Alternative splicing (AS) is an important mechanism of producing transcriptome diversity and microarray techniques are being used increasingly to monitor the splice variants. There exist three types of microarrays interrogating AS events-junction, exon, and tiling arrays. Junction probes have the advantage of monitoring the splice site directly. Johnson et al., performed a genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays (Science 302:2141-2144, 2003), which monitored splicing at every known exon-exon junctions for more than 10,000 multi-exon human genes in 52 tissues and cell lines. Here, we describe an algorithm to deduce the relative concentration of isoforms from the junction array data. Non-negative Matrix Factorization (NMF) is applied to obtain the transcript structure inferred from the expression data. Then we choose the transcript models consistent with the ECgene model of alternative splicing which is based on mRNA and EST alignment. The probe-transcript matrix is constructed using the NMF-consistent ECgene transcripts, and the isoform abundance is deduced from the non-negative least squares (NNLS) fitting of experimental data. Our method can be easily extended to other types of microarrays with exon or junction probes.
Alternative Splicing ; Cell Line ; Exons* ; Humans ; Least-Squares Analysis ; Protein Isoforms ; RNA Precursors ; RNA, Messenger ; Transcriptome

OBJECTIVETo evaluate the comparability and bias of the test results of two detection systems for serum procalcitonin (PCT) under the same laboratory condition.

METHODSAccording to the profile NCCLS-EP9-A, the two systems were used to detect PCT to obtain the correlation coefficient and the liner equation for evaluation of the test result bias.

RESULTS AND CONCLUSIONThe test results of PCT showed no significant difference between the two detection systems (P>005) with a kappa value greater than 0.75. The correlation coefficients of both systems were above 0.975, suggesting a consistency between them for clinical detection of PCT.

Bias ; Blood Chemical Analysis ; methods ; Calcitonin ; blood ; Calcitonin Gene-Related Peptide ; Humans ; Protein Precursors ; blood

The distributions and frequencies of some endocrine cells in the gastrointestinal (GI) tract of ddY mice were studied with immunohistochemical method using 7 types of antisera against bovine chromogranin (BCG), serotonin, gastrin, cholecystokinin (CCK)-8, somatostatin, glucagon and human pancreatic polypeptide (HPP). All of 7 types of immunoreactive (IR) cells were identified. Most of IR cells in the intestinal portion were generally spherical or spindle in shape (open typed cell) while cells showing round in shape (close typed cell) were found in the intestinal gland and stomach regions occasionally. Their relative frequencies were varied according to each portion of GI tract. BCG-IR cells were demonstrated throughout whole GI tract except for the cecum and they were most predominant in the fundus and pylorus. Serotonin-IR cells were detected throughout whole GI tract and they were most predominant cell types in this species of mice. Gastrin-IR cells were restricted to the pylorus and CCK-8-IR cells were demonstrated in the pylorus, duodenum and jejunum with numerous frequencies in the pylorus. Somatostatin-IR cells were detected throughout whole GI tract except for the cecum and rectum and they showed more numerous frequencies in the stomach regions. In addition, glucagon-IR cells were restricted to the fundus, duodenum and jejunum with rare frequencies, and HPP-IR cells were restricted to the rectum only with rare frequency. In conclusion, some strain-dependent unique distributional patterns of gastrointestinal endocrine cells were found in GI tract of ddY mice.
Animals ; Biological Markers/analysis ; Cholecystokinin/analysis ; Chromogranins/analysis ; Enteroendocrine Cells/*cytology/immunology ; Female ; Gastrins/analysis ; Glucagon/analysis ; Immunoenzyme Techniques ; Mice ; Pancreatic Polypeptide/analysis ; Protein Precursors/analysis ; Serotonin/analysis

Neonatal septicemia is one of the major causes of morbidity and mortality worldwide during the neonatal period. It can be classified into two subtypes: early-onset sepsis (EOS) and late-onset sepsis (LOS) depending upon the time of onset. In the western developed countries, group B Streptococcal and Escherichia coli are leading pathogens for EOS, while the most frequent microorganism involved in LOS is coagulase negative Staphylococci, which are different from the domestic data. Clinical manifestations of neonatal septicemia are not specific, so that it is often misdiagnosed. This review describes the progress in diagnostic methods for neonatal septicemia, including blood culture, blood cell counts, cytokine profiles and umbilical cord blood examinations. It provides useful information for early diagnosis and treatment of neonatal septicemia.
Blood Cell Count ; C-Reactive Protein ; analysis ; Calcitonin ; blood ; Cytokines ; blood ; Humans ; Infant, Newborn ; Protein Precursors ; blood ; Sepsis ; blood ; diagnosis

Acute Disease ; Bacterial Translocation ; C-Reactive Protein ; analysis ; Calcitonin ; blood ; Child ; Humans ; Pancreatitis ; diagnosis ; etiology ; therapy ; Protein Precursors ; blood

OBJECTIVE: To investigate the value of C-reactive protein (CRP) and procalcitonin (PCT) in diagnosis of the bacterial infection in acute exacerbations of chronic obstructive pulmonary disease (AECOPD) patients by detecting the change of CRP and PCT. METHODS: A total of 369 AECOPD patients were divided into infective group and non-infective group. The values of CRP, PCT, WBC, N and ESR were tested and compared before and after treatment in each group. RESULTS: Before treatment, the levels of CRP, PCT, WBC, and N in the infective group were significantly higher than that in the non-infective group (P<0.05 or P<0.01), while there was no significant difference in ESR level between the 2 groups (P>0.05). In the infective group, the levels of CRP, PCT, WBC, N and ESR after the treatment were much lower than those before treatment (P<0.05). After treatment, the levels of CRP, PCT, WBC, and N in the infective group were significantly higher compared with that in the non-infective group (P<0.05), while there was no significant difference of ESR level between the 2 groups (P>0.05). There was a positive relationship between PCT and CRP, ESR and WBC (r=0.46, 0.38, 0.20; P<0.05), CRP and WBC as well as N and ESR (r=0.56, 0.43, 0.30; P<0.05). CONCLUSION It is a sensitive method for diagnosis and treatment of the bacterial infection in AECOPD patients through the combination of CRP with PCT and also for evaluation of the prognosis of patients with AECOPD.
Bacterial Infections ; complications ; diagnosis ; C-Reactive Protein ; analysis ; Calcitonin ; analysis ; Calcitonin Gene-Related Peptide ; Humans ; Prognosis ; Protein Precursors ; analysis ; Pulmonary Disease, Chronic Obstructive ; complications ; microbiology

OBJECTIVETo evaluate the diagnostic value of measuring serum C-reactive protein (CRP) and procalcitonin (PCT) levels, within 6 hours after admission to the pediatric intensive care unit (PICU) in children with bloodstream infection (BSI)-associated sepsis and septic infection at other sites.

METHODSA retrospective analysis was performed on 30 children with a confirmed diagnosis of systemic inflammatory response syndrome who were admitted to the Shengjing Hospital of China Medical University between January 2010 and January 2012. Clinical data on serum CRP, PCT and D-dimer levels were collected within 6 hours after admission. The diagnostic values of the indices were determined by comparative analysis.

RESULTSSerum CRP and PCT levels in children with BSI-associated sepsis were significantly higher than in children with septic infection at other sites (P<0.05), but there was no significant difference in serum D-dimer levels between the two groups (P>0.05). Serum PCT level was superior to serum CRP level in distinguishing children with BSI-associated sepsis from those with septic infection at other sites. Serum PCT level could not realistically be used for diagnosing BSI-associated sepsis when it was less than 2 ng/mL (negative predictive value: 100%), but could be reliably used when it was more than 10 ng/mL (positive predictive value: 77%).

CONCLUSIONSSerum PCT level is superior to serum CRP level in distinguishing children with BSI-associated sepsis from those with septic infection at other sites within 6 hours after admission to the PICU. Serum PCT level has a better diagnostic value for BSI-associated sepsis when it is more than 10 ng/mL.

C-Reactive Protein ; analysis ; Calcitonin ; blood ; Calcitonin Gene-Related Peptide ; Child ; Fibrin Fibrinogen Degradation Products ; analysis ; Humans ; Protein Precursors ; blood ; Retrospective Studies ; Sensitivity and Specificity ; Sepsis ; blood ; diagnosis

BACKGROUND: Bloodstream infection (BSI) is associated with a high mortality rate. Since the origin of infection is demonstrated in approximately 2/3rds of cases, early and established biomarkers are warranted. We evaluated the clinical performances of automated procalcitonin (PCT) and C-reactive protein (CRP) assays for the quantitative detection of BSI. Analytical performance of the VIDAS(R) B.R.A.H.M.S PCT assay (bioMerieux, France) was assessed and also compared with the semi-quantitative PCT-Q test (B.R.A.H.M.S Aktiengesellschaft, Germany). METHODS: We prospectively included consecutive patients divided into 3 groups at the Dong-A University Medical Center. Patients were categorized according to the criteria of the American College of Chest Physicians/Society of Critical Care Medicine Consensus Conference (ACCP/SCCM), and also on the basis of catheter-associated bacteremia. RESULTS: A total 77 patients were enrolled. All mean values of PCT and PCT-Q were consistent with the reference value. Measured PCT concentrations showed good linearity (r=0.983). The between-run, within-run, and total imprecisions were below 5%. The PCT levels in gram-negative bacteremia were significantly higher than those in gram-positive bacteremia. Furthermore, the PCT concentrations were significantly different among non-infection, bacteremia, sepsis, severe sepsis, and septic shock groups. Our study showed that PCT >0.3 ng/mL had 95.0% sensitivity and 97.3% specificity, whereas CRP >5.46 mg/dL had 85.0% sensitivity and 86.5% specificity for diagnosing sepsis. CONCLUSIONS: We suggest that, compared with CRP, PCT is a better diagnostic and discriminative biomarker of sepsis categorized according to the ACCP/SCCM. Moreover, catheter-associated bacteremia could be discriminated from sepsis using PCT concentration.
Adult ; Bacteremia/*diagnosis ; Biological Markers/analysis/blood ; C-Reactive Protein/analysis ; Calcitonin/*blood ; Female ; Humans ; Male ; Middle Aged ; Protein Precursors/*blood ; ROC Curve ; Sensitivity and Specificity ; Sepsis/diagnosis

OBJECTIVETo investigate the correlation of hypoproteinemia with inflammation parameters C-reactive protein (CRP), procalcitonin (PCT) and WBC in children with sepsis.

METHODSSeventy-three children with sepsis (including 22 severe sepsis) and 40 non-sepsis children (control group) were enrolled. Serum albumin levels were measured on admission. Based on the level of serum albumin, 73 cases of sepsis were classified into three groups: mild hypoproteinemia, severe hypoproteinemia and normal albumin. Blood CRP, PCT and WBC levels were compared in the three groups. The correlation of CRP, PCT and WBC with serum albumin level was evaluated.

RESULTSSerum albumin levels in the sepsis groups (severe or non-severe) were significantly lower than those in the control group (P<0.05), and the severe sepsis group showed more decreased albumin levels compared with the non-severe sepsis group (P<0.05). Blood CRP, PCT and WBC levels in the mild hypoproteinemia group were higher than those in the normal albumin group (P<0.05), and the severe hypoproteinemia group showed more increased blood CRP, PCT and WBC levels compared with the mild hypoproteinemia group (P<0.05). The incidence of multiple organ failure in the severe hypoproteinemia group was significantly higher than that in the normal albumin group (P<0.05). Serum albumin levels were negatively correlated with blood CRP, PCT and WBC levels.

CONCLUSIONSSerum albumin levels decrease in children with sepsis, and the more serious the illness, the lower serum albumin levels, resulting in a worse prognosis. CRP, PCT and WBC are negatively correlated to serum albumin levels in children with sepsis.

C-Reactive Protein ; analysis ; Calcitonin ; blood ; Calcitonin Gene-Related Peptide ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Leukocyte Count ; Male ; Protein Precursors ; blood ; Sepsis ; blood ; Serum Albumin ; analysis

BACKGROUNDProneurotrophins such as the precursor of nerve growth factor (proNGF) and the precursor of brain-derived neurotrophic factor (proBDNF) interacted with sortilin and p75(NTR) to form a complex capable of activating an apoptotic signaling. We found that the expression of p75(NTR) and sortilin was increased in ischemic retina induced by elevated intraocular pressure (IOP), but the protein expression changes of proNGF and proBDNF in the same situation were not clear. This study aimed to ascertain the protein expression changes of proNGF and proBDNF in ischemic retina induced by elevated IOP.

METHODSExpression of proBDNF and proNGF was examined by double-labeling immunochemistry in normal rat retina, examined using Western blotting and analyzed using statistical methods in ischemic retina induced by elevated IOP.

RESULTSImmunocytochemistry showed that the proBDNF expressed in the ganglion cell layer (GCL) while the proNGF primarily existed in both the nerve fiber layers (NFL) and large ganglion cell bodies of normal rat retina. Western blotting analysis demonstrated that the molecule weights of 28 kD (proBDNF)/25 kD (proNGF) band were increased significantly (P < 0.05) at days 3, 5 and 7 after retinal elevated-IOP-induced ischemia.

CONCLUSIONProBDNF expressed in the GCL and proNGF primarily presented in NFL and large ganglion cell bodies of normal rat retina, the protein expression forms of 28 kD proBDNF and 25 kD proNGF increased in ischemic retina induced by elevated IOP.

Animals ; Blotting, Western ; Brain-Derived Neurotrophic Factor ; analysis ; Immunohistochemistry ; Intraocular Pressure ; physiology ; Ischemia ; metabolism ; Male ; Nerve Growth Factor ; analysis ; Protein Precursors ; analysis ; Rats ; Rats, Wistar ; Retinal Diseases ; metabolism