bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract

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

Abstract

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

Abstract

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

Abstract
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

Abstract

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

Abstract
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

Abstract
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

Abstract

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

Abstract

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

Abstract
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

Abstract

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.
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

AbstractMouse (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.
High End Battery Management Systems for Renewable Energy and EV Applications
Authors: Jung Max , Schwunk Simon 
Published: March 2013

AbstractUsing renewable energies means having to deal with a strongly stochastic behaviour, since for photovoltaics the sun has to shine or for wind generators the wind has to blow. For being able to supply the load any time, storage solutions are needed. Decreasing costs and better availabilities of new battery technologies like lithium-ion therefore result in a growing demand for more sophisticated battery systems in off-grid and grid connected applications. In e.g. off-grid applications, lead-acid battery systems are state of the art. Though, lithium-ion batteries become more popular because of their high energy density and long life time. Another application for electrochemical storage systems are electric vehicles. In all those cases the battery storages need to be managed. But the management of a battery system is not a trivial problem. The batteries must be monitored and controlled, there are challenges regarding safety, electrical isolation and energy efficiency. The article gives an introduction to different architectures of battery management systems (BMS). There are different approaches to design a BMS the article describes in the first part. In the second part, there is a more precise description of the electronic hardware and the software behind a BMS. To understand both function and importance of a BMS, the article introduces in the third part a few applications of BMS in bigger battery packs.
The Competition of Different Measures to Increase Flexibility in Energy Systems with a High Share of Fluctuating Renewable Energy Sources
Authors: Brunner Christoph , Teufel Felix 
Published: March 2013

AbstractThe continuous expansion of electricity generation from intermittent renewable energy sources (RES) is changing the present generation structure that has been designed to follow fluctuating demand considerably. In order to utilise a high share of supply-dependent RES, the future energy system needs to become more flexible than it is today. This paper describes the different flexibility options that can be implemented with regard to their major restrictions as well as their suitability to balance a certain deficit or surplus of RES generation. Furthermore, it outlines the importance of competition between these different balancing measures to meet the required level of flexibility at lowest cost.