bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Arabidopsis Cell Wall Proteoglycan Consists of Pectin and Arabinoxylan Covalently Linked to an Arabinogalactan Protein
Authors: Tan Li , Eberhard Stefan , Pattathil Sivakumar , Warder Clayton , Glushka John , Yuan Chunhua , Hao Zhangying , Zhu Xiang , Avci Utku , Miller Jeffrey S. , Baldwin David , Pham Charles , Orlando Ronald , Darvill Alan , Hahn Michael G. , Kieliszewski Marcia J. , Mohnen Debra 
Published: February 2013

Abstract
Plant cell walls are comprised largely of the polysaccharides cellulose, hemicellulose, and pectin, along with ∼10% protein and up to 40% lignin. These wall polymers interact covalently and noncovalently to form the functional cell wall. Characterized cross-links in the wall include covalent linkages between wall glycoprotein extensins between rhamnogalacturonan II monomer domains and between polysaccharides and lignin phenolic residues. Here, we show that two isoforms of a purified Arabidopsis thaliana arabinogalactan protein (AGP) encoded by hydroxyproline-rich glycoprotein family protein gene At3g45230 are covalently attached to wall matrix hemicellulosic and pectic polysaccharides, with rhamnogalacturonan I (RG I)/homogalacturonan linked to the rhamnosyl residue in the arabinogalactan (AG) of the AGP and with arabinoxylan attached to either a rhamnosyl residue in the RG I domain or directly to an arabinosyl residue in the AG glycan domain. The existence of this wall structure, named ARABINOXYLAN PECTIN ARABINOGALACTAN PROTEIN1 (APAP1), is contrary to prevailing cell wall models that depict separate protein, pectin, and hemicellulose polysaccharide networks. The modified sugar composition and increased extractability of pectin and xylan immunoreactive epitopes in apap1 mutant aerial biomass support a role for the APAP1 proteoglycan in plant wall architecture and function.
ArabidopsisPaired Amphipathic Helix Proteins SNL1 and SNL2 Redundantly Regulate Primary Seed Dormancy via Abscisic Acid–Ethylene Antagonism Mediated by Histone Deacetylation
Authors: Wang Zhi , Cao Hong , Sun Yongzhen , Li Xiaoying , Chen Fengying , Carles Annaick , Li Yong , Ding Meng , Zhang Cun , Deng Xin , Soppe Wim J.J. , Liu Yong-Xiu 
Published: February 2013

AbstractHistone (de)acetylation is a highly conserved chromatin modification that is vital for development and growth. In this study, we identified a role in seed dormancy for two members of the histone deacetylation complex in Arabidopsis thaliana, SIN3-LIKE1 (SNL1) and SNL2. The double mutant snl1 snl2 shows reduced dormancy and hypersensitivity to the histone deacetylase inhibitors trichostatin A and diallyl disulfide compared with the wild type. SNL1 interacts with HISTONE DEACETYLASE19 in vitro and in planta, and loss-of-function mutants of SNL1 and SNL2 show increased acetylation levels of histone 3 lysine 9/18 (H3K9/18) and H3K14. Moreover, SNL1 and SNL2 regulate key genes involved in the ethylene and abscisic acid (ABA) pathways by decreasing their histone acetylation levels. Taken together, we showed that SNL1 and SNL2 regulate seed dormancy by mediating the ABA-ethylene antagonism in Arabidopsis. SNL1 and SNL2 could represent a cross-link point of the ABA and ethylene pathways in the regulation of seed dormancy.
A DEAD Box RNA Helicase Is Critical for Pre-mRNA Splicing, Cold-Responsive Gene Regulation, and Cold Tolerance inArabidopsis
Authors: Guan Qingmei , Wu Jianmin , Zhang Yanyan , Jiang Changhua , Liu Renyi , Chai Chenglin , Zhu Jianhua 
Published: February 2013

AbstractCold stress resulting from chilling and freezing temperatures substantially reduces crop production worldwide. To identify genes critical for cold tolerance in plants, we screened Arabidopsis thaliana mutants for deregulated expression of a firefly luciferase reporter gene under the control of the C-REPEAT BINDING FACTOR2 (CBF2) promoter (CBF2:LUC). A regulator of CBF gene expression1 (rcf1-1) mutant that is hypersensitive to cold stress was chosen for in-depth characterization. RCF1 encodes a cold-inducible DEAD (Asp-Glu-Ala-Asp) box RNA helicase. Unlike a previously reported DEAD box RNA helicase (LOW EXPRESSION OF OSMOTICALLY RESPONSIVE GENES4 [LOS4]) that regulates mRNA export, RCF1 does not play a role in mRNA export. Instead, RCF1 functions to maintain proper splicing of pre-mRNAs; many cold-responsive genes are mis-spliced in rcf1-1 mutant plants under cold stress. Functional characterization of four genes (PSEUDO-RESPONSE REGULATOR5 [PRR5], SHAGGY-LIKE SERINE/THREONINE KINASE12 [SK12], MYB FAMILY TRANSCRIPTION FACTOR CIRCADIAN1 [CIR1], and SPFH/PHB DOMAIN-CONTAINING MEMBRANE-ASSOCIATED PROTEIN [SPFH]) that are mis-spliced in rcf1-1 revealed that these genes are cold-inducible positive (CIR1 and SPFH) and negative (PRR5 and SK12) regulators of cold-responsive genes and cold tolerance. Together, our results suggest that the cold-inducible RNA helicase RCF1 is essential for pre-mRNA splicing and is important for cold-responsive gene regulation and cold tolerance in plants.
Mechanistic models of animal migration behaviour – their diversity, structure and use
Authors: Bauer Silke , Klaassen Marcel 
Published: February 2013

SummaryMigration is a widespread phenomenon in the animal kingdom, including many taxonomic groups and modes of locomotion. Developing an understanding of the proximate and ultimate causes for this behaviour not only addresses fundamental ecological questions but has relevance to many other fields, for example in relation to the spread of emerging zoonotic diseases, the proliferation of invasive species, aeronautical safety as well as the conservation of migrants.Theoretical methods can make important contributions to our understanding of migration, by allowing us to integrate findings on this complex behaviour, identify caveats in our understanding and to guide future empirical research efforts. Various mechanistic models exist to date, but their applications seem to be scattered and far from evenly distributed across taxonomic units.Therefore, we provide an overview of the major mechanistic modelling approaches used in the study of migration behaviour and characterize their fundamental features, assumptions and limitations and discuss their typical data requirements both for model parameterization and for scrutinizing model predictions.Furthermore, we review 155 studies that have used mechanistic models to study animal migration and analyse them with regard to the approaches used and the focal species, and also explore their contribution to advancing current knowledge within six broad migration ecology research themes.This identifies important gaps in our present knowledge, which should be tackled in future research using existing and to‐be developed theoretical approaches.
Quantitative physiology of Lactococcus lactis at extreme low‐growth rates
Authors: Ercan Onur , Smid Eddy J. , Kleerebezem Michiel 
Published: February 2013

SummaryThis paper describes the metabolic adaptation of Lactococcus lactis during the transition from a growing to a non‐growing state using retentostat cultivation. Under retentostat cultivation, the specific growth rate decreased from 0.025 h−1 to 0.0001 h−1 in 42 days, while doubling time increased to more than 260 days. Viability of the overall culture was maintained above 90% but included approximately 20% damaged cells, which had lost their colony forming capacity on solid media. Although culture biomass and viability had reached a steady‐state after 14 days of retentostat cultivation, the morphology of the cells changed from coccus‐to‐rod shape at later stages of retentostat cultivation, by which the cell's surface to volume ratio was estimated to increase 2.4‐fold. Furthermore, the metabolic patterns switched between homolactic and mixed‐acid fermentation during the retentostat cultivation. Retentostat cultivation enabled the calculation of accurate substrate‐ and energy‐related maintenance coefficients and biomass yields under non‐growing conditions, which were in good agreement with those calculated by extrapolation from chemostat cultivations at high dilution rates. In this study, we illustrate how retentostat cultivation allows decoupling of growth and non‐growth associated processes in L. lactis, enabling the analysis of quantitative physiological responses of this bacterium to near zero‐specific growth rates.
Diabetes nurse case management and motivational interviewing for change (DYNAMIC): Results of a 2‐year randomized controlled pragmatic trial (糖尿病护士病例管理以及促进改变的动机性会谈（DYNAMIC）：一项为期2年的实用随机对照研究)
Authors: Gabbay Robert A. , Añel‐Tiangco Raquel M. , Dellasega Cheryl , Mauger David T. , Adelman Alan , Van Horn Deborah H.A. 
Published: February 2013

AbstractBackgroundThe aim of the present study was to determine whether the addition of nurse case managers (NCMs) trained in motivational interviewing (MI) to usual care would result in improved outcomes in high‐risk type 2 diabetes patients.MethodsA 2‐year randomized controlled pragmatic trial randomized 545 patients to usual care control (n = 313) or those who received the intervention (n = 232) with additional practice‐embedded NCM care, including MI‐guided behavior change counseling. The NCMs received intensive MI training with ongoing fidelity assessment.ResultsSystolic blood pressure (SBP) was better in the intervention than usual care group (131 ± 15 vs. 135 ± 18 mmHg, respectively; P < 0.05). Improvements were seen in both the control and intervention groups in terms of HbA1c (from 9.1% to 8.0% and from 8.8% to 7.8%, respectively), low‐density lipoprotein (LDL; from 127 to 100 mg/dL and from 128 to 102 mg/dL, respectively), and diastolic blood pressure (from 78 to 74 mmHg and from 80 to 74 mmHg, respectively). Depression symptom scores were better in the intervention group. The reduction in diabetes‐related distress approached statistical significance.ConclusionsThe NCMs and MI improved SBP and complications screening. The large decrease in HbA1C and LDL in the control group may have obscured any further intervention effect. Although nurses prompted providers for medication titration, strategies to reduce provider clinical inertia may also be needed.
Comparison of autoantibody‐positive and autoantibody‐negative pediatric participants enrolled in the T1D Exchange clinic registry (在1型糖尿病交流中心临床登记的自身抗体阳性与自身抗体阴性的儿科参与者的比较)
Authors: Gerard‐Gonzalez Andrea , Gitelman Stephen E. , Cheng Peiyao , Dubose Stephanie N. , Miller Kellee M. , Olson Beth A. , Redondo Maria J. , Steck Andrea K. , Beck Roy W. 
Published: February 2013

AbstractObjectiveTo compare characteristics of autoantibody (aAb)‐positive and ‐negative cases of type 1 diabetes (T1D) <18 years old in the T1D Exchange clinic registry.MethodsAn aAb‐positive status (n = 6239) required at least one of the aAbs to be positive; an aAb‐negative status (n = 485) required negative results on testing of at least two different aAbs.ResultsThe percentage of males was higher (58% vs 51%; P = 0.002) and total daily insulin dose lower (P = 0.003) in aAb‐negative compared with aAb‐positive groups, but both groups had similar distributions of race–ethnicity, diagnosis age, family history of T1D, ketoacidosis at diagnosis, body mass index at diagnosis and at most recent office visit, and current HbA1c.ConclusionsMale gender and lower total daily insulin dose were more likely in aAb‐negative than aAb‐positive children with T1D, but no other distinguishing characteristics were identified. Further examination of characteristics of aAb‐negative cases may help characterize the heterogeneous nature of T1D.
Restricted variation in plant barcoding markers limits identification in closely related bryophyte species
Authors: Hassel Kristian , Segreto Rossana , Ekrem Torbjørn 
Published: February 2013

AbstractSpecies‐level identification and delimitation of bryophytes using the proposed general barcode markers for land plants has been challenging. Bryophyta (mosses) is the second most species‐rich group of land plants after angiosperms, and it is thus of great importance to find useful barcoding regions also for this group of plants. We investigated how the plastid regions atpF–atpH, rbcL and trnH–psbA and the nuclear ITS2 region performed as barcode markers on closely related bryophyte taxa of selected moss (Bartramia, Distichium, Fissidens, Meesia and Syntrichia) and liverwort (Blepharostoma) genera from boreal and arctic regions. We also evaluated how sequencing success of herbarium specimens is related to length of the sequenced fragment, specimen age and taxonomic group. Sequencing success was higher for shorter fragments and younger herbarium specimens, but was lower than expected in the genera Distichium and Fissidens, indicating imperfect universality of the primers used. None of the studied DNA barcode regions showed a consistent barcode gap across the studied genera. As a single locus, the region atpF–atpH performed slightly better than rbcL and ITS2 and much better than trnH–psbA in terms of grouping conspecific sequences in monophyletic groups. This marker also gave a higher percentage of correct hits when conducting blast searches on a local database of identified sequences. Concatenated data sets of two and three markers grouped more conspecific sequences in monophyletic groups, but the improvement was not great compared with atpF–atpH alone. A discussion of recent studies testing barcode regions for bryophytes is given. We conclude that atpF–atpH, rbcL and ITS2 are to be the most promising barcode markers for mosses.
Molecular mapping of stomatal‐conductance‐related traits in durum wheat (Triticum turgidum ssp. durum)
Authors: Panio G. , Motzo R. , Mastrangelo A.M. , Marone D. , Cattivelli L. , Giunta F. , De Vita P. 
Published: February 2013

AbstractThe most promising traits identified in wheat to raise yield potential via an increase in biomass accumulation are stomatal conductance and stomatal‐conductance‐related traits, such as carbon isotope discrimination (CID) and photosynthetic rate. The evaluation of the extent of genetic variation and the mapping of chromosomal regions controlling these traits are essential for the development of effective breeding strategies in durum wheat. A population of 161 F2‐derived, F8–F9 recombinant inbred lines obtained from a cross between durum wheat (Triticum turgidum ssp. durum) cultivars Ofanto and Cappelli was phenotyped for heading date, plant height, leaf porosity, CID and chlorophyll concentration (estimated through the SPAD index) for 2007/2008 and 2008/2009 seasons, at Ottava, Sardinia (Italy) under irrigated conditions. The genotype mean heritability for leaf porosity, CID and chlorophyll concentration was moderate in size. Six quantitative trait loci were detected for leaf porosity, four for chlorophyll concentration, but only one for CID, because of the small variation expressed in the population for this trait under these experimental conditions. The quantitative trait loci for leaf porosity located on chromosome 3B appear to be more stable with respect to the others, and different microsatellite markers are positioned within the interval of the quantitative trait loci, or in their vicinity, that represent useful tools in programmes for selection assisted by molecular markers.
A new clade of Dickeya spp. plays a major role in potato blackleg outbreaks in North Finland
Authors: Degefu Yeshitila , Potrykus Marta , Golanowska Malgorzata , Virtanen Elina , Lojkowska Ewa 
Published: February 2013

AbstractUntil recently Dickeya was regarded as a pathogen not established in Finland. As a result the blackleg symptom observed on potato was often associated with Pectobacterium atrosepticum. The occurrence of Dickeya spp. on potato in Finland was first reported in 2004. Since then the prevalence of Dickeya has been monitored through surveys and routine test of seed lots produced in the country. The results of monitoring of Dickeya spp. in seed lots produced in Finland between the years 2004 and 2008 indicated a steady increase in the incidence of Dickeya spp. The highest incidence was observed in samples from the 2006 growing season where about 37% were positive for Dickeya spp. The summer in 2006 was one of the warmest summers recorded in 100 years in Finland. The majority of infected lots were imported varieties. Since recently heavy blackleg outbreaks have occurred in production fields in the High Grade (HG) zone. A detailed study of these incidents of blackleg outbreaks in North Finland during the years 2008 and 2010 indicated that Dickeya spp. was the major component in the observed blackleg complex. It was detected and isolated from almost all symptomatic plants investigated. Repetitive sequences PCR (REP‐PCR) and Pulsed Field Gel Electrophoresis (PFGE) analysis of strains isolated in Finland showed identical pattern with those isolated recently in other European countries with a proposed name ‘Dickeya solani’. Moreover, the dnaX gene sequence of the representative strains isolated in Finland indicated 100% similarity to the dnaX sequences of ‘D. solani’. The study presents the first report of a detailed analysis of bacteria involved in potato blackleg complex from natural field outbreaks in North Finland HG zone and characterisation of the ‘D. solani’ strains playing the major role in the disease complex.
Sources of momentum profits in international stock markets
Authors: Park Kyung‐In , Kim Dongcheol 
Published: February 2013

AbstractThis paper examines the sources of momentum profits of countries exhibiting and not exhibiting momentum and compares the differences in the underlying factors determining momentum profits between these two groups of countries. We find remarkable differences in the decomposed components between these two groups of countries. Countries exhibiting momentum show that the cross‐sectional dispersion in unconditional mean returns dominates the negative contribution from the component reflecting the intertemporal behaviour of asset returns. However, this is not the case in countries exhibiting no momentum. Furthermore, countries with greater relative contribution from the cross‐sectional variance in unconditional mean returns tend to have greater momentum profits. Our results may support risk‐based explanations for the momentum phenomenon rather than behavioural finance‐based explanations.
Intercoalescence Time Distribution of Incomplete Gene Genealogies in Temporally Varying Populations, and Applications in Population Genetic Inference
Authors: Chen Hua 
Published: February 2013

SummaryTracing back to a specific time T in the past, the genealogy of a sample of haplotypes may not have reached their common ancestor and may leave m lineages extant. For such an incomplete genealogy truncated at a specific time T in the past, the distribution and expectation of the intercoalescence times conditional on T are derived in an exact form in this paper for populations of deterministically time‐varying sizes, specifically, for populations growing exponentially. The derived intercoalescence time distribution can be integrated to the coalescent‐based joint allele frequency spectrum (JAFS) theory, and is useful for population genetic inference from large‐scale genomic data, without relying on computationally intensive approaches, such as importance sampling and Markov Chain Monte Carlo (MCMC) methods. The inference of several important parameters relying on this derived conditional distribution is demonstrated: quantifying population growth rate and onset time, and estimating the number of ancestral lineages at a specific ancient time. Simulation studies confirm validity of the derivation and statistical efficiency of the methods using the derived intercoalescence time distribution. Two examples of real data are given to show the inference of the population growth rate of a European sample from the NIEHS Environmental Genome Project, and the number of ancient lineages of 31 mitochondrial genomes from Tibetan populations.
Bladder and bowel dysfunction and the resolution of urinary incontinence with successful management of bowel symptoms in children
Authors: Borch Luise , Hagstroem Søren , Bower Wendy F , Siggaard Rittig Charlotte , Rittig Søren 
Published: February 2013

AbstractAimTo investigate the effect of treating defecation problems on urinary incontinence in children suffering from combined urinary bladder and bowel dysfunction (BBD).MethodsWe established a clinical database from medical records of all children referred to the urinary incontinence and gastroenterology outpatient clinics with BBD. The following variables were extracted: symptoms of constipation, faecal incontinence, urinary incontinence, age at onset of symptoms, treatment, including duration and response. All children went through the same treatment protocol. Faecal disorders were treated primarily and once relieved, the daytime incontinence was managed and followed by intervention for nocturnal enuresis.ResultsIn total, 73 children were included in the study. The treatment regimen resulted in resolution of the defecation disorder in 96% of the patients. Of the children with daytime urinary incontinence, 68% had at least a 50% reduction in number of daytime incontinence episodes by successful relief of bowel dysfunction and 27% became completely continent during daytime. Only 17% of the children suffering from enuresis had a significant reduction in number of wet nights after relief of their faecal problem.ConclusionThe empirical treatment approach of managing bowel symptoms before intervening for bladder dysfunction in children with BBD is found to be appropriate.
Postoperative complication rates and invasiveness of laparoscopy‐assisted distal gastrectomy and open distal gastrectomy based on the American Society of Anesthesiologists classification system
Authors: Kawamura Hideki , Tanioka Toshiro , Tahara Munenori , Takahashi Masahiro 
Published: February 2013

AbstractIntroductionWe investigated potential advantages of laparoscopy‐assisted distal gastrectomy (LADG) in high‐risk gastric cancer patients. We examined the differences among various risk groups by comparing the incidence of postoperative complications and invasiveness of LADG with those of open distal gastrectomy (ODG) based on the American Society of Anesthesiologists (ASA) criteria.MethodsA total of 639 patients with stage IA or IB gastric cancer were included in this study. ODG was performed between 2003 and 2005, and LADG was performed between 2006 and 2011.ResultsThe incidence of postoperative complications in the LADG group (ASA1, 5.6%; ASA2, 3.8%; and ASA3, 5.7%) was significantly lower than that in the ODG group in all the ASA classes (ASA1, 16.9%; ASA2, 12.5%; and ASA3, 20%). Changes in the pain scores, body temperatures and blood analyses revealed that LADG was less invasive than ODG in all ASA classes. However, as the ASA class increased, the less invasive nature of LADG decreased.ConclusionLADG may be less invasive than ODG, even in ASA3 patients. Hence, LADG may reduce the incidence of postoperative complications in ASA1, ASA2, and ASA3 patients.