Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells

Spermatogonial stem cells (SSCs) are germline stem cells located along the basement membrane of seminiferous tubules in testes. Recently, SSCs were shown to be reprogrammed into multipotent SSCs (mSSCs). However, both the key factors and biological networks underlying this reprogramming remain elusive. Here, we present transcriptional regulatory networks (TRNs) that control cellular processes related to the SSC-to-mSSC reprogramming. Previously, we established intermediate SSCs (iSSCs) undergoing the transition to mSSCs and generated gene expression profiles of SSCs, iSSCs and mSSCs. By comparing these profiles, we identified 2643 genes that were up-regulated during the reprogramming process and 15 key transcription factors (TFs) that regulate these genes. Using the TF-target relationships, we developed TRNs describing how these TFs regulate three pluripotency-related processes (cell proliferation, stem cell maintenance and epigenetic regulation) during the reprogramming. The TRNs showed that 4 of the 15 TFs (Oct4/Pou5f1, Cux1, Zfp143 and E2f4) regulated cell proliferation during the early stages of reprogramming, whereas 11 TFs (Oct4/Pou5f1, Foxm1, Cux1, Zfp143, Trp53, E2f4, Esrrb, Nfyb, Nanog, Sox2 and Klf4) regulated the three pluripotency-related processes during the late stages of reprogramming. Our TRNs provide a model for the temporally coordinated transcriptional regulation of pluripotency-related processes during the SSC-to-mSSC reprogramming, which can be further tested in detailed functional studies.111Ysciescopuskc

Diagnostic test accuracy: application and practice using R software

The objective of this paper is to describe general approaches of diagnostic test accuracy (DTA) that are available for the quantitative synthesis of data using R software. We conduct a DTA that summarizes statistics for univariate analysis and bivariate analysis. The package commands of R software were “metaprop” and “metabin” for sensitivity, specificity, and diagnostic odds ratio; forest for forest plot; reitsma of “mada” for a summarized receiver-operating characteristic (ROC) curve; and “metareg” for meta-regression analysis. The estimated total effect sizes, test for heterogeneity and moderator effect, and a summarized ROC curve are reported using R software. In particular, we focus on how to calculate the effect sizes of target studies in DTA. This study focuses on the practical methods of DTA rather than theoretical concepts for researchers whose fields of study were non-statistics related. By performing this study, we hope that many researchers will use R software to determine the DTA more easily, and that there will be greater interest in related research

Comparison of Measurement and Prediction of ITU-R Recommendation P.1546

This paper compares measurement with prediction of ITU-R Recommendation P.1546. This recommendation mainly depends on propagation curves which are based on the measurement result. The basic field strength is derived from the curve corresponding to transmitting antenna height, frequency and required distance and then correction factor is added to this. There are two important correction values in this recommendation. First factor is the correction for receiving/mobile antenna height and second factor is the terrain clearance angle (TCA) correction. This paper specially focuses on first correction factor with regard to R which is representative of the height of the ground cover surrounding receiving/mobile antenna. We propose several considerations to enhance the prediction accuracy of ITU-R Recommendation P.1546

Performance of Channel Prediction Using 3D Ray-tracing Scheme Compared to Conventional 2D Scheme

Channel prediction tools using ray-tracing scheme can be used to get information of communication channel instead of channel measurement. Three dimensional (3D) ray-tracing technique is known for the better accuracy compared to two dimensional (2D) ray-tracing. But it requires a lot of calculations, thus 2D simulation has been generally performed. This paper shows how precious 3D ray-tracing predicts the received power indoors compared to 2D one. For this work, wave propagation phenomena are analyzed using Finite Difference Time Domain (FDTD) method and the channel measurement data also will be offered as a standard of comparison

Study on the Effects of Liquid Thermal Media on the Irradiation Capsule of High-Temperature Materials

Irradiation tests of materials at HANARO have usually been conducted using a standard capsule at temperatures of about 300°C for irradiation of materials used at PWR. Thus, the standard capsule uses aluminum as the specimen holder, which acts to dissipate the thermal energy. Future nuclear systems such as a VHTR and SFR require the irradiation tests at a relatively high temperature. As an alternative to aluminum which has been used as the thermal media in a standard material capsule, the characteristics of liquid metals such as NaK and LBE are reviewed. The temperatures of the capsule are affected by the variation of parameters such as the gap and wall thickness of the container. In particular, the external gap is most important in determining the temperature of the specimen. LBE raises the temperature of the specimen higher than NaK at the same configuration of the capsule. Thus, LBE can lessen the gap of the parts and reduce the vibration for a stable long-term test in reactor

Efficient Cell Planning Method by Considering Initial Conditions

This paper focuses on cell planning method and optimal Access Point (AP) location. Cell planning can reduce the adjacent channel interference and minimize the number of AP. So an efficient cell planning method can save cost and time of systems setup. We introduce some methods, compare one another and suggest an efficient method. Existing method is considering a variety of objective functions. So their complexity makes it difficult to design wireless systems. The new method which will be suggested in this paper considering a special condition reduces a lot of calculation quantity

Coordinated Beamforming with Limited BS Cooperation for Multicell Multiuser MIMO Broadcast Channel

The capacity of downlink multi-input multi-output (MIMO) systems is significantly limited by inter-cell co-channel interference (CCI). Improving the erformance of cell edge users who suffers strong inter-cell CCI is still a crucial issue. In this paper, coordinated beamforming (CBF)lgorithm for multicell multiuser MIMO system is proposed to cope with the presence of intel-cell CCI. In multicell environment with MIMO channel, limited base station (BS) cooperation is considered to design optimal transmit and receive beamformers which make interference-free at the receiver. Simulation results show that the proposed algorithms can improve the capacity of cell edge user effectively as well as the overall system capacity for multiuser multicell MIMO system

GarlicESTdb: an online database and mining tool for garlic EST sequences

<p>Abstract</p> <p>Background</p> <p><it>Allium sativum</it>., commonly known as garlic, is a species in the onion genus (<it>Allium</it>), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression.</p> <p>Description</p> <p>GarlicESTdb is an integrated database and mining tool for large-scale garlic (<it>Allium sativum</it>) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The GarlicESTdb web application is freely available at <url>http://garlicdb.kribb.re.kr</url>.</p> <p>Conclusion</p> <p>GarlicESTdb is the first incorporated online information database of EST sequences isolated from garlic that can be freely accessed and downloaded. It has many useful features for interactive mining of EST contigs and datasets from each library, including curation of annotated information, expression profiling, information retrieval, and summary of statistics of functional annotation. Consequently, the development of GarlicESTdb will provide a crucial contribution to biologists for data-mining and more efficient experimental studies.</p

Isolation and Characterization of a Defensin-Like Peptide (Coprisin) from the Dung Beetle, Copris tripartitus

The antibacterial activity of immune-related peptides, identified by a differential gene expression analysis, was investigated to suggest novel antibacterial peptides. A cDNA encoding a defensin-like peptide, Coprisin, was isolated from bacteria-immunized dung beetle, Copris tripartitus, by using differential dot blot hybridization. Northern blot analysis showed that Coprisin mRNA was up-regulated from 4 hours after bacteria injection and its expression level was reached a peak at 16 hours. The deduced amino acid sequence of Coprisin was composed of 80 amino acids with a predicted molecular weight of 8.6 kDa and a pI of 8.7. The amino acid sequence of mature Coprisin was found to be 79.1% and 67.4% identical to those of defensin-like peptides of Anomala cuprea and Allomyrina dichotoma, respectively. We also investigated active sequences of Coprisin by using amino acid modification. The result showed that the 9-mer peptide, LLCIALRKK-NH2, exhibited potent antibacterial activities against Escherichia coli and Staphylococcus aureus

Effects of Dietary Garlic Powder on Growth, Feed Utilization and Whole Body Composition Changes in Fingerling Sterlet Sturgeon,

A 12 week growth study was carried out to investigate the supplemental effects of dietary garlic powder (GP) on growth, feed utilization and whole body composition changes of fingerling sterlet sturgeon Acipenser ruthenus (averaging weight, 5.5 g). Following a 24-h fasting, 540 fish were randomly distributed to each of 18 tanks (30 fish/tank) under a semi-recirculation freshwater system. The GP of 0.5% (GP0.5), 1% (GP1), 1.5% (GP1.5), 2% (GP2) and 3% (GP3) was added to the control diet (GP0) containing 43% protein and 16% lipid. After the feeding trial, weight gain (WG) of fish fed GP1.5, GP2 and GP3 were significantly higher (p<0.05) than those of fish fed GP0, GP0.5 and GP1. Feed efficiency and specific growth rate (SGR) showed a similar trend to WG. Protein efficiency ratio of fish fed GP1.5, GP2, and GP3 were significantly higher (p<0.05) than those of fish groups fed the other diets. A significant difference (p<0.05) was found in whole body composition (moisture, crude protein, crude lipid, ash, and fiber) of fish at the end of the experiment. Significantly higher (p<0.05) protein and lipid retention efficiencies (PRE and LRE) were also found in GP1.5, GP2, and GP3 groups. Broken-line regression model analysis and second order polynomial regression model analysis relation on the basis of SGR and WG indicated that the dietary optimal GP level could be greater than 1.77% and 1.79%, but less than 2.95% and 3.18% in fingerling sterlet sturgeon. The present study suggested that dietary GP for fingerling sterlet sturgeon could positively affect growth performance and protein retention