bluuebunny/crossref_metadata_2025_split huggingface dataset:
An alternative strategy for corn drying (Zea mays) resulted in both energy savings and reduction of fumonisins B1 and B2 contamination
Authors: Yılmaz Neşe , Tuncel Necati Barış 
Published: February 2010

SummaryThe objectives of this study were to investigate the effect of harvest date on fumonisins contamination and to offer an alternative drying procedure with low energy costs. Corn kernel samples above 13% moisture content were dried with hot air (HA), the technique more usually utilised by farmers and compared with infrared and infrared–hot air (IR–HA) combination techniques. The effect of harvest date on fumonisin contamination was found to be significant while drying had no influence. Due to the fact that the corn remains in the field longer than necessary for economic reasons, energy expenses of the drying techniques were calculated in terms of specific energy consumption for unit of evaporated water. It was found that the energy expenses to reduce the moisture level from 15 to 13% with HA drying were higher than the expenses to reduce the moisture level from 29 to 13% with IR–HA drying combination.
Acrylamide content in potato chips on the Italian market determined by liquid chromatography tandem mass spectrometry
Authors: Tateo Fernando , Bononi Monica , Gallone Franco 
Published: February 2010

SummaryAn easy‐to‐use and simplified liquid chromatography‐tandem mass spectrometry (LC‐ESI (+)‐MS/MS) method was adopted to determine the amount of acrylamide in thirty‐two samples of potato chips purchased on the South Italian market in 2009. Extract produced from matrices was directly analysed without derivatisation, the use of isotopically labelled acrylamide or the use of clean up cartridges. Quality analytical data were reported. The limit of detection and limit of quantification were 6 μg kg−1 and 18 μg kg−1, respectively and recovery values ranged from 90.7–96.3%. The relative standard deviation (RSD) ranged between 2.1% and 5.8%. The values ranged between 27 and 1400 μg kg−1 and the arithmetic mean acrylamide content resulted 363 μg kg−1. According to Foot et al. [Food Additives and Contaminants, 24 (2007)(S1), 37] and considering 500 μg kg−1 as the minimum level possible with the actual available mitigation tools, the number of samples showing an acrylamide level higher than 500 μg kg−1 resulted to be 22%. This paper gives a contribution to data collection in response to the monitoring activity of EFSA and following the Commission Recommendation 2007/331/EC: really, the number of Italian samples of potato chips and potato products for which acrylamide values was reported in the ‘results on the monitoring of acrylamide’ of EFSA (http://www.efsa.europa.eu/cs/BlobServer/Report/datex_report_acrylamide_en,0.pdf?ssbinary=true, 2009) issued on 30 April 2009 is very limited.
Thermo‐physical properties of composite bread dough with maize and cassava flours
Authors: Oladunmoye Olufunmilola Olaitan , Ojo Ademola , Akinoso Rahman , Akanbi Charles Taiwo 
Published: February 2010

SummaryComposite wheat–cassava and wheat–maize flours were produced in ratio 100:0. 60:40, 50:50, 40:60 and 0:100 respectively. Thermo‐physical properties of bread dough were determined. For wheat –cassava composite bread dough, moisture content ranged between 44.02 ± 2.04 to 51.31 ± 2.99% dry basis (db), density (1035.2 ± 20.4 to 975.6 ± 12.6 kg m−3), specific heat capacity (2.51 ± 0.61 to 3.01 ± 0.42 kJ kg−1 K) and thermal conductivity (0.362 ± 0.13 to 0.473 ± 0.12 W mK−1). While wheat–maize mixture gave 44.14 ± 1.94 to 45.09 ± 1.26%(db) of moisture content, 981.4 ± 16.3–960.4 ± 22.5 kg m−3 density, 1.77 ± 0.17–2.61 ± 0.63 kJ kg−1 K specific heat capacity and 0.36 ± 0.07–0.39 ± 0.02 W mK−1 thermal conductivity. Effects of substitutions was significant on moisture content and thermal conductivity of dough while non significant influence was recorded on density and specific heat capacity at P < 0.05.
Probiotic lactic acid bacteria from Kung‐Som: isolation, screening, inhibition of pathogenic bacteria
Authors: Hwanhlem Noraphat , Watthanasakphuban Nisit , Riebroy Siriporn , Benjakul Soottawat , H‐Kittikun Aran , Maneerat Suppasil 
Published: February 2010

SummaryLactic acid bacteria (LAB) were isolated from Kung‐Som at various fermentation periods. Only ten strains, named D2SM22, D6SM3, D6SM24, D6SM26, D8SM21, D10SM5, D10SM11, D10SM16, D10SM20 and D16SM26 showed a survival rate of more than 50% under the simulated gastric juice. After being subjected to simulated gastric juice, four strains (D6SM3, D8SM21, D10SM16 and D10SM20) showed a survival rate of more than 50% in simulated small intestinal juices. Growth of strain D6SM3, D8SM21 and D10SM16 under micro‐aerobic and anaerobic conditions was not different. Tested pathogenic strains (Escherichia coli, Staphylococcus aureus, Bacillus cereus, Vibrio parahaemolyticus and Salmonella sp.) were inhibited by probiotic LAB. However, none of strains could produce bacteriocins. All strains were identified as Lactobacillus plantarum. No differences in pH, acidity, LAB count and liking scores between Kung‐Som produced with starter culture and conventional method were observed (P > 0.01).
Determination of simple sugars, malic acid and total phenolic compounds in apple pomace by infrared spectroscopy and PLSR
Authors: Queji Mary D. , Wosiacki Gilvan , Cordeiro Gilcélia A. , Peralta‐Zamora Patricio G. , Nagata Noemi 
Published: February 2010

SummaryThe aim of this work was to develop a fast, versatile, inexpensive and environmentally safe analytical method to quantify simple sugars, malic acid and total phenolic compounds in apple pomace, considering its potential use as a raw material with value instead of as an industrial waste. Diffuse reflectance infrared spectroscopy (DRIFTS) measurements of twenty‐six samples of apple pomace were analysed by partial least squares regression (PLSR), using several signal pre‐processing methods. Multivariate models developed with four to five latent variables (LVs) and based in the MIR (mid‐infrared) region had good prediction for the determination of sucrose, fructose, malic acid and total phenolic compounds, with average errors between 3.9% and 6.6%. By contrast, glucose was better determined by models developed in the NIR (near‐infrared) region and using six LVs, yielding an average error lower than 7.4%. These results confirmed the feasibility of the multivariate spectroscopic approach as an alternative for expensive and time‐consuming conventional chemical methods.
Differential effects of experimental increases in sociality on ectoparasites of free‐ranging raccoons
Authors: Monello Ryan J. , Gompper Matthew E. 
Published: February 2010

Summary1.Parasite transmission depends on the rate at which hosts come into contact with one another or the infectious stages of parasites. However, host contact rates and their influence on parasite transmission are difficult to quantify in natural settings and can fluctuate with host behaviour and the ecological constraints of parasites.2.We investigated how experimental increases in rates of contact and social aggregation affected ectoparasite prevalence and intensity of free‐ranging raccoons (Procyon lotor). Twelve independent raccoon populations were subjected to differential resource provisions for 2 years: a clumped food distribution to aggregate hosts (n = 5 aggregated populations), a dispersed food distribution to control for the effects of food without aggregating hosts (n = 3) and a no food treatment (n = 4).3.Remote cameras indicated that aggregation sizes and rates of contact were three to four times greater in aggregated compared with that in non‐aggregated populations. The number of ticks (adultDermacentor variabilis) on raccoons in aggregated populations was 1·5–2·5 times greater from May to July, the primary time of tick seasonal occurrence. Conversely, louse (Trichodectes octomaculatus) populations werec.40% sparser on male raccoons in aggregated (compared with that in non‐aggregated) populations because of greater overdispersion of lice and a larger number of male hosts harbouring fewer parasites. No treatment‐related differences were found among fleas (Orchopeas howardi).4.These results were not consistent with our current understanding of parasite transmission; greater rates of host sociality led to increases in a parasite that does not rely on host contact for transmission (ticks) and declines in a parasite that depends on host contact for transmission (lice). We concluded thatD. variabilisincreased in aggregated sites because they can detect and seek out hosts and were more likely to drop off after obtaining a blood meal and re‐attach to raccoons in these locations. Several factors may have contributed to sparser louse populations on male hosts, including a dilution effect that lowered per capita infestation levels.5.These results indicate that ectoparasites can interact in unique ways with their hosts that are not consistent with other types of parasite species or models of their transmission.
Population dynamics of an Arctiid caterpillar–tachinid parasitoid system using state‐space models
Authors: Karban Richard , De Valpine Perry 
Published: February 2010

Summary1. Population dynamics of insect host–parasitoid systems are important in many natural and managed ecosystems and have inspired much ecological theory. However, ecologists have a limited knowledge about the relative strengths of species interactions, abiotic effects and density dependence in natural host–parasitoid dynamics. Statistical time‐series analyses would be more informative by incorporating multiple factors, measurement error and noisy dynamics.2. We use a novel maximum likelihood and model‐selection analysis of a state‐space model for host–parasitoid dynamics to examine 21 years of annual census data for woolly bear caterpillars (Platyprepia virginalis) and their locally host‐specific tachinid parasitoids (Thelaira americana).3. Caterpillar densities varied by three orders of magnitude and were driven by density dependence and precipitation from the previous March but not detectably by parasitoids, despite variable and sometimes high (>50%) parasitism.4. Fly fluctuations, as estimated from per cent parasitism, were affected by density dependence and precipitation from the previous July. There was marginal evidence that host abundance drives fly fluctuations as a generic linear effect but no evidence for classical Nicholson–Bailey coupling.5. The state‐space model analysis includes new methods for likelihood calculation and allows a balanced consideration of effect magnitude and statistical significance in a nonlinear model with multiple alternative explanatory variables.
Plio‐Pleistocene diversification and genetic population structure of an endangered lizard (the Blue Mountains water skink, Eulamprus leuraensis) in south‐eastern Australia
Authors: Dubey Sylvain , Shine Richard 
Published: February 2010

AbstractAim  Although climatic fluctuations occurred world‐wide during the Pleistocene, the severity of glacial and drought events – and hence their influence on animal and plant biogeography – differed among regions. Many Holarctic species were forced to warmer‐climate refugia during glacial periods, leaving the genetic signature of recent expansion and gene flow among modern‐day populations. Montane south‐eastern Australia experienced less extreme glaciation, but the effects of drier and colder climatic conditions over this period on biotic distributions, and hence on the present‐day genetic structure of animal and plant populations, are poorly known.Location  South‐eastern Australia.Methods  The endangered Blue Mountains water skink (Eulamprus leuraensis) is a viviparous lizard known from fewer than 40 isolated small swamps at 560–1060 m elevation in south‐eastern Australia. We conducted molecular phylogenetic, dating and population genetics analyses using the mitochondrial NADH dehydrogenase 4 (ND4) of 224 individuals of E. leuraensis sampled across the species’ distribution.Results  Ancient divergences in haplotype groups between lizards from the Blue Mountains and the Newnes Plateau, and strong genetic differences, even between swamps separated by only a few kilometres, suggest that the species has persisted as a series of relatively isolated populations within its current distribution for about a million years. Presumably, habitat patches similar to current‐day swamps persisted throughout glacial–interglacial cycles in this region, allowing the development of high levels of genetic structuring within and among present‐day populations.Main conclusions  Our results suggest that less extreme glacial conditions occurred in the Southern Hemisphere compared with the Northern Hemisphere, allowing cold‐adapted species (such as E. leuraensis) to persist in montane areas. However, additional studies are needed before we can assemble a comprehensive view of the impact of Pleistocene climatic variation on the phylogeography of Southern Hemisphere taxa.
To kill or be killed: how viruses interact with the cell death machinery
Authors: Kaminskyy V. , Zhivotovsky B. 
Published: February 2010

Abstract.  Kaminskyy V, Zhivotovsky B (Karolinska Institutet, Stockholm, Sweden). To kill or be killed: how viruses interact with the cell death machinery (Symposium). J Intern Med 2010; 267: 473–482.A virus (from the Latin virus meaning toxin or poison) is a small infectious agent that can only replicate inside the cells of another organism. Viruses are found wherever there is life and have probably existed since living cells first evolved. Viruses do not have their own metabolism and require a host cell to make new products. The range of structural and biochemical (i.e., cytopathic) effects that viruses have on the host cell is extensive. Most viral infections eventually result in the death of the host cell. The causes of death include cell lysis, alterations to the cell’s surface membrane and various modes of programmed cell death. Some viruses cause no apparent changes to the infected cell. Cells in which the virus is latent and inactive show few signs of infection and often function normally. This causes persistent infection and the virus is often dormant for many months or years. Some viruses can cause cells to proliferate without causing malignancy, whereas others are established causes of cancer. Human organisms use a genetically controlled cell death programme that prevents the spreading of viral infection and kills the virus. Between 19 and 21 November 2009, with sponsorship from the Journal of Internal Medicine, the Swedish Research Foundation and the Swedish Cancer Society hosted a conference in Stockholm entitled: ‘To kill or to be killed. Viral evasion strategies and interference with cell death machinery’. Four comprehensive reviews from this conference are presented in this issue of the Journal of Internal Medicine. These reviews include descriptions of: the modulation of host innate and adaptive immune defenses by cytomegalovirus; the impact of gamma‐chain family cytokines on T cell homoeostasis in HIV‐1 infection and the therapeutic implications; approaches to killing tumours by depriving them of the mechanisms for detoxification; and viral strategies for the evasion of immunogenic cell death.
Viral strategies for the evasion of immunogenic cell death
Authors: Galluzzi L. , Kepp O. , Morselli E. , Vitale I. , Senovilla L. , Pinti M. , Zitvogel L. , Kroemer G. 
Published: February 2010

Abstract.  Galluzzi L, Kepp O, Morselli E, Vitale I, Senovilla L, Pinti M, Zitvogel L, Kroemer G (INSERM, U848; Institut Gustave Roussy; and Université Paris Sud‐XI, Paris, France; Università degli studi di Modena e Reggio Emilia, Modena, Italy; INSERM, U805, Paris, France). Viral strategies for the evasion of immunogenic cell death (Symposium). J Intern Med 2010; 267: 526–542.Driven by co‐evolutionary forces, viruses have refined a wide arsenal of strategies to interfere with the host defences. On one hand, viruses can block/retard programmed cell death in infected cells, thereby suppressing one of the most ancient mechanisms against viral dissemination. On the other hand, multiple viral factors can efficiently trigger the death of infected cells and uninfected cells from the immune system, which favours viral spreading and prevents/limits an active antiviral response, respectively. Moreover, several viruses are able to inhibit the molecular machinery that drives the translocation of calreticulin to the surface of dying cells. Thereby, viruses block the exposure of an engulfment signal that is required for the efficient uptake of dying cells by dendritic cells and for the induction of the immune response. In this review, we discuss a variety of mechanisms by which viruses interfere with the cell death machinery and, in particular, by which they subvert immunogenic cell death.
Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next‐generation sequencing and Sequenom iPLEX MassARRAY genotyping
Authors: BUGGS RICHARD J. A. , CHAMALA SRIKAR , WU WEI , GAO LU , MAY GREGORY D. , SCHNABLE PATRICK S. , SOLTIS DOUGLAS E. , SOLTIS PAMELA S. , BARBAZUK W. BRAD 
Published: February 2010

Abstract Tragopogon miscellus (Asteraceae) is an evolutionary model for the study of natural allopolyploidy, but until now has been under‐resourced as a genetic model. Using 454 and Illumina expressed sequence tag sequencing of the parental diploid species of T. miscellus, we identified 7782 single nucleotide polymorphisms that differ between the two progenitor genomes present in this allotetraploid. Validation of a sample of 98 of these SNPs in genomic DNA using Sequenom MassARRAY iPlex genotyping confirmed 92 SNP markers at the genomic level that were diagnostic for the two parental genomes. In a transcriptome profile of 2989 SNPs in a single T. miscellus leaf, using Illumina sequencing, 69% of SNPs showed approximately equal expression of both homeologs (duplicate homologous genes derived from different parents), 22% showed apparent differential expression and 8.5% showed apparent silencing of one homeolog in T. miscellus. The majority of cases of homeolog silencing involved the T. dubius SNP homeolog (164/254; 65%) rather than the T. pratensis homeolog (90/254). Sequenom analysis of genomic DNA showed that in a sample of 27 of the homeologs showing apparent silencing, 23 (85%) were because of genomic homeolog loss. These methods could be applied to any organism, allowing efficient and cost‐effective generation of genetic markers.
Ecogenomics: using massively parallel pyrosequencing to understand virus ecology
Authors: ROOSSINCK MARILYN J. , SAHA PRASENJIT , WILEY GRAHAM B. , QUAN JIAXI , WHITE JAMES D. , LAI HONGSHING , CHAVARRÍA FELIPE , SHEN GUOAN , ROE BRUCE A. 
Published: February 2010

AbstractEnvironmental samples have been analysed for viruses in metagenomic studies, but these studies have not linked individual viruses to their hosts. We designed a strategy to isolate double‐stranded RNA, a hallmark of RNA virus infection, from individual plants and convert this to cDNA with a unique four nucleotide Tag at each end. Using 96 different Tags allowed us to pool samples and still retain the link to the original sample. We then analysed the sequence of pooled samples using massively parallel sequencing with Roche 454 pyrosequencing such that 384 samples could be assessed per picotiter plate. Using this method we have been able to analyse thousands of plants, and we have discovered several thousand new plant viruses, all linked to their specific plant hosts. Here we describe the method in detail, including the results and analysis for eight pools of samples. This technology will be extremely useful in understanding the full scope of plant virus biodiversity.
Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow
Authors: WOLF JOCHEN B. W. , BAYER TILL , HAUBOLD BERNHARD , SCHILHABEL MARKUS , ROSENSTIEL PHILIP , TAUTZ DIETHARD 
Published: February 2010

AbstractRecent advances in sequencing technology promise to provide new strategies for studying population differentiation and speciation phenomena in their earliest phases. We focus here on the black carrion crow (Corvus [corone] corone), which forms a zone of hybridization and overlap with the grey coated hooded crow (Corvus [corone] cornix). However, although these semispecies are taxonomically distinct, previous analyses based on several types of genetic markers did not reveal significant molecular differentiation between them. We here corroborate this result with sequence data obtained from a set of 25 nuclear intronic loci. Thus, the system represents a case of a very early phase of species divergence that requires new molecular approaches for its description. We have therefore generated RNAseq expression profiles using barcoded massively parallel pyrosequencing of brain mRNA from six individuals of the carrion crow and five individuals from a hybrid zone with the hooded crow. We obtained 856 675 reads from two runs, with average read length of 270 nt and coverage of 8.44. Reads were assembled de novo into 19 552 contigs, 70% of which could be assigned to annotated genes in chicken and zebra finch. This resulted in a total of 7637 orthologous genes and a core set of 1301 genes that could be compared across all individuals. We find a clear clustering of expression profiles for the pure carrion crow animals and disperse profiles for the animals from the hybrid zone. These results suggest that gene expression differences may indeed be a sensitive indicator of initial species divergence.
Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises
Authors: CREER S. , FONSECA V. G. , PORAZINSKA D. L. , GIBLIN‐DAVIS R. M. , SUNG W. , POWER D. M. , PACKER M. , CARVALHO G. R. , BLAXTER M. L. , LAMBSHEAD P. J. D. , THOMAS W. K. 
Published: February 2010

AbstractBiodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well‐acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is confounded by the small size of taxa, morphological convergence and intraspecific variation. However, the most important restricting factor in meiofaunal ecological research is the mismatch between diversity and the number of taxonomists that are able to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular operational taxonomic unit (MOTU)‐based approach has been advocated for en mass meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput afforded by chain termination sequencing. Contemporary pyrosequencing offers a solution to this problem in the form of environmental metagenetic analyses, but this represents a novel field of biodiversity assessment. Here, we provide an overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms. We report two examples of environmental metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical rainforest habitats and provide critical appraisals of the level of putative recombinant DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control measures, environmental metagenetic analyses achieve MOTU formation across the eukaryote domain of life at a fraction of the time and cost of traditional approaches. The effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to elucidate the molecular genetic richness of not only meiofaunal, but also all complex eukaryotic communities.