bluuebunny/crossref_metadata_2025 huggingface dataset:
Documenting the “Flower of Reunification”: Lim Su-gyeong and the memories of Korean border crossing
Authors: Kim Suk-Young
Published: March 2013

In 1989, 20-year-old South Korean college student Lim Su-gyeong crossed the Military Demarcation Line between the two Koreas while thousands of spectators around the world witnessed this controversial act. To this day, citizens of both Koreas cannot cross the border freely without both Korean governments’ permission, which is nearly impossible to obtain. Hence, when Lim visited North Korea, unbeknownst to the South Korean government, to participate in the 13th World Festival of Youth and Students as a one-person delegation representing the League of South Korean University Students, she shocked many with her daring act, which eventually resulted in her imprisonment in South Korea. She was vilified for breaching the National Security Law, therefore causing a huge embarrassment to the South Korean intelligence community, but enjoyed a completely opposite reception in the North. Dubbed the “Flower of Reunification,” Lim was hailed by the North Korean government as a heroic martyr who sacrificed herself at the altar of Korean reunification. Every step of the journey of this unusual South Korean visitor was memorialized in the North Korean documentary film Praise to Lim Su-gyeong, the Flower of Unification ( Janghada, Tongilui kkot Lim Su-gyeong, Naenara Video Jejakso, Pyongyang, 1989), which challenges viewers accustomed to equating the North Korean brand of heroism almost entirely with the canonization of Kim leadership. How does this young South Korean female citizen figure in the long-standing North Korean tradition of identifying male leaders as the legitimate agents of national heroism? What can be gleaned from this North Korean documentary film about how the state remembers the trauma of partition? This article traces the journey of Lim Su-gyeong, one of the most controversial South Korean sojourners to have visited North Korea, as a way of exploring the politics of memory in North Korean documentary film. This article also poses challenges to the overwhelming tendency in scholarship concerning North Korea, which has focused on the figure of the founding father, Kim Il-sung, as the centripetal force of the national personality cult. In the process, the way the North Korean state envisions gender politics and the utopian notion of inter-Korean citizenship will be explored in tandem.
The changing faces of heroines: Korean women in folklore
Authors: Kim Mikyoung
Published: March 2013

This article analyzes the many and changing faces of heroines in Korean folklore by interweaving the Korean cultural ethos of han and the action paradigm of resistance. Kim argues that feminist discourse often relegates alternative modes of resistance to the margins due to Western ethnocentrism and ideological politicization. She analyzes four types of heroines: archetypal, virtuous-but-not-virtuous, pioneering, and hanful resister. In doing so, Kim draws on Giddens’ knowledge and action theorem, which advances the simple equation between consciousness and resistance. Furthermore, Kim explores folklore’s validity as a legitimate commemorative medium. She introduces five memory units (storage/remembering, deletion/forgetting, retrieval, commemorative medium, and commemorative agency) and argues that the genre of folklore serves as a bridge between literature and collective memory scholarship. Since the field of memory studies validates lesser-known historical pasts, folklore deserves careful attention as a legitimate mnemonic medium. Korean folklore, a communal mnemonic result of production, retrieval, and transmission, shows diverse acts of resistance as women link presentism and traditionalism.
The Internet Marketing of Disney Theme Parks
Authors: Auster Carol J. , Michaud Margaret A.
Published: March 2013

The purpose of this study was to analyze the portrayal of gender and race in the images on the official Disney websites used to market five theme parks: the Disneyland Parks in California, Paris, Tokyo, and Hong Kong, and the Magic Kingdom in Florida. This is important because of the growth of e-commerce, Disney’s global influence, and the potential impact on those who view the images. The 452 images that had Disney human characters, human-like characters, animals, cast members, or guests were coded for gender. The main gender hypothesis, that the percentage of male-dominated images would exceed the percentage of female-dominated images, was tested using gender disparity values, which measured the gap between the percentage of male-dominated and female-dominated images. The hypothesis tended to be supported overall, and for most of the resorts (e.g., Florida), lands (e.g., Adventureland), and activities (attractions, entertainment, dining) for human characters, human-like characters, animals, and cast members, but not for guests. Furthermore, the hypotheses that gender disparity values would be highest for images of animals and lowest for images of guests was supported for all five resorts, six of eight lands, and all three activities. Additional analysis also revealed the preponderance of same-sex pairings in parent–child combinations in the images. With regard to race, while the images of some theme parks displayed more racial diversity among their guests than others, in some images, individuals of different races were shown interacting whereas in others they were not. Explanations for these findings and suggestions for future research are discussed.
Outcomes of transplantation using various hematopoietic cell sources in children with Hurler syndrome after myeloablative conditioning
Authors: Boelens Jaap Jan , Aldenhoven Mieke , Purtill Duncan , Ruggeri Annalisa , DeFor Todd , Wynn Robert , Wraith Ed , Cavazzana-Calvo Marina , Rovelli Attilio , Fischer Alain , Tolar Jakub , Prasad Vinod K. , Escolar Maria , Gluckman Eliane , O’Meara Anne , Orchard Paul J. , Veys Paul , Eapen Mary , Kurtzberg Joanne , Rocha Vanderson , Driscoll Timothy A. , Kurtzberg Joanne , Landi Daniel B. , Martin Paul L. , Page Kristin M. , Parikh Suhag H , Prasad Vinod K.
Published: March 2013

Key Points

In HS, patients’ early referral for HCT, with the best available HLA-matched donor offers the best event-free survival. In HS, patients’ HCT with a well-matched unrelated cord blood unit is particularly attractive because the unit is readily available.
Mining for class-specific motifs in protein sequence classification
Authors: Srinivasan Satish M , Vural Suleyman , King Brian R , Guda Chittibabu
Published: March 2013

Background

In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A number of classification methods aim at accurate classification but fail to explain which sequence features indeed contribute to the accuracy. We hypothesize that sequences in lower denominations (n-grams) can be used to explore the sequence landscape and to identify class-specific motifs that discriminate between classes during classification. Discriminative n-grams are short peptide sequences that are highly frequent in one class but are either minimally present or absent in other classes. In this study, we present a new substitution-based scoring function for identifying discriminative n-grams that are highly specific to a class.

Results

We present a scoring function based on discriminative n-grams that can effectively discriminate between classes. The scoring function, initially, harvests the entire set of 4- to 8-grams from the protein sequences of different classes in the dataset. Similar n-grams of the same size are combined to form new n- grams, where the similarity is defined by positive amino acid substitution scores in the BLOSUM62 matrix. Substitution has resulted in a large increase in the number of discriminatory n-grams harvested. Due to the unbalanced nature of the dataset, the frequencies of the n-grams are normalized using a dampening factor, which gives more weightage to the n-grams that appear in fewer classes and vice-versa. After the n-grams are normalized, the scoring function identifies discriminative 4- to 8-grams for each class that are frequent enough to be above a selection threshold. By mapping these discriminative n-grams back to the protein sequences, we obtained contiguous n-grams that represent short class-specific motifs in protein sequences. Our method fared well compared to an existing motif finding method known as Wordspy. We have validated our enriched set of class-specific motifs against the functionally important motifs obtained from the NLSdb, Prosite and ELM databases. We demonstrate that this method is very generic; thus can be widely applied to detect class-specific motifs in many protein sequence classification tasks.

Conclusion

The proposed scoring function and methodology is able to identify class-specific motifs using discriminative n-grams derived from the protein sequences. The implementation of amino acid substitution scores for similarity detection, and the dampening factor to normalize the unbalanced datasets have significant effect on the performance of the scoring function. Our multipronged validation tests demonstrate that this method can detect class-specific motifs from a wide variety of protein sequence classes with a potential application to detecting proteome-specific motifs of different organisms.
Efficient recovery of proteins from multiple source samples after trizol® or trizol®LS RNA extraction and long-term storage
Authors: Simões André ES , Pereira Diane M , Amaral Joana D , Nunes Ana F , Gomes Sofia E , Rodrigues Pedro M , Lo Adrian C , D'Hooge Rudi , Steer Clifford J , Thibodeau Stephen N , Borralho Pedro M , Rodrigues Cecília MP
Published: March 2013

Background

Simultaneous isolation of nucleic acids and proteins from a single biological sample facilitates meaningful data interpretation and reduces time, cost and sampling errors. This is particularly relevant for rare human and animal specimens, often scarce, and/or irreplaceable. TRIzol® and TRIzol®LS are suitable for simultaneous isolation of RNA, DNA and proteins from the same biological sample. These reagents are widely used for RNA and/or DNA isolation, while reports on their use for protein extraction are limited, attributable to technical difficulties in protein solubilisation.

Results

TRIzol®LS was used for RNA isolation from 284 human colon cancer samples, including normal colon mucosa, tubulovillous adenomas, and colon carcinomas with proficient and deficient mismatch repair system. TRIzol® was used for RNA isolation from human colon cancer cells, from brains of transgenic Alzheimer’s disease mice model, and from cultured mouse cortical neurons. Following RNA extraction, the TRIzol®-chloroform fractions from human colon cancer samples and from mouse hippocampus and frontal cortex were stored for 2 years and 3 months, respectively, at −80°C until used for protein isolation.

Simple modifications to the TRIzol® manufacturer’s protocol, including Urea:SDS solubilization and sonication, allowed improved protein recovery yield compared to the TRIzol® manufacturer’s protocol. Following SDS-PAGE and Ponceau and Coomassie staining, recovered proteins displayed wide molecular weight range and staining pattern comparable to those obtainable with commonly used protein extraction protocols. We also show that nuclear and cytosolic proteins can be easily extracted and detected by immunoblotting, and that posttranslational modifications, such as protein phosphorylation, are detectable in proteins recovered from TRIzol®-chloroform fractions stored for up to 2 years at −80°C.

Conclusions

We provide a novel approach to improve protein recovery from samples processed for nucleic acid extraction with TRIzol® and TRIzol®LS compared to the manufacturer`s protocol, allowing downstream immunoblotting and evaluation of steady-state relative protein expression levels. The method was validated in large sets of samples from multiple sources, including human colon cancer and brains of transgenic Alzheimer’s disease mice model, stored in TRIzol®-chloroform for up to two years. Collectively, we provide a faster and cheaper alternative to the TRIzol® manufacturer`s protein extraction protocol, illustrating the high relevance, and wide applicability, of the present protein isolation method for the immunoblot evaluation of steady-state relative protein expression levels in samples from multiple sources, and following prolonged storage.
Promzea: a pipeline for discovery of co-regulatory motifs in maize and other plant species and its application to the anthocyanin and phlobaphene biosynthetic pathways and the Maize Development Atlas
Authors: Liseron-Monfils Christophe , Lewis Tim , Ashlock Daniel , McNicholas Paul D , Fauteux François , Strömvik Martina , Raizada Manish N
Published: March 2013

Background

The discovery of genetic networks and cis-acting DNA motifs underlying their regulation is a major objective of transcriptome studies. The recent release of the maize genome (Zea mays L.) has facilitated in silico searches for regulatory motifs. Several algorithms exist to predict cis-acting elements, but none have been adapted for maize.

Results

A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at http://www.promzea.org and on the Discovery Environment of the iPlant Collaborative website. Promzea was subsequently expanded to include rice and Arabidopsis. Within Promzea, a user enters cDNA sequences or gene IDs; corresponding upstream sequences are retrieved from the maize genome. Predicted motifs are filtered, combined and ranked. Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the gene list and corresponding gene annotations. Promzea was validated in silico using a benchmark data set: the Promzea pipeline showed a 22% increase in nucleotide sensitivity compared to the best standalone program tool, Weeder, with equivalent nucleotide specificity. Promzea was also validated by its ability to retrieve the experimentally defined binding sites of transcription factors that regulate the maize anthocyanin and phlobaphene biosynthetic pathways. Promzea predicted additional promoter motifs, and genome-wide motif searches by Promzea identified 127 non-anthocyanin/phlobaphene genes that each contained all five predicted promoter motifs in their promoters, perhaps uncovering a broader co-regulated gene network. Promzea was also tested against tissue-specific microarray data from maize.

Conclusions

An online tool customized for promoter motif discovery in plants has been generated called Promzea. Promzea was validated in silico by its ability to retrieve benchmark motifs and experimentally defined motifs and was tested using tissue-specific microarray data. Promzea predicted broader networks of gene regulation associated with the historic anthocyanin and phlobaphene biosynthetic pathways. Promzea is a new bioinformatics tool for understanding transcriptional gene regulation in maize and has been expanded to include rice and Arabidopsis.
Cloning and characterization of a novel cold-active glycoside hydrolase family 1 enzyme with β-glucosidase, β-fucosidase and β-galactosidase activities
Authors: Wierzbicka-Woś Anna , Bartasun Paulina , Cieśliński Hubert , Kur Józef
Published: March 2013

Background

Cold-active enzymes, sourced from cold-adapted organisms, are characterized by high catalytic efficiencies at low temperatures compared with their mesophilic counterparts, which have poor activity. This property makes them advantageous for biotechnology applications as it: (i) saves energy costs, (ii) shortens the times for processes operated at low temperatures, (iii) protects thermosensitive substrates or products of the enzymatic reaction, (iv) prevents undesired chemical transformations, and (v) prevents the loss of volatile compounds.

Results

A bglMKg gene that encodes a monomeric cold-active glycoside hydrolase family 1 enzyme with an apparent molecular mass of 50 kDa was isolated by the functional screening of a marine metagenomic library. The BglMKg enzyme was expressed in E. coli, purified by FPLC and characterized. The recombinant BglMKg could effectively hydrolyze various chromogenic substrates and β-linked oligosaccharides, and had remarkably high β-galactosidase, β-glucosidase and β-fucosidase activities. Because of the lack of information about the usefulness of β-fucosidases in industry, further characterization of the enzymatic properties of BglMKg was only carried out with substrates specific for β-glucosidase or β-galactosidase. The BglMKg had maximal β-galactosidase and β-glucosidase activities at approximately 40°C and 45°C, respectively. The optimum pH for β-galactosidase activity was 6.5, whereas the optimum pH for β-glucosidase activity was 7.5. In general, the enzyme was stable below 30°C and from pHs 6.0 to 8.0. The results of the kinetic studies revealed that BglMKg more efficiently hydrolyzed β-glucosidase substrates than β-galactosidase ones.

Conclusions

BglMKg is a small, monomeric, cold-active β-glucosidase with additional enzymatic activities. It was efficiently expressed in E. coli indicating that BglMKg might be a candidate for industrial applications.
Reliability and validity of the Chinese version of the pediatric quality of life inventoryTM (PedsQLTM) 3.0 neuromuscular module in children with Duchenne muscular dystrophy
Authors: Hu Jun , Jiang Li , Hong Siqi , Cheng Li , Kong Min , Ye Yuanzhen
Published: March 2013

Background

The Pediatric Quality of Life InventoryTM (PedsQLTM) is a widely used instrument to measure pediatric health-related quality of life (HRQOL) in children aged 2 to 18 years. The current study aimed to evaluate the reliability and validity of the Chinese version of the PedsQLTM 3.0 Neuromuscular Module in children with Duchenne muscular dystrophy (DMD).

Methods

The PedsQLTM 3.0 Neuromuscular Module was translated into Chinese following PedsQLTM Measurement Model Translation Methodology. The Chinese version scale was administered to 56 children with DMD and their parents, and the psychometric properties were evaluated.

Results

The missing value percentages for each item of the Chinese version scale ranged from 0.00% to 0.54%. Internal consistency reliability approached or exceeded the minimum reliability standard of α = 0.7 (child α = 0.81, parent α = 0.86). Test-retest reliability was satisfactory, with intraclass correlation coefficients (ICCs) of 0.66 for children and 0.88 for parents (P < 0.01). Correlation coefficients between iteims and their hypothesized subscales were higher than those with other subscales (P < 0.05). The subscale of “About My/My Child’s Neuromuscular Disease” significantly related to mobility and stair climbing status (Child t = 2.21, Parent t = 2.83, P < 0.05). The inter-correlations among the Chinese version of the PedsQLTM 3.0 Neuromuscular Module and the PedsQLTM 4.0 Generic Core Scales had medium to large effect sizes (P < 0.05). The child self-report scores were in moderate agreement with the parent proxy-report scores (ICC = 0.51, P < 0.05).

Conclusions

The Chinese version of the PedsQLTM 3.0 Neuromuscular Module has acceptable psychometric properties. It is a reliable measure of disease-specific HRQOL in Chinese children with DMD.
Colon angiolipoma with intussusception: a case report and literature review
Authors: Wang Lei , Chen Ping , Zong Liang , Wang Guang-Yao , Wang Hao
Published: March 2013

Angiolipomas are frequently observed benign tumors. They have a typical vascular component and are often located in subcutaneous tissues, and more rarely, in the gastrointestinal tract. We present the case of a 58-year-old man who complained of abdominal discomfort in the left lower quadrant and two to three bloody stools a day without any obvious etiology. These symptom became more severe in the next three days, due to a large angiolipoma located in the descending colon, which was diagnosed intraoperatively. In a literature review, we found only 22 cases of angiolipomas involving the gastrointestinal tract which are reported in the literature from 1960 to 2012 in PubMed; the key words used in the search are gastrointestinal tract angiolipoma, esophagus, stomach, duodenum, intestine, ileocecal junction, colon, rectum angiolipomas. Colon angiolipoma with intussusception, as seen in this case, is rare and may require emergent surgical intervention.
Juvenile Psoriatic Arthritis (JPsA): juvenile arthritis with psoriasis?
Authors: Butbul Aviel Yonatan , Tyrrell Pascal , Schneider Rayfel , Dhillon Sandeep , Feldman Brian M , Laxer Ronald , Saurenmann Rotraud K , Spiegel Lynn , Cameron Bonnie , Tse Shirley ML , Silverman Earl
Published: March 2013

Background

Following the introduction of the ILAR criteria for juvenile idiopathic arthritis, juvenile psoriatic arthritis (JPsA) has become a better recognized category within the inflammatory arthritides of childhood. There are fewer reports describing the characteristics and long-term outcome of patients with JPsA than other subtypes of JIA.

The aim of our study was to determine the long-term outcome and clinical course of patients with juvenile psoriatic arthritis (JPsA) and to define subgroups of JPsA.

Methods

Clinical records of all patients meeting criteria for JPsA were reviewed and divided into 4 groups depending on their clinical features and onset type. Patient characteristics and clinical features at onset and during follow-up were determined.

Results

The cohort consisted of 119 patients: 65 with oligoarticular-onset (55%; persistent 44 and extended 21), 34 (29%) with RF(-) and 4 (3%) RF(+) polyarticular and 16 (13%) enthesitis-related arthritis (ERA). At diagnosis patients with ERA were oldest and more commonly male (p=0.001 and =0.01 respectively). Patients with a polyarticular course had more involvement of small joints of the hands and wrist when compared to patients with persistent oligoarticular and ERA (p<0.001) while patients with ERA had more hip and sacroiliac arthritis (p<0.001 for both). Nail changes were seen in 66 patients (57%) and were associated with DIP involvement (p=0.0034).

Outcome: Time to first inactive disease on, but not off, therapy was significantly longer among patients with polyarticular course when compared to oligoarticular and ERA (p=0.016 and p=0.48 respectively). Patients with polyarticular course more frequently had contractures during follow-up than other groups (p=0.01).

Conclusion

The long-term outcome of with JPsA was generally good. Patients with JPsA did not appear to form distinct sub-group of patients but rather resembled JIA patients with onset types without psoriasis.
Study on performance of magnetic fluorescent nanoparticles as gene carrier and location in pig kidney cells
Authors: Wang Yan , Cui Haixin , Sun Changjiao , Du Wei , Cui Jinhui , Zhao Xiang
Published: March 2013

We evaluated the performance of green fluorescent magnetic Fe3O4 nanoparticles (NPs) as gene carrier and location in pig kidney cells. When the mass ratio of NPs to green fluorescent protein plasmid DNA reached 1:16 or above, DNA molecules can be combined completely with NPs, which indicates that the NPs have good ability to bind negative DNA. Atomic force microscopy (AFM) experiments were carried out to investigate the binding mechanism between NPs and DNA. AFM images show that individual DNA strands come off of larger pieces of netlike agglomerations and several spherical nanoparticles are attached to each individual DNA strand and interact with each other. The pig kidney cells were labelled with membrane-specific red fluorescent dye 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate and nucleus-specific blue fluorescent dye 4′,6-diamidino-2-phenylindole dihydrochloride. We found that green fluorescent nanoparticles can past the cell membrane and spread throughout the interior of the cell. The NPs seem to locate more frequently in the cytoplasm than in the nucleus.
Global dynamics in a class of discrete-time epidemic models with disease courses
Authors: Wang Lei , Cui Qianqian , Teng Zhidong
Published: March 2013

In this paper, a class of discrete SIRS epidemic models with disease courses is studied. The basic reproduction number

R
0

is computed. The main results on the permanence and extinction of the disease are established. That is, the disease-free equilibrium is globally attractive if

R
0

<
1

, and there exists a unique endemic equilibrium and the disease is also permanent if

R
0

>
1

.

MSC:39A30, 92D30.
The role of autophagy in Parkinson's disease: rotenone-based modeling
Authors: Xiong Nian , Xiong Jing , Jia Min , Liu Ling , Zhang Xiaowei , Chen Zhenzhen , Huang Jinsha , Zhang Zhentao , Hou Lingling , Luo Zhijian , Ghoorah Devina , Lin Zhicheng , Wang Tao
Published: March 2013

Background

Autophagy-mediated self-digestion of cytoplasmic inclusions may be protective against neurodegenerative diseases such as Parkinson’s disease (PD). However, excessive autophagic activation evokes autophagic programmed cell death.

Methods

In this study, we aimed at exploring the role of autophagy in the pathogenesis of rotenone-induced cellular and animal models for PD.

Results

Reactive oxygen species over-generation, mitochondrial membrane potential reduction or apoptosis rate elevation occurred in a dose-dependent fashion in rotenone-treated human neuroblastoma cell line SH-SY5Y. The time- and dose-dependent increases in autophagic marker microtubule-associated protein1 light chain 3 (LC3) expression and decreases in autophagic adaptor protein P62 were observed in this cellular model. LC3-positive autophagic vacuoles were colocalized with alpha-synuclein-overexpressed aggregations. Moreover, the number of autophagic vacuoles was increased in rotenone-based PD models in vitro and in vivo.

Conclusions

These data, along with our previous finding showing rotenone-induced toxicity was prevented by the autophagy enhancers and was aggravated by the autophagy inhibitors in SH-SY5Y, suggest that autophagy contributes to the pathogenesis of PD, attenuates the rotenone toxicity and possibly represents a new subcellular target for treating PD.
Validation of reference genes for expression analysis by quantitative real-time PCR in Leptinotarsa decemlineata (Say)
Authors: Shi Xiao-Qin , Guo Wen-Chao , Wan Pin-Jun , Zhou Li-Tao , Ren Xiang-Liang , Ahmat Tursun , Fu Kai-Yun , Li Guo-Qing
Published: March 2013

Background

L. decemlineata is an exotic invasive insect pest, and invaded in Xinjiang Uygur autonomous region in China in the 1990s from Kazakhstan. It is a notorious defoliator of potato throughout most of the northern Xinjiang in current, and often causes extremely large yield losses of potato.

Results

The expression stability of nine L. decemlineata house-keeping genes (Actin, ACT1 and ACT2; ADP-ribosylation factor, ARF1 and ARF4; TATA box binding protein, TBP1 and TBP2; ribosomal protein RP4 and RP18; translation elongation factor 1α EF1α) was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) in seven developmental stages, three larval tissues and two insecticide treatments. The results were analyzed using three software programs: geNorm, NormFinder and BestKeeper. Although there was no consistent ranking observed among the house-keeping genes across the samples, the overall analysis revealed that RP18, RP4, ARF1, and ARF4 were the four most stable house-keeping genes. In contrast, ACT1 and ACT2, two of the most widely used reference genes, had the least stability. Our results suggest that the combined use of the four most stably expressed genes may produce optimal normalization for qRT-PCR.

Conclusions

The expression stability of the house-keeping genes varies among different developing stages, in different tissues and under different experimental conditions. Our results will enable a more accurate and reliable normalization of qRT-PCR data in L. decemlineata.
Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: Part II – contemporary contextual research
Authors: Bested Alison C , Logan Alan C , Selhub Eva M
Published: March 2013

In recent years there has been a renewed interest concerning the ways in which the gastrointestinal tract – its functional integrity and microbial residents – might influence human mood (e.g. depression) and behavioral disorders. Once a hotbed of scientific interest in the early 20th century, this area lay dormant for decades, in part due to its association with the controversial term ‘autointoxication’. Here we review contemporary findings related to intestinal permeability, small intestinal bacterial overgrowth, lipopolysaccharide endotoxin (LPS) exposure, D-lactic acid, propionic acid, and discuss their relevance to microbiota and mental health. In addition, we include the context of modern dietary habits as they relate to depression, anxiety and their potential interaction with intestinal microbiota.
SNP-based analysis of genetic diversity in anther-derived rice by whole genome sequencing
Authors: Jeong In-Seon , Yoon Ung-Han , Lee Gang-Seob , Ji Hyeon-So , Lee Hyun-Ju , Han Chang-Deok , Hahn Jang-Ho , An Gynheung , Kim Tae-Ho
Published: March 2013

Background

Anther culture has advantage to obtain a homozygous progeny by induced doubling of haploid chromosomes and to improve selection efficiency for invaluable agronomical traits. Therefore, anther culturing is widely utilized to breed new varieties and to induce genetic variations in several crops including rice. Genome sequencing technologies allow the detection of a massive number of DNA polymorphism such as SNPs and Indels between closely related cultivars. These DNA polymorphisms permit the rapid identification of genetic diversity among cultivars and genomic locations of heritable traits. To estimate sequence diversity derived from anther culturing, we performed whole-genome resequencing of five Korean rice accessions, including three anther culture lines (BLB, HY-04 and HY-08), their progenitor cultivar (Hwayeong), and an additional japonica cultivar (Dongjin).

Results

A total of 1,165 × 106 raw reads were generated with over 58× coverage that detected 1,154,063 DNA polymorphisms between the Korean rice accessions and Nipponbare. We observed that in Hwayeong and its progenies, 0.64 SNP was found per one kb of Nipponbare genome, while Dongjin, bred by a conventional breeding method, had a lower number of SNPs (0.45 SNP/kb). Among 1,154,063 DNA polymorphisms, 29,269 non-synonymous SNPs located on 30,013 genes and these genes were functionally classified based on gene ontology (GO). We also analyzed line-specific SNPs which were estimated 1 ~ 3% of the total SNPs. The frequency of non-synonymous SNPs in each accession ranged from 26 SNPs in Hwayeong to 214 SNPs in HY-04.

Conclusions

The genetic difference we detected between the progenies derived from anther culture and their mother cultivar is due to somaclonal variation during tissue culture process, such as karyotype change, chromosome rearrangement, gene amplification and deletion, transposable element, and DNA methylation. Detection of genome-wide DNA polymorphisms by high-throughput sequencer enabled to identify sequence diversity derived from anther culturing and genomic locations of heritable traits. Furthermore, it will provide an invaluable resource to identify molecular markers and genes associated with diverse traits of agronomical importance.
3D angle gathers with plane-wave reverse-time migration
Authors: Tang Bing , Xu Sheng , Zhang Yu
Published: March 2013

Angle domain common image gathers (ADCIGs) from reverse-time migration (RTM) provide new tools for imaging complex geologic structures, such as salt flank or subsalt areas, characterized by multiarrivals. Compared with common image gathers from Kirchoff or Beam migration, the ADCIGs from RTM have the advantage of relying on wave propagation, providing a more reliable input for tomography or amplitude analysis. In practice however, most current wide azimuth surveys (e.g., deep-water regions of the Gulf of Mexico) are acquired with coarsely sampled shot and receiver locations on the surface, which leads to severe angular undersampling. This phenomenon is frequently observed on shallow seismic events in high-resolution 3D ADCIGs from common-shot RTM. In addition, because small offsets are frequently not recorded, seismic events are missing at small incidence angles in angle gathers. We have made a detailed study of the angular sampling issue in 3D angle gathers. We then used plane-wave RTM to generate 3D angle gathers. Plane-wave RTM, with its low-cost and automatic angular interpolation, is a promising solution for improving the quality of 3D angle gathers.
Time to Get Serious About Improving the Safety of Oral Chemotherapy
Authors: Krzyzanowska Monika K.
Published: March 2013

With the increasing use of oral chemotherapy, there has been heightened appreciation of the unique challenges associated, especially in relation to prescribing, dispensing, reimbursement, adherence, and patient and family education.
Posttranslational Processing of Human and Mouse Urocortin 2: Characterization and Bioactivity of Gene Products
Authors: Vaughan Joan M. , Donaldson Cynthia J. , Fischer Wolfgang H. , Perrin Marilyn H. , Rivier Jean E. , Sawchenko Paul E. , Vale Wylie W.
Published: March 2013

Mouse (m) and human (h) urocortin 2 (Ucn 2) were identified by molecular cloning strategies and the primary sequence of their mature forms postulated by analogy to closely related members of the corticotropin-releasing factor (CRF) neuropeptide family. Because of the paucity of Ucn 2 proteins in native tissues, skin, muscle, and pancreatic cell lines were transduced with lentiviral constructs and secretion media were used to isolate and characterize Ucn 2 products and study processing. Primary structures were assigned using a combination of Edman degradation sequencing and mass spectrometry. For mUcn 2, transduced cells secreted a 39 amino acid peptide and the glycosylated prohormone lacking signal peptide; both forms were C-terminally amidated and highly potent to activate the type 2 CRF receptor. Chromatographic profiles of murine tissue extracts were consistent with cleavage of mUcn 2 prohormone to a peptidic form. By contrast to mUcn 2, mammalian cell lines transduced with hUcn 2 constructs secreted significant amounts of an 88 amino acid glycosylated hUcn 2 prohormone but were unable to further process this molecule. Similarly, WM-266-4 melanoma cells that express endogenous hUcn 2 secreted only the glycosylated prohormone lacking the signal peptide and unmodified at the C terminus. Although not amidated, hUcn 2 prohormone purified from overexpressing lines activated CRF receptor 2. Hypoxia and glycosylation, paradigms that might influence secretion or processing of gene products, did not significantly impact hUcn 2 prohormone cleavage. Our findings identify probable Ucn 2 processing products and should expedite the characterization of these proteins in mammalian tissues.
Full- and Half-Gilbert Tessellations with Rectangular Cells
Authors: Burridge James , Cowan Richard , Ma Isaac
Published: March 2013

We investigate the ray-length distributions for two different rectangular versions of Gilbert's tessellation (see Gilbert (1967)). In the full rectangular version, lines extend either horizontally (east- and west-growing rays) or vertically (north- and south-growing rays) from seed points which form a Poisson point process, each ray stopping when another ray is met. In the half rectangular version, east- and south-growing rays do not interact with west and north rays. For the half rectangular tessellation, we compute analytically, via recursion, a series expansion for the ray-length distribution, whilst, for the full rectangular version, we develop an accurate simulation technique, based in part on the stopping-set theory for Poisson processes (see Zuyev (1999)), to accomplish the same. We demonstrate the remarkable fact that plots of the two distributions appear to be identical when the intensity of seeds in the half model is twice that in the full model. In this paper we explore this coincidence, mindful of the fact that, for one model, our results are from a simulation (with inherent sampling error). We go on to develop further analytic theory for the half-Gilbert model using stopping-set ideas once again, with some novel features. Using our theory, we obtain exact expressions for the first and second moments of the ray length in the half-Gilbert model. For all practical purposes, these results can be applied to the full-Gilbert model—as much better approximations than those provided by Mackisack and Miles (1996).
Monotone Policies and Indexability for Bidirectional Restless Bandits
Authors: Glazebrook K. D. , Hodge D. J. , Kirkbride C.
Published: March 2013

Motivated by a wide range of applications, we consider a development of Whittle's restless bandit model in which project activation requires a state-dependent amount of a key resource, which is assumed to be available at a constant rate. As many projects may be activated at each decision epoch as resource availability allows. We seek a policy for project activation within resource constraints which minimises an aggregate cost rate for the system. Project indices derived from a Lagrangian relaxation of the original problem exist provided the structural requirement of indexability is met. Verification of this property and derivation of the related indices is greatly simplified when the solution of the Lagrangian relaxation has a state monotone structure for each constituent project. We demonstrate that this is indeed the case for a wide range ofbidirectionalprojects in which the project state tends to move in a different direction when it is activated from that in which it moves when passive. This is natural in many application domains in which activation of a project ameliorates its condition, which otherwise tends to deteriorate or deplete. In some cases the state monotonicity required is related to the structure of state transitions, while in others it is also related to the nature of costs. Two numerical studies demonstrate the value of the ideas for the construction of policies for dynamic resource allocation, most especially in contexts which involve a large number of projects.
Error Bounds for Small Jumps of Lévy Processes
Authors: Dia E. H. A.
Published: March 2013

The pricing of options in exponential Lévy models amounts to the computation of expectations of functionals of Lévy processes. In many situations, Monte Carlo methods are used. However, the simulation of a Lévy process with infinite Lévy measure generally requires either truncating or replacing the small jumps by a Brownian motion with the same variance. We will derive bounds for the errors generated by these two types of approximation.
Characterizing Heavy-Tailed Distributions Induced by Retransmissions
Authors: Jelenković Predrag R. , Tan Jian
Published: March 2013

Consider a generic data unit of random sizeLthat needs to be transmitted over a channel of unit capacity. The channel availability dynamic is modeled as an independent and identically distributed sequence {A,Ai}i≥1that is independent ofL. During each period of time that the channel becomes available, sayAi, we attempt to transmit the data unit. IfL<Ai, the transmission is considered successful; otherwise, we wait for the next available periodAi+1and attempt to retransmit the data from the beginning. We investigate the asymptotic properties of the number of retransmissionsNand the total transmission timeTuntil the data is successfully transmitted. In the context of studying the completion times in systems with failures where jobs restart from the beginning, it was first recognized by Fiorini, Sheahan and Lipsky (2005) and Sheahan, Lipsky, Fiorini and Asmussen (2006) that this model results in power-law and, in general, heavy-tailed delays. The main objective of this paper is to uncover the detailed structure of this class of heavy-tailed distributions induced by retransmissions. More precisely, we study how the functional relationship ℙ[L>x]-1≈ Φ (ℙ[A>x]-1) impacts the distributions ofNandT; the approximation ‘≈’ will be appropriately defined in the paper based on the context. Depending on the growth rate of Φ(·), we discover several criticality points that separate classes of different functional behaviors of the distribution ofN. For example, we show that if log(Φ(n)) is slowly varying then log(1/ℙ[N>n]) is essentially slowly varying as well. Interestingly, if log(Φ(n)) grows slower than e√(logn)then we have the asymptotic equivalence log(ℙ[N>n]) ≈ - log(Φ(n)). However, if log(Φ(n)) grows faster than e√(logn), this asymptotic equivalence does not hold and admits a different functional form. Similarly, different types of distributional behavior are shown for moderately heavy tails (Weibull distributions) where log(ℙ[N>n]) ≈ -(log Φ(n))1/(β+1), assuming that log Φ(n) ≈ nβ, as well as the nearly exponential ones of the form log(ℙ[N>n]) ≈ -n/(logn)1/γ, γ>0, when Φ(·) grows faster than two exponential scales log log (Φ(n)) ≈nγ.
Bayesian Quickest Detection Problems for Some Diffusion Processes
Authors: Gapeev Pavel V. , Shiryaev Albert N.
Published: March 2013

We study the Bayesian problems of detecting a change in the drift rate of an observable diffusion process with linear and exponential penalty costs for a detection delay. The optimal times of alarms are found as the first times at which the weighted likelihood ratios hit stochastic boundaries depending on the current observations. The proof is based on the reduction of the initial problems into appropriate three-dimensional optimal stopping problems and the analysis of the associated parabolic-type free-boundary problems. We provide closed-form estimates for the value functions and the boundaries, under certain nontrivial relations between the coefficients of the observable diffusion.
Asymptotics of Markov Kernels and the Tail Chain
Authors: Resnick Sidney I. , Zeber David
Published: March 2013

An asymptotic model for the extreme behavior of certain Markov chains is the ‘tail chain’. Generally taking the form of a multiplicative random walk, it is useful in deriving extremal characteristics, such as point process limits. We place this model in a more general context, formulated in terms of extreme value theory for transition kernels, and extend it by formalizing the distinction between extreme and nonextreme states. We make the link between the update function and transition kernel forms considered in previous work, and we show that the tail chain model leads to a multivariate regular variation property of the finite-dimensional distributions under assumptions on the marginal tails alone.
Discrete-Time Semi-Markov Random Evolutions and their Applications
Authors: Limnios Nikolaos , Swishchuk Anatoliy
Published: March 2013

In this paper we introduce discrete-time semi-Markov random evolutions (DTSMREs) and study asymptotic properties, namely, averaging, diffusion approximation, and diffusion approximation with equilibrium by the martingale weak convergence method. The controlled DTSMREs are introduced and Hamilton–Jacobi–Bellman equations are derived for them. The applications here concern the additive functionals (AFs), geometric Markov renewal chains (GMRCs), and dynamical systems (DSs) in discrete time. The rates of convergence in the limit theorems for DTSMREs and AFs, GMRCs, and DSs are also presented.
Finite- and Infinite-Time Ruin Probabilities with General Stochastic Investment Return Processes and Bivariate Upper Tail Independent and Heavy-Tailed Claims
Authors: Guo Fenglong , Wang Dingcheng
Published: March 2013

In this paper we investigate the asymptotic behaviors of the finite- and infinite-time ruin probabilities for a Poisson risk model with stochastic investment returns which constitute a general adapted càdlàg process and heavy-tailed claim sizes which are bivariate upper tail independent. The results of this paper show that the asymptotic ruin probabilities are dominated by the extreme of insurance risk but not by that of investment risk. As applications of the results, we discuss four special cases when the investment returns are determined by a fractional Brownian motion, an integrated Vasicek model, an integrated Cox–Ingersoll–Ross model, and the Heston model.
Approximating the Split Closure
Authors: Fischetti Matteo , Salvagnin Domenico
Published: March 2013

The split closure has been proved in practice to be a very tight approximation of the integer hull formulation of a generic mixed-integer linear program. However, exact separation procedures for optimizing over the split closure have unacceptable computing times in practice; hence, many different heuristic strategies have been proposed in the last few years. In this paper we present a new overall framework for approximating the split closure that merges different ideas from the previous approaches. Computational results prove the effectiveness of the proposed procedure compared to the state of the art, showing that a good approximation of the split closure bound can be obtained with very reasonable computing times.
Stereochemistry and total synthesis of complex myxobacterial macrolides
Authors: Essig Sebastian , Menche Dirk
Published: March 2013

Polyketides are a very diverse family of natural products with an extremely broad range of biological activities and pharmacological properties, including antiproliferative, antibiotic, antifungal, or antiplasmodial activities, and in many cases specific targets are addressed at the molecular level. Their structures are characterized by diverse assemblies of methyl- and hydroxyl-bearing stereogenic centers enabling large numbers of stereochemical permutations, which are often embedded into macrolide rings. This complexity renders the stereochemical assignment and directed total synthesis challenging tasks. Within this review, we will detail practicable approaches for the stereochemical determination of diverse complex polyketides of myxobacterial origin by using computational and NMR methods in combination with novel procedures based on bioinformatics. Furthermore, we have developed efficient preparative strategies for the synthesis of these compounds, which have culminated in several first total syntheses. Key aspects of these various endeavors, which will also focus on the importance of conformational bias in complex polyketide analysis and synthesis, will be discussed within this review in the realm of the potent macrolide antibiotics etnangien and rhizopodin. Along these lines, we will also summarize novel methods for the rapid assembly of key structural elements of polyketides including a novel domino concept relying on a combination of a nucleophilic addition and a Tsuji–Trost reaction.