bluuebunny/crossref_metadata_2025 huggingface dataset:
AN EXTENDED FRAMEWORK FOR PREFERENCE RELATIONS – ERRATUM
Authors: Gustafsson Johan E.
Published: November 2011

It is regretted that the originally published paper (Gustafsson, 2011a) was not the author's final amended version. We apologise for this oversight and reproduce the entire corrected paper here in print and online, with revised notation.
Comparative effects of processing methods on the feeding value of maize in feedlot cattle
Authors: Zinn R. A. , Barreras A. , Corona L. , Owens F. N. , Plascencia A.
Published: November 2011

The primary reason for processing maize is to enhance feeding value. Total tract starch digestion is similar for coarsely processed (dry rolled, cracked) dry maize. Enhancements in starch digestion due to dry rolling maizev.feeding maize whole may be greater in light-weight calves than in yearlings, and when DM intake is restricted ( < 1·5 % of body weight). The net energy (NE) maintain (NEm) and NE gain (NEg) values for whole maize are 8·83 and 6·02 MJ (2·11 and 1·44 Mcal)/kg, respectively. Compared with conventional dry processing (i.e. coarse rolled, cracked), finely processing maize may increase the initial rate of digestion, but does not improve total tract starch digestion. Tempering before rolling (without the addition of steam) may enhance the growth performance response and the NE value of maize. Average total tract starch digestion is similar for high-moisture and steam-flaked maize. However, the proportion of starch digested ruminally is greater (about 8 %) for high-moisture maize. The growth performance response of feedlot cattle to the feeding of high-moisture maize is highly variable. Although the NEmand NEgvalue of whole high-moisture maize was slightly less than that of dry processed maize (averaging 9·04 and 6·44 MJ (2·16 and 1·54 Mcal)/kg, respectively), grinding or rolling high-moisture maize before ensiling increased (6 %) its NE value. Substituting steam-flaked maize for dry processed maize increases average daily gain (6·3 %) and decreases DM intake (5 %). The comparative NEmand NEgvalues for steam-flaked maize at optimal processing (density = 0·34 kg/l) are 10·04 and 7·07 MJ (2·40 and 1·69 Mcal)/kg, respectively. These NE values are greater (3 %) than current tabular values (National Research Council, 2000), being more consistent with earlier standards (National Research Council, 1984). When maize is the primary or sole source of starch in the diet, concentration of starch in faeces (faecal starch, % of DM) of feedlot steers can serve as an indicator of total tract starch digestion, and, hence, the feeding value of maize.
Recording a patient diet over the radical course of radiotherapy for prostate cancer using a diet diary: a feasibility study
Authors: Oates R , McPhee N , Joon M Lim , Schneider-Kolsky M , Kron T
Published: November 2011

Aims: To obtain an estimate of dietary fibre and fluid intake in Australian men undergoing prostate radiotherapy and to establish feasibility and patient compliance with recording normal diet without intervention during the radical course of radiotherapy.

Methods: Eleven participants were enrolled and treated with 74–78 Gray (Gy) to the prostate over 8 weeks. Participants were instructed to record a diary of their food and fluid intake and bowel motions for the duration of treatment. Treating radiation therapists were instructed to initial the diet diary daily. Diet diaries were assessed for compliance by analysing the number of days over the treatment period and the number of diary pages submitted. The diet diaries were analysed for nutrient intake of fibre and fluids.

Results: A total of 10 of 11 participants submitted a diet record for the full duration of treatment with a median compliance of 100% (range 90.4–100%) of days recorded. The mean (standard deviation) of fibre and fluids recorded in the diets were 21.5 g (5.5) and 2227.1 g (733.1), respectively.

Conclusions: It is feasible for patients to record a diet diary over a radical course of prostate radiotherapy. In this study, most patients were highly compliant with submitting a diet record for each day during treatment.
Does gender bias influence awards given by societies?
Authors: Holmes Mary Anne , Asher Pranoti , Farrington John , Fine Rana , Leinen Margaret S. , LeBoy Phoebe
Published: November 2011

AGU is a participant in a U.S. National Science Foundation (NSF)–funded project called Advancing Ways of Awarding Recognition in Disciplinary Societies (AWARDS), which seeks to examine whether gender bias affects selection of recipients of society awards. AGU is interested in learning why there is a higher proportion of female recipients of service and education awards over the past 2 decades. Combined with a lower rate of receipt of research awards, these results suggest that implicit (subconscious) bias in favor of male candidates still influences awardee selection. Six other professional societies (American Chemical Society, American Mathematical Society, American Society of Anesthesiologists, Mathematical Association of America, Society for Neuroscience, and Society for Industrial and Applied Mathematics) are participating in the project. Volunteers from each participant society attended an Association for Women in Science (AWIS)–sponsored workshop in May 2010 to examine data and review literature on best practices for fair selection of society awardees. A draft proposal for implementing these practices will be brought before the AGU Council and the Honors and Recognition Committee at their upcoming meetings.
The language of science and communication with Congress
Authors: Napolitano Grace F.
Published: November 2011

“There are in fact two things, science and opinion; the former begets knowledge, the latter, ignorance.” So stated Hippocrates back in 400 C.E. Today we find ourselves in a tug of war between science and opinion as we try to fashion a path forward on many important societal issues, including the use of science in addressing the water, energy, and climate change issues that are growing in importance. Our job in Congress is making sure we use the knowledge gained from asking questions and apply the responses properly in the decision‐and policy‐making processes. While that all sounds good in theory, the application is at best cumbersome, often leaving us with more questions than answers.
Putting bounds on the drivers of turbulence
Authors: Schultz Colin
Published: November 2011

When fluids with different or continuously varying properties flow next to one another, turbulent flow can emerge. At its most basic, turbulence takes the form of swirling vortices that occur along the flow direction; these vortices are known as a Kelvin‐Helmholtz (K‐H) instability. Superimposed on this two‐dimensional K‐H foundation are a variety of secondary instabilities that extend the mixing into three dimensions and endow it with a more complicated structure. How these secondary instabilities form and the role they play in pulling smoothly flowing fluid into the chaos of turbulence remain an area of active investigation.
Origin of a tidal structure in the thermospheric O/N2 ratio
Authors: Balcerak Ernie
Published: November 2011

One recently recognized way of studying the ionospheric and thermospheric structure is through measurements of the column number density ratio of atomic oxygen to molecular nitrogen (O/N2). Data from the Global Ultraviolet Imager on board the Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED) satellite show that this ratio exhibits a tidal structure. Kil and Paxton found that the 135.6‐nanometer emission produced by the radiative recombination of the oxygen ion contributes to the retrieved O/N2 ratio, and therefore the tidal structure in the O/N2 ratio originates in the ionosphere, not the thermosphere. (Geophysical Research Letters, doi:10.1029/2011GL049432, 2011)
Mean full‐depth summer circulation and transports at the northern periphery of the Atlantic Ocean in the 2000s
Authors: Sarafanov Artem , Falina Anastasia , Mercier Herlé , Sokov Alexey , Lherminier Pascale , Gourcuff Claire , Gladyshev Sergey , Gaillard Fabienne , Daniault Nathalie
Published: November 2011

A mean state of the full‐depth summer circulation in the Atlantic Ocean in the region in between Cape Farewell (Greenland), Scotland and the Greenland‐Scotland Ridge (GSR) is assessed by combining 2002–2008 yearly hydrographic measurements at 59.5°N, mean dynamic topography, satellite altimetry data and available estimates of the Atlantic–Nordic Seas exchange. The mean absolute transports by the upper‐ocean, mid‐depth and deep currents and the Meridional Overturning Circulation (MOCσ = 16.5 ± 2.2 Sv, at σ0= 27.55) at 59.5°N are quantified in the density space. Inter‐basin and diapycnal volume fluxes in between the 59.5°N section and the GSR are then estimated from a box model. The dominant components of the meridional exchange across 59.5°N are the North Atlantic Current (NAC, 15.5 ± 0.8 Sv,σ0 < 27.55) east of the Reykjanes Ridge, the northward Irminger Current (IC, 12.0 ± 3.0 Sv) and southward Western Boundary Current (WBC, 32.1 ± 5.9 Sv) in the Irminger Sea and the deep water export from the northern Iceland Basin (3.7 ± 0.8 Sv, σ0 > 27.80). About 60% (12.7 ± 1.4 Sv) of waters carried in the MOCσ upper limb (σ0< 27.55) by the NAC/IC across 59.5°N (21.1 ± 1.0 Sv) recirculates westward south of the GSR and feeds the WBC. 80% (10.2 ± 1.7 Sv) of the recirculating NAC/IC‐derived upper‐ocean waters gains density ofσ0 > 27.55 and contributes to the MOCσlower limb. Accordingly, the contribution of light‐to‐dense water conversion south of the GSR (∼10 Sv) to the MOCσ lower limb at 59.5°N is one and a half times larger than the contribution of dense water production in the Nordic Seas (∼6 Sv).
Hydrologic consistency as a basis for assessing complexity of monthly water balance models for the continental United States
Authors: Martinez Guillermo F. , Gupta Hoshin V.
Published: November 2011

Methods to select parsimonious and hydrologically consistent model structures are useful for evaluating dominance of hydrologic processes and representativeness of data. While information criteria (appropriately constrained to obey underlying statistical assumptions) can provide a basis for evaluating appropriate model complexity, it is not sufficient to rely upon the principle of maximum likelihood (ML) alone. We suggest that one must also call upon a “principle of hydrologic consistency,” meaning that selected ML structures and parameter estimates must be constrained (as well as possible) to reproduce desired hydrological characteristics of the processes under investigation. This argument is demonstrated in the context of evaluating the suitability of candidate model structures for lumped water balance modeling across the continental United States, using data from 307 snow‐free catchments. The models are constrained to satisfy several tests of hydrologic consistency, a flow space transformation is used to ensure better consistency with underlying statistical assumptions, and information criteria are used to evaluate model complexity relative to the data. The results clearly demonstrate that the principle of consistency provides a sensible basis for guiding selection of model structures and indicate strong spatial persistence of certain model structures across the continental United States. Further work to untangle reasons for model structure predominance can help to relate conceptual model structures to physical characteristics of the catchments, facilitating the task of prediction in ungaged basins.
Preventing hereditary cancers caused by opportunistic carcinogens
Authors: Friedenson Bernard
Published: November 2011

Objectives

Previous studies reported inherited BRCA1/2 deficits appear to cause cancer by impairing normal protective responses to some carcinogens. Opportunistic carcinogens can exploit these deficits by causing chronic inflammation, constant cell death and replacement in a mutagenic environment, DNA crosslinking or double strand breaks. Some of the resulting cancers may be prevented if BRCA1/2 specific carcinogens are identified.

Methods

The literature was systematically searched for carcinogens capable of exploiting deficits in BRCA1/2 pathways. Search criteria were common exposure, available information, required BRCA1/2 pathway repairs, increased risks for any cancer, and effects on stem cells.

Results

Formaldehyde and acetaldehyde are closely related carcinogens and common pollutants that are everywhere. Alcohol metabolism also produces acetaldehyde. High levels of either carcinogen overwhelm normal detoxification systems, cause inflammation, inhibit DNA repair and produce DNA cross links as critical carcinogenic lesions. Searching model system studies revealed both carcinogens activate stem cells, BRCA1/2 pathways and connected BRCA1/2 pathways to myeloid leukemia. For example, the BRCA1-BARD1 complex is required for proper nucleophosmin functions. Nucleophosmin prevents a major subset of acute myeloid leukemia (AML). Next, these concepts were independently tested against risks for myeloid leukemia. Epidemiologic results showed that BRCA2 gene defects inherited on both chromosomes increased risks so dramatically that AML occurs in most children. Using data from 14 studies, known/potential heterozygous BRCA1/BRCA2 mutations increased risks for myeloid leukemias by at least 3 fold in 7 studies and by at least 50% in 12.Acetaldehyde occurs in breast milk. In model studies, excessive acetaldehyde/alcohol exposure affects estrogen metabolism and stimulates alternate alcohol detoxification pathways.These pathways can cause DNA cross linking by releasing oxygen species and activating procarcinogens. Acetaldehyde in rats’ drinking water increased incidence of leukemias, lymphomas,pancreatic cancers and fibroadenomas. Human epidemiologic studies showed increased premenopausal breast cancer risks associated with persistent/high acetaldehyde levels related to alcohol metabolism genotype.

Conclusions

Although it is difficult to prove direct causation, BRCA1/2 mutation carriers may reduce cancer risks by avoiding excessive formaldehyde and acetaldehyde
Oxidation of Met1606 in von Willebrand factor is a risk factor for thrombotic and septic complications in chronic renal failure
Authors: De Filippis Vincenzo , Lancellotti Stefano , Maset Fabio , Spolaore Barbara , Pozzi Nicola , Gambaro Giovanni , Oggianu Laura , Calò Lorenzo A. , De Cristofaro Raimondo
Published: November 2011

CKD (chronic kidney disease) is a life-threatening pathology, often requiring HD (haemodialysis) and characterized by high OS (oxidative stress), inflammation and perturbation of vascular endothelium. HD patients have increased levels of vWF (von Willebrand factor), a large protein (~240 kDa) released as UL-vWF (ultra large-vWF polymers, molecular mass ~20000–50000 kDa) from vascular endothelial cells and megakaryocytes, and responsible for the initiation of primary haemostasis. The pro-haemostatic potential of vWF increases with its length, which is proteolytically regulated by ADAMTS-13 (a disintegrin and metalloproteinase with thrombospondin motifs 13), a zinc-protease cleaving vWF at the single Tyr1605–Met1606 bond, and by LSPs (leucocyte serine proteases), released by activated PMNs (polymorphonuclear cells) during bacterial infections. Previous studies have shown that in vitro oxidation of Met1606 hinders vWF cleavage by ADAMTS-13, resulting in the accumulation of UL-vWF that are not only more pro-thrombotic than shorter vWF oligomers, but also more efficient in binding to bacterial adhesins during sepsis. Notably, HD patients have increased risk of developing dramatic cardiovascular and septic complications, whose underlying mechanisms are largely unknown. In the present study, we first purified vWF from HD patients and then chemically characterized its oxidative state. Interestingly, HD-vWF contains high carbonyl levels and increased proportion of UL-vWF polymers that are also more resistant to ADAMTS-13. Using TMS (targeted MS) techniques, we estimated that HD-vWF contains >10% of Met1606 in the sulfoxide form. We conclude that oxidation of Met1606, impairing ADAMTS-13 cleavage, results in the accumulation of UL-vWF polymers, which recruit and activate platelets more efficiently and bind more tightly to bacterial adhesins, thus contributing to the development of thrombotic and septic complications in CKD.
Nesprin-3: a versatile connector between the nucleus and the cytoskeleton
Authors: Ketema Mirjam , Sonnenberg Arnoud
Published: November 2011

The cytoskeleton is connected to the nuclear interior by LINC (linker of nucleoskeleton and cytoskeleton) complexes located in the nuclear envelope. These complexes consist of SUN proteins and nesprins present in the inner and outer nuclear membrane respectively. Whereas SUN proteins can bind the nuclear lamina, members of the nesprin protein family connect the nucleus to different components of the cytoskeleton. Nesprin-1 and -2 can establish a direct link with actin filaments, whereas nesprin-4 associates indirectly with microtubules through its interaction with kinesin-1. Nesprin-3 is the only family member known that can link the nuclear envelope to intermediate filaments. This indirect interaction is mediated by the binding of nesprin-3 to the cytoskeletal linker protein plectin. Furthermore, nesprin-3 can connect the nucleus to microtubules by its interactions with BPAG1 (bullous pemphigoid antigen 1) and MACF (microtubule–actin cross-linking factor). In contrast with the active roles that nesprin-1, -2 and -4 have in actin- and microtubule-dependent nuclear positioning, the role of nesprin-3 is likely to be more passive. We suggest that it helps to stabilize the anchorage of the nucleus within the cytoplasm and maintain the structural integrity and shape of the nucleus.
Cell autonomous and systemic factors in progeria development
Authors: Osorio Fernando G. , Ugalde Alejandro P. , Mariño Guillermo , Puente Xose S. , Freije José M.P. , López-Otín Carlos
Published: November 2011

Progeroid laminopathies are accelerated aging syndromes caused by defects in nuclear envelope proteins. Accordingly, mutations in the LMNA gene and functionally related genes have been described to cause HGPS (Hutchinson–Gilford progeria syndrome), MAD (mandibuloacral dysplasia) or RD (restrictive dermopathy). Functional studies with animal and cellular models of these syndromes have facilitated the identification of the molecular alterations and regulatory pathways involved in progeria development. We have recently described a novel regulatory pathway involving miR-29 and p53 tumour suppressor which has provided valuable information on the molecular components orchestrating the response to nuclear damage stress. Furthermore, by using progeroid mice deficient in ZMPSTE24 (zinc metalloprotease STE24 homologue) involved in lamin A maturation, we have demonstrated that, besides these abnormal cellular responses to stress, dysregulation of the somatotropic axis is responsible for some of the alterations associated with progeria. Consistent with these observations, pharmacological restoration of the somatotroph axis in these mice delays the onset of their progeroid features, significantly extending their lifespan and supporting the importance of systemic alterations in progeria progression. Finally, we have very recently identified a novel progeroid syndrome with distinctive features from HGPS and MAD, which we have designated NGPS (Néstor–Guillermo progeria syndrome) (OMIM #614008). This disorder is caused by a mutation in BANF1, a gene encoding a protein with essential functions in the assembly of the nuclear envelope, further illustrating the importance of the nuclear lamina integrity for human health and providing additional support to the study of progeroid syndromes as a valuable source of information on human aging.
Bacterial nitrate assimilation: gene distribution and regulation
Authors: Luque-Almagro Víctor M. , Gates Andrew J. , Moreno-Vivián Conrado , Ferguson Stuart J. , Richardson David J. , Roldán M. Dolores
Published: November 2011

In the context of the global nitrogen cycle, the importance of inorganic nitrate for the nutrition and growth of marine and freshwater autotrophic phytoplankton has long been recognized. In contrast, the utilization of nitrate by heterotrophic bacteria has historically received less attention because the primary role of these organisms has classically been considered to be the decomposition and mineralization of dissolved and particulate organic nitrogen. In the pre-genome sequence era, it was known that some, but not all, heterotrophic bacteria were capable of growth on nitrate as a sole nitrogen source. However, examination of currently available prokaryotic genome sequences suggests that assimilatory nitrate reductase (Nas) systems are widespread phylogenetically in bacterial and archaeal heterotrophs. Until now, regulation of nitrate assimilation has been mainly studied in cyanobacteria. In contrast, in heterotrophic bacterial strains, the study of nitrate assimilation regulation has been limited to Rhodobacter capsulatus, Klebsiella oxytoca, Azotobacter vinelandii and Bacillus subtilis. In Gram-negative bacteria, the nas genes are subjected to dual control: ammonia repression by the general nitrogen regulatory (Ntr) system and specific nitrate or nitrite induction. The Ntr system is widely distributed in bacteria, whereas the nitrate/nitrite-specific control is variable depending on the organism.
How neuropilin-1 regulates receptor tyrosine kinase signalling: the knowns and known unknowns
Authors: Zachary Ian C.
Published: November 2011

Essential roles of NRP1 (neuropilin-1) in cardiovascular development and in neuronal axon targeting during embryogenesis are thought to be mediated primarily through binding of NRP1 to two unrelated types of ligands: the VEGF (vascular endothelial growth factor) family of angiogenic cytokines in the endothelium, and the class 3 semaphorins in neurons. A widely accepted mechanism for the role of NRP1 in the endothelium is VEGF binding to NRP1 and VEGFR2 (VEGF receptor 2) and VEGF-dependent formation of complexes or NRP1–VEGFR2 holoreceptors with enhanced signalling activity and biological function. However, although some basic features of this model are solidly based on biochemical and cellular data, others are open to question. Furthermore, a mechanistic account of NRP1 has to accommodate research which emphasizes the diversity of NRP1 functions in different cell types and particularly an emerging role in signalling by other growth factor ligands for RTKs (receptor tyrosine kinases) such as HGF (hepatocyte growth factor) and PDGF (platelet-derived growth factor). It is uncertain, however, whether the model of NRP1–RTK heterocomplex formation applies in all of these situations. In the light of these developments, the need to explain mechanistically the role of NRP1 in signalling is coming increasingly to the fore. The present article focuses on some of the most important unresolved questions concerning the mechanism(s) through which NRP1 acts, and highlights recent findings which are beginning to generate insights into these questions.
Role of Fur on cyanide tolerance of Pseudomonas pseudoalcaligenes CECT5344
Authors: Becerra Gracia , Blasco Rafael , Quesada Alberto , Merchán Faustino , Igeño M. Isabel
Published: November 2011

Pseudomonas pseudoalcaligenes CECT5344 can be used in cyanide bioremediation processes because it grows at pH 9.5 using 2.0 mM cyanide at the sole nitrogen source. Cyanide strongly binds to metals creating iron-deprivation conditions. The bacterium responds to the presence of cyanide by inducing several processes such as siderophore synthesis for iron capture, cyanide-insensitive respiration system and defence mechanisms against oxidative stress. Since high concentrations of cyanide cause iron deficiency and because iron is an essential nutrient, bacterial growth in the presence of cyanide requires an efficient iron uptake. Fur is a global transcription factor that regulates a diversity of biological processes such as iron homoeostasis, TCA (tricarboxylic acid) cycle metabolism and oxidative stress response. Fur's regulation of iron uptake and storage genes should play a significant role in the lives of these bacteria. In the present review, current knowledge of Fur is summarized.
Anaerobic ammonium oxidation (anammox) in different natural ecosystems
Authors: Hu Bao-lan , Shen Li-dong , Xu Xiang-yang , Zheng Ping
Published: November 2011

Anammox (anaerobic ammonium oxidation), which is a reaction that oxidizes ammonium to dinitrogen gas using nitrite as the electron acceptor under anoxic conditions, was an important discovery in the nitrogen cycle. The reaction is mediated by a specialized group of planctomycete-like bacteria that were first discovered in man-made ecosystems. Subsequently, many studies have reported on the ubiquitous distribution of anammox bacteria in various natural habitats, including anoxic marine sediments and water columns, freshwater sediments and water columns, terrestrial ecosystems and some special ecosystems, such as petroleum reservoirs. Previous studies have estimated that the anammox process is responsible for 50% of the marine nitrogen loss. Recently, the anammox process was reported to account for 9–40% and 4–37% of the nitrogen loss in inland lakes and agricultural soils respectively. These findings indicate the great potential for the anammox process to occur in freshwater and terrestrial ecosystems. The distribution of different anammox bacteria and their contribution to nitrogen loss have been described in different natural habitats, demonstrating that the anammox process is strongly influenced by the local environmental conditions. The present mini-review summarizes the current knowledge of the ecological distribution of anammox bacteria, their contribution to nitrogen loss in various natural ecosystems and the effects of major influential factors on the anammox process.
Metabolic adaptation ofPseudomonas pseudoalcaligenesCECT5344 to cyanide: role of malate–quinone oxidoreductases, aconitase and fumarase isoenzymes
Authors: Igeño M. Isabel , Becerra Gracia , Guijo M. Isabel , Merchán Faustino , Blasco Rafael
Published: November 2011

In general, the biodegradation of a toxic compound by a micro-organism requires the concurrence of, at least, two features in the biological system: first, the capability of the micro-organism to metabolize the toxic compound, and secondly, the capacity to resist its toxic effect. Pseudomonas pseudoalcaligenes CECT5344 is a bacterium used in the biodegradation of cyanide because it is capable to use it as a nitrogen source. The present review is mainly focused on the putative role of iron-containing enzymes of the tricarboxylic acid cycle in cyanide resistance by P. pseudoalcaligenes CECT5344.
The nuclear envelope and its involvement in cellular stress responses
Authors: Malhas Ashraf N. , Vaux David J.
Published: November 2011

The nuclear envelope is not only important for the structural integrity of the nucleus, but also involved in a number of cellular functions. It has been shown to be important for maintaining and controlling chromatin organization, sequestering transcription factors, replication, transcription and signalling. The nuclear envelope is thus important for development and differentiation, and some of its components are essential for cell viability. Among the many functions which are emerging for the nuclear envelope is its involvement in protecting the cell against different types of cellular stress. In the present paper, we review key findings which describe the roles of nuclear envelope components in responses to common types of stress conditions.
Evolvement of LEM proteins as chromatin tethers at the nuclear periphery
Authors: Brachner Andreas , Foisner Roland
Published: November 2011

The nuclear envelope in eukaryotic cells has important roles in chromatin organization. The inner nuclear membrane contains over 60 transmembrane proteins. LEM [LAP2 (lamina-associated polypeptide 2)/emerin/MAN1] domain-containing proteins of the inner nuclear membrane are involved in tethering chromatin to the nuclear envelope and affect gene expression. They contain a common structural, bihelical motif, the so-called LEM domain, which mediates binding to a conserved chromatin protein, BAF (barrier to autointegration factor). Interestingly, this domain is highly related to other bihelical motifs, termed HeH (helix–extension–helix) and SAP {SAF (scaffold attachment factor)/acinus/PIAS [protein inhibitor of activated STAT (signal transducer and activator of transcription)]} motifs, which are directly linked to DNA. In the present paper, we summarize evidence that the LEM motif evolved from the HeH and SAP domains concomitantly with BAF. In addition, we discuss the potential evolution of HeH/SAP and LEM domain-containing proteins and their role in chromatin tethering and gene regulation from unicellular eukaryotes to mammals.
A non-stationary model for high power impulse magnetron sputtering discharges
Authors: Kozák Tomáš , Dagmar Pajdarová Andrea
Published: November 2011

We present a non-stationary model proposed for high power impulse magnetron sputtering discharges, which is based on a global description of the plasma processes. The model takes into account a typical structure of magnetron discharges by dividing the plasma volume into two zones, the magnetically confined high-density zone above the target racetrack and the bulk plasma zone, where the transport of particles onto the substrate and the chamber walls dominates. The comparisons of the calculated data with measured results for distinct experimental conditions in two different high power impulse magnetron sputtering systems show a good agreement, suggesting that all relevant plasma processes were correctly incorporated into the model equations. The model can be used to gain a more detailed insight into the complicated processes in such types of discharges and to predict the influence of various process parameters on the deposition characteristics.
Higher-order (2 + 4) Korteweg-de Vries-like equation for interfacial waves in a symmetric three-layer fluid
Authors: Kurkina O. E. , Kurkin A. A. , Soomere T. , Pelinovsky E. N. , Rouvinskaya E. A.
Published: November 2011

We address a specific but possible situation in natural water bodies when the three-layer stratification has a symmetric nature, with equal depths of the uppermost and the lowermost layers. In such case, the coefficients at the leading nonlinear terms of the modified Korteweg-de Vries (mKdV) equation vanish simultaneously. It is shown that in such cases there exists a specific balance between the leading nonlinear and dispersive terms. An extension to the mKdV equation is derived by means of combination of a sequence of asymptotic methods. The resulting equation contains a cubic and a quintic nonlinearity of the same magnitude and possesses solitary wave solutions of different polarity. The properties of smaller solutions resemble those for the solutions of the mKdV equation, whereas the height of the taller solutions is limited and they become table-like. It is demonstrated numerically that the collisions of solitary wave solutions to the resulting equation are weakly inelastic: the basic properties of the counterparts experience very limited changes but the interactions are certainly accompanied by a certain level of radiation of small-amplitude waves.
Weak commutation relations of unbounded operators and applications
Authors: Bagarello Fabio , Inoue Atsushi , Trapani Camillo
Published: November 2011

Four possible definitions of the commutation relation [S, T] = 11 of two closable unbounded operators S, T are compared. The weak sense of this commutator is given in terms of the inner product of the Hilbert space \documentclass[12pt]{minimal}\begin{document}${\mathcal H}$\end{document}H where the operators act. Some consequences on the existence of eigenvectors of two numberlike operators are derived and the partial O*-algebra generated by S, T is studied. Some applications are also considered.
Global hyperbolicity is stable in the interval topology
Authors: Navarro J. J. Benavides , Minguzzi E.
Published: November 2011

We prove that global hyperbolicity is stable in the interval topology on the spacetime metrics. We also prove that every globally hyperbolic spacetime admits a Cauchy hypersurface which remains Cauchy under small perturbations of the spacetime metric. Moreover, we prove that if the spacetime admits a complete timelike Killing field, then the light cones can be widened preserving both global hyperbolicity and the Killing property of the field.
Spin-adapted open-shell time-dependent density functional theory. III. An even better and simpler formulation
Authors: Li Zhendong , Liu Wenjian
Published: November 2011

The recently proposed spin-adapted time-dependent density functional theory (S-TD-DFT) [Z. Li and W. Liu, J. Chem. Phys. 133, 064106 (2010)]10.1063/1.3463799 resolves the spin-contamination problem in describing singly excited states of high spin open-shell systems. It is an extension of the standard restricted open-shell Kohn-Sham-based TD-DFT which can only access those excited states due to singlet-coupled single excitations. It is also far superior over the unrestricted Kohn-Sham-based TD-DFT (U-TD-DFT) which suffers from severe spin contamination for those excited states due to triplet-coupled single excitations. Nonetheless, the accuracy of S-TD-DFT for high spin open-shell systems is still inferior to TD-DFT for well-behaved closed-shell systems. The reason can be traced back to the violation of the spin degeneracy conditions (SDC) by approximate exchange-correlation (XC) functionals. Noticing that spin-adapted random phase approximation (S-RPA) can indeed maintain the SDC by virtue of the Wigner-Eckart theorem, a hybrid ansatz combining the good of S-TD-DFT and S-RPA can immediately be envisaged. The resulting formalism, dubbed as X-TD-DFT, is free of spin contamination and can also be viewed as a S-RPA correction to the XC kernel of U-TD-DFT. Compared with S-TD-DFT, X-TD-DFT leads to much improved results for the low-lying excited states of, e.g., \documentclass[12pt]{minimal}\begin{document}${\rm N}_2^+$\end{document}N2+, yet with much reduced computational cost. Therefore, X-TD-DFT can be recommended for routine calculations of excited states of high spin open-shell systems.
Mutation-induced fold switching among lattice proteins
Authors: Holzgräfe Christian , Irbäck Anders , Troein Carl
Published: November 2011

Recent experiments uncovered a mutational pathway between two proteins, along which a single mutation causes a switch in fold. Searching for such paths between real proteins remains, despite this achievement, a true challenge. Here, we analyze fold switching in the minimalistic hydrophobic/polar model on a square lattice. For this analysis, we generate a comprehensive sequence-structure database for chains of length ⩽ 30, which exceeds previous work by five units. Single-mutation-induced fold switching turns out to be quite common in the model. The switches define a fold network, whose topology is roughly similar to what one would expect for a set of randomly connected nodes. In the combinatorially challenging search for fold switches between two proteins, a tempting strategy is to only consider paths containing the minimum number of mutations. Such a restricted search fails to correctly identify 40% of the single-mutation-linked fold pairs that we observe. The thermodynamic stability is correlated with mutational stability and is, on average, markedly reduced at the observed fold switches.
Conditional stability theorem for the one dimensional Klein-Gordon equation
Authors: Demirkaya Aslihan , Stanislavova Milena
Published: November 2011

The paper addresses the conditional non-linear stability of the steady state solutions of the one-dimensional Klein-Gordon equation for large time. We explicitly construct the center-stable manifold for the steady state solutions using the modulation method of Soffer and Weinstein and Strichartz type estimates. The main difficulty in the one-dimensional case is that the required decay of the Klein-Gordon semigroup does not follow from Strichartz estimates alone. We resolve this issue by proving an additional weighted decay estimate and further refinement of the function spaces, which allows us to close the argument in spaces with very little time decay.
Thermoelectric conversion via laser-induced voltage in highly textured polycrystalline NaxCoO2 ceramic
Authors: Yan G. W. , Yu L. , Wang Y. , Zhang H. , Zhang P. X. , Habermeier H.-U.
Published: November 2011

We have studied and analyzed the laser-induced voltage effect in highly c-axis-oriented polycrystalline NaxCoO2. The textured and layered stacking NaxCoO2 (x ∼ 0.7) bulks were prepared by a solid-state reaction process. Under the irradiation on Na0.67CoO2 bulk surface with pulsed laser (λ = 248 nm), the induced voltage signals were observed on the inclined surface with rise time 30 ns–43 ns and peak voltage 200 mV–500 mV; the voltage peak values show a linear dependence of laser energy densities. The crystal grains orientation plays a critical role in voltage peak value whether in film or texture bulk. The transverse voltage signal brings the information of thermoelectric anisotropy. In NaxCoO2 band structure, the Fermi surface is different in the ab plane and along the c axis, leading to anisotropy of Seebeck coefficient. Additionally, the artificial structure of the inclined surface for highly textured bulk enables us to obtain a transverse voltage on inclined surface. These results demonstrated the layered textured bulk has potential applications in waste-heat conversion via transverse thermoelectric effect.
Talbot-Lau x-ray interferometry for high energy density plasma diagnostic
Authors: Stutman D. , Finkenthal M.
Published: November 2011

High resolution density diagnostics are difficult in high energy density laboratory plasmas (HEDLP) experiments due to the scarcity of probes that can penetrate above solid density plasmas. Hard x-rays are one possible probe for such dense plasmas. We study the possibility of applying an x-ray method recently developed for medical imaging, differential phase-contrast with Talbot-Lau interferometers, for the diagnostic of electron density and small-scale hydrodynamic instabilities in HEDLP experiments. The Talbot method uses micro-periodic gratings to measure the refraction and ultra-small angle scatter of x-rays through an object and is attractive for HEDLP diagnostic due to its capability to work with incoherent and polychromatic x-ray sources such as the laser driven backlighters used for HEDLP radiography. Our paper studies the potential of the Talbot method for HEDLP diagnostic, its adaptation to the HEDLP environment, and its extension of high x-ray energy using micro-periodic mirrors. The analysis is illustrated with experimental results obtained using a laboratory Talbot interferometer.
Energy harvesting properties of all-thin-film multiferroic cantilevers
Authors: Onuta Tiberiu-Dan , Wang Yi , Long Christian J. , Takeuchi Ichiro
Published: November 2011

We have measured electromagnetic energy harvesting properties of all-thin-film magnetoelectric (ME) heterostructures on Si cantilevers. The devices are built on a silicon oxide/nitride/oxide stack, and the ME layers consist of a magnetostrictive Fe0.7Ga0.3 thin film and a Pb(Zr0.52Ti0.48)O3 piezoelectric thin film. The harvested peak power at 1 Oe is 0.7 mW/cm3 (RMS) at the resonant frequency (3.8 kHz) with a load of 12.5 kΩ. The resonant frequency was found to display DC bias magnetic field dependence indicative of a magnetization canting with respect to the cantilever easy axis as a result of interplay between the anisotropy and Zeeman energies.
Interchain coupled chain dynamics of poly(ethylene oxide) in blends with poly(methyl methacrylate): Coupling model analysis
Authors: Ngai K. L. , Wang Li-Min
Published: November 2011

Quasielastic neutron scattering and molecular dynamics simulation data from poly(ethylene oxide) (PEO)/poly(methyl methacrylate) (PMMA) blends found that for short times the self-dynamics of PEO chain follows the Rouse model, but at longer times past tc = 1–2 ns it becomes slower and departs from the Rouse model in dependences on time, momentum transfer, and temperature. To explain the anomalies, others had proposed the random Rouse model (RRM) in which each monomer has different mobility taken from a broad log-normal distribution. Despite the success of the RRM, Diddens et al. [Eur. Phys. Lett. 95, 56003 (2011)] extracted the distribution of friction coefficients from the MD simulations of a PEO/PMMA blend and found that the distribution is much narrower than expected from the RRM. We propose a simpler alternative explanation of the data by utilizing alone the observed crossover of PEO chain dynamics at tc. The present problem is just a special case of a general property of relaxation in interacting systems, which is the crossover from independent relaxation to coupled many-body relaxation at some tc determined by the interaction potential and intermolecular coupling/constraints. The generality is brought out vividly by pointing out that the crossover also had been observed by neutron scattering from entangled chains relaxation in monodisperse homopolymers, and from the segmental α-relaxation of PEO in blends with PMMA. The properties of all the relaxation processes in connection with the crossover are similar, despite the length scales of the relaxation in these systems are widely different.
Quantitative analysis of the guest-concentration dependence of the mobility in a disordered fluorene-arylamine host-guest system in the guest-to-guest regime
Authors: Nicolai H. T. , Hof A. J. , Lu M. , Blom P. W. M. , de Vries R. J. , Coehoorn R.
Published: November 2011

The charge transport in a polyspirobifluorene derivative with copolymerized N,N,N′,N′-tetraaryldiamino biphenyl (TAD) hole transport units is investigated as a function of the TAD content. For TAD concentrations larger than 5%, guest-to-guest transport is observed. It is demonstrated that in this regime the charge carrier density dependent mobility can be described consistently with the extended Gaussian disorder model, with a density of hopping sites which is proportional to the TAD concentration and comparable to the molecular density.
Autistic Architecture: The Fall of the Icon and the Rise of the Serial Object of Architecture
Authors: Kaika Maria
Published: November 2011

In this contribution I sketch a framework for interpreting the parallel process of banalisation of old and proliferation of new ‘iconic’ corporate architecture as the Janus-faced manifestation of a qualitative shift in the relationship between capital and architecture. Highlighting the change from place-bound, place-loyal urban elites to footloose transnational elites, I argue that after the 1970s the need to develop a new set of building specifications and use values to accommodate the requirements of a new urban economy was matched by an equally pressing need to institute a new set of symbolic values for a new generation of elites. Drawing upon Castoriadis's work, I conceptualise architecture as the narrativisation of the desires of elites during a given era, and as a key component in instituting a society's radical imaginary during moments of change. Within this framework, I argue that despite their common commitment to spectacular design, there are a number of significant differences between contemporary and earlier corporate ‘icons’. Discerning the distinct symbolic, material, and social role of contemporary corporate buildings, I challenge their identification as ‘iconic’ architecture and place them instead under a new category, which I term ‘autistic architecture’.
Assaying History: Creating Temporal Junctions through Urban Exploration
Authors: Garrett Bradley L
Published: November 2011

This paper discusses the role of encounters with the past in the practice of urban exploration through ethnographic research undertaken with communities of urban explorers. Urban exploration is an activity intimately connected with places that have largely reached the end of their capitalist use-life. In this paper I argue that the practice enticingly complicates understandings of places by unveiling unexpected material traces and immaterial affordances that build resilient personal attachments where the ‘present’ tangibly intersects with the ‘past’. In the process urban exploration exposes possibilities for a cultural use-life of abandoned buildings beyond the event of abandonment, with or without formal historical interpretation.
Standing-up Vineyards: The Political Relevance of Tuscan Wine Production
Authors: Certomà Chiara
Published: November 2011

This paper investigates the philosophical and political assumptions supporting the commonly held view of ‘place identity’, exemplarily represented by the Tuscany region in Italy and its wine. It focuses on the production process of one of the most expensive and highly rated Italian wines, the Brunello di Montalcino, produced in the southeast of Tuscany. The Brunello di Montalcino wine area in Tuscany has a leading role in Italian wine production, and it represents an enormously successful example of place authenticity protection, promoting high-quality standards of economic solidarity and a fulfilling sense of well-being. This paper puts into question the romantic and fascinating image of Tuscany by offering an alternative portrait of the material-semiotic networks constituting the specificity of this place. The case for the analysis is provided by the diplomatic impasse between Italy and the United States in 2008. Anomalies in the wine production process were detected by a massive use of technological control devices; this put in ‘danger’ the reputation of the Italian wine makers and overturned the tradition, local authenticity, and identity of Tuscan wines—and eventually the identity of the Tuscany region itself. In reconstructing the way in which Brunello di Montalcino wine materially shapes politics, economic relations, social behaviours, landscape, cultural production and international narratives, the paper analyses the related material-semiotic networks. These analyses show that local identity does not naturally grow out of the soil but is generated and preserved by a long retinue of global-based practices and connections. Brunello, a symbol of authentic Tuscany, only exists as Brunello and can be enjoyed as such through the mediation of a large apparatus of very specific scientific knowledge, laboratory practices and protocols, administrative procedures at different geographical scales, and certificates and licences. Paradoxically, we need the global to protect the local.