bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical properties of host material for phosphor computational modeling
Authors: Yao Ge , Berry Mary T. , May P. Stanley , Kilin Dmitri S.
Published: July 2012

The lanthanide ions doped hexagon (β)‐NaYF4 nanocrystals exhibit photoluminescence outputs, where β‐NaYF4 with a strong cation disorder serve as host substance. The ab initio computation of β‐NaYF4 with different atomic sizes NamYmF4m, for m = 3, 6, 12, 24, 48, or 96 in periodic boundary conditions is simulated based on density functional theory with the generalized gradient approximation. With the increase of unit sizes, the energy of highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), energy gap, and energy per atom exhibit asymptotic convergence as well as the interatomic distances. The calculation of first ionization energy appreciates the prediction of the Koopmans' theorem. The investigation of orbital's spatial distribution proves the ligand (F− −1e → F) to metal (Y3+ +1e → Y2+) transition during the excitations mainly through the p → d path. Two families of lifetimes are observed in the simulated results from the optical absorption spectrum, which indicates that transitions can be divided by two categories. © 2012 Wiley Periodicals, Inc.
ENSO effects on δ18O, δ2H and d‐excess values in precipitation across the U.S. using a high‐density, long‐term network (USNIP)
Authors: Welker Jeffrey M.
Published: July 2012

RATIONALE

Isotope (δ18O and δ2H values) ratios in precipitation have been central to understanding changes in Earth's climate as recorded in ice, coral, speleothems, lake varves and long‐lived plants. Understanding how climate phases (i.e. ENSO) affect the spatial and temporal patterns of δ18O and δ2H values in precipitation has, however, been uncertain across the USA.

METHODS

A spatial precipitation isotope network (USNIP) has been established that aims to: (1) characterize the δ18O, δ2H and d‐excess values in precipitation across the USA with the highest spatially dense network of measurements yet undertaken; (2) quantify the annual and seasonal patterns of precipitation δ18O and δ2H values that may be affected by ENSO climate phases; and (3) provide a new isotope database for scientific studies that can be incorporated into NEON, BASIN, GNIP, and IsoMAP.

RESULTS

On average, precipitation δ18O and δ2H values are very low in the northern Rocky Mountain region (~ −15‰ δ18O, and ~ −120‰ δ2H), and precipitation δ18O and δ2H values are relatively higher along the Gulf Coast (~ −5‰ δ18O and −10‰ δ2H) and in the Southeast. During El Niño periods the precipitation δ18O and δ2H values are lowest in northwest Montana, with precipitation that is depleted in 18O and 2H extending into northern Colorado, while moisture that is enriched in 18O and 2H continues to dominate the Gulf Coast. The annual average differences between the climate phases generally show especially depleted 18O and 2H in precipitation across the Rocky Mountain region during El Niño, compared with Neutral periods.

CONCLUSIONS

Detailed spatial and seasonal patterns of δ18O, δ2H and d‐excess values provide fine‐scale resolution not previously recognized. Climate phases of ENSO have major effects on the spatial patterns of δ18O, δ2H and d‐excess values, being especially important on a seasonal basis in the Desert Southwest. Copyright © 2012 John Wiley & Sons, Ltd.
LONG‐TERM COTTONWOOD FOREST DYNAMICS ALONG THE UPPER MISSOURI RIVER, USA
Authors: Scott M. L. , Auble G. T. , Dixon M. D. , Carter Johnson W. , Rabbe L. A.
Published: July 2012

The upper Missouri River bottomland in north‐central Montana, USA, retains much of the physical character it had when traversed by Lewis and Clark around 1805. We used geospatial data to quantify long‐term changes in the distribution of bottomland vegetation, land use patterns and channel planform for a 257‐rkm segment of the Missouri River above Fort Peck Reservoir. This segment is less ecologically altered than downstream segments, but two dams completed in the mid‐1950s have decreased the frequency and magnitude of floods. The area of forest is sparse because of geomorphic setting but, contrary to public perception, has remained relatively constant during the past century. However, the stability of forest area obscures its spatial and temporal dynamics. We used state and transition models to quantify fates and sources of forest during two periods: 1890s–1950s and 1950s–2006. Total forest area was 6% greater in 2006 than it was in the 1890s, largely due to reduced forest loss to erosional processes and gains related to progressive channel narrowing. Channel narrowing resulted in part from human‐caused peak flow attenuation. A modified transition matrix, used to examine future steady‐state conditions, projected little change in forest area; however, these projections are likely an overestimate. The extent to which 2006 forest area represents a transient adjustment to a new flow regime versus a dynamic, quasi–steady state will be determined by the long‐term interplay among hydrologic factors, channel processes, water management and land use practices. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
AN INVADER WITHIN AN ALTERED LANDSCAPE: ONE CATFISH, TWO RIVERS AND AN INTER‐BASIN WATER TRANSFER SCHEME
Authors: Kadye W. T. , Booth A. J.
Published: July 2012

African sharptooth catfish Clarias gariepinus has become established as a non‐native invasive species in Eastern Cape, South Africa, where it was translocated primarily through an inter‐basin water transfer scheme into the Great Fish and Sundays rivers. This study examined the patterns in catfish distribution and abundance, and compared trophic niches in relation to the ichthyofauna of the two rivers. Correspondence analysis revealed upstream to downstream gradients associated with the spatial distribution in species richness for most species within the mainstream and mainstream to tributary gradients that were associated mostly with the spatial distribution of native minnows in both rivers. Catfish was predicted to occur widely within the mainstream habitats and to decrease progressively from mainstreams to tributaries. Based on classification and regression trees, the physico‐chemical environment was found to be a good proxy for predicting the occurrence and abundance of catfish. Although non‐significant relationships were observed between catfish and other native fish species abundances, the study suggests potential impact due to predation and interference in habitats where the invader co‐occurs with other fishes. Comparisons of trophic niches indicated higher trophic diversity for the mainstream ichthyofauna than the tributary communities in both rivers, suggesting an upstream to downstream continuum in community structure and resource availability. Catfish within the invaded mainstream had comparable trophic niches and similar dispersion patterns among individuals for both rivers, but indicated differences in shapes of scatter. This suggests that the catfish exhibited a differential response, probably in relation to resource availability, that may be indicative of its dietary plasticity. The study suggests the proliferation of catfish and its probable impact within the mainstream flow‐altered habitats where invasion resistance was possibly reduced. Comparisons of trophic niches provided information on its probable impact at different scales and the potential risk of invasion of tributaries inhabited by native minnow species. Copyright © 2012 John Wiley & Sons, Ltd.
Catalytic pyrolysis of biomass for transportation fuels
Authors: Lappas Angelos A. , Kalogiannis Kostas G. , Iliopoulou Eleni F. , Triantafyllidis Kostas S. , Stefanidis Stylianos D.
Published: July 2012

Application of heterogeneous catalysis in biomass pyrolysis seems to be one of the most promising methods to improve bio‐oil quality by minimizing its undesirable properties (high viscosity, corrosivity, instability, etc.) and producing renewable crude (bio‐crude). This bio‐crude could finally lead to transportation fuels using existing refinery processes (such as hydrotreating). A plethora of catalytic materials have been investigated in the literature as catalysts for the biomass catalytic pyrolysis process. Among them, microporous (zeolitic) or mesoporous (Al‐MCM‐41) acid materials have been tested, either promoted or not with several transition metals. Lately, basic materials are also suggested. For this process, a circulating fluid bed reactor seems to be the most effective technology, since it offers continuous catalyst regeneration. The research till today shows that catalysts based on ZSM‐ are the most promising. With these catalysts, bio‐oil yield up to about 30 wt% (on dry biomass) with about 21 wt% oxygen can be produced. However, tailoring of catalyst properties such as acidity/basicity and porosity characteristics is still needed to develop an optimized catalyst.

This article is categorized under:

Bioenergy > Science and Materials

Bioenergy > Climate and Environment

Energy and Climate > Science and Materials
Wind conditions and resource assessment
Authors: Petersen Erik Lundtang , Troen Ib
Published: July 2012

The development of wind power as a competitive energy source requires resource assessment of increasing accuracy and detail (including not only the long‐term ‘raw’ wind resource, but also turbulence, shear, and extremes), and in areas of increasing complexity. This in turn requires the use of the most advanced large‐scale meteorological models and data together with a chain of modeling tools linking the large‐scale dynamics via the mesoscales to site‐specific wind conditions. These wind conditions (at a given wind turbine site and height) are a complex function of ‘the weather’ statistics and of influence from features at smaller scales such as hills and mountains, surface roughness conditions, surface thermal properties, and specific nearby obstacles such as ‘other’ wind turbines.

This article is categorized under:

Bioenergy > Science and Materials

Energy and Development > Science and Materials
Effects of Inbreeding on Skeletal Size and Fluctuating Asymmetry of Peromyscus polionotus Mice
Authors: Lacy Robert C. , Alaks Glen
Published: July 2012

Measurements of size and asymmetry in morphology might provide early indications of damaging effects of inbreeding or other genetic changes in conservation breeding programs. We examined the effects of inbreeding on size and fluctuating asymmetry (FA) in skull and limb bone measurements in experimental populations of three subspecies of Peromyscus polionotus mice that had previously been shown to suffer significant reductions in reproductive success when inbred. Inbreeding caused significant depression in mean size in two of the subspecies (P. p. rhoadsi and P. p. subgriseus), but the effects were smaller in the third (P. p. leucocephalus). Inbreeding caused an increase in FA of just one of eight bilateral traits in one subspecies (P. p. rhoadsi). Inbreeding depression in size was more easily detected than the effects of inbreeding on FA. FA may be much less sensitive to inbreeding and other stresses than are more direct measures of fitness such as reproductive output and body mass growth rate. Given the large sample sizes and statistical complexity required to assess changes to typically very small levels of FA in captive populations, FA will not likely provide a useful measure of inbreeding depression in captive populations. Zoo Biol. 32:125‐133, 2013. © 2012 Wiley Periodicals, Inc.
Synthesis and Surface‐Active Properties of F‐Alkylated Polar Loops
Authors: Khalfallah Ali , Boughariou Boutheina , Hedhli Ahmed
Published: July 2012

The synthesis of double tail surfactants having crown ethers as polar heads was performed by reacting di‐F‐alkyl mercaptosuccinate on cyclic polyethylene glycol maleates. Surface tension and critical micelle concentration (CMC) were determined for these new surfactants. According to CMC values, the solubility in water is higher with perfluoroalkyl surfactants having a bigger loop size and shorter hydrophobic chains.
N‐terminal tyrosine phosphorylation of caveolin‐2 negates anti‐proliferative effect of transforming growth factor beta in endothelial cells
Authors: Abel Britain , Willoughby Cara , Jang Sungchan , Cooper Laura , Xie Leike , Vo-Ransdell Chi , Sowa Grzegorz
Published: July 2012

Here we show that tyrosine phosphorylation of caveolin‐2 (Cav‐2) negatively regulates the anti‐proliferative function of transforming growth factor beta (TGF‐beta) in endothelial cells. In contrast to wild‐type‐Cav‐2, retroviral re‐expression of Y19/27F‐Cav‐2 in Cav‐2 knockout endothelial cells did not affect anti‐proliferative effect of TGF‐beta compared to empty vector. Conversely, although less effective than wild‐type, re‐expression of S23/36A‐Cav‐2 reduced the effect of TGF‐beta compared to empty vector. This differential effect of tyrosine and serine phosphorylation mutants of Cav‐2 correlated with TGF‐beta‐induced Smad3 phosphorylation and transcriptional activation of plasminogen activator inhibitor‐1. Thus tyrosine‐phosphorylated Cav‐2 counteracts anti‐proliferative effect of TGF‐beta in endothelial cells.
tRNA concentration fine tunes protein solubility
Authors: Fedyunin Ivan , Lehnhardt Lothar , Böhmer Nadine , Kaufmann Paul , Zhang Gong , Ignatova Zoya
Published: July 2012

Clusters of codons pairing to low‐abundance tRNAs synchronize the translation with co‐translational folding of single domains in multidomain proteins. Although proven with some examples, the impact of the ribosomal speed on the folding and solubility on a global, cell‐wide level remains elusive. Here we show that upregulation of three low‐abundance tRNAs in Escherichia coli increased the aggregation propensity of several cellular proteins as a result of an accelerated elongation rate. Intriguingly, alterations in the concentration of the natural tRNA pool compromised the solubility of various chaperones consequently rendering the solubility of some chaperone‐dependent proteins.
The importance of flavodoxin for environmental stress tolerance in photosynthetic microorganisms and transgenic plants. Mechanism, evolution and biotechnological potential
Authors: Lodeyro Anabella F. , Ceccoli Romina D. , Pierella Karlusich Juan J. , Carrillo Néstor
Published: July 2012

Ferredoxins are electron shuttles harboring iron–sulfur clusters which participate in oxido‐reductive pathways in organisms displaying very different lifestyles. Ferredoxin levels decline in plants and cyanobacteria exposed to environmental stress and iron starvation. Flavodoxin is an isofunctional flavoprotein present in cyanobacteria and algae (not plants) which is induced and replaces ferredoxin under stress. Expression of a chloroplast‐targeted flavodoxin in plants confers tolerance to multiple stresses and iron deficit. We discuss herein the bases for functional equivalence between the two proteins, the reasons for ferredoxin conservation despite its susceptibility to aerobic stress and for the loss of flavodoxin as an adaptive trait in higher eukaryotes. We also propose a mechanism to explain the tolerance conferred by flavodoxin when expressed in plants.
Increased expression of tryptophan‐5‐hydroxylase 1, but not 2, in brainstem as a result of intrauterine malnutrition
Authors: Manjarrez‐Gutiérrez Gabriel , Martínez‐Radilla Karina , Boyzo‐Montes de Oca Alfonso , Orozco‐Suárez Sandra , Hernández‐Rodríguez Jorge
Published: July 2012

The aim of this study was to determine whether intrauterine malnutrition (IUM) produces a change in the expression of tryptophan‐5‐hydroxylase (TPH) 1 and/or 2 as the primary mechanism to explain the observed chronic cerebral acceleration of the synthesis of 5‐hydroxytryptamine (5‐HT). We used an IUM model and controls with ages of 1, 15 and 21 days. The brainstem was obtained to determine l‐tryptophan, 5‐HT and TPH activity. Expression of TPH1 and TPH2 via specific antibodies for each was also evaluated by immunocytochemistry and Western blot. Malnourished offspring had a significant elevation of l‐Trp, TPH activity and 5‐HT in the brainstem. Both isoforms (1 and 2) of TPH were expressed from birth in both groups; however, TPH1 expression was significantly higher in offspring with IUM in relation to the controls. Importantly, these malnourished offspring showed reduced expression of TPH2 compared to controls. It was confirmed that IUM produces an increase in 5‐HT in the brainstem and also showed increased expression of TPH1 at birth, with decreased expression of TPH2. These findings together allow us to propose that chronic elevation of synthesis of 5‐HT observed in the brain of the offspring with IUM is probably due to a change in the expression and activity of TPH1 induced from fetal life.
Oxidative stress in Niemann‐Pick type C patients: a protective role of N‐butyl‐deoxynojirimycin therapy
Authors: Ribas Graziela S. , Pires Ricardo , Coelho Janice Carneiro , Rodrigues Daiane , Mescka Caroline Paula , Vanzin Camila S. , Biancini Giovana B. , Negretto Giovanna , Wayhs Carlos A.Y. , Wajner Moacir , Vargas Carmen R.
Published: July 2012

Niemann‐Pick type C (NPC) is a rare neurodegenerative disorder biochemically characterized by the accumulation of cholesterol and glycosphingolipids in late endosomes and lysosomes of the affected patients. N‐butyl‐deoxynojirimycin is the only approved drug for patients with NPC disease. It inhibits glycosphingolipid synthesis, therefore reducing intracellular lipid storage. Although the mechanisms underlying the neurologic damage in the NPC disease are not yet well established, in vitro and in vivo studies suggest an involvement of reactive species in the pathophysiology of this disease. In this work we aimed to evaluate parameters of lipid and protein oxidation, measured by thiobarbituric acid‐reactive species (TBA‐RS) and protein carbonyl formation, respectively, as well as the enzymatic and non‐enzymatic antioxidant defenses in plasma, erythrocytes and fibroblasts from NPC1 patients, at diagnosis and during treatment with N‐butyl‐deoxynojirimycin. We found a significant increase of TBA‐RS in plasma and fibroblasts, as well as increased protein carbonyl formation and decreased total antioxidant status (TAS) in plasma of untreated NPC1 patients as compared to the control group. In addition, erythrocyte glutathione peroxidase (GSH‐Px) activity was increased, whereas CAT and SOD activities were normal in these patients. We also observed that patients treated with N‐butyl‐deoxynojirimycin normalized plasma TBA‐RS and TAS, as well as erythrocyte GSH‐Px activity. Taken together, the present data indicate that oxidative stress is increased in patients with NPC1 disease and that treatment with N‐butyl‐deoxynojirimycin is able to confer protection against this pathological process.
Real option valuation of abandoned farmland
Authors: Nishihara Michi
Published: July 2012

This paper investigates the decision‐making process of an owner of abandoned farmland that is currently restricted to agricultural use but will be available for nonagricultural use in the future. I make a real option valuation of the abandoned farmland taking prospective land conversion into consideration. Results from the model calibration demonstrate that a slight probability of land conversion greatly increases the land value and discourages the owner from cultivating the land. Further, the results show that a small gap in the anticipation of land conversion prevents the owner from selling or leasing the land to a more efficient farmer.
Origin of glacial ridges (OIS 6) in the Kaskaskia Sublobe, southwestern Illinois, USA
Authors: Webb Nathan D. , Grimley David A. , Phillips Andrew C. , Fouke Bruce W.
Published: July 2012

The origin of Illinois Episode (OIS 6) glacial ridges (formerly: ‘Ridged Drift’) in the Kaskaskia Basin of southwestern Illinois is controversial despite a century of research. Two studied ridges, containing mostly fluvial sand (OSL ages: ~ 150 ± 19 ka), with associated debris flows and high-angle reverse faults, are interpreted as ice-walled channels. A third studied ridge, containing mostly fine-grained till, is arcuate and morainal. The spatial arrangement of various ridge types can be explained by a glacial sublobe in the Kaskaskia Basin, with mainly fine-grained ridges along the sublobe margins and coarse-grained glaciofluvial ridges in a paleodrainage network within the sublobe interior. Illinois Episode till fabric and striation data demonstrate southwesterly ice flow that may diverge near the sublobe terminus. The sublobe likely formed as glacial ice thinned and receded from its maximum extent. The Kaskaskia Basin contains some of the best-preserved Illinois Episode constructional glacial landforms in the North American midcontinent. Such distinctive features probably result from ice flow and sedimentation into this former lowland, in addition to minimal postglacial erosion. Other similar OIS 6 glacial landforms may exist in association with previously unrecognized sublobes in the midcontinent, where paleo-lowlands might also have focused glacial sedimentation.
The Economic Dynamics of Law
Authors: Driesen David M.
Published: July 2012

This book offers a dynamic theory of law and economics focused on change over time, aimed at avoiding significant systemic risks (like financial crises and climate disruption) and implemented through a systematic analysis of law's economic incentives and how people actually respond to them. This theory offers a new vision of law as fundamentally a macro-level enterprise establishing normative commitments and a framework for numerous private transactions, rather than as an analogue to a market transaction. It explains how neoclassical law and economics sparked decades of deregulation culminating in the 2008 financial collapse. It then shows how economic dynamic theory helps scholars and policymakers make wise choices about how to avoid future catastrophes while keeping open a robust set of economic opportunities, with individual chapters addressing the law and economics of financial regulation, contract, property, intellectual property, antitrust, national security and climate disruption.
India in the World Economy
Authors: Roy Tirthankar
Published: July 2012

Cross-cultural exchange has characterized the economic life of India since antiquity. Its long coastline has afforded convenient access to Asia and Africa as well as trading partnerships formed in the exchange of commodities ranging from textiles to military technology and from opium to indigo. In a journey across two thousand years, this enthralling book, written by a leading South Asian historian, describes the ties of trade, migration, and investment between India and the rest of the world and shows how changing patterns of globalization have reverberated in economic policy, politics, and political ideology within India. Along the way, the book asks three major questions: Is this a particularly Indian story? When did the big turning points happen? And is it possible to distinguish the modern from the pre-modern pattern of exchange? These questions invite a new approach to the study of Indian history by placing the region at the center of the narrative. This is global history written on India's terms, and, as such, the book invites Indian, South Asian, and global historians to rethink both their history and their methodologies.
Relational Knowledge Discovery
Authors: Müller M. E.
Published: July 2012

What is knowledge and how is it represented? This book focuses on the idea of formalising knowledge as relations, interpreting knowledge represented in databases or logic programs as relational data and discovering new knowledge by identifying hidden and defining new relations. After a brief introduction to representational issues, the author develops a relational language for abstract machine learning problems. He then uses this language to discuss traditional methods such as clustering and decision tree induction, before moving onto two previously underestimated topics that are just coming to the fore: rough set data analysis and inductive logic programming. Its clear and precise presentation is ideal for undergraduate computer science students. The book will also interest those who study artificial intelligence or machine learning at the graduate level. Exercises are provided and each concept is introduced using the same example domain, making it easier to compare the individual properties of different approaches.
Societies of Wolves and Free-ranging Dogs
Authors: Spotte Stephen
Published: July 2012

Wolves are charismatic emblems of wilderness. Dogs, which descended from wolves, are models of urbanity. Do free-ranging dogs revert to pack living or are their societies only reminiscent of a wolfish heritage? Focusing on behavioral ecology, this is the first book to assess societies of both gray wolves and domestic dogs living as urban strays and in the feral state. It provides a comprehensive review of wolf genetics, particularly of New World wolves and their mixture of wolf, coyote and dog genomes. Spotte draws on the latest scientific findings across the specialized fields of genetics, sensory biology, reproductive physiology, space use, foraging ecology and socialization. This interdisciplinary approach provides a solid foundation for a startling and original comparison of the social lives of wolves and free-ranging dogs. Supplementary material, including a full glossary of terms, is available online at www.cambridge.org/9781107015197.
Winning and Losing on the Western Front
Authors: Boff Jonathan
Published: July 2012

The 'Hundred Days' campaign of 1918 remains a neglected aspect of the First World War. Why was the German army defeated on the Western Front? Did its morale collapse or was it beaten by the improved military effectiveness of a British army which had climbed a painful 'learning curve' towards modern combined arms warfare? This revealing insight into the crucial final months of the First World War uses state-of-the-art methodology to present a rounded case study of the ability of both armies to adapt to the changing realities they faced. Jonathan Boff draws on both British and German archival sources, some of them previously unseen, to examine how representative armies fought during the 'Hundred Days' campaign. Assessing how far the application of modern warfare underpinned the British army's part in the Allied victory, the book highlights the complexity of modern warfare and the role of organisational behaviour within it.
Unsteady nearshore natural convection induced by constant isothermal surface heating
Authors: Mao Yadan , Lei Chengwang , Patterson John C.
Published: July 2012

The present investigation is concerned with natural convection in a wedge-shaped domain induced by constant isothermal heating at the water surface. Complementary to the study of daytime heating by solar radiation relevant to nearshore regions of lakes and reservoirs previously reported by the same authors, this study focuses on sensible heating imposed by the atmosphere when it is warmer than the water body. A semi-analytical approach coupled with scaling analysis and numerical simulation is adopted to resolve the problem. Two flow regimes are identified depending on the comparison between the Rayleigh number and the inverse of the square of the bottom slope. For the lower Rayleigh number regime, the entire flow domain eventually becomes isothermal and stationary. For the higher Rayleigh number regime, the flow domain is composed of two distinct subregions, a conductive subregion near the shore and a convective subregion offshore. Within the conductive subregion, the maximum local flow velocity occurs when the thermal boundary layer reaches the local bottom, and the subregion eventually becomes isothermal and stationary. In the offshore convective subregion, a steady state is reached with a distinct thermal boundary layer below the surface and a steady flow velocity. The dividing position between the two subregions and the major time and velocity scales governing the flow development in both subregions are proposed by the scaling analysis and validated by corresponding numerical simulation.
Group B streptococcal colonization and the risk of pre-eclampsia
Authors: MULLA Z. D. , ANNAVAJJHALA V. , GONZALEZ-SANCHEZ J. L. , SIMON M. R. , NUWAYHID B. S.
Published: July 2012

To determine if there was an association between recto-vaginal group B streptococcus (GBS) colonization and pre-eclampsia, two cross-sectional studies were conducted using statewide hospital databases. The first study analysed data from the state of Florida, USA, and included 190 645 women who were discharged in 2001. This dataset was used to generate the hypothesis that GBS colonization is associated with pre-eclampsia. The second study tested the GBS hypothesis using the records of 577 153 women who delivered in 2004 or 2005 in Texas, USA. Adjusted odds ratios (aOR) for the outcome of pre-eclampsia comparing GBS-positive to GBS-negative women were calculated using logistic regression. The aOR for the association between GBS carriage and pre-eclampsia was 0·71 [95% confidence interval (CI) 0·65–0·77] in the Florida dataset. In the Texas dataset, the overall prevalence of GBS carriage was 14·1% while the overall prevalence of pre-eclampsia was 4·0%. GBS carriers were 31% less likely than non-carriers to have pre-eclampsia (aOR 0·69, 95% CI 0·66–0·72) in Texas. In two large statewide analyses, GBS carriage was inversely associated with pre-eclampsia. A sensitivity analysis revealed that misclassification of GBS status is not a likely explanation of our findings.
Does milk fortification increase the risk of necrotising enterocolitis in preterm infants with congenital heart disease?
Authors: Malhotra Atul , Veldman Alex , Menahem Samuel
Published: July 2012

Prematurity and low birth weight adds to the risk of serious congenital heart disease in infants. It may also delay surgical intervention, especially when cardiopulmonary bypass is required, or where an aortopulmonary shunt is necessary to maintain adequate oxygenation. In this setting, neonatologists are faced with the challenge of accelerating the infant's growth to allow for early surgery. We describe the cases of two infants in whom an attempt to fortify the feeds was associated with necrotising enterocolitis, with a lethal outcome in one. The outcome suggests caution in fortifying feeds in premature infants with serious congenital heart disease.
VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets
Authors: Morganella Sandro , Ceccarelli Michele
Published: July 2012

Summary: Identification of genetic alterations of tumor cells has become a common method to detect the genes involved in development and progression of cancer. In order to detect driver genes, several samples need to be simultaneously analyzed. The Cancer Genome Atlas (TCGA) project provides access to a large amount of data for several cancer types. TGCA is an invaluable source of information, but analysis of this huge dataset possess important computational problems in terms of memory and execution times. Here, we present a R/package, called VegaMC (Vega multi-channel), that enables fast and efficient detection of significant recurrent copy number alterations in very large datasets. VegaMC is integrated with the output of the common tools that convert allele signal intensities in log R ratio and B allele frequency. It also enables the detection of loss of heterozigosity and provides in output two web pages allowing a rapid and easy navigation of the aberrant genes. Synthetic data and real datasets are used for quantitative and qualitative evaluation purposes. In particular, we demonstrate the ability of VegaMC on two large TGCA datasets: colon adenocarcinoma and glioblastoma multiforme. For both the datasets, we provide the list of aberrant genes which contain previously validated genes and can be used as basis for further investigations.

Availability: VegaMC is a R/Bioconductor Package, available at http://bioconductor.org/packages/release/bioc/html/VegaMC.html.

Contact:  morganella@unisannio.it

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Network inference using steady-state data and Goldbeter–koshland kinetics
Authors: Oates Chris J , Hennessy Bryan T , Lu Yiling , Mills Gordon B , Mukherjee Sach
Published: July 2012

Motivation: Network inference approaches are widely used to shed light on regulatory interplay between molecular players such as genes and proteins. Biochemical processes underlying networks of interest (e.g. gene regulatory or protein signalling networks) are generally nonlinear. In many settings, knowledge is available concerning relevant chemical kinetics. However, existing network inference methods for continuous, steady-state data are typically rooted in statistical formulations, which do not exploit chemical kinetics to guide inference.

Results: Herein, we present an approach to network inference for steady-state data that is rooted in non-linear descriptions of biochemical mechanism. We use equilibrium analysis of chemical kinetics to obtain functional forms that are in turn used to infer networks using steady-state data. The approach we propose is directly applicable to conventional steady-state gene expression or proteomic data and does not require knowledge of either network topology or any kinetic parameters. We illustrate the approach in the context of protein phosphorylation networks, using data simulated from a recent mechanistic model and proteomic data from cancer cell lines. In the former, the true network is known and used for assessment, whereas in the latter, results are compared against known biochemistry. We find that the proposed methodology is more effective at estimating network topology than methods based on linear models.

Availability:  mukherjeelab.nki.nl/CODE/GK_Kinetics.zip

Contact:  c.j.oates@warwick.ac.uk; s.mukherjee@nki.nl

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Triclinic modification of diaquabis(5-carboxy-1H-imidazole-4-carboxylato-κ2N3,O4)iron(II)
Authors: Ohshima Eriko , Yoshida Kazuki , Sugiyama Kazumasa , Uekusa Hidehiro
Published: July 2012

The title compound, [Fe(C5H3N2O4)2(H2O)2], is a triclinic modification of a monoclinic form recently reported by Duet al.[Acta Cryst.(2011), E67, m997]. The FeIIion lies at an inversion center and is coordinated by two N and two O atoms from two 5-carboxy-1H-imidazole-4-carboxylate ligands intranspositions, together with two water molecules, completing a slightly distorted octahedral coordination. Intermolecular N—H...O hydrogen bonding between the N—H group of the imidazole ring and the deprotonated carboxylate group builds a chain of 5-carboxy-1H-imidazole-4-carboxylate anions along the [101] direction. The water molecules form intermolecular hydrogen bonds to O—C and O=C sites of the carboxylate group in adjacent layers.
(Ethanolato-κO)[N′-(3-methoxy-2-oxidobenzylidene-κO2)benzohydrazidato-κ2N′,O]oxidovanadium(V)
Authors: Chen Xiao-Hua , Wu Qiong-Jie , Chen Li-Juan , Yang Ming-Xing
Published: July 2012

In the title complex, [V(C15H12N2O4)(C2H5O)O], the VVion is coordinated by an oxide O atom, an ethanolate anion and two O atoms and one N atom from the tridentate benzohydrazidate dianion in a distorted square-pyramidal geometry; the V atom is displaced by 0.4748 (8) Å from the basal plane towards the axial oxide O atom. An intramolecular O—H...N hydrogen bond occurs in the benzohydrazidate ligand. Weak intermolecular C—H...O hydrogen bonding is present in the crystal.
Dimethyl 2,2′-[2,2′-bi(1H-1,3-benzimidazole)-1,1′-diyl]diacetate
Authors: Guo Huai-Ling , Liu Jia-Cheng , Xiao Chao-Hu , Pang Ting , Cao Ping
Published: July 2012

The whole molecule of the title compound, C20H18N4O4, is generated by an inversion center. The benzimidazole ring mean plane make a dihedral angle of 89.4 (8)° with the plane passing through the acetate group (COO). In the crystal, molecules are linkedviaweak C—H...O hydrogen bonds and π–π interactions [centroid–centroid distance = 3.743 (3) Å] involving inversion-related benzimidazole groups.
(1S,3R,8R)-2,2-Dibromo-3,7,7,10-tetramethyltricyclo[6.4.0.01,3]dodec-9-ene
Authors: Benharref Ahmed , El Ammari Lahcen , Lassaba Essêdiya , Ourhriss Najia , Berraho Moha
Published: July 2012

The title compound, C16H24Br2, was synthesized from β-himachalene (3,5,5,9-tetramethyl-2,4a,5,6,7,8-hexahydro-1H-benzocycloheptene), which was isolated from the essential oil of the Atlas cedar (Cedrus Atlantica). The molecule is built up from two fused six- and seven-membered rings and an additional three-membered ring from the reaction of β-himachalene with dibromocarbene. The six-membered ring shows a screw-boat conformation, whereas the seven-membered ring displays a boat conformation; the dihedral angle between the mean planes through the rings is 57.9 (4)°. The absolute structure was established unambiguously from anomalous dispersion effects.
Pharmacokinetics and pharmacodynamics of turoctocog alfa and N8‐GP in haemophilia A dogs
Authors: Agersø H. , Stennicke H. R. , Pelzer H. , Olsen E. N. , Merricks E. P. , deFriess N. A. , Nichols T. C. , Ezban M.
Published: July 2012

The objective of the present study was to evaluate the pharmacokinetic (PK) and pharmacodynamic (PD) profiles of the new recombinant FVIII compound turoctocog alfa and a Glyco‐PEGylated FVIII derivative thereof (N8‐GP) in Haemophilia A dogs. Six haemophilic dogs divided into two groups were included in the study. Each dog was administered a dose of 125 U kg−1, blood samples were collected at predetermined time points for both pharmacokinetic (FVIII measured by one‐stage aPTT assay) and pharmacodynamic [whole blood clotting time (WBCT)] evaluations. After intravenous administration to haemophilic dogs, the plasma concentration at the first sampling point was comparable for turoctocog alfa and N8‐GP, and the clearance was estimated to be 6.5 and 3.9 mL h−1kg−1 for turoctocog alfa and N8‐GP respectively. Both turoctocog alfa and N8‐GP were able to reduce the WBCT time to normal levels (<20 min), however, the reduced clearance was reflected in the WBCT, which returned to baseline at a later time point for N8‐GP as compared with dogs dosed with turoctocog alfa. The clearance was 40% reduced for N8‐GP as compared with turoctocog alfa. Simulations of a multiple dosing regimen in dogs, suggest that to maintain WBCT <20 min N8‐GP can be dosed at reduced intervals, e.g. with 4 days between doses, whereas turoctocog alfa will have to be dosed with 2½ day between doses. Data thereby supports N8‐GP as an alternative to standard rFVIII replacement therapy, with a more convenient dosing regimen.
Nurses' intervention goal categories for persons with spinal cord injury based on the International Classification of Functioning, Disability and Health: an international Delphi survey
Authors: Boldt Christine , Velstra Inge‐Marie , Brach Mirjam , Linseisen Elisabeth , Cieza Alarcos
Published: July 2012

Aim

To examine whether the International Classification of Functioning, Disability and Health can be used as standard language to express intervention goals on the part of nurses caring for persons with spinal cord injury.

Background

This classification is multipurpose and is designed to organize a wide range of health‐related information that can be used in any healthcare context and especially by interdisciplinary teams.

Design

A three‐round, consensus‐building, electronic‐mail survey using the Delphi technique.

Methods

In the Delphi process spinal cord injury nurses were asked to name the problems, resources, and aspects of the environment that they address when treating patients with spinal cord injury. The answers were linked to the categories of the International Classification of Functioning, Disability and Health. The study was carried out in 2007.

Results

Nurses (N = 35) from 17 countries provided 823 answers that were linked to a set of 143 categories, 24 personal factors, and 51 concepts categorized as ‘Not‐covered’, of which 32 were areas of fundamental importance to nurses. These were mainly risks that persons with spinal cord injury may face, such as the risk for future impairments.

Conclusion

The use of the data set resulting from this study should help determine and document the needs that pertain to spinal cord injury nursing on an international level. Future research should confirm the usefulness of such a data set in clinical practice and can contribute to the update process of the International Classification of Functioning, Disability and Health.
Structural insight in histo‐blood group binding by the F18 fimbrial adhesin FedF
Authors: Moonens Kristof , Bouckaert Julie , Coddens Annelies , Tran Thao , Panjikar Santosh , De Kerpel Maia , Cox Eric , Remaut Han , De Greve Henri
Published: July 2012

F18‐positive enterotoxigenic and Shiga toxin‐producing Escherichia coli are responsible for post‐weaning diarrhoea and oedema disease in pigs and lead to severe production losses in the farming industry. F18 fimbriae attach to the small intestine of young piglets by latching onto glycosphingolipids with A/H blood group determinants on type 1 core. We demonstrate the N‐terminal domain of the F18 fimbrial subunit FedF to be responsible for ABH‐mediated attachment and present its X‐ray structure in ligand‐free form and bound to A and B type 1 hexaoses. The FedF lectin domain comprises a 10‐stranded immunoglobulin‐like β‐sandwich. Three linear motives, Q47‐N50, H88‐S90 and R117‐T119, form a shallow glycan binding pocket near the tip of the domain that is selective for type 1 core glycans in extended conformation. In addition to the glycan binding pocket, a polybasic loop on the membrane proximal surface of FedF lectin domain is shown to be required for binding to piglet enterocytes. Although dispensable for ABH glycan recognition, the polybasic surface adds binding affinity in the context of the host cell membrane, a mechanism that is proposed to direct ABH–glycan binding to cell‐bound glycosphingolipids and could allow bacteria to avoid clearance by secreted glycoproteins.
The coming of age of the LeuO regulator
Authors: Hernández‐Lucas Ismael , Calva Edmundo
Published: July 2012

LeuO is a quiescent genetic regulator present in many bacteria, which forms part of the H‐NS regulon. LeuO in turn has been proposed to activate a subset of genes of the regulon by antagonizing H‐NS. In the paper by Dillon et al., binding of LeuO to the S. Typhimurium genome was observed by ChIP‐chip to some of the previously described LeuO‐regulated genes, upon growth under stress conditions. However, studies at a higher LeuO concentration from a cloned inducible promoter rendered many more binding sites, pointing towards the importance of the abundance of the regulator in the cell, in a given moment. Binding of LeuO was observed not only to intergenic sequences, but in the majority of cases to intragenic sequences, and co‐binding was observed with H‐NS in many sites and with RNA polymerase to the majority of sites. The authors define a binding motif that allowed the detection of several other LeuO‐regulated genes that were not detected by ChIP‐chip, which were possibly missed because LeuO binds and bridges distal sites, in those instances. The observations reported open new questions regarding the mode of action for LeuO.
Factors shaping the spatial variation of weed communities across a landscape mosaic
Authors: ALIGNIER A , PETIT S
Published: July 2012

Alignier A & Petit S (2012). Factors shaping the spatial variation of weed communities across a landscape mosaic. Weed Research.52, 402–410.

The spatial pattern of weeds within field is widely accepted to be aggregated, but few studies have assessed the spatial structure of weed communities at the landscape scale. Using a combination of aggregation measures and similarity indices, this study aimed at inferring the processes behind the spatial patterning of weed communities. We analysed spatial variation in the species composition of weed communities to understand how similarity in weed composition varies with field and spatial effects. Weeds were surveyed in a regular grid sampling a 110 ha landscape mosaic made up of 24 fields. We showed that weed composition similarity among samples exhibited an aggregated pattern at the mosaic scale, of up to 400 m. Similarity in weed composition varied mainly among fields, but also within field according to the distance from the field border. The decay in species similarity was influenced both by field and spatial effects. Spatial effect remains signifi‐cant after controlling for field effect. These findings provide support for the hypothesis that niche relationships and dispersal processes are both involved in the spatial patterning of weed species composition at the mosaic scale.
Identification of a dicer homologue gene (DCL2) in Nicotiana tabacum
Authors: Udriste A. A. , Stan V. , Radu G. L. , Tabler M. , Cucu N.
Published: July 2012

Eukaryotes possess a mechanism that generates small interfering RNA (siRNA) and microRNA (miRNA) and use these to regulate gene expression at the transcriptional or post‐transcriptional level. These small RNAs (21–24nt) are processed from long double‐stranded RNA precursors by type III RNase enzymes, referred to as DICER or DICER‐LIKE proteins (DCLs). In Arabidopsis, there are four DCL genes and their role in small RNA biogenesis and silencing has been the subject of intense study. DCL2 is less well studied than the other DCL proteins although it is known to play a role in formation of natural antisense siRNA and may be involved in transitive silencing of transgene transcripts. This study provides basic genomic information on DCL2 in the Nicotiana tabacum (NtDCL2) gene family and its probable roles in plant growth and development.
Histochemical Distribution of Digestive Enzymes in the Intestine of the Common Two‐Banded SeaBream, Diplodus vulgaris, Geoffroy St‐Hilaire 1817
Authors: Tlak Gajger I. , Nejedli S. , Kozarić Z.
Published: July 2012

The histochemical localization of non‐specific esterase, alkaline and acid phosphatase as well as aminopeptidase in the intestine of the free‐living common two‐banded sea bream (Diplodus vulgaris) was investigated. Fish were caught near the town of Zadar (Adriatic Sea, Croatia). Samples of pyloric caeca and three parts of the intestine proper (anterior, middle and posterior) were used for the description of non‐specific esterase, alkaline and acid phosphatase as well as aminopeptidase. Non‐specific esterase activity was found in the cytoplasm of enterocytes in pyloric caeca and in all investigated intestinal segments. The activity was stronger in the anterior and posterior part of the intestine than in the pyloric caeca and middle segment of the intestine. Intestinal alkaline phosphatase was detected in brush border of enterocytes of all investigated intestinal segments. Enzymatic activity gradually decreased in a posterior direction. Acid phosphatase activity was observed as a fine granular reaction product in the supranuclear region of enterocytes. This activity was almost equal in pyloric caeca as well as in the anterior intestinal segment, while it was stronger in the middle and posterior intestinal segment. Aminopeptidase was present along the intestinal epithelium brush border in all investigated parts of the digestive tube. The intensity of aminopeptidase increased posteriorly. The possible role of investigated enzymes in intracellular digestion and transport is discussed.