TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants

Genome-wide association studies have shown that common genetic variants associated with complex diseases are mostly located in non-coding regions, which may not be causal. In addition, the limited number of validated non-coding functional variants makes it difficult to develop an effective supervised learning model. Therefore, improving the accuracy of predicting non-coding causal variants has become critical. This study aims to build a transfer learning-based machine learning method for predicting regulatory variants to overcome the problem of limited sample size. This paper presents a supervised learning method transfer support vector machine (TSVM) for massively parallel reporter assays (MPRA) validated regulatory variants prediction. First, uses a convolutional neural network to extract features with transfer learning. Second, the extracted features are selected by random forest method. Third, the selected features are used to train support vector machine for classification. We performed scale sensitivity experiments on the MPRA dataset and validated the effectiveness of transfer learning. The model achieves the Mcc of 0.326 and the AUC of 0.720, which are higher than the state-of-the-art method. The source code of our proposed TSVM can be found in https://github.com/biomg/TSVM.

WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites

RNA-binding proteins are important for the process of cell life activities. High-throughput technique experimental method to discover RNA-protein binding sites is time-consuming and expensive. Deep learning is an effective theory for predicting RNA-protein binding sites. Using weighted voting method to integrate multiple basic classifier models can improve model performance. Thus, in our study, we propose a weighted voting deep learning model (WVDL), which uses weighted voting method to combine convolutional neural network (CNN), long short term memory network (LSTM) and residual network (ResNet). First, the final forecast result of WVDL outperforms the basic classifier models and other ensemble strategies. Second, WVDL can extract more effective features by using weighted voting to find the best weighted combination. And, the CNN model also can draw the predicted motif pictures. Third, WVDL gets a competitive experiment result on public RBP-24 datasets comparing with other state-of-the-art methods. The source code of our proposed WVDL can be found in https://github.com/biomg/WVDL.

CRMSNet: a deep learning model that uses convolution and residual multi-head self-attention block to predict RBPs for RNA sequence

RNA-binding proteins (RBPs) play significant roles in many biological life activities, many algorithms and tools are proposed to predict RBPs for researching biological mechanisms of RNA-protein binding sites. Deep learning algorithms based on traditional machine learning get better result for predicting RBPs. Recently, deep learning method fused with attention mechanism has attracted huge attention in many fields and gets competitive result. Thus, attention mechanism module may also improve model performance for predicting RNA-protein binding sites. In this study, we propose convolutional residual multi-head self-attention network (CRMSNet) that combines CNN, ResNet and multi-head self-attention blocks to find RBPs for RNA sequence. First, CRMSNet incorporates convolutional neural networks, recurrent neural networks and multi-head self-attention block. Second, CRMSNet can draw binding motif pictures from the convolutional layer parameters. Third, attention mechanism module combines the local and global RNA sequence information for capturing long sequence feature. CRMSNet gets competitive AUC (area under the ROC curve) result in a large-scale dataset RBP-24. And CRMSNet experiment result is also compared with other state-of-the-art methods. The source code of our proposed CRMSNet method can be found in https://github.com/biomg/CRMSNet. This article is protected by copyright. All rights reserved.

MCNN: Multiple Convolutional Neural Networks for RNA-Protein Binding Sites Prediction

Computational prediction of the RBP bound sites using features learned from existing annotation knowledge is an effective method because high-throughput experiments are complex, expensive and time-consuming. Many methods have been proposed to predict RNA-protein binding sites. However, the partial information of RNA sequence is not fully used. In this study, we propose multiple convolutional neural networks (MCNN) method, which predicts RNA-protein binding sites by integrating multiple convolutional neural networks constructed by RNA sequence information extracted from windows with different lengths. First, MCNN trains multiple CNNs base on RNA sequences extracted by different window lengths. Second, MCNN can extract more binding patterns of RBPs by combining these trained multiple CNNs previously. Third, MCNN only uses RNA base sequence information for RNA-protein binding sites prediction, which extracts sequence binding features and predicts the result with same architecture. This avoids the information loss of feature extraction step. Our proposed MCNN demonstrates a competitive performance comparing with other methods on a large-scale dataset derived from CLIP-seq, which is an effective method for RNA-protein binding sites prediction. The source code of our proposed MCNN method can be found in https://github.com/biomg/MCNN.

Microtubule integrity regulates Pak leading to Ras-independent activation of Raf-1. insights into mechanisms of Raf-1 activation

Growth factors activate Raf-1 by engaging a complex program, which requires Ras binding, membrane recruitment, and phosphorylation of Raf-1. The present study employs the microtubule-depolymerizing drug nocodazole as an alternative approach to explore the mechanisms of Raf activation. Incubation of cells with nocodazole leads to activation of Pak1/2, kinases downstream of small GTPases Rac/Cdc42, which have been previously indicated to phosphorylate Raf-1 Ser(338). Nocodazole-induced stimulation of Raf-1 is augmented by co-expression of small GTPases Rac/Cdc42 and Pak1/2. Dominant negative mutants of these proteins block activation of Raf-1 by nocodazole, but not by epidermal growth factor (EGF). Thus, our studies define Rac/Cdc42/Pak as a module upstream of Raf-1 during its activation by microtubule disruption. Although it is Ras-independent, nocodazole-induced activation of Raf-1 appears to involve the amino-terminal regulatory region in which the integrity of the Ras binding domain is required. Surprisingly, the Raf zinc finger mutation (C165S/C168S) causes a robust activation of Raf-1 by nocodazole, whereas it diminishes Ras-dependent activation of Raf-1. We also show that mutation of residues Ser(338) to Ala or Tyr(340)-Tyr(341) to Phe-Phe immediately amino-terminal to the catalytic domain abrogates activation of both the wild type and zinc finger mutant Raf by both EGF/4beta-12-O-tetradecanoylphorbol-13-acetate and nocodazole. Finally, an in vitro kinase assay demonstrates that the zinc finger mutant serves as a better substrate of Pak1 than the wild type Raf-1. Collectively, our results indicate that 1) the zinc finger exerts an inhibitory effect on Raf-1 activation, probably by preventing phosphorylation of (338)SSYY(341); 2) such inhibition is first overcome by an unknown factor binding in place of Ras-GTP to the amino-terminal regulatory region in response to nocodazole; and 3) EGF and nocodazole utilize different kinases to phosphorylate Ser(338), an event crucial for Raf activation.

Biomarker risk assessment and bladder cancer detection in a cohort exposed to benzidine

BACKGROUND

Cancer screening with highly sensitive, specific biomarkers that reflect molecular phenotypic alterations is an attractive strategy for cancer control. We examined whether biomarker profiles could be used for risk assessment and cancer detection in a cohort of Chinese workers occupationally exposed to benzidine and at risk for bladder cancer.

METHODS

The cohort consisted of 1788 exposed and 373 nonexposed workers, followed from 1991 through 1997. We assayed urothelial cells from voided urine samples for DNA ploidy (expressed as the 5C-exceeding rate [DNA 5CER]), the bladder tumor-associated antigen p300, and a cytoskeletal protein (G-actin). Workers were stratified into different risk groups (high, moderate, and low risk) at each examination based on a predefined biomarker profile. For workers who developed bladder cancer, tumor risk assessment was analyzed from samples collected 6-12 months before the cancer diagnosis. The associations between risk group and subsequent development of bladder cancer were analyzed by Cox proportional hazards regression analysis and logistic analysis, after adjustment. All statistical tests were two-sided.

RESULTS

Twenty-eight bladder cancers were diagnosed in exposed workers and two in nonexposed workers. For risk assessment, DNA 5CER had 87.5% sensitivity, 86.5% specificity, an odds ratio (OR) of 46.2 (95% confidence interval [CI] = 8.1 to 867.0), and a risk ratio (RR) of 16.2 (95% CI = 7.1 to 37.0); p300 had 50.0% sensitivity, 97.9% specificity, an OR of 40.0 (95% CI = 9.0 to 177.8), and an RR of 37.9 (95% CI = 16.8 to 85.3). The risk of developing bladder cancer was 19.6 (95% CI = 8.0 to 47.9) times higher in workers positive for either the DNA 5CER or p300 biomarkers than in workers negative for both biomarkers and 81.4 (95% CI = 33.3 to 199.3) times higher in workers positive for both biomarkers. G-actin was a poor marker of individual risk.

CONCLUSIONS

Occupationally exposed workers at risk for bladder cancer can be individually stratified, screened, monitored, and diagnosed based on predefined molecular biomarker profiles.

Identification of two pairs of spatially approximated residues within the carboxyl terminus of secretin and its receptor

The carboxyl-terminal domains of secretin family peptides have been shown to contain key determinants for high affinity binding to their receptors. In this work, we have examined the interaction between carboxyl-terminal residues within secretin and the prototypic secretin receptor. We previously utilized photoaffinity labeling to demonstrate spatial approximation between secretin residue 22 and the receptor domain that includes the first 30 residues of the amino terminus (Dong, M., Wang, Y., Pinon, D. I., Hadac, E. M., and Miller, L. J. (1999) J. Biol. Chem. 274, 903-909). Here, we further refined the site of labeling with the p-benzoyl-phenylalanine (Bpa(22)) probe to receptor residue Leu(17) using progressive cleavage of wild type and mutant secretin receptors (V13M and V16M) and sequence analysis. We also developed a new probe incorporating a photolabile Bpa at position 26 of secretin, closer to its carboxyl terminus. This analogue was also a potent agonist (EC(50) = 72 +/- 6 pm) and bound to the secretin receptor specifically and with high affinity (K(i) = 10.3 +/- 2.4 nm). It covalently labeled the secretin receptor at a single site saturably and specifically. This was localized to the segment between residues Gly(34) and Ala(41) using chemical and enzymatic cleavage of labeled wild type and A41M mutant receptor constructs and immunoprecipitation of epitope-tagged receptor fragments. Radiochemical sequencing identified the site of covalent attachment as residue Leu(36). These new insights, along with our recent report of contact between residue 6 within the amino-terminal half of secretin and this same amino-terminal region of this receptor (Dong, M., Wang, Y., Hadac, E. M., Pinon, D. I., Holicky, E. L., and Miller, L. J. (1999) J. Biol. Chem. 274, 19161-19167), support a key role for this region, making the molecular details of this interaction of major interest.

[Clinical analysis of glucose dysbolism in 162 cases with Cushing syndrome]

OBJECTIVE

To understand the characteristic of steroid diabetes by the analysis for clinical data of 162 cases with Cushing syndrome (CS) proved by pathological report.

METHODS

Retrospective analysis for the data of CS about age of CS onset, duration of CS, body mass index (BMI), 24 hours urine free cortisol (24 h UFC), pathological report, fasting blood glucose (FBG) pre- and post-operation, family history of diabetes, treatment of glucose dysbolism (GD) pre- and post-operation.

RESULTS

The onset age and duration of CS in GD group was obviously earlier and longer than normal glucose (NG) group. BMI and 24 h UFC were no difference between two groups. Besides adrenal adenocarcinoma, no difference was found in types of pathology. FBG of diabetes pre-operation was obviously lower than post-operation. After operation, most diabetes need not on drug treatment. Only one secondary diabetes has family history.

CONCLUSIONS

Steroid diabetes easily occurs in patients who is senility and suffer longer course of CS. No relation to diabetic family history, concentric obesity, the level of UFC and benign types of pathology. Therapeutical emphasis of steroid diabetes is radical cure of CS.

[Mechanisms of opioid receptor-induced elevation in intracellular calcium by confocal laser scanning microscopy]

OBJECTIVE

To determine the acute and chronic effects of opioid receptor agonists on the intracellular free calcium concentration ([Ca2+]i) in NG-LNCXiNOS cells, stably expressing iNOS gene, and regulation of G-protein on opioid-induced response in [Ca2+]i.

METHODS

A single cell [Ca2+]i is measured by confocal laser scanning microscopy using Ca(2+)-sensitive dye Fluo-3 as an new calcium fluorescent probe.

RESULTS

DPDPE(D-Pen2, D-Pen5-enkephalin), a delta-opioid receptor agonist, and morphine acutely induced the increase in [Ca2+]i of NG-LNCXiNOS cells. The elevation in [Ca2+]i by DPDPE could be abolished with naloxone. Pretreatment of the cells with pertussis toxin (PTX) at 100 ng/ml for 24 hours almost completely blocked morphine-evoked response. In contrast to acute effect of opioid agonists on [Ca2+]i, the cells exposed to 1 mumol/L DPDPE or 10 mumol/L morphine for 48 hours also appeared to raise [Ca2+]i. However, the elevation in [Ca2+]i was not greater than that caused by acute effect of DPDPE or morphine. After cell "withdrawal" was precipitated by the addition of 10 mumol/L naloxone, the increase in [Ca2+]i could further be intensified.

CONCLUSIONS

The opioid agonist-induced increase in [Ca2+]i is mediated by opioid receptor and regulated though PTX-sensitive G-protein. The attenuation of this response in chronically treated cells with opioid agonist is associated with receptor desensitization.

[Prevention and treatment of bladder tumors recurrence with furtulon]

OBJECTIVE

To inquire into the value of oral furtulon therapy for bladder tumors.

METHODS

103 patients were randomized into four groups and have been undergoing a long term follow-ups.

RESULTS

Recurrent rate of oral furtulon therapy for bladder tumors (8.8%) and instillation of mitomycin C for preventing the recurrence of bladder tumors (12.5%) as compared to recurrent rate of control group(40%), which was statistically significant(P < 0.01). Overall, 4 patients (33.3%) had an effective response with furtulon.

CONCLUSIONS

Furtulon has more effective for treatment and prophylaxis of bladder tumors.

[Effect of nitric oxide synthase inhibitor on signal transduction pathway of opiate tolerance and dependence in NG108-15 cells expressing iNOS gene]

OBJECTIVE

To investigate the role of adenylate cyclase (AC)-cAMP system and Ca2+ system and NO-cGMP signal system and the effects of a NOS inhibitor, NG-nitro-L-arginine (L-NNA) in the neuronal mechanisms of opioid tolerance and dependence.

METHODS

The experiments were performed in five groups: control group; opioid agonist group; opioid agonist + nalonoxe group; L-NNA + opioid agonist group and L-NNA + opioid agonist + nalonoxe group. The intracellular cAMP and cGMP levels were measured by 3H-cAMP protein binding assay and 3H-cGMP radioimmunoassay, respectively. NOS activity was determined by the conversion of 3H-arginine to 3H-citrulline. The change of [Ca2+]i was studied by the laser scanning confocal microscopy technique. iNOS protein expression was detected using immunohistochemistry with monoclonal antibody of iNOS, and imaging analysis was performed.

RESULTS

Long-term administration of high-selective delta-opioid receptor agonist DPDPE and precipitation of opioid withdrawal by naloxone significantly induced increase of cAMP level and [Ca2+]i in NG-LNCXiNOS cells with stable expression of iNOS gene. The cytosolic iNOS activity and cGMP generation were enhanced by DPDPE dose-dependently. 10(-4) mol/L L-NNA could block opioid agonist-induced AC-cAMP desensitization and activity of NO-cGMP second messenger pathway, but it could not reduce opioid-induced elevation of [Ca2+]i. Furthermore, L-NNA decreased iNOS-specific protein expression in DPDPE-induced tolerance and naloxone-precipited withdrawal cells.

CONCLUSION

NOS inhibitor may attenuate the development of opioid tolerance and withdrawal via the negative regulation of AC-cAMP system and NO-cGMP system. It can be clinically used to prevent opiate tolerance and addiction.

Clinical observation on 41 cases of threatened and habitual abortion treated by blood activation and stasis removal

41 cases of pregnancy diagnosed as belonging to 4 subtypes of blood stasis, namely, qi stagnant, qi deficient, pernicious cold condensing and heat accumulating, suffering from womb leak, stirred fetus and fetal slip (threatened and habitual abortion) were treated by the method of blood activation and stasis removal in accordance with diagnostic typing. The treatment proved effective in 34 cases, the effective rate reaching 82.9%, with no significant differences either between threatened and habitual abortions or among the groups of cases with different syndromes. The treatment resulted in varying degrees of improvement in blood rheology and the level of serum (human) chorionic gonadotropin (HCG). Follow-up examination of 28 patients who had reacted favorably to the treatment and whose pregnancy had ended in normal deliveries revealed that none of the newborns differed significantly from the normal.

[Use of appendix to restore a ureter: report of 2 cases]

In two cases the appendix was utilised as a substitute for part of the left ureter. Case one used the appendix as a conduit from the upper left ureter to the right one to treat the megaureter, and the other one used the appendix as a connection to join the two transected openings of the left ureter to treat the obstruction caused by the chronic ureteritis of the left ureter. Long-term observation after the operation showed satisfactory functions of kidneys. We suggested that the appendix is an autologus tissue whose active peristalsis, little mucous absorption along with its easy performance make this method highly valuable and practical.

1 alpha,25-Dihydroxyvitamin D (calcitriol) inhibits the invasiveness of human prostate cancer cells

1 alpha,25-Dihydroxyvitamin D (1,25 D; also know as calcitriol), the hormonal form of vitamin D, can inhibit the proliferation and promote the differentiation of human prostate adenocarcinoma cells. However, little is known about the effects of 1,25 D on the invasive ability of prostate cancer cells. We used an in vitro bioassay of cell invasion (Amgel assay) to examine the effects of 1,25 D and a "noncalcemic" vitamin D analogue, 1,25-dihydroxy-16-ene-23-yne-cholecalciferol (16-23-D3), on the invasiveness of three well-characterized human prostate carcinoma cell lines: DU 145, PC-3, and LNCaP. PC-3 and LNCaP cells were poorly invasive in Amgel and were hardly affected by treatment with 1,25 D or 16-23-D3 (< 3%). Conversely, DU 145 cells were highly invasive in Amgel, and their invasion was markedly inhibited by 1,25 D and 16-23-D3 (maximally 66 and 59.4% respectively). This effect was both dose-dependent, with maximal inhibition at 1 x 10(-7) M and 72 h. Significant inhibition of invasion was observed at physiological levels of 1,25 D. Neither proliferative indices nor cell cycle kinetics were altered during the experimental exposure. Treatment with 1,25 D and 16-23-D3 caused a selective decrease in the secreted levels of type IV collagenases (MMP-2 and MMP-9). These findings support the hypothesis that 1,25 D reduces the risk of invasive prostate cancer and suggest a role for vitamin D compounds in the chemoprevention of invasive prostate cancer.

[Isolation of human herpes virus 6 from peripheral blood of renal transplant recipients]

One strain of the viruses was isolated from preipheral blood lymphocytes (PBL) of a renal transplant recipient. PBL isolated from blood samples were cocultured with the PHA actived cord blood lymphocytes (CBL). Two of twelve recipient's samples found cytopathic effect after 10 to 14 days. Examination of ultrathin-sections of the virus infected cells by electron microscope showed herpes-like virus particles. Detection of indirect immunofluorescences with McAbs against HHV-6 was positive in the infected cells.

[The expression of rat brain constitutive nitric oxide synthase in NG108-15 cell]

Full length cDNA of rat brain cNOS was inserted into the polylinker area of pRC/CMV with specific orientation and an eukaryocyte expression vector pCMVcNOS was obtained. The existence of cNOS gene was demonstrated by PCR amplification, using pCMVcNOS gene as the model and primers designed in accord with the internal sequence of cNOS gene. The insertion and orientation of pCMVcNOS were further verified by enzymatic cleavage. NG108-15 cells were transfected with pCMVcNOS by calcium phosphate DNA coprecipitation and lipofectin transfection. G418 resistant monoclonal cells were selected with a culture medium containing 600 micrograms/ml G418. NOS activity of each clone was assayed by monitoring the conversion of 3H-Arginine to 3H-Citrulline. High expression cell lines were selected through measurement of the cytosol and particulate NOS activity. Out of 42 resistant monoclonal cell lines, 3 stable high expression clones have been finally selected. The increase of expressed cytosol NOS was more obvious. The result showed that the cell lines expressing cNOS at a high level had been obtained.

[Symptoms, FEV1/FVC, and peak flow as indices of the control of asthma]

In a cross-sectional study, we evaluated success in the control of asthma as defined by criteria for symptoms, for FEV1/FVC, and for peak flow rates. One hundred and three patients with chronic asthma who had been treated with inhaled steroids were studied. Chest tightness, dyspnea, wheezing, sputum production, and coughing were each scored from 1 (worst) to 5 (best). Symptoms were said to have been controlled if the symptoms scores for the preceding 4 weeks were greater than or equal to 20; FEV1/FVC was said to be under control if it was greater than or equal to 70% when measured in the clinic; peak flow was said to have been controlled if the lowest peak flow in the preceding 4 weeks was greater than or equal to 80% of the highest measured value. Symptoms were controlled in 72% of the patients, FEV/FVC was under control in 83%, and peak flow was controlled in 66%. The patients were grouped by severity of disease into four classes, and these percentages did not differ significantly among the classes. In 22 out of 74 (30%) patients in whom symptoms were controlled, peak flow was not controlled. Furthermore, in 18 out of 64 (28%) patients in whom symptoms and FEV/FVC were controlled, peak flow was not controlled. We concluded that in treating asthma, not should symptoms be controlled, but peak flow should also be measured each day to avoid undertreatment.

Production of recombinant proteins in Chinese hamster ovary cells using a protein-free cell culture medium

The growth-factor prototrophic Chinese hamster ovary (CHO) SSF3 cell line was previously adapted for growth in serum-free media. Here we present a newly designed medium which allows these cells to grow in the absence of any exogenously added growth factors. To investigate the capacity of CHO SSF3 cells for the efficient production of recombinant proteins in protein-free media, expression plasmids containing either a human single chain urokinase-type plasminogen activator (uPA)-encoding cDNA or a humanized immunoglobulin G (IgG) kappa light chain cDNA were introduced by transfection. The tryptophan synthase (trpB) gene of Escherichia coli was used as a dominantly acting selection marker allowing the cells to survive in a medium containing indole in place of tryptophan. Some of the clones obtained exhibited a stable uPA expression over a period of several months under selective conditions and the yields were up to 74 mg of uPA/l in a bioreactor and the productivity was around 40 mg/day per 10(9) cells. The yields of IgG light chains were up to 118 mg/l and the productivity was in the order of 56 mg/day per 10(9) cells in a bioreactor. These results demonstrate the potential of CHO SSF3 cells for the efficient production of recombinant proteins under protein-free conditions.

Field molecular epidemiology. Feasibility of monitoring for the malignant bladder cell phenotype in a benzidine-exposed occupational cohort

Modern molecular and cellular biology have provided powerful new approaches to study cancer in the research laboratory, but these techniques have not been used extensively in field studies or in screening of high-risk occupational cohorts. The primary objective of this study was to demonstrate the use of cellular and molecular methods in combination with medical and epidemiologic methods to identify cancer cases, risk factors, and markers in a previously identified and defined cohort of Chinese workers exposed to benzidine. The screening of exposed workers included occupational, medical, and smoking histories to identify exogenous risk factors, a limited physical examination, Papanicolaou (PAP) urinary cytology, measurement of urine pH, quantitative fluorescence image analysis (QFIA) cytology to detect DNA hyperploidy, and quantitative fluorescence to detect expression of a low-grade bladder tumor-associated antigen (p300) by exfoliated urothelial cells and elevated expression of the neu oncogene product (p185). Detailed analysis of the accuracy of epidemiologic data and the adequacy of samples and accuracy of molecular techniques was carried out. Three groups were included in this study: group 1 included 23 bladder cancer cases who had previously been exposed to benzidine and served as two surrogates for late-emerging disease; group 2 consisted of 20 subjects with previous exposure history but not previously diagnosed with bladder cancer; and group 0 was the nonexposure and nonbladder cancer controls. The results showed that accurate questionnaire data and urine samples can be obtained at remote sites. Among the 20 group 2 subjects, two displayed abnormal findings by both QFIA cytology and p300 expression and were later confirmed to have bladder cancer.(ABSTRACT TRUNCATED AT 250 WORDS)