Bayesian Robust Tensor Factorization for Incomplete Multiway Data

We propose a generative model for robust tensor factorization in the presence of both missing data and outliers. The objective is to explicitly infer the underlying low-CP-rank tensor capturing the global information and a sparse tensor capturing the local information (also considered as outliers), thus providing the robust predictive distribution over missing entries. The low-CP-rank tensor is modeled by multilinear interactions between multiple latent factors on which the column sparsity is enforced by a hierarchical prior, while the sparse tensor is modeled by a hierarchical view of Student-$t$ distribution that associates an individual hyperparameter with each element independently. For model learning, we develop an efficient closed-form variational inference under a fully Bayesian treatment, which can effectively prevent the overfitting problem and scales linearly with data size. In contrast to existing related works, our method can perform model selection automatically and implicitly without need of tuning parameters. More specifically, it can discover the groundtruth of CP rank and automatically adapt the sparsity inducing priors to various types of outliers. In addition, the tradeoff between the low-rank approximation and the sparse representation can be optimized in the sense of maximum model evidence. The extensive experiments and comparisons with many state-of-the-art algorithms on both synthetic and real-world datasets demonstrate the superiorities of our method from several perspectives.Comment: in IEEE Transactions on Neural Networks and Learning Systems, 201

A fast and highly sensitive blood culture PCR method for clinical detection of Salmonella enterica serovar Typhi

<p>Abstract</p> <p>Background</p> <p><it>Salmonella </it>Typhi causes an estimated 21 million new cases of typhoid fever and 216,000 deaths every year. Blood culture is currently the gold standard for diagnosis of typhoid fever, but it is time-consuming and takes several days for isolation and identification of causative organisms. It is then too late to initiate proper antibiotic therapy. Serological tests have very low sensitivity and specificity, and no practical value in endemic areas. As early diagnosis of the disease and prompt treatment are essential for optimal management, especially in children, a rapid sensitive detection method for typhoid fever is urgently needed. Although PCR is sensitive and rapid, initial research indicated similar sensitivity to blood culture and lower specificity. We developed a fast and highly sensitive blood culture PCR method for detection of <it>Salmonella </it>Typhi, allowing same-day initiation of treatment after accurate diagnosis of typhoid.</p> <p>Methods</p> <p>An ox bile tryptone soy broth was optimized for blood culture, which allows the complete lysis of blood cells to release intracellular bacteria without inhibiting the growth of <it>Salmonella </it>Typhi. Using the optimised broth <it>Salmonella </it>Typhi bacteria in artificial blood samples were enriched in blood culture and then detected by a PCR targeting the <it>fliC-d </it>gene of <it>Salmonella </it>Typhi.</p> <p>Results</p> <p>Tests demonstrated that 2.4% ox bile in blood culture not only lyzes blood cells completely within 1.5 hours so that the intracellular bacteria could be released, but also has no inhibiting effect on the growth of <it>Salmonella </it>Typhi.</p> <p>Three hour enrichment of <it>Salmonella </it>Typhi in tryptone soya broth containing 2.4% ox bile could increase the bacterial number from 0.75 CFU per millilitre of blood which is similar to clinical typhoid samples to the level which regular PCR can detect. The whole blood culture PCR assay takes less than 8 hours to complete rather than several days for conventional blood culture.</p> <p>Conclusions</p> <p>This novel blood culture PCR method is superior in speed and sensitivity to both conventional blood culture and PCR assays. Its use in clinical diagnosis may allow early detection of the causative organism and facilitate initiation of prompt treatment among patients with typhoid fever.</p

Effects of lncRNA PKD2-2-3 on cell proliferation, clone formation, migration, and invasion of lung adenocarcinoma

Background and purpose: Long non-coding RNA (lncRNA) is abnormally expressed in lung adenocarcinoma patients, and closely related to tumor occurrence, development and chemotherapy resistance. In this study, we mainly investigated the biological function of lncRNA PKD2-2-3 and verified its effect on the proliferation, colony formation, migration and invasion in lung adenocarcinoma. Methods: Three pairs of lung adenocarcinoma tissues and adjacent tissues were analyzed based on expression profiling Affymetrix® GeneChip Human Transcriptome Array 2.0 (HTA2.0), and we focused on lncRNA PKD2-2-3 that showed most significant difference between lung adenocarcinoma issues and adjacent tissues. Besides, we found the upregulated expression of lncRNA PKD2-2-3 in lung adenocarcinoma tissues and suggested the relation of lncRNA PKD2-2-3 expression with prognosis by using GSE19188 and GSE30219 data in Gene Expression Omnibus (GEO) database. Real-time fluorescence quantitative polymerase chain reaction (RTFQ-PCR) was used to detect the expression of lncRNA PKD2-2-3 in cell lines including HBE, A549 and PC9. After using siRNAs to decrease the expression of lncRNA PKD2-2-3 in A549 and PC9, we detected cell proliferation and colony formation by cell counting kit-8 (CCK-8) assay and colony formation assay. Effects of lncRNA PKD2-2-3 on migration and invasion in lung adenocarcinoma cells were detected by wound-healing assay and transwell assay, respectively. Moreover, we detected expression levels of E-cadherin and N-cadherin that were epithelial-mesenchymal transition (EMT) related genes by Western blot. The effect of lncRNA PKD2-2-3 on the formation and growth of lung adenocarcinoma in vivo was verified by subcutaneous transplantation tumor model. Results: LncRNA PKD2-2-3 was highly expressed in lung adenocarcinoma tissue, and was positively associated with poor prognosis of lung adenocarcinoma patients. Compared with human bronchial epithelial cells (HBE), lncRNA PKD2-2-3 was overexpressed in A549 and PC9. The proliferation, colony formation, migration and invasion of lung adenocarcinoma cells were significantly inhibited when decreasing the expression level of lncRNA PKD2-2-3. Western blot also showed that the expression level of E-cadherin was increased, while the level of N-cadherin was decreased after lncRNA PKD2-2-3 knockdown. Subcutaneous tumor transplantation experiments showed that lncRNA PKD2-2-3 knockdown inhibited the growth of lung adenocarcinoma in vivo. Conclusion: LncRNA PKD2-2-3 expression was upregulated in lung adenocarcinoma tissues, and it was associated with poor prognosis of lung adenocarcinoma patients. Overexpression of lncRNA PKD2-2-3 promoted the proliferation, colony formation, migration and invasion of lung adenocarcinoma cells. LncRNA PKD2-2-3 level was closely related to EMT process in lung adenocarcinoma in vitro and in vivo

The influence of employees' perception of over-qualification on career compromise: Mediated by role conflict and sense of relative deprivation

In the external environment with the increasing level of education, there is a general phenomenon of excess qualification in the employment market. This research discusses employee career compromise from the perspective of employee over-qualification based on resource conservation theory and self-regulation theory. Combined with the survey data, a structural equation model (SEM) is constructed, and the mediation effect of relative deprivation and role conflict is analyzed according to the causal mediation model. The research find that employees' perception of over-qualification has three ways to affect employees' career compromise. First, employees' perception of over-qualification has a significant positive impact on their career compromise behavior through employees' emotions and self-cognition. Second, role conflict plays a partial intermediary role between the perception of over-qualification and career compromise by positively affecting career compromise behavior. Third, the sense of relative deprivation plays a partial intermediary role between the perception of over-qualification and career compromise by negatively affecting career compromise behavior. According to the research conclusions, the following suggestions are put forward. Enterprises need to establish a scientific employment mechanism to achieve talent-post matching and fundamentally reduce the phenomenon of over-qualifications. The company should pay attention to employee training, actively guide employees' career planning, instruct employees to correctly understand the sense of over-qualification and play a positive role in guiding employees' career planning

Structure, morphology and magnetic properties of flowerlike gamma-Fe2O3@NiO core/shell nanocomposites synthesized from different precursor concentrations

The flowerlike gamma-Fe2O3@NiO core/shell nanocomposites are synthesized by the two-step method. Their structure and morphology can be controlled by tuning the precursor concentration. Microstructural analysis reveals that all the samples have distinct core/shell structure without impurities, and the NiO shells are built of many irregular nanosheets which enclose the surface of gamma-Fe2O3 core. As the precursor concentration decreases (i.e., more NiO content), the NiO grain grows significantly, and the thickness of NiO shells increases. Magnetic experiments are performed to analyze the influences of different microstructures on magnetic properties of samples and we have the following two results. First, at 5 K, along with increasing thickness of NiO shell, the saturation magnetization increases, while the residual magnetization decreases slightly. Second, the hysteresis loops under cooling field demonstrate that the value of exchange bias effect fluctuates between 13 Oe and 17 Oe. This is mainly because of the NiO shell that (i) is composed of irregular nanosheets with disordered orientations, and (ii) does not form a complete coating around gamma-Fe2O3 core

Transcriptome analysis reveals the molecular basis of the response to acute hypoxic stress in blood clam Scapharca broughtonii

Hypoxia tolerance and adaptive regulation are important for aquatic animals, especially for species with poor mobility, such as most bivalves. Previous studies have confirmed that the blood clam Scapharca broughtonii has strong hypoxia resistance. However, the molecular mechanism supporting its hypoxic tolerance is still largely limited. To further screen the genes and their potential regulation of hypoxia tolerance, the transcriptome changes of S. broughtonii after acute hypoxic stress were explored by RNA sequencing. In this study, the average value of Q30 is 92.89%, indicating that the quality of sequencing is relatively high. The Unigenes obtained were annotated using four databases, namely Interpo, KEGG, Swisspro and TrEMBL. The annotation rates in these four databases were 71.82%, 75.95%, 92.98%, and 79.26%, respectively. And also, there were 649 DEGs in group B (dissolved oxygen (DO) of 2.5 mg/L) compared with group D (DO of 7.5 mg/L), among which 252 were up-regulated, and 397 were down-regulated. There were 965 DEGs in group A (DO of 0.5 mg/L), 2.5 mg/L, and 7.5 mg/L, compared with group B, among which 530 were up-regulated, and 435 were down-regulated. Meanwhile, there were 2,040 DEGs in group A compared with group D, among which 901 were up-regulated, and 1,139 were down-regulated. The main metabolic-related pathways of KEGG enriched in this study included Insulin secretion, Insulin signaling pathway, MAPK signal transduction pathway, and PPAR signaling pathway. These pathways may be critical metabolic pathways to solve energy demand and rebuild energy balance in S. broughtonii under hypoxic conditions. This study preliminarily clarified the response of S. broughtonii to hypoxia stress on the molecular levels, providing a reference for the following study on the response laws of related genes and pathways under environmental stress of S. broughtonii

A radiomics nomogram for predicting cytokeratin 19–positive hepatocellular carcinoma: a two-center study

ObjectivesWe aimed to construct and validate a radiomics-based nomogram model derived from gadoxetic acid–enhanced magnetic resonance (MR) images to predict cytokeratin (CK) 19–positive (+) hepatocellular carcinoma (HCC) and patients’ prognosis.MethodsA two-center and time-independent cohort of 311 patients were retrospectively enrolled (training cohort, n = 168; internal validation cohort, n = 72; external validation cohort, n = 71). A total of 2286 radiomic features were extracted from multisequence MR images with the uAI Research Portal (uRP), and a radiomic feature model was established. A combined model was established by incorporating the clinic-radiological features and the fusion radiomics signature using logistic regression analysis. Receiver operating characteristic curve (ROC) was used to evaluate the predictive efficacy of these models. Kaplan–Meier survival analysis was used to assess 1-year and 2-year progression-free survival (PFS) and overall survival (OS) in the cohort.ResultsBy combining radiomic features extracted in DWI phase, arterial phase, venous and delay phase, the fusion radiomics signature achieved AUCs of 0.865, 0.824, and 0.781 in the training, internal, and external validation cohorts. The final combined clinic-radiological model showed higher AUC values in the three datasets compared with the fusion radiomics model. The nomogram based on the combined model showed satisfactory prediction performance in the training (C-index, 0.914), internal (C-index, 0.855), and external validation (C-index, 0.795) cohort. The 1-year and 2-year PFS and OS of the patients in the CK19+ group were 76% and 73%, and 78% and 68%, respectively. The 1-year and 2-year PFS and OS of the patients in the CK19-negative (−) group were 81% and 77%, and 80% and 74%, respectively. Kaplan–Meier survival analysis showed no significant differences in 1-year PFS and OS between the groups (P = 0.273 and 0.290), but it did show differences in 2-year PFS and OS between the groups (P = 0.032 and 0.040). Both PFS and OS were lower in CK19+ patients.ConclusionThe combined model based on clinic-radiological radiomics features can be used for predicting CK19+ HCC noninvasively to assist in the development of personalized treatment