bluuebunny/crossref_metadata_2025 huggingface dataset:
Airborne validation of cirrus cloud properties derived from CALIPSO lidar measurements: Optical properties
Authors: Hlavka Dennis L. , Yorks John E. , Young Stuart A. , Vaughan Mark A. , Kuehn Ralph E. , McGill Matthew J. , Rodier Sharon D.
Published: April 2012

The Cloud‐Aerosol Lidar Infrared Pathfinder Satellite Observations (CALIPSO) satellite was successfully launched in April 2006 to study cloud and aerosol layers using range‐resolved laser remote sensing. Dedicated flights were conducted from July 26 to August 14, 2006 using the airborne Cloud Physics Lidar (CPL) to validate the CALIPSO lidar (CALIOP) data products. This paper presents results from coincident ice cloud measurements of lidar ratio, extinction coefficient, and optical depth. Flight segment case studies are shown as well as statistics for all coincident measurements during this CALIPSO‐CloudSat Validation Experiment (CC‐VEX). For the penetrated portion of opaque layers, CALIOP estimates of lidar ratio and extinction are substantially lower than the corresponding CPL values. Significant differences were also found for measurements of horizontally aligned ice, where different instrument viewing geometries precluded meaningful comparisons. After filtering the data set to exclude these discrepancies, overall CALIOP lidar ratio and extinction averages compared favorably to within 1% of overall CPL averages. When restricting the data further to exact coincident in‐cloud point‐pairs, CALIOP lidar ratios remained close to CPL values, averaging 2.1% below CPL, and the retrieved extinction and optical depth averaged 14.7% above CPL values, a result partially of higher average CALIOP attenuated backscatter but still a respectably close match.
Ozone and alkyl nitrate formation from the Deepwater Horizon oil spill atmospheric emissions
Authors: Neuman J. A. , Aikin K. C. , Atlas E. L. , Blake D. R. , Holloway J. S. , Meinardi S. , Nowak J. B. , Parrish D. D. , Peischl J. , Perring A. E. , Pollack I. B. , Roberts J. M. , Ryerson T. B. , Trainer M.
Published: April 2012

Ozone (O3), alkyl nitrates (RONO2), and other photochemical products were formed in the atmosphere downwind from the Deepwater Horizon (DWH) oil spill by photochemical reactions of evaporating hydrocarbons with NOx (=NO + NO2) emissions from spill response activities. Reactive nitrogen species and volatile organic compounds (VOCs) were measured from an instrumented aircraft during daytime flights in the marine boundary layer downwind from the area of surfacing oil. A unique VOC mixture, where alkanes dominated the hydroxyl radical (OH) loss rate, was emitted into a clean marine environment, enabling a focused examination of O3 and RONO2 formation processes. In the atmospheric plume from DWH, the OH loss rate, an indicator of potential O3 formation, was large and dominated by alkanes with between 5 and 10 carbons per molecule (C5–C10). Observations showed that NOx was oxidized very rapidly with a 0.8 h lifetime, producing primarily C6–C10 RONO2 that accounted for 78% of the reactive nitrogen enhancements in the atmospheric plume 2.5 h downwind from DWH. Both observations and calculations of RONO2 and O3 production rates show that alkane oxidation dominated O3 formation chemistry in the plume. Rapid and nearly complete oxidation of NOx to RONO2 effectively terminated O3 production, with O3 formation yields of 6.0 ± 0.5 ppbv O3 per ppbv of NOx oxidized. VOC mixing ratios were in large excess of NOx, and additional NOx would have formed additional O3 in this plume. Analysis of measurements of VOCs, O3, and reactive nitrogen species and calculations of O3 and RONO2 production rates demonstrate that NOx‐VOC chemistry in the DWH plume is explained by known mechanisms.
Step changes in the flood frequency curve: Process controls
Authors: Rogger M. , Pirkl H. , Viglione A. , Komma J. , Kohl B. , Kirnbauer R. , Merz R. , Blöschl G.
Published: April 2012

Empirical distribution functions of flood peaks in small catchments sometimes show discontinuities in the slope; that is, the largest flood peaks are significantly larger than the rest of the record. The aim of this paper is to understand whether these discontinuities, or step changes, can be a consistent effect of hydrological processes. We conducted field surveys in two Austrian alpine catchments 73 km2in size to map the spatial patterns of surface runoff generation and hydrogeologic storage. On the basis of this information, we selected the parameters of a distributed continuous runoff model, which is designed to simulate well the point when the storage capacity of the catchment is exhausted. Then we calibrated a stochastic rainfall model and performed Monte Carlo simulations of runoff to generate flood frequency curves for the two catchments. The curves exhibit a step change around a return period of 30 years. An analysis of the storage capacities suggests that this step change is due to a threshold of storage capacity being exceeded, which causes fast surface runoff in large parts of the catchments. The threshold occurs when the storage within the catchment is spatially rather uniform. To identify step changes, reliable estimates of the catchment storage capacity are needed on the basis of detailed hydrogeological information. The occurrence of a step change is of importance for estimating low‐probability floods since the flood estimates with the step change accounted for can be significantly different from those based on commonly used distribution functions. We therefore suggest that step changes in the flood frequency curve of small catchments can be real and their possible presence should be taken into account in design flood estimation.
Influence of rock fragment coverage on soil erosion and hydrological response: Laboratory flume experiments and modeling
Authors: Jomaa S. , Barry D. A. , Heng B. C. P. , Brovelli A. , Sander G. C. , Parlange J.‐Y.
Published: April 2012

Two laboratory flume experiments on the effect of surface rock fragments on precipitation‐driven soil erosion yields were carried out. The total sediment concentration, the concentration of seven individual size classes, and the flow discharge were measured. Digital terrain models (DTMs) were generated before and after one of the experiments. The results revealed that the rock fragments protected the soils from raindrop detachment and retarded the overland flow, therefore decreasing its sediment transport capacity. Rock fragments were found to affect selectively the different size classes in a manner that changed according to the time scale. For short times, the rock fragment coverage reduced erosion of the finer particles (<20 μm). For the midsize classes the protection decreased, while erosion of the larger size classes (>100 μm) was unaffected. At long times the rock fragment cover decreased the concentration of the individual size classes in proportion to effective rainfall intensity and the area exposed to raindrops. An area‐based modification of the Hairsine and Rose (H‐R) soil erosion model was employed to analyze the experimental data. The H‐R model predictions agreed well with the measured sediment concentrations when high rainfall intensity and low rock fragment cover were used. Predictions were instead less accurate with low rainfall intensity and high rock fragment cover. The DTM results showed that the presence of rock fragments on the soil surface led to increased soil compaction, perhaps due to higher soil moisture content (from greater infiltration) within the rock fragment‐covered flumes.
On the sub‐decadal variability of South Atlantic Antarctic Intermediate Water
Authors: McCarthy G. D. , King B. A. , Cipollini P. , McDonagh E. L. , Blundell J. R. , Biastoch A.
Published: April 2012

Variability of Antarctic Intermediate Water salinity in the South Atlantic is investigated on interannual and intradecadal timescales. Novel observations of slow, westward propagating salinity anomalies in Argo data are presented. The features have no corresponding signal in temperature and are anomalous in density. Analysis of 40 years of model output supports the existence of these westward propagating salinity anomalies and indicates that they are typical occurrences in time. The features are intensified in a latitude band around 30°S associated with the propagation of Agulhas rings. However, the features are much larger than Agulhas rings and occur on decadal timescales in the model. They propagate westward with speeds of 2.3 cm/s in observations, and 1.7 cm/s in model data. They are more consistent with planetary waves than with the advection of large‐scale salinity anomalies. The observation of these features has implications for the interpretation of salinity anomalies, such as the linking of hydrological cycle changes to salinity changes.
Toroidal hydromagnetic waves in an axi‐symmetric magnetic field
Authors: Webb G. M. , McKenzie J. F. , Hu Q. , Zank G. P.
Published: April 2012

Hydromagnetic wave equations are derived for toroidal Alfvén waves in a background, axi‐symmetric magnetic field. In the case, where the spatial variations in the wave equations are along the background magnetic field, the equations can be re‐cast in Klein‐Gordon equation forms, with cut‐off frequency ωc. For harmonic, constant frequency solutions, the Klein Gordon equation reduces to a Sturm‐Liouville equation. We compute the eigenvalues and eigenfunctions appropriate for the Earth's dipole magnetic field, which are relevant for geomagnetic pulsations. It is suggested that the breather type Alfvén eigenmodes, obtained from the analysis may describe ultra low frequency Alfvénic pulsations (e.g. Pc and Pi pulsations) observed in space and on the ground with frequencies ranging from a few milli‐Herz (mHz) to a few Hz). The wave equations for the velocity and magnetic field perturbations can be re‐written in terms of Elsässer variables. The resultant wave equations are a special case of the wave mixing equations for Alfvénic fluctuations used to describe locally incompressible turbulence in the solar wind. The canonical wave energy equation for the backward and forward waves, and wave reflection and transmission coefficients are briefly discussed. The equations can also be cast in the form of a Dirac equation, in the Weyl spinor form, in which the mass in the Dirac equation is identified with the wave mixing coefficient for the backward and forward waves.
Short‐term transport variability of the Antarctic Circumpolar Current from satellite gravity observations
Authors: Bergmann I. , Dobslaw H.
Published: April 2012

Ocean bottom pressure gradients deduced from the satellite gravity mission Gravity Recovery and Climate Experiment (GRACE) were previously shown to provide barotropic transport variations of the Antarctic Circumpolar Current (ACC) with up to monthly resolution. Here, bottom pressure distributions from GRACE with monthly (GFZ RL04) and higher temporal resolution (CNES/GRGS with 10 days, ITG‐GRACE2010 with daily resolution) are evaluated over the ACC area. Even on time scales shorter than 10 days, correlations with in situ bottom pressure records frequently exceed 0.6 with positive explained variances, giving evidence that high‐frequency nontidal ocean mass variability is captured by the daily ITG‐GRACE2010 solutions not already included in the applied background models. Bottom pressure is subsequently taken to calculate the barotropic component of the ACC transport variability across Drake Passage. For periods longer than 30 days, transport shows high correlations between 0.4 and 0.5 with several tide gauge records along the coast of Antarctica. Still significant correlations around 0.25 are obtained even for variability with periods shorter than 10 days. Since transport variations are predominantly affected by time‐variable surface winds, GRACE‐based transports are contrasted against an atmospheric index of the Southern Annular Mode (SAM), which represents the Southern Hemispheric wind variability. Correlations between the SAM and GRACE‐based transports are consistently higher than correlations between any of the available sea level records in all frequency bands considered, indicating that GRACE is indeed able to accurately observe a hemispherically consistent pattern of bottom pressure (and hence ACC transport) variability that is otherwise at least partially masked in tide gauge records due to local weather effects, sea ice presence and steric signals.
Rogue waves in crossing seas: The Louis Majesty accident
Authors: Cavaleri L. , Bertotti L. , Torrisi L. , Bitner‐Gregersen E. , Serio M. , Onorato M.
Published: April 2012

We analyze the sea state conditions during which the accident of the cruise ship Louis Majesty took place. The ship was hit by a large wave that destroyed some windows at deck number five and caused two fatalities. Using the wave model (WAM), driven by the Consortium for Small‐Scale Modelling (COSMO‐ME) winds, we perform a detailed hindcast of the local wave conditions. The results reveal the presence of two comparable wave systems characterized almost by the same frequency. We discuss such sea state conditions in the framework of a system of two coupled Nonlinear Schrödinger (CNLS) equations, each of which describe the dynamics of a single spectral peak. For some specific parameters, we discuss the breather solutions of the CNLS equations and estimate the maximum wave amplitude. Even though, due to the lack of measurements, it is impossible to establish the nature of the wave that caused the accident, we show that the angle between the two wave systems during the accident was close to the condition for which the maximum amplitude of the breather solution is observed.
An improved radiance simulation for hyperspectral infrared remote sensing of Asian dust
Authors: Han Hyo‐Jin , Sohn Byung‐Ju , Huang Hung‐Lung , Weisz Elisabeth , Saunders Roger , Takamura Tamio
Published: April 2012

The fast Radiative Transfer for Television Infrared Observation Satellite (TIROS) Operational Vertical Sounder (RTTOV) (Version 9.3) model was used for simulating the effect of East Asian dust on top of atmosphere radiances. The size distribution of Asian dust was retrieved from nine years of sky radiometer measurements at Dunhunag located in the east of Taklimakan desert of China. The default surface emissivity in RTTOV was replaced by the geographically and monthly varying data from University of Wisconsin (UW)/Cooperative Institute for Meteorological Satellite Studies (CIMSS) infrared surface spectral emissivities. For a given size distribution and surface emissivity, the effects of three refractive indices of Optical Properties of Aerosols and Clouds (OPAC) mineral aerosol, dust‐like aerosol by Volz, and High Resolution Transmission (HITRAN) quartz were examined. Results indicate that the specification of surface emissivity using geographically and monthly varying UW/CIMSS data significantly improved the performance of the simulation of AIRS brightness temperature (TB) difference (BTD) between window channels, in comparison to the results from the use of default emissivity value of 0.98 in the RTTOV model, i.e., increase of the correlation coefficient from 0.1 to 0.83 for BTD between 8.9 μm and 11 μm, and from 0.31 to 0.61 for BTD between 3.8 μm and 11 μm. On the other hand, the use of Asian dust size distributions contributed to a general reduction of radiance biases over dust‐sensitive window bands. A further improvement of the TB simulations has been made by considering the Volz refractive index, suggesting that hyperspectral infrared remote sensing of Asian dust can be improved using the proper optical properties of the dust and surface emissivity.
Density and porosity of the lunar crust from gravity and topography
Authors: Huang Qian , Wieczorek Mark A.
Published: April 2012

Newly obtained gravity and topography data of the Moon, combined with a lithospheric flexure model that considers both surface and subsurface loading, are used to place constraints on the density of the upper crust from a localized spectral admittance analysis. Subsurface loads are found to be relatively unimportant in the highlands, and when subsurface loads are neglected, the best fitting bulk densities for a number of highland regions are found to vary from 2590 to 2870 kg m−3, with a mean value of 2691 kg m−3. Crustal rock densities estimated from geochemical considerations and global iron and titanium abundances imply somewhat greater densities, which we interpret as porosity affecting the gravity‐derived bulk density estimates. The average porosity in the upper few kilometers of crust is calculated to be about 7.7%, which is consistent with porosity estimates of impact‐fractured meteorites and terrestrial impact craters.
New Vary‐Chap profile of the topside ionosphere electron density distribution for use with the IRI model and the GIRO real time data
Authors: Nsumei Patrick , Reinisch Bodo W. , Huang Xueqin , Bilitza Dieter
Published: April 2012

A new Vary‐Chap function is introduced for the empirical modeling of the electron density N(h) profile in the topside ionosphere that uses a shape function S(h) in the generalized Chapman function. The Vary‐Chap profile extends the bottomside profile that is specified by the IRI model or measured by the Global Ionospheric Radio Observatory (GIRO) to the altitude of the ISIS‐2 satellite. Some 80,000 topside profiles, measured by the topside sounder on the ISIS‐2 satellite were analyzed, and the shape function S(h) was calculated for each profile. A parameterized function S*(h), composed of two sub‐functions S1(h) and S2(h), is fitted to the measured S(h) profile using three free parameters. At altitudes just above the F2 layer peak height hmF2, the shape function S1 controls S(h), and at greater altitudes S2 controls S(h). The height of the intersection of S1 and S2 is defined as the transition height hT indicating the transition from an O+ to an H+‐dominated profile shape. The observed transition heights range from ∼500 km to 800 km.
Lessons Learned From EHDI: Where Do We Go From Here?
Authors: Bradham Tamala S. , Houston K. Todd , Muñoz Karen
Published: April 2012

Over the past 60 years, experts have made tremendous strides to establish and strengthen early hearing detection and intervention (EHDI) programs in all 50 states and the U.S. territories. Today, approximately 97% of all newborns are screened for hearing loss prior to discharge from a birthing center or hospital (White, Forsman, Eichwald, & Muñoz, 2010). This level of hearing screening is a significant achievement that requires ongoing collaboration among program administrators, policymakers, service providers, and, most importantly, families and children with hearing loss. Although we have learned many lessons that have strengthened the efficiency of the EHDI system, challenges do remain. In this paper, we will share lessons learned in the trenches and provide insights into where we go from here.
Pragmatic Language in Autism and Fragile X Syndrome: Genetic and Clinical Applications
Authors: Losh Molly , Martin Gary E. , Klusek Jessica , Hogan-Brown Abigail L.
Published: April 2012

Evidence suggests a strong genetic basis to autism. Our research program focuses on identifying genetically meaningful phenotypes in autism through family-genetic and cross-population methods, with a particular focus on language and social phenotypes that have been shown to aggregate in families of individuals with autism. In this article, we discuss recent findings from family study research implicating particular language and personality features as markers for genetic liability to autism and Fragile X syndrome and Fragile X Mental Retardation 1 (FMR1)–related variation in relatives. We conclude with consideration of the clinical implications of such findings.
The Relationship Between Client-Centered Goal-Setting and Treatment Outcomes
Authors: Womack Jennifer L.
Published: April 2012

Shifting definitions of health and well-being, prompted by the World Health Organization's International Classification of Functioning (2001), have stimulated changes in traditional clinician-client relationships in rehabilitation. Among these changes, in keeping with the concept of client-centered care, is a trend toward more collaborative goal-setting and joint determination of intervention plans. Evidence suggests that supporting clients' autonomy in prioritizing personally meaningful goals leads to increased engagement in intervention, less emotional anxiety about the rehabilitation process, and improved treatment outcomes. Supporting people with aphasia in a process of collaborative goal formulation may also serve to alter treatment priorities so that they address more relevant communication challenges embedded in post-rehabilitation life.
Use of Life Interests and Values (LIV) Cards for Self-Determination of Aphasia Rehabilitation Goals
Authors: Helm-Estabrooks Nancy , Whiteside Janet
Published: April 2012

The concepts of self-determination and autonomy are now recognized as powerful factors in the ways people respond to rehabilitation. In this paper, we define these concepts and demonstrate that when self-determination and autonomy are incorporated into treatment delivery approaches, patient compliance, outcomes, and satisfaction improve. Determining the rehabilitation goals of people with aphasia (PWA) is typically challenging, because their communication problems often interfere with valid responding to interviews and questionnaires. The Life Interest and Values (LIV) cards described in this paper were developed as a way to circumvent the linguistic problems of PWA and allow them to choose goals for rehabilitation. We also describe the use of the LIV cards in an intensive aphasia rehabilitation program, how the activities chosen by participants were established as reimbursable goals with measureable outcomes, and case studies illustrating this process.
Stress and Coping in Parents of Children and Adolescents with Spinal Muscular Atrophy
Authors: von Gontard A. , Rudnik-Schöneborn S. , Zerres K.
Published: April 2012

Chronic illness and disability is not only associated with higher rates of behavioural problems in children, but also parental stress which requires active coping. The aim of the study was to analyse stress and coping, as well as their mediating variables, in parents of children and adolescents with Spinal Muscular Atrophy (SMA).

96 children and adolescents with SMA aged 6;0 to 18;11 years were compared to 59 age, sex and SES matched controls. Parental stress was measured with the QRS, coping with the F-COPES and social support with the F-SOZU questionnaires.

Parental stress was significantly higher in the SMA families for the total score and all subscales of the QRS. Stress was higher in families with severely affected SMA types I and II. The greatest percentage of variance contributing to stress could be explained by lack of social support, degree of disability and behavioural problems in the child. Although social support was reduced, the actual coping abilities of the families did not differ.

Families with children and adolescents with SMA show high degrees of stress and strain which are associated with the severity of the disease, reduced social support and child behaviour. Despite these stresses they manage and cope no differently from families with healthy children.
Extending the timescale and range of ecosystem services through paleoenvironmental analyses, exemplified in the lower Yangtze basin
Authors: Dearing John A. , Yang Xiangdong , Dong Xuhui , Zhang Enlou , Chen Xu , Langdon Peter G. , Zhang Ke , Zhang Weiguo , Dawson Terence P.
Published: April 2012

In China, and elsewhere, long-term economic development and poverty alleviation need to be balanced against the likelihood of ecological failure. Here, we show how paleoenvironmental records can provide important multidecadal perspectives on ecosystem services (ES). More than 50 different paleoenvironmental proxy records can be mapped to a wide range of ES categories and subcategories. Lake sediments are particularly suitable for reconstructing records of regulating services, such as soil stability, sediment regulation, and water purification, which are often less well monitored. We demonstrate the approach using proxy records from two sets of lake sediment sequences in the lower Yangtze basin covering the period 1800–2006, combined with recent socioeconomic and climate records. We aggregate the proxy records into a regional regulating services index to show that rapid economic growth and population increases since the 1950s are strongly coupled to environmental degradation. Agricultural intensification from the 1980s onward has been the main driver for reducing rural poverty but has led to an accelerated loss of regulating services. In the case of water purification, there is strong evidence that a threshold has been transgressed within the last two decades. The current steep trajectory of the regulating services index implies that regional land management practices across a large agricultural tract of eastern China are critically unsustainable.
Bacteriophage T4 polynucleotide kinase triggers degradation of mRNAs
Authors: Durand Sylvain , Richard Graziella , Bontems François , Uzan Marc
Published: April 2012

The bacteriophage T4-encoded RegB endoribonuclease is produced during the early stage of phage development and targets mostly (but not exclusively) the Shine–Dalgarno sequences of early genes. In this work, we show that the degradation of RegB-cleaved mRNAs depends on a functional T4 polynucleotide kinase/phosphatase (PNK). The 5′-OH produced by RegB cleavage is phosphorylated by the kinase activity of PNK. This modification allows host RNases G and E, with activity that is strongly stimulated by 5′-monophosphate termini, to attack mRNAs from the 5′-end, causing their destabilization. The PNK-dependent pathway of degradation becomes effective 5 min postinfection, consistent with our finding that several minutes are required for PNK to accumulate after infection. Our work emphasizes the importance of the nature of the 5′ terminus for mRNA stability and depicts a pathway of mRNA degradation with 5′- to 3′-polarity in cells devoid of 5′–3′ exonucleases. It also ascribes a role for T4 PNK during normal phage development.
The role of plant viroids in diseases - new developments.
Authors: Serio F. di , Torchetti E. M. , Flores R. , Navarro B.
Published: April 2012

Viroids are tiny infectious agents of plants, consisting exclusively of a small (246-401 nucleotides) circular RNA lacking protein-coding ability. Likely mimicking structural features of cellular RNAs, they can redirect the pre-existing host transcription and RNA trafficking machineries for their own replication and spread, and by doing so they eventually elicit severe diseases. Therefore, in addition to causing phytopathological problems, viroids also offer opportunities for basic research on cellular RNA-based networks. After briefly summarizing the biological, molecular and epidemiological properties of viroids, this review focuses on relevant novelties of these infectious agents, with major emphasis on the molecular pathways presumably mediating viroid pathogenesis and on current phytosanitary emergences in Europe associated with the dissemination of viroids potentially causing severe diseases in vegetable crops.
The American withdrawal from Iraq: ways and means for remaining behind
Authors: al-Hamid Raed
Published: April 2012

This article examines the 2011 withdrawal of United States’ regular military forces from Iraq in the context of Gen. David H. Petraeus strategy of the ‘surge’ and co-opting Sunni fighters against forces aligned with al-Qāʿidah through brokering tribal alliances and adding members of the majālis al-ṣaḥwah (‘awakening councils’) to government pay rosters. It is argued here that Petraeus’s strategy of the ‘surge’ was numerically insignificant and – even if he did order US fighting units back onto the streets – was only partly effective. Various factors and internal Iraqi dynamics played a more decisive role in the outcome of events that ultimately gave the Nuri Maliki government a free hand to work in unofficial cooperation with Shiʿite militias to leave major Sunni neighbourhoods in Baghdad depopulated or abandoned and which transformed the capital into a predominantly Shiʿite city. American withdrawal from Iraq was dictated by the need to redeploy US military personnel and material in Afghanistan, which coincided with a new rhetorical framework under Barack Obama for working with the Islamic world that diverged from George W. Bush’s categorizations under his ‘War on Terror’ as well as the recommendations of the new May 2010 National Security Strategy, which set down the broad outlines for withdrawal. Despite the formal military withdrawal, a palpable American presence remains in Iraq through private security firms as well as a constellation of various agreements and deals concluded with mega-corporations and other, not to mention the largest US embassy in the world with its various support apparatuses. While the troop withdrawal of regular forces has taken place and permitted redeployment in Afghanistan, the ways which the Americans have devised to remain behind are many and their de facto presence, albeit in more ‘civil’ forms, is still very much a ‘fact on the ground’.
Detailed analysis of the phenomenon of political corruption in Algeria: causes, repercussions and reform
Authors: Limam Mohammed Halim
Published: April 2012

Corruption in present-day Algeria has become so rife that it has gone from what Algerians once sardonically termed the ‘sport of the elite’ to being the ‘national sport’. Not only has it reached epidemic proportions at all levels, it has become a culture unto itself, endemic to the country. Because most documented instances of major corruption and scandals have been linked to official branches, apparatuses and persons of the state, and because most have occurred and would not have been possible without some sort of official sanction, corruption in Algeria is ipso facto political. The mechanisms and networks of corruption are many and interlocking, revolving around and feeding on bribery, clientelism, tribalism, nepotism, webs of personal interest and loyalties. The crisis is multifaceted with international dimensions as well, given the collusion of multinational corporations and the intersection of power and vast revenues deriving from oil rent that has also permitted, through an overinflated and ineffectual state bureaucracy, a fertile environment for the pernicious phenomenon. Privatization; the opening of Algerian markets to direct foreign investment and liberalization of trade in response to structural reforms demanded by international monetary institutions during the 1990s; what was effectively a vicious and disastrous civil war in the wake of the suspension of the 1992 elections; as well as globalization have all factored in reinforcing old forms of corruption and promoting new ones. Elite coteries, crony capitalism, and a new generation of ambitious intermediaries and young opportunistic entrepreneurs, such as Rafiq ‘Abd al-Mu’min Khalifa (convicted head of the al-Khalifa Group), have become the new players in billion-dollar schemes of graft, theft and embezzlement of unprecedented proportions. Furthermore, court cases and judicial proceedings have often taken on the aspect of farce when arrests are made and charges brought against minor officials, leaving those higher-up and known to have been party to illicit activities and dealings above the law in the realm of the ‘untouchables’. Significantly, the road to reform, which must necessarily be political in the first instance, is fraught with obstacles, not the least of which is that favouritism is institutionalized in the letter of Algerian law. With good reason, Algerians in general have become highly circumspect with candidates and an electoral process that are open to every tactic of manipulation. This article provides valuable insider information into the specifics and mechanics of Algerian corruption, which even the ruling elite has been obliged to admit constitutes the primary threat to the stability and continuity of the state. The research and distillation of conclusions in this article are drawn from the full-length Arabic-language book by Muḥammad Ḥalīm Līm ām entitled Ẓāhirat al-Fasād al-Siyāsī fī al-Jazāʾir: al-Asbāb wa al-Āthār wa al-Iṣlāḥ. Beirut: Center for Arab Unity Studies (CAUS), 2011.
Egypt’s Muslim Brotherhood and the January 25 Revolution: new political party, new circumstances
Authors: Farag Mona
Published: April 2012

This paper highlights the Muslim Brotherhood’s experience in Egyptian elections since the 1980s with an emphasis on their last attempts during the Hosni Mubarak era in 2010 and in light of their most recent showing in the 2011 elections. This summary reveals how past electoral activities and failures have positioned this organization the better to capitalize on the newfound democratic climate in a post-revolution Egypt and perform well during the 2011 parliamentary elections. Drawing on these and more recent sources, an attempt is also made to bring the features of today’s Egypt’s political field into clear focus in the wake of the January 25 revolution and the subsequent emergence of newly formed political parties on the Egyptian scene. The paper concludes with a broad assessment of the prospects for the political future of the Muslim Brotherhood in view of its showing in the initial phase of elections for the People’s Assembly that took place in November 2011.
On the conservatism of post-Jungian criticism: competing concepts of the symbol in Freud, Jung and Walter Benjamin
Authors: Charles Matthew
Published: April 2012

The renewed interest in analytical psychology by academics working in the humanities has led to the emergence of a post-Jungian field of cultural criticism, at the theoretical core of which stands Jung's theory of symbolism. This article examines the centrality of symbolism to both Freud and Jung's psychology and explains how the differing concepts of the symbol lead to their divergent theories of interpretation in psychology and art criticism. Acknowledging the advantages of Jung's more expansive account of the symbol, it argues that Walter Benjamin's critical engagement with Jung nonetheless provides a useful correction to the problematic conservatism inherent to his concept of the symbol and its contemporary application.
Convergence analysis of a class of massively parallel direction splitting algorithms for the Navier-Stokes equations in simple domains
Authors: Guermond Jean-Luc , Minev Peter , Salgado Abner
Published: April 2012

We provide a convergence analysis for a new fractional time-stepping technique for the incompressible Navier-Stokes equations based on direction splitting. This new technique is of linear complexity, unconditionally stable and convergent, and suitable for massive parallelization.
Bpipe: a tool for running and managing bioinformatics pipelines
Authors: Sadedin Simon P. , Pope Bernard , Oshlack Alicia
Published: April 2012

Summary: Bpipe is a simple, dedicated programming language for defining and executing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, Bpipe is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.

Availability and implementation: Bpipe is freely available from http://bpipe.org under a BSD License.

Contact:  simon.sadedin@mcri.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
ChemSpot: a hybrid system for chemical named entity recognition
Authors: Rocktäschel Tim , Weidlich Michael , Leser Ulf
Published: April 2012

Motivation: The accurate identification of chemicals in text is important for many applications, including computer-assisted reconstruction of metabolic networks or retrieval of information about substances in drug development. But due to the diversity of naming conventions and traditions for such molecules, this task is highly complex and should be supported by computational tools.

Results: We present ChemSpot, a named entity recognition (NER) tool for identifying mentions of chemicals in natural language texts, including trivial names, drugs, abbreviations, molecular formulas and International Union of Pure and Applied Chemistry entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a hybrid approach combining a Conditional Random Field with a dictionary. It achieves an F1 measure of 68.1% on the SCAI corpus, outperforming the only other freely available chemical NER tool, OSCAR4, by 10.8 percentage points.

Availability: ChemSpot is freely available at: http://www.informatik.hu-berlin.de/wbi/resources

Contact:  leser@informatik.hu-berlin.de
Multiple potential regulatory sites of TLR4 activation induced by LPS as revealed by novel inhibitory human TLR4 mAbs
Authors: Tsukamoto Hiroki , Fukudome Kenji , Takao Shoko , Tsuneyoshi Naoko , Ihara Hideyuki , Ikeda Yoshitaka , Kimoto Masao
Published: April 2012

Recognition of LPS by the toll-like receptor 4 (TLR4)/MD-2 complex is a trigger of innate immune defense against bacterial invasion. However, excessive immune activation by this receptor complex causes septic shock and autoimmunity. Manipulation of TLR4 signaling represents a potential therapy that would avoid the detrimental consequences of unnecessary immune responses. In this study, we established two novel mAbs that inhibit LPS-induced human TLR4 activation. HT52 and HT4 mAbs inhibited LPS-induced nuclear factor-κB activation in TLR4/MD-2-expressing Ba/F3-transfected cells and cytokine production and up-regulation of CD86 in the human cell line U373 and PBMCs. These inhibitory activities were stronger than that of HTA125 mAb, which we previously reported. Immunofluorescent and biochemical studies using TLR4 deletion mutants revealed that HT52 and HT4 recognized spatially distinct regions on TLR4 irrespective of MD-2 association. The HT52 and HTA125 epitopes were localized within aa 50–190, while the HT4 epitope was formed only by the full length of TLR4. In addition, we demonstrated that HT52 and HT4 failed to compete with LPS for binding to TLR4/MD-2 but inhibited LPS-induced TLR4 internalization. Inhibitory activities were not due to the interaction with the Fcγ receptor CD32. Our finding that binding of mAbs to at least two distinct regions on TLR4 inhibits LPS-dependent activation provides a novel method for manipulating TLR4 activation and also a rationale for designing drugs targeted to TLR4.
Digital clocks: simple Boolean models can quantitatively describe circadian systems
Authors: Akman Ozgur E. , Watterson Steven , Parton Andrew , Binns Nigel , Millar Andrew J. , Ghazal Peter
Published: April 2012

The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be entrained to the external 24-h day–night cycle, enabling organisms to optimally time biochemical processes relative to dawn and dusk. In recent years, computational models based on differential equations have become useful tools for dissecting and quantifying the complex regulatory relationships underlying the clock's oscillatory dynamics. However, optimizing the large parameter sets characteristic of these models places intense demands on both computational and experimental resources, limiting the scope of
in silico
studies. Here, we develop an approach based on Boolean logic that dramatically reduces the parametrization, making the state and parameter spaces finite and tractable. We introduce efficient methods for fitting Boolean models to molecular data, successfully demonstrating their application to synthetic time courses generated by a number of established clock models, as well as experimental expression levels measured using luciferase imaging. Our results indicate that despite their relative simplicity, logic models can (i) simulate circadian oscillations with the correct, experimentally observed phase relationships among genes and (ii) flexibly entrain to light stimuli, reproducing the complex responses to variations in daylength generated by more detailed differential equation formulations. Our work also demonstrates that logic models have sufficient predictive power to identify optimal regulatory structures from experimental data. By presenting the first Boolean models of circadian circuits together with general techniques for their optimization, we hope to establish a new framework for the systematic modelling of more complex clocks, as well as other circuits with different qualitative dynamics. In particular, we anticipate that the ability of logic models to provide a computationally efficient representation of system behaviour could greatly facilitate the reverse-engineering of large-scale biochemical networks.
Feeding habits and trophic ecology of Dasyatis longa (Elasmobranchii: Myliobatiformes): sexual, temporal and ontogenetic effects
Authors: López‐García J. , Navia A. F. , Mejía‐Falla P. A. , Rubio E. A.
Published: April 2012

Sexual, ontogenic and temporal effects in the diet of Dasyatis longa were evaluated to determine feeding habits and trophic ecology. Numeric indices and the index of relative importance were applied to establish the feeding strategy of the species. Independence of the diet with respect to sex, dry or rainy season and size was evaluated with contingency tables, correspondence analysis and multivariate analysis (MANOVA). The trophic relationships of D. longa (by sex and size intervals) were determined using Levin's niche breadth index and the Pianka's diet overlap index and their significance was determined by null models. The trophic level for each size interval and the species was also calculated. Dasyatis longa showed a narrow niche breadth feeding mainly on shrimps and fishes and its diet was dependent on size, but not on sex or season. Juvenile individuals (class I) fed on shrimps, sub‐adults (class II) on fishes and adults (class III) on stomatopods. Significant overlaps between size classes I and II and classes II and III were found. The trophic level shows D. longa to be a secondary or tertiary consumer. Due to considerable fishing pressures on shrimps, the principal prey of D. longa, it will be important to determine their ability to adapt to changes in prey populations.
Diel temperature patterns of juvenile lemon sharks Negaprion brevirostris, in a shallow‐water nursery
Authors: DiGirolamo A. L. , Gruber S. H. , Pomory C. , Bennett W. A.
Published: April 2012

The relatively complex pattern of temperature selection exhibited by juvenile lemon sharks Negaprion brevirostris in the North Sound differed markedly from many previously described responses of fish preferenda. Thermal data demonstrated that juvenile N. brevirostris did not attempt to behaviourally maintain a constant eccritic temperature. Rather, juveniles selected progressively warmer temperatures throughout the day until reaching the highest temperatures available, and then moved to cooler temperatures during late evening and early morning hours. It is possible that by exploiting habitat thermal heterogeneity juvenile N. brevirostris prolong activities such as feeding or digestion well into the cooler parts of the evening. The complex pattern of temperature occupation by juvenile N. brevirostris within the thermally heterogeneous North Sound nursery is probably linked to key daily activities such as prey capture, predator avoidance and digestive efficiency.
Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D‐loop region
Authors: Menezes M. R. , Kumar G. , Kunal S. P.
Published: April 2012

Genetic structure of skipjack tuna Katsuwonus pelamis from the Indian region was investigated using sequence data of mitochondrial DNA (mtDNA) D‐loop region. A total of 315 individuals were sampled from six major fishing grounds around the east and west coasts of India including the Andaman (Port Blair) and Lakshadweep (Minicoy) Islands. Nucleotide and gene diversities were high in all the sample collections. Significant genetic heterogeneity was observed for the mtDNA sequence data among sites (φST = 0·0273, P < 0·001). Analysis of molecular variance (AMOVA) showed significant genetic variation among four groups (φCT = 0·0261, P < 0·05) which was also supported by spatial AMOVA results. The null hypothesis of single panmictic population of K. pelamis along the Indian coast can thus be rejected. Phylogenetic analysis of the mtDNA sequence data showed the presence of four clades of K. pelamis in the Indian waters. There was no clear pattern, however, of haplotypes and geographic location among samples. The results of this study suggest the occurrence of four genetically differentiated groups of K. pelamis across the coastal waters of India.
Human microdose evaluation of the novel EP1 receptor antagonist GSK269984A
Authors: Ostenfeld Thor , Beaumont Claire , Bullman Jonathan , Beaumont Maria , Jeffrey Phillip
Published: April 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• The microdose administration of novel drug candidates to humans in early development is currently undergoing evaluation as a cost‐efficient approach to the early assessment of pharmacokinetics (PK) before the commitment of resources required to support formal phase 1 studies.

• The microdose approach assumes that PK can be extrapolated linearly over the full range of exposures achieved with sub‐pharmacological doses up to the therapeutic dose range.

• Few microdose studies have been undertaken in the context of pharmaceutical drug development and their precise role in the selection of candidates for further clinical evaluation at therapeutic doses has yet to be fully substantiated.

WHAT THIS STUDY ADDS

• The present study describes the elective application of a human microdose study with a novel EP1 receptor antagonist, GSK269984A, to address a critical development liability posed by uncertainty with respect to the predicted human PK profile.

• Microdose data revealed a favourable PK profile, consistent with a clinically acceptable dosing regimen. These data support the value of undertaking a microdose study early in the drug discovery process to facilitate risk evaluation and to enable decision‐making.

AIM The primary objective was to evaluate the pharmacokinetics (PK) of the novel EP1 antagonist GSK269984A in human volunteers after a single oral and intravenous (i.v.) microdose (100 µg).

METHOD GSK269984A was administered to two groups of healthy human volunteers as a single oral (n= 5) or i.v. (n= 5) microdose (100 µg). Blood samples were collected for up to 24 h and the parent drug concentrations were measured in separated plasma using a validated high pressure liquid chromatography‐tandem mass spectrometry method following solid phase extraction.

RESULTS Following the i.v. microdose, the geometric mean values for clearance (CL), steady‐state volume of distribution (Vss) and terminal elimination half‐life (t1/2) of GSK269984A were 9.8 l h−1, 62.8 l and 8.2 h. Cmax and AUC(0,∞) were 3.2 ng ml−1 and 10.2 ng ml−1 h, respectively; the corresponding oral parameters were 1.8 ng ml−1 and 9.8 ng ml−1 h, respectively. Absolute oral bioavailability was estimated to be 95%. These data were inconsistent with predictions of human PK based on allometric scaling of in vivo PK data from three pre‐clinical species (rat, dog and monkey).

CONCLUSION For drug development programmes characterized by inconsistencies between pre‐clinical in vitro metabolic and in vivo PK data, and where uncertainty exists with respect to allometric predictions of the human PK profile, these data support the early application of a human microdose study to facilitate the selection of compounds for further clinical development.