Proteomic profiling of protein expression changes after 3 months-exercise in ESRD patients on hemodialysis.

The prevalence of chronic kidney disease (CKD) is steadily increasing, and it is a global health burden. Exercise has been suggested to improve physical activity and the quality of life in patients with CKD, eventually reducing mortality. This study investigated the change in physical performance after exercise in dialysis-dependent patients with CKD and analyzed differentially expressed proteins before and after the exercise. Plasma samples were collected at enrollment and after 3 months of exercise. Liquid chromatography with tandem mass spectrometry analysis and data-independent acquisition results were analyzed to determine the significantly regulated proteins. A total of 37 patients on dialysis were recruited, and 16 were randomized to exercise for 3 months. The hand grip strength and the walking speed significantly improved in the exercise group. Proteome analysis revealed 60 significantly expressed proteins after 3 months of exercise. In the protein functional analysis, the significantly expressed proteins were involved in the immune response. Also, some of the key significantly expressed proteins [(M Matrix metallopeptidase 9 (MMP-9), Activin A Receptor Type 1B (ACVR1B), Fetuin B (FETUB)] were validated via an enzyme-linked immunosorbent assay. Our results showed that exercise in dialysis-dependent patients with CKD could improve their physical performance. These results indicated that this beneficial effect of exercise in these populations could be associated with immune response.

Effect of acupuncture on Lipopolysaccharide-induced anxiety-like behavioral changes: involvement of serotonin system in dorsal Raphe nucleus.

BACKGROUND: Acupuncture has been used as a common therapeutic tool in many disorders including anxiety and depression. Serotonin transporter (SERT) plays an important role in the pathology of anxiety and other mood disorders. The aim of this study was to evaluate the effects of acupuncture on lipopolysaccharide (LPS)-induced anxiety-like behaviors and SERT in the dorsal raphe nuclei (DRN). METHODS: Rats were given acupuncture at ST41 (Jiexi), LI11 (Quchi) or SI3 (Houxi) acupoint in LPS-treated rats. Anxiety-like behaviors of elevated plus maze (EPM) and open field test (OFT) were measured and expressions of SERT and/or c-Fos were also examined in the DRN using immunohistochemistry. RESULTS: The results showed that 1) acupuncture at ST41 acupoint, but neither LI11 nor SI3, significantly attenuated LPS-induced anxiety-like behaviors in EPM and OFT, 2) acupuncture at ST41 decreased SERT expression increased by LPS in the DRN. CONCLUSIONS: Our results suggest that acupuncture can ameliorate anxiety-like behaviors, possibly through regulation of SERT in the DRN.

Simple binary segmentation frameworks for identifying variation in DNA copy number.

BACKGROUND: Variation in DNA copy number, due to gains and losses of chromosome segments, is common. A first step for analyzing DNA copy number data is to identify amplified or deleted regions in individuals. To locate such regions, we propose a circular binary segmentation procedure, which is based on a sequence of nested hypothesis tests, each using the Bayesian information criterion. RESULTS: Our procedure is convenient for analyzing DNA copy number in two general situations: (1) when using data from multiple sources and (2) when using cohort analysis of multiple patients suffering from the same type of cancer. In the first case, data from multiple sources such as different platforms, labs, or preprocessing methods are used to study variation in copy number in the same individual. Combining these sources provides a higher resolution, which leads to a more detailed genome-wide survey of the individual. In this case, we provide a simple statistical framework to derive a consensus molecular signature. In the framework, the multiple sequences from various sources are integrated into a single sequence, and then the proposed segmentation procedure is applied to this sequence to detect aberrant regions. In the second case, cohort analysis of multiple patients is carried out to derive overall molecular signatures for the cohort. For this case, we provide another simple statistical framework in which data across multiple profiles is standardized before segmentation. The proposed segmentation procedure is then applied to the standardized profiles one at a time to detect aberrant regions. Any such regions that are common across two or more profiles are probably real and may play important roles in the cancer pathogenesis process. CONCLUSIONS: The main advantages of the proposed procedure are flexibility and simplicity.

A SATS algorithm for jointly identifying multiple differentially expressed gene sets.

A gene set in DNA microarrays is a group of genes that share a common biological function, chromosomal location, or regulation. This paper discusses the problem of jointly identifying multiple differentially expressed gene sets associated with a phenotype of interest from many hundreds of pre-defined gene sets in a microarray experiment. We propose a null hypothesis that any group of gene sets from the experiment is not differentially expressed. The hypothesis is applicable to a real microarray experiment, where only a fraction of gene sets examined in the experiment are differentially expressed. To test this hypothesis, we provide an algorithm called set association for tail strength (SATS). SATS assigns the tail-strength statistic (TS) to each gene set to measure differential expression that is related to the phenotype of interest, combines the statistics into an overall association measure of multiple gene sets by utilizing a set-association method, and then calculates the significance of the overall measure by conducting sample permutations. SATS performs a simultaneous significance test on several gene sets, while controlling the Type I error rate. As multiple gene sets work together toward the significance, SATS can capture correlations across gene sets that should be considered in assessing joint statistical significance.

Hydroxyapatite scaffolds processed using a TBA-based freeze-gel casting/polymer sponge technique.

A novel freeze-gel casting/polymer sponge technique has been introduced to fabricate porous hydroxyapatite scaffolds with controlled "designer" pore structures and improved compressive strength for bone tissue engineering applications. Tertiary-butyl alcohol (TBA) was used as a solvent in this work. The merits of each production process, freeze casting, gel casting, and polymer sponge route were characterized by the sintered microstructure and mechanical strength. A reticulated structure with large pore size of 180-360 microm, which formed on burn-out of polyurethane foam, consisted of the strut with highly interconnected, unidirectional, long pore channels (approximately 4.5 microm in dia.) by evaporation of frozen TBA produced in freeze casting together with the dense inner walls with a few, isolated fine pores (<2 microm) by gel casting. The sintered porosity and pore size generally behaved in an opposite manner to the solid loading, i.e., a high solid loading gave low porosity and small pore size, and a thickening of the strut cross section, thus leading to higher compressive strengths.

Biomimetic whisker-shaped apatite coating of titanium powder.

Biomimetic apatite coatings on chemically modified titanium powder have been processed and the resulting coating layers evaluated in terms of morphology, composition and structure, using TF-XRD, XPS, SEM, TEM and FTIR analysis. After 7 days immersion in a simulated body fluid (SBF), nanometer-sized fine precipitates with an amorphous whisker-like phase and a Ca/P atomic ratio of 1.94 were obtained on the external surface of the titanium particles. When the immersion time in SBF was extended to 16 days, the coating layer consisted of the whisker-like nanostructured crystals of carbonated hydroxyapatite with a atomic ratio of 3; in such a case, a double coating layer was developed. The double layer could be divided into two regions and could be clearly distinguished: an inner dense region (approximately 200 nm in thickness) which may include hard agglomerated crystals and an outer less dense region (> 500 nm in thickness) in which crystals are loosely distributed.

Rosiglitazone stimulates the release and synthesis of insulin by enhancing GLUT-2, glucokinase and BETA2/NeuroD expression.

Peroxisome proliferator-activated receptor (PPAR)-gamma is a member of the nuclear receptor superfamily, and its ligands, the thiazolidinediones, might directly stimulate insulin release and insulin synthesis in pancreatic beta-cells. In the present study, we examined the effects of rosiglitazone (RGZ) on insulin release and synthesis in pancreatic beta-cell (INS-1). Insulin release and synthesis were stimulated by treatment with RGZ for 24h. RGZ upregulated the expressions of GLUT-2 and glucokinase (GCK). Moreover, it was found that RGZ increased the expression of BETA2/NeuroD gene which could regulate insulin gene expression. These results suggest that RGZ could stimulate the release and synthesis of insulin through the upregulation of GLUT-2, GCK, and BETA2/NeuroD gene expression.

Effects of activin A on pancreatic ductal cells in streptozotocin-induced diabetic rats.

BACKGROUND: The shortage of islets for transplantation has led to find alternative insulin producing cells. Pancreatic progenitor cells in the duct have the potential to grow and differentiate into endocrine cells. In this study, we examined whether activin A can promote the expansion and/or differentiation of ductal cells into insulin-producing cells. METHODS: Pancreatic ductal cells were treated with activin A for differentiation into endocrine cells, and transplanted into the renal subcapsular space of streptozotocin (STZ)-induced diabetic rats. The identity of the endocrine cells was confirmed by immunostaining and analysis of the expression of transcription factors and endocrine genes by reverse-transcriptase polymerase chain reaction. RESULTS: Activin A treatment significantly increased the DNA synthesis and the expression of insulin I, insulin II, PDX-1, Nkx 6.1, Glut-2, Pax-4, Pax-6, and Ngn-3. De novo synthesis of insulin in activin A-treated ductal cells was observed by the immunocytochemical detection of C-peptide and the differentiated ductal cells secreted significantly increased amount of insulin compared to nontreated ductal cells in response to glucose stimulation. When activin A-treated ductal cells were transplanted on STZ-induced diabetic rats, blood glucose levels were normalized and the removal of the transplanted kidney resulted in return to hyperglycemia. CONCLUSIONS: The pancreatic ductal cells could be efficiently differentiated into insulin secreting cells by activin A treatment in vitro and normalize hyperglycemia in vivo.

Distribution of eschars on the body of scrub typhus patients: a prospective study.

Eschar is an important finding for the diagnosis of scrub typhus. The IFA test for possible scrub typhus was performed. The presence or absence of eschar was thoroughly examined. Among the 176 scrub typhus cases confirmed by IFA, 162 (92.0%) cases had eschar; 128 patients (79.5%) had eschars on the front of the body. Eschars were primarily detected in males within 30 cm below the umbilicus (19 patients, 35.8%). Distributions on the lower extremities and the front chest above the umbilicus were 22.6% (12 patients) and 20.8% (11 patients), respectively. A different pattern was seen in females. The most prevalent area was the front chest above the umbilicus, which accounted for 40.7% (44 patients) of all the detected eschars. Our study is the first report of a schematic diagram that shows the differences between the males and females with respect to eschar location in scrub typhus patients.

Clinical usefulness of eschar polymerase chain reaction for the diagnosis of scrub typhus: a prospective study.

BACKGROUND: The aim of this study was to determine the diagnostic utility of performing eschar polymerase chain reaction (PCR) for the diagnosis of scrub typhus through a prospective comparison of eschar PCR results with indirect immunofluorescent antibody assay (IFA) results. METHODS: We conducted a multicenter prospective study involving patients with possible scrub typhus. Whole-blood samples and eschars were obtained for serological evaluation and PCR. A new crust was formed several days later at the site of the removed eschar. The newly formed crust was taken for performance of the second eschar PCR. Additional blood samples and eschars were collected, if possible, at 1-week intervals for 1 month after antibiotic treatment. RESULTS: We prospectively studied 135 patients with possible scrub typhus. Of these patients, 118 had scrub typhus confirmed on the basis of either a single indirect immunofluorescent specific immunoglobulin M titer against Orientia tsutsugamushi of > or = 1:10 or a > or = 4-fold increase in the follow-up titer. The results of nested PCR assay of the eschars demonstrated a sensitivity of 0.86 (95% confidence interval, 0.78-0.92) and a specificity of 1 (95% confidence interval, 0.05-1). Among the 50 patients who showed positive results of eschar PCR at admission, 46 (92%) also showed positive results for the follow-up PCR test of the newly formed eschar after the treatment with antibiotics. CONCLUSIONS: The eschar PCR assay was useful as a rapid and reliable test to confirm the diagnosis of scrub typhus, even though the patients received treatment with appropriate antibiotics, such as macrolides, quinolones, and tetracycline, which are all active against Orientia and Rickettsia species.

Usefulness of nested PCR for the diagnosis of scrub typhus in clinical practice: A prospective study.

The aims of this study were to determine the diagnostic accuracy and clinical usefulness of using nested polymerase chain reaction (PCR) for the diagnosis of scrub typhus through a prospective comparison of nested PCR and indirect immunofluorescent antibody assay (IFA). We conducted a multi-center prospective study of patients who were suffering with possible scrub typhus infection. Whole blood samples were collected for PCR testing, and sera were obtained for serology evaluation using the indirect IFA and the passive hemagglutination assay (PHA). We prospectively studied 135 patients with possible scrub typhus. One hundred eighteen patients were confirmed as having scrub typhus, 7 patients were undetermined, and 10 patients were confirmed as having other diseases. The results of nested PCR assay showed a sensitivity of 82.2% and a specificity of 100%. Ninety-six of the 118 patients were positive for IgM on their admission day. Of the 22 patients who were negative for IgM antibody at admission, 19 had positive results for nested PCR of the buffy coat. The nested PCR assay of the buffy coat is useful as a rapid and reliable test for confirming the diagnosis of scrub typhus.

Hepatic Infarction Caused by Portal Vein Thrombophlebitis Misdiagnosed as Infiltrative Hepatic Malignancy with Neoplastic Thrombus.

Portal vein thrombosis (PVT) is a form of venous thrombosis that usually presents in chronic form without any sequalae in patients with hepatocellular carcinoma (HCC) or liver cirrhosis. Accurate differential diagnosis of bland PVT from neoplastic PVT is an important step for planning treatment options, but the acute form can be challenging. Here we present a case of acute hepatic infarction caused by acute bland PVT combined with pylephlebitis, which was misdiagnosed as infiltrative hepatic malignancy with neoplastic PVT owing to the perplexing imaging results and elevated tumor markers.

A Simple Rank Product Approach for Analyzing Two Classes.

The rank product statistic has been widely used to detect differentially expressed genes in replicated microarrays and a one-class setting. The objective of this article is to apply a rank product statistic to approximate the P-value of differential expression in a two-class setting, such as in normal and cancer cells. For this purpose, we introduce a simple statistic that compares the P-values of each class's rank product statistic. Its null distribution is straightforwardly derived using the change-of-variable technique.

First human trial of pancreatic islet allo-transplantation in Korea--focus on re-transplantation.

Over the past 20 years, allo-transplantation of islet or whole pancreas for reaching and sustaining near-normoglycemia, as close as possible to the physiological model, have been undertaken. As previously known, even though islet transplantation is possible as a safe re-transplant, it is not well known whether re-transplantation of islets is suitable for patients who have lost the grafted islet function. We have performed a human islet allo-transplantation and re-transplantation on an IDDM patient for the first time in Asia and Korea. The recipient was a 32-year-old male and his insulin requirement was 75-85 U per day. After islet transplantation, the basal C-peptide increased from 0.6 to 2.1 ng/ml and insulin requirement decreased from 80 to 36 U per day, indicating that the grafted islets were functional. However, the grafted islets lost function 70 days after the transplantation. So, we performed re-transplantation of the islets. After the re-transplantation, the glucose profile became more stable and frequent episodes of severe hypoglycemia completely disappeared. His severe neuropathic pain improved dramatically and he could engage his ordinary daily life without any antineuropathic drugs. The success of this re-transplantation is one step closer to becoming a viable alternative for the millions of individuals who are suffering from diabetes.

Grouped False-Discovery Rate for Removing the Gene-Set-Level Bias of RNA-seq.

In recent years, RNA-seq has become a very competitive alternative to microarrays. In RNA-seq experiments, the expected read count for a gene is proportional to its expression level multiplied by its transcript length. Even when two genes are expressed at the same level, differences in length will yield differing numbers of total reads. The characteristics of these RNA-seq experiments create a gene-level bias such that the proportion of significantly differentially expressed genes increases with the transcript length, whereas such bias is not present in microarray data. Gene-set analysis seeks to identify the gene sets that are enriched in the list of the identified significant genes. In the gene-set analysis of RNA-seq, the gene-level bias subsequently yields the gene-set-level bias that a gene set with genes of long length will be more likely to show up as enriched than will a gene set with genes of shorter length. Because gene expression is not related to its transcript length, any gene set containing long genes is not of biologically greater interest than gene sets with shorter genes. Accordingly the gene-set-level bias should be removed to accurately calculate the statistical significance of each gene-set enrichment in the RNA-seq. We present a new gene set analysis method of RNA-seq, called FDRseq, which can accurately calculate the statistical significance of a gene-set enrichment score by the grouped false-discovery rate. Numerical examples indicated that FDRseq is appropriate for controlling the transcript length bias in the gene-set analysis of RNA-seq data. To implement FDRseq, we developed the R program, which can be downloaded at no cost from http://home.mju.ac.kr/home/index.action?siteId=tyang.

Differences in clinical features according to Boryoung and Karp genotypes of Orientia tsutsugamushi.

BACKGROUND: Scrub typhus is an infectious disease caused by Orientia tsutsugamushi. The differences in virulence of O. tsutsugamushi prototypes in humans are still unknown. We investigated whether there are any differences in the clinical features of the Boryoung and Karp genotypes. METHODOLOGY/PRINCIPAL FINDINGS: Patients infected with O. tsutsugamushi, as Boryoung and Karp clusters, who had visited 6 different hospitals in southwestern Korea were prospectively compared for clinical features, complications, laboratory parameters, and treatment responses. Infected patients in the Boryoung cluster had significantly more generalized weakness, eschars, skin rashes, conjunctival injection, high albumin levels, and greater ESR and fibrinogen levels compared to the Karp cluster. The treatment response to current antibiotics was significantly slower in the Karp cluster as compared to the Boryoung cluster. CONCLUSION: The frequency of occurrence of eschars and rashes may depend on the genotype of O. tsutsugamushi.

Delayed improvement of insulin secretion after autologous islet transplantation in partially pancreatectomized patients.

The purpose of this study was to evaluate the effects of autologous islet transplantation (ITx) on glucose homeostasis and insulin secretory function after partial pancreatectomy (Px). Fourteen nondiabetic patients who underwent distal Px and autologous ITx for benign pancreatic tumors were enrolled in the study (Px + ITx group). Fourteen normal glucose-tolerant controls and 6 Px without ITx controls were recruited, and all groups were followed over a 24-month period. They performed the 75-g oral glucose tolerance test and the 1-mg glucagon stimulation test. Hemoglobin A(1c) was measured, and indices of insulin secretion were calculated. In the Px + ITx group, insulin secretion increased after a nadir at 6 months. Glucose tolerance, which had been abruptly impaired immediately after Px, recovered until 6 months and stabilized thereafter. As a result, differences in glucose intolerance emerged between the subjects in the Px group and those in the Px + ITx group at 24 months after Px. Characteristic variables in the better insulin secretory subjects in the Px + ITx group included younger age, less extensive pancreas resection, and a greater number of total islets. In summary, delayed amelioration of glucose intolerance was induced by autologous ITx after partial Px, even with a small number of islets.

The simple classification of multiple cancer types using a small number of significant genes.

BACKGROUND AND OBJECTIVE: The problems involved in the classification of cancers have recently received a great deal of attention in the context of DNA microarrays. We propose a simple procedure for classifying or predicting the cancer types of test samples when multiple cancer types and many genes are present. METHOD: The procedure sequentially combines a gene-sort algorithm and a predictive likelihood-based classifier. Genes that have homogeneous patterns of expression measurements across cancer types are of limited interest. Therefore, this algorithm orders genes on the basis of strong heterogeneous patterns. The proposed classifier then selects the first few genes, which are sufficient to classify most training samples correctly via cross validation. Test samples were classified using only the selected genes. RESULTS AND CONCLUSION: This predictive likelihood-based classifier performs well and is simple to understand. Empirical examination revealed good classification accuracy using relatively few genes.

A tree-based model for homogeneous groupings of multinomials.

The motivation of this paper is to provide a tree-based method for grouping multinomial data according to their classification probability vectors. We produce an initial tree by binary recursive partitioning whereby multinomials are successively split into two subsets and the splits are determined by maximizing the likelihood function. If the number of multinomials k is too large, we propose to order the multinomials, and then build the initial tree based on a dramatically smaller number k-1 of possible splits. The tree is then pruned from the bottom up. The pruning process involves a sequence of hypothesis tests of a single homogeneous group against the alternative that there are two distinct, internally homogeneous groups. As pruning criteria, the Bayesian information criterion and the Wilcoxon rank-sum test are proposed. The tree-based model is illustrated on genetic sequence data. Homogeneous groupings of genetic sequences present new opportunities to understand and align these sequences.