bluuebunny/crossref_metadata_2025 huggingface dataset:
Origins of 210Pb‐226Ra disequilibria in basalts: New insights from the 1978 Asal Rift eruption
Authors: Turner Simon , Reagan Mark , Vigier Nathalie , Bourdon Bernard
Published: June 2012

There has been much debate as to whether 210Pb‐226Ra disequilibria in young volcanic rocks result from partial melting, cumulate interaction or magma degassing. Here we present new data from basalts erupted in 1978 from Ardoukoba volcano in the Asal Rift. The (210Pb/226Ra)t ratios are very low (0.2 to 0.6) and appear to correlate negatively with (226Ra/230Th). Invariant (230Th/238U) and (231Pa/235U) ratios require similar melting rates, porosities, and extents for all parental magmas. Thus, the range in (226Ra/230Th), which is negatively correlated with Th concentration, reflects fractional crystallization over millennia after the magmas were emplaced into the crust. This precludes the 210Pb deficits from resulting from partial melting. Instead, the 210Pb deficits must have formed subsequent to magma differentiation and are interpreted to reflect several decades of magma degassing. Many young basalts erupted in a variety of tectonic settings are similarly depleted in 210Pb with respect to 226Ra, suggesting that they continuously degas over a period of a few to several decades, perhaps reflecting the time required to rise to the surface from deeper reservoirs. In some of these basalts, gas accumulation leads to the shallowest, most evolved, and earliest erupting magmas having the highest (210Pb/226Ra) ratios and sometimes 210Pb excesses.
Euler potentials for two current sheets along ambient uniform magnetic field
Authors: Romashets E. P. , Vandas M.
Published: June 2012

Euler potentials of two current sheets of finite width parallel or antiparallel to each other and aligned with a uniform ambient magnetic field are constructed analytically. It is shown how analytic treatment can be simplified using complex number analysis. Our approach generalizes results obtained earlier for a system of two line currents (wires). In the present solution the latter system represents a limiting case, and differences between results from configurations with sheets/wires are discussed. The solution is applied for study of bouncing motion of particles trapped between mirror points of this field structure. The result can be applied to Birkeland currents and to laboratory plasma experiments.
Pore structure model for elastic wave velocities in fluid‐saturated sandstones
Authors: David E. C. , Zimmerman R. W.
Published: June 2012

During hydrostatic compression conducted within the elastic regime, P and S‐wave velocities measured on porous rock samples generally increase with pressure and reach asymptotic values at high pressures. The increase in velocities can be attributed to the gradual closure of compliant cracks, in which case the high‐pressure velocities reflect only the influence of the stiff, non‐closable pores. A procedure is presented to extract the complete pore aspect ratio distribution from the pressure dependence of dry velocities, assuming that the rock contains a distribution of cracks with different aspect ratios, and one family of stiff pores having an aspect ratio that generally will lie between 0.01 and 1. The model is able to invert successfully many sets of experimental data on dry sandstones taken from the literature. The pore aspect ratio distribution inverted from dry data can then be used to predict saturated velocities as functions of pressure, by introducing fluid into the pores. For ultrasonic velocity measurements that are performed at high frequencies in the laboratory (∼ MHz), the predictions of saturated velocities using effective medium theories match well the experimental data for a good number of sandstone data sets. The saturated velocities thus predicted are always more accurate than those predicted from the Gassmann relations, which underpredict the saturated velocities by a large amount. These results are only weakly dependent on the choice of the effective medium theory.
Measuring aerobic respiration in stream ecosystems using the resazurin‐resorufin system
Authors: González‐Pinzón Ricardo , Haggerty Roy , Myrold David D.
Published: June 2012

The use of smart tracers to study hydrologic systems is becoming more widespread. Smart tracers are compounds that irreversibly react in the presence of a process or condition under investigation. Resazurin (Raz) is a smart tracer that undergoes an irreversible reduction to resorufin (Rru) in the presence of cellular metabolic activity. We quantified the relationship between the transformation of Raz and aerobic bacterial respiration in pure culture experiments using two obligate aerobes and two facultative anaerobes, and in colonized surface and shallow (<10 cm) hyporheic sediments using reach‐scale experiments. We found that the transformation of Raz to Rru was nearly perfectly (minr2 = 0.986), positively correlated with aerobic microbial respiration in all experiments. These results suggest that Raz can be used as a surrogate to measure respiration in situ and in vivoat different spatial scales, thus providing an alternative to investigate mechanistic controls of solute transport and stream metabolism on nutrient processing. Lastly, a comparison of respiration and mass‐transfer rates in streams suggests that field‐scale respiration is controlled by the slower of respiration and mass transfer, highlighting the need to understand both biogeochemistry and physics in stream ecosystems.
Interplay of oxygen-evolution kinetics and photovoltaic power curves on the construction of artificial leaves
Authors: Surendranath Yogesh , Bediako D. Kwabena , Nocera Daniel G.
Published: June 2012

An artificial leaf can perform direct solar-to-fuels conversion. The construction of an efficient artificial leaf or other photovoltaic (PV)-photoelectrochemical device requires that the power curve of the PV material and load curve of water splitting, composed of the catalyst Tafel behavior and cell resistances, be well-matched near the thermodynamic potential for water splitting. For such a condition, we show here that the current density-voltage characteristic of the catalyst is a key determinant of the solar-to-fuels efficiency (SFE). Oxidic Co and Ni borate (Co-B
i
and Ni-B
i
) thin films electrodeposited from solution yield oxygen-evolving catalysts with Tafel slopes of 52 mV/decade and 30 mV/decade, respectively. The consequence of the disparate Tafel behavior on the SFE is modeled using the idealized behavior of a triple-junction Si PV cell. For PV cells exhibiting similar solar power-conversion efficiencies, those displaying low open circuit voltages are better matched to catalysts with low Tafel slopes and high exchange current densities. In contrast, PV cells possessing high open circuit voltages are largely insensitive to the catalyst’s current density-voltage characteristics but sacrifice overall SFE because of less efficient utilization of the solar spectrum. The analysis presented herein highlights the importance of matching the electrochemical load of water-splitting to the onset of maximum current of the PV component, drawing a clear link between the kinetic profile of the water-splitting catalyst and the SFE efficiency of devices such as the artificial leaf.
Neurokinin Bs and neurokinin B receptors in zebrafish-potential role in controlling fish reproduction
Authors: Biran Jakob , Palevitch Ori , Ben-Dor Shifra , Levavi-Sivan Berta
Published: June 2012

The endocrine regulation of vertebrate reproduction is achieved by the coordinated actions of several peptide neurohormones, tachykinin among them. To study the evolutionary conservation and physiological functions of neurokinin B (NKB), we identified tachykinin (tac) andtac receptor(NKBR) genes from many fish species, and cloned two cDNA forms from zebrafish. Phylogenetic analysis showed that piscine Tac3s and mammalian neurokinin genes arise from one lineage. High identity was found among different fish species in the region encoding the NKB; all shared the common C-terminal sequence. Although the piscine Tac3 gene encodes for two putative tachykinin peptides, the mammalian ortholog encodes for only one. The second fish putative peptide, referred to as neurokinin F (NKF), is unique and found to be conserved among the fish species when tested in silico.tac3awas expressed asymmetrically in the habenula of embryos, whereas in adults zebrafishtac3a-expressing neurons were localized in specific brain nuclei that are known to be involved in reproduction. Zebrafishtac3amRNA levels gradually increased during the first few weeks of life and peaked at pubescence. Estrogen treatment of prepubertal fish elicited increases intac3a,kiss1,kiss2, andkiss1raexpression. The synthetic zebrafish peptides (NKBa, NKBb, and NKF) activated Tac3 receptors via both PKC/Ca2+and PKA/cAMP signal-transduction pathways in vitro. Moreover, a single intraperitoneal injection of NKBa and NKF significantly increased leuteinizing hormone levels in mature female zebrafish. These results suggest that the NKB/NKBR system may participate in neuroendocrine control of fish reproduction.
Warming accelerates decomposition of decades-old carbon in forest soils
Authors: Hopkins Francesca M. , Torn Margaret S. , Trumbore Susan E.
Published: June 2012

Global climate carbon-cycle models predict acceleration of soil organic carbon losses to the atmosphere with warming, but the size of this feedback is poorly known. The temperature sensitivity of soil carbon decomposition is commonly determined by measuring changes in the rate of carbon dioxide (CO
2
) production under controlled laboratory conditions. We added measurements of carbon isotopes in respired CO
2
to constrain the age of carbon substrates contributing to the temperature response of decomposition for surface soils from two temperate forest sites with very different overall rates of carbon cycling. Roughly one-third of the carbon respired at any temperature was fixed from the atmosphere more than 10 y ago, and the mean age of respired carbon reflected a mixture of substrates of varying ages. Consistent with global ecosystem model predictions, the temperature sensitivity of the carbon fixed more than a decade ago was the same as the temperature sensitivity for carbon fixed less than 10 y ago. However, we also observed an overall increase in the mean age of carbon respired at higher temperatures, even correcting for potential substrate limitation effects. The combination of several age constraints from carbon isotopes showed that warming had a similar effect on respiration of decades-old and younger (<10 y) carbon but a greater effect on decomposition of substrates of intermediate (between 7 and 13 y) age. Our results highlight the vulnerability of soil carbon to warming that is years-to-decades old, which makes up a large fraction of total soil carbon in forest soils globally.
Elemental nitrogen partitioning in dense interstellar clouds
Authors: Daranlot Julien , Hincelin Ugo , Bergeat Astrid , Costes Michel , Loison Jean-Christophe , Wakelam Valentine , Hickson Kevin M.
Published: June 2012

Many chemical models of dense interstellar clouds predict that the majority of gas-phase elemental nitrogen should be present as N
2
, with an abundance approximately five orders of magnitude less than that of hydrogen. As a homonuclear diatomic molecule, N
2
is difficult to detect spectroscopically through infrared or millimeter-wavelength transitions. Therefore, its abundance is often inferred indirectly through its reaction product N
2
H
+
. Two main formation mechanisms, each involving two radical-radical reactions, are the source of N
2
in such environments. Here we report measurements of the low temperature rate constants for one of these processes, the N + CN reaction, down to 56 K. The measured rate constants for this reaction, and those recently determined for two other reactions implicated in N
2
formation, are tested using a gas-grain model employing a critically evaluated chemical network. We show that the amount of interstellar nitrogen present as N
2
depends on the competition between its gas-phase formation and the depletion of atomic nitrogen onto grains. As the reactions controlling N
2
formation are inefficient, we argue that N
2
does not represent the main reservoir species for interstellar nitrogen. Instead, elevated abundances of more labile forms of nitrogen such as NH
3
should be present on interstellar ices, promoting the eventual formation of nitrogen-bearing organic molecules.
Regulatory T cells use programmed death 1 ligands to directly suppress autoreactive B cells in vivo
Authors: Gotot Janine , Gottschalk Catherine , Leopold Sonny , Knolle Percy A. , Yagita Hideo , Kurts Christian , Ludwig-Portugall Isis
Published: June 2012

The mechanisms by which regulatory T cells (Tregs) suppress autoantibody production are unclear. Here we have addressed this question using transgenic mice expressing model antigens in the kidney. We report that Tregswere essential and sufficient to suppress autoreactive B cells in an antigen-specific manner and to prevent them from producing autoantibodies. Most of this suppression was mediated through the inhibitory cell-surface-molecule programmed death-1 (PD-1). Suppression required PD-1 expression on autoreactive B cells and expression of the two PD-1 ligands on Tregs. PD-1 ligation inhibited activation of autoreactive B cells, suppressed their proliferation, and induced their apoptosis. Intermediate PD-1+cells, such as T helper cells, were dispensable for suppression. These findings demonstrate in vivo that Tregsuse PD-1 ligands to directly suppress autoreactive B cells, and they identify a previously undescribed peripheral B-cell tolerance mechanism against tissue autoantigens.
Enhanced cellulose degradation by targeted integration of a cohesin-fused β-glucosidase into the
Clostridium thermocellum
cellulosome
Authors: Gefen Gilad , Anbar Michael , Morag Ely , Lamed Raphael , Bayer Edward A.
Published: June 2012

The conversion of recalcitrant plant-derived cellulosic biomass into biofuels is dependent on highly efficient cellulase systems that produce near-quantitative levels of soluble saccharides. Similar to other fungal and bacterial cellulase systems, the multienzyme cellulosome system of the anaerobic, cellulolytic bacterium
Clostridium thermocellum
is strongly inhibited by the major end product cellobiose. Cellobiose-induced inhibition can be relieved via its cleavage to noninhibitory glucose by the addition of exogenous noncellulosomal enzyme β-glucosidase; however, because the cellulosome is adsorbed to the insoluble substrate only a fraction of β-glucosidase would be available to the cellulosome. Towards this end, we designed a chimeric cohesin-fused β-glucosidase (BglA-CohII) that binds directly to the cellulosome through an unoccupied dockerin module of its major scaffoldin subunit. The β-glucosidase activity is thus focused at the immediate site of cellobiose production by the cellulosomal enzymes. BglA-CohII was shown to retain cellobiase activity and was readily incorporated into the native cellulosome complex. Surprisingly, it was found that the native
C. thermocellum
cellulosome exists as a homooligomer and the high-affinity interaction of BglA-CohII with the scaffoldin moiety appears to dissociate the oligomeric state of the cellulosome. Complexation of the cellulosome and BglA-CohII resulted in higher overall degradation of microcrystalline cellulose and pretreated switchgrass compared to the native cellulosome alone or in combination with wild-type BglA in solution. These results demonstrate the effect of enzyme targeting and its potential for enhanced degradation of cellulosic biomass.
Leaf fossil record suggests limited influence of atmospheric CO
2
on terrestrial productivity prior to angiosperm evolution
Authors: Boyce C. Kevin , Zwieniecki Maciej A.
Published: June 2012

Declining CO
2
over the Cretaceous has been suggested as an evolutionary driver of the high leaf vein densities (7–28 mm mm
−2
) that are unique to the angiosperms throughout all of Earth history. Photosynthetic modeling indicated the link between high vein density and productivity documented in the modern low-CO
2
regime would be lost as CO
2
concentrations increased but also implied that plants with very low vein densities (less than 3 mm mm
−2
) should experience substantial disadvantages with high CO
2
. Thus, the hypothesized relationship between CO
2
and plant evolution can be tested through analysis of the concurrent histories of alternative lineages, because an extrinsic driver like atmospheric CO
2
should affect all plants and not just the flowering plants. No such relationship is seen. Regardless of CO
2
concentrations, low vein densities are equally common among nonangiosperms throughout history and common enough to include forest canopies and not just obligate shade species that will always be of limited productivity. Modeling results can be reconciled with the fossil record if maximum assimilation rates of nonflowering plants are capped well below those of flowering plants, capturing biochemical and physiological differences that would be consistent with extant plants but previously unrecognized in the fossil record. Although previous photosynthetic modeling suggested that productivity would double or triple with each Phanerozoic transition from low to high CO
2
, productivity changes are likely to have been limited before a substantial increase accompanying the evolution of flowering plants.
Geographic axes and the persistence of cultural diversity
Authors: Laitin David D. , Moortgat Joachim , Robinson Amanda Lea
Published: June 2012

Jared Diamond’sGuns, Germs, and Steel[Diamond J, (1997)Guns, Germs, and Steel(WW Norton, NY)] has provided a scientific foundation for answering basic questions, such as why Eurasians colonized the global South and not the other way around, and why there is so much variance in economic development across the globe. Diamond’s explanatory variables are: (i) the susceptibility of local wild plants to be developed for self-sufficient agriculture; (ii) the domesticability of large wild animals for food, transport, and agricultural production; and (iii) the relative lengths of the axes of continents with implications for the spread of human populations and technologies. This third “continental axis” thesis is the most difficult of Diamond’s several explanatory factors to test, given that the number of continents are too few for statistical analysis. This article provides a test of one observable implication of this thesis, namely that linguistic diversity should be more persistent to the degree that a geographic area is oriented more north-south than east-west. Using both modern states and artificial geographic entities as the units of analysis, the results provide significant confirmation of the relationship between geographic orientation and cultural homogenization. Beyond providing empirical support for one observable implication of the continental axis theory, these results have important implications for understanding the roots of cultural diversity, which is an important determinant of economic growth, public goods provision, local violence, and social trust.
Quelques Considérations sur la Traduction Médicale et Pharmaceutique
Authors: Sliosberg Anatole
Published: June 2012

Summary
The technical translator needs to possess three fundamental qualities: a complete mastery of his own language; a cultural background enabling him to translate clearly what are often poorly drafted original texts; a thorough knowledge of the language translated, with its variations and idiomatic expressions. These often vary from one country to another, as well as from one historical period to another. Many terms of English origin are often mistranslated into other languages, and there are also certain peculiarities of language employed by groups of individuals, for example, drug-addicts' slang.
Technical knowledge is obviously essential and
in medicine and pharmacy involves a wide range of science. Designations can vary from one language to another, even in anatomical descriptions and in certain clinical syndromes. Difficulty may arise in the case of words derived from the same root, but not having the same meaning, depending on the language used. This is illustrated by examples in the tables of the text. The designation of diseases and symptoms by proper names also constitutes a difficulty for the translator, as such terms have different meanings according to the language concerned.
Abbreviations are ever increasing in number and often confusing as they are not identical in the different languages; furthermore, each may have several meanings. Authors should use a clear style, devoid of vernacular terms and popular words, as well as of eponyms and arbitrary abbreviations.
Kurzf
assung
Der technische Übersetzer mußüber drei wesent-liche Fähigkeiten verfügen: eine vollkommene Beherrschung seiner Muttersprache; eine Allge-meinbildung, die ihm erlaubt, die oft schlecht geschriebenen Texte in eine klare Form zu über-tragen; gründliche Kenntnis der übersetzten Sprache, ihrer Variationen und idiomatischen Be-griffe, die sich oft von einem Land zum anderen und von Epoche zu Epoche andern. Viele Aus-drücke englischen Ursprungs sind oft schlecht in andere Sprachen übersetzt und auch charakteri-stische Spracheigenheiten einiger Personengruppen, wie z. B. die Sprache der Süchtigen.
Fall der Medizin und der Pharmazie umfassen sie eine ganze Reihe verschiedener Wissenschafts-bereiche. Die Bezeichnungen andern sich von ei-ner Sprache zur anderen, selbst für die Anatomie und für gewisse klinische Syndrome. Hinzu kommen Ausdrücke, die zwar denselben Stamm, in verschiedenen Sprachen jedoch verschiedene Be-deutungen besitzen; der Text enthalt Tabellen mit Beispielen. Eine weitere Schwierigkeit für den Übersetzer bildet die Bezeichnung von Krankheiten und Symptomen mit Eigennamen; auch hier sind die Ausdrücke in den verschiedenen Idiomen nicht dieselben.
Als letztes sind die immer haufiger auftretenden Abkürzungen zu erwahnen, die oft verwirren, da sie in den verschiedenen Sprachen nicht iden-tisch sind und da autëerdem jede einzelne Ab-kürzung mehrere Bedeutungen haben kann. Autoren sollen klar schreiben, ohne mundartliche Sprachbegriffe, ohne triviale Worte, ohne Epo-nyme oder willkürlich geformte Abkürzungen zu verwenden.
The Kahn-Priddy Theorem and the homotopy of the three-sphere
Authors: Beben Piotr , Theriault Stephen
Published: June 2012

Let

p
p

be an odd prime. The least nontrivial

p
p

-torsion homotopy group of

S

3

S^{3}

occurs in dimension

2
p

2p

and is of order

p
p

. This induces a map

f
:

P

2
p
+
1

(
p
)
→

S

3

f\colon P^{2p+1}(p)\rightarrow S^{3}

, where

P

2
p
+
1

(
p
)

P^{2p+1}(p)

is a mod-

p
p

Moore space. An important conjecture related to the Kahn-Priddy Theorem is that the double loops on the three-connected cover of

f
f

has a right homotopy inverse. We prove a weaker but still useful property: if

X
X

is the cofiber of

f
f

, then the double loop on the three-connected cover of the inclusion

S

3

→
X

S^{3}\rightarrow X

is null homotopic.
Health economic assessment of ferric carboxymaltose in patients with iron deficiency and chronic heart failure based on the FAIR‐HF trial: an analysis for the UK
Authors: Gutzwiller Florian S. , Schwenkglenks Matthias , Blank Patricia R. , Braunhofer Peter G. , Mori Claudio , Szucs Thomas D. , Ponikowski Piotr , Anker Stefan D.
Published: June 2012

Aims

The purpose of this study was to evaluate the cost‐effectiveness of iron repletion using intravenous (i.v.) ferric carboxymaltose (FCM) in chronic heart failure (CHF) patients with iron deficiency with or without anaemia. Cost‐effectiveness was studied from the perspective of the National Health Service in the UK.

Methods and results

A model‐based cost‐effectiveness analysis was used to compare iron repletion with FCM with no iron treatment. Using data from the FAIR‐HF trial and publicly available sources and publications, per patient costs and clinical effectiveness of FCM were estimated compared with placebo. Cost assessment was based on study drug and administration costs, cost of CHF treatment, and hospital length of stay. The incremental cost‐effectiveness ratio (ICER) of FCM use was expressed as cost per quality‐adjusted life year (QALY) gained, and sensitivity analyses were performed on the base case. The time horizon of the analysis was 24 weeks. Mean QALYs were higher in the FCM arm (difference 0.037 QALYs; bootstrap‐based 95% confidence interval 0.017–0.060). The ICER of FCM compared with placebo was €4414 per QALY gained for the FAIR‐HF dosing regimen. Sensitivity analyses confirmed the base case result to be robust.

Conclusion

From the UK payers’ perspective, managing iron deficiency in CHF patients using i.v. FCM was cost‐effective in this analysis. The base case ICER was clearly below the threshold of €22 200–€33 300/QALY gained (£20 000–£30 000) typically used by the UK National Institute for Health and Clinical Excellence and proved to be robust in sensitivity analysis. Improved symptoms and better quality of life contributed to this result.
Risk adjustment of heroin treatment outcomes for comparative performance assessment in England
Authors: Marsden John , Eastwood Brian , Jones Hayley , Bradbury Colin , Hickman Matthew , Knight Jonathan , Randhawa Kulvir , White Martin ,   the National Drug Treatment Monitoring System Outcomes Study Group
Published: June 2012

Aims

Variability in effectiveness of treatment for substance abuse disorder (SUD) is an important and understudied issue. This study aimed to quantify the extent of outcome variability in the English SUD treatment system after adjusting for potential confounding variables.

Design

Prospective cohort study using data from the English national drug treatment outcome monitoring database.

Setting

All 149 administrative areas delivering publicly funded SUD services in the National Health Service and non‐governmental sector.

Participants

New adult admissions between January 2008 and October 2010 with illicit heroin‐related problems in all administrative areas, with an in‐treatment review conducted between 5 and 26 weeks (mean = 129.5 days; SD = 40.0) up to 30 April 2011 (n = 65 223; 75.6% of eligible clients). Individuals were divided randomly to form model developmental and internal validation samples. These were contrasted with an independent (external) sample of the same population admitted to treatment between November 2010 and April 2011 and followed to 31 October 2011 (n = 13 797; 81.4% of those eligible).

Measurements and analysis

The outcome measure was self‐reported illicit heroin use, categorized as abstinent or deteriorated (the latter by Reliable Change Index), each risk‐adjusted by person‐level (demographics, clinical severity and treatment complexity) and area‐level (SUD prevalence, social deprivation and severity averages) covariates by multivariable logistic regression using multiply imputed outcome and covariate data. Risk‐adjusted models were assessed by information criteria and discrimination (c‐index). Standardized outcome rates were compared by funnel plot with 95% and 99% control limits.

Findings

Models of heroin abstinence (48.4%) and deterioration (3.2%) were comparable across the developmental and validation samples (c‐index = 0.70–0.71 and 0.82–0.87), with 79.2 and 94.0%, respectively, of the 149 treatment areas falling within 95% control limits. At the 99% limit, seven areas (4.7%) achieved abstinence rates above the national average, and eight had relatively poor abstinence rates (5.4%). At the 99% control limit, one area achieved very low deterioration outcomes and two (1.3%) were worse that the average. Risk adjustment served to increase abstinence rates in good performing areas by 0.63% and reduce abstinence rates by 0.37% in poor performing areas, and by 0.12% and 0.18%, respectively, for deterioration.

Conclusion

There is some exceptional variability in the apparent effectiveness of the English treatment system for substance use disorders. It is important to determine the source of this variability in order to inform drug treatment delivery and its evaluation both in England and overseas.
Regulation of thyroid hormone sensitivity by differential expression of the thyroid hormone receptor during Xenopus metamorphosis
Authors: Nakajima Keisuke , Fujimoto Kenta , Yaoita Yoshio
Published: June 2012

During amphibian metamorphosis, a series of dynamic changes occur in a predetermined order. Hind limb morphogenesis begins in response to low levels of thyroid hormone (TH) in early prometamorphosis, but tail muscle cell death is delayed until climax, when TH levels are high. It takes about 20 days for tadpoles to grow from early prometamorphosis to climax. To study the molecular basis of the timing of tissue‐specific transformations, we introduced thyroid hormone receptor (TR) expression constructs into tail muscle cells of Xenopus tadpoles. The TR‐transfected tail muscle cells died upon exposure to a low level of thyroxine (T4). This cell death was suggested to be mediated by type 2 iodothyronine deiodinase (D2) that converts T4 to T3—the more active form of TH. D2 mRNA was induced in the TR‐overexpressing cells by low levels of TH. D2 promoter contains a TH‐response element (TRE) with a lower affinity for TR. These results show that the TR transfection confers the ability to respond to physiological concentrations of TH at early prometamorphosis to tail muscle cells through D2 activity and promotes TH signaling. We propose the positive feedback loop model to amplify the cell's ability to respond to low levels of T4.
Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics
Authors: Helmy Mohamed , Sugiyama Naoyuki , Tomita Masaru , Ishihama Yasushi
Published: June 2012

We have developed a novel bioinformatics method called mass spectrum sequential subtraction (MSSS) to search large peptide spectra datasets produced by liquid chromatography/mass spectrometry (LC‐MS/MS) against protein and large‐sized nucleotide sequence databases. The main principle in MSSS is to search the peptide spectra set against the protein database, followed by removal of the spectra corresponding to the identified peptides to create a smaller set of the remaining peptide spectra for searching against the nucleotide sequences database. Therefore, we reduce the number of spectra to be searched to limit the peptide search space. Comparing MSSS and conventional search approach using a dataset of 27 LC‐MS/MS runs of rice culture cells indicated that MSSS reduced the search queries to 50% and the search time to 75% on average. In addition, MSSS had no effect on the identification false‐positive rate (FPR) or the novel peptide sequences identification ability. We used MSSS to analyze another dataset of 34 LC‐MS/MS runs, resulting in identifying additional 74 novel peptides. Proteogenomic analysis with these additional peptides yielded 47 new genomic features in 24 rice genes plus 24 intergenic peptides. These results show that the utility of MSSS in searching large databases with large MS/MS datasets for proteogenomics.
The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements
Authors: Staton S. Evan , Bakken Bradley H. , Blackman Benjamin K. , Chapman Mark A. , Kane Nolan C. , Tang Shunxue , Ungerer Mark C. , Knapp Steven J. , Rieseberg Loren H. , Burke John M.
Published: June 2012

Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing Gypsy LTR retrotransposons (‘chromoviruses’), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.
Obesity in asthma: more neutrophilic inflammation as a possible explanation for a reduced treatment response
Authors: Telenga E. D. , Tideman S. W. , Kerstjens H. A. M. , Hacken N. H. T. ten , Timens W. , Postma D. S. , van den Berge M.
Published: June 2012

Background

The incidence of asthma and obesity is increasing worldwide, and reports suggest that obese patients have more severe asthma. We investigated whether obese asthma patients have more severe airway obstruction and airway hyper‐responsiveness and a different type of airway inflammation than lean asthmatics. Furthermore, we assessed the effect of obesity on corticosteroid treatment response.

Methods

Patient data from four well‐documented asthma cohorts were pooled (n = 423). We evaluated FEV1, bronchial hyper‐responsiveness (PC20) to either methacholine/histamine or adenosine 5′‐monophosphate (AMP) (differential) cell counts in induced sputum and blood and corticosteroid treatment response in 118 patients.

Results

At baseline, FEV1, PC20 methacholine or histamine, and PC20 AMP values were comparable in 63 obese (BMI ≥30 kg/m2) and 213 lean patients (BMI <25 kg/m2). Obese patients had significantly higher blood neutrophils. These higher blood neutrophils were only seen in obese women and not in obese men. After a two‐week treatment with corticosteroids, we observed less corticosteroid‐induced improvement in FEV1%predicted in obese patients than in lean patients (median 1.7% vs 6.3% respectively, P = 0.04). The percentage of sputum eosinophils improved significantly less with higher BMI (P = 0.03), and the number of blood neutrophils increased less in obese than in lean patients (0.32 x103/μl vs 0.57 x103/μl, P = 0.046).

Conclusions

We found no differences in asthma severity between obese and nonobese asthmatics. Interestingly, obese patients demonstrated more neutrophils in sputum and blood than nonobese patients. The smaller improvement in FEV1 and sputum eosinophils suggests a worse corticosteroid treatment response in obese asthmatics.
Evidence for a genetic interaction in allergy‐related responsiveness to vitamin D deficiency
Authors: Vimaleswaran K. S. , Cavadino A. , Hyppönen E.
Published: June 2012

Background

The hormonal form of vitamin D affects both adaptive and innate immune functions involved in the development of allergies. Certain genotypes have been seen to alter the association between vitamin D deficiency (VDD) and the risk of food sensitization in children.

Methods

We examined 27 functional single nucleotide polymorphisms (SNPs) in/near selected candidate genes for association with total immunoglobulin E (IgE) and effect modification by 25‐hydroxyvitamin D in the 1958 British birth cohort (aged 45 years, n = 4921). A cut‐off value of 50 nmol/L was used to define VDD.

Results

Four SNPs (in FCER1A, IL13, and CYP24A1) and three SNPs (in IL4 and CYP24A1) were associated with total IgE and specific IgE, respectively, after correction for multiple testing. As in a previous study, MS4A2 (rs512555, Pinteraction = 0.04) and IL4 (rs2243250, Pinteraction = 0.02), and their composite score (Pinteraction = 0.009) modified the association between VDD and allergy‐related outcome. Vitamin D deficiency was associated with higher total IgE only in the carriers of the ‘C’ allele (IL4), which is present in 86% of white Europeans, while only 26% of Chinese and <20% of some African populations are carriers.

Conclusions

Our study on white European adults was consistent with a previous study on children from largely non‐white ethnic groups, suggesting that IL4 and MS4A2 genotypes modify the association between VDD and allergy risk. The risk allele in IL4 is present in nearly 90% of white Europeans, while less than a quarter are carriers in some other populations, highlighting the need to consider possible ethnic differences in allergy‐related responsiveness to VDD.
Restoration of humoral immunity after intravenous immunoglobulin replacement therapy in heart recipients with post‐transplant antibody deficiency and severe infections
Authors: Carbone J. , Sarmiento E. , Del Pozo N. , Rodriguez‐Molina J.J. , Navarro J. , Fernandez‐Yañez J. , Palomo J. , Villa A. , Muñoz P. , Fernandez‐Cruz E.
Published: June 2012

IgG hypogammaglobulinemia is a risk factor for infection in heart recipients. We assessed reconstitution of humoral immunity after non‐specific intravenous immunoglobulin (IVIg) replacement therapy administered to treat secondary IgG hypogammaglobulinemia in heart recipients with severe infections. The study population comprised 55 heart recipients who were administered IVIg (IVIg group) and 55 heart recipients with no severe infectious complications (control group). An event was defined as a severe infection requiring intravenous drug therapy during the first year after transplantation. The IVIg protocol comprised non‐specific 5% pasteurized IVIg at a dose of 300–400 mg/kg/months. IgG titers were lower in the IVIg group than in controls at seven d (577 vs. 778 mg/dL, p < 0.001) and at one month (553 vs. 684, p = 0.003). After IVIg therapy, IgG concentrations were similar in both groups at three months (681 vs. 737, p = 0.25) and at six months (736 vs. 769, p = 0.46). At three months, the IVIg group had higher levels of antitetanus toxoid and anti‐HBs (ELISA, 2.07 ± 2.11 vs. 0.60 ± 1.24 mg/dL [p = 0.003] and 42 ± 40 vs. 11 ± 31 IU/mL [p = 0.005], respectively) than controls. The mean number of infectious complications was significantly lower after IVIG therapy in the IVIG group. IVIg was associated with restoration of humoral immunity in heart recipients with post‐transplant IgG hypogammaglobulinemia and severe infections.
Health care follow‐up by live kidney donors more than three yr post‐nephrectomy
Authors: Weng Francis L. , Reese Peter P. , Waterman Amy D. , Soto Angelo G. , Demissie Kitaw , Mulgaonkar Shamkant
Published: June 2012

Background

Live kidney donors are advised to follow up regularly with healthcare providers to monitor kidney function and to diagnose and treat relevant comorbidities. We sought to determine the frequency and correlates of follow‐up care among live kidney donors.

Methods

We sent a mailed questionnaire to 606 live kidney donors from a single center who were at least three yr post‐nephrectomy.

Results

We received usable responses from 276 (45.5%), at a median of 6.2 yr post‐donation. Compared with non‐responders, responding donors were more likely to be older (p < 0.001), female (p = 0.002), white (p < 0.001), and married to the recipient (p < 0.001). In the prior year, 87.7% of respondents reported seeing a physician or other healthcare professional, and 79.0% had seen a “general doctor” such as their primary care provider. In univariable analyses of live kidney donors who responded to our survey, lack of medical follow‐up in the past year was associated with younger age, current lack of health insurance, and infrequent contact with the transplant recipient.

Conclusions

Most responding live kidney donors had seen a healthcare provider within the past year. To improve donors’ follow‐up, transplant centers can consider targeting donors who are younger or lack health insurance.
Access to renal transplantation in the diabetic population–effect of comorbidities and body mass index
Authors: Patibandla Bhanu K. , Narra Akshita , DeSilva Ranil , Chawla Varun , Goldfarb‐Rumyantzev Alexander S.
Published: June 2012

Background

In this study, we hypothesized that higher level of comorbidity and greater body mass index (BMI) may mediate the association between diabetes and access to transplantation.

Methods

We used data from the United States Renal Data System (01/01/2000–24/09/2007; n = 619 151). We analyzed two outcomes using Cox model: (i) time to being placed on the waiting list or transplantation without being listed and (ii) time to transplantation after being listed. Two primary Cox models were developed based on different levels of adjustment.

Results

In Cox models adjusted for a priori defined potential confounders, history of diabetes was associated with reduced transplant access (compared with non‐diabetic population) – both for wait‐listing/transplant without being listed (hazard ratio, HR = 0.80, p < 0.001) and for transplant after being listed (HR = 0.72, p < 0.001). In Cox models adjusted for BMI and comorbidity index along with the potential confounders, history of diabetes was associated with shorter time to wait‐listing or transplantation without being listed (HR = 1.07, p < 0.001), and there was no significant difference in time to transplantation after being listed (HR = 1.01, p = 0.42).

Conclusion

We demonstrated that higher level of comorbidity and greater BMI mediate the association between diabetes and reduced access to transplantation.
Severe Legionnaire's disease caused by Legionella longbeachae in a long‐term renal transplant patient: the importance of safe living strategies after transplantation
Authors: Wright A.J. , Humar A. , Gourishankar S. , Bernard K. , Kumar D.
Published: June 2012

Legionella species are intracellular gram‐negative bacilli that require specific culture media for growth. Transplant recipients with impaired cellular immunity are at particular risk for infection with this pathogen. Most human disease is caused by Legionella pneumophila; disease caused by non‐L. pneumophila species is reported mainly in immunosuppressed patients with the exception of Legionella longbeachae. L. longbeachae is a common cause of Legionnaires' disease in Australia and New Zealand, and is associated with exposure to potting soil. We report the case of a patient, 26 years post kidney transplant, who presented with severe and rapidly progressive respiratory illness. L. longbeachae serogroup 1 was isolated from respiratory cultures. Further investigation revealed that she had significant soil exposure before the onset of illness. We highlight the importance of following safe living strategies to prevent exposure‐related illness even in long‐term transplant recipients.
Colonizing the world in spite of reduced MHC variation
Authors: GANGOSO L. , ALCAIDE M. , GRANDE J. M. , MUÑOZ J. , TALBOT S. L. , SONSTHAGEN S. A. , SAGE G. K. , FIGUEROLA J.
Published: June 2012

The major histocompatibility complex (MHC), which harbours the most polymorphic vertebrate genes, plays a critical role in the host–pathogen coevolutionary arms race. However, the extent to which MHC diversity determines disease susceptibility and long‐term persistence of populations is currently under debate, as recent studies have demonstrated that low MHC variability does not necessarily hamper population viability. However, these studies typically assayed small and decimated populations in species with restricted distribution, thereby making inferences about the evolutionary potential of these populations difficult. Here, we show that MHC impoverishment has not constrained the ecological radiation and flourishing of falcons (Aves: Falconidae) worldwide. We found two remarkably different patterns of MHC variation within the genus Falco. Whereas MHC variation in kestrels (the basal group within the genus) is very high, falcons exhibit ancestrally low intra‐ and interspecific MHC variability. This pattern is not due to the inadvertent survey of paralogous genes or pseudogenes. Further, patterns of variation in mitochondrial or other nuclear genes do not indicate a generalized low level of genome‐wide variability among falcons. Although a relative contribution of genetic drift cannot be completely ruled out, we propose the falcons went through an evolutionary transition, driven and maintained by natural selection, from primarily highly variable towards low polymorphic and slow‐evolving MHC genes with a very specific immune function. This study highlights that the importance of MHC diversity cannot be generalized among vertebrates, and hints at the evolution of compensatory immune mechanisms in falcons to cope with emerging and continuously evolving pathogens.
Functional analysis of a WRKY transcription factor involved in transcriptional activation of the DBAT gene in Taxus chinensis
Authors: Li S. , Zhang P. , Zhang M. , Fu C. , Yu L.
Published: June 2012

Although the regulation of taxol biosynthesis at the transcriptional level remains unclear, 10‐deacetylbaccatin III‐10 β‐O‐acetyl transferase (DBAT) is a critical enzyme in the biosynthesis of taxol. The 1740 bp fragment 5′‐flanking sequence of the dbat gene was cloned from Taxus chinensis cells. Important regulatory elements needed for activity of the dbat promoter were located by deletion analyses in T. chinensis cells. A novel WRKY transcription factor, TcWRKY1, was isolated with the yeast one‐hybrid system from a T. chinensis cell cDNA library using the important regulatory elements as bait. The gene expression of TcWRKY1 in T. chinensis suspension cells was specifically induced by methyl jasmonate (MeJA). Biochemical analysis indicated that TcWRKY1 protein specifically interacts with the two W‐box (TGAC) cis‐elements among the important regulatory elements. Overexpression of TcWRKY1 enhanced dbat expression in T. chinensis suspension cells, and RNA interference (RNAi) reduced the level of transcripts of dbat. These results suggest that TcWRKY1 participates in regulation of taxol biosynthesis in T. chinensis cells, and that dbat is a target gene of this transcription factor. This research also provides a potential candidate gene for engineering increased taxol accumulation in Taxus cell cultures.
Chilo partellus (Swinhoe) (Lepidoptera: Pyralidae) a new invasive species in Israel
Authors: Ben‐Yakir D. , Chen M. , Sinev S. , Seplyarsky V.
Published: June 2012

Chilo partellus, the spotted stem borer (SSB), is reported for the first time from the fields of sorghum and corn in Israel. Spotted stem borer larvae were first discovered in July 2010 on sorghum and corn plants in the Western Galilee. The new pest had spread all over northern Israel by the end of 2011. The identity of the new pest was confirmed using the morphology of the dissected male genitalia and its attraction to SSB sex pheromone.