julilili42/papers huggingface dataset:
Diffraction and Interference of a Bose–Einstein Condensate Scattered from an Atom Chip‐Based Magnetic Lattice
2011-02-09

This chapter describes the particular example of a condensate reflected from a surface that carries a micro-fabricated magnetic lattice. The lattice diffracts the condensate and splits it into a number of momentum classes. The experiment is elementary because it realizes the matter wave analog of an optical reflecting diffraction grating. The chapter begins with a technical description of the experimental apparatus and the magnetic grating for diffraction experiments. It gives special emphasis to the magnetic field configuration near meandering conductors and to the wave mechanics of diffraction. The chapter describes experimental data of BEC diffraction and interference and analyzes them with an analytic phase-imprinting model. A full three-dimensional simulation of the Gross-Pitaevskii equation is used to verify the regimes in which this model is valid. Controlled Vocabulary Terms Bose-Einstein condensation; diffraction gratings
Broad‐spectrum antimicrobial peptide resistance by MprF‐mediated aminoacylation and flipping of phospholipids
2011-02-10

Summary Bacteria are frequently exposed to cationic antimicrobial peptides (CAMPs) from eukaryotic hosts (host defence peptides) or from prokaryotic competitors (bacteriocins). However, many bacteria, among them most of the major human pathogens, achieve CAMP resistance by MprF, a unique enzyme that modifies anionic phospholipids with l ‐lysine or l ‐alanine thereby introducing positive charges into the membrane surface and reducing the affinity for CAMPs. The lysyl or alanyl groups are derived from aminoacyl tRNAs and are usually transferred to phosphatidylglycerol (PG). Recent studies with MprF from Staphylococcus aureus demonstrated that production of Lys‐PG only leads to CAMP resistance when an additional flippase domain of MprF is present that translocates Lys‐PG and exposes it at the outer leaflet of the membrane. Thus, MprF exerts two specific functions that have hardly been found in other bacterial proteins. MprF proteins are crucial virulence factors of many human pathogens, which recommends them as targets for new anti‐virulence drugs. Intriguingly, specific point mutations in mprF cause resistance to the CAMP‐like antibiotic daptomycin in a yet unclear way that may involve altered Lys‐PG synthesis and/or Lys‐PG flipping capacities. Thus, a thorough characterization of MprF domains and functions will help to unravel how bacteria maintain and protect their cytoplasmic membranes.
The Changing Nature of International Institutions in Europe: the Challenge of the European Union
2011-02-10

The European Union is often compared to other political systems in order to better understand its basic features and how they structure politics. This article argues that this focus on comparative politics instils a domestic bias into the study of the EU, which also ignores the impact of enlargement. To remedy this, a comparison is suggested between the order of the EU as a regional international society and the order of the traditional, global international society as analysed by the English School of International Relations, and in particular by Hedley Bull. It is argued that the primary goal of the international order of the society of states, the preservation of states as its fundamental units, has been replaced by the goal of the preservation of peace in Europe. Consequently, the five core institutions of international order identified by Bull (balance of power, international law, diplomacy, war and great powers) have been modified or replaced. The new institutions of the European order are identified as the pooling of sovereignty, the acquis communautaire, multi-managerialism, pacific democracy, member state coalitions and multiperspectivity. These sustain and enlarge a regional international society that not only combines international and domestic elements, but transforms politics to such an extent that it should better be called a multiperspectival society, confounding Bull's expectation that the European integration will either lead to a European state or falter. This has potential ramifications for the organisation of international society at large, although whether the transformative potential of the EU can be realised remains to be seen, and will be decided above all in the EU's treatment of its own borders. Â© 2011 Taylor & Francis.
Alanine Zipper-Like Coiled-Coil Domains Are Necessary for Homotypic Dimerization of Plant GAGA-Factors in the Nucleus and Nucleolus
2011-02-10

GAGA-motif binding proteins control transcriptional activation or repression of homeotic genes. Interestingly, there are no sequence similarities between animal and plant proteins. Plant BBR/BPC-proteins can be classified into two distinct groups: Previous studies have elaborated on group I members only and so little is known about group II proteins. Here, we focused on the initial characterization of AtBPC6, a group II protein from Arabidopsis thaliana. Comparison of orthologous BBR/BPC sequences disclosed two conserved signatures besides the DNA binding domain. A first peptide signature is essential and sufficient to target AtBPC6-GFP to the nucleus and nucleolus. A second domain is predicted to form a zipper-like coiled-coil structure. This novel type of domain is similar to Leucine zippers, but contains invariant alanine residues with a heptad spacing of 7 amino acids. By yeast-2-hybrid and BiFC-assays we could show that this Alanine zipper domain is essential for homotypic dimerization of group II proteins in vivo. Interhelical salt bridges and charge-stabilized hydrogen bonds between acidic and basic residues of the two monomers are predicted to form an interaction domain, which does not follow the classical knobs-into-holes zipper model. FRET-FLIM analysis of GFP/RFP-hybrid fusion proteins validates the formation of parallel dimers in planta. Sequence comparison uncovered that this type of domain is not restricted to BBR/BPC proteins, but is found in all kingdoms.
Effect of dexamethasone on Na+/Ca2+ exchanger in dendritic cells
2011-02-10

Ca + -dependent signaling regulates the function of dendritic cells (DCs), antigen-presenting cells linking innate and adaptive immunity. The activity of DCs is suppressed by glucocorticoids, potent immunosuppressive hormones. The present study explored whether the glucocorticoid dexamethasone influences the cytosolic Ca 2+ concentration ([Ca 2+ ] i ) in DCs. To this end, DCs were isolated from mouse bone marrow. According to fura-2 fluorescence, exposure of DCs to lipopolysaccharide (LPS, 100 ng/ml) increased [Ca 2+ ] i , an effect significantly blunted by overnight incubation with 10 nM dexamethasone before LPS treatment. Dexamethasone did not affect the Ca 2+ content of intracellular stores, sarco(endo)plasmic reticulum Ca 2+ -ATPase (SERCA)2 and SERCA3 expression, ryanodine receptor (RyR)1 expression, or Ca 2+ entry through store-operated Ca 2+ channels. In contrast, dexamethasone increased the transcript level and the membrane protein abundance of the Na + /Ca 2+ exchanger NCX3. The activity of Na + /Ca 2+ exchangers was assessed by removal of extracellular Na + in the presence of external Ca 2+ , a maneuver triggering the Ca 2+ influx mode. Indeed, Na + removal resulted in a rapid transient increase of [Ca 2+ ] i and induced an outwardly directed current as measured in whole cell patch-clamp experiments. Dexamethasone significantly augmented the increase of [Ca 2+ ] i and the outward current following removal of extracellular Na + . The NCX blocker KB-R7943 reversed the inhibitory effect of dexamethasone on LPS-induced increase in [Ca 2+ ] i . Dexamethasone blunted LPS-induced stimulation of CD86 expression and TNF-α production, an effect significantly less pronounced in the presence of NCX blocker KB-R7943. In conclusion, our results show that glucocorticoid treatment blunts LPS-induced increase in [Ca 2+ ] i in DCs by increasing expression and activity of Na + /Ca 2+ exchanger NCX3. The effect contributes to the inhibitory effect of the glucocorticoid on DC maturation.
THE pp → ppπ0π0 REACTION AND ITS LIMITING CASE, FUSION TO QUASI-BOUND 2He, IN SEARCH OF THE ABC EFFECT
2011-02-10

The π 0 π 0 production in pp -collisions has been investigated in exclusive and kinematically complete measurements from threshold up to T p = 1.4 GeV . For incident energies T p &gt; 1 GeV , i.e. in the region beyond the Roper excitation, the ΔΔ excitation process takes over. The data are well explained by the t-channel ΔΔ process dominated by pion exchange. There is no low-mass enhancement (ABC effect) in the π 0 π 0 -invariant mass distribution beyond that given by the conventional t-channel ΔΔ process. This is also true for the limiting case, where the protons are in the quasi-bound 2 He state.
THE ABC EFFECT AND ITS ENERGY DEPENDENCE IN THE DOUBLE-PIONIC FUSION TO 4He
2011-02-10

The double-pionic fusion reactions dd → 4 He π 0 π 0 and dd → 4 He π + π - were measured exclusively and kinematically complete with the WASA detector at COSY. The measurements were performed in the energy range T p = 0.8 - 1.4 GeV covering thus the full energy region, where the so-called ABC effect – a peculiar low-mass enhancement in the ππ-invariant mass spectrum – was observed previously in inclusive measurements. Our findings for the double-pionic fusion to 4 He are in accordance with the observations for the basic pn → dπ 0 π 0 reaction pointing to the same fundamental mechanism. In both cases we observe that the ABC effect is associated with a peak in the energy dependence of the total cross section. In the 4 He case the peak structure in the total cross section is broadened in comparison to the deuteron case. This is consistent with both Fermi motion of the basic pn system within 4 He and with collision broadening as it is known, e.g., from excitations of the Δ resonance in nuclei.
Determination of the in vivo redox potential using roGFP and fluorescence spectra obtained from one-wavelength excitation
2011-02-10

The analysis of molecular processes in living (plant) cells such as signal transduction, DNA replication, carbon metabolism and senescence has been revolutionized by the use of green fluorescent protein (GFP) and its variants as specific cellular markers. Many cell biological processes are accompanied by changes in the intracellular redox potential. To monitor the redox potential, a redox-sensitive mutant of GFP (roGFP) was created, which shows changes in its optical properties in response to changes in the redox state of its surrounding medium. For a quantitative analysis in living systems, it is essential to know the optical properties of roGFP in vitro. Therefore, we applied spectrally resolved fluorescence spectroscopy on purified roGFP exposed to different redox potentials to determine shifts in both the absorption and the emission spectra of roGFP. Based on these in vitro findings, we introduce a new approach using one-wavelength excitation to use roGFP for the in vivo analysis of cell biological processes. We demonstrate the ability this technique by investigating chloroplast-located Grx1-roGFP2 expressing Arabidopsis thaliana cells as example for dynamically moving intracellular compartments. This is not possible with the two-wavelength excitation technique established so far, which hampers a quantitative analysis of highly mobile samples due to the time delay between the two measurements and the consequential displacement of the investigated area.
WHAT IS THE NATURE OF THE ABC EFFECT?
2011-02-10

The ABC effect — an intriguing low-mass enhancement in the ππ invariant mass spectrum — is known from inclusive measurements of two-pion production in nuclear fusion reactions. Exclusive measurements have been carried out at CELSIUS/WASA and WASA-at-COSY for the fusion reactions leading to d, 3 He and 4 He . They all reveal this effect to be of isoscalar nature and associated with a narrow Lorentzian-shaped structure in the total cross section. The latter could point to the formation of an isoscalar resonance, which couples to the pn channel as well as to an intermediate ΔΔ state.
A Third Metal Is Required for Catalytic Activity of the Signal-transducing Protein Phosphatase M tPphA
2011-02-11

Protein phosphatase M (PPM) regulates key signaling pathways in prokaryotes and eukaryotes. Novel structures of bacterial PPM members revealed three divalent metal ions in their catalytic centers. The function of metal 3 (M3) remained unclear. To reveal its function, we created variants of tPphA from Thermosynechococcus elongatus in all metal-coordinating residues, and multiple variants were created for the M3 coordinating Asp-119 residue. The structures of variants D119A and D193A were resolved, showing loss of M3 binding but unaffected binding of M1 and M2 in the catalytic center of D119A, with the nucleophilic water molecule in the correct place. The catalytic activity of this variant was highly impaired. This and further structure-function analyses showed that M3 is required for catalysis by providing a water molecule as a proton donor during catalysis. Mutation of the homologue Asp residue in human PP2Cα also caused loss of function, suggesting a general requirement of M3 in PPM-catalyzed reactions.
Valuation And Market Timing In Private M&A Transactions
2011-02-11

&lt;p class="MsoNormal" style="text-align: justify; margin: 0in 0.5in 0pt; mso-pagination: none;"&gt;&lt;span style="font-size: 10pt; mso-bidi-font-size: 12.0pt;"&gt;&lt;span style="font-family: Times New Roman;"&gt;The objective of this case is to teach and initiate a classroom discussion about the optimal market timing for the sale of a mid-cap privately held firm.&lt;span style="mso-spacerun: yes;"&gt;&amp;nbsp; &lt;/span&gt;The discussion is facilitated by a real world case example that focuses on the sale of a Little Rock, AK based plastic injection molding company with approximately $20 million in revenues.&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p class="MsoNormal" style="text-align: justify; margin: 0in 0.5in 0pt; mso-pagination: none;"&gt;&lt;span style="font-size: 8pt;"&gt;&lt;span style="font-family: Times New Roman;"&gt;&amp;nbsp;&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p class="MsoNormal" style="text-align: justify; margin: 0in 0.5in 0pt; mso-pagination: none;"&gt;&lt;span style="font-size: 10pt; mso-bidi-font-size: 12.0pt;"&gt;&lt;span style="font-family: Times New Roman;"&gt;Theoretical and practical issues central to receiving maximum price in relation to selling at the right time are addressed.&lt;span style="mso-spacerun: yes;"&gt;&amp;nbsp; &lt;/span&gt;Considered are the desired time to close the deal from the owner&amp;rsquo;s point of view, the time required for successful completion of the sale process, business conditions in this industry, firm-specific business conditions, and ability of agents to time this market.&lt;span style="mso-spacerun: yes;"&gt;&amp;nbsp; &lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p class="MsoNormal" style="text-align: justify; margin: 0in 0.5in 0pt; mso-pagination: none;"&gt;&lt;span style="font-size: 8pt;"&gt;&lt;span style="font-family: Times New Roman;"&gt;&amp;nbsp;&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;&lt;p class="MsoNormal" style="text-align: justify; margin: 0in 0.5in 0pt; mso-pagination: none;"&gt;&lt;span style="font-size: 10pt; mso-bidi-font-size: 12.0pt;"&gt;&lt;span style="font-family: Times New Roman;"&gt;This case also discusses various reasons for the sale of private companies and the effect of respective sale motives on the placement of these firms.&lt;span style="mso-spacerun: yes;"&gt;&amp;nbsp; &lt;/span&gt;Principally, the retirement decision by the owners of small privately held firms as the most frequent reason for the sale of these companies is explored.&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;
Transcranial Electrical Currents to Probe EEG Brain Rhythms and Memory Consolidation during Sleep in Humans
2011-02-14

Previously the application of a weak electric anodal current oscillating with a frequency of the sleep slow oscillation (∼0.75 Hz) during non-rapid eye movement sleep (NonREM) sleep boosted endogenous slow oscillation activity and enhanced sleep-associated memory consolidation. The slow oscillations occurring during NonREM sleep and theta oscillations present during REM sleep have been considered of critical relevance for memory formation. Here transcranial direct current stimulation (tDCS) oscillating at 5 Hz, i.e., within the theta frequency range (theta-tDCS) is applied during NonREM and REM sleep. Theta-tDCS during NonREM sleep produced a global decrease in slow oscillatory activity conjoint with a local reduction of frontal slow EEG spindle power (8-12 Hz) and a decrement in consolidation of declarative memory, underlining the relevance of these cortical oscillations for sleep-dependent memory consolidation. In contrast, during REM sleep theta-tDCS appears to increase global gamma (25-45 Hz) activity, indicating a clear brain state-dependency of theta-tDCS. More generally, results demonstrate the suitability of oscillating-tDCS as a tool to analyze functions of endogenous EEG rhythms and underlying endogenous electric fields as well as the interactions between EEG rhythms of different frequencies.
CyLoP-1: A Novel Cysteine-Rich Cell-Penetrating Peptide for Cytosolic Delivery of Cargoes
2011-02-14

Cell-penetrating peptides (CPPs) may have impli-cations in biomedical sciences by improving the delivery of a wide variety of drugs through the membrane barrier. CPPs are generally taken up by endocytotic pathways, and vesicular encapsulation is a limiting factor in the area of intracellular targeting. A novel, cationic cysteine-rich CPP, CyLoP-1, has been developed exhibiting distinguished diffused cytosolic distribution along with endosomal uptake at low micromolar concentrations. Comparative uptake analysis with known CPPs showed CyLoP-1 as a promising delivery vector to access the cytosol in a variety of cell types. In addition to the positively charged residues, the presence of cysteines and tryptophans proved to be essential to maintain its functionality. Also, the oxidation status of the cysteines played an important role for the uptake efficiency of CyLoP-1, with the disulfide-containing form being more effective. The distinct feature of CyLoP-1 to enter the cytosol was further explored by the covalent attachment of cargoes of different nature and sizes. In particular, induction of caspase-3 activity (indicating apoptosis) by a CyLoP-1-SmacN7 conjugate proved successful delivery of the pro-apoptotic cargo to its site of action in the cytosol. Efficient intracellular delivery into the entire cytosol already at low micromolar concentrations makes CyLoP-1 a promising candidate for cytosolic delivery of cargoes of small sizes. Thus, this peptide might prove to be useful for efficient transmembrane delivery of agents directed to cytosolic targets.
Tracking progress towards safe motherhood: meeting the benchmark yet missing the goal? An appeal for better use of health‐system output indicators with evidence from Zambia and Sri Lanka
2011-02-14

Summary Objectives Indicators of health‐system outputs, such as Emergency Obstetric Care (EmOC) density, have been proposed for monitoring progress towards reducing maternal mortality, but are currently underused. We seek to promote them by demonstrating their use at subnational level, evaluating whether they differentiate between a high‐maternal‐mortality country (Zambia) and a low‐maternal‐mortality country (Sri Lanka) and assessing whether benchmarks are set at the right level. Methods We compared national and subnational density of health facilities, EmOC facilities and health professionals against current benchmarks for Zambia and Sri Lanka. For Zambia, we also examined geographical accessibility by linking health facility data to population data. Results Both countries performed similarly in terms of EmOC facility density, implying this indicator, as currently used, fails to discriminate between high‐ and low‐maternal‐mortality settings. In Zambia, the WHO benchmarks for doctors/midwives were met overall, but distribution between provinces was highly unequal. Sri Lanka overshot the suggested benchmarks by three times for midwives and over 30 times for doctors. Geographical access in Zambia – which is much less densely populated than Sri Lanka – was poor, less than half the population lived within 15 km of an EmOC facility. Conclusions Current health‐system output indicators and benchmarks on EmOC need revision to enhance discriminatory power and should be adapted for different population densities. Subnational disaggregation and assessing geographical access can identify gaps in EmOC provision and should be routinely considered. Increased use of an improved set of output indicators is crucial for guiding international efforts towards reducing maternal mortality.
Sebacinales Everywhere: Previously Overlooked Ubiquitous Fungal Endophytes
2011-02-15

Inconspicuous basidiomycetes from the order Sebacinales are known to be involved in a puzzling variety of mutualistic plant-fungal symbioses (mycorrhizae), which presumably involve transport of mineral nutrients. Recently a few members of this fungal order not fitting this definition and commonly referred to as 'endophytes' have raised considerable interest by their ability to enhance plant growth and to increase resistance of their host plants against abiotic stress factors and fungal pathogens. Using DNA-based detection and electron microscopy, we show that Sebacinales are not only extremely versatile in their mycorrhizal associations, but are also almost universally present as symptomless endophytes. They occurred in field specimens of bryophytes, pteridophytes and all families of herbaceous angiosperms we investigated, including liverworts, wheat, maize, and the non-mycorrhizal model plant Arabidopsis thaliana. They were present in all habitats we studied on four continents. We even detected these fungi in herbarium specimens originating from pioneering field trips to North Africa in the 1830s/40s. No geographical or host patterns were detected. Our data suggest that the multitude of mycorrhizal interactions in Sebacinales may have arisen from an ancestral endophytic habit by specialization. Considering their proven beneficial influence on plant growth and their ubiquity, endophytic Sebacinales may be a previously unrecognized universal hidden force in plant ecosystems.
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
2011-02-15

The MEGAN program now allows the interactive analysis and comparison of the taxonomical and functional content of multiple datasets. As a stand-alone tool, MEGAN provides an alternative to web portals for scientists that have concerns about uploading their unpublished data to a website.