bluuebunny/crossref_metadata_2025 huggingface dataset:
TEL (ETV6)-AML1 (RUNX1) Initiates Self-Renewing Fetal Pro-B Cells in Association with a Transcriptional Program Shared with Embryonic Stem Cells in Mice
Authors: Tsuzuki Shinobu , Seto Masao
Published: November 2012

The initial steps involved in the pathogenesis of acute leukemia are poorly understood. The TEL-AML1 fusion gene usually arises before birth, producing a persistent and covert preleukemic clone that may convert to precursor B cell leukemia following the accumulation of secondary genetic “hits.” Here, we show that TEL-AML1 can induce persistent self-renewing pro-B cells in mice. TEL-AML1+ cells nevertheless differentiate terminally in the long term, providing a “window” period that may allow secondary genetic hits to accumulate and lead to leukemia. TEL-AML1-mediated self-renewal is associated with a transcriptional program shared with embryonic stem cells (ESCs), within which Mybl2, Tgif2, Pim2, and Hmgb3 are critical and sufficient components to establish self-renewing pro-B cells. We further show that TEL-AML1 increases the number of leukemia-initiating cells that are generated in collaboration with additional genetic hits, thus providing an overall basis for the development of novel therapeutic and preventive measures targeting the TEL-AML1-associated transcriptional program.
Whence genes in pieces: reconstruction of the exon–intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes
Authors: Koonin Eugene V. , Csuros Miklos , Rogozin Igor B.
Published: November 2012

In eukaryotes, protein‐coding sequences are interrupted by non‐coding sequences known as introns. During mRNA maturation, introns are excised by the spliceosome and the coding regions, exons, are spliced to form the mature coding region. The intron densities widely differ between eukaryotic lineages, from 6 to 7 introns per kb of coding sequence in vertebrates, some invertebrates and green plants, to only a few introns across the entire genome in many unicellular eukaryotes. Evolutionary reconstructions using maximum likelihood methods suggest intron‐rich ancestors for each major group of eukaryotes. For the last common ancestor of animals, the highest intron density of all extant and extinct eukaryotes was inferred, at 120–130% of the human intron density. Furthermore, an intron density within 53–74% of the human values was inferred for the last eukaryotic common ancestor. Accordingly, evolution of eukaryotic genes in all lines of descent involved primarily intron loss, with substantial gain only at the bases of several branches including plants and animals. These conclusions have substantial biological implications indicating that the common ancestor of all modern eukaryotes was a complex organism with a gene architecture resembling those in multicellular organisms. Alternative splicing most likely initially appeared as an inevitable result of splicing errors and only later was employed to generate structural and functional diversification of proteins. WIREs RNA 2013, 4:93–105. doi: 10.1002/wrna.1143

This article is categorized under:

RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution
Long non‐coding RNAs in stem cell pluripotency
Authors: Ng Shi‐Yan , Stanton Lawrence W.
Published: November 2012

Pluripotency refers to the self‐renewal of undifferentiated embryonic stem cells (ESCs), and is maintained by a tightly regulated gene regulatory network involving an intricate interplay between transcription factors and their genomic targets, as well as epigenetic processes that influence gene expression. Long non‐coding RNAs (lncRNAs) are newly discovered members of gene regulatory networks that govern a variety of cell functions. Defined as RNA transcripts larger than 200 nucleotides, lncRNAs have little or no protein‐coding capacity and have been shown to act via various mechanisms, and are important in a variety of biological functions. Recent reports have described the discovery of pluripotent lncRNAs involved in the maintenance and induction of stem cell pluripotency. Here, we discuss how lncRNAs may integrate into the pluripotency network, as well as prominent questions in this emerging field. WIREs RNA 2013, 4:121–128. doi: 10.1002/wrna.1146

This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications

Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs

RNA in Disease and Development > RNA in Development
The curious case of miRNAs in circulation: potential diagnostic biomarkers?
Authors: Duttagupta Radha , Jones Keith W.
Published: November 2012

The pervasive occurrence of cell‐free miRNAs in circulation suggests that these species play an emerging role as regulatory molecules in the secretory environment. Are these molecules released fortuitously with no clear biological intent? Or do they constitute a regulatory architecture that has evolved to modulate gene expression using the highways and byways of the circulatory system? The study of circulating miRNAs continues to increase our understanding of the regulation of genomes. The diversity of acellular miRNAs from a functional perspective is discussed, and in particular we explore their utility in a clinical setting as blood‐based biomarkers for diseases. WIREs RNA 2013, 4:129–138. doi: 10.1002/wrna.1149

This article is categorized under:

RNA in Disease and Development > RNA in Disease
Modeling vaccination and targeted removal of white‐tailed deer in Michigan for bovine tuberculosis control
Authors: Cosgrove Melinda K. , Campa Henry , Ramsey David S. L. , Schmitt Stephen M. , O'brien Daniel J.
Published: November 2012

White‐tailed deer (Odocoileus virginianus) in Michigan, USA, is one of the few species in the world considered a maintenance host for bovine tuberculosis (TB). Prevalence of TB over the past decade has remained steady in Deer Management Unit (DMU) 452 and new control strategies are needed to further reduce prevalence or eradicate the disease. There is little public support for large‐scale culling of deer in Michigan, and vaccination is being considered as a potential management tool. Our goal was to evaluate the use of vaccination and/or targeted removal via live‐trapping as TB control measures and how changes in vaccine parameters affect prevalence reduction. We used a spatially explicit stochastic individual‐based model of TB dynamics in white‐tailed deer to evaluate 39 management scenarios for their ability to 1) reach a 95% probability of eradication, and 2) lower TB prevalence over 30 years. We found continuation of current management would not result in a detectable prevalence reduction, nor would treatment of a “hot‐spot” of infection within DMU 452. Application frequency played a larger role in prevalence reduction than vaccine efficacy, guaranteed immunity period, or half‐life. Vaccination (alone or with targeted removal) applied annually throughout DMU 452 was necessary for a detectable reduction in prevalence. Projected costs for application over DMU 452 would exceed US$1.5 million annually. Vaccination will be costly and require long‐term commitment, but the economic losses associated with allowing TB to persist in Michigan could outweigh vaccination costs. © 2012 The Wildlife Society.
Comparison of Antioxidant Capacities of Rosmarinate Alkyl Esters in Riboflavin Photosensitized Oil‐in‐Water Emulsions
Authors: Lee Jae Hwan , Panya Atikorn , Laguerre Mickaël , Bayrasy Christelle , Lecomte Jérôme , Villeneuve Pierre , Decker Eric A.
Published: November 2012

Effects of the alkyl chain length of rosmarinate alkyl esters on the oxidative stability in photosensitized oil‐in‐water (O/W) emulsions were determined by lipid hydroperoxides and headspace volatile analyses. Antioxidant capacities of 20 μM rosmarinate esters with alkyl chain length of 0, 4, 8, 12, 18, and 20 were tested in O/W emulsion containing stripped soybean oil, Tween 20 as an emulsifier, and riboflavin as a photosensitizer. Synergistic or antagonistic effects of 20 μM α‐tocopherol in the presence of rosmarinate alkyl esters were also determined. Samples containing rosmarinate with 4 and 8 alkyl esters showed lower lipid hydroperoxides and headspace volatiles than those without rosmarinate and those with 0, 12, 18, and 20 alkyl esters, which indicates that phenolic free radical scavengers showed antioxidant capacities non‐linearly in riboflavin photosensitized O/W emulsions. Antagonistic rather than synergistic effects were observed in all rosmarinate alkyl esters with α‐tocopherol in current conditions although rosmarinates with 4, 8, and 12 alkyl esters showed better antioxidant capacities than those with other alkyl chain length. The results of this study clearly showed that rosmarinates need the proper length of non‐polar groups to show optimum antioxidant capacities in O/W emulsions with Tween 20 as an emulsifier under riboflavin photosensitization.
A GENERATION OF ORPHANS: THE SOCIO-ECONOMIC CRISIS IN CÔTE D'IVOIRE AS SEEN THROUGH POPULAR MUSIC
Authors: Schumann Anne
Published: November 2012

Côte d'Ivoire has travelled full circle from economic success (from 1960 to about 1979) to failure (from the 1980s onwards) in little more than a generation. In the early 1990s, Zouglou, today Côte d'Ivoire's internationally best-known music, emerged at the university residences of the University of Abidjan in the Yopougon quarter. The young people who were to become the ‘Zouglou generation’ were precisely the generation that bore the brunt of this economic deterioration. Zouglou was born at a time when, as a result of an unprecedented economic crisis and the attendant structural adjustment measures, university students experienced a general downgrading not only as students but also as future graduates hoping to find employment. In addition, the number of students and school pupils who were unable to complete their education grew considerably during this time. As this article demonstrates, these phenomena had a profound influence on the development of the philosophy associated with Zouglou music. Accordingly, Zouglou singers have called themselves the ‘sacrificed generation’. Indeed, the many songs about orphans in Zouglou music can be read as a symbolic statement about this experience: the sense that Ivoirian youth have been abandoned by their elders, their families and the political authorities is unmistakable in the words of Zouglou songs consoling such (metaphorical) orphans. Zouglou music has become an important platform through which this generation has been able to express itself, as well as a site for oral street poetry and collective catharsis. The article discusses the content of these songs, as well as interviews with Zouglou singers on this matter, to investigate how Zouglou, as a cultural phenomenon, grew out of the experience of a generation.
Study of the effect exerted by fructo-oligosaccharides from yacon (Smallanthus sonchifolius) root flour in an intestinal infection model with Salmonella Typhimurium
Authors: Velez Eva , Castillo Natalia , Mesón Oscar , Grau Alfredo , Bibas Bonet María E. , Perdigón Gabriela
Published: November 2012

Beneficial effects of prebiotics like inulin and fructo-oligosaccharides (FOS) have been proven in health and nutrition. Yacon (Smallanthus sonchifolius), an Andean crop, contains FOS (50–70 % of its dry weight) and, therefore, is considered a prebiotic. Commercial FOS can up-regulate total secretory IgA (S-IgA) in infant mice, prevent infection with Salmonella in swine or enhance immune response for Salmonella vaccine in a mouse model. Previously, we found that administration of yacon root flour regulates gut microbiota balance and has immunomodulatory effects without inflammatory responses. The aim of the present paper is to analyse if yacon prevents enteric infection caused by a strain of Salmonella enteritidis serovar Typhimurium (S. Typhimurium) in a mouse model. BALB/c mice were supplemented with yacon flour (45 d), challenged with S. Typhimurium and killed to study pathogen translocation, total and specific IgA production by ELISA, presence of IgA and other cytokines and Toll-like receptor 4 (TLR4) and clustor of differentiation 206 (CD206) receptors positive cells by immunofluorescence and histological changes. Yacon flour administration had a protective effect from 15 to 30 d of treatment. We found a peak of total S-IgA production without translocation of the pathogen for these periods. At 30 d, there was an increase in IL-6 and macrophage inflammatory proteins-1α+ cells and expression of the receptors CD206 and TLR4. Yacon flour did not have incidence in pathogen-specific S-IgA production. Longer periods (45 d) of administration had no protective effect. Therefore, yacon can prevent enteric infection caused by S. Typhimurium when given up to 30 d; this effect would be mediated by enhancing non-specific immunity, such as total S-IgA, that improves the immunological intestinal barrier.
Making and Breaking the Working Class: Worker Recruitment in the National Textile Industry in Interwar Egypt
Authors: Hammad Hanan
Published: November 2012

This article examines how worker mediation to secure jobs for relatives and co-villagers in the nationalist textile industry influenced working-class formation in interwar Egypt. Mediation was conducted out of a sense of communal commitment or for commission, or indeed both. The fact that rank-and-file workers were able to intervene in the recruitment process reveals that workers were successfully able to manoeuvre in such a way as to balance their unjust work relations with the huge mill and to manipulate its system. On the other hand, this method of recruitment became a source of violence among workers when they fought one another, sometimes fatally, whenever one side failed to respect the terms of the financial arrangements agreed. In most cases it strengthened the communal solidarity based on kinship and geographical origin. In both cementing and distracting from working-class solidarity, worker interference in the recruitment processes was part of the developing sense of social transformation and bonding among a distinctive and connected professional community that hoarded its own bargaining power.
European Reactions to the Homestead Act
Authors: Dovring Folke
Published: November 2012

Contemporary reaction to the Homestead Act was complex in the United States, and the judgment of posterity has included much negative criticism. Whatever the real merits and defects of the Act, its impact on public opinion in Europe was not necessarily in keeping with the facts as they unfolded in America. European reactions to the famous Act are much less known than is the case with American public and expert opinion on the same subject. Standard literature on emigration and on the American image in Europe invariably stresses political freedom and economic opportunity as main motives for emigration. The Homestead Act is in most cases mentioned only in passing, as one among several factors in the motivation of prospective emigrants. In some cases it is claimed to have been a major motive but without evidence to bear out how important it was.
Museveni and the 2011 Ugandan election: did the money matter?
Authors: Conroy-Krutz Jeffrey , Logan Carolyn
Published: November 2012

In February 2011, Ugandan President Yoweri Museveni resoundingly won re-election. In the aftermath of the vote, which many had predicted would be competitive, analysts and opposition supporters ascribed Museveni's victory to massive pre-election spending on public goods, creation of new administrative districts, and vote buying. While the opposition could not compete with Museveni and his National Resistance Movement in access to resources, our analyses of survey data, from two pre-election surveys conducted by Afrobarometer in November/December 2010 and January 2011, and a pre- and post-election panel study, find little evidence that Museveni benefited significantly from public goods outlays, district creation, and vote buying. Additionally, we find little evidence that fear and intimidation were responsible for the results. Instead, the data suggest that Museveni's re-election was driven by an uninspiring opposition slate, widespread satisfaction with macro-economic growth, and an improved security situation, particularly in the Northern Region.
Evidence for interspecific hybridisation in pteridophytes with subterranean mycoparasitic gametophytes
Authors: Wagner W. H. , Wagner F. S. , Beitel Joseph M.
Published: November 2012

Synopsis

Pteridophytes with subterranean sexual stages exist in five families. Their prothalli grow underground without light, nourished by fungi, and are rounded, massive, and without chlorophyll. Various authors have suggested that such gametophytes may inhibit outbreeding ability and that minor variations may therefore form in colonies through inbreeding.

This paper questions these ideas. The subterranean condition is believed to be suited to fields, grassy meadows, and other habitats subject to seasonal drying. The parenchymatous thallus makes possible water storage. Water can flow between some particles. Sperm may be carried by mass flow in various directions and can evidently swim as much as 2 cm. Close clumping of underground gametophytes appears to be no less common than in surficial gametophytes and evidence exists that hybridisation occurs.

No evidence has been detected that outbreeding is inhibited, and we conclude that it is successful and that cross-fertilisation is no less common among underground gametophytes than among surface gametophytes. Numerous examples are listed from Lycopodiales, Psilotales, and Ophioglossales.
COST: Cognitive State Test, a brief screening battery for Alzheimer disease in illiterate and literate patients
Authors: Babacan-Yildiz Gulsen , Isik Ahmet T. , Ur Emel , Aydemir Emine , Ertas Can , Cebi Merve , Soysal Pinar , Gursoy Esra , Kolukisa Mehmet , Kocaman Gulsen , Celebi Arif
Published: November 2012

Background: The aim was to develop a brief screening battery, Cognitive State Test (COST), for detecting the presence of dementia in both illiterate and literate patients and to assess its validity and reliability.

Methods: COST is a cognitive screening tool that consists of almost all cognitive domains. It takes 5–7 minutes to administer, and has a maximum score of 30. Data were obtained from 114 healthy volunteers and 74 Alzheimer dementia (AD) patients. Subjects’ age divided into two groups: A1: <65 years; and A2: ≥65 years and their education level divided into three groups: E1: illiterate; E2: 1–5 years; and E3: ≥6 years. For assessing concurrent validity, total COST score was compared to the Clinical Dementia Rating (CDR), the Mini Mental State Examination (MMSE), the Montreal Cognitive Assessment (MoCA), and Basic Activities of Daily Living (BADL). Sensitivity and specificity were determined through a discriminant analysis using the Receiver Operating Characteristic (ROC) curves. Internal consistency was measured using Cronbach's coefficient α.

Results: For normal and AD subjects, mean age was 64.9±9.8 years (50 women and 64 men) and 67.2±13.2 years (55 women and 19 men), respectively. Schooling ranged from 0–15 years (mean 5.7±4.2 and 3.3±3.8 years, respectively), and 21 and 37 subjects were illiterate, respectively. The COST significantly and positively correlated with MMSE and MoCA, and significantly and inversely correlated with CDR, the Geriatric Depression Scale (GDS), and BADL. In the E1, E2, and E3 education groups, the optimal cut-off points of COST chosen for diagnosis of AD were 23/24 (sensitivity: 81%, specificity: 99%), 24/25 (sensitivity: 75%, specificity: 86%), and 26/27 (sensitivity: 77%, specificity: 84%), respectively. When illiterate and literate subjects were then pooled, the optimal cut-off score of COST was 24/25, which yielded a sensitivity of 81% and a specificity of 87%. Reliability of the COST was good (0.86).

Conclusion: The COST is a valid and reliable screening battery for detection of dementia both in the illiterate and the literate Alzheimer patients.
Cardiac magnetic resonance imaging in a premature baby with interrupted aortic arch and aortopulmonary window
Authors: Tzifa Aphrodite , Komnou Areti , Loggitsi Dimitra
Published: November 2012

Aortopulmonary window is a communication between the main pulmonary artery and the ascending aorta in the presence of two separate semilunar valves. The combination of an aortopulmonary window with interrupted aortic arch is rare. We discuss the unique case of an extremely premature infant weighing 1.7 kilograms who underwent cardiovascular magnetic resonance imaging as a pre-operative assessment in a high-field open 1.0 Tesla magnetic resonance imaging system as a one-stop investigation before complete repair.
When Pressure is Positive: A Literature Review of the Prehospital Use of Continuous Positive Airway Pressure
Authors: Williams Brett , Boyle Malcolm , Robertson Nicole , Giddings Coco
Published: November 2012

Background

Heart failure poses a significant burden of disease, resulting in 2,658 Australian deaths in 2008, and listed as an associated cause of death in a further 14,466 cases. Common in the hospital setting, continuous positive airway pressure (CPAP) therapy is a non-invasive ventilation technique used to prevent airway collapse and manage acute pulmonary edema (APO). In the hospital setting, CPAP has been known to decrease the need for endotracheal intubation in patients with APO. Therefore the objective of this literature review was to identify the effectiveness of CPAP therapy in the prehospital environment.

Methods

A review of selected electronic medical databases (Cochrane, Medline, EMBASE, and CINAHL) was conducted from their commencement date through the end of May 2012. Inclusion criterion was any study type reporting the use of CPAP therapy in the prehospital environment, specifically in the treatment of heart failure and acute pulmonary edema. References of relevant articles were also reviewed.

Results

The literature search located 1,253 articles, 12 of which met the inclusion criteria. The majority of studies found that the use of CPAP therapy in the prehospital environment is associated with reduced short-term mortality as well as reduced rates of endotracheal intubation. Continuous positive airway pressure therapy was also shown to improve patient vital signs during prehospital transport and reduce myocardial damage.

Discussion

The studies conducted of prehospital use of CPAP to manage APO have all demonstrated improvement in patient outcomes in the short term.

Conclusion

Available evidence suggests that the use of CPAP therapy in the prehospital environment may be beneficial to patients with acute pulmonary edema as it can potentially decrease the need for endotracheal intubation, improve vital signs during transport to hospital, and improve short-term mortality.

WilliamsB, BoyleM, RobertsonN, GiddingsC. When pressure is positive: a literature review of the prehospital use of continuous positive airway pressure. Prehosp Disaster Med.2013;28(1):1-10.
Magnetic anisotropy, magnetostatic interactions and identification of magnetofossils
Authors: Li Jinhua , Wu Wenfang , Liu Qingsong , Pan Yongxin
Published: November 2012

Single‐domain magnetite particles produced by magnetotactic bacteria (MTB) and aligned in chains, called magnetosomes, are potentially important recorders of paleomagnetic, paleoenvironmental and paleolife signals. Rock magnetic properties related to the anisotropy of magnetosome chains have been widely used to identify fossilized magnetosomes (magnetofossils) preserved in geological materials. However, ambiguities exist when linking magnetic properties to the chain structure because of the complexity of chain integrity and magnetostatic interactions among magnetofossils that results from chain collapse during post‐depositional diagenesis. In this paper, magnetic properties of three sets of samples containing extracted magnetosomes of the culturedMagnetospirillum magneticumstrain AMB‐1 were analyzed to determine how chain integrity and particle concentration influence magnetic properties. Intact MTB and well‐dispersed magnetosome chains are characterized by strong magnetic anisotropy and weak magnetostatic interactions, but progressive chain breakup and particle clumping significantly increase the degree of magnetostatic interaction. This results in a change of the magnetic signature toward properties typical of interacting, single‐domain particles, i.e., a decrease of the ratio of anhysteretic remanent magnetization to the saturation isothermal remanent magnetization, decreasing in the crossing point of the Wohlfarth‐Cisowski test and in the delta ratio between losses of field and zero‐field cooled remanent magnetization across the Verwey transition, as well as vertical broadening of the first‐order reversal curve distribution. We propose a new diagram that summarizes the Verwey transition properties, with diagnostic limits for intact and collapsed chains of magnetosomes. This diagram can be used, in conjunction with other parameters, to identify unoxidized magnetofossils in sediments and rocks.
Multidecadal climate variability in Brazil's Nordeste during the last 3000 years based on speleothem isotope records
Authors: Novello Valdir F. , Cruz Francisco W. , Karmann Ivo , Burns Stephen J. , Stríkis Nicolás M. , Vuille Mathias , Cheng Hai , Lawrence Edwards R. , Santos Roberto V. , Frigo Everton , Barreto Eline A. S.
Published: November 2012

We present the first high resolution, approximately ∼4 years sample spacing, precipitation record from northeastern Brazil (hereafter referred to as ‘Nordeste’) covering the last ∼3000 yrs from 230Th‐dated stalagmites oxygen isotope records. Our record shows abrupt fluctuations in rainfall tied to variations in the intensity of the South American summer monsoon (SASM), including the periods corresponding to the Little Ice Age (LIA), the Medieval Climate Anomaly (MCA) and an event around 2800 yr B.P. Unlike other monsoon records in southern tropical South America, dry conditions prevailed during the LIA in the Nordeste. Our record suggests that the region is currently undergoing drought conditions that are unprecedented over the past 3 millennia, rivaled only by the LIA period. Using spectral, wavelet and cross‐wavelet analyses we show that changes in SASM activity in the region are mainly associated with variations of the Atlantic Multidecadal Oscillation (AMO) and to a lesser degree caused by fluctuations in tropical Pacific SST. Our record also shows a distinct periodicity around 210 years, which has been linked to solar variability.
Low‐frequency spiciness variations in the tropical Pacific Ocean observed during 2003–2012
Authors: Li Yuanlong , Wang Fan , Sun Yan
Published: November 2012

Large‐scale spiciness variations in the Pacific Ocean during 2003–2012 are well recorded in the Argo‐based Grid Point Value of the Monthly Objective Analysis (MOAA GPV) dataset. Pronounced interannual spiciness anomalies between 25.0–25.5σθare detected near the outcropping areas in the eastern subtropics of both hemispheres. Differing from previous model results, the observed subtropical variations are more powerful in the North Pacific. While these subtropical signals diffuse quickly as propagating equatorward, large‐magnitude anomalies are generated in the off‐equatorial tropics (10°–14°N and 3°–7°S) under intensive current perturbation and further communicated to the central equatorial Pacific via interior‐ocean meridional flow. Although along‐equator signal propagation to the eastern Pacific upwelling zones is not discernable, appearance of spiciness anomalies leads to low‐frequency thermal variations in the central equatorial Pacific, which may play a role in the increasingly frequent occurrences of ENSO‐Modoki events.
Transport of the plasma sheet electrons to the geostationary distances
Authors: Ganushkina N. Y. , Amariutei O. A. , Shprits Y. Y. , Liemohn M. W.
Published: November 2012

The transport and acceleration of low‐energy electrons (50–250 keV) from the plasma sheet to the geostationary orbit were investigated. Two moderate storm events, which occurred on 6–7 November 1997 and 12–14 June 2005, were modeled using the Inner Magnetosphere Particle Transport and Acceleration model (IMPTAM) with the boundary set at 10 RE in the plasma sheet. The output of the IMPTAM was compared to the observed electron fluxes in four energy ranges (50–225 keV) measured by the Synchronous Orbit Particle Analyzer instrument onboard the Los Alamos National Laboratory spacecraft. It was found that the large‐scale convection in combination with substorm‐associated impulsive fields is the drivers of the transport of plasma sheet electrons from 10 RE to geostationary orbit at 6.6 RE during storm times. The addition of radial diffusion had no significant influence on the modeled electron fluxes. At the same time, the modeled electron fluxes are one (two) order(s) smaller than the observed ones for 50–150 keV (150–225 keV) electrons, respectively, most likely due to inaccuracy of electron boundary conditions. The loss processes due to wave‐particle interactions were not considered. The choice of the large‐scale convection electric field model used in simulations did not have a significant influence on the modeled electron fluxes, since there is not much difference between the equipotential contours given by the Volland‐Stern and the Boyle et al. (1997) models at distances from 10 to 6.6 RE in the plasma sheet. Using the TS05 model for the background magnetic field instead of the T96 model resulted in larger deviations of the modeled electron fluxes from the observed ones due to specific features of the TS05 model. The increase in the modeled electron fluxes can be as large as two orders of magnitude when substorm‐associated electromagnetic fields were taken into account. The obtained model distribution of low‐energy electron fluxes can be used as an input to the radiation belt models. This seed population for radiation belts will affect the local acceleration up to relativistic energies.
Evolution of auroral acceleration types inferred from two‐satellite coincidences
Authors: Newell P. T. , Sotirelis T. , Mitchell E. J.
Published: November 2012

The relationship between monoenergetic electron acceleration and broadband electron acceleration is uncertain, although some have speculated that the latter is a temporal transient, and may evolve into the former. Here we have taken advantage of DMSP satellite coincidences to investigate the issue. We consider 1668 cases where one DMSP satellite observed an electron acceleration event covering at least 2 s, hence as many discrete accelerated spectra, and a second satellite subsequently observed an electron acceleration at the same location. The spatial coincidence required was tight, with a maximum separation of 0.1° magnetic latitude and 0.15 h magnetic local time. Time separations of 0–10 min were considered in 1 min bins, with auroral acceleration flagged as either monoenergetic, broadband, or a mixture of both. Within the first temporal bin (0–1 min), the second satellite had a high probability of observing the same type of aurora as the first, establishing consistency. When the first satellite observed monoenergetic aurora, the second satellite also observed monoenergetic aurora (about 80% of the time), and this continued to up to about 10 min of UT separation. In most of the other 20% of the cases, the second satellite also recorded monoenergetic acceleration but with an additional mixture of broadband acceleration. Thus monoenergetic aurora does not seem to typically evolve on a time scale of minutes. However, when the first satellite encounter was with broadband acceleration, the second encounter was highly time‐dependent, with broadband dominating the second satellite encounter only in the 0–1 min bin. Between 1 and 5 min, the probability of observing a mixture of auroral types jumped, and after 6 min, the auroral acceleration was nearly as likely to be monoenergetic as broadband. Finally, if the first satellite encountered a mixture of acceleration, the second encounter was progressively more likely to be entirely monoenergetic aurora as time increased. These results are consistent with the idea that broadband aurora may be inherently a transient, and often progresses to monoenergetic aurora, while the latter is quasi‐static.
Waveguide properties recovered from shallow diffractions in common offset GPR
Authors: Strobach Elmar , Harris Brett D. , Dupuis J. Christian , Kepic Anton W.
Published: November 2012

Near‐surface heterogeneities produce diffractions in common offset ground‐penetrating radar (GPR) data from the Gnangara Groundwater Mound, north of Perth, Western Australia. These diffracted wavefields can be enhanced and show a dispersion pattern if they propagate along a waveguide caused by a low velocity surface layer, such as moist sand on top of dry sand. Until now, GPR waveguide dispersion has been analyzed and inverted using common midpoint data. Using numerical modeling, we demonstrate that the same dispersion information can also be recovered from a diffracted electromagnetic wavefield recorded with common offset geometry. Frequency‐slowness analysis of shallow diffractions in common offset GPR field data reveals high resolution dispersion curves. Inverting picked dispersion maxima to modeled curves (i.e., modal wave propagation in waveguide layer) allows estimation of waveguide height and velocities of waveguide and the underlying material. Data analysis in the frequency‐wavenumber domain provides an alternative technique for extracting dispersion curves. Preliminary results validate this approach, which could be favorable in large‐scale applications due to minimal processing requirement and inherent yet adjustable spatial averaging. The differences between waveguide parameters recovered from two surveys appear to be consistent with seasonal changes in moisture content and lateral changes due to variations in depositional environment. Our approach presents a new method to quantify the shallow dielectric permittivity structure of the subsurface from common offset gathers—the most commonly acquired type of GPR data. Potential applications of this method include estimation of shallow moisture distribution, early target identification for unexploded ordnance (UXO) detection, concrete slab characterization, pedological investigations, or planetary exploration.
Low‐degree structure in Mercury's planetary magnetic field
Authors: Anderson Brian J. , Johnson Catherine L. , Korth Haje , Winslow Reka M. , Borovsky Joseph E. , Purucker Michael E. , Slavin James A. , Solomon Sean C. , Zuber Maria T. , McNutt Ralph L.
Published: November 2012

The structure of Mercury's internal magnetic field has been determined from analysis of orbital Magnetometer measurements by the MESSENGER spacecraft. We identified the magnetic equator on 531 low‐altitude and 120 high‐altitude equator crossings from the zero in the radial cylindrical magnetic field component,Bρ. The low‐altitude crossings are offset 479 ± 6 km northward, indicating an offset of the planetary dipole. The tilt of the magnetic pole relative to the planetary spin axis is less than 0.8°. The high‐altitude crossings yield a northward offset of the magnetic equator of 486 ± 74 km. A field with only nonzero dipole and octupole coefficients also matches the low‐altitude observations but cannot yield off‐equatorialBρ= 0 at radial distances greater than 3520 km. We compared offset dipole and other descriptions of the field with vector field observations below 600 km for 13 longitudinally distributed, magnetically quiet orbits. An offset dipole with southward directed moment of 190 nT‐RM3yields root‐mean‐square (RMS) residuals below 14 nT, whereas a field with only dipole and octupole terms tuned to match the polar field and the low‐altitude magnetic equator crossings yields RMS residuals up to 68 nT. Attributing the residuals from the offset‐dipole field to axial degree 3 and 4 contributions we estimate that the Gauss coefficient magnitudes for the additional terms are less than 4% and 7%, respectively, relative to the dipole. The axial alignment and prominent quadrupole are consistent with a non‐convecting layer above a deep dynamo in Mercury's fluid outer core.
Macroroughness and variations in reach‐averaged flow resistance in steep mountain streams
Authors: Nitsche M. , Rickenmann D. , Kirchner J. W. , Turowski J. M. , Badoux A.
Published: November 2012

Steep mountain streams typically feature macroroughness elements like large immobile boulders or channel‐spanning bedforms such as step‐pool sequences. The effects of macroroughness on resistance and flow velocity are not well understood and appropriate field parameters for representing macroroughness in flow velocity equations have not been identified. The prediction of flow velocity in rough and steep streams therefore remains challenging. We measured flow velocity and several macroroughness parameters, i.e., boulder concentration, boulder diameter and protrusion, and roughness of longitudinal channel profiles in six reaches of steep mountain streams with plane bed/riffle, step‐pool, and cascade channel morphologies. The between‐site variations in flow resistance can be explained to a large degree by nondimensionalization of discharge and flow velocity using channel slope and a characteristic roughness length. Using any of our roughness parameters as the characteristic roughness length, this nondimensionalization leads to a similarity collapse of the entire data set. The remaining differences in flow resistance among the streams are related to dimensionless measures of macroroughness that describe the concentration of boulders or step density in a reach. Boulder concentration represents the measure best describing the data and is used in a simple regression equation for flow velocity. The predictions were better than predictions by the variable power law equation proposed by Ferguson. Although the regression might not be statistically significant, the observed trends suggest that boulder concentration partly explains the residual variance of between‐site variation of flow resistance.
Cell cycle regulation by the intrinsically disordered proteins p21 and p27
Authors: Yoon Mi-Kyung , Mitrea Diana M. , Ou Li , Kriwacki Richard W.
Published: November 2012

Today, it is widely accepted that proteins that lack highly defined globular three-dimensional structures, termed IDPs (intrinsically disordered proteins), play key roles in myriad biological processes. Our understanding of how intrinsic disorder mediates biological function is, however, incomplete. In the present paper, we review disorder-mediated cell cycle regulation by two intrinsically disordered proteins, p21 and p27. A structural adaptation mechanism involving a stretchable dynamic linker helix allows p21 to promiscuously recognize the various Cdk (cyclin-dependent kinase)–cyclin complexes that regulate cell division. Disorder within p27 mediates transmission of an N-terminal tyrosine phosphorylation signal to a C-terminal threonine phosphorylation, constituting a signalling conduit. These mechanisms are mediated by folding upon binding p21/p27′s regulatory targets. However, residual disorder within the bound state contributes critically to these functional mechanisms. Our studies provide insights into how intrinsic protein disorder mediates regulatory processes and opportunities for designing drugs that target cancer-associated IDPs.
An emerging role for LRRK2 in the immune system
Authors: Dzamko Nicolas , Halliday Glenda M.
Published: November 2012

Missense mutations in LRRK2 (leucine-rich repeat kinase 2) contribute significantly to autosomal dominant PD (Parkinson's disease). Genome-wide association studies have suggested further that mutations in LRRK2 comprise a risk factor for sporadic PD. How LRRK2 contributes to PD, however, is largely unknown. Recent work has shown that LRRK2 is highly expressed in tissue and circulating immune cells and is suggestive of a potential role for LRRK2 in innate immunity. These studies and their potential implications for PD are discussed in the present paper.
Human leucine-rich repeat kinase 1 and 2: intersecting or unrelated functions?
Authors: Civiero Laura , Bubacco Luigi
Published: November 2012

Mutations in LRRK2 (leucine-rich repeat kinase 2) are associated with both familial and sporadic PD (Parkinson's disease). LRRK1 (leucine-rich repeat kinase 1) shares a similar domain structure with LRRK2, but it is not linked to PD. LRRK proteins belong to a gene family known as ROCO, which codes for large proteins with several domains. All ROCO proteins have a ROC (Ras of complex proteins) GTPase domain followed by a domain of unknown function [COR (C-terminal of ROC)]. LRRK2, LRRK1 and other ROCO proteins also possess a kinase domain. To date, the function of LRRK1 and both the physiological and the pathological roles of LRRK2 are only beginning to unfold. The comparative analysis of these two proteins is a strategy to single out the specific properties of LRRKs to understand their cellular physiology. This comparison is the starting point to unravel the pathways that may lead to PD and eventually to develop therapeutic strategies for its treatment. In the present review, we discuss recently published results on LRRK2 and its paralogue LRRK1 concerning their evolutionary significance, biochemical properties and potential functional roles.
LRRK2 and autophagy: a common pathway for disease
Authors: Manzoni Claudia
Published: November 2012

LRRK2 (leucine-rich repeat kinase 2) is an enzyme implicated in human disease, containing kinase and GTPase functions within the same multidomain open reading frame. Dominant mutations in the LRRK2 gene are the most common cause of familial PD (Parkinson's disease). Additionally, in genome-wide association studies, the LRRK2 locus has been linked to risk of PD, Crohn's disease and leprosy, and LRRK2 has also been linked with cancer. Despite its association with human disease, very little is known about its pathophysiology. Recent reports suggest a functional association between LRRK2 and autophagy. Implications of this set of data for our understanding of LRRK2′s role in physiology and disease are discussed in the present paper.
MASL1: a neglected ROCO protein
Authors: Dihanich Sybille
Published: November 2012

The human ROCO proteins are a family of four proteins characterized by a conserved supradomain: a Ras-like GTPase domain. This domain consists of ROC (Ras of complex proteins) occurring in tandem with a COR (C-terminal of ROC) domain. Together, these proteins are linked to various pathologies including cancer and PD (Parkinson's disease). Despite an increasing research focus on these proteins, their functions in general, and their specific roles in disease, are still unknown. In the case of MASL1 (malignant fibrous histiocytoma amplified sequences with leucine-rich tandem repeats 1), a predicted oncoprotein in MFHs (malignant fibrous histiocytomas), there is a particular lack of information available in the literature. The aim of the present review is therefore to summarize the existing information on MASL1 and also to compile data that could be linked to MASL1 and thus help our understanding of this neglected ROCO protein.
The GTPase function of LRRK2
Authors: Taymans Jean-Marc
Published: November 2012

LRRK2 (leucine-rich repeat kinase 2) is a large protein encoding multiple functional domains, including two catalytically active domains, a kinase and a GTPase domain. The LRRK2 GTPase belongs to the Ras-GTPase superfamily of GTPases, more specifically to the ROC (Ras of complex proteins) subfamily. Studies with recombinant LRRK2 protein purified from eukaryotic cells have confirmed that LRRK2 binds guanine nucleotides and catalyses the hydrolysis of GTP to GDP. LRRK2 is linked to PD (Parkinson's disease) and GTPase activity is impaired for several PD mutants located in the ROC and COR (C-terminal of ROC) domains, indicating that it is involved in PD pathogenesis. Ras family GTPases are known to function as molecular switches, and several studies have explored this possibility for LRRK2. These studies show that there is interplay between the LRRK2 GTPase function and its kinase function, with most data pointing towards a role for the kinase domain as an upstream regulator of ROC. The GTPase function is therefore a pivotal functionality within the LRRK2-mediated signalling cascade which includes partners encoded by other LRRK2 domains as well as other cellular signalling partners. The present review examines what is known of the enzymatic properties of the LRRK2 GTPase, the interplay between ROC and other LRRK2 domains, and the interplay between ROC and other cellular proteins with the dual goal to understand how LRRK2 GTPase affects cellular functions and point to future research venues.
Disordered stoichiometric nanorods and ordered off-stoichiometric nanoparticles in n-type thermoelectric Bi2Te2.7Se0.3
Authors: Carlton Chris E. , Kuryak Chris A. , Liu Wei-shu , Ren Zhifeng , Chen Gang , Shao-Horn Yang
Published: November 2012

N-type Bi2Te2.7Se0.3 bulk thermoelectric materials with peak ZT values up to ∼1 were examined by transmission electron microscopy and electron diffraction. Two nanostructural features were found: (i) a structural modulation of ∼10 nm, which consisted of nanorods with crystalline and nearly amorphous regions, having the rod axes normal to (0,1,5)-type planes, and wave vector normal to (1,0,10)-type planes and (ii) non-stoichiometric ordered Bi-rich nanoparticles. The presence of the structural modulation was not influenced by the ion milling energy or temperature in this study while the non-stoichiometric ordered nanoparticles were only observed when ion milling at low temperatures and low energy was used. It is proposed that both the structural modulation of ∼10 nm and the presence of non-stoichiometric nanoparticles are responsible for the low lattice thermal conductivity (∼0.6 W/mK) of the Bi2Te2.7Se0.3 bulk thermoelectric materials studied.
A comprehensive study of hole collection in heterojunction solar cells
Authors: Crandall Richard S. , Iwaniczko Eugene , Li Jian V. , Page Mathew R.
Published: November 2012

We conduct a systematic investigation into the mechanism of hole collection in amorphous/crystalline silicon heterojunctions solar cells using transient-capacitance techniques. The devices are formed by depositing undoped amorphous silicon (i layer) followed by p-type amorphous silicon on n-type crystalline silicon wafers. For i layers varying from 3.2 to 96 nm, we find only a factor of four change in hole collection-rate at low temperature where thermal emission over the valence band offset is precluded. We conclude that holes traverse the i layer by hopping through defects rather than direct tunneling through the entire i layer. This process is weakly thermally activated with a rate above 1 × 104 s−1 at room temperature. Near room temperature and with thick i layers, we observe hole collection with a high activation energy that depends on measurement conditions. We demonstrate that hopping through defects is the dominant mode of hole collection for solar cell operation at room temperature and above.
On the breaking of a plasma wave in a thermal plasma. I. The structure of the density singularity
Authors: Bulanov Sergei V. , Esirkepov Timur Zh. , Kando Masaki , Koga James K. , Pirozhkov Alexander S. , Nakamura Tatsufumi , Bulanov Stepan S. , Schroeder Carl B. , Esarey Eric , Califano Francesco , Pegoraro Francesco
Published: November 2012

The structure of the singularity that is formed in a relativistically large amplitude plasma wave close to the wave breaking limit is found by using a simple waterbag electron distribution function. The electron density distribution in the breaking wave has a typical “peakon” form. The maximum value of the electric field in a thermal breaking plasma is obtained and compared to the cold plasma limit. The results of computer simulations for different initial electron distribution functions are in agreement with the theoretical conclusions. The after-wavebreak regime is then examined, and a semi-analytical model of the density evolution is constructed. Finally the results of two dimensional particle in cell simulations for different initial electron distribution functions are compared, and the role of thermal effects in enhancing particle injection is noted.