DoSurvive: A webtool for investigating the prognostic power of a single or combined cancer biomarker

We present DoSurvive, a user-friendly survival analysis web tool and a cancer prognostic biomarker centered database. DoSurvive is the first database that allows users to perform multivariant survival analysis for cancers with customized gene/patient list. DoSurvive offers three survival analysis methods, Log rank test, Cox regression and accelerated failure time model (AFT), for users to analyze five types of quantitative features (mRNA, miRNA, lncRNA, protein and methylation of CpG islands) with four survival types, i.e. overall survival, disease-specific survival, disease-free interval, and progression-free interval, in 33 cancer types. Notably, the implemented AFT model provides an alternative method for genes/features which failed the proportional hazard assumption in Cox regression. With the unprecedented number of survival models implemented and high flexibility in analysis, DoSurvive is a unique platform for the identification of clinically relevant targets for cancer researcher and practitioners. DoSurvive is freely available at http://dosurvive.lab.nycu.edu.tw/.

Global survival trends for brain tumors, by histology: analysis of individual records for 556,237 adults diagnosed in 59 countries during 2000-2014 (CONCORD-3)

BACKGROUND

Survival is a key metric of the effectiveness of a health system in managing cancer. We set out to provide a comprehensive examination of worldwide variation and trends in survival from brain tumors in adults, by histology.

METHODS

We analyzed individual data for adults (15-99 years) diagnosed with a brain tumor (ICD-O-3 topography code C71) during 2000-2014, regardless of tumor behavior. Data underwent a 3-phase quality control as part of CONCORD-3. We estimated net survival for 11 histology groups, using the unbiased nonparametric Pohar Perme estimator.

RESULTS

The study included 556,237 adults. In 2010-2014, the global range in age-standardized 5-year net survival for the most common sub-types was broad: in the range 20%-38% for diffuse and anaplastic astrocytoma, from 4% to 17% for glioblastoma, and between 32% and 69% for oligodendroglioma. For patients with glioblastoma, the largest gains in survival occurred between 2000-2004 and 2005-2009. These improvements were more noticeable among adults diagnosed aged 40-70 years than among younger adults.

CONCLUSIONS

To the best of our knowledge, this study provides the largest account to date of global trends in population-based survival for brain tumors by histology in adults. We have highlighted remarkable gains in 5-year survival from glioblastoma since 2005, providing large-scale empirical evidence on the uptake of chemoradiation at population level. Worldwide, survival improvements have been extensive, but some countries still lag behind. Our findings may help clinicians involved in national and international tumor pathway boards to promote initiatives aimed at more extensive implementation of clinical guidelines.

The effect of androgen on wool follicles and keratin production in Hetian sheep

To investigate the optimal androgen concentration for culturing Hetian sheep wool follicle and to detect effects of androgen concentration on wool follicle cell proliferation and apoptosis using immunofluorescence labeling and real-time quantitative fluorescence determinations of wool keratin-associated protein gene expression levels. Wool follicles were isolated by microdissection and wool follicles and skin pieces were cultured in various concentrations of dihydrotestosterone (DHT) in culture medium. Next, daily lengthwise growth measurements of wool follicles were obtained using a microscopic micrometer. Cultured Hetian wool follicles were stained using the SACPIC method to reveal wool follicle structure, while sheep skin slices were used to observe cell proliferation by immunostaining and cell apoptosis using the TUNEL method. At the molecular biological level, keratin-associated protein (Kap) gene expression was studied using wool follicles cultured for various numbers of days in vitro. Effects of androgen concentrations on Hetian wool follicle growth and development were experimentally studied. EdU proliferation assays revealed that androgen promoted cell proliferation within wool follicle dermal papillae. TUNEL apoptosis detection demonstrated that androgen treatment could delay cell apoptosis. Quantitative reverse transcription polymerase chain reaction (qPCR) results demonstrated that gene expression level patterns of Hetian mountain sheep super-high sulfur protein. Kap1.1, KIF1.2, Kap2.12 and Kap4.2 gene expression level of the mountainous experimental group was significantly higher than plains Hetian sheep. An androgen concentration of 100 nM can promote the growth of Hetian wool follicle cells in vitro, resulting in overexpression of some genes of the Kap family.

N-acetylgalactosamine-6-sulfatase (GALNS), Similar to Glycodelin, Is a Potential General Biomarker for Multiple Malignancies

BACKGROUND/AIM

The aim of this study was to evaluate N-acetylgalactosamine-6-sulfatase (GALNS) as a new biomarker candidate for detecting lung cancer. Glycodelin or PAEP, the serum levels of which are known to be elevated in lung and other cancers, served as a benchmark for comparison.

PATIENTS AND METHODS

A total of 170 serum samples from healthy controls and patients with pneumonia, lung cancer, breast cancer, colon cancer, liver cancer, and head and neck cancer were analyzed for the levels of GALNS and PAEP by ELISA.

RESULTS

The median serum levels of GALNS and PAEP in all cancer types as well as pneumonia patients were significantly higher than those of the healthy controls.

CONCLUSION

In addition to previously known cancers, the median serum levels of PAEP were also found to be higher in liver and head and neck cancer patients. GALNS and PAEP are promising general biomarkers for multiple cancers and deserve further evaluation.

PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms

Background

Next-generation sequencing promises the de novo genomic and transcriptomic analysis of samples of interests. However, there are only a few organisms having reference genomic sequences and even fewer having well-defined or curated annotations. For transcriptome studies focusing on organisms lacking proper reference genomes, the common strategy is de novo assembly followed by functional annotation. However, things become even more complicated when multiple transcriptomes are compared.

Results

Here, we propose a new analysis strategy and quantification methods for quantifying expression level which not only generate a virtual reference from sequencing data, but also provide comparisons between transcriptomes. First, all reads from the transcriptome datasets are pooled together for de novo assembly. The assembled contigs are searched against NCBI NR databases to find potential homolog sequences. Based on the searched result, a set of virtual transcripts are generated and served as a reference transcriptome. By using the same reference, normalized quantification values including RC (read counts), eRPKM (estimated RPKM) and eTPM (estimated TPM) can be obtained that are comparable across transcriptome datasets. In order to demonstrate the feasibility of our strategy, we implement it in the web service PARRoT. PARRoT stands for Pipeline for Analyzing RNA Reads of Transcriptomes. It analyzes gene expression profiles for two transcriptome sequencing datasets. For better understanding of the biological meaning from the comparison among transcriptomes, PARRoT further provides linkage between these virtual transcripts and their potential function through showing best hits in SwissProt, NR database, assigning GO terms. Our demo datasets showed that PARRoT can analyze two paired-end transcriptomic datasets of approximately 100 million reads within just three hours.

Conclusions

In this study, we proposed and implemented a strategy to analyze transcriptomes from non-reference organisms which offers the opportunity to quantify and compare transcriptome profiles through a homolog based virtual transcriptome reference. By using the homolog based reference, our strategy effectively avoids the problems that may cause from inconsistencies among transcriptomes. This strategy will shed lights on the field of comparative genomics for non-model organism. We have implemented PARRoT as a web service which is freely available at http://parrot.cgu.edu.tw.

Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing

BACKGROUND

Whole genome sequence construction is becoming increasingly feasible because of advances in next generation sequencing (NGS), including increasing throughput and read length. By simply overlapping paired-end reads, we can obtain longer reads with higher accuracy, which can facilitate the assembly process. However, the influences of different library sizes and assembly methods on paired-end sequencing-based de novo assembly remain poorly understood.

RESULTS

We used 250 bp Illumina Miseq paired-end reads of different library sizes generated from genomic DNA from Escherichia coli DH1 and Streptococcus parasanguinis FW213 to compare the assembly results of different library sizes and assembly approaches. Our data indicate that overlapping paired-end reads can increase read accuracy but sometimes cause insertion or deletions. Regarding genome assembly, merged reads only outcompete original paired-end reads when coverage depth is low, and larger libraries tend to yield better assembly results. These results imply that distance information is the most critical factor during assembly. Our results also indicate that when depth is sufficiently high, assembly from subsets can sometimes produce better results.

CONCLUSIONS

In summary, this study provides systematic evaluations of de novo assembly from paired end sequencing data. Among the assembly strategies, we find that overlapping paired-end reads is not always beneficial for bacteria genome assembly and should be avoided or used with caution especially for genomes containing high fraction of repetitive sequences. Because increasing numbers of projects aim at bacteria genome sequencing, our study provides valuable suggestions for the field of genomic sequence construction.

ChIPseek, a web-based analysis tool for ChIP data

Background

Chromatin is a dynamic but highly regulated structure. DNA-binding proteins such as transcription factors, epigenetic and chromatin modifiers are responsible for regulating specific gene expression pattern and may result in different phenotypes. To reveal the identity of the proteins associated with the specific region on DNA, chromatin immunoprecipitation (ChIP) is the most widely used technique. ChIP assay followed by next generation sequencing (ChIP-seq) or microarray (ChIP-chip) is often used to study patterns of protein-binding profiles in different cell types and in cancer samples on a genome-wide scale. However, only a limited number of bioinformatics tools are available for ChIP datasets analysis.

Results

We present ChIPseek, a web-based tool for ChIP data analysis providing summary statistics in graphs and offering several commonly demanded analyses. ChIPseek can provide statistical summary of the dataset including histogram of peak length distribution, histogram of distances to the nearest transcription start site (TSS), and pie chart (or bar chart) of genomic locations for users to have a comprehensive view on the dataset for further analysis. For examining the potential functions of peaks, ChIPseek provides peak annotation, visualization of peak genomic location, motif identification, sequence extraction, and comparison between datasets. Beyond that, ChIPseek also offers users the flexibility to filter peaks and re-analyze the filtered subset of peaks. ChIPseek supports 20 different genome assemblies for 12 model organisms including human, mouse, rat, worm, fly, frog, zebrafish, chicken, yeast, fission yeast, Arabidopsis, and rice. We use demo datasets to demonstrate the usage and intuitive user interface of ChIPseek.

Conclusions

ChIPseek provides a user-friendly interface for biologists to analyze large-scale ChIP data without requiring any programing skills. All the results and figures produced by ChIPseek can be downloaded for further analysis. The analysis tools built into ChIPseek, especially the ones for selecting and examine a subset of peaks from ChIP data, provides invaluable helps for exploring the high through-put data from either ChIP-seq or ChIP-chip. ChIPseek is freely available at http://chipseek.cgu.edu.tw.

Radiation doses of cerebral blood volume measurements using C-arm CT: A phantom study

BACKGROUND AND PURPOSE

Parenchymal blood volume measurement by C-arm CT facilitates in-room peritherapeutic perfusion evaluation. However, the radiation dose remains a major concern. This study aimed to compare the radiation dose of parenchymal blood volume measurement using C-arm CT with that of conventional CTP using multidetector CT.

MATERIALS AND METHODS

A biplane DSA equipped with C-arm CT and a Rando-Alderson phantom were used. Slab parenchymal blood volume (8-cm scanning range in a craniocaudal direction) and whole-brain parenchymal blood volume with identical scanning parameters, except for scanning ranges, were undertaken on DSA. Eighty thermoluminescent dosimeters were embedded into 22 organ sites of the phantom. We followed the guidelines of the International Commission on Radiation Protection number 103 to calculate the effective doses. For comparison, 8-cm CTP with the same phantom and thermoluminescent dosimeter distribution was performed on a multidetector CT. Two repeat dose experiments with the same scanning parameters and phantom and thermoluminescent dosimeter settings were conducted.

RESULTS

Brain-equivalent dose in slab parenchymal blood volume, whole-brain parenchymal blood volume, and CTP were 52.29 ± 35.31, 107.51 ± 31.20, and 163.55 ± 89.45 mSv, respectively. Variations in the measurement of an equivalent dose for the lens were highest in slab parenchymal blood volume (64.5%), followed by CTP (54.6%) and whole-brain parenchymal blood volume (29.0%). The effective doses of slab parenchymal blood volume, whole-brain parenchymal blood volume, and CTP were 0.87 ± 0.55, 3.91 ± 0.78, and 2.77 ± 1.59 mSv, respectively.

CONCLUSIONS

The dose measurement conducted in the current study was reliable and reproducible. The effective dose of slab parenchymal blood volume is about one-third that of CTP. With the advantages of on-site and immediate imaging availability and saving procedural time and patient transportation, slab parenchymal blood volume measurement using C-arm CT can be recommended for clinical application.

Large precursor tolerance database search - a simple approach for estimation of the amount of spectra with precursor mass shifts in proteomic data

Mass measurement and precursor mass assignment are independent processes in proteomic data acquisition. Due to misassignments to C-13 peak, or for other reasons, extensive precursor mass shifts (i.e., deviations of the measured from calculated precursor neutral masses) in LC-MS/MS data obtained with the high-accuracy LTQ-Orbitrap mass spectrometers have been reported in previous studies. Although computational methods for post-acquisition reassignment to monoisotopic mass have been developed to curate the MS/MS spectra prior to database search, a simpler method for estimating the fraction of spectra with precursor mass shift so as to determine whether the data require curation remains desirable. Here, we provide the evidence that an easy approach, which applies a large precursor tolerance (2.1Da or higher) in SEQUEST search against a forward and decoy protein sequence database and then filters the data with PeptideProphet peptide identification probability (p≥0.9), could detect most of the MS/MS spectra containing inaccurate precursor masses. Furthermore, through the implementation of artificial mass shifts on 4000 randomly selected MS/MS spectra, which originally had accurate precursor mass assigned by the mass spectrometers, we demonstrated that the accuracy of the precursor mass has almost negligible influence on the efficacy and fidelity of peptide identification.

BIOLOGICAL SIGNIFICANCE

Integral precursor mass shift is a known problem and thus proteomic data should be handled and analyzed properly to avoid losing important protein identification and/or quantification information. A quick and easy approach for estimating the number of MS/MS spectra with inaccurate precursor mass assignments would be helpful for evaluating the performance of the instrument, determining whether the data requires curation prior to database search or should be searched with specific search parameter(s). Here we demonstrated most of the MS/MS spectra with inaccurate mass assignments (integral or non-integral changes) that could be easily identified by database search with large precursor tolerance windows.

Can iterative reconstruction improve imaging quality for lower radiation CT perfusion? Initial experience

BACKGROUND AND PURPOSE

Initial results using IR for CT of the head showed satisfactory subjective and objective imaging quality with a 20-40% radiation dose reduction. The aim of our study was to compare the influence of IR and FBP algorithms on perfusion parameters at standard and lowered doses of CTP.

MATERIALS AND METHODS

Forty patients with unilateral carotid stenosis post-carotid stent placement referred for follow-up CTP were divided into 2 groups (tube currents were 100 mAs in group A and 80 mAs in group B). Datasets were reconstructed with IR and FBP algorithms; and SNRs of gray matter, white matter, and arterial and venous ROIs were compared. CBF, CBV, and MTT means and SNRs were evaluated by using linear regression, and qualitative imaging scores were compared across the 2 algorithms.

RESULTS

The mean effective radiation dose of group B (2.06 mSv) was approximately 20% lower than that of group A (2.56 mSv). SNRs for ROIs in the dynamic contrast-enhanced images were significantly higher than those for the FBP images. Correlations of the SNRs for CBF, CBV, and MTT across the 2 algorithms were moderate (R² = 0.46, 0.23, and 0.44, respectively). ROIs in gray matter rather than the IR algorithm predicted increasing SNRs in all CBF, CBV, and MTT maps. Two cases of significant restenosis were confirmed in both algorithms. CBV, CBF, and MTT imaging scores did not differ significantly across algorithms or groups.

CONCLUSIONS

Lower dose CTP (20% below normal dose) without IR can effectively identify oligemic tissue in poststenting follow-up. IR does not alter the absolute values or increase the SNRs of perfusion parameters. Other methods should be attempted to improve SNRs in settings with low tube currents.

Three dimensional microfluidics with embedded microball lenses for parallel and high throughput multicolor fluorescence detection

We report a 3D microfluidic device with 32 detection channels and 64 sheath flow channels and embedded microball lens array for high throughput multicolor fluorescence detection. A throughput of 358 400 cells/s has been accomplished. This device is realized by utilizing solid immersion micro ball lens arrays for high sensitivity and parallel fluorescence detection. High refractive index micro ball lenses (n = 2.1) are embedded underneath PDMS channels close to cell detection zones in channels. This design permits patterning high N.A. micro ball lenses in a compact fashion for parallel fluorescence detection on a small footprint device. This device also utilizes 3D microfluidic fabrication to address fluid routing issues in two-dimensional parallel sheath focusing and allows simultaneous pumping of 32 sample channels and 64 sheath flow channels with only two inlets.

Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates

Background

Researches have been conducted for the identification of differentially expressed genes (DEGs) by generating and mining of cDNA expressed sequence tags (ESTs) for more than a decade. Although the availability of public databases make possible the comprehensive mining of DEGs among the ESTs from multiple tissue types, existing studies usually employed statistics suitable only for two categories. Multi-class test has been developed to enable the finding of tissue specific genes, but subsequent search for cancer genes involves separate two-category test only on the ESTs of the tissue of interest. This constricts the amount of data used. On the other hand, simple pooling of cancer and normal genes from multiple tissue types runs the risk of Simpson's paradox. Here we presented a different approach which searched for multi-cancer DEG candidates by analyzing all pertinent ESTs in all categories and narrowing down the cancer biomarker candidates via integrative analysis with microarray data and selection of secretory and membrane protein genes as well as incorporation of network analysis. Finally, the differential expression patterns of three selected cancer biomarker candidates were confirmed by real-time qPCR analysis.

Results

Seven hundred and twenty three primary DEG candidates (p-value < 0.05 and lower bound of confidence interval of odds ratio ≧ 1.65) were selected from a curated EST database with the application of Cochran-Mantel-Haenszel statistic (CMH). GeneGO analysis results indicated this set as neoplasm enriched. Cross-examination with microarray data further narrowed the list down to 235 genes, among which 96 had membrane or secretory annotations. After examined the candidates in protein interaction network, public tissue expression databases, and literatures, we selected three genes for further evaluation by real-time qPCR with eight major normal and cancer tissues. The higher-than-normal tissue expression of COL3A1, DLG3, and RNF43 in some of the cancer tissues is in agreement with our in silico predictions.

Conclusions

Searching digitized transcriptome using CMH enabled us to identify multi-cancer differentially expressed gene candidates. Our methodology demonstrated simultaneously analysis for cancer biomarkers of multiple tissue types with the EST data. With the revived interest in digitizing the transcriptomes by NGS, cancer biomarkers could be more precisely detected from the ESTs. The three candidates identified in this study, COL3A1, DLG3, and RNF43, are valuable targets for further evaluation with a larger sample size of normal and cancer tissue or serum samples.

FastAnnotator--an efficient transcript annotation web tool

BACKGROUND

Recent developments in high-throughput sequencing (HTS) technologies have made it feasible to sequence the complete transcriptomes of non-model organisms or metatranscriptomes from environmental samples. The challenge after generating hundreds of millions of sequences is to annotate these transcripts and classify the transcripts based on their putative functions. Because many biological scientists lack the knowledge to install Linux-based software packages or maintain databases used for transcript annotation, we developed an automatic annotation tool with an easy-to-use interface.

METHODS

To elucidate the potential functions of gene transcripts, we integrated well-established annotation tools: Blast2GO, PRIAM and RPS BLAST in a web-based service, FastAnnotator, which can assign Gene Ontology (GO) terms, Enzyme Commission numbers (EC numbers) and functional domains to query sequences.

RESULTS

Using six transcriptome sequence datasets as examples, we demonstrated the ability of FastAnnotator to assign functional annotations. FastAnnotator annotated 88.1% and 81.3% of the transcripts from the well-studied organisms Caenorhabditis elegans and Streptococcus parasanguinis, respectively. Furthermore, FastAnnotator annotated 62.9%, 20.4%, 53.1% and 42.0% of the sequences from the transcriptomes of sweet potato, clam, amoeba, and Trichomonas vaginalis, respectively, which lack reference genomes. We demonstrated that FastAnnotator can complete the annotation process in a reasonable amount of time and is suitable for the annotation of transcriptomes from model organisms or organisms for which annotated reference genomes are not avaiable.

CONCLUSIONS

The sequencing process no longer represents the bottleneck in the study of genomics, and automatic annotation tools have become invaluable as the annotation procedure has become the limiting step. We present FastAnnotator, which was an automated annotation web tool designed to efficiently annotate sequences with their gene functions, enzyme functions or domains. FastAnnotator is useful in transcriptome studies and especially for those focusing on non-model organisms or metatranscriptomes. FastAnnotator does not require local installation and is freely available at http://fastannotator.cgu.edu.tw.

VIP DB--a viral protein domain usage and distribution database

During the viral infection and replication processes, viral proteins are highly regulated and may interact with host proteins. However, the functions and interaction partners of many viral proteins have yet to be explored. Here, we compiled a VIral Protein domain DataBase (VIP DB) to associate viral proteins with putative functions and interaction partners. We systematically assign domains and infer the functions of proteins and their protein interaction partners from their domain annotations. A total of 2,322 unique domains that were identified from 2,404 viruses are used as a starting point to correlate GO classification, KEGG metabolic pathway annotation and domain-domain interactions. Of the unique domains, 42.7% have GO records, 39.6% have at least one domain-domain interaction record and 26.3% can also be found in either mammals or plants. This database provides a resource to help virologists identify potential roles for viral protein. All of the information is available at http://vipdb.cgu.edu.tw.

Interrogation of alternative splicing events in duplicated genes during evolution

Background

Gene duplication provides resources for developing novel genes and new functions while retaining the original functions. In addition, alternative splicing could increase the complexity of expression at the transcriptome and proteome level without increasing the number of gene copy in the genome. Duplication and alternative splicing are thought to work together to provide the diverse functions or expression patterns for eukaryotes. Previously, it was believed that duplication and alternative splicing were negatively correlated and probably interchangeable.

Results

We look into the relationship between occurrence of alternative splicing and duplication at different time after duplication events. We found duplication and alternative splicing were indeed inversely correlated if only recently duplicated genes were considered, but they became positively correlated when we took those ancient duplications into account. Specifically, for slightly or moderately duplicated genes with gene families containing 2 - 7 paralogs, genes were more likely to evolve alternative splicing and had on average a greater number of alternative splicing isoforms after long-term evolution compared to singleton genes. On the other hand, those large gene families (contain at least 8 paralogs) had a lower proportion of alternative splicing, and fewer alternative splicing isoforms on average even when ancient duplicated genes were taken into consideration. We also found these duplicated genes having alternative splicing were under tighter evolutionary constraints compared to those having no alternative splicing, and had an enrichment of genes that participate in molecular transducer activities.

Conclusions

We studied the association between occurrences of alternative splicing and gene duplication. Our results implicate that there are key differences in functions and evolutionary constraints among singleton genes or duplicated genes with or without alternative splicing incidences. It implies that the gene duplication and alternative splicing may have different functional significance in the evolution of speciation diversity.

Ambient and personal dose assessment of a container inspection site using a mobile X-ray system

Ambient monitor and phantom studies of absorbed and effective doses by TLDs were carried out in a non-intrusive inspection station for containers, Terminal I, of Taichung harbor, Taiwan. The doses from the X-ray scan in the control room and driver waiting room, located outside of the radiation control area, were quite small and could not be distinguished from the natural background radiation. The doses in the driver cab and the inspector cab of the X-ray scan car were also within background radiation levels. The protection wall, a 40-cm thick concrete barrier, can effectively attenuate the intensity of the primary X-ray scan. The possible effective dose of a person in the container or trailer is about 3.15 ± 0.23 μSv/scan and 2.31 ± 0.38 μSv/scan. This dose is below the annual background dose. If someone was to be scanned by the X-ray, the effective dose would be at an acceptable level.

Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis

Background

sRNAs, which belong to the non-coding RNA family and range from approximately 50 to 400 nucleotides, serve various important gene regulatory roles. Most are believed to be trans-regulating and function by being complementary to their target mRNAs in order to inhibiting translation by ribosome occlusion. Despite this understanding of their functionality, the global properties associated with regulation by sRNAs are not yet understood. Here we use topological analysis of sRNA targets in terms of protein-protein interaction and transcription-regulatory networks in Escherichia coli to shed light on the global correlation between sRNA regulation and cellular control networks.

Results

The analysis of sRNA targets in terms of their networks showed that some specific network properties could be identified. In protein-protein interaction network, sRNA targets tend to occupy more central positions (higher closeness centrality, p-val = 0.022) and more cliquish (larger clustering coefficient, p-val = 0.037). The targets of the same sRNA tend to form a network module (shorter characteristic path length, p-val = 0.015; larger density, p-val = 0.019; higher in-degree ratio, p-val = 0.009). Using the transcription-regulatory network, sRNA targets tend to be under multiple regulation (higher indegree, p-val = 0.013) and the targets usually are important to the transfer of regulatory signals (higher betweenness, p-val = 0.012). As was found for the protein-protein interaction network, the targets that are regulated by the same sRNA also tend to be closely knit within the transcription-regulatory network (larger density, p-val = 0.036), and inward interactions between them are greater than the outward interactions (higher in-degree ratio, p-val = 0.023). However, after incorporating information on predicted sRNAs and down-stream targets, the results are not as clear-cut, but the overall network modularity is still evident.

Conclusions

Our results indicate that sRNA targeting tends to show a clustering pattern that is similar to the human microRNA regulation associated with protein-protein interaction network that was observed in a previous study. Namely, the sRNA targets show close interaction and forms a closely knit network module for both the protein-protein interaction and the transcription-regulatory networks. Thus, targets of the same sRNA work in a concerted way toward a specific goal. In addition, in the transcription-regulatory network, sRNA targets act as "multiplexor", accepting regulatory control from multiple sources and acting accordingly. Our results indicate that sRNA targeting shows different properties when compared to the proteins that form cellular networks.

DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection

BACKGROUND

Orthologs are genes derived from the same ancestor gene loci after speciation events. Orthologous proteins usually have similar sequences and perform comparable biological functions. Therefore, ortholog identification is useful in annotations of newly sequenced genomes. With rapidly increasing number of sequenced genomes, constructing or updating ortholog relationship between all genomes requires lots of effort and computation time. In addition, elucidating ortholog relationships between distantly related genomes is challenging because of the lower sequence similarity. Therefore, an efficient ortholog detection method that can deal with large number of distantly related genomes is desired.

RESULTS

An efficient ortholog detection pipeline DODO (DOmain based Detection of Orthologs) is created on the basis of domain architectures in this study. Supported by domain composition, which usually directly related with protein function, DODO could facilitate orthologs detection across distantly related genomes. DODO works in two main steps. Starting from domain information, it first assigns protein groups according to their domain architectures and further identifies orthologs within those groups with much reduced complexity. Here DODO is shown to detect orthologs between two genomes in considerably shorter period of time than traditional methods of reciprocal best hits and it is more significant when analyzed a large number of genomes. The output results of DODO are highly comparable with other known ortholog databases.

CONCLUSIONS

DODO provides a new efficient pipeline for detection of orthologs in a large number of genomes. In addition, a database established with DODO is also easier to maintain and could be updated relatively effortlessly. The pipeline of DODO could be downloaded from http://140.109.42.19:16080/dodo_web/home.htm.

Stabilizing oils from smoked pink salmon (Oncorhynchus gorbuscha)

Smoking of meats and fish is one of the earliest preservation technologies developed by humans. In this study, the smoking process was evaluated as a method for reducing oxidation of pink salmon (Oncorhynchus gorbuscha) oils and also maintaining the quality of oil in aged fish prior to oil extraction. Salmon heads that were subjected to high temperatures (95 degrees C) during smoking unexpectedly produced oils with fewer products of oxidation than their unprocessed counterparts, as measured by peroxide value (PV), thiobarbituric acid reactive substances (TBARS), and fatty acids (FA). Higher temperatures and longer smoking times resulted in correspondingly lower quantities of oxidative products in the oils. Fatty acid methyl ester (FAME) analysis of smoke-processed oils confirmed that polyunsaturated fatty acids (PUFA) were not being destroyed. Smoke-processing also imparted antioxidant potential to the extracted oils. Even when antioxidants, such as ethoxyquin or butylated hydroxytoluene, were added to raw oils, the smoke-processed oils still maintained lower levels of oxidation after 14 d of storage. However, decreased antioxidant capacity of smoke-processed oils was noted when they were heated above 75 degrees C. Vitamin studies supported the antioxidant results, with smoke-processed oils displaying higher levels of alpha-tocopherol than raw oils. Results suggest that smoking salmon prior to oil extraction can protect valuable PUFA-rich oils from oxidation. Improved preservation methods for marine oils may extend their usefulness when added as a supplement to enhance levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in foods.

A wearable mobihealth care system supporting real-time diagnosis and alarm

This paper describes a wearable mobihealth care system aiming at providing long-term continuous monitoring of vital signs for high-risk cardiovascular patients. We use a portable patient unit (PPU) and a wearable shirt (WS) to monitor electrocardiogram (ECG), respiration (acquired with respiratory inductive plethysmography, RIP), and activity. Owing to integrating fabric sensors and electrodes endowed with electro-physical properties into the WS, long-term continuous monitoring can be realized without making patients feel uncomfortable and restricting their mobility. The PPU analyzes physiological signals in real time and determines whether the patient is in danger or needs external help. The PPU will alert the patient and an emergency call will be automatically established with a medical service center (MSC) when life-threatening arrhythmias or falls are detected. With advanced gpsOne technology, the patient can be located and rescued immediately whether he/she is indoors or outdoors in case of emergency.

Proteome Analysis of Halobacterium sp. NRC-1 Facilitated by the Biomodule Analysis Tool BMSorter

To better understand the extremely halophilic archaeon Halobacterium species NRC-1, we analyzed its soluble proteome by two-dimensional liquid chromatography coupled to electrospray ionization tandem mass spectrometry. A total of 888 unique proteins were identified with a ProteinProphet probability (P) between 0.9 and 1.0. To evaluate the biochemical activities of the organism, the proteomic data were subjected to a biological network analysis using our BMSorter software. This allowed us to examine the proteins expressed in different biomodules and study the interactions between pertinent biomodules. Interestingly an integrated analysis of the enzymes in the amino acid metabolism and citrate cycle networks suggested that up to eight amino acids may be converted to oxaloacetate, fumarate, or oxoglutarate in the citrate cycle for energy production. In addition, glutamate and aspartate may be interconverted from other amino acids or synthesized from citrate cycle intermediates to meet the high demand for the acidic amino acids that are required to build the highly acidic proteome of the organism. Thus this study demonstrated that proteome analysis can provide useful information and help systems analyses of organisms.

Development and characterization of a new tropical marine fish cell line from grouper, Epinephelus coioides susceptible to iridovirus and nodavirus

The development and characterization of a new tropical marine fish cell line (GS), derived from the spleen of orange spotted grouper, Epinephelus coioides is described. The GS cells grow well in Leibovitz's L-15 medium supplemented with 10% foetal bovine serum, and have been subcultured more than 200 times. The optimal growth temperature was 27 degrees C. The GS cell culture consisted of mostly fibroblastic cells. The modal diploid chromosome number was 48. GS cell cultures showed advanced cytopathic effects after infection with a pathogenic grouper iridovirus (Singapore grouper iridovirus, SGIV) or with a grouper nodavirus (Epinephelus tauvina nervous necrosis virus, ETNNV). Analysis by transmission electron microscopy showed a large number of SGIV and ETNNV particles in the cytoplasm of virus-infected cells, respectively, indicative of high sensitivity to these two viruses. Immunofluorescence microscopy showed that iridovirus-infected GS cells reacted strongly with monoclonal antibody against the grouper iridovirus. It is suggested that the GS cell line has good potential as a diagnostic tool for isolation and propagation of iridovirus and nodavirus. When the GS cells were transfected with pEGFP vector DNA, significant fluorescent signals were observed suggesting that the GS cell line can be used as a useful tool for transgenic and genetic manipulation studies.

Antioxidant supplementation may improve renal transplant function: A preliminary report

Dysfunction of the renal graft may not only be due to rejection but also other causes such as ischemia and reperfusion injury and calcineurin inhibitor nephrotoxicity. Antioxidant free radical scavengers may decrease oxidative stress and lipid peroxidation. Previous animal studies suggest that vitamins C (ascorbic acid) and E (alpha-tocopherol) are both strong antioxidants, that decrease oxidative stress caused by ischemia-reperfusion injury and calcineurin inhibitor nephrotoxicity. But there have been only limited reports about clinical efficacy. We report five cases supplemented with vitamin C (500 mg per day), vitamin E (500 mg per day), or both. After a 1- to 3-month prescription, the serum creatinine level decreased more than 20% from the original value. Interestingly, one patient had this experience: he ceased vitamin E for 1 month due to noncompliance. The serum creatinine level increased more than 50%. When he took vitamin E again, his serum creatinine level declined and returned to the previous level. From our limited experience, antioxidant supplementation with vitamin C or E may improve renal transplant function, especially in grafts donated from marginal donors.

Effect of 5-methoxypsoralen (5-MOP) on cell apoptosis and cell cycle in human hepatocellular carcinoma cell line

The chemopreventive role of 5-methoxypsoralen (5-MOP) in the human hepatocellular carcinoma (HCC) cell line was investigated by studying the regulation of proliferation and apoptosis in HCC (J5) cells. Morphological analysis, cell viability assay, DNA analysis and cell-cycle analysis suggest that there are at least three modes of the suppressive effects shown by 5-MOP: (a) kills J5 cells directly; (b) induces apoptosis by arresting J5 cells at the G2/M phase in the cell cycle; (c) induces apoptosis through an independent pathway with cell-cycle arrest at 24-72 h of exposure. Further immunoblot analysis demonstrated that inhibition of cyclin B1 by 5-MOP may play an important role in G2/M arrest of J5 cells and provides an additional way to prevent cells from entering the M phase and undergoing apoptosis. 5-MOP therefore appears to exert its anticarcinogenic properties by cytotoxic effect, inducing apoptosis and inhibiting proliferation in the human hepatocellular carcinoma cell line.

Evaluating geometric accuracy of multi-platform stereotactic neuroimaging in radiosurgery

We used a spherical phantom to evaluate geometric accuracy in multi-platform stereotactic neuroimaging for radiosurgery. The phantom consisted of two plastic 16-cm-diameter hemispheres in which an exchangeable 8-cm plastic functional cube was incorporated. The functional cube contained cylinder and point targets. The targets were filled with a mixed aqueous solution of 2-mM copper sulfate and 300-mg/ml iodinated contrast medium and were visible on both MR and X-ray images. Two MR scanners and a biplane X-ray angio-suite were used to scan the phantom stereotactically in two sessions of the experiment. The angio-suite was equipped with digital subtraction and distortion-correction software. The resulting stereotactic images were transferred to a dose-planning computer for length measurement and coordinate determination of the targets. The mean errors of the measured cylinder length on distortion non-corrected X-ray stereotactic images were 0.24 +/- 0.14 and 0.73 +/- 0.10 mm, respectively, in the experiments; on distortion-corrected images 0.22 +/- 0.10 and 0.35 +/- 0.39 mm. They were 0.50 +/- 0.24, 0.25 +/- 0.19 and 0.49 +/- 0.34, 0.23 +/- 0.25 mm, respectively, of the two MR scanners. The mean errors of coordinate determination of point targets between the stereotactic MR and the distortion-corrected X-ray images were 0.70 +/- 0.18, 0.52 +/- 0.22 and 0.76 +/- 0.25, 0.40 +/- 0.10 mm, respectively, in the experiments. We found that the overall geometric errors of target delineation between stereotactic MR and X-ray images were in the submillimeter range. The current study validates the multi-platform and multi-facility stereotactic neuroimaging practice and ensures imaging accuracy in radiosurgery.

Estimation of mean-glandular dose from monitoring breast entrance skin air kerma using a high sensitivity metal oxide semiconductor field effect transistor (MOSFET) dosimeter system in mammography

Estimation of mean-glandular dose (MGD) has been investigated in recent years due to the potential risks of radiation-induced carcinogenesis associated with the mammographic examination for diagnostic radiology. In this study, a new technique for immediate readout of breast entrance skin air kerma (BESAK) using high sensitivity MOSFET dosimeter after mammographic projection was introduced and a formula for the prediction of tube output with exposure records was developed. A series of appropriate conversion factors was applied to the MGD determination from the BESAK. The study results showed that signal response of the high sensitivity MOSFET exhibited excellent linearity within mammographic dose ranges, and that the energy dependence was less than 3% for each anode/filter combination at the tube potentials 25-30 kV. Good agreement was observed between the BESAK and the tube exposure output measurement for breasts thicker than 30 mm. In addition, the air kerma estimated from our prediction formula provided sufficient accuracy for thinner breasts. The average MGD from 120 Asian females was 1.5 mGy, comparable to other studies. Our results suggest that the high sensitivity MOSFET dosimeter system is a good candidate for immediately readout of BESAK after mammographic procedures.

Characterization of high-sensitivity metal oxide semiconductor field effect transistor dosimeters system and LiF:Mg,Cu,P thermoluminescence dosimeters for use in diagnostic radiology

Monitoring radiation exposure during diagnostic radiographic procedures has recently become an area of interest. In recent years, the LiF:Mg,Cu,P thermoluminescence dosimeter (TLD-100H) and the highly sensitive metal oxide semiconductor field effect transistor (MOSFET) dosimeter were introduced as good candidates for entrance skin dose measurements in diagnostic radiology. In the present study, the TLD-100H and the MOSFET dosimeters were evaluated for sensitivity, linearity, energy, angular dependence, and post-exposure response. Our results indicate that the TLD-100H dosimeter has excellent linearity within diagnostic energy ranges and its sensitivity variations were under 3% at tube potentials from 40Vp to 125kVp. Good linearity was also observed with the MOSFET dosimeter, but in low-dose regions the values are less reliable and were found to be a function of the tube potentials. Both dosimeters also presented predictable angular dependence in this study. Our findings suggest that the TLD-100H dosimeter is more appropriate for low-dose diagnostic procedures such as chest and skull projections. The MOSFET dosimeter system is valuable for entrance skin dose measurement with lumbar spine projections and certain fluoroscopic procedures.

Dynamic evaluation of absorbed dose to the bladder wall with a balloon-bladder phantom during a study using [(18)F]fluorodeoxyglucose positron emission imaging

An accurate evaluation of the absorbed dose to the bladder wall from 2-[(18)F]fluoro-2-deoxy-d-glucose (FDG) is clinically important because the bladder is considered as a critical organ in most positron emission tomography (PET) studies that cumulate about 20% of the total activity injection during image procedures. In the MIRD calculation, no allowance is made for the inclusion of all the dynamic parameters that affect the actual dose to the bladder wall to be taken in the dose assessment. The goal of the study is to propose a dose evaluation model by using a dynamic bladder phantom and time-activity curves from the bladder PET imaging. The proposed model takes all dynamic parameters into account and provides a much more accurate dose estimation to the bladder. In this study, the lowest dose to the bladder wall was obtained at the conditions of having a larger initial volume for the bladder contents and a higher production rate for urine. It is then advised patients to drink a bulk amount of water before the FDG injection or after urine voiding to facilitate urine production and to enlarge the bladder surface area, which are the most crucial steps in reducing the dose to the bladder wall. In our study, the voiding schedule in dose calculation plays certain roles although it is much more critical in the conventional MIRD calculation. The model estimated that the lowest dose to the bladder would occur at an initial void about 40 min after the FDG injection and the urine voiding was as complete as possible.

Immunodominance and tumor escape

Cancers in mouse and man express multiple tumor-specific as well as tumor-associated antigens. Immunodominance in the host response to these antigens can result in successive selection of heritable antigen loss variants. Immunodominance may also prevent the development of responses to new tumor-specific antigens that may arise during tumor progression. Some tumor-specific antigens are retained during tumor progression possibly because they are essential for survival of the malignant phenotype. Immunodominance may allow cancer cells to escape even after loss of a single MHC Class I allele because cross-presentation of the retained antigen by this allele that must be expressed on the surrounding antigen presenting cells sustains the immunodominant response. This prevents effective responses to secondary antigens that may remain as potential targets. Immunization with in vitro selected cancer cell variants that lack the immunodominant antigen can break the immunodominance and prevent escape of cancers from host immunity.

Correlations between peripheral differential leukocyte counts and carotid atherosclerosis in non-smokers

Substantial evidence clearly indicates the immuno-inflammatory nature of atherosclerosis and the important roles of monocytes and other leukocytes in atherogenesis. The relationship between atherosclerosis and the peripheral monocyte count, however, has been equivocal and uncertain so far. One possible reason may be an opposing effect of different major risk factors of atherosclerosis on the monocyte count, e.g. smoking increases the monocyte count while hypercholesterolemia is accompanied by a lower monocyte count. Since smoking is well shown to increase leukocyte counts prominently in weeks, our study included only non-smokers who participated in a health check program at our hospital from 1996 to 1998 and had received a carotid duplex study with extra payment. Our results revealed the followings: In male non-smokers (n=571), the presence of carotid atherosclerosis was associated with significant increases in the counts of all leukocyte, neutrophil, and monocyte (P<0.005,<0.001 and <0.05, respectively), and, after adjustments for age and body mass index, there were significant positive links between these three leukocyte counts and the severity of carotid atherosclerosis, judged by either the sum score of all carotid plaques or the score of the most severe carotid plaque. On the contrary, in female non-smokers (n=614), there was no significant link between differential leukocyte counts and either the presence or severity of carotid atherosclerosis. These results are compatible with recently recognized sex differences in the mechanism and pathophysiology of atherosclerosis, and together with relevant results in the literature, suggest that monocytes and neutrophils are the main types of leukocytes involved in atherosclerosis.

Tracking the common ancestry of antigenically distinct cancer variants

In the months and years after first diagnosis, cancers often show an increase in their malignancy such as faster growth, resistance to chemo- and/or hormonal therapy, and loss of antigens targeted by immunotherapy. Our objective was to develop a model in which one can track the changes occurring as a result of in vivo immune selection, such as the loss of antigen, the emergence of previously hidden antigens, or the acquisition of new tumor-specific antigens. In this study, we used the primary UV-induced murine tumor 8101, which consists predominantly of regressor tumor cells that express the immunodominant mutant p68 antigen, but this tumor also contains progressor variants that have lost this antigen. To search for tumor-specific antigens on the immune escape progressors, we raised CD8+ T cells specific for these variants. We found that one of the escape variants expressed a previously unrecognized, unique tumor-specific antigen. However, this unique antigen was not readily detectable on any of the other 8101 lines we tested. To prove that these antigenically distinct cancer variants had indeed been derived from the same tumor and neither represented new tumors nor contaminations by other cell lines, we used unique tumor-specific p53 mutations as a lineage-specific marker to demonstrate that these antigenically distinct progressor variants were derived from the 8101 tumor. Because p53 mutations occur very early during UV carcinogenesis and vary from tumor to tumor, they provide convenient reliable markers for tracking the origin of cancers arising after immune selection or immunotherapy.

Polyclonal anticardiolipin antibodies purified from sera of patients with active systemic lupus erythematosus induce apoptosis of the cultured glomerular mesangial cells

OBJECTIVE

To test the effect of anticardiolipin antibodies (aCL) on cultured glomerular mesangial cells with regard to their expression of apoptosis-related genes.

METHODS

aCL purified from active lupus sera by cardiolipin micelles were incubated with cultured rodent mesangial cells (RMC). Morphological changes of the RMC were observed. The genomic DNA was extracted for the detection of apoptosis. The total cell RNA was extracted for detection of Fas, c-myc, p53, and bcl-2 transcripts by reverse transcription-polymerase chain reaction.

RESULTS

aCL (100 GPL-U/0.1 mg protein/ml) bound to RMC more prominent than human IgG (100 microg/ml). The antibodies suppressed RMC proliferation in a dose-dependent manner. The RMC were undergoing apoptosis as evidenced by morphologic changes, fluoresceinannexin V staining and appearance of nucleosome-sized DNA fragments. RMC spontaneously express p53 and c-myc but not Fas or bcl-2. aCL (100 GPL-U/ml) enhanced the expression of Fas but not other apoptosis-related genes and suppressed the intracellular tyrosine phosphorylation.

CONCLUSIONS

Binding of aCL can induce apoptosis of the RMC. The aCL may be implicated in the pathogenesis of lupus nephritis.

DDE in eggs of two crocodile species from Belize

Organochlorine (OC) residues were recently detected in nonviable Morelet's crocodile (Crocodylus moreletii) eggs from northern Belize. To further the assessment of contaminant exposure in Belizean crocodiles, nonviable Morelet's crocodile eggs (n = 11) from southern Belize and American crocodile (Crocodylus acutus) eggs (n = 12) from the coastal zones of Belize were screened for 20 OCs. Results indicated p,p-DDE to be the most prevalent OC (96% occurrence) in eggs examined, with concentrations ranging from 5 to 372 ng/g. These concentrations are similar to those observed in crocodile eggs (10-180 ng/g) from northern Belize. A general trend toward higher DDE concentrations in Morelet's crocodile eggs (mean = 103 ppb) compared with American crocodile eggs (mean = 31 ppb) was observed. However, this trend may be due to site-specific contamination rather than differences in interspecific susceptibility to chemical exposure. Other OCs detected in crocodile eggs included the parent compound, p,p-DDT, and its metabolite, p, p-DDD.

Immunological enhancement of primary tumor development and its prevention

While it has been known for decades that the growth of tumor transplants can be enhanced immunologically, the potential significance of these previous findings to the development of primary tumors and the mechanisms of tumor enhancement has remained obscure. This review will summarize recent experiments indicating that primary tumor development can be enhanced by active immunization. The evidence suggests that antibodies, B cells and CD4+ T cells can play a critical role in enhancing the development of primary, tumors, whereas endogenous interferon-gamma (IFNgamma) can counteract enhancement. Thus, we envision two possible functions of IFNgamma: (i) preventing B cell and antibody enhancement and (ii) counteracting tumor promotion independent of T and B cells.

The in vitro immunomodulatory effects of sulfasalazine on human polymorphonuclear leukocytes, mononuclear cells, and cultured glomerular mesangial cells

Sulfasalazine (SSA) was investigated for its effects on phagocytic activity of normal human polymorphonuclear neutrophils (PMN), proliferation of mononuclear cells (MNC) and cultured glomerular mesangial cells. At concentrations from 25 to 100 microM, it inhibited phagocytic activity of PMN and the 3H-thymidine incorporation of phytohemagglutinin (PHA)-stimulated human MNC in a dose-dependent manner. At comparable concentrations, sulfapyridine and 5-aminosalicylic acid, two of its major metabolites, did not show similar effects. SSA exhibited an inhibitory effect on both mouse and rat mesangial cells but at rather higher concentrations (0.5 mM). Excretion of interleukin (IL)-8 by lipopolysaccharide (LPS)-stimulated PMN was also markedly deterred in a dose-dependent manner but excretion of IL-8 by LPS-stimulated MNC was not interfered by SSA. Production of tumor necrosis factor (TNF)-alpha and IL-1beta by mouse mesangial cells was not blocked by SSA but production of IL-4 by these cells was inhibited by it (>0.1 mM). Inhibition of MNC was not due directly to cytotoxic effect of SSA on these cells as shown by fluorescein diacetate stain. Collectively, SSA inhibits phagocytosis and IL-8 excretion by PMN as well as mitogen-stimulated MNC reaction. On the other hand, at high concentrations, it inhibits glomerular mesangial cells and their IL-4 excretion but not TNF-alpha and IL-1beta excretion. These results can account for minimal nephrotoxic characteristic of SSA and suggest that it may be helpful in the treatment of immune-mediated glomerulonephritis.

Evaluation of equivalent dose to working staff with oxygen-15-water in positron emission tomographic studies

With its short physical half-life and allowing for higher dosage injections, oxygen-15 labeled water has become increasingly important in many clinical applications. However, the use of oxygen-15 labeled water could potentially result in radiation exposures to working staff exceeding regulatory limits. In this study, thermoluminescent dosimeters (LiF-100H) were attached at various parts of the body to measure the accumulated equivalent doses of a physician and to evaluate the radiation risk to the sensitive organs which could receive as many as 10 intravenous injections of (15)O-water for each subject studied. The results showed that during the injections, the hands of a physician received the highest dose, which was about 25.8 times that of the routine chest X-ray dose. If protective shieldings were provided during injection, about 83% of the dose could be effectively reduced. Even without any protective shielding, the estimated maximum dose to the physician was still within the regulatory limit, 50 mSv/year, suggested by ICRP 60. In conclusion, reducing excess radiation exposure to workers, by minimizing the time spent in close contact with patients, increasing the distance from the source and providing suitable protective shielding would be the most effective approach.

Increased excretions of beta2-microglobulin, IL-6, and IL-8 and decreased excretion of Tamm-Horsfall glycoprotein in urine of patients with active lupus nephritis

Tubulointerstitial nephritis is a less frequently recognized but important complication of systemic lupus erythematosus. We have investigated the cytokine beta2-microglobulin (beta2M) and Tamm-Horsfall glycoprotein (THG) excretions in the urine of systemic lupus erythematosus patients to identify indices for evaluation of tubulointerstitial inflammation in lupus nephritis (LN). Daily urine was collected from 15 patients with active LN, from 12 patients with inactive LN, and from 17 normal subjects. The amounts of soluble interleukin (IL) 2 receptor, IL-6, IL-8, beta2M, and THG in urine were measured. Beta2M and THG were regarded as indicators of proximal and distal renal tubule function, respectively. The urinary excretions of IL-6 and IL-8 were significantly higher in patients with active LN than in those with inactive LN and in normal individuals. The excretion of soluble IL-2 receptor in all three groups of subjects was not significantly different. On the other hand, the excretion of beta2M in patients with LN was significantly higher than that in normal individuals. The excretion of beta2M in patients with active or inactive LN was not significantly different. The THG excretion was lower in patients with active LN and tubulointerstitial inflammation as compared with patients with inactive LN or normal individuals. Six patients underwent pulse cyclophosphamide therapy during the course of experiments. Five of them showed a decrease in IL-8 and IL-6 excretions in urine after the treatment. The excretions of beta2M and THG in urine, in addition to IL-6 and IL-8, can reflect the renal inflammatory activity in patients with lupus tubulointerstitial nephritis as well as in those having lupus glomerulonephritis.

Organochlorine contaminants in Morelet's crocodile (Crocodylus moreletii) eggs from Belize

Non-viable eggs of Morelet's crocodile (Crocodylus moreletii) were collected from Gold Button (GBL) and New River lagoons (NRL) in northern Belize and screened for organochlorine (OC) compounds using gas chromatography (GC) with electron capture detection (ECD). All egg samples from both lagoons (n = 24) tested positive for one or more OCs. Primary contaminants were p,p-DDE and methoxychlor, detected in 100% and 29% of the eggs examined, respectively. Concentrations of individual OC contaminants ranged from 1 ppb (ng chemical/g egg) to > 0.5 ppm (microgram chemical/g egg). Total concentrations of OCs (sum of all OCs) for one egg collected from a nest at GBL reached as high as 0.7 ppm. Sediment samples from both lagoons also tested positive for OCs (lindane, aldrin, methoxychlor, heptachlor epoxide, p,p-DDT, among others). Nest media (soil and plant material) collected from crocodile nests at GBL were positive for p,p-DDT, methoxychlor, aldrin, endosulfan II, and endrin aldehyde. Based on the 24 egg samples analyzed to date, crocodiles from both lagoons are being exposed to OCs. Such exposure may present a health threat to populations of crocodiles in Central America.

Factors affecting the first recurrence of noncardioembolic ischemic stroke

Studies of the factors affecting the first recurrence of ischemic stroke have reported inconsistent findings. Types of initial stroke and the racial differences in study samples are among the explanations that may account for this inconsistency. The aims of this study were to estimate the cumulative recurrence rates of noncardioembolic ischemic stroke and identify the factors that influence the first recurrence of noncardioembolic ischemic stroke in the Taiwanese Chinese population. Four hundred and sixty-six patients with noncardioembolic ischemic stroke from thirteen hospitals in Taiwan were followed up in this study to ascertain first recurrence of noncardioembolic ischemic stroke between October 1992 and April 1995. The Kaplan-Meier method was used to estimate the cumulative recurrence rate. The Cox regression model was used to ascertain the significant factors affecting the first recurrence of noncardioembolic ischemic stroke. The overall cumulative recurrence rate was 10.5% (49/466) from the follow-up period of 30 months. After adjustment for age, sex, treatment modes, and variables pertinent to blood pressure, the site of brain lesion remained a significant factor. The relative risk of first recurrence for the basal ganglion vs. the region of middle cerebral artery was 3.06 (95% CI: 1.29-7.26). The brain lesion site was demonstrated to be an independent predictor of risk for the first recurrence of noncardioembolic ischemic stroke among the Taiwanese Chinese population. Whether this finding was also seen in other populations should be corroborated in future research.

Evaluation of the dose to the bladder wall using a dynamic balloon-bladder phantom and TLD measurements in 18F-FDG PET studies

[18F]-2-deoxyglucose (18F-FDG) is one of the most useful radiopharmaceuticals in clinical positron emission tomographic imaging. Its final metabolic destination is the bladder, which accumulates the highest absorbed dose in the body during imaging. The aims of this study were to develop a dynamic bladder phantom to emulate the dynamic response of the bladder and to evaluate changes in the dose to the bladder wall during the imaging procedure. 18F-FDG of various concentrations can be drip-fed intravenously to the balloon-bladder at different uptake phases or extracted from the phantom during voiding. A dose evaluation model, introducing the concept of photon energy flux conversion into the dose calculation, is thus developed for clinical evaluation. The dose to the bladder wall using the proposed model is comparable to that measured using a thermoluminescence dosimeter (TLD), with a less than 5% discrepancy. The main advantages of the model are the use of the dose conversion factor, phi TLD, which is determined from real TLD measurements, and the ability to consider the dynamic characteristics of the bladder. To overcome the problems of diverse dose distributions among subjects, time-activity information provided by clinical bladder imaging is required, so that the method can be applied to other radiopharmaceuticals.

Outer membrane proteins as a carrier for detoxified lipooligosaccharide conjugate vaccines for nontypeable Haemophilus influenzae

Nontypeable Haemophilus influenzae (NTHi) is a common cause of otitis media and respiratory tract infections. Outer membrane proteins (OMP) and lipooligosaccharide (LOS) are major surface antigens of NTHi and potential vaccine candidates. De-O-acylated LOS (dLOS) or oligosaccharide (OS) was coupled to total OMP to form dLOS-OMP and OS-OMP conjugates, while a dLOS-tetanus toxoid (TT) was synthesized for comparison. These conjugates were evaluated in mice and rabbits for immunogenicity. dLOS-OMP elicited a better boostable antibody response against LOS than did dLOS-TT, while OS-OMP was not immunogenic. Formulation of the conjugates with Ribi adjuvant significantly enhanced the immunogenicity of dLOS-OMP and dLOS-TT but not that of OS-OMP. In addition, rabbit antisera elicited by dLOS-OMP but not dLOS-TT (or OMP alone) demonstrated bactericidal activity against 40% of the NTHi strains tested. These results indicate that dLOS is a better derivative of LOS than OS and that OMP is a good carrier for NTHi LOS-based conjugate vaccines.

Cardiac-specific overexpression of RhoA results in sinus and atrioventricular nodal dysfunction and contractile failure

RhoA is a low-molecular-weight GTPase that has been implicated in the regulation of hypertrophic cardiac muscle cell growth. To study the role of RhoA in control of cardiac function in vivo, transgenic mice expressing wild-type and constitutively activated forms of RhoA under the control of the cardiac-specific alpha-myosin heavy chain promoter were generated. Transgene-positive mice expressing high levels of either wild-type or activated RhoA showed pronounced atrial enlargement and manifested a lethal phenotype, often preceded by generalized edema, with most animals dying over the course of a few weeks. Echocardiographic analysis of visibly healthy wild-type RhoA transgenic mice revealed no significant change in left ventricular function. As their condition deteriorated, significant dilation of the left ventricular chamber and associated decreases in left ventricular contractility were detected. Heart rate was grossly depressed in both wild-type and activated RhoA-expressing mice, even prior to the onset of ventricular failure. Electrocardiography showed evidence of atrial fibrillation and atrioventricular block. Interestingly, muscarinic receptor blockade with atropine did not elicit a positive chronotropic response in the transgenic mice. We suggest that RhoA regulates cardiac sinus and atrioventricular nodal function and that its overexpression results in bradycardia and development of ventricular failure.

Estimation of organ dose equivalents from residents of radiation-contaminated buildings with Rando phantom measurements

Since August 1996, a dose reconstruction model has been conducted with thermoluminescent dosimeter (TLD)-embedded chains, belts and badges for external dose measurements on the residents in radiation-contaminated buildings. The TLD dosimeters, worn on the front of the torso, would not be adequate for dose measurement in cases when the radiation is anisotropic or the incident angles of radiation sources are not directed in the front-to-back direction. The shielding and attenuation by the body would result in the dose equivalent estimation being somewhat skewed. An organ dose estimation method with a Rando phantom under various exposure geometries is proposed. The conversion factors, obtained from the phantom study, may be applicable to organ dose estimations for residents in the contaminated buildings if the incident angles correspond to the phantom simulation results. There is a great demand for developing a mathematical model or Monte Carlo calculation to deal with complicated indoor layout geometry problems involving ionizing radiation. Further research should be directed toward conducting laboratory simulation by investigating the relationship between doses delivered from multiple radiation sources. It is also necessary to collaborate with experimental biological dosimetry, such as chromosome aberration analysis, fluorescence in situ hybridization (FISH) and retrospective ESR-dosimetry with teeth, applied to the residents, so that the organ dose equivalent estimations may be more reliable for radio-epidemiological studies.