Germline HLA landscape does not predict efficacy of pembrolizumab monotherapy across solid tumor types.

We evaluated the impact of class I and class II human leukocyte antigen (HLA) genotypes, heterozygosity, and diversity on the efficacy of pembrolizumab. Seventeen pembrolizumab clinical trials across eight tumor types and one basket trial in patients with advanced solid tumors were included (n > 3,500 analyzed). Germline DNA was genotyped using a custom genotyping array. HLA diversity (measured by heterozygosity and evolutionary divergence) across class I loci was not associated with improved response to pembrolizumab, either within each tumor type evaluated or across all patients. Similarly, HLA heterozygosity at each class I and class II gene was not associated with response to pembrolizumab after accounting for the number of tests conducted. No conclusive association between HLA genotype and response to pembrolizumab was identified in this dataset. Germline HLA genotype or diversity alone is not an important independent determinant of response to pembrolizumab and should not be used for clinical decision-making in patients treated with pembrolizumab.

Hepatocellular carcinoma patients with high circulating cytotoxic T cells and intra-tumoral immune signature benefit from pembrolizumab: results from a single-arm phase 2 trial.

BACKGROUND: A limited number of studies have characterized genomic properties of hepatocellular carcinoma (HCC) patients in response to anti-PD-1 immunotherapy. METHODS: Herein, we performed comprehensive molecular characterization of immediate (D-42 to D-1) pre-treatment tumor biopsy specimens from 60 patients with sorafenib-failed HCC in a single-arm prospective phase II trial of pembrolizumab. Objective response rate was the primary efficacy endpoint. We used whole-exome sequencing, RNA sequencing, and correlative analysis. In addition, we performed single-cell RNA sequencing using peripheral blood mononuclear cells. RESULTS: The overall response rate of pembrolizumab in sorafenib-failed HCC patients was 10% ([6/60] 95% CI, 2.4-17.6). In a univariate analysis using clinicopathological features, female gender, PD-L1 positivity, and low neutrophil-to-lymphocyte ratio (NLR) were identified as contributing factors to pembrolizumab response. Somatic mutations in CTNNB1 and genomic amplifications in MET were found only in non-responders. Transcriptional profiles through RNA sequencing identified that pembrolizumab responders demonstrated T cell receptor (TCR) signaling activation with expressions of MHC genes, indicating increased levels of T cell cytotoxicity. In single-cell sequencing from 10 pre- and post-treatment peripheral blood mononuclear cells (PBMCs), patients who achieved a partial response or stable disease exhibited immunological shifts toward cytotoxic CD8+ T cells. Conversely, patients with progressive disease showed an increased number of both CD14+ and CD16+ monocytes and activation of neutrophil-associated pathways. CONCLUSIONS: Taken together, HCC patients with infiltration of cytotoxic T cells, along with increased active circulating CD8+ T cells during pembrolizumab treatment and down-regulation of neutrophil-associated markers, significantly benefited from pembrolizumab treatment. TRIAL REGISTRATION: NCT#03163992 (first posted: May 23, 2017).

Temperature change and electricity consumption of the group living: A case study of college students.

The relationship between energy use and climate change is the center of analysis about mitigation and adaptation. Yet current studies of the electricity-climate relationship focus on developed countries. Little was known about the energy-use behavior in group living. By using college students' monthly electricity-use data from September 2018 to August 2019 in Beijing, China, we build a weighted least square regression model and found a U-shaped relationship between temperature and electricity consumption. The results show that one additional day of temperature exceeding 30 °C would cause a 16.8% increase in monthly electricity consumption with reference to 18-22 °C while one additional day of temperature below -6 °C will increase it by 6%. The magnitudes of temperature effect on electricity are much greater than those in Shanghai and California. Further, we find that building structures, such as windows orientation and floor height, play important roles in the temperature-electricity relationship. Finally, we predict the changes in electricity use in a collection of Representative Concentration Pathways (RCP). It finds that the electricity use in summer in north China would increase by 72.8% in RCP 4.5, 79.5% in RCP6.0, and 91.2% in RCP8.5. Our study could be extended to the urban area in northern China, and indicates how the electricity use would respond to climate change in the Beijing-Tianjin-Hebei Urban Agglomeration, covering 8.1% of China's population and 8.4% of gross domestic product. Climate change impact on electricity use in residential and commercial sectors is significant and varying in regions. To achieve sustainable and environmental-friendly development, building structures could play a more effective role in energy-saving and adaptation to climate change.

High PD-L1 expression in gastric cancer (GC) patients and correlation with molecular features.

BACKGROUND: The programmed death receptor ligand 1 (PD-L1) immunohistochemistry (IHC) 22C3 pharmDx assay is a widely used selection method for pembrolizumab treatment in gastric cancer (GC) patients, especially in the U.S. The present study investigated the relationship between PD-L1 expression and the clinical features, molecular markers, and molecular subtypes of GC. METHODS: PD-L1 expression was assessed based on combined positive score (CPS) using PD-L1 IHC 22C3 pharmDx in the Asian Cancer Research Group (ACRG) GC cohort (N = 300), which has been previously genomically profiled. PD-L1 positivity was defined as PD-L1 CPS ≥ 1. The association between PD-L1 expression and clinical features, tumor burden, and molecular subtypes (ACRG and The Cancer Genome Atlas [TCGA]) was analyzed. RESULTS: Of the 300 tumors, 178 (59.3 %) had PD-L1 CPS ≥ 1 and 122 (40.7 %) had PD-L1 CPS < 1. PD-L1 CPS ≥ 1 was significantly associated with stage I tumor (P = 0.022), high microsatellite instability (MSI-H) (P < 0.001), Epstein-Barr virus (EBV) positivity (P = 0.008), and positive Helicobacter pylori status (P = 0.001). PD-L1 CPS ≥ 1 was observed in 96/193 (49.7 %) EBV-negative/microsatellite stable (MSS) tumors. In gene expression profiling, PD-L1 CPS was highly correlated with mutational load (P < 0.001) as well as EBV (P < 0.001) and MSI subtypes (P < 0.001); 27/300 (9%) GC patients had a very high PD-L1 (≥ 20) score (MSI-H, n = 10; EBV, n = 6; and non-EBV/MSS, n = 11). OS was longer in patients with PD-L1 CPS ≥ 1 tumors than in those with PD-L1 CPS < 1 tumors (median OS not reached vs. 40 months; P = 0.008; log-rank test). CONCLUSIONS: PD-L1 is expressed in 59.3 % of GC patients and is associated with MSI and EBV positivity. These results provide a basis for identifying GC patients who may benefit from anti-PD-1/PD-L1 therapy.

Efficacy and safety of clopidogrel only vs. clopidogrel added proton pump inhibitors in the treatment of patients with coronary heart disease after percutaneous coronary intervention: A systematic review and meta-analysis.

BACKGROUND: Controversy still exists that whether clopidogrel should add proton pump inhibitors (PPIs) in patients with coronary heart disease after percutaneous coronary intervention (PCI). The aim of this study was to evaluate the efficacy and safety of clopidogrel added proton pump inhibitors (PPIs) vs. clopidogrel for the treatment of patients with coronary heart disease after percutaneous coronary intervention (PCI). METHODS AND RESULTS: We systematically searched PubMed, EMBASE, Web of Science, the Chinese Biomedical Medical Literature database, and the Cochrane Library for all clinical trials that were published on this topic through October 2018. We specifically selected the clinical trials that evaluated the efficacy and safety of clopidogrel added proton pump inhibitors vs. clopidogrel in the treatment of patients with coronary heart disease after PCI. RevMan 5.0 software was used for quantitative data analyses.15 randomized controlled trials including 50,366 patients were included. The meta-analysis results showed that compared with the clopidogrel added PPI group, the non-PPI group had significantly less risk of MACE[RR = 0.82,95%CI:0.77-0.88], myocardial infarction recurrence[RR = 0.72,95%CI:0.57-0.90], stent thrombosis[RR = 0.71,95%CI:0.56-0.92], Target vessel revascularization (TVR)[RR = 0.77,95%CI:0.63-0.93] and stroke [RR = 0.72,95%CI:0.67-0.76]. The risks of all cause death [RR = 1.14,95%CI:0.85-1.51], cardiovascular death [RR = 1.14, 95% CI: 0.85-1.52], bleedings events [RR = 1.60,95%CI:0.53-4.81] were similar in the two groups. CONCLUSIONS: The patients in the non-PPI group were observed to be associated with less risk of MACE, myocardial infarction recurrence, stent thrombosis, target vessel revascularization (TVR) and stroke. And the two groups had similar all cause death, cardiovascular death, bleedings events.

Correlation between the expression of Drp1 in vascular endothelial cells and inflammatory factors in hypertension rats.

The objective of this study was to investigate the expression level of dynamin-related protein 1 (Drp1) in vascular endothelium of hypertension rats and its correlation with expression of inflammatory factors. Twenty spontaneous hypertension rats (SHR) were randomly divided into SHR group (n=10) and inhibition group (MD group, n=10), and the Sprague Dawley rats were enrolled as the control group (C group, n=10). For rats in the MD group, Mdivi-1, a mitochondrial division inhibitor, was given in dosage of 25 mg/kg. After 4 weeks of administration, blood pressure was measured via tail-artery blood pressure measurement. The blood samples collected from the abdominal aorta of rats were used to assay the C-reaction protein (CRP) concentration in serum through radioimmunoassay. Hematoxylin and eosin (H&E) staining was performed for sections of thoracic aorta for morphological observation and measurement of medial thickness. Enzyme-linked immunosorbant assay (ELISA), semi-quantitative real-time polymerase chain reaction (RT-PCR) and western blotting was carried out for detecting the expression levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α). Drp1 and monocyte chemotactic protein 1 (MCP-1). After 4 weeks of drug administration, the blood pressure in the MD group was significantly higher (P<0.01). The medial thickness of the thoracic aorta in the MD group was significantly decreased in comparison with the SHR group (P<0.01). The results of ELISA showed that compared with the SHR group, the expression levels of IL-6 and TNF-α in the MD group were remarkably decreased (P<0.01). Semi-quantitative RT-PCR results indicated that the mRNA expression levels of Drp1 and MCP-1 in the MD group were significantly lower than those in the SHR group (P<0.05). In the SHR rats, after administration of Mdivi-1, the expression of Drp1 is decreased, which contributes to the alleviation in inflammatory reactions and protects the vessels in SHR rats.

Systematic identification of cancer-related long noncoding RNAs and aberrant alternative splicing of quintuple-negative lung adenocarcinoma through RNA-Seq.

OBJECTIVES: Lung adenocarcinoma (LUAD) is a common subtype of non-small cell lung cancer prevalent in Asia. There is a dearth of understanding regarding the transcriptome landscape of LUAD without primary known driver mutations. In this study, LUAD samples without well-known driver mutations occurring in EGFR, KRAS, ALK, ROS1 or RET (quintuple-negative) were used for transcriptome study with a focus on long noncoding RNAs (lncRNAs), alternative splicing and gene fusions. MATERIALS AND METHODS: 24 pairs of LUAD and adjacent normal samples and 13 tumor-only samples derived from 37 quintuple-negative patients were used. Differentially expressed lncRNA transcripts were detected by paired t-test and were validated by qPCR. Functions of lncRNAs were predicted by co-expressed mRNAs. Aberrant splicing events in LUAD were identified using MISO. In addition, gene fusions were screened by SOAPfuse. RESULTS AND CONCLUSION: In total, 90 and 153 up- or down-regulated lncRNA transcripts were detected in LUAD samples in comparison with the adjacent normal samples. The most significantly differentially expressed lncRNA transcript was ENST00000598996.1 (FENDRR) down-regulated in LUAD. By lncRNA-mRNA co-expression analysis, functions of 14 lncRNAs were predicted. The predicted functions included vasculature development, immune response, cell cycle and respiratory gaseous exchange. Furthermore, six co-expressed pairs of lncRNAs and their nearby protein coding genes were identified as associated with lung development. This study also identified two highly recurrent (22 in 24) differential exon skipping events occurring in MYH14 and ESYT2 with exon including isoforms of both genes up-regulated in isoform percentage in LUAD samples. On the other hand, two out of 24 LUAD samples possessed the driver mutation exon 14 skipping of MET. The transcriptional alterations of LUAD samples without well-known driver mutations identified in the study can be used as references for future research. The translational values of these transcriptional changes are also worthy of further investigation.

Comprehensive Characterization of Oncogenic Drivers in Asian Lung Adenocarcinoma.

INTRODUCTION: The incidence rate of lung adenocarcinoma (LUAD), the predominant histological subtype of lung cancer, is elevated in Asians, particularly in female nonsmokers. The mutation patterns in LUAD in Asians might be distinct from those in LUAD in whites. METHODS: We profiled 271 resected LUAD tumors (mainly stage I) to characterize the genomic landscape of LUAD in Asians with a focus on female nonsmokers. RESULTS: Mutations in EGFR, KRAS, erb-b2 receptor tyrosine kinase 2 gene (ERBB2), and BRAF; gene fusions involving anaplastic lymphoma receptor tyrosine kinase gene (ALK), ROS1, and ret proto-oncogene (RET); and Met Proto-Oncogene Tyrosine Kinase (MET) exon 14 skipping were the major drivers in LUAD in Asians, exhibiting mutually exclusive and differing prevalence from those reported in studies of LUAD in non-Asians. In addition, we identified a novel mutational signature of XNX (the mutated base N in the middle flanked by two identical bases at the 5' and 3' positions) that was overrepresented in LUAD tumors in nonsmokers and negatively correlated with the overall mutational frequency. CONCLUSIONS: In this cohort, approximately 85% of individuals have known driver mutations (EGFR 59.4%, KRAS 7.4%, ALK 7.4%, ERBB2 2.6%, ROS1 2.2%, RET 2.2%, MET 1.8%, BRAF 1.1%, and NRAS 0.4%). Seventy percent of smokers and 90% of nonsmokers had defined oncogenic drivers matching the U.S. Food and Drug Administration-approved targeted therapies.

Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets.

Hepatocellular carcinoma (HCC) is an aggressive and deadly cancer. The molecular pathogenesis of the disease remains poorly understood. To better understand HCC biology and explore potential biomarkers and therapeutic targets, we investigated the whole transcriptome of HCC. Considering the genetic heterogeneity of HCC, four datasets from four studies consisting of 15 pairs of HCC and adjacent normal samples were analyzed. We observed that the number of lncRNAs expressed in each HCC sample was consistently greater than the adjacent normal sample. Moreover, 15 lncRNAs were identified expressed in five to seven HCC tissues but were not detected in any adjacent normal tissue. Differential expression analysis detected 35 up- and 80 down-regulated lncRNAs in HCC samples compared with adjacent normal samples. In addition, five differentially expressed lncRNAs were predicted to play a role in oxidation and reduction process. With regard to splicing alterations, we identified nine highly recurrent differential splicing events belonging to eight genes USO1, RPS24, CCDC50, THNSL2, NUMB, FN1 (two events), SLC39A14 and NR1I3. Of them, splicing alterations of SLC39A14 and NR1I3 were reported for the association with HCC for the first time. The splicing dysregulation in HCC may be influenced by three splicing factors ESRP2, CELF2 and SRSF5 which were significantly down-regulated in HCC samples. This study revealed uncharacterized aspects of HCC transcriptome and identified important lncRNAs and splicing isoforms with the potential to serve as biomarkers and therapeutic targets for the disease.

An effective analytic method for detecting tissue-specific genes in RNA-seq experiments.

AIM: To develop an analytic method for identifying tissue-specific (TS) genes from RNA-seq data. MATERIALS & METHODS: Based on a negative binomial distribution, we develop a statistical method containing consecutive procedures incorporating data variability from replicates in each tissue. RESULTS: Simulations show that our approach can effectively identify at least 94% of the truly TS genes if the sample size is 3 and at least 84% of the TS genes detected by our method are truly TS genes. We illustrated the utility of our method in an in-house RNA-seq project and produced sensible results. CONCLUSION: Our approach not only directly works on discrete data but also naturally incorporates data variability. It works effectively for detecting TS genes.

Genome-wide identification of RNA editing in hepatocellular carcinoma.

We did whole-transcriptome sequencing and whole-genome sequencing on nine pairs of Hepatocellular carcinoma (HCC) tumors and matched adjacent tissues to identify RNA editing events. We identified mean 26,982 editing sites with mean 89.5% canonical A→G edits in each sample using an improved bioinformatics pipeline. The editing rate was significantly higher in tumors than adjacent normal tissues. Comparing the difference between tumor and normal tissues of each patient, we found 7 non-synonymous tissue specific editing events including 4 tumor-specific edits and 3 normal-specific edits in the coding region, as well as 292 edits varying in editing degree. The significant expression changes of 150 genes associated with RNA editing were found in tumors, with 3 of the 4 most significant genes being cancer related. Our results show that editing might be related to higher gene expression. These findings indicate that RNA editing modification may play an important role in the development of HCC.

Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by whole-genome sequencing.

Gastric cancer (GC) is the second most common cause of cancer-related deaths. It is known to be a heterogeneous disease with several molecular and histological subtypes. Here we perform whole-genome sequencing of 49 GCs with diffuse (N=31) and intestinal (N=18) histological subtypes and identify three mutational signatures, impacting TpT, CpG and TpCp[A/T] nucleotides. The diffuse-type GCs show significantly lower clonality and smaller numbers of somatic and structural variants compared with intestinal subtype. We further divide the diffuse subtype into one with infrequent genetic changes/low clonality and another with relatively higher clonality and mutations impacting TpT dinucleotide. Notably, we discover frequent and exclusive mutations in Ephrins and SLIT/ROBO signalling pathway genes. Overall, this study delivers new insights into the mutational heterogeneity underlying distinct histologic subtypes of GC that could have important implications for future research in the diagnosis and treatment of GC.

O-GlcNAcylation under hypoxic conditions and its effects on the blood-retinal barrier in diabetic retinopathy.

An increase in O-linked N-acetylglucosamine (O-GlcNAc) protein modifications has been observerd in db/db mouse retinas. O-GlcNAc-modified proteins in the db/db mouse retina have been shown to be localized in the ganglion cell layer, the inner nuclear layer, the retina pigment epithelium (RPE) layer and the inner plexiform layer, in which hypoxia-inducible factor 1α (HIF1α) has also been shown to be localized. In the current study, we examined whether hypoxia increases O-GlcNAcylation in retinal vascular cells under high glucose conditions and whether HIF1α activation is consistent with the response to and activation of O-GlcNAcylation in retinal lesions in diabetic retinopathy. In addition, the effects of O-GlcNAcylation on the blood-retinal barrier were verified in vitro by the inhibition of O-GlcNAcylation. A time-dependent increase in the O-GlcNAcylation in bovine retinal vascular endothelial cells (BRVECs) was observed following incubation of the cells with high glucose medium (glucose 4.5 g/l) under hypoxic (1-3% O2) conditions. Hypoxia-induced BRVEC O-GlcNAcylation was not observed when the BRVECs were transfected with siRNA targeting O-GlcNAc transferase (OGT) or treated with alloxan (an OGT inhibitor) prior to exposure to high glucose. The increase in BRVEC O-GlcNAcylation induced by high glucose, as well as by thiamet G [an O-GlcNAcase (OGA) inhibitor] led to a reduction in occludin expression levels in vitro, which was prevented by treatment with OGT siRNA and alloxan. In conclusion, the current study demonstrates the relationship between O-GlcNAc glycosylation and hypoxia during diabetic retinopathy and that hyperglycemia induced O2 consumption activates HIF1α and O-GlcNAc modification protein in the same retinal layer. The reduced protein BRVEC O-GlcNAcylation levels exert protective effects on the blood-retinal barrier and thus represent a potential therapeutic target for the treatment of diabetic retinopathy.

RNA-seq identified a super-long intergenic transcript functioning in adipogenesis.

RNA transcripts are generally classified into polyA-plus and polyA-minus subgroups due to the presence or absence of a polyA tail at the 3' end. Even though a number of physiologically and pathologically important polyA-minus RNAs have been recently identified, a systematic analysis of the expression and function of these transcripts in adipogenesis is still elusive. To study the potential function of the polyA-minus RNAs in adipogenesis, a dynamic expressional profiling was performed in the induced differentiation of 3T3-L1 cells. In addition to identifying thousands of novel intergenic transcripts, differentiation-synchronized expression was characterized for many of them. Among these, several large intergenic transcripts were found to be upregulated by more than 19-fold during differentiation. Further study demonstrated a fat tissue-specific expression pattern for these regions and identified an adipogenesis-associated long non-coding RNA. Collectively, these lines of evidence contribute to the characterization of a super-long intergenic transcript functioning in adipogenesis.

WebLab: a data-centric, knowledge-sharing bioinformatic platform.

With the rapid progress of biological research, great demands are proposed for integrative knowledge-sharing systems to efficiently support collaboration of biological researchers from various fields. To fulfill such requirements, we have developed a data-centric knowledge-sharing platform WebLab for biologists to fetch, analyze, manipulate and share data under an intuitive web interface. Dedicated space is provided for users to store their input data and analysis results. Users can upload local data or fetch public data from remote databases, and then perform analysis using more than 260 integrated bioinformatic tools. These tools can be further organized as customized analysis workflows to accomplish complex tasks automatically. In addition to conventional biological data, WebLab also provides rich supports for scientific literatures, such as searching against full text of uploaded literatures and exporting citations into various well-known citation managers such as EndNote and BibTex. To facilitate team work among colleagues, WebLab provides a powerful and flexible sharing mechanism, which allows users to share input data, analysis results, scientific literatures and customized workflows to specified users or groups with sophisticated privilege settings. WebLab is publicly available at http://weblab.cbi.pku.edu.cn, with all source code released as Free Software.

[The effects of different occluder selection on cardiac remodeling post transcatheter closure in patients with secundum atrial septal defect].

OBJECTIVE: To evaluate the effects on cardiac remodeling post transcatheter closure by Amplatzer septal occluder selected by oval circumference formula in patients with atrial septal defect (ASD). METHODS: A total of 146 patients with ASD (68 males,mean 33.5 years) treated by transcatheter closure with the Amplatzer occluder were enrolled in this study. The diameter of defects was corrected with the oval circumference formula (group A, 73 cases) or by echocardiography (group B, 73 cases). Cardiac remodeling was assessed by transthoracic echocardiography (TTE) before the procedure, 3 days, 3 months and 6 months after ASD closure. RESULTS: The mean ASD diameter was similar between the two groups [(20.16 +/- 4.98) mm vs. (21.36 +/- 5.69) mm, P > 0.05] and the mean diameter of the selected occluder of group A was significantly smaller than that in group B [(21.95 +/- 6.78) mm vs. (25.85 +/- 6.75) mm, P < 0.05]. Procedural success rate was identical between the two groups (97.3%) and the defects were completely occluded and there was no residual shunt during the 6 months follow up period, there were also no complications during and after the procedure. The lateral diameter of right atrial (RALD), the diastolic diameter of right ventricle (RVDD), RALD/LALD, RVDD/LVDD and pulmonary diameter (PD) were significantly decreased while the lateral diameter of left atrial (LALD) and left ventricle (LVDD) were significantly increased post ASD closure in both groups. At 6 months follow up, RALD decreased by (18.63 +/- 10.59)% in group A versus (10.14 +/- 6.59)% in group B, LALD increased by (13.42 +/- 8.38)% in group A versus (9.28 +/- 4.95)% in group B and RALD/LALD ratio decreased by (26.35 +/- 11.24)% in group A versus (13.98 +/- 8.96)% in groups B (all P < 0.05). CONCLUSION: ASD occluder selection based on the oval circumferen ce formula is superior to that made by echocardiography in terms of more favorable cardiac remodeling post ASD closure.

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

Recent transcriptome studies have revealed that a large number of transcripts in mammals and other organisms do not encode proteins but function as noncoding RNAs (ncRNAs) instead. As millions of transcripts are generated by large-scale cDNA and EST sequencing projects every year, there is a need for automatic methods to distinguish protein-coding RNAs from noncoding RNAs accurately and quickly. We developed a support vector machine-based classifier, named Coding Potential Calculator (CPC), to assess the protein-coding potential of a transcript based on six biologically meaningful sequence features. Tenfold cross-validation on the training dataset and further testing on several large datasets showed that CPC can discriminate coding from noncoding transcripts with high accuracy. Furthermore, CPC also runs an order-of-magnitude faster than a previous state-of-the-art tool and has higher accuracy. We developed a user-friendly web-based interface of CPC at http://cpc.cbi.pku.edu.cn. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation.

Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP).

MOTIVATION: The rapid accumulation of single amino acid polymorphisms (SAPs), also known as non-synonymous single nucleotide polymorphisms (nsSNPs), brings the opportunities and needs to understand and predict their disease association. Currently published attributes are limited, the detailed mechanisms governing the disease association of a SAP remain unclear and thus, further investigation of new attributes and improvement of the prediction are desired. RESULTS: A SAP dataset was compiled from the Swiss-Prot variant pages. We extracted and demonstrated the effectiveness of several new biologically informative attributes including the structural neighbor profiles that describe the SAP's microenvironment, nearby functional sites that measure the structure-based and sequence-based distances between the SAP site and its nearby functional sites, aggregation properties that measure the likelihood of protein aggregation and disordered regions that consider whether the SAP is located in structurally disordered regions. The new attributes provided insights into the mechanisms of the disease association of SAPs. We built a support vector machines (SVMs) classifier employing a carefully selected set of new and previously published attributes. Through a strict protein-level 5-fold cross-validation, we attained an overall accuracy of 82.61%, and an MCC of 0.60. Moreover, a web server was developed to provide a user-friendly interface for biologists. AVAILABILITY: The web server is available at http://sapred.cbi.pku.edu.cn/

[Development of multi-channels cardiac electrophysiological polygraph with LabVIEW as software platform and its clinical application].

Polygraph has become a necessary instrument in interventional cardiology and fundamental research of medicine up to the present. In this study, a LabView development system (DS) (developed by NI in U.S.) used as software platform, a DAQ data acquisition module and universal computer used as hardware platform, were creatively coupled with our self-made low noise multi-channels preamplifier to develop Multi-channels electrocardiograph. The device possessed the functions such as real time display of physiological process, digit highpass and lowpass, 50Hz filtered and gain adjustment, instant storing, random playback and printing, and process control stimulation. Besides, it was small-sized, economically practical and easy to operate. It could advance the spread of cardiac intervention treatment in hospitals.