bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinematic analysis of deformed structures in a tectonic mélange: a key unit for the manifestation of transpression along the Zagros Suture Zone, Iran
Authors: FAGHIH ALI , KUSKY TIMOTHY , SAMANI BABAK
Published: June 2012

Kinematic analysis of mélange fabrics provides critical information concerning tectonic processes and evaluation of the kinematics of ancient relative plate motion. Systematic kinematic analysis of deformed structures within a tectonic mélange exposed along the Zagros Suture Zone elucidates that this zone is an ancient transpressional boundary. The mélange is composed of a greywacke and mudstone matrix surrounding various lenses, blocks and ribbons of radiolarian chert, limestone, sandstone, pillow lava, tuff, serpentinite, shale and marl. The deformation fabrics of the mélange suggest that the mélange units were tectonically accreted at shallow levels within a subduction complex, resulting in layer-parallel extension and shearing along a NW–SE-trending suture that juxtaposes the Afro-Arabian continent to the south and the Central Iranian microcontinents to the north. The tectonic mélange is characterized by subhorizontal layer-parallel extension and subsequent heterogeneous non-coaxial shear resulting in alternating asymmetric and layer-parallel extensional fabrics such as P–Y fabrics and boudinaged layers. Kinematic data suggest that the mélange formed during oblique subduction of the Neo-Tethys oceanic lithosphere in Late Cretaceous time. Kinematic shear sense indicators reveal that the slip direction (N9°E to N14°E) during accretion-related deformations reflects the relative plate motion between the Afro-Arabian continent and Central Iranian microcontinents during Late Cretaceous to Miocene times.
Ethnische Bildungsungleichheit in der frühen Kindheit: Ergebnisse aus dem Projekt ESKOM-V
Authors: Becker Birgit
Published: June 2012

Zusammenfassung: Viele Studien haben in Deutschland die Existenz ethnischer Bildungsungleichheit auf verschiedenen Stufen im deutschen Bildungssystem nachgewiesen. Die Grundlage dafür wird jedoch wahrscheinlich schon in der Zeit vor Schulbeginn gelegt. Das DFG-Projekt „Erwerb von sprachlichen und kulturellen Kompetenzen von Migrantenkindern in der Vorschulzeit“ (ESKOM-V) beschäftigt sich mit ethnischen Unterschieden in der frühen Bildung. In diesem Längsschnittprojekt wurden ca. 1000 Kinder ab dem 3. Lebensjahr bis zum Beginn der Schulzeit regelmäßig verschiedenen standardisierten Tests unterzogen und ihre Eltern jeweils in persönlichen Interviews befragt, wobei etwa die Hälfte der Familien einen türkischen Migrationshintergrund hat. Der vorliegende Beitrag gibt einen Kurzüberblick über das Projekt ESKOM-V und stellt einige zentrale Ergebnisse zu ethnischen Unterschieden im Bereich der frühen Bildung vor. Dabei wird insbesondere auf die Bildungsinstitution Kindergarten eingegangen. Es zeigt sich, dass Kinder mit türkischem Migrationshintergrund im Durchschnitt etwas später den Kindergarten beginnen und auch Kindergärten mit ungünstigeren Lernbedingungen besuchen als deutsche Kinder. Ethnische Kompetenzunterschiede sind bereits im Alter von drei Jahren festzustellen, insbesondere im Bereich der deutschen Sprachfähigkeiten. Der Kindergartenbesuch hat bei türkischstämmigen Kindern einen positiven Einfluss auf den Erwerb der deutschen Sprache, wobei es jedoch auch auf die konkreten Rahmenbedingungen in den Einrichtungen ankommt.
Spatial variation of englacial radar attenuation: Modeling approach and application to the Vostok flowline
Authors: MacGregor Joseph A. , Matsuoka Kenichi , Waddington Edwin D. , Winebrenner Dale P. , Pattyn Frank
Published: June 2012

Constraining the spatial variation of englacial radar attenuation is critical for accurate inference of the spatial variation of the englacial and basal properties of ice sheets from radar returned power. Here we evaluate attenuation models that account for spatial variations in ice temperature and chemistry and test them along the flowline that passes through the Vostok ice core site, Antarctica. The simplest model, often used but rarely valid, assumes a uniform attenuation rate everywhere along the flowline, so that total attenuation is proportional to ice thickness. The next simplest model uses spatially varying temperatures predicted by an ice‐flow model and assumes uniform chemistry. Additional models account for spatially varying chemistry using englacial stratigraphy. We find that the roundtrip attenuation to the bed can easily differ by 10 dB or more between the uniform attenuation‐rate model and models that account for variable ice temperature. Such differences are sufficient to confound the delineation of dry and wet beds. Also including spatial variations in chemistry produces smaller differences (<10 dB), but the magnitude of these differences depends on the relative importance of dry and wet deposition of impurities in the past. Accounting for dry‐deposited impurities requires ice‐flow modeling and results in larger differences from all other models, which assume uniform chemistry or wet deposition only. These results indicate that modeling the spatial variation of attenuation requires a spatially varying temperature model in order to infer bed conditions from bed returned power accurately, and that both ice core data and radar stratigraphy are also strongly desirable.
Interannual variability of primary production and dissolved organic nitrogen storage in the North Pacific Subtropical Gyre
Authors: Luo Ya‐Wei , Ducklow Hugh W. , Friedrichs Marjorie A. M. , Church Matthew J. , Karl David M. , Doney Scott C.
Published: June 2012

The upper ocean primary production measurements from the Hawaii Ocean Time series (HOT) at Station ALOHA in the North Pacific Subtropical Gyre showed substantial variability over the last two decades. The annual average primary production varied within a limited range over 1991–1998, significantly increased in 1999–2000 and then gradually decreased afterwards. This variability was investigated using a one‐dimensional ecosystem model. The long‐term HOT observations were used to constrain the model by prescribing physical forcings and lower boundary conditions and optimizing the model parameters against data using data assimilation. The model reproduced the general interannual pattern in the observed primary production, and mesoscale variability in vertical velocity was identified as a major contributing factor to the interannual variability in the simulation. Several strong upwelling events occurred in 1999, which brought up nitrate at rates several times higher than other years and elevated the model primary production. Our model results suggested a hypothesis for the observed interannual variability pattern of primary production at Station ALOHA: Part of the upwelled nitrate input in 1999 was converted to and accumulated as semilabile dissolved organic nitrogen (DON), and subsequent recycling of this semilabile DON supported enhanced primary productivity for the next several years as the semilabile DON perturbation was gradually removed via export.
Regional assessment of the parameter‐dependent performance of CAM4 in simulating tropical clouds
Authors: Zhang Yuying , Xie Shaocheng , Covey Curt , Lucas Donald D. , Gleckler Peter , Klein Stephen A. , Tannahill John , Doutriaux Charles , Klein Richard
Published: June 2012

Representation of clouds remains among the largest uncertainties in climate models and thus climate projections. Clouds vary significantly over different climate regimes and are controlled by different dynamics and physics. Using the cloud simulator output from perturbed‐parameter ensemble climate runs with prescribed monthly sea surface temperature, this study examines the performance of the Community Atmosphere Model version 4 (CAM4) in simulating clouds over different tropical regions. Perturbing 28 selected parameters shows that model performance is quite sensitive to parameter values in different cloud regimes. Carefully adjusting these parameters could lead to a better simulation of clouds over many regions compared with the default model. Latin hypercube runs that pseudo‐randomly sample the 28 parameters simultaneously have much wider spread and more spatial variations than the runs with parameters varied One‐At‐a‐Time (OAT), suggesting the importance of non‐linearities and interactions among parameters associated with different physical processes. The perturbed parameters have a relatively large impact on the mean bias compared to the pattern error.
The changing impact of El Niño on US winter temperatures
Authors: Yu Jin‐Yi , Zou Yuhao , Kim Seon Tae , Lee Tong
Published: June 2012

In this study, evidence is presented from statistical analyses, numerical model experiments, and case studies to show that the impact on US winter temperatures is different for the different types of El Niño. While the conventional Eastern‐Pacific El Niño affects winter temperatures primarily over the Great Lakes, Northeast, and Southwest US, the largest impact from Central‐Pacific El Niño is on temperatures in the northwestern and southeastern US. The recent shift to a greater frequency of occurrence of the Central‐Pacific type has made the Northwest and Southeast regions of the US most influenced by El Niño. It is shown that the different impacts result from differing wave train responses in the atmosphere to the sea surface temperature anomalies associated with the two types of El Niño.
Spatial and energy distributions of X‐ray emissions from leaders in natural and rocket triggered lightning
Authors: Schaal M. M. , Dwyer J. R. , Saleh Z. H. , Rassoul H. K. , Hill J. D. , Jordan D. M. , Uman M. A.
Published: June 2012

Energetic radiation is known to be produced by lightning. To investigate these emissions, ground‐based observations are being conducted at the International Center for Lightning Research and Testing (ICLRT) at Camp Blanding, FL where measurements of energetic radiation from both natural and rocket‐triggered lightning discharges are recorded. In the present study, data from two natural negative cloud‐to‐ground stepped leaders and one rocket‐triggered “chaotic” dart leader are analyzed in detail to investigate X‐ray energy spectra and spatial X‐ray distributions around the source. These measurements are compared with Monte Carlo simulations of runaway electron propagation with the goal of understanding the underlying mechanism of runaway electron production and their role in lightning initiation and propagation. We show that the energetic electrons that produce X‐rays exhibit a characteristic energy less than 3 MeV for two natural and one rocket‐triggered leaders investigated. In addition to studying these three leaders, energetic electron luminosity, total energy, and energetic electron per meter are compared to the following return stroke currents for 28 leaders from 12 different triggered flashes. Electron luminosity is found to increase exponentially with return stroke current up to about 10 kA and to be roughly constant for larger currents. The maximum electron luminosity, which is determined indirectly through X‐ray luminosities, is on the order of 1017 electrons/s, which is less than the value found from theoretical calculations.
Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life
Authors: Thole Sebastian , Kalhoefer Daniela , Voget Sonja , Berger Martine , Engelhardt Tim , Liesegang Heiko , Wollherr Antje , Kjelleberg Staffan , Daniel Rolf , Simon Meinhard , Thomas Torsten , Brinkhoff Thorsten
Published: June 2012

Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.
Novel atypical PKC inhibitors prevent vascular endothelial growth factor-induced blood–retinal barrier dysfunction
Authors: Titchenell Paul M. , Lin Cheng-Mao , Keil Jason M. , Sundstrom Jeffrey M. , Smith Charles D. , Antonetti David A.
Published: June 2012

Pro-inflammatory cytokines and growth factors such as VEGF (vascular endothelial growth factor) contribute to the loss of the BRB (blood–retinal barrier) and subsequent macular oedema in various retinal pathologies. VEGF signalling requires PKCβ [conventional PKC (protein kinase C)] activity; however, PKCβ inhibition only partially prevents VEGF-induced endothelial permeability and does not affect pro-inflammatory cytokine-induced permeability, suggesting the involvement of alternative signalling pathways. In the present study, we provide evidence for the involvement of aPKC (atypical PKC) signalling in VEGF-induced endothelial permeability and identify a novel class of inhibitors of aPKC that prevent BRB breakdown in vivo. Genetic and pharmacological manipulations of aPKC isoforms were used to assess their contribution to endothelial permeability in culture. A chemical library was screened using an in vitro kinase assay to identify novel small-molecule inhibitors, and further medicinal chemistry was performed to delineate a novel pharmacophore. We demonstrate that aPKC isoforms are both sufficient and required for VEGF-induced endothelial permeability. Furthermore, these specific, potent, non-competitive, small-molecule inhibitors prevented VEGF-induced tight junction internalization and retinal endothelial permeability in response to VEGF in both primary culture and in rodent retina. The results of the present study suggest that aPKC inhibition with 2-amino-4-phenyl-thiophene derivatives may be developed to preserve the BRB in retinal diseases such as diabetic retinopathy or uveitis, and the BBB (blood–brain barrier) in the presence of brain tumours.
Human YKL-39 is a pseudo-chitinase with retained chitooligosaccharide-binding properties
Authors: Schimpl Marianne , Rush Christina L. , Betou Marie , Eggleston Ian M. , Recklies Anneliese D. , van Aalten Daan M. F.
Published: June 2012

The chitinase-like proteins YKL-39 (chitinase 3-like-2) and YKL-40 (chitinase 3-like-1) are highly expressed in a number of human cells independent of their origin (mesenchymal, epithelial or haemapoietic). Elevated serum levels of YKL-40 have been associated with a negative outcome in a number of diseases ranging from cancer to inflammation and asthma. YKL-39 expression has been associated with osteoarthritis. However, despite the reported association with disease, the physiological or pathological role of these proteins is still very poorly understood. Although YKL-39 is homologous to the two family 18 chitinases in the human genome, it has been reported to lack any chitinase activity. In the present study, we show that human YKL-39 possesses a chitinase-like fold, but lacks key active-site residues required for catalysis. A glycan screen identified oligomers of N-acetylglucosamine as preferred binding partners. YKL-39 binds chitooligosaccharides and a newly synthesized derivative of the bisdionin chitinase-inhibitor class with micromolar affinity, through a number of conserved tryptophan residues. Strikingly, the chitinase activity of YKL-39 was recovered by reverting two non-conservative substitutions in the active site to those found in the active enzymes, suggesting that YKL-39 is a pseudo-chitinase with retention of chitinase-like ligand-binding properties.
Effect of homomeric P450–P450 complexes on P450 function
Authors: Reed James R. , Connick J. Patrick , Cheng Dongmei , Cawley George F. , Backes Wayne L.
Published: June 2012

Previous studies have shown that the presence of one P450 enzyme can affect the function of another. The goal of the present study was to determine if P450 enzymes are capable of forming homomeric complexes that affect P450 function. To address this problem, the catalytic activities of several P450s were examined in reconstituted systems containing NADPH–POR (cytochrome P450 reductase) and a single P450. CYP2B4 (cytochrome P450 2B4)-, CYP2E1 (cytochrome P450 2E1)- and CYP1A2 (cytochrome P450 1A2)-mediated activities were measured as a function of POR concentration using reconstituted systems containing different concentrations of P450. Although CYP2B4-dependent activities could be explained by a simple Michaelis–Menten interaction between POR and CYP2B4, both CYP2E1 and CYP1A2 activities generally produced a sigmoidal response as a function of [POR]. Interestingly, the non-Michaelis behaviour of CYP1A2 could be converted into a simple mass-action response by increasing the ionic strength of the buffer. Next, physical interactions between CYP1A2 enzymes were demonstrated in reconstituted systems by chemical cross-linking and in cellular systems by BRET (bioluminescence resonance energy transfer). Cross-linking data were consistent with the kinetic responses in that both were similarly modulated by increasing the ionic strength of the surrounding solution. Taken together, these results show that CYP1A2 forms CYP1A2–CYP1A2 complexes that exhibit altered catalytic activity.
Ser262 determines the chloride-dependent colour tuning of a new halorhodopsin from Haloquadratum walsbyi
Authors: Fu Hsu-Yuan , Chang Yung-Ning , Jheng Ming-Jin , Yang Chii-Shen
Published: June 2012

Light is an important environmental signal for all organisms on earth because it is essential for physiological signalling and the regulation of most biological systems. Halophiles found in salt-saturated ponds encode various archaeal rhodopsins and thereby harvest various wavelengths of light either for ion transportation or as sensory mediators. HR (halorhodopsin), one of the microbial rhodopsins, senses yellow light and transports chloride or other halides into the cytoplasm to maintain the osmotic balance during cell growth, and it exists almost ubiquitously in all known halobacteria. To date, only two HRs, isolated from HsHR (Halobacterium salinarum HR) and NpHR (Natronomonas pharaonis HR), have been characterized. In the present study, two new HRs, HmHR (Haloarcula marismortui HR) and HwHR (Haloquadratum walsbyi HR), were functionally overexpressed in Escherichia coli, and the maximum absorbance (λmax) of the purified proteins, the light-driven chloride uptake and the chloride-binding affinity were measured. The results showed them to have similar properties to two HRs reported previously. However, the λmax of HwHR is extremely consistent in a wide range of salt/chloride concentrations, which had not been observed previously. A structural-based sequence alignment identified a single serine residue at 262 in HwHR, which is typically a conserved alanine in all other known HRs. A Ser262 to alanine replacement in HwHR eliminated the chloride-independent colour tuning, whereas an Ala246 to serine mutagenesis in HsHR transformed it to have chloride-independent colour tuning similar to that of HwHR. Thus Ser262 is a key residue for the mechanism of chloride-dependent colour tuning in HwHR.
microRNA-29b contributes to pre-eclampsia through its effects on apoptosis, invasion and angiogenesis of trophoblast cells
Authors: Li Pengfei , Guo Wei , Du Leilei , Zhao Junli , Wang Yaping , Liu Liu , Hu Yali , Hou Yayi
Published: June 2012

PE (pre-eclampsia), a pregnancy-specific disorder, is characterized by increased trophoblast cell death and deficient trophoblast invasion and reduced trophoblast-mediated remodelling of spiral arteries. The present study was performed to determine the function of miR-29b (microRNA-29b) in trophoblast cells and its underlying role in the pathogenesis of PE. The prediction of miR-29b target genes was performed using computer-based programs, including Targetscan, Pictar and miRBase. The function of these target genes was analysed further by gene ontology (GO). The effects of miR-29b on apoptosis, and invasion and angiogenesis of trophoblast cell lines (HTR-8/SVneo, BeWo and JAR) were examined by flow cytometry and Matrigel assay respectively. We found that miR-29b induced apoptosis and inhibited invasion and angiogenesis of trophoblast cells. Further studies confirmed that miR-29b regulated the expression of MCL1 (myeloid cell leukaemia sequence 1), MMP2 (encoding matrix metallproteinase 2), VEGFA (vascular endothelial growth factor A) and ITGB1 (integrin β1) genes by directly binding to their 3′-UTRs (untranslated regions). Moreover, we identified that there was an inverse correlation between miR-29b and its target genes in subjects with PE. Taken together, these findings support a novel role for miR-29b in invasion, apoptosis and angiogenesis of trophoblast cells, and miR-29b may become a new potential therapeutic target for PE.
Parent-Implemented Enhanced Milieu Teaching With Preschool Children Who Have Intellectual Disabilities
Authors: Kaiser Ann P. , Roberts Megan Y.
Published: June 2012

Purpose

The purpose of this study was to compare the effects of enhanced milieu teaching (EMT) implemented by parents and therapists versus therapists only on the language skills of preschool children with intellectual disabilities (IDs), including children with Down syndrome and children with autism spectrum disorders.

Method

Seventy-seven children were randomly assigned to 2 treatments (parent + therapist EMT or therapist-only EMT) and received 36 intervention sessions. Children were assessed before, immediately after, 6 months after, and 12 months after intervention. Separate linear regressions were conducted for each standardized and observational measure at each time point.

Results

Parents in the parent + therapist group demonstrated greater use of EMT strategies at home than untrained parents in the therapist-only group, and these effects maintained over time. Effect sizes for observational measures ranged from
d
= 0.10 to
d
= 1.32 favoring the parent + therapist group, with the largest effect sizes found 12 months after intervention.

Conclusion

Findings from this study indicate generally that there are benefits to training parents to implement naturalistic language intervention strategies with preschool children who have ID and significant language impairments.
Speech Perception in Noise by Children With Cochlear Implants
Authors: Caldwell Amanda , Nittrouer Susan
Published: June 2012

Purpose

Common wisdom suggests that listening in noise poses disproportionately greater difficulty for listeners with cochlear implants (CIs) than for peers with normal hearing (NH). The purpose of this study was to examine phonological, language, and cognitive skills that might help explain speech-in-noise abilities for children with CIs.

Method

Three groups of kindergartners (NH, hearing aid wearers, and CI users) were tested on speech recognition in quiet and noise and on tasks thought to underlie the abilities that fit into the domains of phonological awareness, general language, and cognitive skills. These last measures were used as predictor variables in regression analyses with speech-in-noise scores as dependent variables.

Results

Compared to children with NH, children with CIs did not perform as well on speech recognition in noise or on most other measures, including recognition in quiet. Two surprising results were that (a) noise effects were consistent across groups and (b) scores on other measures did not explain any group differences in speech recognition.

Conclusions

Limitations of implant processing take their primary toll on recognition in quiet and account for poor speech recognition and language/phonological deficits in children with CIs. Implications are that teachers/clinicians need to teach language/phonology directly and maximize signal-to-noise levels in the classroom.
Centennial to millennial geomagnetic field variations
Authors: Korte Monika , Muscheler Raimund
Published: June 2012

Reconstructions of the geomagnetic field in the past represent a useful tool not only to investigate the geodynamo process, but also to estimate the effect of geomagnetic shielding for any studies on cosmogenic radionuclides and galactic cosmic rays. A number of new millennial-scale geomagnetic field reconstructions have been published over the last years, based on improved global archeo- and paleomagnetic data compilations. Here we review several spherical harmonic models and compare their dipole field predictions to reconstructions based on virtual axial dipole moments and virtual geomagnetic poles. Dipole intensity estimates from cosmogenic radionuclide production records, with suitable filtering to minimise the solar influence, have also been included in the comparison to provide independent information about variations in the strength of the geomagnetic field. However, due to differences among geomagnetic models and between 14C and 10Be production records this comparison is fairly inconclusive with respect to multi-centennial variations. Different geomagnetic dipole tilt reconstructions agree well for much of the Holocene, but dipole moment estimates still differ substantially. Recent spherical harmonic models for the past 3 and 10 kyrs have improved considerably compared to earlier versions. Nevertheless at present we recommend to test if any interpretation depends on the choice of model.
Seedling survivorship of temperate grassland perennials is remarkably resistant to projected changes in rainfall
Authors: Perring Michael P. , Hovenden Mark J.
Published: June 2012

Recruitment is central to the maintenance of any plant population, particularly in disturbed or drought-prone environments. Recruitment relies on both seedling emergence and subsequent survival to establishment, processes susceptible to changes in soil water potential. Here, we use an existing relationship between seedling survivorship and soil water potential from the TasFACE global change impacts experiment situated in Tasmanian grassland, elucidate relationships between rainfall and soil water potential, and then simulate seedling survivorship responses to potential changes in both the amount and seasonal distribution of precipitation. Annual rainfall was a poor predictor of survivorship, suggesting the importance of seasonal and daily distribution of rain in determining establishment patterns. Modelled seedling survivorship was remarkably resistant to declines in rainfall, with a rainfall reduction of 40% reducing survivorship only by ~10%. Reducing spring rainfall only markedly reduced seedling survivorship when the rain removed was not added to winter rainfall. Our results show that soil water recharge during winter is critical to seedling survivorship of perennial species at the study site. Providing rainfall regimes allow recharge to occur, seedling survivorship of perennial grassland species may be maintained despite large reductions in rainfall, indicating that these grassland species may have an inherent capacity that limits the impacts of reductions in rainfall.
Seasonal differences of urban organic aerosol composition – an ultra-high resolution mass spectrometry study
Authors: Rincón Angela G. , Calvo Ana I. , Dietzel Mathias , Kalberer Markus
Published: June 2012

Environmental contextUnderstanding the molecular composition and chemical transformations of organic aerosols during atmospheric aging is a major challenge in atmospheric chemistry. Ultra-high resolution mass spectrometry can provide detailed information on the molecular composition of organic aerosols. Aerosol samples collected in summer and winter at an urban site are characterised and compared in detail with respect to the elemental composition of their components, especially nitrogen- and sulfur-containing compounds, and are discussed with respect to atmospheric formation processes.
AbstractOrganic compounds are major constituents of atmospheric aerosol particles. The understanding of their chemical composition, their properties and reactivity are important for assessing aerosol effects upon both global climate change and human health. The composition of organic aerosols is poorly understood, mainly due to its highly complex chemical composition of several thousand compounds. There is currently no analytical technique available covering a wide enough chemical space to characterise this large number of organic compounds. In recent years ultra-high resolution mass spectrometry has been increasingly used to explore the chemical complexity in organic aerosols from laboratory and ambient samples. In the present study ambient particles <1 µm were collected at an urban site in Cambridge, UK, from August to December 2009. The water-soluble organic fraction of the filters was separated from inorganic ions following a procedure developed for humic-like substance isolation. Ultra-high resolution mass spectrometry analyses were performed in negative and positive polarity. Data in the mass range of m/z 50–350 were analysed for their elemental composition. Summer samples generally contained more components than winter samples. The large number of compounds was subdivided into groups according to their elemental composition. Up to 80 % of the peaks contain nitrogen and sulfur functional groups and only ~20 % of the compounds contain only C, H and O atoms. In summer the fraction of compounds with oxidised nitrogen and sulfur groups increases compared with winter indicating a photo-chemical formation route of these multifunctional compounds. In addition to oxidised nitrogen compounds a large number of amines was identified.
Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system
Authors: Walldén Karin , Williams Robert , Yan Jun , Lian Pei W. , Wang Luchun , Thalassinos Konstantinos , Orlova Elena V. , Waksman Gabriel
Published: June 2012

Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer of antibiotic resistance. The VirB4 ATPase of the T4S system is essential for both the assembly of the system and substrate transfer. In this article, we present the crystal structure of the C-terminal domain of
Thermoanaerobacter pseudethanolicus
VirB4. This structure is strikingly similar to that of another T4S ATPase, VirD4, a protein that shares only 12% sequence identity with VirB4. The VirB4 domain purifies as a monomer, but the full-length protein is observed in a monomer-dimer equilibrium, even in the presence of nucleotides and DNAs. We also report the negative stain electron microscopy structure of the core complex of the T4S system of the
Escherichia coli
pKM101 plasmid, with VirB4 bound. In this structure, VirB4 is also monomeric and bound through its N-terminal domain to the core’s VirB9 protein. Remarkably, VirB4 is observed bound to the side of the complex where it is ideally placed to play its known regulatory role in substrate transfer.
Activation of the Hippo pathway by CTLA-4 regulates the expression of Blimp-1 in the CD8+T cell
Authors: Thaventhiran James E. D. , Hoffmann Anja , Magiera Lukasz , de la Roche Maike , Lingel Holger , Brunner-Weinzierl Monika , Fearon Douglas T.
Published: June 2012

During the primary response, the commitment of the CD8+T cell to Blimp-1 expression and the terminal differentiation that Blimp-1 induces must be timed so as not to impair the process of clonal expansion. We determined whether the Hippo pathway, which links cell–cell contact to differentiation in other cell lineages, controls Blimp-1 expression. Activating the CD8+T cell with antigen and IL-2 causes expression of the core Hippo pathway components, including the pivotal transcriptional cofactor Yap. Contact between activated CD8+T cells induces Hippo pathway-mediated Yap degradation and Blimp-1 expression; a Hippo-resistant, stable form of Yap suppresses Blimp-1 expression. Cytotoxic T lymphocyte antigen 4 (CTLA-4) and CD80 comprise the receptor–ligand pair that mediates contact-dependent Hippo pathway activation. In vivo, CD8+T cells expressing Hippo resistant-Yap or lacking CTLA-4 have diminished expression of the senescence marker, KLRG1, during a viral infection. The CTLA-4/Hippo pathway/Blimp-1 system may couple terminal differentiation of CD8+T cell with the magnitude of clonal expansion.
Conserved features of intermediates in amyloid assembly determine their benign or toxic states
Authors: Krishnan Rajaraman , Goodman Jessica L. , Mukhopadhyay Samrat , Pacheco Chris D. , Lemke Edward A. , Deniz Ashok A. , Lindquist Susan
Published: June 2012

Some amyloid-forming polypeptides are associated with devastating human diseases and others provide important biological functions. For both, oligomeric intermediates appear during amyloid assembly. Currently we have few tools for characterizing these conformationally labile intermediates and discerning what governs their benign versus toxic states. Here, we examine intermediates in the assembly of a normal, functional amyloid, the prion-determining region of yeast Sup35 (NM). During assembly, NM formed a variety of oligomers with different sizes and conformation-specific antibody reactivities. Earlier oligomers were less compact and reacted with the conformational antibody A11. More mature oligomers were more compact and reacted with conformational antibody OC. We found we could arrest NM in either of these two distinct oligomeric states with small molecules or crosslinking. The A11-reactive oligomers were more hydrophobic (as measured by Nile Red binding) and were highly toxic to neuronal cells, while OC-reactive oligomers were less hydrophobic and were not toxic. The A11 and OC antibodies were originally raised against oligomers of Aβ, an amyloidogenic peptide implicated in Alzheimer’s disease (AD) that is completely unrelated to NM in sequence. Thus, this natural yeast prion samples two conformational states similar to those sampled by Aβ, and when assembly stalls at one of these two states, but not the other, it becomes extremely toxic. Our results have implications for selective pressures operating on the evolution of amyloid folds across a billion years of evolution. Understanding the features that govern such conformational transitions will shed light on human disease and evolution alike.
Feeling close and doing well: The prevalence and motivational effects of interpersonally engaging emotions in Mexican and European American cultural contexts
Authors: Savani Krishna , Alvarez Ayme , Mesquita Batja , Markus Hazel Rose
Published: June 2012

Two studies investigate whether interpersonally engaging emotions—those that bring the self closer to others (e.g., affection, shame)—are central to the model of self and relationships prevalent in Mexican cultural contexts. Study 1 demonstrated that compared to people in European American contexts, people in Mexican contexts were more likely to report experiencing interpersonally engaging emotions and less likely to report experiencing interpersonally disengaging emotions. Study 2 found that interpersonally engaging emotions had a substantial influence on performance motivation in Mexican contexts—Mexican participants solved more word search puzzles after recalling instances in which they experienced positive interpersonally engaging emotions, and fewer after recalling negative interpersonally disengaging emotions; in contrast, there were no differences by condition for European Americans. These findings significantly extend previous research by documenting the implications of relational concerns (e.g., simpatia, personalismo) for emotion and motivation in Mexican contexts, and are the first to demonstrate the motivational effects of interpersonally engaging emotions.
HELPING VALUES AND CIVIC ENGAGEMENT
Authors: Purdam K. , Tranmer M.
Published: June 2012

In this article we examine generalised helping and specifically the importance people attach to helping other people, the extent to which they help in practice and their perceptions of how much people living locally help each other. We consider the extent to which the value of help is associated with other civic engagement activities such as, for example, volunteering, signing a petition and contacting a politician. Our findings suggest that the importance people attach to helping others and the extent to which they help in practice (in terms of helping with or attending activities in their local area) varies considerably across Europe. People are more likely to see helping other people as important than actually help in practice. However, helping in practice is more strongly associated than helping as a value, with other civic engagement activities. It seems that the value of help is detached from what people do in their everyday lives. Both the value of help and helping in practice are associated with the extent to which people in their local area are perceived to help each other. Our findings concerning generalised helping have important implications for the understanding of civic society and the contribution citizens can make.
Nuclear-localized focal adhesion kinase regulates inflammatory VCAM-1 expression
Authors: Lim Ssang-Taek , Miller Nichol L.G. , Chen Xiao Lei , Tancioni Isabelle , Walsh Colin T. , Lawson Christine , Uryu Sean , Weis Sara M. , Cheresh David A. , Schlaepfer David D.
Published: June 2012

Vascular cell adhesion molecule–1 (VCAM-1) plays important roles in development and inflammation. Tumor necrosis factor–α (TNF-α) and focal adhesion kinase (FAK) are key regulators of inflammatory and integrin–matrix signaling, respectively. Integrin costimulatory signals modulate inflammatory gene expression, but the important control points between these pathways remain unresolved. We report that pharmacological FAK inhibition prevented TNF-α–induced VCAM-1 expression within heart vessel–associated endothelial cells in vivo, and genetic or pharmacological FAK inhibition blocked VCAM-1 expression during development. FAK signaling facilitated TNF-α–induced, mitogen-activated protein kinase activation, and, surprisingly, FAK inhibition resulted in the loss of the GATA4 transcription factor required for TNF-α–induced VCAM-1 production. FAK inhibition also triggered FAK nuclear localization. In the nucleus, the FAK-FERM (band 4.1, ezrin, radixin, moesin homology) domain bound directly to GATA4 and enhanced its CHIP (C terminus of Hsp70-interacting protein) E3 ligase–dependent polyubiquitination and degradation. These studies reveal new developmental and anti-inflammatory roles for kinase-inhibited FAK in limiting VCAM-1 production via nuclear localization and promotion of GATA4 turnover.
Membrane bending is critical for the stability of voltage sensor segments in the membrane
Authors: Callenberg Keith M. , Latorraca Naomi R. , Grabe Michael
Published: June 2012

The interaction between membrane proteins and the surrounding membrane is becoming increasingly appreciated for its role in regulating protein function, protein localization, and membrane morphology. In particular, recent studies have suggested that membrane deformation is needed to stably accommodate proteins harboring charged amino acids in their transmembrane (TM) region, as it is energetically prohibitive to bury charge in the hydrophobic core of the bilayer. Unfortunately, current computational methods are poorly equipped for describing such deformations, as atomistic simulations are often too short to observe large-scale membrane reorganization and most continuum approaches assume a flat membrane. Previously, we developed a method that overcomes these shortcomings by using elasticity theory to characterize equilibrium membrane distortions in the presence of a TM protein, while using traditional continuum electrostatic and nonpolar energy models to determine the energy of the protein in the membrane. Here, we linked the elastostatics, electrostatics, and nonpolar numeric solvers to permit the calculation of energies for nontrivial membrane deformations. We then coupled this procedure to a robust search algorithm that identifies optimal membrane shapes for a TM protein of arbitrary chemical composition. This advance now permits us to explore a host of biological phenomena that were beyond the scope of our original method. We show that the energy required to embed charged residues in the membrane can be highly nonadditive, and our model provides a simple mechanical explanation for this nonadditivity. Our results also predict that isolated voltage sensor segments do not insert into rigid membranes, but membrane bending dramatically stabilizes these proteins in the bilayer despite their high charge content. Additionally, we use the model to explore hydrophobic mismatch with regard to nonpolar peptides and mechanosensitive channels. Our method is in quantitative agreement with molecular dynamics simulations at a tiny fraction of the computational cost.
A bioimage informatics approach to automatically extract complex fungal networks
Authors: Obara Boguslaw , Grau Vicente , Fricker Mark D.
Published: June 2012

Motivation: Fungi form extensive interconnected mycelial networks that scavenge efficiently for scarce resources in a heterogeneous environment. The architecture of the network is highly responsive to local nutritional cues, damage or predation, and continuously adapts through growth, branching, fusion or regression. These networks also provide an example of an experimental planar network system that can be subjected to both theoretical analysis and experimental manipulation in multiple replicates. For high-throughput measurements, with hundreds of thousands of branches on each image, manual detection is not a realistic option, especially if extended time series are captured. Furthermore, branches typically show considerable variation in contrast as the individual cords span several orders of magnitude and the compressed soil substrate is not homogeneous in texture making automated segmentation challenging.

Results: We have developed and evaluated a high-throughput automated image analysis and processing approach using Phase Congruency Tensors and watershed segmentation to characterize complex fungal networks. The performance of the proposed approach is evaluated using complex images of saprotrophic fungal networks with 105–106 edges. The results obtained demonstrate that this approach provides a fast and robust solution for detection and graph-based representation of complex curvilinear networks.

Availability and implementation: The Matlab toolbox is freely available through the Oxford e-Research Centre website: http://www.oerc.ox.ac.uk/research/bioimage/software

Contacts:  boguslaw.obara@oerc.ox.ac.uk
Hominin cognitive evolution: identifying patterns and processes in the fossil and archaeological record
Authors: Shultz Susanne , Nelson Emma , Dunbar Robin I. M.
Published: June 2012

As only limited insight into behaviour is available from the archaeological record, much of our understanding of historical changes in human cognition is restricted to identifying changes in brain size and architecture. Using both absolute and residual brain size estimates, we show that hominin brain evolution was likely to be the result of a mix of processes; punctuated changes at approximately 100 kya, 1 Mya and 1.8 Mya are supplemented by gradual within-lineage changes in
Homo erectus
and
Homo sapiens sensu lato
. While brain size increase in
Homo
in Africa is a gradual process, migration of hominins into Eurasia is associated with step changes at approximately 400 kya and approximately 100 kya. We then demonstrate that periods of rapid change in hominin brain size are not temporally associated with changes in environmental unpredictability or with long-term palaeoclimate trends. Thus, we argue that commonly used global sea level or Indian Ocean dust palaeoclimate records provide little evidence for either the variability selection or aridity hypotheses explaining changes in hominin brain size. Brain size change at approximately 100 kya is coincident with demographic change and the appearance of fully modern language. However, gaps remain in our understanding of the external pressures driving encephalization, which will only be filled by novel applications of the fossil, palaeoclimatic and archaeological records.
Language, gesture, skill: the co-evolutionary foundations of language
Authors: Sterelny Kim
Published: June 2012

This paper defends a gestural origins hypothesis about the evolution of enhanced communication and language in the hominin lineage. The paper shows that we can develop an incremental model of language evolution on that hypothesis, but not if we suppose that language originated in an expansion of great ape vocalization. On the basis of the gestural origins hypothesis, the paper then advances solutions to four classic problems about the evolution of language: (i) why did language evolve only in the hominin lineage? (ii) why is language use an evolutionarily stable form of informational cooperation, despite the fact that hominins have diverging evolutionary interests? (iii) how did stimulus independent symbols emerge? (iv) what were the origins of complex, syntactically organized symbols? The paper concludes by confronting two challenges: those of testability and of explaining the gesture-to-speech transition; crucial issues for any gestural origins hypothesis
Transmission fidelity is the key to the build-up of cumulative culture
Authors: Lewis Hannah M. , Laland Kevin N.
Published: June 2012

Many animals have socially transmitted behavioural traditions, but human culture appears unique in that it is cumulative, i.e. human cultural traits increase in diversity and complexity over time. It is often suggested that high-fidelity cultural transmission is necessary for cumulative culture to occur through refinement, a process known as ‘ratcheting’, but this hypothesis has never been formally evaluated. We discuss processes of information transmission and loss of traits from a cognitive viewpoint alongside other cultural processes ofnovel invention(generation of entirely new traits),modification(refinement of existing traits) andcombination(bringing together two established traits to generate a new trait). We develop a simple cultural transmission model that does not assume major evolutionary changes (e.g. in brain architecture) and show that small changes in the fidelity with which information is passed between individuals can lead to cumulative culture. In comparison, modification and combination have a lesser influence on, and novel invention appears unimportant to, the ratcheting process. Our findings support the idea that high-fidelity transmission is the key driver of human cumulative culture, and that progress in cumulative culture depends more on trait combination than novel invention or trait modification.