Effect of Age on Allergen Responses of Allergic Patients in Southern Taiwan

To survey airborne and food allergen patterns in southern Taiwan and to analyze the effect of age on response to different allergens, we tested samples from 4,411 allergic patients at Kaohsiung Medical University Hospital using the MAST-CLA test (new Taiwan panel). A total of 2,212 (50.1%) samples showed a positive response. We grouped allergic patients into five age groups. Milk and egg white were the main food allergens in the younger groups (< 3 years old and 3-6 years old). Shrimp, crab, and shellfish were the main allergens in the groups aged 7-12, 13-18, and more than 18 years. Among airborne allergens, house dust and mites Dermatophagoides farinae and D. pteronyssinus were the main allergens in all age groups, whereas the frequency of response to cockroach allergen was low in the group aged less than 3 years, but increased in the other age groups. There was a sharp increase in the frequency of response to airborne allergens after 3 years old and a sharp decrease in response to food allergens. Among subjects allergic to both airborne and food allergens, there was a positive MAST-CLA rate of 19.9% to 26% (all five age groups, no significant difference). When we compared our results with those from Taipei Veterans General Hospital in northern Taiwan, there were significant differences for yeast, peanut, feather mix, dog dander, cockroach, D. farinae and D. pteronyssinus allergens (p < 0.01). These differences were probably caused by differences in patient location, patient age, disease patterns and allergen panels

Sequence features involved in the mechanism of 3' splice junction wobbling

Background Alternative splicing is an important mechanism mediating the diversified functions of genes in multicellular organisms, and such event occurs in around 40-60% of human genes. Recently, a new splice-junction wobbling mechanism was proposed that subtle modifications exist in mRNA maturation by alternatively choosing at 5'- GTNGT and 3'- NAGNAG, which created single amino acid insertion and deletion isoforms. Results By browsing the Alternative Splicing Database information, we observed that most 3' alternative splice site choices occur within six nucleotides of the dominant splice site and the incidence significantly decreases further away from the dominant acceptor site. Although a lower frequency of alternative splicing occurs within the intronic region (alternative splicing at the proximal AG) than in the exonic region (alternative splicing at the distal AG), alternative AG sites located within the intronic region show stronger potential as the acceptor. These observations revealed that the choice of 3' splice sites during 3' splicing junction wobbling could depend on the distance between the duplicated AG and the branch point site (BPS). Further mutagenesis experiments demonstrated that the distance of AG-to-AG and BPS-to-AG can greatly influence 3' splice site selection. Knocking down a known alternative splicing regulator, hSlu7, failed to affect wobble splicing choices. Conclusion Our results implied that nucleotide distance between proximal and distal AG sites has an important regulatory function. In this study, we showed that occurrence of 3' wobble splicing occurs in a distance-dependent manner and that most of this wobble splicing is probably caused by steric hindrance from a factor bound at the neighboring tandem motif sequence

Elevated 1- α

A uremic patient developed hypercalcemia after tuberculosis infection, and his ionized calcium levels correlated with 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) levels. We performed further studies to determine whether monocytes are alternative sites of 1,25(OH)2D3 conversion beyond renal tubular cells. Using an ex vivo bioassay, in this study, we found that 1-α hydroxylase (CYP27B1) activity in monocytes is significantly higher in patients with active tuberculosis (TB) than in those with frequent TB contact. However, when monocytes from patients with active TB were restimulated with antigen derived from Mycobacterium tuberculosis, less 1,25(OH)2D3 was observed. In contrast, the level of 1,25(OH)2D3 was unchanged in those with frequent TB contact. We conclude that monocytes may be an alternative source of 1-α hydroxylase that could convert 25-hydroxyvitamin D3 to the more active 1,25(OH)2D3

DYNAMIC KEY BLOCK DECISION WITH SPATIO-TEMPORAL ANALYSIS FOR WYNER-ZIV VIDEO CODING

ABSTRACT Wyner-Ziv coding has been recognized as the most popular method up to now. For traditional WZC, side information is generated from intra-coded frames for use in the decoding of WZ frames. The unit for intra-coding is a frame and the distance between key-frames is kept constant. In this paper, the unit for intra-coding is a block, and the temporal distance between two consecutive key blocks can varying with time. A block is assigned a mode (WZ or intra-coded), depending on the result of spatio-temporal analysis, and encoded in an alternative manner. This strategy improves the overall coding efficiency, while maintaining a low encoder complexity. The performance gain can achieve up to 6 dB with respect to the traditional pixel-domain WZC

Activation of Endothelial Cells by Antiphospholipid Antibodies—A Possible Mechanism Triggering Thrombosis in Patients with Antiphospholipid Syndrome

Antiphospholipid syndrome (APS) is an antibody-mediated hypercoagulable state characterized by recurrent venous and arterial thromboembolic events. The presence of serum antibodies are collectively termed as antiphospholipid antibodies (aPL) and is the hallmark of the disease. Interest in the pathogenesis has mostly been focused on the blood coagulation factor. However, endothelial cells might play an important role. When stimulated, cell membrane would flip to expose negatively charged phospholipids and activation markers such as adhesive molecules may appear. We consider that these changes may play an important role in the initiation of the thrombotic process when endothelial cells encounter aPL. In this study, we incubated human umbilical vein endothelial cells (HUVECs) with IgG isolated from patients with APS and found that the HUVECs were activated by the expression of negatively charged phospholipids, as shown by high annexin V binding and negative propidium iodide staining and by an increase in the level of intracellular cell adhesion molecule-1 on the cell surface. The above findings indicate that endothelial cells can be activated on exposure to aPL and trigger the thrombotic event

Quantitative measures of functional outcomes and quality of life in patients with C5 palsy

AbstractBackgroundIt is generally understood that postoperative C5 palsy can occur with anterior or posterior decompression surgery, but functional measures of the palsy have not been well documented. This study aimed to investigate the incidence of C5 palsy in different surgical procedures, examine the correlations between muscle strength, upper extremity functional measures, and health-related quality of life, and to observe potential risk factors contributing to C5 palsy.MethodsOur investigation involved a retrospective study design. A total of 364 patients who underwent decompression surgery were indicated within the selected exclusion criteria. Additionally, 12 C5 palsy patients were recruited. The relationships between the manual muscle test (MMT), the action research arm test (ARAT), the Jebsen test of hand function (JTHF), and the European quality of life-5 dimensions (EQ-5D) were studied, and univariate analyses were performed to search possible risk factors and recovery investigation.ResultsThe data analyzed in the 12 cases and C5 palsy incidences (3.3%) were: 0.7% in anterior procedures (n = 2), 8.8% in posterior procedures (n = 6), and 36.4% in combined procedures (n = 4). Moderate-to-high correlations were observed between the ARAT, JTHF, EQ-5D visual analog scale scores, and MMT (r = 0.636–0.899). There were significant differences in patient age, etiology of cervical lesion, variable decompression procedures, and the number of decompression levels between the C5 palsy and non-C5 palsy groups. For female patients (p = 0.018) and number of decompression levels (p = 0.028), there were significant differences between the complete recovery and the incomplete recovery groups.ConclusionPatients undergoing combined anterior–posterior decompression surgery had the highest incidence of C5 palsy, and correlations between the ARAT, JTHF, EQ-5D visual analog scale clinical tools, and MMT scores supported these findings. Female status and lower decompression levels could also be predictive factors for complete recovery, although additional research is needed to substantiate these findings

UMARS: Un-MAppable Reads Solution

[[abstract]]Background: Un-MAppable Reads Solution (UMARS) is a user-friendly web service focusing on retrieving valuable information from sequence reads that cannot be mapped back to reference genomes. Recently, next-generation sequencing (NGS) technology has emerged as a powerful tool for generating high-throughput sequencing data and has been applied to many kinds of biological research. In a typical analysis, adaptor-trimmed NGS reads were first mapped back to reference sequences, including genomes or transcripts. However, a fraction of NGS reads failed to be mapped back to the reference sequences. Such un-mappable reads are usually imputed to sequencing errors and discarded without further consideration.Methods: We are investigating possible biological relevance and possible sources of un-mappable reads. Therefore, we developed UMARS to scan for virus genomic fragments or exon-exon junctions of novel alternative splicing isoforms from un-mappable reads. For mapping un-mappable reads, we first collected viral genomes and sequences of exon-exon junctions. Then, we constructed UMARS pipeline as an automatic alignment interface.Results: By demonstrating the results of two UMARS alignment cases, we show the applicability of UMARS. We first showed that the expected EBV genomic fragments can be detected by UMARS. Second, we also detected exon-exon junctions from un-mappable reads. Further experimental validation also ensured the authenticity of the UMARS pipeline. The UMARS service is freely available to the academic community and can be accessed via http://musk.ibms.sinica.edu.tw/UMARS/.Conclusions: In this study, we have shown that some un-mappable reads are not caused by sequencing errors. They can originate from viral infection or transcript splicing. Our UMARS pipeline provides another way to examine and recycle the un-mappable reads that are commonly discarded as garbage

Discovery and characterization of medaka miRNA genes by next generation sequencing platform

Background MicroRNAs (miRNAs) are endogenous non-protein-coding RNA genes which exist in a wide variety of organisms, including animals, plants, virus and even unicellular organisms. Medaka (Oryzias latipes) is a useful model organism among vertebrate animals. However, no medaka miRNAs have been investigated systematically. It is beneficial to conduct a genome-wide miRNA discovery study using the next generation sequencing (NGS) technology, which has emerged as a powerful sequencing tool for high-throughput analysis. Results In this study, we adopted ABI SOLiD platform to generate small RNA sequence reads from medaka tissues, followed by mapping these sequence reads back to medaka genome. The mapped genomic loci were considered as candidate miRNAs and further processed by a support vector machine (SVM) classifier. As result, we identified 599 novel medaka pre-miRNAs, many of which were found to encode more than one isomiRs. Besides, additional minor miRNAs (also called miRNA star) can be also detected with the improvement of sequencing depth. These quantifiable isomiRs and minor miRNAs enable us to further characterize medaka miRNA genes in many aspects. First of all, many medaka candidate pre-miRNAs position close to each other, forming many miRNA clusters, some of which are also conserved across other vertebrate animals. Secondly, during miRNA maturation, there is an arm selection preference of mature miRNAs within precursors. We observed the differences on arm selection preference between our candidate pre-miRNAs and their orthologous ones. We classified these differences into three categories based on the distribution of NGS reads. Finally, we also investigated the relationship between conservation status and expression level of miRNA genes. We concluded that the evolutionally conserved miRNAs were usually the most abundant ones. Conclusions Medaka is a widely used model animal and usually involved in many biomedical studies, including the ones on development biology. Identifying and characterizing medaka miRNA genes would benefit the studies using medaka as a model organism