bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of habitat quality and size on extinction in experimental populations
Authors: Griffen Blaine D , Drake John M
Published: June 2008

Stochastic population theory makes clear predictions about the effects of reproductive potential and carrying capacity on characteristic time-scales of extinction. At the same time, the effects of habitat size and quality on reproduction and regulation have been hotly debated. To trace the causal relationships among these factors, we looked at the effects of habitat size and quality on extinction time in experimental populations ofDaphnia magna. Replicate model systems representative of a broad-spectrum consumer foraging on a continuously supplied resource were established under crossed treatments of habitat size (two levels) and habitat quality (three levels) and monitored until eventual extinction of all populations. Using statistically derived estimates of key parameters, we related experimental treatments to persistence time through their effect on carrying capacity and the population growth rate. We found that carrying capacity and the intrinsic rate of increase were each influenced similarly by habitat size and quality, and that carrying capacity and the intrinsic rate of increase were in turn both correlated with time to population extinction. We expected habitat quality to have a greater influence on extinction. However, owing to an unexpected effect of habitat size on reproductive potential, habitat size and quality were similarly important for population persistence. These results support the idea that improving the population growth rate or carrying capacity will reduce extinction risk and demonstrate that both are possible by improving habitat quality or increasing habitat size.
Tissue-specific regulation of SIRT1 by calorie restriction
Authors: Chen Danica , Bruno Joanne , Easlon Erin , Lin Su-Ju , Cheng Hwei-Ling , Alt Frederick W. , Guarente Leonard
Published: June 2008

Calorie restriction (CR) has been reported to increase SIRT1 protein levels in mice, rats, and humans, and elevated activity of SIRT1 orthologs extends life span in yeast, worms, and flies. In this study, we challenge the paradigm that CR induces SIRT1 activity in all tissues by showing that activity of this sirtuin in the liver is, in fact, reduced by CR and activated by a high-caloric diet. We demonstrate this change both by assaying levels of SIRT1 and its small molecule regulators, NAD and NADH, as well as assessing phenotypes of a liver-specific SIRT1 knockout mouse on various diets. Our findings suggest that designing CR mimetics that target SIRT1 to provide uniform systemic benefits may be more complex than currently imagined.
EagleView: A genome assembly viewer for next-generation sequencing technologies
Authors: Huang Weichun , Marth Gabor
Published: June 2008

The emergence of high-throughput next-generation sequencing technologies (e.g., 454 Life Sciences [Roche], Illumina sequencing [formerly Solexa sequencing]) has dramatically sped up whole-genome de novo sequencing and resequencing. While the low cost of these sequencing technologies provides an unparalleled opportunity for genome-wide polymorphism discovery, the analysis of the new data types and huge data volume poses formidable informatics challenges for base calling, read alignment and genome assembly, polymorphism detection, as well as data visualization. We introduce a new data integration and visualization tool EagleView to facilitate data analyses, visual validation, and hypothesis generation. EagleView can handle a large genome assembly of millions of reads. It supports a compact assembly view, multiple navigation modes, and a pinpoint view of technology-specific trace information. Moreover, EagleView supports viewing coassembly of mixed-type reads from different technologies and supports integrating genome feature annotations into genome assemblies. EagleView has been used in our own lab and by over 100 research labs worldwide for next-generation sequence analyses. The EagleView software is freely available for not-for-profit use at http://bioinformatics.bc.edu/marthlab/EagleView.
CpG dinucleotides and the mutation rate of non-CpG DNA
Authors: Walser Jean-Claude , Ponger Loïc , Furano Anthony V.
Published: June 2008

The neutral mutation rate is equal to the base substitution rate when the latter is not affected by natural selection. Differences between these rates may reveal that factors such as natural selection, linkage, or a mutator locus are affecting a given sequence. We examined the neutral base substitution rate by measuring the sequence divergence of ∼30,000 pairs of inactive orthologous L1 retrotransposon sequences interspersed throughout the human and chimpanzee genomes. In contrast to other studies, we related ortholog divergence to the time (age) that the L1 sequences resided in the genome prior to the chimpanzee and human speciation. As expected, the younger orthologs contained more hypermutable CpGs than the older ones because of their conversion to TpGs (and CpAs). Consequently, the younger orthologs accumulated more CpG mutations than the older ones during the ∼5 million years since the human and chimpanzee lineages separated. But during this same time, the younger orthologs also accumulated more non-CpG mutations than the older ones. In fact, non-CpG and CpG mutations showed an almost perfect (R2 = 0.98) correlation for ∼97% of the ortholog pairs. The correlation is independent of G + C content, recombination rate, and chromosomal location. Therefore, it likely reflects an intrinsic effect of CpGs, or mutations thereof, on non-CpG DNA rather than the joint manifestation of the chromosomal environment. The CpG effect is not uniform for all regions of non-CpG DNA. Therefore, the mutation rate of non-CpG DNA is contingent to varying extents on local CpG content. Aside from their implications for mutational mechanisms, these results indicate that a precise determination of a uniform genome-wide neutral mutation rate may not be attainable.
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
Authors: Mavrich Travis N. , Ioshikhes Ilya P. , Venters Bryan J. , Jiang Cizhong , Tomsho Lynn P. , Qi Ji , Schuster Stephan C. , Albert Istvan , Pugh B. Franklin
Published: June 2008

Most nucleosomes are well-organized at the 5′ ends of S. cerevisiae genes where “−1” and “+1” nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified by the genome is less clear. Here we establish and inter-relate rules governing genomic nucleosome organization by sequencing DNA from more than one million immunopurified S. cerevisiae nucleosomes (displayed at http://atlas.bx.psu.edu/). Evidence is presented that the organization of nucleosomes throughout genes is largely a consequence of statistical packing principles. The genomic sequence specifies the location of the −1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3′ NFR that is present at >95% of all genes. 3′ NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3′ NFRs in gene looping.
Quantitative 1H Nuclear Magnetic Resonance Metabolite Profiling as a Functional Genomics Platform to Investigate Alkaloid Biosynthesis in Opium Poppy
Authors: Hagel Jillian M. , Weljie Aalim M. , Vogel Hans J. , Facchini Peter J.
Published: June 2008

Opium poppy (Papaver somniferum) produces a diverse array of bioactive benzylisoquinoline alkaloids and has emerged as a versatile model system to study plant alkaloid metabolism. The plant is widely cultivated as the only commercial source of the narcotic analgesics morphine and codeine. Variations in plant secondary metabolism as a result of genetic diversity are often associated with perturbations in other metabolic pathways. As part of a functional genomics platform, we used 1H nuclear magnetic resonance (NMR) metabolite profiling for the analysis of primary and secondary metabolism in opium poppy. Aqueous and chloroform extracts of six different opium poppy cultivars were subjected to chemometric analysis. Principle component analysis of the 1H NMR spectra for latex extracts clearly distinguished two varieties, including a low-alkaloid variety and a high-thebaine, low-morphine cultivar. Distinction was also made between pharmaceutical-grade opium poppy cultivars and a condiment variety. Such phenotypic differences were not observed in root extracts. Loading plots confirmed that morphinan alkaloids contributed predominantly to the variance in latex extracts. Quantification of 34 root and 21 latex metabolites, performed using Chenomx NMR Suite version 4.6, showed major differences in the accumulation of specific alkaloids in the latex of the low-alkaloid and high-thebaine, low-morphine varieties. Relatively few differences were found in the levels of other metabolites, indicating that the variation was specific for alkaloid metabolism. Exceptions in the low-alkaloid cultivar included an increased accumulation of the alkaloid precursor tyramine and reduced levels of sucrose, some amino acids, and malate. Real-time polymerase chain reaction analysis of 42 genes involved in primary and secondary metabolism showed differential gene expression mainly associated with alkaloid biosynthesis. Reduced alkaloid levels in the condiment variety were associated with the reduced abundance of transcripts encoding several alkaloid biosynthetic enzymes.
Histone Modifications and Expression of Light-Regulated Genes in Arabidopsis Are Cooperatively Influenced by Changing Light Conditions
Authors: Guo Lan , Zhou Junli , Elling Axel A. , Charron Jean-Benoit F. , Deng Xing Wang
Published: June 2008

Here, we analyzed the effects of light regulation on four selected histone modifications (H3K4me3, H3K9ac, H3K9me2, and H3K27me3) and the relationship of these histone modifications with the expression of representative light-regulated genes. We observed that the histone modifications examined and gene transcription were cooperatively regulated in response to changing light environments. Using H3K9ac as an example, our analysis indicated that histone modification patterns are set up very early and are relatively stable during Arabidopsis (Arabidopsis thaliana) seedling development. Distinct photoreceptor systems are responsible for mediating the effects of different light qualities on histone modifications. Moreover, we found that light regulation of gene-specific histone modifications involved the known photomorphogenesis-related proteolytic system defined by the pleiotropic CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETOLIATED proteins and histone modification enzymes (such as HD1). Furthermore, our data suggest that light-regulated changes in histone modifications might be an intricate part of light-controlled gene transcription. Thus, it is possible that variations in histone modifications are an important physiological component of plant responses to changing light environments.
Intergrowth of several solid phases from the Y–Ni–B–C system in a large YNi2B2C crystal
Authors: Weissbach Torsten , Leisegang Tilmann , Kreyssig Andreas , Frontzek Matthias , Hoffmann Jens-Uwe , Souptel Dmitri , Köhler Anke , Behr Günter , Paufler Peter , Meyer Dirk C.
Published: June 2008

A YNi2B2C single crystal containing traces of foreign phases was inspected by means of neutron and X-ray diffraction as well as scanning electron microscopy and X-ray spectroscopy methods. The diffraction patterns obtained from the experiments look similar to those expected for a superstructure. Nevertheless, they can be interpreted as crystallographically oriented precipitations of YB2C2and Ni2B within the YNi2B2C crystal, formed during the cooling process. The orientation relation between the lattices was obtained from experimental neutron and X-ray data. Structure refinements of the collected X-ray data were performed by separation of the intensity data of the individual phases. Scanning electron microscopy images of the inclusions found on a polished cross section of the crystal are presented; their chemical composition was determined using wavelength-dispersive X-ray analysis.
Anomalous small-angle scattering from nanoquasicrystalline precipitates in Zr80Pt20ribbons
Authors: Okuda Hiroshi , Fukumoto Takefumi , Saida Junji , Ochiai Shojiro , Sasaki Sono , Masunaga Hiroyasu
Published: June 2008

Anomalous small-angle X-ray scattering (ASAXS) profiles of Zr80Pt20ribbons have been measured at the ZrKabsorption edge. By annealing the melt-spun ribbons at 800 K, well defined SAXS patterns from nanoquasicrystals were observed, although the compositions of the quasicrystals (QC) and the amorphous matrix have previously been reported to be the same. The SAXS intensities were found to show a small anomalous effect at the ZrKedge. Contrast analysis suggested that the origin of the small-angle scattering is a small compositional fluctuation coupled with a small density difference, which enhances SAXS intensity but reduces the anomalous effect. A constant ASAXS intensity ratio for QC microstructure suggests that the ratio of the composition difference to the density difference between QC and the amorphous matrix is almost constant for the ZrPt ribbons examined here.
Conformational richness and multiple Z′ in salt co-crystal of N-methylpiperidine betaine with N-methylpiperidine betaine hexafluorosilicate
Authors: Thaimattam Ram , Szafran Miroslaw , Dega-Szafran Zofia , Jaskolski Mariusz
Published: June 2008

The co-crystal structure of N-methylpiperidine betaine with N-methylpiperidine betaine hexafluorosilicate represents an unusual case of a salt co-crystal with a high Z′ value (3), unexpected conformational variability, and with nearly 50% of its contents disordered. The betaine units from the salt and co-crystal formers are paired into several homoconjugated dimers via very short, linear O−...H+...O− bridges. These hydrogen bonds are the dominating interactions in the co-crystal structure, in variance with the simple hexafluorosilicate salt, which has a structure governed by COOH...F hydrogen bonds. The SiF^{2-}_6 anion in the co-crystal structure has only C—H...F interactions with the betaine units. The zwitterion:cation:anion stoichiometry is 3:3:1.5. Some of the betaine units display disorder, but each case is different. One of the SiF_6^{2-} anions is ordered while possessing exact crystallographic symmetry. The other one is disordered in a general position. In addition, there are three water molecules in the crystal structure. One is fully ordered, one has an H atom disordered in two positions and the third one occupies two alternative positions with unequal populations.
Orientational ordering in the low-temperature stable phases of deuterated thiophene
Authors: Damay F. , Rodríguez-Carvajal J. , André D. , Dunstetter F. , Szwarc H.
Published: June 2008

The stable structures of deuterated thiophene C4D4S were investigated at 155 (phase III), 115 (phase IV), 100 and 1.5 K (phase V) by neutron powder diffraction. At 155 K, thiophene is orthorhombic with space group Pbnm. Although there is some degree of in-plane orientational disorder, molecules begin to order along two symmetrically equivalent main orientations. At 115 K the structure is incommensurate, with a wavevector q ≃ 0.55a*. At 100 K and below, there is a doubling of the a cell parameter and the structure space group is P21. For the first time, it is shown that, unlike C4H4S, phase V of C4D4S is not an orientational glass: thiophene molecules are perfectly ordered and are oriented within the molecular plane along two alternating directions, corresponding to the two main orientations observed at 155 K. This ordering probably originates in the slowing down of the in-plane reorientational dynamics upon deuteration.
OPUS‐Rota: A fast and accurate method for side‐chain modeling
Authors: Lu Mingyang , Dousis Athanasios D. , Ma Jianpeng
Published: June 2008

In this paper, we introduce a fast and accurate side‐chain modeling method, named OPUS‐Rota. In a benchmark comparison with the methods SCWRL, NCN, LGA, SPRUCE, Rosetta, and SCAP, OPUS‐Rota is shown to be much faster than all the methods except SCWRL, which is comparably fast. In terms of overallχ1andχ1+2accuracies, however, OPUS‐Rota is 5.4 and 8.8 percentage points better, respectively, than SCWRL. Compared with NCN, which has the best accuracy in the literature, OPUS‐Rota is 1.6 percentage points better for overallχ1+2but 0.3 percentage points weaker for overallχ1. Hence, our algorithm is much more accurate than SCWRL with similar execution speed, and it has accuracy comparable to or better than the most accurate methods in the literature, but with a runtime that is one or two orders of magnitude shorter. In addition, OPUS‐Rota consistently outperforms SCWRL on the Wallner and Elofsson homology‐modeling benchmark set when the sequence identity is greater than 40%. We hope that OPUS‐Rota will contribute to high‐accuracy structure refinement, and the computer program is freely available for academic users.
Effects of surface‐to‐volume ratio of proteins on hydrophilic residues: Decrease in occurrence and increase in buried fraction
Authors: Shirota Matsuyuki , Ishida Takashi , Kinoshita Kengo
Published: June 2008

The size of a protein is an important factor for understanding the sequence–structure relationship, and it affects both the amino acid composition and the residue burial of proteins. However, it is usually measured as the number of amino acids, although these effects would result from the reduction of surface regions relative to the volume of core regions in larger proteins. In addition, although these two effects are dependent on each other, they have been studied separately. In this study, we investigated them by considering the surface‐to‐volume ratio (SVR), and observed the correlation between them. We found that the reduction of several hydrophilic residues is more strongly correlated with SVR than with protein size (the number of amino acids) and that SVR directly affects the amino acid composition. The difference as a descriptor between SVR and size is also supported by the observation that the secondary structural elements correlate completely differently with SVR and with size. Furthermore, for the four most hydrophilic residues, glutamine, arginine, glutamic acid, and lysine, balances between the decrease in composition and the increase in core burial were observed. We found that the burial of glutamine and arginine became accelerated at SVR = 0.3 Å−1 (approximately 132 residues) as the protein size increased, but that lysine has an upper limit of 0.9% for its occurrence in the core. The uniqueness of lysine was also elucidated by comparison with the burial environments of the four hydrophilic residues.
Atomic structure of the cross‐β spine of islet amyloid polypeptide (amylin)
Authors: Wiltzius Jed J.W. , Sievers Stuart A. , Sawaya Michael R. , Cascio Duilio , Popov Dmitriy , Riekel Christian , Eisenberg David
Published: June 2008

Human islet amyloid polypeptide (IAPP or amylin) is a 37‐residue hormone found as fibrillar deposits in pancreatic extracts of nearly all type II diabetics. Although the cellular toxicity of IAPP has been established, the structure of the fibrillar form found in these deposits is unknown. Here we have crystallized two segments from IAPP, which themselves form amyloid‐like fibrils. The atomic structures of these two segments, NNFGAIL and SSTNVG, were determined, and form the basis of a model for the most commonly observed, full‐length IAPP polymorph.
Experiences of Younger Siblings of Young Men in Prison
Authors: Meek Rosie
Published: June 2008

Whilst the detrimental effects of forced separation through incarceration have been explored in the context of parent–child relationships, little is known about the social and psychological impact of having a sibling in custody. The present research was carried out in order to develop a better understanding of the needs and experiences of children who have a sibling in prison and is based on an interpretative phenomenological analysis of the accounts of eight young people (age 9–17, mean = 13 years) with an older brother in custody. The interviews revealed a series of themes, including the emotional response to a sibling being taken into custody, a reluctance to disclose information to teachers and peers, and perceptions of own behaviour in the light of the sibling's experiences of the criminal justice system. Findings are discussed in relation to policy implications and recommendations for those working with young people, and suggestions are made for future research directions.
Significance of sentinel node biopsy in the management of squamous cell carcinoma arising from recessive dystrophic epidermolysis bullosa
Authors: ROKUNOHE Akiko , NAKANO Hajime , AIZU Takayuki , KANEKO Takahide , NAKAJIMA Koji , IKENAGA Satsuki , MATSUZAKI Yasushi , MURAI Takaya , TAMAI Katsuto , SAWAMURA Daisuke
Published: June 2008

The most life‐threatening complication developing in patients with recessive dystrophic epidermolysis bullosa (RDEB) is squamous cell carcinoma (SCC). To improve patient prognosis, early detection of regional lymph node metastasis is required. Herein, we report a patient diagnosed with non‐Hallopeau–Siemens RDEB who developed SCC on the left foot with inguinal lymph node swelling. Use of the sentinel node biopsy (SNB) technique favorably minimized defective damage to the inguinal region in this case. Genetic analysis identified one novel COL7A1 mutation, a maternal c.238G > C (p.A80P) and one previously reported mutation, a paternal c.3631C > T (p.Q1211X). A published work review demonstrated that no COL7A1 mutations specific for SCC development in RDEB have previously been identified. It remains unclear if SNB in combination with gene diagnosis is beneficial for the management of SCC in RDEB patients, however, because of the limited number of case reports. To address this issue, COL7A1 mutational analysis should be performed in as many cases of RDEB as possible.
Immunoglobulin A pemphigus associated with immunoglobulin A gammopathy and lung cancer
Authors: PETROPOULOU Haritini , POLITIS George , PANAGAKIS Pantelis , HATZIOLOU Eftihia , ARONI Kiriaki , KONTOCHRISTOPOULOS George
Published: June 2008

Immunoglobulin (Ig)A pemphigus is a rare disease marked by a vesiculopustular eruption characterized by intercellular IgA deposition in the epidermis. It has clinical and histopathological heterogeneity and encompasses two subgroups: subcorneal pustular dermatosis type and intraepidermal neutrophilic IgA dermatosis type. IgA pemphigus has been rarely associated with monoclonal IgA paraprotein, myeloma and B‐cell lymphoma in the past. We report the first case, to our knowledge, of a 47‐year‐old male patient with a subcorneal pustular dermatosis type of IgA pemphigus associated with IgA gammopathy and lung cancer.
Lymphocutaneous type of nocardiosis caused by Nocardia brasiliensis: A case report and review of primary cutaneous nocardiosis caused by N. brasiliensis reported in Japan
Authors: FUKUDA Hidetsugu , SAOTOME Atsuko , USAMI Nao , URUSHIBATA Osamu , MUKAI Hideki
Published: June 2008

Nocardiosis is a mixed suppurative and granulomatous inflammatory disease caused by infection with Nocardia organisms, a group of aerobic actinomycetes. We recently encountered a 25‐year‐old woman with posttraumatic nocardiosis of the lower extremities. The clinical symptoms noted during her first visit included erythematous swelling of the right knee accompanied by white maceration of the center of the knee and erosions, shallow ulcers and satellite pustules. In addition, multiple erythematous areas (up to the size of the tip of the thumb) were linearly distributed on the right thigh. These lesions were painful, and right inguinal lymphadenopathy was also noted. No lesion was found in internal organs such as the lungs. Histopathologically, signs of nonspecific granulomatous inflammation were observed, as well as several filamentous branching bacilli positive on Grocott stain. The organisms isolated from culture of pus were acid‐fast, Gram‐positive long rods. The isolated strain was finally identified as Nocardia brasiliensis. The patient was therefore diagnosed with lymphocutaneous type of primary cutaneous nocardiosis caused by N. brasiliensis. Drip infusion of flomoxef sodium was initially performed to treat her condition. Because of exacerbation of erythematous swelling of the right knee and an increase in number of pustules, treatment was switched to oral minocycline hydrochloride therapy. The disease healed 9 weeks after the start of oral minocycline hydrochloride therapy. Our patient was free of systemic immunosuppression and was neither under 10 nor over 65 years of age. She may therefore be considered a rare case of lymphocutaneous type of nocardiosis. We present this case and discuss reported cases of primary cutaneous nocardiosis due to N. brasiliensis in Japan.
Effects of sample attrition in a longitudinal study of the association between alcohol intake and all‐cause mortality
Authors: Thygesen Lau C. , Johansen Christoffer , Keiding Niels , Giovannucci Edward , Grønbæk Morten
Published: June 2008

Background and aims  Longitudinal studies show higher mortality among abstainers and heavy drinkers than among light and moderate alcohol consumers. The influence on this association of missing information on alcohol intake due to attrition (dropout) has not been examined previously. The aims of this study were to characterize participants who dropped out and to evaluate whether the missing information influenced the association between alcohol intake and all‐cause mortality.

Design and participants  Data on the 18 974 participants in the Copenhagen City Heart Study, with four measures of alcohol intake and other life‐style factors during 28 years of follow‐up, were linked with nation‐wide registers on socio‐economic covariates, mortality and disease incidence. Logistic regression was used to describe life‐style and socio‐economic determinants of attrition, and Poisson regression was used to evaluate how attrition affected the association between alcohol intake and mortality. The statistical methods used for dealing with missing values were complete case analysis, carry last observation forward, simple imputations, multiple imputation and weighting.

Findings  Abstinence and high alcohol intake, current smoking, physical inactivity and high body mass index increased the odds of dropping out, whereas being married, more years of education, skilled occupation, high income and large residential area decreased the odds. Attrition was associated with increased mortality and incidence rates of heart disease, lung and upper digestive tract cancers and alcoholic liver diseases. Increased mortality among abstainers and heavy drinkers was observed with all methods used for handling missing data on alcohol intake.

Conclusions  Attrition was non‐random, and the observed association between alcohol intake and all‐cause mortality did not differ by statistical method for handling missing data.
Comparison of cardiac output measurement using the CardioQPTM oesophageal Doppler with cardiac output measurement using thermodilution technique in children during heart catheterisation*
Authors:   Working Group on Non‐invasive Haemodynamic Monitoring in Paediatrics:, Knirsch W. , Kretschmar O. , Tomaske M. , Stutz K. , Nagdyman N. , Balmer C. , Schmitz A. , Berger F. , Bauersfeld U. , Weiss M.
Published: June 2008

The minimally invasive CardioQPTM oesophageal Doppler probe estimates cardiac output by measuring blood flow velocity in the descending aorta. Individual variables to enter are patient’s age, weight and height. We measured cardiac output simultaneously with CardioQP and pulmonary artery catheter thermodilution techniques during heart catheterisation in 40 paediatric patients with congenital heart defects. Median [range] age was 8.2 years [0.5–16.7 years], cardiac output values measured by thermodilution and CardioQP were 3.6 l.min−1 [1.2–7.1 l.min−1] and 3.0 l.min−1 [0.7–6.7 l.min−1], respectively. These values showed only moderate correlation (r = 0.809; p < 0.0001). Bias and precision were 0.66 l.min−1 and 1.79 l.min−1 (95% limits of agreement: −1.13 to +2.45 l.min−1). Based on our preliminary experience, cardiac output values measured by CardioQP in children do not reliably represent cardiac output values compared with the thermodilution technique. We suggest measurement of individual aortic diameter to improve performance of the CardioQP.
Thyroid storm in a polytrauma patient
Authors: Wilkinson J. N.
Published: June 2008

We report the case of a 38 year‐old woman who presented initially as the driver in a road traffic accident with a Glasgow Coma Score of 14, agitated, tachycardic, tachypnoeic and hypertensive. The combination of an abdominal CT scan and clinical findings led to the decision to perform an emergency laparotomy. Her persisting symptoms and laboratory results revealed her to be manifesting acute thyroid storm; TSH of < 0.10 IU.l−1, free T4 of 59.8 pmol.l−1 and free T3 of 20.20 pmol.l−1.
Clinical and molecular characterisation of a prospectively collected cohort of children and adolescents with polycythemia vera
Authors: Cario Holger , Schwarz Klaus , Herter Jan M. , Komrska Vladimir , McMullin Mary F. , Minkov Milen , Niemeyer Charlotte , Pospisilova Dagmar , Reinhard Harald , Debatin Klaus‐Michael , Pahl Heike L.
Published: June 2008

The clinical, haematological, molecular and treatment data of eight paediatric patients with polycythemia vera (PV) were collected prospectively. One patient developed PV after treatment for large‐cell anaplastic lymphoma. Budd‐Chiari syndrome was diagnosed in two patients, necessitating orthotopic liver transplantation in one and transjugular portosystemic shunting in the other. The remaining patients presented with non‐specific symptoms. Endogenous erythroid colonies were detected in all cases examined. The JAK2V617F mutation was found in six patients; two patients displayed JAK2 exon 12 mutations, including one novel mutation (JAK2H538‐K539delinsI). CD177 (PRV‐1) mRNA expression was increased in three of five patients tested.
Serum hepcidin levels are innately low in HFE‐related haemochromatosis but differ between C282Y‐homozygotes with elevated and normal ferritin levels
Authors: Van Dijk Boukje A. C. , Laarakkers Coby M. M. , Klaver Siem M. , Jacobs Esther M. G. , Van Tits Lambertus J. H. , Janssen Mirian C. H. , Swinkels Dorine W.
Published: June 2008

HFE C282Y‐homozygosity has been associated with low hepcidin expression, leading to increased ferritin levels. However, serum hepcidin protein levels have not been documented in humans. In the current study, we compared serum hepcidin levels of newly diagnosed HFE C282Y‐homozygotes with (N = 15) and without (N = 7) elevated serum ferritin levels to levels of 40 controls (20 heterozygotes and 20 wild types). In addition, hepcidin levels of four C282Y homozygotes were investigated during the course of all phlebotomy treatment phases. Serum hepcidin levels were lower in HFE C282Y‐homozygotes (median; 25th–75th percentile: 1·88; 0·78–2·77 nmol/l) compared to controls (2·74; 1·45–5·39). Hepcidin/ferritin ratios were also lower in homozygotes. Homozygotes with an elevated serum ferritin had a higher serum hepcidin but a lower hepcidin/ferritin ratio than those with normal ferritin (2·28; 1·62–3·23 nmol/l hepcidin vs. 0·80; 0·60–1·29 and 3·63; 2·72–7·59 pmol hepcidin/μg ferritin vs. 13·2; 5·15–14·2). Serum hepcidin decreased during the depletion phase of phlebotomy and remained low during maintenance. This study showed that serum hepcidin is innately low in HFE‐related haemochromatosis. Elevated ferritin levels were associated with increased hepcidin levels while erythropoiesis lead to lower hepcidin levels. During depletion, therefore, hepcidin levels are decreased, which may exacerbate intestinal iron absorption.
Array comparative genome hybridization analysis of acute lymphoblastic leukaemia and acute megakaryoblastic leukaemia in patients with Down syndrome
Authors: Lo Ken C. , Chalker Jane , Strehl Sabine , Neat Michael , Smith Owen , Dastugue Nicole , Kearney Lyndal , Izraeli Shai , Kempski Helena , Cowell John K.
Published: June 2008

Twenty‐five cases of B‐cell precursor acute lymphoblastic leukaemia (ALL) from Down syndrome (DS) patients were analyzed using array comparative genomic hybridization (aCGH) and compared with two other subgroups of non‐DS patients with ALL; five cases with high‐hyperdiploidy (HH) and nine cases with ETV6‐RUNX1 positive clones. Seven cases of DS‐acute megakaryoblastic leukaemia (AMKL) were also included, DS‐ALL cases showed relatively stable karyotypes with cryptic losses and gains that most frequently involved chromosomes X, 1, 2, 9, 11, 16, and 17. The most consistent change involved a deletion in 2p, spanning region Chr2:88273220‐91084234, which in some cases appeared to be homozygous. ALL from non‐DS patients showed a similar overall karyotypic stability, although gains of chromosome 21 were infrequent in the ETV6‐RUNX1 positive cases. The most consistent change in this group involved a 12p deletion, where Chr12:10383878‐16017619 defined the common region of overlap. All HH‐ALL karyotypes showed variable gains of chromosome 21. This overall analysis supports the suggestion that, although constitutional trisomy 21 predisposes to ALL/AMKL, the cytogenetic changes associated with DS‐ALL in particular, are most similar to those found in non‐DS ETV6‐RUNX1 positive ALL. The HH‐ALL group, however, undergoes distinct karyotypic evolution not dependent on chromosome translocation/deletion events.
The rarity concept and the commonness of rarity in freshwater zooplankton
Authors: HESSEN DAG O. , WALSENG BJØRN
Published: June 2008

1. Regional distribution, frequency of occurrence and relative abundance were scored in 2467 Norwegian lakes for all the recorded 130 species of crustacean zooplankton. The majority of species were rare in the sense that 65% of species were recorded in fewer than 10% of localities. Only six species were recorded in more than 50% of localities, and the median number of species in a given locality was 14 (i.e. 10% of the total species pool).

2. Abundances of all species were scored according to the fraction of lakes in which they were recorded, their geographical range of distribution, and their numerical abundance. Typically the most rare species were rare by all three criteria, and vice versa for the common species, pointing to rarity as an inherent property of some species. For some species this rarity reflects being on the edge of their distributional range, while for others rarity seems to be a consequence of their life cycle strategies.

3. Some of the truly rare species have high dispersal rates and high colonization abilities, but are rapidly replaced by other species. Others are confined to specific habitats, often highly eutrophic, pointing to highly specialized niche adaptations.

4. A major cause for the few truly common species seems to be the limited number of species that are able to coexist within a given locality, reflecting ‘the ghost of competition past’ and predation pressure.

5. While species composition and species richness may reflect colonization abilities and stochastic events, the presence or absence of species is not only a random lottery but also a consequence of species‐specific attributes.
Novel role of nectin: implication in the co‐localization of JAM‐A and claudin‐1 at the same cell–cell adhesion membrane domain
Authors: Kuramitsu Kaori , Ikeda Wataru , Inoue Naoya , Tamaru Yoshiyuki , Takai Yoshimi
Published: June 2008

Tight junctions (TJs) are formed at the apical side of adherens junctions (AJs) in epithelial cells. Major cell adhesion molecules (CAMs) at TJs are JAM and claudin, whereas major CAMs at AJs are nectin and cadherin. We previously showed that nectin initially forms cell–cell adhesion and then recruits cadherin to the nectin‐based cell–cell adhesion sites to form AJs, followed by the recruitment of JAM and claudin to the apical side of AJs to form TJs. We investigated the roles of nectin in the formation of TJs by expressing various combinations of CAMs in L fibroblasts with no TJs or AJs. Co‐expression of one of the AJ CAMs and one of the TJ CAMs formed two separate cell–cell adhesion membrane domains (CAMDs). Co‐expression of nectin‐3 and E‐cadherin formed the same CAMD, but co‐expression of JAM‐A and claudin‐1 did not form the same CAMD. Co‐expression of JAM‐A and claudin‐1 with nectin‐3, but not E‐cadherin, made them form the same CAMD, which was separated from the nectin‐based CAMD. Nectin‐3 required afadin, a nectin‐ and F‐actin‐binding protein, for this ability. In conclusion, nectin plays a novel role in the co‐localization of JAM and claudin at the same CAMD.
Crustal‐scale prestack depth imaging of the 1994 and 1999 LARSE surveys
Authors: Thornton Michael , Zhou Hua‐wei
Published: June 2008

While seismic imaging for crustal and mantle structures has traditionally relied on surface wave and refraction data, the use of reflection data for crustal‐scale targets has been largely limited to the common midpoint (CMP) stack techniques. The rapid increase in the number of seismograph array deployments in recent years in crustal and mantle seismology has reached a level such that a re‐examination of the imaging techniques is becoming necessary. In this paper we show the advantage of prestack depth imaging for crustal reflection studies, based on data from two reflection surveys of the Los Angeles Regional Seismic Experiment (LARSE) to map faults and crustal‐scale structures. Our analysis indicates that the quality of the previous images of these surveys is limited by the CMP stack technique. For comparison, we present here depth images of the same LARSE data using wave equation prestack depth imaging and a tomographic velocity model based on first arrivals of the LARSE surveys and local earthquakes. Our new images are considerably improved over previous images in terms of resolution and reflector continuity. The new images show reflectors throughout the crust and suggest truncations in the Moho associated with the San Andreas Fault. A series of bright reflector segments, which are associated with the San Gabriel and San Andreas faults have been identified and might represent reflections from the fault zones. Our results suggest that the presence of high noise level, strong lateral velocity heterogeneity and wide angle geometry argue for, rather than against, the use of prestack depth imaging over the simple CMP stack techniques. As demonstrated in this study, it is now viable to conduct prestack depth imaging of crustal reflection data using a velocity model based on earthquake first arrivals thanks to the dense acquisition deployment.
Modeling the effects of fire and climate change on carbon and nitrogen storage in lodgepole pine (Pinus contorta) stands
Authors: SMITHWICK E. A. H. , RYAN M. G. , KASHIAN D. M. , ROMME W. H. , TINKER D. B. , TURNER M. G.
Published: June 2008

The interaction between disturbance and climate change and resultant effects on ecosystem carbon (C) and nitrogen (N) fluxes are poorly understood. Here, we model (using CENTURY version 4.5) how climate change may affect C and N fluxes among mature and regenerating lodgepole pine (Pinus contortavar.latifoliaEngelm. ex S. Wats.) stands that vary in postfire tree density following stand‐replacing fire. Both young (postfire) and mature stands had elevated forest production and net N mineralization under future climate scenarios relative to current climate. Forest production increased 25% [Hadley (HAD)] to 36% [Canadian Climate Center (CCC)], compared with 2% under current climate, among stands that varied in stand age and postfire density. Net N mineralization increased under both climate scenarios, e.g., +19% to 37% (HAD) and +11% to 23% (CCC), with greatest increases for young stands with sparse tree regeneration. By 2100, total ecosystem carbon (live+dead+soils) in mature stands was higher than prefire levels, e.g., +16% to 19% (HAD) and +24% to 28% (CCC). For stands regenerating following fire in 1988, total C storage was 0–9% higher under the CCC climate model, but 5–6% lower under the HAD model and 20–37% lower under the Control. These patterns, which reflect variation in stand age, postfire tree density, and climate model, suggest that although there were strong positive responses of lodgepole pine productivity to future changes in climate, C flux over the next century will reflect complex relationships between climate, age structure, and disturbance‐recovery patterns of the landscape.
Impacts of climate change on fire activity and fire management in the circumboreal forest
Authors: FLANNIGAN MIKE , STOCKS BRIAN , TURETSKY MERRITT , WOTTON MIKE
Published: June 2008

Forest fires are a significant and natural element of the circumboreal forest. Fire activity is strongly linked to weather, and increased fire activity due to climate change is anticipated or arguably has already occurred. Recent studies suggest a doubling of area burned along with a 50% increase in fire occurrence in parts of the circumboreal by the end of this century. Fire management agencies' ability to cope with these increases in fire activity is limited, as these organizations operate with a narrow margin between success and failure; a disproportionate number of fires may escape initial attack under a warmer climate, resulting in an increase in area burned that will be much greater than the corresponding increase in fire weather severity. There may be only a decade or two before increased fire activity means fire management agencies cannot maintain their current levels of effectiveness.
Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest
Authors: WALDROP MARK P. , HARDEN JENNIFER W.
Published: June 2008

Boreal forests contain significant quantities of soil carbon that may be oxidized to CO2 given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short‐term effects of wildfire to the long‐term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both 13C lignin decomposition and microbial respiration in incubation studies. Taken together, these results indicate that reductions in fungal biomass in postfire soils and lower soil moisture in nonpermafrost soils reduced the potential of soil heterotrophs to decompose soil carbon. Although in the field increased rates of microbial respiration can be observed in postfire soils due to warmer soil conditions, reductions in fungal biomass and activity may limit rates of decomposition.
Meeting US biofuel goals with less land: the potential of Miscanthus
Authors: HEATON EMILY A. , DOHLEMAN FRANK G. , LONG STEPHEN P.
Published: June 2008

Biofuels from crops are emerging as a Jekyll & Hyde – promoted by some as a means to offset fossil fuel emissions, denigrated by others as lacking sustainability and taking land from food crops. It is frequently asserted that plants convert only 0.1% of solar energy into biomass, therefore requiring unacceptable amounts of land for production of fuel feedstocks. The C4 perennial grass Miscanthus×giganteus has proved a promising biomass crop in Europe, while switchgrass (Panicum virgatum) has been tested at several locations in N. America. Here, replicated side‐by‐side trials of these two crops were established for the first time along a latitudinal gradient in Illinois. Over 3 years of trials, Miscanthus×giganteus achieved average annual conversion efficiencies into harvestable biomass of 1.0% (30 t ha−1) and a maximum of 2.0% (61 t ha−1), with minimal agricultural inputs. The regionally adapted switchgrass variety Cave‐in‐Rock achieved somewhat lower yields, averaging 10 t ha−1. Given that there has been little attempt to improve the agronomy and genetics of these grasses compared with the major grain crops, these efficiencies are the minimum of what may be achieved. At this 1.0% efficiency, 12 million hectares, or 9.3% of current US cropland, would be sufficient to provide 133 × 109 L of ethanol, enough to offset one‐fifth of the current US gasoline use. In contrast, maize grain from the same area of land would only provide 49 × 109 L, while requiring much higher nitrogen and fossil energy inputs in its cultivation.
CH4 emission with differences in atmospheric CO2 enrichment and rice cultivars in a Japanese paddy soil
Authors: LOU YUNSHENG , INUBUSHI KAZUYUKI , MIZUNO TAKAYUKI , HASEGAWA TOSHIHIRO , LIN YANHUNG , SAKAI HIDEMITSU , CHENG WEIGUO , KOBAYASHI KAZUHIKO
Published: June 2008

A pot experiment was conducted to investigate CH4 emissions from a sandy paddy soil as influenced by rice cultivars and atmospheric CO2 elevation. The experiment with two CO2 levels, 370 μL L−1 (ambient) and 570 μL L−1 (elevated), was performed in a climatron, located at the National Institute for Agro‐Environmental Sciences, Tsukuba, Japan. Four rice cultivars were tested in this experiment, including IR65598, IR72, Dular and Koshihikari. Tiller number, root length and grain yield were clearly larger under elevated CO2 than under ambient CO2. IR72 and Dular showed significantly higher tiller number, root length and grain yield than Koshihikari and IR65598. Average daily CH4 fluxes under elevated CO2 were significantly larger by 10.9–23.8% than those under ambient CO2, and varied with the cultivars in the sequence Dular ≧ IR72>IR65598 ≧ Koshihikari. Dissolved organic C (DOC) content in the soil was obviously higher under elevated CO2 than under ambient CO2 and differed among the cultivars, in the sequence IR72>Dular>Koshihikari>IR65598. The differences in average daily CH4 fluxes between CO2 levels and among the cultivars were related to different root exudation as DOC content, root length and tiller number. This study indicated that Koshihikari should be a potential cultivar for mitigating CH4 emission and simultaneously keeping stable grain yield, because this cultivar emitted lowest CH4 emission and produced medium grain yield.