm. Compared with a modular fault repair method based on the genetic algorithm, the ID-IPSO routing-based fault repair method has greater advantages and can save 39.3% of the completion time on average in the completion of complex experiments. When the ratio of faulty electrodes is less than 12% and 23%, the modular and ID-IPSO routing-based fault repair methods, respectively, can guarantee a 100% failure repair rate. The utilization rate of the electrodes is 18% higher than that of the modular method, and the average electrode usage time is 17%. Therefore, the ID-IPSO routing-based fault repair method can accommodate more faulty electrodes for the same fault repair rate; the experiment completion time is shorter, the average number of electrodes is lower, and the security performance is better.

PURPOSE: It is generally accepted that inflammation has a role in the progression of many central nervous system (CNS) diseases, although the mechanisms through which this occurs remain unclear. Among mitogen-activated protein kinase (MAPK) targets, mitogen- and stress-activated protein kinase (MSK1) has been thought to be involved in the pathology of inflammatory gene expression. In this study, the roles of MSK1 activation in neuroinflammation were investigated. METHODS: The bacterial lipopolysaccharide (LPS)-induced brain injury model was performed on Sprague-Dawley rats. The dynamic expression changes and the cellular location of p-MSK1 in the brain cortex were detected by Western blot and immunofluorescence staining. The synthesis of inflammatory cytokines in astrocytes was detected by enzyme-linked immunosorbent assay (ELISA). RESULTS: Phosphorylated MSK1 (p-MSK1 Thr-581) was induced significantly after intracerebral injection of LPS into the lateral ventricles of the rat brain. Specific upregulation of p-MSK1 in astrocytes was also observed in inflamed cerebral cortex. At 1 day after LPS stimulation, iNOS, TNFα expression, and the astrocyte marker glial fibrillary acidic protein (GFAP) were increased significantly. Also, in vitro studies indicated that the upregulation of p-MSK1 (Thr-581) may be involved in the subsequent astrocyte inflammatory process, following LPS challenge. Using an enzyme-linked immunosorbent assay (ELISA), it was confirmed that treatment with LPS in primary astrocytes stimulated the synthesis of inflammatory cytokines, through MAPKs signaling pathways. In cultured primary astrocytes, both knock-down of total MSK1 by small interfering RNAs (siRNA) or specific mutation of Thr-581 resulted in higher production of certain cytokines, such as TNFα and IL-6. CONCLUSIONS: Collectively, these results suggest that MSK1 phosphorylation is associated with the regulation of LPS-induced brain injury and possibly acts as a negative regulator of inflammation.

Moment invariants have been extensively studied and widely used in object recognition. The pioneering investigation of moment invariants in pattern recognition was due to Hu, where a set of moment invariants for similarity transformation were developed using the theory of algebraic invariants. This paper details a comparative analysis on several modifications of the original Hu moment invariants which are used to describe and retrieve two-dimensional (2D) shapes with a single closed contour. The main contribution of this paper is that we propose several different weighting functions to calculate the central moment according to human visual processing. The comparative results are detailed through experimental analysis. The results suggest that the moment invariants improved by weighting functions can get a better retrieval performance than the original one does.