julilili42/papers huggingface dataset:
The BLLAST field experiment: Boundary-Layer Late Afternoon and Sunset Turbulence
2014-10-16

Abstract. Due to the major role of the sun in heating the earth's surface, the atmospheric planetary boundary layer over land is inherently marked by a diurnal cycle. The afternoon transition, the period of the day that connects the daytime dry convective boundary layer to the night-time stable boundary layer, still has a number of unanswered scientific questions. This phase of the diurnal cycle is challenging from both modelling and observational perspectives: it is transitory, most of the forcings are small or null and the turbulence regime changes from fully convective, close to homogeneous and isotropic, toward a more heterogeneous and intermittent state. These issues motivated the BLLAST (Boundary-Layer Late Afternoon and Sunset Turbulence) field campaign that was conducted from 14 June to 8 July 2011 in southern France, in an area of complex and heterogeneous terrain. A wide range of instrumented platforms including full-size aircraft, remotely piloted aircraft systems, remote-sensing instruments, radiosoundings, tethered balloons, surface flux stations and various meteorological towers were deployed over different surface types. The boundary layer, from the earth's surface to the free troposphere, was probed during the entire day, with a focus and intense observation periods that were conducted from midday until sunset. The BLLAST field campaign also provided an opportunity to test innovative measurement systems, such as new miniaturized sensors, and a new technique for frequent radiosoundings of the low troposphere. Twelve fair weather days displaying various meteorological conditions were extensively documented during the field experiment. The boundary-layer growth varied from one day to another depending on many contributions including stability, advection, subsidence, the state of the previous day's residual layer, as well as local, meso- or synoptic scale conditions. Ground-based measurements combined with tethered-balloon and airborne observations captured the turbulence decay from the surface throughout the whole boundary layer and documented the evolution of the turbulence characteristic length scales during the transition period. Closely integrated with the field experiment, numerical studies are now underway with a complete hierarchy of models to support the data interpretation and improve the model representations.
Fluid mixing from below in unconformity-related hydrothermal ore deposits
2014-10-16

This research was partly funded by German Research Foundation (DFG) grant BO 1776/8 and was carried out within the framework of DGMK (German Society for Petroleum and Coal Science and Technology) project 718, funded by the companies ExxonMobil Production Deutschland GmbH, GDF SUEZ E&P Deutschland GmbH, RWE Dea AG, and Wintershall Holding GmbH. Assistance by Simone Kaulfuss, Gabi Stoschek, Sara Ladenburger, Mathias Burisch, and Bernd Steinhilber with sample preparation and crush-leach analyses is gratefully acknowledged. We thank Steve Cox and two anonymous reviewers for their critical comments.
A Sialic Acid Binding Site in a Human Picornavirus
2014-10-16

The picornaviruses coxsackievirus A24 variant (CVA24v) and enterovirus 70 (EV70) cause continued outbreaks and pandemics of acute hemorrhagic conjunctivitis (AHC), a highly contagious eye disease against which neither vaccines nor antiviral drugs are currently available. Moreover, these viruses can cause symptoms in the cornea, upper respiratory tract, and neurological impairments such as acute flaccid paralysis. EV70 and CVA24v are both known to use 5-N-acetylneuraminic acid (Neu5Ac) for cell attachment, thus providing a putative link between the glycan receptor specificity and cell tropism and disease. We report the structures of an intact human picornavirus in complex with a range of glycans terminating in Neu5Ac. We determined the structure of the CVA24v to 1.40 Å resolution, screened different glycans bearing Neu5Ac for CVA24v binding, and structurally characterized interactions with candidate glycan receptors. Biochemical studies verified the relevance of the binding site and demonstrated a preference of CVA24v for α2,6-linked glycans. This preference can be rationalized by molecular dynamics simulations that show that α2,6-linked glycans can establish more contacts with the viral capsid. Our results form an excellent platform for the design of antiviral compounds to prevent AHC.
Atmospheric hydrogen peroxide and Eoarchean iron formations
2014-10-16

Abstract It is widely accepted that photosynthetic bacteria played a crucial role in Fe( II ) oxidation and the precipitation of iron formations ( IF ) during the Late Archean–Early Paleoproterozoic (2.7–2.4 Ga). It is less clear whether microbes similarly caused the deposition of the oldest IF at ca . 3.8 Ga, which would imply photosynthesis having already evolved by that time. Abiological alternatives, such as the direct oxidation of dissolved Fe( II ) by ultraviolet radiation may have occurred, but its importance has been discounted in environments where the injection of high concentrations of dissolved iron directly into the photic zone led to chemical precipitation reactions that overwhelmed photooxidation rates. However, an outstanding possibility remains with respect to photochemical reactions occurring in the atmosphere that might generate hydrogen peroxide (H 2 O 2 ), a recognized strong oxidant for ferrous iron. Here, we modeled the amount of H 2 O 2 that could be produced in an Eoarchean atmosphere using updated solar fluxes and plausible CO 2 , O 2 , and CH 4 mixing ratios. Irrespective of the atmospheric simulations, the upper limit of H 2 O 2 rainout was calculated to be &lt;10 6 molecules cm −2 s −1 . Using conservative Fe( III ) sedimentation rates predicted for submarine hydrothermal settings in the Eoarchean, we demonstrate that the flux of H 2 O 2 was insufficient by several orders of magnitude to account for IF deposition (requiring ~10 11 H 2 O 2 molecules cm −2 s −1 ). This finding further constrains the plausible Fe( II ) oxidation mechanisms in Eoarchean seawater, leaving, in our opinion, anoxygenic phototrophic Fe( II )‐oxidizing micro‐organisms the most likely mechanism responsible for Earth's oldest IF .
Ophthalmic Rosacea: Case Report in a Child and Treatment Recommendations
2014-10-16

Abstract We report a rare case of rosacea with ocular involvement in a child that remitted with prolonged anti‐inflammatory oral tetracycline therapy and provide general expert recommendations. A 14‐year‐old girl presented with discrete papules and pustules on both cheeks with blepharitis and conjunctivitis. Ophthalmologic examination confirmed bilateral severe blepharitis, as well as a corneal infiltrate in the right eye with additional neovascularization. The diagnosis of rosacea with ocular involvement was made. In addition to the existing antibiotic and anti‐inflammatory topical eye therapy, systemic treatment with minocycline 50 mg twice a day was started. After marked improvement, the dose was reduced to 50 mg once a day. After further amelioration, treatment was switched to maintenance therapy with 40 mg of prolonged‐release doxycycline. Three years after a 12‐month course of anti‐inflammatory therapy, the patient remained recurrence free.
All1371 is a polyphosphate-dependent glucokinase in Anabaena sp. PCC 7120
2014-10-16

The polyphosphate glucokinases can phosphorylate glucose to glucose 6-phosphate using polyphosphate as the substrate. ORF all1371 encodes a putative polyphosphate glucokinase in the filamentous heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Here, ORF all1371 was heterologously expressed in Escherichia coli , and its purified product was characterized. Enzyme activity assays revealed that All1371 is an active polyphosphate glucokinase that can phosphorylate both glucose and mannose in the presence of divalent cations in vitro . Unlike many other polyphosphate glucokinases, for which nucleoside triphosphates (e.g. ATP or GTP) act as phosphoryl group donors, All1371 required polyphosphate to confer its enzymic activity. The enzymic reaction catalysed by All1371 followed classical Michaelis–Menten kinetics, with k cat = 48.2 s −1 at pH 7.5 and 28 °C and K M = 1.76 μM and 0.118 mM for polyphosphate and glucose, respectively. Its reaction mechanism was identified as a particular multi-substrate mechanism called the ‘bi-bi ping-pong mechanism’. Bioinformatic analyses revealed numerous polyphosphate-dependent glucokinases in heterocyst-forming cyanobacteria. Viability of an Anabaena sp. PCC 7120 mutant strain lacking all1371 was impaired under nitrogen-fixing conditions. GFP promoter studies indicate expression of all1371 under combined nitrogen deprivation. All1371 might play a substantial role in Anabaena sp. PCC 7120 under these conditions.
The Salmonella effector protein SpvC, a phosphothreonine lyase is functional in plant cells
2014-10-17

Salmonella is one of the most prominent causes of food poisoning and growing evidence indicates that contaminated fruits and vegetables are an increasing concern for human health. Successful infection demands the suppression of the host immune system, which is often achieved via injection of bacterial effector proteins into host cells. In this report we present the function of Salmonella effector protein in plant cell, supporting the new concept of trans-kingdom competence of this bacterium. We screened a range of Salmonella Typhimurium effector proteins for interference with plant immunity. Among these, the phosphothreonine lyase SpvC attenuated the induction of immunity-related genes when present in plant cells. Using in vitro and in vivo systems we show that this effector protein interacts with and dephosphorylates activated Arabidopsis Mitogen-activated Protein Kinase 6 (MPK6), thereby inhibiting defense signaling. Moreover, the requirement of Salmonella SpvC was shown by the decreased proliferation of the ΔspvC mutant in Arabidopsis plants. These results suggest that some Salmonella effector proteins could have a conserved function during proliferation in different hosts. The fact that Salmonella and other Enterobacteriaceae use plants as hosts strongly suggests that plants represent a much larger reservoir for animal pathogens than so far estimated.
Surgical treatment of neurogenic stress urinary incontinence: A systematic review of quality assessment and surgical outcomes
2014-10-18

Background There are many opinions but little firm knowledge about the optimal treatment of neurogenic stress urinary incontinence (NSUI). Objective To scrutinize the quality and surgical outcomes of the available treatment modalities in the published literature. Evidence Acquisition A systematic review of the published literature from Pub Med and Web of Science was undertaken for studies describing surgical treatment of NSUI between 1990 and 2013. A checklist of criteria of methodological and reporting quality of interventions in urological publications was applied to assess quality of the retrieved publications. Surgical outcomes of success, failure, and reoperation were calculated. Statistical analyses included one‐way ANOVA and post‐hoc tests to determine significant differences between groups. Evidence Synthesis Thirty studies were identified with Level 3 evidence. The quality of reporting was 43–81%, with significantly higher quality noted in studies published after 2002 (64% vs. 45%, P &lt; 0.0001). None of the studies followed a randomized controlled trial (RCT) design. Three primary surgical procedures were used in 29 of 30 studies: artificial urinary sphincter (AUS), urethral slings, and urethral bulking agents. One study used a ProACT device. AUS was considered more successful than urethral bulking agents (77 ± 15% vs. 27 ± 20%, P = 0.002). Urethral bulking agents reported higher failures than urethral sling procedures (49 ± 16% vs. 21 ± 19%, P = 0.016) and AUS (21 ± 19% vs. 10 ± 11%, P &lt; 0.002). Conclusions The quality of evidence obtained from non‐RCTs is modest. Surgeries for NSUI have relatively high success rates but also high complication rates in this highly heterogeneous population. More studies using modern techniques are required to update our knowledge. Neurourol. Urodynam. 35:21–25, 2016 . © 2014 Wiley Periodicals, Inc.
Multimodel ensembles of wheat growth: many models are better than one
2014-10-20

Abstract Crop models of crop growth are increasingly used to quantify the impact of global changes due to climate or crop management. Therefore, accuracy of simulation results is a major concern. Studies with ensembles of crop models can give valuable information about model accuracy and uncertainty, but such studies are difficult to organize and have only recently begun. We report on the largest ensemble study to date, of 27 wheat models tested in four contrasting locations for their accuracy in simulating multiple crop growth and yield variables. The relative error averaged over models was 24–38% for the different end‐of‐season variables including grain yield ( GY ) and grain protein concentration ( GPC ). There was little relation between error of a model for GY or GPC and error for in‐season variables. Thus, most models did not arrive at accurate simulations of GY and GPC by accurately simulating preceding growth dynamics. Ensemble simulations, taking either the mean (e‐mean) or median (e‐median) of simulated values, gave better estimates than any individual model when all variables were considered. Compared to individual models, e‐median ranked first in simulating measured GY and third in GPC . The error of e‐mean and e‐median declined with an increasing number of ensemble members, with little decrease beyond 10 models. We conclude that multimodel ensembles can be used to create new estimators with improved accuracy and consistency in simulating growth dynamics. We argue that these results are applicable to other crop species, and hypothesize that they apply more generally to ecological system models.
Analysis of Phosphorylation-Dependent Protein–Protein Interactions of Histone H3
2014-10-20

Multiple posttranslational modifications (PTMs) of histone proteins including site-specific phosphorylation of serine and threonine residues govern the accessibility of chromatin. According to the histone code theory, PTMs recruit regulatory proteins or block their access to chromatin. Here, we report a general strategy for simultaneous analysis of both of these effects based on a SILAC MS scheme. We applied this approach for studying the biochemical role of phosphorylated S10 of histone H3. Differential pull-down experiments with H3-tails synthesized from l- and d-amino acids uncovered that histone acetyltransferase 1 (HAT1) and retinoblastoma-binding protein 7 (RBBP7) are part of the protein network, which interacts with the unmodified H3-tail. An additional H3-derived bait containing the nonhydrolyzable phospho-serine mimic phosphonomethylen-alanine (Pma) at S10 recruited several isoforms of the 14-3-3 family and blocked the recruitment of HAT1 and RBBP7 to the unmodified H3-tail. Our observations provide new insights into the many functions of H3S10 phosphorylation. In addition, the outlined methodology is generally applicable for studying specific binding partners of unmodified histone tails.
High-throughput tri-colour flow cytometry technique to assess Plasmodium falciparum parasitaemia in bioassays
2014-10-20

An improved methodology for high-throughput assessment of P. falciparum parasitaemia under culture conditions that could be useful in different bioassays, including ADCI and growth inhibition assays has been developed.
Synergistic Effects of Trace Amounts of Water in the Enantiodiscrimination Processes by Lipodex E: A Spectroscopic and Computational Investigation
2014-10-20

Abstract Nuclear magnetic resonance (NMR) investigations on mixtures containing octakis(3‐ O ‐butanoyl‐2,6‐di‐ O ‐pentyl)‐γ‐cyclodextrin (Lipodex E) and each enantiomer of methyl‐2‐chloropropionate (MCP) ascertained the role of trace amounts of water in the enantiodiscrimination processes. Water is deeply included into the cyclodextrin and favors the formation of the inclusion complex with ( S )‐MCP, whereas ( R )‐MCP is only slightly affected, thus causing a significant increase of NMR differentiation. Molecular dynamics simulations were performed to shed light on the possible behavior of Lipodex E in different conditions (i.e., solvent, inclusion complexes), providing energetic and atomistic details that are in agreement with NMR observations. Chirality 27:95–103, 2014 . © 2014 Wiley Periodicals, Inc.
On ethical leadership impact: The role of follower mindfulness and moral emotions
2014-10-21

With the present paper, we aim to provide new conceptual insights and empirical evidence on ethical leadership contingencies: we analyze under what conditions ethical leadership can positively impact follower discretionary work behaviors (extra effort and helping). We argue that followers vary in terms of their sensitivity toward and processing of moral information, as conveyed by ethical leaders, and that these individual differences determine the strength of the link between ethical leadership and follower discretionary work behaviors. In a multisource study with 135 leader–follower dyads, we examine two prototypical examples of affective and cognitive individual differences that involve a heightened inclination toward morality: follower moral emotions and follower mindfulness. Our findings indicate that ethical leadership is more strongly related to follower extra effort and helping at higher levels of follower moral emotions and higher levels of follower mindfulness. We discuss the implications of this moral information processing perspective on ethical leadership for research and managerial practice.
Isolated Assessment of Translation or Rotation Severely Underestimates the Effects of Subject Motion in fMRI Data
2014-10-21

Subject motion has long since been known to be a major confound in functional MRI studies of the human brain. For resting-state functional MRI in particular, data corruption due to motion artefacts has been shown to be most relevant. However, despite 6 parameters (3 for translations and 3 for rotations) being required to fully describe the head's motion trajectory between timepoints, not all are routinely used to assess subject motion. Using structural (n = 964) as well as functional MRI (n = 200) data from public repositories, a series of experiments was performed to assess the impact of using a reduced parameter set (translationonly and rotationonly) versus using the complete parameter set. It could be shown that the usage of 65 mm as an indicator of the average cortical distance is a valid approximation in adults, although care must be taken when comparing children and adults using the same measure. The effect of using slightly smaller or larger values is minimal. Further, both translationonly and rotationonly severely underestimate the full extent of subject motion; consequently, both translationonly and rotationonly discard substantially fewer datapoints when used for quality control purposes ("motion scrubbing"). Finally, both translationonly and rotationonly severely underperform in predicting the full extent of the signal changes and the overall variance explained by motion in functional MRI data. These results suggest that a comprehensive measure, taking into account all available parameters, should be used to characterize subject motion in fMRI.
Epidural electrocorticography for monitoring of arousal in locked-in state
2014-10-21

Electroencephalography (EEG) often fails to assess both the level (i.e., arousal) and the content (i.e., awareness) of pathologically altered consciousness in patients without motor responsiveness. This might be related to a decline of awareness, to episodes of low arousal and disturbed sleep patterns, and/or to distorting and attenuating effects of the skull and intermediate tissue on the recorded brain signals. Novel approaches are required to overcome these limitations. We introduced epidural electrocorticography (ECoG) for monitoring of cortical physiology in a late-stage amytrophic lateral sclerosis patient in completely locked-in state (CLIS). Despite long-term application for a period of six months, no implant-related complications occurred. Recordings from the left frontal cortex were sufficient to identify three arousal states. Spectral analysis of the intrinsic oscillatory activity enabled us to extract state-dependent dominant frequencies at <4, ~7 and ~20 Hz, representing sleep-like periods, and phases of low and elevated arousal, respectively. In the absence of other biomarkers, ECoG proved to be a reliable tool for monitoring circadian rhythmicity, i.e., avoiding interference with the patient when he was sleeping and exploiting time windows of responsiveness. Moreover, the effects of interventions addressing the patient's arousal, e.g., amantadine medication, could be evaluated objectively on the basis of physiological markers, even in the absence of behavioral parameters. Epidural ECoG constitutes a feasible trade-off between surgical risk and quality of recorded brain signals to gain information on the patient's present level of arousal. This approach enables us to optimize the timing of interactions and medical interventions, all of which should take place when the patient is in a phase of high arousal. Furthermore, avoiding low-responsiveness periods will facilitate measures to implement alternative communication pathways involving brain-computer interfaces (BCI).
SLy2 controls the antibody response to pneumococcal vaccine through an IL‐5Rα‐dependent mechanism in B‐1 cells
2014-10-21

The adaptor protein SLy2 (Src homology domain 3 lymphocyte protein 2) is located on human chromosome 21 and was reported to be among a group of genes amplified in Down's syndrome (DS) patients. DS patients characteristically show an impaired immunity to pneumococcal infections. However, molecular mechanisms linking gene amplifications with specific DS phenotypes remain elusive. To investigate the effect of SLy2 gene amplification on the mammalian immune system, we studied SLy2 overexpressing transgenic‐ SLy2 (TG) mice. We found that baseline immunoglobulin M (IgM) levels as well as IgM responses following Pneumovax immunizations were reduced in TG mice. Moreover, B‐1 cells, the major natural IgM‐producing population in mice, were reduced in the peritoneal cavity of TG mice, while other immune cell compartments were unaltered. Mechanistically, SLy2 overexpression attenuated the expression of the IL‐5 receptor α chain on B‐1 cells, resulting in decreased B‐1 cell numbers and decreased differentiation into Ab‐secreting cells. Since B‐1 cells essentially contribute to immunity against Streptococcus pneumoniae , the present study provides a novel molecular link between SLy2 expression and pneumococcal‐specific IgM responses in vivo. These studies suggest that the adaptor protein SLy2 is a potential future target for immunomodulatory strategies for pneumococcal infections.