bluuebunny/crossref_metadata_2025_split huggingface dataset:
Practicalities of estimating carbon sequestration - boreal coniferous forests.
Authors: Berg B. , McClaugherty C. , Santo A. V. de 
Published: February 2009

Abstract

We have reviewed literature on the topic 'carbon sequestration in forest soils'. We review a theory/model for the sequestration process based on pine (
Pinus
) needle litter that is transformed into stable matter during decomposition. The decomposition process is divided into two phases with lignified tissue in the latter developing a recalcitrance with a calculable limit value for decomposition. This is just one of several possible models, this one developed for boreal forests. It appears likely that part of the stabilization process is related to oxygen limitation for micro-organisms, high concentrations of heavy metals developed during decomposition and/or allelopathic effects that suppress the decomposition process and allow an accumulation of organic matter. We divide the concept into
primary sequestration
and
secondary sequestration
. Primary sequestration occurs in an organic layer, e.g. a humus layer, and is a process that encompasses the stabilization of decomposing plant litter remains and their accumulation. This layer is vulnerable to e.g. fire and other disturbances. Secondary sequestration occurs in the mineral soil, where the buildup of sequestered carbon is a slower process. This carbon material was leached from the organic layers and has become adsorbed to mineral particles and thus stabilized. We may consider the concept stability as a very relative one. Stability appears to be related to a set of conditions on e.g. environment and micro-organisms. It may also be related to nutrients in the litter and/or environment. The review is based on available data and has its focus on coniferous boreal and northern temperate forests.
The role of vitamin E in the diet.
Authors: Shrapnel B. S. 
Published: February 2009

Abstract
The last decade has seen many developments in our understanding of vitamin E, its transport and metabolism, and its potential role in the prevention of chronic disease. Of the eight fat-soluble substances comprising vitamin E, α-tocopherol has emerged as central to vitamin E activity in the body, its concentration in the plasma being governed by α-tocopherol transfer protein and maintained in a narrow range. Although new insights into the role of habitual fat intake in determining human requirements for vitamin E have been gained, uncertainties remain and estimates of requirements differ considerably between authorities. Investigation of the potential of this potent chain-breaking antioxidant to prevent or delay conditions thought to be associated with oxidative stress, including cardiovascular disease, cancer, Alzheimer's disease and Parkinson's disease, has challenged nutritionists to reconsider optimal intakes of vitamin E. High-dose supplementation has proved ineffective in reducing risk and may even be associated with increased risk; yet, new evidence suggests that a lifetime diet rich in α-tocopherol may provide protection against heart disease and cancer. Intakes of α-tocopherol are low in some western populations, which may in part be the result of advice to consume low-fat diets, intended to help address rising rates of obesity. An increased focus on fat quality, consistent with advice stemming from the cardiovascular literature, will help ensure adequate intakes of vitamin E in the context of diets moderate in total fat.
Geminivirus resistance breeding in common bean.
Authors: Blair M. W. , Morales F. J. 
Published: February 2009

Abstract

Common bean (
Phaseolus vulgaris
L.) is among the most important food staples worldwide, mainly because of its relatively high protein content and other valuable nutritional qualities. Unfortunately, common beans are highly susceptible to plant viruses in general, including one of the largest families of plant viruses known as the
Geminiviridae
. These viruses, unlike most RNA plant viruses, possess a DNA genome that allows these pathogens to replicate in the nucleus of their plant host cells, thus, causing major damage to susceptible legume crops. Although some geminiviruses, belonging to two (
Mastrevirus
and
Curtovirus
) of the four genera that compose the
Geminiviridae
, can be transmitted by leafhoppers (Cicadellidae) to common bean, most geminiviruses that attack legumes belong to the genus
Begomovirus
, and are transmitted by the whitefly
Bemisia tabaci
(Genn.). In fact, the type species of this genus is bean golden yellow mosaic virus (BGYMV), which attacks over a million hectares of common bean grown in the lowlands and mid-altitude valleys of Central America, southern Mexico, the Caribbean region and northern South America. Another begomovirus, bean golden mosaic virus (BGMV), affects over two million hectares of common bean in Brazil, northern Argentina and the lowlands of Bolivia, in South America. In this region, bean dwarf mosaic virus (BDMV) has also caused the loss of thousands of hectares of highly valuable common bean genotypes in northwestern Argentina. In northwestern Mexico, thousands of hectares of common bean have been under the constant attack of a begomovirus related to a virus originally described in cucurbits, squash leaf curl virus (SLCV), in southwestern USA, currently known in Mexico as bean calico mosaic virus (BCaMV). Fortunately, none of these viruses is present in Eastern Africa, where the common bean is also a major food staple. Another Old World begomovirus reported to attack common bean both in the Old and New World, is tomato yellow leaf curl virus (TYLCV). This review describes the different breeding approaches followed since the 1970s to introduce resistance to begomoviruses infecting important legume crops, particularly common bean. This has been a challenging process, considering that no immune genotypes have been identified in more than 30000 common bean genotypes exposed to begomoviruses, such as BGMV or BGYMV.
How have opinions about GMOs changed over time? The situation in the European Union and the USA.
Authors: Bonny S. 
Published: February 2009

Abstract
This text examines changes in opinions on genetically modified organisms (GMOs) over the past ten years in the EU and the USA. Divergence in opinion on this topic makes it difficult to define common policies and has led to conflicts. The results of diverse surveys and polls taken repeatedly over several years, for example the Eurobarometer polls in the EU, have been used to carry out a meta-analysis of opinions on GMOs. First of all, the data used as well as questions of method and the numerous difficulties arising from such an approach are presented. In the second part, the points of view in the USA and the EU are compared for those years when identical questions were asked on both sides of the Atlantic, demonstrating the differences associated with location. Then, changes in opinions on GMOs over time are analysed, focusing in turn on the USA and then the EU countries. To conclude, we examine whether there is a certain convergence or a widening gap over time between views in the USA and the EU. As regards biotechnology, there is a slight convergence of views over the last few years, Americans having become a little less optimistic and Europeans relatively more optimistic. However, in Europe, the level of opposition to GMOs remains very high and is even growing in some countries.
Food-drug interaction: the case of grapefruit juice.
Authors: Uesawa Y. 
Published: February 2009

Abstract
Here, we present an overview of two decades of work on the interactions between grapefruit juice (GFJ) and drugs, particularly on the mechanisms of these interactions and the interacting components in GFJ. We describe classical examples where GFJ enhances intestinal absorption of drugs, as well as newly discovered interactions with the inhibition of intestinal absorption. Work aimed at understanding the causal compounds in GFJ highlights the relationship between human physiology and food and is clinically important. Further understanding of this interaction may allow patients and their doctors to stop worrying about drug interactions with GFJ.
Feeding the immune system: the role of micronutrients in restoring resistance to infections.
Authors: Maggini S. , Beveridge S. , Sorbara P. J. P. , Senatore G. 
Published: February 2009

Abstract

The immune system protects the body against pathogens and cancer cells, thereby defending it against infections and diseases via three main components: epithelial barriers, immune cells and proteins including antibodies. Immune defences are constantly active and consist of a complex network of coordinated biological responses. Therefore, the immune system needs to be fed properly with energy sources and essential micronutrients serving as cofactors in the development, maintenance and expression of the immune response. The general nutritional status of an individual modulates immune functions, and immunocompetence is regarded as a measure of adequate nutrition. Low levels of vitamins, minerals and trace elements lead to suppressed immunity, predisposing individuals to infections, which in turn aggravate the nutritional status, leading to a vicious cycle. Supplying the deficient micronutrients with the diet or a dietary supplement can re-establish immune function. A sufficient and balanced diet should cover the overall micronutrient requirements. However, many population segments both in developing and industrialized countries do not get adequate amounts of essential micronutrients through the diet. Current environmental and geopolitical developments (i.e. global economic crisis, rice crisis and other food shortages, the increase in maize cultivation for ethanol production, etc.) are exacerbating problems of nutritional status in many parts of the world and represent a serious threat to nutritional health. This review focuses on nutritional aspects of the immune system and discusses the roles of vitamins A, D, E, C, B
6
, B
12
and folate as well as of the trace elements selenium, zinc, iron and copper in supporting the body's natural defence system and restoring resistance to infections by enhancing the three levels of immunity: epithelial barriers, immune cells and antibody production.
Gender and Eloquence in Ercole de' Roberti'sPortia and Brutus
Authors: Cox Virginia 
Published: February 2009

AbstractA commonplace of modern feminist scholarship holds that fifteenth-century Italian humanists regarded the figure of the articulate women with hostility and suspicion. This position is insufficiently nuanced: while it may have been true to some extent in republican contexts, it was emphatically not the case in the secular princely courts, where women's capacity for eloquence was frequently a subject of praise. Humanistic attitudes toward female eloquence are examined here with special reference to Ercole de’ Roberti's representation of the classical heroine Portia in oratorical guise in his Portia and Brutus, painted at the court of Ferrara in the late 1480s or early ’90s. The article contextualizes Roberti's painting with regard to its classical literary sources, to contemporary practices of female oratory, and to the cultural and social self-positioning of the work's probable patron, Duchess Eleonora d'Aragona.
“The Root is Hidden and the Material Uncertain”: The Challenges of Prosecuting Witchcraft in Early Modern Venice*
Authors: Seitz Jonathan 
Published: February 2009

AbstractThe rich archival records of the Holy Office of the Inquisition in Venice have yielded much information about early modern society and culture. The transcripts of witchcraft trials held before the Inquisition reveal the complexities of early modern conceptions of natural and supernatural. The tribunal found itself entirely unable to convict individuals charged with performing harmful magic, or maleficio, as different worldviews clashed in the courtroom. Physicians, exorcists, and inquisitors all had different approaches to distinguishing natural phenomena from supernatural, and without a consensus guilty verdicts could not be obtained.
Boosting for high-dimensional time-to-event data with competing risks
Authors: Binder Harald , Allignol Arthur , Schumacher Martin , Beyersmann Jan 
Published: February 2009

AbstractMotivation: For analyzing high-dimensional time-to-event data with competing risks, tailored modeling techniques are required that consider the event of interest and the competing events at the same time, while also dealing with censoring. For low-dimensional settings, proportional hazards models for the subdistribution hazard have been proposed, but an adaptation for high-dimensional settings is missing. In addition, tools for judging the prediction performance of fitted models have to be provided.Results: We propose a boosting approach for fitting proportional subdistribution hazards models for high-dimensional data, that can e.g. incorporate a large number of microarray features, while also taking clinical covariates into account. Prediction performance is evaluated using bootstrap.632+ estimates of prediction error curves, adapted for the competing risks setting. This is illustrated with bladder cancer microarray data, where simultaneous consideration of both, the event of interest and competing events, allows for judging the additional predictive power gained from incorporating microarray measurements.Availability: The proposed boosting approach is implemented in the R package CoxBoost and prediction error estimation in the package peperr, both available from CRAN.Contact: binderh@fdm.uni-freiburg.de
Predicting helix–helix interactions from residue contacts in membrane proteins
Authors: Lo Allan , Chiu Yi-Yuan , Rødland Einar Andreas , Lyu Ping-Chiang , Sung Ting-Yi , Hsu Wen-Lian 
Published: February 2009

AbstractMotivation: Helix–helix interactions play a critical role in the structure assembly, stability and function of membrane proteins. On the molecular level, the interactions are mediated by one or more residue contacts. Although previous studies focused on helix-packing patterns and sequence motifs, few of them developed methods specifically for contact prediction.Results: We present a new hierarchical framework for contact prediction, with an application in membrane proteins. The hierarchical scheme consists of two levels: in the first level, contact residues are predicted from the sequence and their pairing relationships are further predicted in the second level. Statistical analyses on contact propensities are combined with other sequence and structural information for training the support vector machine classifiers. Evaluated on 52 protein chains using leave-one-out cross validation (LOOCV) and an independent test set of 14 protein chains, the two-level approach consistently improves the conventional direct approach in prediction accuracy, with 80% reduction of input for prediction. Furthermore, the predicted contacts are then used to infer interactions between pairs of helices. When at least three predicted contacts are required for an inferred interaction, the accuracy, sensitivity and specificity are 56%, 40% and 89%, respectively. Our results demonstrate that a hierarchical framework can be applied to eliminate false positives (FP) while reducing computational complexity in predicting contacts. Together with the estimated contact propensities, this method can be used to gain insights into helix-packing in membrane proteins.Availability: http://bio-cluster.iis.sinica.edu.tw/TMhit/Contact: tsung@iis.sinica.edu.twSupplementary information: Supplementary data are available at Bioinformatics online.
Shark depredation rates in pelagic longline fisheries: a case study from the Northwest Atlantic
Authors: MacNeil M. Aaron , Carlson John K. , Beerkircher Lawrence R. 
Published: February 2009

Abstract
MacNeil, M. A., Carlson, J. K., and Beerkircher, L. R. 2009. Shark depredation rates in pelagic longline fisheries: a case study from the Northwest Atlantic. – ICES Journal of Marine Science, 66: 708–719. A suite of modelling approaches was employed to analyse shark depredation rates from the US Atlantic pelagic longline fishery. As depredation events are relatively rare, there are a large number of zeroes in pelagic longline data and conventional generalized linear models (GLMs) may be ineffective as tools for statistical inference. GLMs (Poisson and negative binomial), two-part (delta-lognormal and truncated negative binomial, T-NB), and mixture models (zero-inflated Poisson, ZIP, and zero-inflated negative binomial, ZINB) were used to understand the factors that contributed most to the occurrence of depredation events that included a small proportion of whale damage. Of the six distribution forms used, only the ZIP and T-NB models performed adequately in describing depredation data, and the T-NB and ZINB models outperformed the ZIP models in bootstrap cross-validation estimates of prediction error. Candidate T-NB and ZINB model results showed that encounter probabilities were more strongly related to large-scale covariates (space, season) and that depredation counts were correlated with small-scale characteristics of the fishery (temperature, catch composition). Moreover, there was little evidence of historical trends in depredation rates. The results show that the factors contributing to most depredation events are those already controlled by ships' captains and, beyond novel technologies to repel sharks, there may be little more to do to reduce depredation loss in the fishery within current economic and operational constraints.
Thin scattering layers observed by airborne lidar
Authors: Churnside James H. , Donaghay Percy L. 
Published: February 2009

Abstract
Churnside, J. H., and Donaghay, P. L. 2009. Thin scattering layers observed by airborne lidar. – ICES Journal of Marine Science, 66: 778–789. More than 2000 km of thin (<3 m) optical scattering layers were identified in 80 000 km of airborne lidar data collected from a variety of oceanic and coastal waters. The spatial characteristics of thin layers varied dramatically from (i) those that were self-contained features consistently <3–4 m thick over their 1–12 km extent to (ii) those that were clearly parts of much longer layers that had gaps and/or regions where the layer became more intense and much thicker than the 3-m criterion. The characteristics of the lidar signal suggest that plankton was the most likely source of scattering. Examples from upwelling regions, areas with large fresh-water influx, and warm-core eddies are presented. The results are quite consistent with the characteristics observed in studies of thin plankton layers in fjords and near-coastal waters. These layers exhibit great spatial variability that is difficult to observe using traditional methods, and examples of layer perturbations by both linear and non-linear internal waves are presented. The results suggest that airborne lidar can be a powerful tool not only for detecting and mapping the spatial extent of thin scattering layers and linking their occurrence to larger scale physical processes, but also for tracking their evolution over time and guiding the ship-based sampling needed to understand their composition, dynamics, and impacts. Such a capability will be crucial in future studies designed to test the hypothesis that thin plankton layers have the spatial extent and intensity to play a key role in controlling the recruitment of fish larvae, biogeochemical cycling, trophic transfer processes, plankton biodiversity, and harmful algal bloom dynamics.
Cellular distributions of molecules with altered expression specific to thyroid proliferative lesions developing in a rat thyroid carcinogenesis model
Authors: Woo Gye‐Hyeong , Takahashi Miwa , Inoue Kaoru , Fujimoto Hitoshi , Igarashi Katsuhide , Kanno Jun , Hirose Masao , Nishikawa Akiyoshi , Shibutani Makoto 
Published: February 2009

To identify differentially regulated molecules related to early and late stages of tumor promotion in a rat two‐stage thyroid carcinogenesis model by an antithyroid agent, sulfadimethoxine, microarray‐based microdissected lesion‐specific gene expression profiling was carried out. Proliferative lesions for profiling were divided into two categories: (i) focal follicular cell hyperplasias (FFCH) and adenomas (Ad) as early lesions; and (ii) carcinomas (Ca) as more advanced. In both cases, gene expression was compared with that in surrounding non‐tumor follicular cells. Characteristically, upregulation of cell cycle‐related genes in FFCH + Ad, downregulation of genes related to tumor suppression and transcription inhibitors of inhibitor of DNA binding (Id) family proteins in Ca, and upregulation of genes related to cell proliferation and tumor progression in common in FFCH + Ad and Ca, were detected. The immunohistochemical distributions of molecules included in the altered expression profiles were further examined. In parallel with microarray data, increased localization of ceruloplasmin, cyclin B1, and cell division cycle 2 homolog A, and decreased localization of poliovirus receptor‐related 3 and Id3 were observed in all types of lesion. Although inconsistent with the microarray data, thyroglobulin immunoreactivity appeared to reduce in Ca. The results thus suggest cell cycling facilitation by induction of M‐phase‐promoting factor consisting of cyclin B1 and cell division cycle 2 homolog A and generation of oxidative responses as evidenced by ceruloplasmin accumulation from an early stage, as well as suppression of cell adhesion involving poliovirus receptor‐related 3 and inhibition of cellular differentiation regulated by Id3. Decrease of thyroglobulin in Ca may reflect dedifferentiation with progression. (Cancer Sci 2009; 100: 617–625)
Overexpression of EIF‐5A2 predicts tumor recurrence and progression in pTa/pT1 urothelial carcinoma of the bladder
Authors: Luo Jun‐Hang , Hua Wen‐Feng , Rao Hui‐Lan , Liao Yi‐Ji , Kung Hsiang‐Fu , Zeng Yi‐Xin , Guan Xin‐Yuan , Chen Wei , Xie Dan 
Published: February 2009

The authors investigated the status of abnormalities of eIF‐5A2 gene in superficial (pTa/pT1) urothelial carcinoma of the bladder (UC), as well as its correlation with clinicopathologic variables and patient outcome. The methods of immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), reverse transcription‐polymerase chain reaction (RT‐PCR) and Wetern blotting were utilized to examine protein/mRNA(messenger RNA) expression and amplification of eIF‐5A2 in a cohort of pTa/pT1 UCs. Overexpression of EIF‐5A2 was examined by IHC in 38/112 (33.9%) pTa/pT1 UCs. A significant association of overexpression of EIF‐5A2 with shortened UC patient recurrence‐free survival (P = 0.002), as well as with shortened progression‐free survival (P = 0.004), was demonstrated. Importantly, multivariate Cox regression analysis revealed that EIF‐5A2 expression provided a significant independent prognostic parameter either in tumor recurrence (P = 0.002) or in tumor progression (P = 0.007). FISH results demonstrated that eIF‐5A2 amplification was detected in 5/59 of the informative UCs; in each of the five cases with eIF‐5A2 amplification, overexpression of EIF‐5A2 was observed. In the remaining 54 UCs without eIF‐5A2 amplification, 16 cases were also observed to have overexpression of EIF‐5A2. In 13 pairs of UC and adjacent normal tissues, eight UCs were examined and showed up‐regulated eIF‐5A2 mRNA by RT‐PCR, while increased expression of EIF‐5A2 protein was only detected in 4/8 UCs by Western blotting. These findings suggest that overexpression of EIF‐5A2, as detected by IHC, may predict tumor recurrence and progression in pTa/pT1 UC patients, and the protein expression of eIF‐5A2 might be regulated not only by gene amplification, but also by other molecular mechanisms. (Cancer Sci 2009; 100: 896–902)