bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of soil moisture initialization for decadal predictions under different regional climatic conditions in Europe
Authors: Khodayar S. , Sehlinger A. , Feldmann H. , Kottmeier Ch. 
Published: July 2014

ABSTRACTThe impact of soil initialization is investigated through perturbation simulations with the regional climate model Consortium for Small‐scale Modelling (COSMO) and the Climate Limited‐area Modelling (COSMO–CLM). The focus of the investigation is to assess the sensitivity of simulated extreme periods, dry and wet, to soil moisture initialization in different climatic regions over Europe and to establish the necessary spin‐up time within the framework of decadal predictions for these regions. Sensitivity experiments consisted of a reference simulation from 1968 to 1999 and five simulations from 1972 to 1983. The Effective Drought Index (EDI) is used to select and quantify drought status in the reference run to establish the simulation time period for the sensitivity experiments. Different soil initialization procedures are investigated. The sensitivity of the decadal predictions to soil moisture initial conditions is investigated through the analysis of water cycle components' (WCC) variability. In an episodic timescale, the local effects of soil moisture on the boundary layer and the propagated effects on the large‐scale dynamics are analysed. The results show: (1) COSMO–CLM reproduces the observed features of the drought index. (2) Soil moisture initialization exerts a relevant impact on WCC, e.g. precipitation distribution and intensity. (3) Regional characteristics strongly impact the response of the WCC. Precipitation and evapotranspiration deviations are larger for humid regions. (4) The initial soil conditions (wet/dry), the regional characteristics (humid/dry) and the annual period (wet/dry) play a key role in the time that soil needs to restore quasi‐equilibrium and the impact on the atmospheric conditions. Humid areas, and for all regions, a humid initialization, exhibit shorter spin‐up times, also soil reacts more sensitive when initialized during dry periods. (5) The initial soil perturbation may markedly modify atmospheric pressure field, wind circulation systems and atmospheric water vapour distribution affecting atmospheric stability conditions, thus modifying precipitation intensity and distribution even several years after the initialization.
Neonatal medical exposures and characteristics of low birth weight hepatoblastoma cases: A report from the Children's Oncology Group
Authors: Turcotte Lucie M. , Georgieff Michael K. , Ross Julie A. , Feusner James H. , Tomlinson Gail E. , Malogolowkin Marcio H. , Krailo Mark D. , Miller Nicole , Fonstad Rachel , Spector Logan G. 
Published: July 2014

AbstractBackgroundHepatoblastoma is a malignancy of young children. Low birth weight is associated with significantly increased risk of hepatoblastoma and neonatal medical exposures are hypothesized as contributors. This study represents the largest case–control study of hepatoblastoma to date and aimed to define the role of neonatal exposures in hepatoblastoma risk among low birth weight children.ProcedureIncident hepatoblastoma cases who were born <2,500 g (N = 60), diagnosed between 2000 and 2008, were identified through the Children's Oncology Group. Controls were recruited through state birth registries (N = 51). Neonatal medical exposures were abstracted from medical records. Subjects from the Vermont Oxford Network were used for further comparisons, as were existing reports on neonatal medical exposures.ResultsCase–control comparisons were hindered by poor matching within birth weight strata. Cases were smaller and received more aggressive neonatal treatment compared to controls, and reflected high correlation levels between birth weight and treatments. Similar difficulty was encountered when comparing cases to Vermont Oxford Network subjects; cases were smaller and required more aggressive neonatal therapy. Furthermore, it appears hepatoblastoma cases were exposed to a greater number of diagnostic X‐rays than in case series previously reported in the neonatal literature.ConclusionsThis study presents the largest case series of hepatoblastoma in <2,500 g birth weight infants with accompanying neonatal medical exposure data. Findings confirm that birth weight is highly correlated with exposure intensity, and neonatal exposures are themselves highly correlated, which hampers the identification of a causal exposure among hepatoblastoma cases. Experimental models or genetic susceptibility testing may be more revealing of etiology. Pediatr Blood Cancer 2014;61:2018–2023. © 2014 Wiley Periodicals, Inc.
Synthesis and characterization of double hydrophilic block copolymers containing semi‐rigid and flexible segments
Authors: Savage Alice M. , Ullrich Elizabeth , Chin Stacey M. , Kiernan Zachary , Kost Caitlyn , Turner S. Richard 
Published: July 2014

ABSTRACT3‐Methyl‐(E)‐stilbene (3MSti) and 4‐(diethylamino)‐(E)‐stilbene (DEASti) monomers are synthesized and polymerized separately with maleic anhydride (MAn) in a strictly alternating fashion using reversible addition‐fragmentation chain transfer (RAFT) polymerization techniques. The optimal RAFT chain transfer agents (CTAs) for each copolymerization affect the reaction kinetics and CTA compatibilities. Psuedo‐first order polymerization kinetics are demonstrated for the synthesis of poly((3‐methyl‐(E)‐stilbene)‐alt‐maleic anhydride) (3MSti‐alt‐MAn) with a thiocarbonylthio CTA (methyl 2‐(dodecylthiocarbonothioylthio)−2‐methylpropionate, TTCMe). In contrast, a dithioester CTA (cumyl dithiobenzoate, CDB) controls the synthesis of poly((4‐(diethylamino)‐(E)‐stilbene)‐alt‐maleic anhydride) (DEASti‐alt‐MAn) with pseudo‐first order polymerization kinetics. DEASti‐alt‐MAn is chain extended with 4‐acryloylmorpholine (ACMO) to synthesize diblock copolymers and subsequently converted to a double hydrophilic polyampholyte block copolymers (poly((4‐(diethylamino)‐(E)‐stilbene)‐alt‐maleic acid))‐b‐acryloylmorpholine) (DEASti‐alt‐MA)‐b‐ACMO) via acid hydrolysis. The isoelectric point and dissociation behavior of these maleic acid‐containing copolymers are determined using ζ‐potential and acid–base titrations, respectively. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015, 53, 219–227
From reactor to rheology in industrial polymers
Authors: Read Daniel J. 
Published: July 2014

ABSTRACTThis article reviews current efforts towards quantitative prediction of rheological properties of industrial polymer resins, based upon their polydisperse branched molecular structure. This involves both an understanding of how reactor and reaction conditions influence the distribution of chain lengths and branch placement (which is the province of reactor engineering) and an understanding of how the molecular structures in turn give rise to the rheology (the province of polymer physics). Both fields are reviewed at an introductory level, focussing in particular on developments in theoretical prediction of rheology for both entangled model polymers and industrial polymers. Finally, we discuss three classes of reaction for which the fields of reactor engineering and polymer physics have been truly combined to produce predictions from reactor to rheology. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys.2015,53, 123–141
Symptoms of posttraumatic stress in Australian women with ovarian cancer
Authors: Shand Lyndel K. , Brooker Joanne E. , Burney Sue , Fletcher Jane , Ricciardelli Lina A. 
Published: July 2014

AbstractObjectiveThe aim of the study was to assess the prevalence and nature of symptoms of posttraumatic stress disorder (PTSD) in women with ovarian cancer. A further aim was to examine the demographic, medical and psychosocial factors associated with PTSD symptoms.MethodOne hundred and eight women with ovarian cancer were assessed for PTSD, quality of life, depression, anxiety, posttraumatic growth, optimism, coping and social support.ResultsClinically significant symptoms were experienced by 9.25% of participants for PTSD, 5.6% for depression and 13.9% for anxiety. Poorer quality of life was associated with total PTSD symptoms, and avoidance and intrusive symptoms. Depression was associated with avoidance and intrusive symptoms. Anxiety was associated with total, avoidance, intrusive and hyperarousal symptoms. Finally, coping by substance use/self‐blame was associated with total, avoidance and hyperarousal PTSD symptoms.ConclusionsLevels of PTSD in women with ovarian cancer were equivalent to that of the general population. Poorer quality of life, depression, anxiety and maladaptive coping, characterised by avoidance, substance use and self‐blame, were associated with increased symptoms of PTSD. Copyright © 2014 John Wiley & Sons, Ltd.
Double trouble—Buffer selection and His‐tag presence may be responsible for nonreproducibility of biomedical experiments
Authors: Majorek Karolina A. , Kuhn Misty L. , Chruszcz Maksymilian , Anderson Wayne F. , Minor Wladek 
Published: July 2014

AbstractThe availability of purified and active protein is the starting point for the majority of in vitro biomedical, biochemical, and drug discovery experiments. The use of polyhistidine affinity tags has resulted in great increases of the efficiency of the protein purification process, but can negatively affect structure and/or activity measurements. Similarly, buffer molecules may perturb the conformational stability of a protein or its activity. During the determination of the structure of a Gcn5‐related N‐acetyltransferase (GNAT) from Pseudomonas aeruginosa (PA4794), we found that both HEPES and the polyhistidine affinity tag bind (separately) in the substrate‐binding site. In the case of HEPES, the molecule induces conformational changes in the active site, but does not significantly affect enzyme activity. In contrast, the uncleaved His‐tag does not induce major conformational changes but acts as a weak competitive inhibitor of peptide substrate. In two other GNAT enzymes, we observed that the presence of the His‐tag had a strong influence on the activity of these proteins. The influence of protein preparation on functional studies may affect the reproducibility of experiments in other laboratories, even when changes between protocols seem at first glance to be insignificant. Moreover, the results presented here show how critical it is to adjust the experimental conditions for each protein or family of proteins, and investigate the influence of these factors on protein activity and structure, as they may significantly alter the effectiveness of functional characterization and screening methods. Thus, we show that a polyhistidine tag and the buffer molecule HEPES bind in the substrate‐binding site and influence the conformation of the active site and the activity of GNAT acetyltransferases. We believe that such discrepancies can influence the reproducibility of some experiments and therefore could have a significant “ripple effect” on subsequent studies.
Dopamine‐induced α‐synuclein oligomers show self‐ and cross‐propagation properties
Authors: Planchard Matthew S. , Exley Sarah E. , Morgan Sarah E. , Rangachari Vijayaraghavan 
Published: July 2014

AbstractAmyloid aggregates of α‐synuclein (αS) protein are the predominant species present within the intracellular inclusions called Lewy bodies in Parkinson's disease (PD) patients. Among various aggregates, the low‐molecular weight ones broadly ranging between 2 and 30 mers are known to be the primary neurotoxic agents responsible for the impairment of neuronal function. Recent research has indicated that the neurotransmitter dopamine (DA) is one of the key physiological agents promoting and augmenting αS aggregation, which is thought to be a significant event in PD pathologenesis. Specifically, DA is known to induce the formation of soluble oligomers of αS, which in turn are responsible for inducing several important cellular changes leading to cellular toxicity. In this report, we present the generation, isolation, and biophysical characterization of five different dopamine‐derived αS oligomers (DSOs) ranging between 3 and 15 mers, corroborating previously published reports. More importantly, we establish that these DSOs are also capable of replication by self‐propagation, which leads to the replication of DSOs upon interaction with αS monomers, a process similar to that observed in mammilian prions. In addition, DSOs are also able to cross‐propagate amyloid‐β (Aβ) aggregates involved in Alzheimer's disease (AD). Interestingly, while self‐propagation of DSOs occur with no net gain in protein structure, cross‐propagation proceeds with an overall gain in β‐sheet conformation. These results implicate the involvement of DSOs in the progression of PD, and, in part, provide a molecular basis for the observed co‐existence of AD‐like pathology among PD patients.
Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake
Authors: Kumar Abhinav , Punta Marco , Axelrod Herbert L. , Das Debanu , Farr Carol L. , Grant Joanna C. , Chiu Hsiu‐Ju , Miller Mitchell D. , Coggill Penelope C. , Klock Heath E. , Elsliger Marc‐André , Deacon Ashley M. , Godzik Adam , Lesley Scott A. , Wilson Ian A. 
Published: July 2014

AbstractCrystal structures of three members (BACOVA_00364 from Bacteroides ovatus, BACUNI_03039 from Bacteroides uniformis and BACEGG_00036 from Bacteroides eggerthii) of the Pfam domain of unknown function (DUF4488) were determined to 1.95, 1.66, and 1.81 Å resolutions, respectively. The protein structures adopt an eight‐stranded, calycin‐like, β‐barrel fold and bind an endogenous unknown ligand at one end of the β‐barrel. The amino acids interacting with the ligand are not conserved in any other protein of known structure with this particular fold. The size and chemical environment of the bound ligand suggest binding or transport of a small polar molecule(s) as a potential function for these proteins. These are the first structural representatives of a newly defined PF14869 (DUF4488) Pfam family.
Topographic control of stratified flows: upstream jets, blocking and isolating layers
Authors: Winters Kraig B. , Armi Laurence 
Published: July 2014

AbstractOptimal solutions to the nonlinear, hydrostatic, Boussinesq equations are developed for steady, density-stratified, topographically controlled flows characterized by blocking and upstream influence. These flows are jet-like upstream of an isolated obstacle and are contained within an asymmetric, thinning stream tube that is accelerated as it passes over the crest. A stagnant, nearly uniform-density isolating layer, surrounded by a bifurcated uppermost streamline, separates the accelerated flow from an uncoupled flow above. The flows are optimal in the sense that, for a given stratification, the solutions maximize the topographic rise above the blocking level required for hydraulic control while minimizing the total energy of the flow. Hydraulic control is defined mathematically by the asymmetry of the accelerated flow as it passes the crest. A subsequent analysis of the Taylor–Goldstein equation shows that these sheared, non-uniformly stratified flows are indeed subcritical upstream, critical at the crest, and supercritical downstream with respect to gravest-mode, long internal waves. The flows obtained are relevant to arrested wedge flows, selective withdrawal, stratified towing experiments, tidal flow over topography and atmospheric flows over mountains.
The Saint with Indra's Sword: Khruubaa Srivichai and Buddhist Millenarianism in Northern Thailand
Authors: Bowie Katherine 
Published: July 2014

AbstractDespite a growing literature revealing the presence of millenarian movements in both Theravada and Mahayana Buddhist societies, scholars have been remarkably reluctant to consider the role of messianic beliefs in Buddhist societies. Khruubaa Srivichai (1878–1938) is the most famous monk of northern Thailand and is widely revered as atonbun, or saint. Althoughtonbunhas been depoliticized in the modern context, the term also refers to a savior who is an incarnation of the coming Maitreya Buddha. In 1920 Srivichai was sent under arrest to the capital city of Bangkok to face eight charges. This essay focuses on the charge that he claimed to possess the god Indra's sword. Although this charge has been widely ignored, it was in fact a charge of treason. In this essay, I argue that the treason charge should be understood within the context of Buddhist millenarianism. I note the saint/savior tropes in Srivichai's mytho-biography, describe the prevalence of millenarianism in the region, and detail the political economy of the decade of the 1910s prior to Srivichai's detention. I present evidence to show that the decade was characterized by famine, dislocation, disease, and other disasters of both natural and social causes. Such hardships would have been consistent with apocalyptic omens in the Buddhist repertoire portending the advent of Maitreya. Understanding Srivichai in this millenarian context helps to explain both the hopes of the populace and the fears of the state during that tumultuous decade.
Resource Politics and State-Society Relations: Why Are Certain States More Inclusive than Others?
Authors: Sato Jin 
Published: July 2014

AbstractWhy do some states resort to more exclusive top-down management of natural resources, while others tend to be more inclusive and solicit participation from civil society? By rejecting the simple characterization of the state within the narrow spectrum of “weak” and “strong,” this article investigates resource-mediated relations in the peripheral social groups that the state has sought to transform as part of the process of modernization. Focusing on Siam and Japan, I highlight alternative explanations based on ethnicity and labor, bureaucratic mindset, and agro-ecological conditions. I argue that the more embedded nature of the labor force in resources sectors made it necessary for the Japanese government to engage with marginal people, whereas the enclave nature of such sectors in Siam allowed elites to establish a distinctively exclusive system. While the Japanese state quickly learned to accommodate people at the fringes through its recognition and acceptance of existing customs in the management of resources, and even facilitated the creation of local organizations such as forest unions, the Siamese were consistently more exclusionary and even oppressed indigenous groups living at the state's territorial periphery. Resource interventions targeted at the fringes of land and society in Japan and Siam produced lasting effects on state-society relations that have extended far beyond their original intention of securing resource procurement. Understanding the historical roots of such relations offers a fresh perspective from which to explain why state inaction prevails in the present debate on state devolution in Thailand.
Molecular nature of chemically and physically induced mutants in plants: a review
Authors: Nawaz Zarqa , Shu Qingyao 
Published: July 2014

More than 3200 new mutant varieties have been bred and used by millions of farmers, which has significantly contributed to world food security. A lot more mutants have also served as tools for gene discovery and functional analysis. Recent genomic approaches including TILLING (Targeting Induced Local Lesions In Genome) have enabled screening of mutations at the molecular level. This review describes the molecular nature of chemically and physically induced mutations and their repercussions. Analyses of TILLING reports indicate that chemically induced mutations are mostly nucleotide substitutions, but that mutation frequencies fluctuate among plant species ranging from one DNA lesion per 300 kbp inArabidopsisto one DNA lesion per 30 kbp in bread wheat, which reciprocate with an increase in ploidy levels. The majority (>95%) of chemically induced DNA lesions are silent or missense mutations. Mutations induced by physical mutagens seem to be more diverse, including single-nucleotide substitutions, insertions, inversions and translocations, although short deletions ( < 15 bp) are relatively more predominant. The proportion of complex mutations (translocation, inversions, etc.) may increase with an increase in the linear energy transfer of radiations. In addition, the implications of these findings for the roles of induced mutants in breeding and gene function analysis are briefly discussed.
Cloning and characterization of Ku70 and Ku80 homologues involved in DNA repair process in wheat (Triticum aestivum L.)
Authors: Gu Jiayu , Wang Qing , Cui Meng , Han Bing , Guo Huijun , Zhao Linshu , Xie Yongdun , Song Xiyun , Liu Luxiang 
Published: July 2014

Error-prone repair of radiation-induced DNA double-strand breaks (DSBs) results in DNA mutation that is essential for mutation breeding. Non-homologous end joining might be the principal DSB repair mechanism in eukaryotes, which is mediated and activated by Ku protein, a heterodimer of 70 and 80 kDa subunits. In this study, on the basis of complementary DNA (cDNA), the genomic sequences of TaKu70 and TaKu80 genes in all the three genomes of wheat were characterized. Only single-nucleotide substitutions and no insertions or deletions were detected in the exons of TaKu70 and TaKu80 genes. The size of the introns exhibited a slight variation between the sequences. Yeast two-hybrid analysis demonstrated that TaKu70 and TaKu80 formed a heterodimer, and electrophoretic mobility shift assays revealed that this heterodimer bound to double-stranded DNA, but not to single-stranded DNA. The quantitative polymerase chain reaction analysis revealed that the expression of TaKu70 and TaKu80 genes was up-regulated under γ-ray irradiation in a dose-dependent manner in the seedlings of wheat. These results suggest that TaKu70 and TaKu80 form a functional heterodimer and are associated with the repair of the induced DSBs in wheat.
De novo transcriptome assembly of Vitis flexuosa grapevines inoculated with Elsinoe ampelina
Authors: Ahn Soon Young , Kim Seon Ae , Jo Sung Hwan , Yun Hae Keun 
Published: July 2014

In this study, the transcriptome of Vitis flexuosa leaves inoculated with Elsinoe ampelina was analysed to identify useful genes and elucidate their function and differential expression patterns through assembly and annotation gene ontology of data from sequencing short reads on the Illumina platform. We assembled ~121 million high-quality trimmed reads using Velvet and Oases with optimal parameters into a non-redundant set of 70,899 transcripts ( ≥ 200 bp in length). The transcripts exhibited an average length of 1138 bp and a N50 length of 1695 bp, with the largest contig length being 9623 bp. Functional categorization revealed the conservation of genes involved in various molecular functions, including protein binding (21.1%) and oxidoreductase activity (11.7%), in V. flexuosa. The V. flexuosa transcript set generated in this study will serve as a resource for gene discovery and development of functional molecular markers.