julilili42/papers huggingface dataset:
BIR2 affects complex formation of BAK1 with ligand binding receptors in plant defense
2014-04-29

BAK1 is a multifunctional leucine-rich repeat receptor kinase (LRR-RLK) that exerts its function by interacting with multiple ligand binding receptors and thereby influences diverse processes varying from brassinosteroid perception via PAMP and DAMP perception to cell death control. We recently identified a new BAK1 interacting protein, BIR2, that is also a LRR-RLK but, in contrast to BAK1, negatively regulates BAK1-dependent PAMP responses. While brassinosteroid responses are not affected by BIR2, cell death is negatively regulated as described for BAK1. BIR2 is released from BAK1 after ligand perception, increasing the pool of free BAK1 that is available to form complexes with activated ligand binding receptors. Individual ligands can only partially release BAK1 from BIR2. After exposition to a cocktail of ligands, almost the complete amount of BAK1 can be released indicating that BAK1 exists, together with BIR2, in subpools that can be individually addressed by specific ligands. These data support the idea that BAK1 exists in preformed complexes with its ligand binding receptor partners. Overexpression of BIR2 results in reduced complex formation of BAK1 with FLS2, showing that BIR2 negatively regulates BAK1 complex formation with ligand binding receptors.
Neutrophil homeostasis and its regulation by danger signaling
2014-04-29

Abstract Hematopoiesis in general is demand driven and adaptive, but in contrast to erythropoiesis or thrombocytopoiesis, our knowledge on how neutrophil production is adapted to individual needs remains incomplete. Recently, neutrophil homeostasis has been shown to depend on danger receptors, macrophages, and even circadian rhythms. Puzzle pieces for a broader view of neutrophil homeostasis accumulate, and we will herein try to put seemingly contradictory evidence in a perspective of neutrophil homeostasis and emergency granulopoiesis determined by innate immunologic signaling.
bZIPs and WRKYs: two large transcription factor families executing two different functional strategies
2014-04-30

bZIPs and WRKYs are two important plant transcription factor (TF) families regulating diverse developmental and stress-related processes. Since a partial overlap in these biological processes is obvious, it can be speculated that they fulfill non-redundant functions in a complex regulatory network. Here, we focus on the regulatory mechanisms that are so far described for bZIPs and WRKYs. bZIP factors need to heterodimerize for DNA-binding and regulation of transcription, and based on a bioinformatics approach, bZIPs can build up more than the double of protein interactions than WRKYs. In contrast, an enrichment of the WRKY DNA-binding motifs can be found in WRKY promoters, a phenomenon which is not observed for the bZIP family. Thus, the two TF families follow two different functional strategies in which WRKYs regulate each other's transcription in a transcriptional network whereas bZIP action relies on intensive heterodimerization.
Colonization of Medical Devices by Coagulase-Negative Staphylococci
2014-04-30

In 1981, intravenous catheters infected with staphylococci by perfusion were investigated by scanning electron microscopy (SEM) to demonstrate the mode of adhesion. Bacterial cells, primarily those of staphylococci, followed by Acinetobacter calcoaceticus and Pseudomonas aeruginosa, were shown to be attached to the inner surface of the catheter. The thickest bacterial layers were found in catheters infected by coagulase-negative staphylococci (CoNS). Right heart flow-directed catheters removed from 18 critically ill patients after an average of 2.6 days after insertion were covered by a bacterial biofilm. In a neonatal intensive care unit, CoNS caused the majority of the nosocomial bacteremias. A study of arterial and central venous catheters removed from patients after 1 to 14 days revealed an extensive biofilm on all 42 arterial and 26 central venous catheters. By using special biofilm culture recovery methods, it was shown that 81% of the catheters were colonized by bacteria growing in slime-enclosed biofilms. It was speculated that the colonization represents a nidus for infection and bacteremia in these patients. Staphylococci also produced biofilm on polyvinyl chloride (PVC) endotracheal tubes used in neonates. Adherence of staphylococci to various intravascular catheter materials was investigated; these materials were composed of silicone elastomer, thermoplastic polyurethane, and polyurethane coated with Hydromer, a coating that absorbs water and provides a hydrophilic sheath around the catheter. Production of slime is necessary for Staphylococcus epidermidis colonization and is also observed with many other pathogens, including S. aureus.
Neurosharing: large-scale data sets (spike, LFP) recorded from the hippocampal-entorhinal system in behaving rats
2014-04-30

<ns4:p>Using silicon-based recording electrodes, we recorded neuronal activity of the dorsal hippocampus and dorsomedial entorhinal cortex from behaving rats. The entorhinal neurons were classified as principal neurons and interneurons based on monosynaptic interactions and wave-shapes. The hippocampal neurons were classified as principal neurons and interneurons based on monosynaptic interactions, wave-shapes and burstiness. The data set contains recordings from 7,736 neurons (6,100 classified as principal neurons, 1,132 as interneurons, and 504 cells that did not clearly fit into either category) obtained during 442 recording sessions from 11 rats (a total of 204.5 hours) while they were engaged in one of eight different behaviours/tasks. Both original and processed data (time stamp of spikes, spike waveforms, result of spike sorting and local field potential) are included, along with metadata of behavioural markers. Community-driven data sharing may offer cross-validation of findings, refinement of interpretations and facilitate discoveries.</ns4:p>
Corporate Taxes and Internal Borrowing within Multinational Firms
2014-04-30

This study develops a theoretical model of a multinational firm with an internal capital market. Hypotheses regarding the role of local versus foreign characteristics such as profit tax rates, lack of institutional quality, financial underdevelopment, and productivity for internal debt financing at the level of foreign affiliates are derived and assessed empirically in a panel dataset covering the universe of German multinationals. We show that differences in nontax incentives given by fundamentals in local and foreign markets can offset or reinforce tax incentives. The results point at a many times higher tax-sensitivity of internal debt financing compared to previous research. (JEL F23, G32, H25)
Feeling before knowing why: The role of the orbitofrontal cortex in intuitive judgments—an MEG study
2014-04-30

In theory, intuitive decisions are made immediately, without conscious, reasoned thought. They are experienced as decisions based on hunches that cannot be explicitly described but, nevertheless, guide subsequent action. Investigating the underlying neural mechanisms, previous research has found the orbitofrontal cortex (OFC) to be crucial to intuitive processes, but its specific role has remained unclear. On the basis of a two-stage conceptualization of intuition suggested by Bowers, Regehr, Balthazard, and Parker Cognitive Psychology, 22, 72-110 (1990), we attempt to clarify the OFC's role in intuitive processing. We propose that it functions as an early integrator of incomplete stimulus input guiding subsequent processing by means of a coarse representation of the gist of the information. On the subjective level, this representation would be perceived as a (gut) feeling biasing the decision. Our aim in the present study was to test this neural model and rule out alternative explanations of OFC activation in intuitive judgments. We used magnetoencephalography (MEG) to record participants' electromagnetic brain responses during a visual coherence judgment task. As in earlier studies, the OFC was found to be activated when participants perceived coherence. Using MEG, it could be shown that this increase in activation began earlier in the OFC than in temporal object recognition areas. Moreover, the present study demonstrated that OFC activation was independent of physical stimulus characteristics, task requirements, and participants' explicit recognition of the stimuli presented. These results speak to the OFC's fundamental role in the early steps of intuitive judgments and suggest the proposed neural model as a promising starting point for future investigations.
T-cell immunity in the aging human
2014-04-30

Immunosenescence is an ill-defined term commonly used to describe the differences observed between younger and older individuals in a broad range of immune parameters. Humans and mice are the best-studied, but indications of immunosenescence have also been reported in primates, dogs, cats and horses
Ataxia meets chorioretinal dystrophy and hypogonadism: Boucher-Neuhäuser syndrome due toPNPLA6mutations: Figure 1
2014-04-30

A 37-year-old woman presented with progressive visual loss and primary amenorrhoea due to hypogonadotropic hypogonadism since 14 years of age. These symptoms were followed by cerebellar ataxia and lower limb spasticity, leading to wheelchair dependency at the age of 30 years. At examination at the age of 37 years, her vision was reduced to perception of hand motion, thus meeting the criteria of legal blindness (defined as visual acuity <20/400). This progressive visual loss was caused by chorioretinal degeneration as demonstrated by fundoscopy and optical coherence tomography (figure 1). Whereas patellar tendon reflexes were increased, Achilles tendon reflexes were ...
Ecology of Siderophores
2014-04-30

This chapter attempts to illustrate the occurrence of siderophores within different bacterial genera and explains the relationship between environmental factors and the biological function of siderophores, which may be summarized under the term of The ecology of siderophores may be considered in the context of an ecological niche defined by low iron availability and by the expression of high-affinity siderophore-mediated iron transport systems by the organisms that occupy this niche. The chapter focuses on selected aerobic, chemoorganotrophic bacterial groups, which represent only a part of the currently known bacteria. Streptomycetes are known to utilize polymeric carbohydrates such as starch, chitin, and cellulose, which are abundant in the upper layers of soils. Although plants are generally not able to use fungal and bacterial siderophores as iron sources, there are reports showing optimal utilization by mono- and dicotyledonous plants of some fungal mono- and dihydroxamates, which originate from partial degradation of fungal trihydroxamate siderophores. Many bacteria that inhabit the intestinal tracts of vertebrate hosts produce siderophores, although the question whether ferric siderophore transport is required in the gut still remains. The currently known bacterial siderophores and their producing organisms are listed in the chapter. An example of an absolute requirement for hydroxamate siderophores is the soil bacterium Microbacterium flavescens JG9 (previously classified as Arthrobacter or Aureobacterium), which is often used as a bioassay organism. It is an interesting fact that enzymes for siderophore biosynthesis are found among bacteria as well fungi.
The future of the European Union
2014-04-30

This article develops an assessment of the present-day European crisis management, referring to Wolfgang Streeck’s recent interpretation of the European ‘consolidation state’ as an attempt to install a ‘Hayekian’ regime of liberalized transnational markets. This article arrives at a diagnosis different from Streeck’s: if there has been a ‘Hayekian’ regime, it had already developed after the collapse of the Bretton Woods system in 1973 and the subsequent dismantling of capital controls in the USA and Europe. As it appeared in the financial crisis of 2007–2008, the ultimate practical test of the Hayekian vision was dramatically negative. European crisis management, as it is still largely occupied with the imperative to maintain the solvency of troubled Euro states vis-à-vis the capital markets, is not following a Hayekian script. Rather, it is confronted with the challenge of removing the debris of the collapse of the former Hayekian regime, taking the form of zombie banks and large uncovered capital claims. To master this challenge, not only intact European institutions and transnational cooperation in Europe would be required, but also much more democratic pressure from below.
Ferrous Iron Transport
2014-04-30

Transport systems for both ferric and ferrous iron have been identified in bacteria. Many bacteria produce siderophores to mobilize insoluble ferric iron from their surroundings. One of the first ferrous iron transport systems identified in bacteria, Feo, was found in Escherichia coli. The major transport protein FeoB contains a typical nucleotide-binding motif in the first 160 N-terminal amino acid residues, and there are at least 7 carboxy-terminal α-helices that embed the protein in the cytoplasmic membrane. Although there is evidence that the transport of ferrous iron is energized by ATP hydrolysis, the nucleotide-binding motif in FeoB has more similarities to the GTP-binding sites found in Ras proteins and elongation factors than to the ATP-binding sites in bacterial ABC transporters. Although it is clear that FeoB and the associated GTPase activity are required for ferrous iron transport, the mechanism of transport and precise function of FeoB are unknown. FeoB homologs are found in genomes of archaea and gram-positive and gram-negative bacteria (COGs, or phylogenetic classification of proteins encoded in complete genomes). It has been shown that FeoB-dependent ferrous iron transport in Synechocystis sp. strain PCC6803 is induced under iron-limiting growth conditions. Ferrous iron uptake is also important in the presence of oxygen since many bacteria can reduce extracellular ferric iron. The striking similarity of Feo to G proteins and the wide distribution of this protein make future research on the function of this protein in ferrous iron transport an exciting task.
Pilot Study for Reconstruction of Soft Tissues: Muscle Cross‐Sectional Area of the Forearm Estimated from Cortical Bone for a Neolithic Sample
2014-04-30

ABSTRACT On a basis of a method for muscle cross‐sectional area estimation from cortical bone area that was previously developed (Slizewski et al. Anat Rec 2013; 296:1695–1707), we reconstructed muscle cross‐sectional area at 65% of radius length for a sample of Neolithic human remains from the Linear Pottery Culture (ca. 5,700–4,900 years BC). Muscle cross‐sectional area estimations for the Neolithic sample were compared to in vivo measurements from a recent human sample. Results demonstrate that the Neolithic individuals had larger muscle cross‐sectional area relative to radius length than the contemporary humans and that their forearms were more muscular and robust. We also found significant differences in relative muscle cross‐sectional area between Neolithic and recent children that indicate different levels of physical stress and isometric activities. Our results fit into the framework of studies previously published about the sample and the Linear Pottery Culture. Therefore, the new approach was successfully applied to an archaeological sample for the first time here. Results of our pilot study indicate that muscle cross‐sectional area estimation could in the future supplement other anthropological methods currently in use for the analysis of postcranial remains. Anat Rec, 297:1103–1114, 2014. © 2014 Wiley Periodicals, Inc.
FFT simulation of dynamic recrystallization in polar ice
2014-04-30

Research on ice flow is a key to understand how climate changes affect polar ice. Numerical modelling provides&#13;\\na better insight into the mechanics of ice from the microstructure to the ice sheet scale. The mechanics of polar ice are very sensitive to temperature changes mainly due to active recrystallization processes, as the material is very close to its melting point. We present numerical simulations that predict the microstructural evolution of ice polycrystals during deformation and dynamic recrystallization at large strain, using a full-field approach.&#13;\\nThe crystal plasticity code (Lebensohn, 2001) is used to calculate the response of a polycrystalline aggregate that deforms by dislocation glide, applying a Fast Fourier Transform (FFT). The coupling between FFT and the ELLE microstructural evolution platform allows us to include recrystallization in the aggregate, which is simulated by means of two main processes: (1) recovery and subgrain rotation, which locally reduces the crystal misorientation, and (2) grain boundary migration, which is driven by grain boundary curvature and intra-grain strain energies.&#13;\\nThis contribution presents a comparison of numerical simulations under pure and simple shear conditions up to&#13;\\nhigh strain at different strain rates. The results show a strong effect of the recrystallization on the final microstructure. Dynamic recrystallization masks the strain rate and finite strain heterogeneity resulting from the strong slip anisotropy of ice. However, this strong effect does not significantly modify the single-maximum pattern of c-axes that are distributed at a low angle to the shortening direction in both pure and simple shear. In both cases, recrystallization produces larger and more equidimensional grains, with smooth boundaries.&#13;\\n&#13;\\nReferences:&#13;\\nR. A. Lebensohn. N-site modelling of a 3D viscoplastic polycrystal using Fast Fourier Transform. 2001. Acta&#13;\\nMaterialia 49, pp 2723-2737.
Ferrichrome- and Citrate-Mediated Iron Transport
2014-04-30

Iron transport through the outer membrane as ferrichrome- and ferric citrate-siderophore complexes is catalyzed by the FhuA and FecA proteins and across the cytoplasmic membrane by the FhuCDB and FecBCDE proteins, respectively. The energy for transport across the outer membrane is provided by the proton motive force of the cytoplasmic membrane, and the energy for transport across the cytoplasmic membrane is provided by ATP hydrolysis. Energy transfer from the cytoplasmic membrane to the outer membrane is mediated by the TonB-ExbB-ExbD proteins. Knowledge about the proteins that transport ferric siderophores, their interaction, and their subcellular location provides insights into the transport mechanism, but much work remains to be done before an understanding of the molecular mechanism of substrate translocation across the outer membrane and the cytoplasmic membrane is gained. Although crystal structures of the proteins in the entire pathway are now available (FhuA in the outer membrane, FhuD in the periplasm, and BtuCD in the cytoplasmic membrane), they provide only a framework for a detailed biochemical and genetic analysis. Crystal structures are static, yet transport is a dynamic process involving many rearrangements of amino acid side chains and entire polypeptide regions.
Neurosharing: large-scale data sets (spike, LFP) recorded from the hippocampal-entorhinal system in behaving rats
2014-04-30

Using silicon-based recording electrodes, we recorded neuronal activity of the dorsal hippocampus and dorsomedial entorhinal cortex from behaving rats. The entorhinal neurons were classified as principal neurons and interneurons based on monosynaptic interactions and wave-shapes. The hippocampal neurons were classified as principal neurons and interneurons based on monosynaptic interactions, wave-shapes and burstiness. The data set contains recordings from 7,736 neurons (6,100 classified as principal neurons, 1,132 as interneurons, and 504 cells that did not clearly fit into either category) obtained during 442 recording sessions from 11 rats (a total of 204.5 hours) while they were engaged in one of eight different behaviours/tasks. Both original and processed data (time stamp of spikes, spike waveforms, result of spike sorting and local field potential) are included, along with metadata of behavioural markers. Community-driven data sharing may offer cross-validation of findings, refinement of interpretations and facilitate discoveries.
Brain communication in a completely locked-in patient using bedside near-infrared spectroscopy
2014-05-01

Amyotrophic lateral sclerosis (ALS) can result in the locked-in state (LIS), characterized by paralysis, and eventual respiratory failure, compensated by artificial ventilation,1 or the completely LIS (CLIS), with additional total paralysis of eye muscles. Brain–computer interfaces (BCIs) have been used to allow paralyzed people to regain basic communication,2 although current EEG-based BCIs have not succeeded with CLIS patients.3 We present Class IV case evidence to establish that communication in the CLIS is possible with a metabolic BCI based on near-infrared spectroscopy (NIRS).
Tools and Strategies to Match Peptide-Ligand Receptor Pairs
2014-05-01

Peptide signals have emerged as an important class of regulators in cell-to-cell communication in plants. Several families of small, secreted proteins with a conserved C-terminal Pro-rich motif have been identified as functional peptide signals in Arabidopsis thaliana. These proteins are presumed to be trimmed proteolytically and undergo posttranslational modifications, such as hydroxylation of Pro residues and glycosylation, to form mature, bioactive signals. Identification and matching of such ligands with their respective receptors remains a major challenge since the genes encoding them often show redundancy and low expression restricted to a few cells or particular developmental stages. To overcome these difficulties, we propose the use of ectopic expression of receptor genes in suitable plant cells like Nicotiana benthamiana for testing ligand candidates in receptor output assays and in binding studies. As an example, we used the IDA peptide HAE/HSL2 receptor signaling system known to regulate floral organ abscission. We demonstrate that the oxidative burst response can be employed as readout for receptor activation by synthetic peptides and that a new, highly sensitive, nonradioactive labeling approach can be used to reveal a direct correlation between peptide activity and receptor affinity. We suggest that these approaches will be of broad value for the field of ligand-receptor studies in plants.
A Nasal Epithelial Receptor for Staphylococcus aureus WTA Governs Adhesion to Epithelial Cells and Modulates Nasal Colonization
2014-05-01

Nasal colonization is a major risk factor for S. aureus infections. The mechanisms responsible for colonization are still not well understood and involve several factors on the host and the bacterial side. One key factor is the cell wall teichoic acid (WTA) of S. aureus, which governs direct interactions with nasal epithelial surfaces. We report here the first receptor for the cell wall glycopolymer WTA on nasal epithelial cells. In several assay systems this type F-scavenger receptor, termed SREC-I, bound WTA in a charge dependent manner and mediated adhesion to nasal epithelial cells in vitro. The impact of WTA and SREC-I interaction on epithelial adhesion was especially pronounced under shear stress, which resembles the conditions found in the nasal cavity. Most importantly, we demonstrate here a key role of the WTA-receptor interaction in a cotton rat model of nasal colonization. When we inhibited WTA mediated adhesion with a SREC-I antibody, nasal colonization in the animal model was strongly reduced at the early onset of colonization. More importantly, colonization stayed low over an extended period of 6 days. Therefore we propose targeting of this glycopolymer-receptor interaction as a novel strategy to prevent or control S. aureus nasal colonization.