bluuebunny/crossref_metadata_2025 huggingface dataset:
Pre‐mRNA modifications and their role in nuclear processing
Authors: Martinez Nicole M. , Gilbert Wendy V.
Published: September 2018

Background

Cellular non‐coding RNAs are extensively modified post‐transcriptionally, with more than 100 chemically distinct nucleotides identified to date. In the past five years, new sequencing based methods have revealed widespread decoration of eukaryotic messenger RNA with diverse RNA modifications whose functions in mRNA metabolism are only beginning to be known.

Results

Since most of the identified mRNA modifying enzymes are present in the nucleus, these modifications have the potential to function in nuclear pre‐mRNA processing including alternative splicing. Here we review recent progress towards illuminating the role of pre‐mRNA modifications in splicing and highlight key areas for future investigation in this rapidly growing field.

Conclusions

Future studies to identify which modifications are added to nascent pre‐mRNA and to interrogate the direct effects of individual modifications are likely to reveal new mechanisms by which nuclear pre‐mRNA processing is regulated.
Climatic variables drive temporal patterns of α and β diversities of dung beetles
Authors: Ferreira S.C. , da Silva P.G. , Paladini A. , Di Mare R.A.
Published: September 2018

Understanding the mechanisms underpinning spatiotemporal diversity patterns of biological communities is a major goal of ecology. We aimed to test two ecological hypotheses: (i) temporal patterns of β-diversity will mostly be driven by nestedness, with a loss of species from summer to winter, and (ii) nestedness values will correlate with climatic variables instead of turnover values, indicating either a loss of species during winter or a gain of species during summer. We sampled dung beetles using standardized sampling protocols along a year in four Atlantic forest sites: two at the northwest and two at the central region of Rio Grande do Sul state, southern Brazil. We partitioned temporal patterns of β-diversity into turnover and nestedness in order to investigate if community changes are driven by species substitution or gain/loss across time. Our results highlighted five main findings: (i) dung beetle composition varied more with sites than site geographic position; (ii) there was almost one and a half ‘true’ dung beetle assemblages regarding the spatial distribution of species weighed by abundance; (iii) we found a positive influence of mean temperature and a negative influence of relative humidity on both species richness and abundance; (iv) both spatial and temporal dissimilarity among sites were dominated by species replacement, while the relative importance of nestedness was higher in temporal than spatial patterns; (v) there was an effect of precipitation and relative humidity on temporal patterns of β-diversity components, but these effects were site-dependent. Contrary to our expectations, the β-diversity component of turnover dominated both spatial and temporal patterns in dung beetle dissimilarity among sites and months. Distinct climatic variables affected differently the α-diversity and β-diversity components of dung beetle assemblages. Partitioning β-diversity into temporal components is a promising approach to unveil patterns of the community dynamics and to produce insights on mechanisms underlying such patterns.
THE CONTRIBUTION OF LEGISLATIVE DRAFTING TO THE RULE OF LAW
Authors: Sales Philip
Published: September 2018

Drafters of legislation occupy an important position of constitutional significance, involving the translation of political will into legal form. They help clarify and refine the instructions from politicians and create statutory schemes which are internally coherent and have external coherence with wider legal and constitutional values. They begin the process of disciplining and refining political will through application of constitutional reason, which is then continued at the stage of interpretation of statutes by the courts. Drafters of legislation thus contribute to the formal rule of law values of predictability and certainty and also to more substantive values of fairness and respect for constitutional principles and rights. The better the drafting of legislation, the smoother the integration of democracy and the rule of law and the less need there is for interstitial law-making by judges in the interpretive exercise.
BOUNDEDNESS OF M-ESTIMATORS FOR LINEAR REGRESSION IN TIME SERIES
Authors: Johansen Søren , Nielsen Bent
Published: September 2018

We show boundedness in probability uniformly in sample size of a general M-estimator for multiple linear regression in time series. The positive criterion function for the M-estimator is assumed lower semicontinuous and sufficiently large for large argument. Particular cases are the Huber-skip and quantile regression. Boundedness requires an assumption on the frequency of small regressors. We show that this is satisfied for a variety of deterministic and stochastic regressors, including stationary and random walks regressors. The results are obtained using a detailed analysis of the condition on the regressors combined with some recent martingale results.
Reduced susceptibility in leptospiral strains of bovine origin might impair antibiotic therapy
Authors: Correia L. , Loureiro A. P. , Lilenbaum W.
Published: September 2018

Leptospirosis is a worldwide zoonotic disease determined by pathogenic spirochetes of the genusLeptospira. The control of bovine leptospirosis involves several measures including antibiotic treatment of carriers. Despite its importance, few studies regarding antimicrobial susceptibility of strains from bovine origin have been conducted. The aim of this study was to determine thein vitrosusceptibility ofLeptospirastrains obtained from cattle in Rio de Janeiro, Brazil, against the main antibiotics used in bovine veterinary practice. A total of 23Leptospiraspp. strains were investigated for minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) using broth macrodilution. At the species level, there were not differences in MIC susceptibility except for tetracycline (P< 0.05). Nevertheless, at the serogroup level, differences in MIC were observed among Sejroe strains, mainly for ceftiofur, doxycycline and in MBC for streptomycin (P< 0.05). One strain presented MBC values above maximum plasmatic concentration described for streptomycin and was classified as presenting reduced susceptibility. Efficacy of antimicrobial therapy on bovine leptospirosis could be compromised due to occurrence of infection byLeptospirastrains presenting reduced susceptibility.
Compliance, toxicity and efficacy in weekly versus 3-weekly cisplatin concurrent chemoradiation in locally advanced head and neck cancer
Authors: Muzumder Sandeep , Srikantia Nirmala , Vashishta Ganesha Dev , Udayashankar Avinash H. , Raj John Michael , Sebastian M. G. John , Kainthaje Prashanth Bhat
Published: September 2018

Aim

Weekly low-dose cisplatin is routinely used in concurrent chemoradiation (CCRT) in locally advanced head and neck cancer (LAHNC), despite 3-weekly cisplatin being the standard of care. We compared compliance, toxicity and efficacy in weekly versus 3-weekly cisplatin CCRT in LAHNC.

Materials and methods

In this retrospective study, weekly cisplatin 50 mg flat dose was compared with 3-weekly cisplatin 100 mg/m2, when given in CCRT in LAHNC with curative intent. The study outcome was compliance, toxicity, loco-regional control (LRC), disease-free survival (DFS) and overall survival (OS).

Results

Eighty-four patients received CCRT from January 2013 to June 2017, 40 in weekly and 44 in 3-weekly arm. There was no difference between the arms not completing scheduled radiation therapy or chemotherapy. Patient receiving 200 mg/m2 cisplatin is higher in 3-weekly arm compared with weekly arm (75 versus 40·9%; p<0·0015). Compared with 3-weekly arm, more patient in weekly arm developed grade ≥3 mucositis (52·5 versus 15·9%, p=0·0004), day care intravenous hydration (82·5 versus 38·6% <0·0001) and in-patient admission (55·0 versus 18·2%; p=0·0004). The 2-year LRC, DFS and OS in weekly versus 3-weekly arm were: 70 versus 61·4% (p=0·406); 67·5 versus 56·8% (p=0·314); 67·5 versus 61·4% (p=0·558), respectively. The median time to LRR, DFs and OS was not reached.

Conclusions

Weekly cisplatin is comparable with 3-weekly cisplatin in terms of compliance, disease control and survival, but with increased grade 3 mucositis and higher admissions for supportive care.
Modelling the emission of HNCO towards IRAS16293-2422 using a new set of collisional coefficients
Authors: Hernández-Gómez A. , Sahnoun E. , Caux E. , Wiesenfeld L. , Loinard L. , Bottinelli S. , Hammami K.
Published: September 2018

Isocyanic acid (HNCO) is a simple molecule containing the four main atoms essential for life and can be considered as a prebiotic molecule. To model the HNCO emission in the IRAS16293-2422 class 0 low-mass protostar, we used a new set of HNCO collisional coefficients with ortho-H2and para-H2, computed from a set of rotational excitation quenching rates between HNCO and H2based on a novel potential energy surface for the rigid molecules interactions. We present here the HNCO Potential Energy Surface used to compute this new set of collisional coefficients and the result of the IRAS16293-2422 HNCO spectrum modelling using them.
Chemical modelling of N-bearing COMs in star-forming regions
Authors: Quénard David , Jiménez-Serra Izaskun , Viti Serena , Holdship Jonathan
Published: September 2018

The study of complex organic molecules, and more specifically those of prebiotic interest, is important to understand the chemical richness of star-forming regions. The chemistry of nitrogen bearing molecules such as formamide or methyl isocyanate is poorly constrained. We study different chemical pathways to form and destroy these molecules from both the gas phase and grain surface chemistry. From comparison with observations of four different relevant astrophysical regions, we show that both the gas phase and grain surface chemistry are required to explain the observed abundances of these species.
Methanol formation in TW Hya and future prospects for detecting larger complex molecules in disks with ALMA
Authors: Walsh Catherine , Vissapragada Shreyas , McGee Harry
Published: September 2018

Gas-phase methanol was recently detected in a protoplanetary disk for the first time with ALMA. The peak abundance and distribution of methanol observed in TW Hya differed from that predicted by chemical models. Here, the chemistry of methanol gas and ice is calculated using a physical model tailored for TW Hya with the aim to contrast the results with the recent detection in this source. New pathways for the formation of larger complex molecules (e.g., ethylene glycol) are included in an updated chemical model, as well as the fragmentation of methanol ice upon photodesorption. It is found that including fragmentation upon photodesorption improves the agreement between the peak abundance reached in the chemical models with that observed in TW Hya (∼10−11 with respect to H2); however, the model predicts that the peak in emission resides a factor of 2 − 3 farther out in the disk than the ALMA images. Reasons for the persistent differences in the gas-phase methanol distribution between models and the observations of TW Hya are discussed. These include the location of the ice reservoir which may coincide with the compact mm-dust disk (≲ 60 au) and sources of gas-phase methanol which have not yet been considered in models. The possibility of detecting larger molecules with ALMA is also explored. Calculations of the rotational spectra of complex molecules other than methanol using a parametric model constrained by the TW Hya observations suggest that the detection of individual emission lines of complex molecules with ALMA remains challenging. However, the signal-to-noise ratio can be enhanced via stacking of multiple transitions which have similar upper energy levels.
ALMA observations of Titan’s atmospheric chemistry and seasonal variation
Authors: Cordiner M. A. , Lai J. C. , Teanby N. A. , Nixon C. A. , Palmer M. Y. , Charnley S. B. , Thelen A. E. , Molter E. M. , Kisiel Z. , Vuitton V. , Irwin P. G. J. , Mumma M. J.
Published: September 2018

Results are presented from our ongoing studies of Titan using ALMA during the period 2012-2015, including a confirmation of the previous detection of vinyl cyanide (C2H3CN), as well as the first spatial map for this species on Titan. Simultaneous mapping of HC3N, CH3CN and C2H5CN reveal characteristic abundance patterns for each species that provide insight into their individual photochemical lifetimes, and help inform our understanding of Titan’s unique, time-variable atmospheric chemistry and global circulation. A time-sequence of HC3N maps covering 38 months reveals a dramatic change in the distribution of this gas consistent with high-altitude photochemical production followed by advection towards the southern (winter) pole, combined with rapid loss in the north after Titan’s 2009 seasonal equinox. The 2015 C2H3CN and C2H5CN maps show abundance peaks in Titan’s southern hemisphere, similar to those observed for the short-lived HC3N molecule. The longer-lived CH3CN, on the other hand, remains more concentrated in the north.
Chemical Change in the Disk Forming Region of IRAS 16293–2422 Studied with ALMA
Authors: Oya Yoko
Published: September 2018

We have analyzed rotational spectral line emission of OCS, CH3OH, HCOOCH3, and H2CS observed toward the low-mass Class 0 protostar IRAS 16293–2422 (Source A and B) at a sub-arcsecond resolution with ALMA. Significant chemical differentiation is found at a 50 au scale. OCS is found to trace the infalling-rotating envelope, while COM distributions are concentrated around the inner part of the envelope. The kinematic structure in Source A is explained with a ballistic model, and the protostellar mass and the radius of the centrifugal barrier are evaluated to be ~0.75 M⊙ and ~50 au, respectively. This study has revealed that the centrifugal barrier plays a central role not only in the disk formation but also in the associated chemical evolution.
Chemical Tracers of Dynamics in Low-Mass Protostellar Objects
Authors: Yamamoto Satoshi , Oya Yoko , Sakai Nami
Published: September 2018

Recent progress in astrochemistry of low-mass protostellar sources is reviewed. In particular, we focus on disk formation processes and associated chemical changes at a 50 au scale, which is extensively being studied with ALMA. A small scale chemical differentiation sensitively reflects changes in physical conditions, and hence, it provides us with unique opportunities of chemical diagnostics of disk-forming regions. Complex physical and chemical pictures of disk formation revealed by observations are summarized, and future prospects are discussed.
SO survey of massive cores
Authors: Zinchenko Igor , Henkel Christian
Published: September 2018

We present the results of a survey of several tens of dense high mass star forming (HMSF) cores in three transitions of the SO molecule at 30 and 100 GHz with the 100-m Effelsberg and 20-m Onsala radio telescopes. The physical parameters of the cores are estimated from the line ratios and column densities. Relative abundances are derived as well.
Ultraluminous Extragalactic Chemistry
Authors: Ruiz Sergio Martín
Published: September 2018

At a distance of 77 Mpc, the Ultralumious galaxy Arp 220 is the closest extragalactic equivalent to Galactic hot cores. The low resolution SMA survey showed a highly excited confusion limited spectrum. The new ALMA snapshot spectral scan opens the possibility of chemically resolve the two nuclei at unprecedented sensitivity. When completed, it will be the widest survey ever done towards an extragalactic object. The model of Band 6 and 7 data already shows the chemical similarities between the interacting nuclei which may provide clues on the similar heating sources. Vibrationally excited transitions may be tracing the deeply embedded dust obscured active nuclei and/or hot compact star burst. This vibrational emission is the brightest ever measured in an extragalactic object, and even so compared with Galactic hot cores. In fact, the eastern one is the brightest in such vibrational emission. Water mega-maser emission also points towards a very compact sources likely related to star forming clumps within both Arp 220 nuclei.
Chemical Evolution of Turbulent Multiphase Molecular Clouds
Authors: Valdivia Valeska , Hennebelle Patrick , Godard Benjamin , Gerin Maryvonne , Lesaffre Pierre , Le Bourlot Jacques
Published: September 2018

Molecular clouds are essentially made up of atomic and molecular hydrogen, which in spite of being the simplest molecule in the ISM plays a key role in the chemical evolution of molecular clouds. Since its formation time is very long, the H2 molecules can be transported by the turbulent motions within the cloud toward low density and warm regions, where its enhanced abundance can boost the abundances of molecules with high endothermicities.

We present high resolution simulations where we include the evolution of the molecular gas under the effect of the dynamics, and we analyze its impact on the abundance of CH+.
Simulations of branched carbon-chain chemistry in star-forming regions
Authors: Garrod Robin T.
Published: September 2018

The detection of iso-propyl cyanide (i-C3H7CN) toward the Galactic Center hot-core source Sgr B2(N) (by Belloche et al. 2014) marked the first interstellar detection of an aliphatic molecule with a branched carbon-chain structure. Surprisingly, this branched form was found to have an almost equal abundance with its straight-chain homologue, normal-propyl cyanide (i:n = 0.40 ± 0.06). The detection of this first example of an interstellar molecule with a side-chain raises the question as to how prominent such structures may be in interstellar chemistry, and whether the large branched-to-straight chain ratio is maintained for even larger molecules.

Here are presented recently published models that simulate the chemistry occurring in Sgr B2(N) using a chemical network that explicitly includes the straight-chain and branched forms of propyl cyanide (normal/iso) and butyl cyanide (normal/iso/sec/tert), as well as butane (n/i) and pentane (n/i/neo). Formation is assumed to occur on dust-grain surfaces, but a full complement of destruction mechanisms is included both on the grains and in the gas phase.

The models suggest that branched structures become increasingly dominant as molecular sizes increase. In the case of butyl cyanide, the sec form is at least ∼2 times more abundant than the straight-chain normal form, and together the branched forms dominate normal-butyl cyanide by a factor of at least 3. The results for the larger alkanes suggest similarly large ratios of branched to straight-chain molecules. A key set of reactions in the surface/ice chemistry of interstellar nitriles is found to be the addition of the CN radical to unsaturated hydrocarbons, especially acetylene and ethene. The models also predict that the dominant, sec form of butyl cyanide reaches a peak abundance equal to that of n-propyl cyanide, albeit with a smaller emission radius. This makes s-C4H9CN a good candidate for detection. New ALMA observations to search for this molecule are ongoing.
Gas vs dust radial extent in disks: the importance of their thermal interplay
Authors: Facchini Stefano
Published: September 2018

A key parameter governing the secular evolution of protoplanetary disks is their outer radius. In this paper, the feedback of realistic dust grain size distributions onto the gas emission is investigated. Models predict that the difference of dust and gas extents as traced by CO is primarily caused by differences in the optical depth of lines vs continuum. The main effect of radial drift is the sharp decrease in the intensity profile at the outer edge. The gas radial extent can easily range within a factor of 2 for models with different turbulence. A combination of grain growth and vertical settling leads to thermal de-coupling between gas and dust at intermediate scale-heights. A proper treatment of the gas thermal structure within dust gaps will be fundamental to disentangle surface density gaps from gas temperature gaps.
Monte Carlo Modeling of Astrophysically-Relevant Temperature-Programmed Desorption Experiments
Authors: Clements Aspen R. , Cooke Ilsa , Garrod Robin T.
Published: September 2018

The formation of molecules in the interstellar medium is significantly driven by grain chemistry, ranging from simple (e.g. H2) to relatively complex (e.g. CH3OH) products. The movement of atoms and molecules on amorphous ice surfaces is not well constrained, and this is a quintessential component of surface chemistry. We show that ice structure created by utilizing an off-lattice Monte Carlo kinetics model is highly dependent on deposition parameters (i.e. angle, rate, and temperature). The model, thus far, successfully predicts the densities of deposition rate- and temperature-dependent laboratory experiments. The simulations indicate, when angle and deposition rate increase, the density decreases. On the other hand, temperature has the opposite effect and will increase the density. We can make ices with desired densities and monitor how molecules, like CO, percolate through H2O ice pores. The strength of this model lies in the ability to replicate TPD-like experiments by monitoring molecules diffusing on and desorbing from user-defined surfaces.
Zooming in on the Chemistry of Protoplanetary Disks with ALMA
Authors: Cleeves L. Ilsedore
Published: September 2018

During the first few ~Myr of a young stars life, it is encircled by a disk made up of molecular gas, dust, and ice – the building blocks for future planetary systems. How/when these disks form planets and what sets the planets initial compositions remain key outstanding questions in disk science. In recent years, major leaps in sensitivity and spatial resolution afforded by the Atacama Large Millimeter/Submillimeter Array (ALMA) have revolutionized our understanding of protoplanetary disks chemical composition and physical properties, revealing in some cases complex radial, vertical, and azimuthal structure in the dust and gas. In this contribution, I review recent observational results and new theoretical puzzles, and how these fit into a newly emerging picture of the disk environment.
Chemical and kinematic complexity of the very young star-forming region Serpens Main observed with ALMA
Authors: Tychoniec Łukasz , Hull Charles L. H. , Tobin John J. , van Dishoeck Ewine F.
Published: September 2018

The youngest low-mass protostars are known to be chemically rich, accreting matter most vigorously, and producing the most powerful outflows. Molecules are unique tracers of these phenomena. We use ALMA to study several outflow sources in the Serpens Main region. The most luminous source, Ser-SMM1, shows the richest chemical composition, but some complex molecules are also present in S68N. No emission from complex organics is detected toward Ser-emb 8N, which is the least luminous in the sample. We discuss whether these differences reflect an evolutionary effect or whether they are due to different physical structures. We also analyze the outflow structure from these young protostars by comparing emission of CO and SiO. EHV molecular jets originating from SMM1-a,b and Ser-emb 8N contrast with no such activity from S68N, which on the other hand presents a complex outflow structure.
Political Mobilization in American Congregations: A Religious Economies Perspective
Authors: Djupe Paul A. , Neiheisel Jacob R.
Published: September 2018

It has become an article of faith that congregations in America play an important role in the political mobilization of the faithful, but the reasons why congregations themselves provide political opportunities are not well understood. We unite various strands of work about congregational political engagement under the canopy of the religious economies model. Using the 2001 U.S. Congregational Life Study and 1998 National Congregations Study datasets, we show that market forces shape churches’ provision of political goods, suggesting that the congregational embrace of political activities should be understood not as a politically strategic exercise, but as another way to reach out to new members and retain current ones.
Reducing mental health-related stigma in primary health care settings in low- and middle-income countries: a systematic review
Authors: Heim E. , Kohrt B. A. , Koschorke M. , Milenova M. , Thornicroft G.
Published: September 2018

Aims

This systematic review compiled evidence on interventions to reduce mental health-related stigma in primary health care (PHC) in low- and middle-income countries (LMICs). Studies targeting PHC staff (including non-professionals) were included. Primary outcomes were stigmatising attitudes and discriminatory behaviours.

Methods

Data collection included two strategies. First, previous systematic reviews were searched for studies that met the inclusion criteria of the current review. Second, a new search was done, covering the time since the previous reviews, i.e. January 2013 to May 2017. Five search concepts were combined in order to capture relevant literature: stigma, mental health, intervention, PHC staff and LMICs. A qualitative analysis of all included full-texts was done with software MAXQDA. Full-texts were analysed with regards to the content of interventions, didactic methods, mental disorders, cultural adaptation, type of outcome measure and primary outcomes. Furthermore, a risk of bias assessment was undertaken.

Results

A total of 18 studies were included. Risk of bias was rated as high in most included studies. Only six studies had tested their intervention against a control condition, two of which had used random allocation. Most frequently used interventions were lectures providing theoretical information. Many studies also used interactive methods (N= 9), discussed case studies (N= 8) or used role plays (N= 5). Three studies reported that they had used clinical practice and supervision. Results of these studies were mixed. No or little effects were found for brief training interventions (e.g. 1 h to 1 day). Longer training interventions with more sophisticated didactic methods produced statistically significant changes in validated stigma questionnaires. These results have to be interpreted with caution due to risk of bias. Methods for cultural adaptation of interventions were rarely documented.

Conclusions

More rigorous trials are needed in LMICs to test interventions that target discriminatory behaviours in relationship with patients. Cultural adaptation of stigma interventions and structural/institutional factors should be more explicitly addressed in such trials.
Turbulent Mixing in a Far‐Field Plume During the Transition to Upwelling Conditions: Microstructure Observations From an AUV
Authors: Fisher Alexander W. , Nidzieko Nicholas J. , Scully Malcolm E. , Chant Robert J. , Hunter Elias J. , Mazzini Piero L. F.
Published: September 2018

A REMUS 600 autonomous underwater vehicle was used to measure turbulent mixing within the far‐field Chesapeake Bay plume during the transition to upwelling. Prior to the onset of upwelling, the plume was mixed by a combination of energetic downwelling winds and bottom‐generated shear resulting in a two‐layer plume structure. Estimates of turbulent dissipation and buoyancy flux from a nose‐mounted microstructure system indicate that scalar exchange within the plume was patchy and transient, with direct wind mixing constrained to the near surface by stratification within the plume. Changing wind and tide conditions contributed to temporal variability. Following the separation of the upper plume from the coast, alongshore shear became a significant driver of mixing on the shoreward edge of the plume.
The Role of Melting Snow in the Ocean Surface Heat Budget
Authors: Duffy George , Bennartz Ralf
Published: September 2018

We estimate the cooling flux from snow melting in the ocean through CloudSat satellite snowfall retrievals and reanalysis data. For snowfall events with less than 0.01 mm/hr, this flux is inconsequential. Melting snow begins to compete with other ocean surface heat fluxes as snowfall rates increase beyond 0.1 mm/hr, and it may often become the dominant heat flux as snowfall rates approach and exceed 1 mm/hr. The largest monthly average values of the melting snow cooling flux occur in winter months, approaching −10 W/m2 in both hemispheres. To determine the regional influence of melting snow on a seasonal basis, we calculate an impact metric that gauges the cooling flux of melting snow against the net flux in the ocean. This metric can be between 20% and 30% in the Northern Hemisphere during March, April, May; the Southern Ocean during March, April, May and September, October, November; and in high‐latitude polar oceans during sea ice freeze up seasons.
Dawnside Wedge Current System Formed During Intense Geomagnetic Storms
Authors: Ohtani S. , Gjerloev J. W. , Anderson B. J. , Kataoka R. , Troshichev O. , Watari S.
Published: September 2018

We investigate the formation and development of a large‐scale current system in the dawn sector during intense geomagnetic storms. Four events are selected based on the historical ranking of the westward deflections of the morningside midlatitude magnetic field. For each event the polar distribution of equivalent currents indicates a significant intensification of the westward electrojet (WEJ), which initially takes place at postmidnight and then extends eastward covering the entire dawn sector. The longitudinal confinement of the enhanced WEJ suggests that it closes with downward and upward field‐aligned currents (FACs) at its eastern and western ends, respectively, and therefore, the entire system may be envisioned as a wedge current. It is noted, however, that the primary closure of FACs is meridional, and those upward and downward FACs are considered to be unbalanced parts of the R1 and R2 currents. In one event dipolarization was observed in the dawnside plasma sheet near the magnetic conjugate point of the enhanced WEJ, and in another event a major auroral expansion was observed in the entire dawn sector. It is therefore suggested that the formation of the wedge current system and the subsequent expansion toward dayside is an ionospheric projection of the tail current reduction extending toward the dawnside flank. This wedge current system is similar to the substorm wedge current system except that it is centered at dawn. The recurrent formation of this dawnside current wedge in intense storms suggests that this is another distinct constituent of the storm time current system.
Decadal Variability of Eddy Characteristics and Energetics in the Kuroshio Extension: Unstable Versus Stable States
Authors: Yang Haiyuan , Qiu Bo , Chang Ping , Wu Lixin , Wang Shengpeng , Chen Zhaohui , Yang Yun
Published: September 2018

Using the Estimating Circulation and Climate of the Ocean Phase II product, this study investigates the eddy characteristics and energetics in two dynamical regimes within the Kuroshio Extension (KE) region. Based on the empirical orthogonal function analysis, it is found that the decadal evolution of eddy kinetic energy in the KE region is characterized by a delayed negative correlation between the upstream and downstream. Besides the out‐of‐phase change in eddy activity levels, eddy characteristics and energetics in the upstream KE are also different from those in the downstream. In the upstream region, eddies are stretched in the zonal direction and the unstable state is characterized by strong eddy‐shedding processes. During these processes, cyclonic eddies are found to be formed in the first quasi‐stationary meander and finally pinched off from the KE jet. Energy budget illustrates that the eddy shedding processes are triggered by baroclinic instability, while barotropic instability becomes the dominated energy source after the meander is fully developed. Accompanied by the generation of cyclonic eddies, significant inverse energy cascade is detected. When the upstream KE is stable, the eddy activity is dominated by baroclinic instability and the inverse energy cascade occurs similarly. Distinct from the upstream, eddies in the downstream KE tend to be stretched in the meridional direction and the decadal variability of eddy kinetic energy in this region is mainly regulated by the upstream through lateral advection.
Organization and Oscillations in Simulated Shallow Convective Clouds
Authors: Dagan Guy , Koren Ilan , Kostinski Alex , Altaratz Orit
Published: September 2018

Physical insights into processes governing temporal organization and evolution of cloud fields are of great importance for climate research. Here using large eddy simulations with a bin microphysics scheme, we show that warm convective cloud fields exhibit oscillations with two distinct periods (~10 and ~90 min, for the case studied here). The shorter period dominates the nonprecipitating phase, and the longer period is related to the precipitating phase. We show that rain processes affect the domain's thermodynamics, hence forcing the field into a low‐frequency recharge‐discharge cycle of developing cloudiness followed by precipitation‐driven depletion. The end result of precipitation is stabilization of the lower atmosphere by warming of the cloudy layer (due to latent heat release) and cooling of the subcloud layer (by rain evaporation, creating cold pools). As the thermodynamic instability weakens, so does the cloudiness, and the rain ceases. During the nonprecipitating phase of the cycle, surface fluxes destabilize the boundary layer until the next precipitation cycle. Under conditions that do not allow development of precipitation (e.g., high aerosol loading), high‐frequency oscillations dominate the cloud field. Clouds penetrating the stable inversion layer trigger gravity waves with a typical period of ~10 min. In return, the gravity waves modulate the clouds in the field by modifying the vertical velocity, temperature, and humidity fields. Subsequently, as the polluted nonprecipitating simulations evolve, the thermodynamic instability increases and the cloudy layer deepens until precipitation forms, shifting the oscillations from high to low frequency. The organization of cold pools and the spatial scale related to these oscillations are explored.
Predicting Effective Diffusion Coefficients in Mudrocks Using a Fractal Model and Small‐Angle Neutron Scattering Measurements
Authors: Busch A. , Kampman N. , Bertier P. , Pipich V. , Feoktystov A. , Rother G. , Harrington J. , Leu L. , Aertens M. , Jacops E.
Published: September 2018

The determination of effective diffusion coefficients of gases or solutes in the water‐saturated pore space of mudrocks is time consuming and technically challenging. Yet reliable values of effective diffusion coefficients are important to predict migration of hydrocarbon gases in unconventional reservoirs, dissipation of (explosive) gases through clay barriers in radioactive waste repositories, mineral alteration of seals to geological CO2 storage reservoirs, and contaminant migration through aquitards. In this study, small‐angle and very small angle neutron scattering techniques have been utilized to determine a range of transport properties in mudrocks, including porosity, pore size distributions, and surface and volume fractal dimensions of pores and grains, from which diffusive transport parameters can be estimated. Using a fractal model derived from Archie's law, we calculate effective diffusion coefficients from these parameters and compare them to laboratory‐derived effective diffusion coefficients for CO2, H2, CH4, and HTO on either the same or related mudrock samples. The samples include Opalinus Shale from the underground laboratory in Mont Terri, Switzerland, Boom Clay from a core drilled in Mol, Belgium, and a marine claystone cored in Utah, USA. The predicted values were compared to laboratory diffusion measurements. The measured and modeled diffusion coefficients show good agreement, differing generally by less than factor 5. Neutron or X‐ray scattering analysis is therefore proposed as a novel method for fast, accurate estimation of effective diffusion coefficients in mudrocks, together with simultaneous measurement of multiple transport parameters including porosity, pore size distributions, and surface areas, important for (reactive) transport modeling.
Structure of the herpes simplex virus type 2 C-capsid with capsid-vertex-specific component
Authors: Wang Jialing , Yuan Shuai , Zhu Dongjie , Tang Hao , Wang Nan , Chen Wenyuan , Gao Qiang , Li Yuhua , Wang Junzhi , Liu Hongrong , Zhang Xinzheng , Rao Zihe , Wang Xiangxi
Published: September 2018

Herpes simplex viruses (HSVs) cause human oral and genital ulcer diseases. Patients with HSV-2 have a higher risk of acquiring a human immunodeficiency virus infection. HSV-2 is a member of the α-herpesvirinae subfamily that together with the β- and γ-herpesvirinae subfamilies forms the Herpesviridae family. Here, we report the cryo-electron microscopy structure of the HSV-2 C-capsid with capsid-vertex-specific component (CVSC) that was determined at 3.75 Å using a block-based reconstruction strategy. We present atomic models of multiple conformers for the capsid proteins (VP5, VP23, VP19C, and VP26) and CVSC. Comparison of the HSV-2 homologs yields information about structural similarities and differences between the three herpesviruses sub-families and we identify α-herpesvirus-specific structural features. The hetero-pentameric CVSC, consisting of a UL17 monomer, a UL25 dimer and a UL36 dimer, is bound tightly by a five-helix bundle that forms extensive networks of subunit contacts with surrounding capsid proteins, which reinforce capsid stability.
A fully protected hydrogenase/polymer-based bioanode for high-performance hydrogen/glucose biofuel cells
Authors: Ruff Adrian , Szczesny Julian , Marković Nikola , Conzuelo Felipe , Zacarias Sónia , Pereira Inês A. C. , Lubitz Wolfgang , Schuhmann Wolfgang
Published: September 2018

Hydrogenases with Ni- and/or Fe-based active sites are highly active hydrogen oxidation catalysts with activities similar to those of noble metal catalysts. However, the activity is connected to a sensitivity towards high-potential deactivation and oxygen damage. Here we report a fully protected polymer multilayer/hydrogenase-based bioanode in which the sensitive hydrogen oxidation catalyst is protected from high-potential deactivation and from oxygen damage by using a polymer multilayer architecture. The active catalyst is embedded in a low-potential polymer (protection from high-potential deactivation) and covered with a polymer-supported bienzymatic oxygen removal system. In contrast to previously reported polymer-based protection systems, the proposed strategy fully decouples the hydrogenase reaction form the protection process. Incorporation of the bioanode into a hydrogen/glucose biofuel cell provides a benchmark open circuit voltage of 1.15 V and power densities of up to 530 µW cm−2 at 0.85 V.
A PECTIN METHYLESTERASE gene at the maize Ga1 locus confers male function in unilateral cross-incompatibility
Authors: Zhang Zhaogui , Zhang Baocai , Chen Zhibin , Zhang Dongmei , Zhang Huairen , Wang Hang , Zhang Yu’e , Cai Darun , Liu Juan , Xiao Senlin , Huo Yanqing , Liu Jie , Zhang Lanjun , Wang Mingming , Liu Xu , Xue Yongbiao , Zhao Li , Zhou Yihua , Chen Huabang
Published: September 2018

Unilateral cross-incompatibility (UCI) is a unidirectional inter/intra-population reproductive barrier when both parents are self-compatible. MaizeGametophyte factor1(Ga1) is an intraspecific UCI system and has been utilized in breeding. However, the mechanism underlying maize UCI specificity has remained mysterious for decades. Here, we report the cloning ofZmGa1P, a pollen-expressedPECTIN METHYLESTERASE(PME) gene at theGa1locus that can confer the male function in the maize UCI system. Homozygous transgenic plants expressingZmGa1Pin aga1background can fertilizeGa1-Splants and can be fertilized by pollen ofga1plants. ZmGa1P protein is predominantly localized to the apex of growing pollen tubes and may interact with another pollen-specific PME protein, ZmPME10-1, to maintain the state of pectin methylesterification required for pollen tube growth inGa1-Ssilks. Our study discloses a PME-mediated UCI mechanism and provides a tool to manipulate hybrid breeding.
Real-world retrospective cohort study ARCTIC shows burden of comorbidities in Swedish COPD versus non-COPD patients
Authors: Ställberg Björn , Janson Christer , Larsson Kjell , Johansson Gunnar , Kostikas Konstantinos , Gruenberger Jean-Bernard , Gutzwiller Florian S. , Jorgensen Leif , Uhde Milica , Lisspers Karin
Published: September 2018

This study aimed to generate real-world evidence to assess the burden of comorbidities in COPD patients, to effectively manage these patients and optimize the associated healthcare resource allocation. ARCTIC is a large, real-world, retrospective cohort study conducted in Swedish COPD patients using electronic medical record data collected between 2000 and 2014. These patients were studied for prevalence of various comorbidities and for association of these comorbidities with exacerbations, mortality, and healthcare costs compared with an age-, sex-, and comorbidities-matched non-COPD reference population. A total of 17,479 patients with COPD were compared with 84,514 non-COPD reference population. A significantly higher prevalence of various comorbidities was observed in COPD patients 2 years post-diagnosis vs. reference population, with the highest percentage increase observed for cardiovascular diseases (81.8% vs. 30.7%). Among the selected comorbidities, lung cancer was relatively more prevalent in COPD patients vs. reference population (relative risk, RR = 5.97, p < 0.0001). Ischemic heart disease, hypertension, depression, anxiety, sleep disorders, osteoporosis, osteoarthritis, and asthma caused increased mortality rates in COPD patients. Comorbidities that were observed to be significantly associated with increased number of severe exacerbations in COPD patients included heart failure, ischemic heart disease, depression/anxiety, sleep disorders, osteoporosis, lung cancer, and stroke. The cumulative healthcare costs associated with comorbidities over 2 years after the index date were observed to be significantly higher in COPD patients (€27,692) vs. reference population (€5141) (p < 0.0001). The data support the need for patient-centered treatment strategies and targeted healthcare resource allocation to reduce the humanistic and economic burden associated with COPD comorbidities.
Comparative study of the toxicity between three non-steroidal anti-inflammatory drugs and their UV/Na2S2O8 degradation products on Cyprinus carpio
Authors: Gao Xingsheng , Geng Jinju , Du Yourong , Li Shaoli , Wu Gang , Fu Yingying , Ren Hongqiang
Published: September 2018

The efficiency of advanced oxidation processes (AOPs) for disposing of non-steroidal anti-inflammatory drugs (NSAIDs) has been widely studied, but the environmental fates and effects of the NSAIDs and their degradation products (DPs) are poorly understood. In this study, the efficiency of ultraviolet light/Na2S2O8 (UV/PS) in degrading three NSAIDs—diclofenac, naproxen, and ibuprofen—and the toxicity of their DPs on Cyprinus carpio (C. carpio) was investigated. Results showed that the three NSAIDs can be completely removed (removal rate > 99.9%) by UV/PS, while the mineralization rate of the NSAIDs was only 28%. When C. carpio were exposed to 0.1 μM NSAIDs, 10 μM persulfate (PS), and 0.1 μM DPs of the NSAIDs for 96 h, respectively, the toxicity effects are as the NSAID DPs > PS > NSAIDs. Research results into the time-dependent effect of NSAID DPs on C. carpio demonstrated that obvious toxicity effects were observed in the first 48 hours, and the toxicity effects strengthened over time. NSAID DPs may have more severe toxicity effects than NSAIDs on C. carpio; therefore, the operating conditions of UV/PS must be optimized to eliminate the ecotoxicity of DPs.
A Remember/Know Examination of Free-recall Reveals Dissociative Roles of Item- and Context-Information over Time
Authors: Sadeh Talya , Moran Rani , Stern Yonatan , Goshen-Gottstein Yonatan
Published: September 2018

It is well-established that the ability to freely recall information is driven by the extent to which the context at encoding is reinstated at retrieval. Still, when asked to judge the subjective quality of one’s memories giving Remember/Know (R/K) judgments, people tend to classify a substantial proportion of recalls as being devoid of context. We suggest that R- and K-recalls differ with regard to their reliance on context- and item-information, with R-recalls driven primarily by contextual-information (e.g., associations evoked by the study-items) and K-recalls driven primarily by information pertaining to the items (e.g., semantic information). Memory was tested both immediately after study and in a final free-recall test conducted ~20 minutes after encoding—a timescale which is akin to real-life events. In line with our predictions, as compared to K-recalls, R-recalls show stronger contextual effects, but similarly strong item-related effects over these timescales. Furthermore, drawing on theories regarding the forgetting of item- and contextual information, we hypothesized and found that R- and K-recalls are differentially affected by the passage of time. Our findings provide several converging pieces of evidence for differential roles of item and contextual information in driving recall and thus highlight the need to extend longstanding theories of free-recall to account for cases in which recall relies less on context.
Auxin sensing is a property of an unstructured domain in the Auxin Response Factor ETTIN of Arabidopsis thaliana
Authors: Simonini Sara , Mas Philippe J. , Mas Caroline M. V. S. , Østergaard Lars , Hart Darren J.
Published: September 2018

The plant hormone auxin regulates numerous aspects of the plant life cycle. Auxin signalling is mediated by auxin response factors (ARFs) that dimerise with modulating Aux/IAA repressors. ARF3 (ETTIN or ETT) is atypical as it does not interact with Aux/IAA repressors. It is proposed to be a non-canonical auxin sensor, regulating diverse functions essential for development. This sensing ability relies on a unique C-terminal ETT specific domain (ES domain). Alignments of ETT orthologues across the angiosperm phylum revealed that the length and sequence identities of ES domains are poorly conserved. Computational predictors suggested the ES domains to be intrinsically disordered, explaining their tolerance of insertions, deletions and mutations during evolution. Nevertheless, five highly conserved short linear motifs were identified suggesting functional significance. High-throughput library screening identified an almost full-length soluble ES domain that did not bind auxin directly, but exhibited a dose-dependent response in a yeast two-hybrid system against the Arabidopsis INDEHISCENT (IND) transcription factor. Circular dichroism confirmed the domain was disordered. The identification and purification of this domain opens the way to the future characterisation of the ETT auxin-sensing mechanism in planta and an improved understanding of auxin-mediated regulation.
Author Correction: Major ocular trauma in Taiwan: 2002–2004 versus 2012–2014
Authors: Chang Yi-Sheng , Teng Yu-Ti , Huang Yi-Hsun , Liu Mei-Ling , Hung Jia-Horung , Hsu Sheng-Min , Huang Fu-Chin , Shih Min-Hsiu , Chen Wan-Ju , Lai Chun-Chieh , Hsiao Shu-Fang , Wang Shih-Hao , Tseng Sung-Huei
Published: September 2018

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