bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting hydraulic properties of seasonally impounded soils
Authors: PATIL N. G. , RAJPUT G. S. , NEMA R. K. , SINGH R. B. 
Published: October 2009

SUMMARYAgricultural crop management decisions often require data on hydraulic properties of soils. Little information is available on hydraulic properties of clay soils that are impounded by rainwater (known as ‘Haveli’ lands) every year during the monsoon season in large tracts of Madhya Pradesh in India. Estimating hydraulic properties using global pedotransfer functions (PTFs) is one possible way to collect such information. Rules in the widely used global PTF Rosetta were executed to obtain estimates of two important hydraulic properties, namely soil water retention characteristics (SWRC) and saturated hydraulic conductivity (Ks). SWRC estimates obtained with maximum input (particle size distribution, bulk density, field capacity and permanent wilting point) in Rosetta were relatively closer to the laboratory-measured data as compared with the estimates obtained with lower levels of input. Root mean square error (RMSE) of estimates ranged from 0·01 to 0·05 m3/m3. Hierarchical PTFs to predictKsfrom basic soil properties were derived using statistical regression and artificial neural networks. Evaluation of these indicated that neural PTFs were acceptable and hence could be used without loss of accuracy.
Hard-to-Value Stocks, Behavioral Biases, and Informed Trading
Authors: Kumar Alok 
Published: October 2009

AbstractThis paper uses investor-level data to provide direct evidence for an intuitive but surprisingly untested proposition that investors make larger investment mistakes when valuation uncertainty is higher and stocks are more difficult to value. Using multiple measures of valuation uncertainty and multiple behavioral bias proxies, I show that individual investors exhibit stronger behavioral biases when stocks are harder to value and when market-level uncertainty is higher. I also find that informed trading intensity is higher among stocks where individual investors exhibit stronger behavioral biases. Collectively, these results indicate that uncertainty at both stock and market levels amplifies individual investors’ behavioral biases and that relatively better informed investors attempt to exploit those biases.
Support for the mutual maintenance of pain and post-traumatic stress disorder symptoms
Authors: Liedl A. , O'Donnell M. , Creamer M. , Silove D. , McFarlane A. , Knaevelsrud C. , Bryant R. A. 
Published: October 2009

BackgroundPain and post-traumatic stress disorder (PTSD) are frequently co-morbid in the aftermath of a traumatic event. Although several models attempt to explain the relationship between these two disorders, the mechanisms underlying the relationship remain unclear. The aim of this study was to investigate the relationship between each PTSD symptom cluster and pain over the course of post-traumatic adjustment.MethodIn a longitudinal study, injury patients (n=824) were assessed within 1 week post-injury, and then at 3 and 12 months. Pain was measured using a 100-mm Visual Analogue Scale (VAS). PTSD symptoms were assessed using the Clinician-Administered PTSD Scale (CAPS). Structural equation modelling (SEM) was used to identify causal relationships between pain and PTSD.ResultsIn a saturated model we found that the relationship between acute pain and 12-month pain was mediated by arousal symptoms at 3 months. We also found that the relationship between baseline arousal and re-experiencing symptoms, and later 12-month arousal and re-experiencing symptoms, was mediated by 3-month pain levels. The final model showed a good fit [χ2=16.97, df=12, p>0.05, Comparative Fit Index (CFI)=0.999, root mean square error of approximation (RMSEA)=0.022].ConclusionsThese findings provide evidence of mutual maintenance between pain and PTSD.
Influence of soil, topography and substrates on differences in wood decomposition between one-hectare plots in lowland tropical moist forest in Central Amazonia
Authors: de Toledo José Julio , Magnusson William Ernest , de Castilho Carolina Volkmer 
Published: October 2009

Abstract:Understanding how wood decomposition varies spatially at the mesoscale (between 1-ha plots) may improve carbon flux estimates in Amazonian forests. An experiment was carried out to test the influence of soil, slope, above-ground tree live biomass (biomass), fine-litter mass and characteristics of neighbouring trees on the variation of wood decomposition between 1-ha plots in four species of tropical trees that vary in wood density (Manilkara huberi – 0.86 g cm−3, Couratari guianensis – 0.54 g cm−3, Hura crepitans – 0.32 g cm−3 and Parkia pendula – 0.29 g cm−3). A wood sample from each species (30 × 5 × 2.5 cm) was placed in each of 71 plots within 64 km2 of terra firme tropical moist forest in Reserva Florestal Adolpho Ducke. One year later, samples were collected and weighed. The effects of specificity of decomposers was measured by the association of decomposition with the wood density and with the taxonomic group of the nearest tree with dbh ≥30 cm. Wood decomposition was independent of soil (texture and nutrients), slope, biomass and fine-litter mass at the mesoscale, except for C. guianensis, which showed greater decomposition in locations with greater biomass. Decomposition was also independent of wood density and taxonomic group of nearby large trees. In general, none of the variables was useful as a predictor of wood decomposition at the scale larger than 1 ha. Thus, the use of models that include soil and topography to improve estimates of carbon flux are limited because wood decomposition does not follow similar mesoscale patterns to that of biomass and fine-litter decomposition. Also, the results indicate that wood decomposition is more likely to be associated with generalist decomposers than with specialists associated with neighbouring trees.
Early effect of elevated nitrogen input on above-ground net primary production of a lower montane rain forest, Panama
Authors: Adamek Markus , Corre Marife D. , Hölscher Dirk 
Published: October 2009

Abstract:To evaluate N limitation on above-ground net primary production in a tropical lower montane rain forest, an N fertilization experiment was conducted for 2 y. The study site is located at 1200–1300 m asl in the Fortuna forest reserve in western Panama and has a mature, mixed-species stand growing on an Andisol soil. Control and N-fertilized (125 kg urea-N ha−1 y−1) treatments were represented by four replicate plots (each 40 × 40 m, separated by at least 40 m). Stem diameter growth was analysed by diameter at breast height classes and also for the three most abundant species. The three species did not respond to N addition. The response of stem growth and above-ground woody biomass production to N fertilization varied among dbh classes. Stem growth of trees of 10–30 cm dbh increased only in the first year of N addition while trees of 30–50 cm dbh responded in the second year of N addition, which may be due to differences in light conditions between years. Trees >50 cm dbh did not respond during 2 years of N addition. As a result, the overall stem growth and above-ground woody biomass production were not affected by N fertilization. Annual total fine litterfall increased in the first year of N fertilization, while annual leaf litterfall increased in both years of N addition. Above-ground net primary production, of which total fine litterfall constituted 68%, also increased only in the first year of N addition. The magnitude and timing of response of stem diameter growth and litterfall suggest that these aspects of above-ground productivity are not uniformly limited by N availability.
Can one invasion lead to another? Niche space and the future of Southwestern U.S. riparian zones
Authors: Reynolds Lindsay , Cooper David 
Published: October 2009

Abstract
Background/Question/Methods:
Invasive species are increasingly problematic world-wide. Scientists working to understand why invasive species are successful must first understand the processes of invasion. Invasion facilitation and empty niche exploitation are key processes that have not been well-studied in species rich ecosystems such as riparian areas. In the southwestern United States (U.S.) two prominent invaders of riparian habitats are the exotic woody plant species tamarisk (Tamarix ramosissima, T. chinensis, and their hybrids) and Russian olive (Eleagnus angustifolia). These plants were introduced by humans throughout the southwest around 1900. Both tamarisk and Russian olive have invaded the ephemeral stream system in Canyon de Chelly National Monument, Arizona. We worked in sites within Canyon de Chelly and throughout the region to address the following questions: (1) does Russian olive have a broader niche than cottonwood and tamarisk? And (2) can cottonwood and tamarisk facilitate Russian olive invasion by providing shaded habitat? We analyzed riparian tree seedling requirements in a controlled experiment, and performed empirical field studies at sites in Canyon de Chelly, and throughout the Colorado Plateau region.

Results/Conclusions:
Our controlled experiment and field surveys indicate that Russian olive can establish and survive under shadier and drier conditions than tamarisk and native cottonwood. Russian olive survival was significantly higher in dense shade, and low soil moisture treatments than tamarisk and cottonwood. In the field, we found Russian olive establishing on a local and regional scale, up to 8 meters above the stream channel, in sites where flooding cannot occur. It established under dense canopies of tamarisk, cottonwood and Russian olive. Tamarisk and native riparian plants species seedlings cannot establish in these dry, shady habitats. Russian olive is limited only by seed dispersal in southwestern riparian ecosystems. Although Russian olive did not show a preference for shaded habitat and is therefore not being facilitated by cottonwood and tamarisk, our results demonstrate it has a much broader niche than cottonwood and tamarisk. Some researchers suggest that native cottonwood trees are undergoing population declines and invasive tamarisk trees have invaded all possible habitats in the southwestern US. The potential for continued Russian olive invasions in southwestern riparian ecosystems is tremendous. Russian olive will likely increase in abundance while tamarisk and cottonwood decrease along rivers in the southwestern US. Generalist exotic species that have broader niches than native species have the potential to exclude native species and create novel ecosystems where community composition is dominated by exotic species.
A putrescine–anthracene conjugate: a paradigm for selective drug delivery
Authors: Palmer Andrew J. , Ghani Radiah A. , Kaur Navneet , Phanstiel Otto , Wallace Heather M. 
Published: October 2009

Increased polyamine concentrations play an important role in the development of cancer at all stages, from initiation through to maintenance of the transformed phenotype. One way cancer cells accumulate increased concentrations of polyamines is by increased uptake of preformed polyamines via their PTS (polyamine transport system). The PTS is promiscuous and will transport a range of polyamine-based molecules. Therefore it may be that cytotoxic drugs could be attached to polyamine vectors and targeted selectively to cancer cells by utilizing the PTS. The aim of the present study was to investigate the potential of Ant 4, a putrescine–anthracene conjugate, to target cytotoxic agents to human cancer cells as a paradigm for a novel method of selective drug delivery. Ant 4 induced cytotoxicity after only 24 h exposure. Apoptosis was the predominant type of cell death, with mechanistic studies revealing that oxidative stress and DNA damage may have a part to play. For the first time, uptake of Ant 4 via the PTS was demonstrated both directly and indirectly in human cell lines. In addition, Ant 4 significantly reduced putrescine uptake, demonstrating that this conjugate not only used the PTS, but also could successfully compete with its native polyamine for uptake. However, the most interesting finding was the intracellular depletion of the polyamine pools, providing an additional mode of toxicity for Ant 4 and the possibility that this molecule may act as a ‘double-edged sword’: preventing cell growth by delivery of the toxic moiety and by depletion of intracellular polyamine content.
A di-arginine motif contributes to the ER localization of the type I transmembrane ER oxidoreductase TMX4
Authors: Roth Doris , Lynes Emily , Riemer Jan , Hansen Henning G. , Althaus Nils , Simmen Thomas , Ellgaard Lars 
Published: October 2009

The thiol-disulfide oxidoreductases of the PDI (protein disulfide isomerase) family assist in disulfide-bond formation in the ER (endoplasmic reticulum). In the present study, we have shown that the previously uncharacterized PDI family member TMX4 (thioredoxin-like transmembrane 4) is an N-glycosylated type I membrane protein that localizes to the ER. We also demonstrate that TMX4 contains a single ER-luminal thioredoxin-like domain, which, in contrast with similar domains in other PDIs, is mainly oxidized in living cells. The TMX4 transcript displays a wide tissue distribution, and is strongly expressed in melanoma cells. Unlike many type I membrane proteins, TMX4 lacks a typical C-terminal di-lysine retrieval signal. Instead, the cytoplasmic tail has a conserved di-arginine motif of the RXR type. We show that mutation of the RQR sequence in TMX4 to KQK interferes with ER localization of the protein. Moreover, whereas the cytoplasmic region of TMX4 confers ER localization to a reporter protein, the KQK mutant of the same protein redistributes to the cell surface. Overall, features not commonly found in other PDIs characterize TMX4 and suggest unique functional properties of the protein.
Adjusting for clinical covariates improves the ability of B‐type natriuretic peptide to distinguish cardiac from non‐cardiac dyspnoea: a sub‐study of HEARD‐IT
Authors: Rogers R. Kevin , Stehlik Josef , Stoddard Gregory J. , Greene Thomas , Collins Sean P. , Peacock W. Frank , Maisel Alan D. , Clopton Paul , Michaels Andrew D. 
Published: October 2009

AimsWe sought to create a model that adjusts B‐type natriuretic peptide (BNP) for specific covariates to better distinguish cardiac from non‐cardiac dyspnoea.Methods and resultsHEARD‐IT was a multicentre, prospective study of the diagnostic utility of acoustic cardiography in the emergency department. Dyspnoeic patients more than 40 years were eligible. Two cardiologists independently adjudicated the HF outcome. Using logistic regression, a model adjusting BNP for pertinent covariates was developed (n = 740). The mean age was 66 ± 13 years. Age, gender, ethnicity, body mass index, blood urea nitrogen, and creatinine affected BNP levels independently of HF. The model adjusting BNP for these covariates improved the area under receiver operator characteristic curve for HF compared with BNP alone (0.948, 95% CI 0.934–0.963 vs. 0.937, 95% CI 0.920–0.954; P = 0.004). Net reclassification improvement, a novel metric of model performance, was 3.5% for those without HF (P = 0.05) compared with conventional, unadjusted BNP cut‐offs. Thirteen of 116 (11%) patients without HF, but with unadjusted BNP values ≥100 pg/mL, were correctly reclassified as not having HF with the adjusted BNP model.ConclusionAdjusting BNP for important covariates may improve its ability to distinguish cardiac from non‐cardiac dyspnoea.
Effects of microstructures on mesoscopic morphological transitions in deposition growth models
Authors: Sánchez Pedro A. , Sintes Tomás , Piro Oreste , Cartwright Julyan H. E. 
Published: October 2009

We study the influence of competing microstructure symmetries on the emergence of different morphologies during the growth by vapour deposition of thin solid films. We perform extensive numerical simulations with a minimal model that includes different microstructures, as well as thermal surface diffusion, to compute the corresponding structure zone model (SZM) and analyse, with statistical physics techniques, the details of transitional morphologies at border zones. We show that the maximum coordination number of the underlying microstructure provides a classification of the statistics of the transitional morphologies at the border between zones I (porous structures) and II (columnar faceted structures) of the SZM.
Replication Protein A (RPA1a) Is Required for Meiotic and Somatic DNA Repair But Is Dispensable for DNA Replication and Homologous Recombination in Rice
Authors: Chang Yuxiao , Gong Liang , Yuan Wenya , Li Xingwang , Chen Guoxing , Li Xianghua , Zhang Qifa , Wu Changyin 
Published: October 2009

AbstractReplication protein A (RPA), a highly conserved single-stranded DNA-binding protein in eukaryotes, is a stable complex comprising three subunits termed RPA1, RPA2, and RPA3. RPA is required for multiple processes in DNA metabolism such as replication, repair, and homologous recombination in yeast (Saccharomyces cerevisiae) and human. Most eukaryotic organisms, including fungi, insects, and vertebrates, have only a single RPA gene that encodes each RPA subunit. Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), however, possess multiple copies of an RPA gene. Rice has three paralogs each of RPA1 and RPA2, and one for RPA3. Previous studies have established their biochemical interactions in vitro and in vivo, but little is known about their exact function in rice. We examined the function of OsRPA1a in rice using a T-DNA insertional mutant. The osrpa1a mutants had a normal phenotype during vegetative growth but were sterile at the reproductive stage. Cytological examination confirmed that no embryo sac formed in female meiocytes and that abnormal chromosomal fragmentation occurred in male meiocytes after anaphase I. Compared with wild type, the osrpa1a mutant showed no visible defects in mitosis and chromosome pairing and synapsis during meiosis. In addition, the osrpa1a mutant was hypersensitive to ultraviolet-C irradiation and the DNA-damaging agents mitomycin C and methyl methanesulfonate. Thus, our data suggest that OsRPA1a plays an essential role in DNA repair but may not participate in, or at least is dispensable for, DNA replication and homologous recombination in rice.
Flexible Tools for Gene Expression and Silencing in Tomato
Authors: Fernandez Ana I. , Viron Nicolas , Alhagdow Moftah , Karimi Mansour , Jones Matthew , Amsellem Ziva , Sicard Adrien , Czerednik Anna , Angenent Gerco , Grierson Donald , May Sean , Seymour Graham , Eshed Yuval , Lemaire-Chamley Martine , Rothan Christophe , Hilson Pierre 
Published: October 2009

Abstract
As a genetic platform, tomato (Solanum lycopersicum) benefits from rich germplasm collections and ease of cultivation and transformation that enable the analysis of biological processes impossible to investigate in other model species. To facilitate the assembly of an open genetic toolbox designed to study Solanaceae, we initiated a joint collection of publicly available gene manipulation tools. We focused on the characterization of promoters expressed at defined time windows during fruit development, for the regulated expression or silencing of genes of interest. Five promoter sequences were captured as entry clones compatible with the versatile MultiSite Gateway format: PPC2, PG, TPRP, and IMA from tomato and CRC from Arabidopsis (Arabidopsis thaliana). Corresponding transcriptional fusions were made with the GUS gene, a nuclear-localized GUS-GFP reporter, and the chimeric LhG4 transcription factor. The activity of the promoters during fruit development and in fruit tissues was confirmed in transgenic tomato lines. Novel Gateway destination vectors were generated for the transcription of artificial microRNA (amiRNA) precursors and hairpin RNAs under the control of these promoters, with schemes only involving Gateway BP and LR Clonase reactions. Efficient silencing of the endogenous phytoene desaturase gene was demonstrated in transgenic tomato lines producing a matching amiRNA under the cauliflower mosaic virus 35S or PPC2 promoter. Lastly, taking advantage of the pOP/LhG4 two-component system, we found that well-characterized flower-specific Arabidopsis promoters drive the expression of reporters in patterns generally compatible with heterologous expression. Tomato lines and plasmids will be distributed through a new Nottingham Arabidopsis Stock Centre service unit dedicated to Solanaceae resources.
A Cytoplasmically Inherited Barley Mutant Is Defective in Photosystem I Assembly Due to a Temperature-Sensitive Defect in ycf3 Splicing
Authors: Landau Alejandra Mabel , Lokstein Heiko , Scheller Henrik Vibe , Lainez Verónica , Maldonado Sara , Prina Alberto Raúl 
Published: October 2009

Abstract
A cytoplasmically inherited chlorophyll-deficient mutant of barley (Hordeum vulgare) termed cytoplasmic line 3 (CL3), displaying a viridis (homogeneously light-green colored) phenotype, has been previously shown to be affected by elevated temperatures. In this article, biochemical, biophysical, and molecular approaches were used to study the CL3 mutant under different temperature and light conditions. The results lead to the conclusion that an impaired assembly of photosystem I (PSI) under higher temperatures and certain light conditions is the primary cause of the CL3 phenotype. Compromised splicing of ycf3 transcripts, particularly at elevated temperature, resulting from a mutation in a noncoding region (intron 1) in the mutant ycf3 gene results in a defective synthesis of Ycf3, which is a chaperone involved in PSI assembly. The defective PSI assembly causes severe photoinhibition and degradation of PSII.
Systematic review: distribution of advanced neoplasia according to polyp size at screening colonoscopy
Authors: HASSAN C. , PICKHARDT P. J. , KIM D. H. , DI GIULIO E. , ZULLO A. , LAGHI A. , REPICI A. , IAFRATE F. , OSBORN J. , ANNIBALE B. 
Published: October 2009

SummaryBackground  The impact of not referring sub‐centimetre polyps identified at CT colonography upon the efficacy of colorectal cancer screening remains uncertain.Aim  To determine the distribution of advanced neoplasia according to polyp size in a screening setting.Methods  Published studies reporting the distribution of advanced adenomas in asymptomatic screening cohorts according to polyp size were identified by MEDLINE and EMBASE searches. Predefined outputs were the screening rates of advanced adenomas represented by diminutive (≦5 mm), small (6–9 mm), sub‐centimetre (<10 mm) and large (≧10 mm) polyp sizes.Results  Data from four studies with 20 562 screening subjects met the primary inclusion criteria. Advanced adenomas were detected in 1155 (5.6%) subjects (95% CI = 5.3–5.9), corresponding to diminutive, small and large polyps in 4.6% (95% CI = 3.4–5.8), 7.9% (95% CI = 6.3–9.4) and 87.5% (95% CI = 86–89.4) of cases respectively. The frequency of advanced lesions among patients whose largest polyp was diminutive, small, sub‐centimetre and large in size was 0.9%, 4.9%, 1.7% and 73.5% respectively.Conclusions  Based on this systematic review, a 6‐mm polyp size threshold for polypectomy referral would identify over 95% of subjects with advanced adenomas, whereas a 10‐mm threshold would identify 88% of cases. Aliment Pharmacol Ther 31, 210–217