julilili42/papers huggingface dataset:
Plant cytokinesis: a tale of membrane traffic and fusion
2015-01-26

Cytokinesis separates the forming daughter cells. Higher plants have lost the ability to constrict the plasma membrane (PM) in the division plane. Instead, trans-Golgi network (TGN)-derived membrane vesicles are targeted to the centre of the division plane and generate, by homotypic fusion, the partitioning membrane named cell plate (CP). The CP expands in a centrifugal fashion until its margin fuses with the PM at the cortical division site. Mutant screens in Arabidopsis have identified a cytokinesis-specific syntaxin named KNOLLE and an interacting Sec1/Munc18 (SM) protein named KEULE both of which are required for vesicle fusion during cytokinesis. KNOLLE is only made during M-phase, targeted to the division plane and degraded in the vacuole at the end of cytokinesis. Here we address mechanisms of KNOLLE trafficking and interaction of KNOLLE with different soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor (SNARE) partners and with SM-protein KEULE, ensuring membrane fusion in cytokinesis.
PART is part of Alzheimer disease
2015-01-27

It has been proposed that tau aggregation confined to entorhinal cortex and hippocampus, with no or only minimal Aβ deposition, should be considered as a 'primary age-related tauopathy' (PART) that is not integral to the continuum of sporadic Alzheimer disease (AD). Here, we examine the evidence that PART has a pathogenic mechanism and a prognosis which differ from those of AD. We contend that no specific property of the entorhinal-hippocampal tau pathology makes it possible to predict either a limited progression or the development of AD, and that biochemical differences await an evidence base. On the other hand, entorhinal-hippocampal tau pathology is an invariant feature of AD and is always associated with its development. Rather than creating a separate disease entity, we recommend the continued use of an analytical approach based on NFT stages and Aβ phases with no inference about hypothetical disease processes.
H.E.S.S. reveals a lack of TeV emission from the supernova remnant Puppis A
2015-01-27

Context. Puppis A is an interesting ~4 kyr-old supernova remnant (SNR) that shows strong evidence of interaction between the forward shock and a molecular cloud. It has been studied in detail from radio frequencies to high-energy (HE, 0.1−100 GeV) γ-rays. An analysis of the Fermi-LAT data has shown extended HE -ray emission with a 0.2−100 GeV spectrum exhibiting no significant deviation from a power law, unlike most of the GeV-emitting SNRs known to be interacting with molecular clouds. This makes it a promising target for imaging atmospheric Cherenkov telescopes (IACTs) to probe the -ray emission above 100 GeV. Aims. Very-high-energy (VHE, E ≥ 0.1 TeV) -ray emission from Puppis A has been, for the first time, searched for with the High Energy Stereoscopic System (H.E.S.S.). Methods. Stereoscopic imaging of Cherenkov radiation from extensive air showers is used to reconstruct the direction and energy of the incident γ-rays in order to produce sky images and source spectra. The profile likelihood method is applied to find constraints on the existence of a potential break or cutoff in the photon spectrum. Results. The analysis of the H.E.S.S. data does not reveal any significant emission towards Puppis A. The derived upper limits on the differential photon flux imply that its broadband -ray spectrum must exhibit a spectral break or cutoff. By combining Fermi-LAT and H.E.S.S. measurements, the 99% confidence-level upper limits on such a cutoff are found to be 450 and 280 GeV, assuming a power law with a simple exponential and a sub-exponential cutoff, respectively. It is concluded that none of the standard limitations (age, size, radiative losses) on the particle acceleration mechanism, assumed to be continuing at present, can explain the lack of VHE signal. The scenario in which particle acceleration has ceased some time ago is considered as an alternative explanation. The HE/VHE spectrum of Puppis A could then exhibit a break of non-radiative origin (as observed in several other interacting SNRs, albeit at somewhat higher energies), owing to the interaction with dense and neutral material, in particular towards the NE region.
On the Codes Related to the Higman-Sims Graph
2015-01-27

All linear codes of length over a field which admit the Higman-Sims simple group HS in its rank representation are determined. By group representation theory it is proved that they can all be understood as submodules of the permutation module where denotes the vertex set of the Higman-Sims graph. This module is semisimple if and absolutely indecomposable otherwise. Also if the submodule lattice is determined explicitly. The binary case is studied in detail under coding theoretic aspects. The HS-orbits in the subcodes of dimension are computed explicitly and so also the weight enumerators are obtained. The weight enumerators of the dual codes are determined by MacWilliams transformation. Two fundamental methods are used: Let be the endomorphism determined by an adjacency matrix. Then in the HS-orbits are determined as -images of certain low weight vectors in which carry some special graph configurations. The second method consists in using the fact that is a Klein four group under addition, if denotes the code generated by and a Higman vector of weight 50 associated to a heptad in the shortened Golay code , and denotes the doubly even subcode of . Using the mentioned observation about and the results on the HS-orbits in a model of G. Higman's geometry is constructed, which leads to a direct geometric proof that G. Higman's simple group is isomorphic to HS. Finally, it is shown that almost all maximal subgroups of the Higman-Sims group can be understood as stabilizers in HS of codewords in .
On the Codes Related to the Higman-Sims Graph
2015-01-27

All linear codes of length over a field which admit the Higman-Sims simple group HS in its rank representation are determined. By group representation theory it is proved that they can all be understood as submodules of the permutation module where denotes the vertex set of the Higman-Sims graph. This module is semisimple if and absolutely indecomposable otherwise. Also if the submodule lattice is determined explicitly. The binary case is studied in detail under coding theoretic aspects. The HS-orbits in the subcodes of dimension are computed explicitly and so also the weight enumerators are obtained. The weight enumerators of the dual codes are determined by MacWilliams transformation. Two fundamental methods are used: Let be the endomorphism determined by an adjacency matrix. Then in the HS-orbits are determined as -images of certain low weight vectors in which carry some special graph configurations. The second method consists in using the fact that is a Klein four group under addition, if denotes the code generated by and a "Higman vector" of weight 50 associated to a heptad in the shortened Golay code , and denotes the doubly even subcode of . Using the mentioned observation about and the results on the HS-orbits in a model of G. Higman's geometry is constructed, which leads to a direct geometric proof that G. Higman's simple group is isomorphic to HS. Finally, it is shown that almost all maximal subgroups of the Higman-Sims group can be understood as stabilizers in HS of codewords in .
Topological order and the vacuum of Yang-Mills theories
2015-01-27

We study, for Yang-Mills theories discretized on a lattice, a\\nnon-local topological order parameter, the center flux . We show that:\\ni) well defined topological sectors classified by \\ncan only exist in the ordered phase of ; ii) depending on the dimension\\n and action chosen, the center flux exhibits a critical\\nbehaviour sharing striking features with the Kosterlitz-Thouless type of\\ntransitions, although belonging to a novel universality class; iii) such\\ncritical behaviour does not depend on the temperature . Yang-Mills theories\\ncan thus exist in two different continuum phases, characterized by an either\\ntopologically ordered or disordered vacuum; this reminds of a quantum phase\\ntransition, albeit controlled by the choice of symmetries and not by a physical\\nparameter.\\n
Left Dorsal Speech Stream Components and Their Contribution to Phonological Processing
2015-01-28

Models propose an auditory-motor mapping via a left-hemispheric dorsal speech-processing stream, yet its detailed contributions to speech perception and production are unclear. Using fMRI-navigated repetitive transcranial magnetic stimulation (rTMS), we virtually lesioned left dorsal stream components in healthy human subjects and probed the consequences on speech-related facilitation of articulatory motor cortex (M1) excitability, as indexed by increases in motor-evoked potential (MEP) amplitude of a lip muscle, and on speech processing performance in phonological tests. Speech-related MEP facilitation was disrupted by rTMS of the posterior superior temporal sulcus (pSTS), the sylvian parieto-temporal region (SPT), and by double-knock-out but not individual lesioning of pars opercularis of the inferior frontal gyrus (pIFG) and the dorsal premotor cortex (dPMC), and not by rTMS of the ventral speech-processing stream or an occipital control site. RTMS of the dorsal stream but not of the ventral stream or the occipital control site caused deficits specifically in the processing of fast transients of the acoustic speech signal. Performance of syllable and pseudoword repetition correlated with speech-related MEP facilitation, and this relation was abolished with rTMS of pSTS, SPT, and pIFG. Findings provide direct evidence that auditory-motor mapping in the left dorsal stream causes reliable and specific speech-related MEP facilitation in left articulatory M1. The left dorsal stream targets the articulatory M1 through pSTS and SPT constituting essential posterior input regions and parallel via frontal pathways through pIFG and dPMC. Finally, engagement of the left dorsal stream is necessary for processing of fast transients in the auditory signal.
The Lipid-Modifying Multiple Peptide Resistance Factor Is an Oligomer Consisting of Distinct Interacting Synthase and Flippase Subunits
2015-01-28

ABSTRACT Phospholipids are synthesized at the inner leaflet of the bacterial cytoplasmic membrane but have to be translocated to the outer leaflet to maintain membrane lipid bilayer composition and structure. Even though phospholipid flippases have been proposed to exist in bacteria, only one such protein, MprF, has been described. MprF is a large integral membrane protein found in several prokaryotic phyla, whose C terminus modifies phosphatidylglycerol (PG), the most common bacterial phospholipid, with lysine or alanine to modulate the membrane surface charge and, as a consequence, confer resistance to cationic antimicrobial agents such as daptomycin. In addition, MprF is a flippase for the resulting lipids, Lys-PG or Ala-PG. Here we demonstrate that the flippase activity resides in the N-terminal 6 to 8 transmembrane segments of the Staphylococcus aureus MprF and that several conserved, charged amino acids and a proline residue are crucial for flippase function. MprF protects S. aureus against the membrane-active antibiotic daptomycin only when both domains are present, but the two parts do not need to be covalently linked and can function in trans . The Lys-PG synthase and flippase domains were each found to homo-oligomerize and also to interact with each other, which illustrates how the two functional domains may act together. Moreover, full-length MprF proteins formed oligomers, indicating that MprF functions as a dimer or larger oligomer. Together our data reveal how bacterial phospholipid flippases may function in the context of lipid biosynthetic processes. IMPORTANCE Bacterial cytoplasmic membranes are crucial for maintaining and protecting cellular integrity. For instance, they have to cope with membrane-damaging agents such as cationic antimicrobial peptides (CAMPs) produced by competing bacteria (bacteriocins), secreted by eukaryotic host cells (defensins), or used as antimicrobial therapy (daptomycin). The MprF protein is found in many Gram-positive, Gram-negative, and even archaeal commensals or pathogens and confers resistance to CAMPs by modifying anionic phospholipids with amino acids, thereby compromising the membrane interaction of CAMPs. Here we describe how MprF does not only modify phospholipids but uses an additional, distinct domain for translocating the resulting lysinylated phospholipids to the outer leaflet of the membrane. We reveal critical details for the structure and function of MprF, the first dedicated prokaryotic phospholipid flippase, which may pave the way for targeting MprF with new antimicrobials that would not kill bacteria but sensitize them to antibiotics and innate host defense molecules.
Das Vermögen der Familie des Mannum-mēšu-liṣṣur
2015-01-28

Abstract: The family of Mannum-mēšu-liṣṣur belongs to the wealthy and well known families from Old Babylonian Nippur. This article will trace the development of its property through the eight documented generations spanning 150 years in total (Lipit-Enlil d to Samsu-iluna 29, ca. 1871–1721 B. C.). The study is based on 30 legal documents mentioning members of the family, and thus forming the archive of Mannum-mēšu-liṣṣur. Special attention will be paid to the inheritance documents.
Parton-to-pion fragmentation reloaded
2015-01-29

We present a new, comprehensive global analysis of parton-to-pion\\nfragmentation functions at next-to-leading order accuracy in QCD. The obtained\\nresults are based on the latest experimental information on single-inclusive\\npion production in electron-positron annihilation, lepton-nucleon\\ndeep-inelastic scattering, and proton-proton collisions. An excellent\\ndescription of all data sets is achieved, and the remaining uncertainties in\\nparton-to-pion fragmentation functions are estimated based on the Hessian\\nmethod. Extensive comparisons to the results from our previous global analysis\\nare performed.\\n
Generalization of word meanings during infant sleep
2015-01-29

Abstract Sleep consolidates memory and promotes generalization in adults, but it is still unknown to what extent the rapidly growing infant memory benefits from sleep. Here we show that during sleep the infant brain reorganizes recent memories and creates semantic knowledge from individual episodic experiences. Infants aged between 9 and 16 months were given the opportunity to encode both objects as specific word meanings and categories as general word meanings. Event-related potentials indicate that, initially, infants acquire only the specific but not the general word meanings. About 1.5 h later, infants who napped during the retention period, but not infants who stayed awake, remember the specific word meanings and, moreover, successfully generalize words to novel category exemplars. Independently of age, the semantic generalization effect is correlated with sleep spindle activity during the nap, suggesting that sleep spindles are involved in infant sleep-dependent brain plasticity.
Regulatory T-Cell Impairment in Cystic Fibrosis Patients with Chronic Pseudomonas Infection
2015-01-29

Patients with CF who have chronic P. aeruginosa infection show an age-dependent, quantitative, and qualitative impairment of Tregs. Modulation of Tregs represents a novel strategy to rebalance T-cell responses, dampen inflammation, and ultimately improve outcomes for patients with infective CF lung disease.
Systematic re-evaluation of genes from candidate gene association studies in migraine using a large genome-wide association data set
2015-01-29

Background Before the genome-wide association (GWA) era, many hypothesis-driven candidate gene association studies were performed that tested whether DNA variants in genes that had been selected based on prior knowledge about migraine pathophysiology were associated with migraine. Most studies involved small sample sets without robust replication, thereby making the risk of false-positive findings high. Genome-wide marker data of thousands of migraine patients and controls from the International Headache Genetics Consortium provide a unique opportunity to re-evaluate key findings from candidate gene association studies (and other non-GWA genetic studies) in a much larger data set. Methods We selected 21 genes from published candidate gene association studies and six additional genes from other non-GWA genetic studies in migraine. Single nucleotide polymorphisms (SNPs) in these genes, as well as in the regions 500 kb up- and downstream, were inspected in IHGC GWAS data from 5175 clinic-based migraine patients with and without aura and 13,972 controls. Results None of the SNPs in or near the 27 genes, including the SNPs that were previously found to be associated with migraine, reached the Bonferroni-corrected significance threshold; neither when analyzing all migraine patients together, nor when analyzing the migraine with and without aura patients or males and females separately. Conclusion The available migraine GWAS data provide no clear evidence for involvement of the previously reported most promising candidate genes in migraine.
Morphology and connectivity of the small bistratified A8 amacrine cell in the mouse retina
2015-01-29

ABSTRACT Amacrine cells comprise ∼30 morphological types in the mammalian retina. The synaptic connectivity and function of a few γ‐aminobutyric acid (GABA)ergic wide‐field amacrine cells have recently been studied; however, with the exception of the rod pathway‐specific AII amacrine cell, the connectivity of glycinergic small‐field amacrine cells has not been investigated in the mouse retina. Here, we studied the morphology and connectivity pattern of the small‐field A8 amacrine cell. A8 cells in mouse retina are bistratified with lobular processes in the ON sublamina and arboreal dendrites in the OFF sublamina of the inner plexiform layer. The distinct bistratified morphology was first visible at postnatal day 8, reaching the adult shape at P13, around eye opening. The connectivity of A8 cells to bipolar cells and ganglion cells was studied by double and triple immunolabeling experiments by using various cell markers combined with synaptic markers. Our data suggest that A8 amacrine cells receive glutamatergic input from both OFF and ON cone bipolar cells. Furthermore, A8 cells are coupled to ON cone bipolar cells by gap junctions, and provide inhibitory input via glycine receptor (GlyR) subunit α1 to OFF cone bipolar cells and to ON A‐type ganglion cells. Measurements of spontaneous glycinergic postsynaptic currents and GlyR immunolabeling revealed that A8 cells express GlyRs containing the α2 subunit. The results show that the bistratified A8 cell makes very similar synaptic contacts with cone bipolar cells as the rod pathway‐specific AII amacrine cell. However, unlike AII cells, A8 amacrine cells provide glycinergic input to ON A‐type ganglion cells. J. Comp. Neurol. 523:1529–1547, 2015. © 2015 Wiley Periodicals, Inc.
Prodrugs of Reverse Fosmidomycin Analogues
2015-01-29

Fosmidomycin inhibits IspC (Dxr, 1-deoxy-d-xylulose 5-phosphate reductoisomerase), a key enzyme in nonmevalonate isoprenoid biosynthesis that is essential in Plasmodium falciparum. The drug has been used successfully to treat malaria patients in clinical studies, thus validating IspC as an antimalarial target. However, improvement of the drug's pharmacodynamics and pharmacokinetics is desirable. Here, we show that the conversion of the phosphonate moiety into acyloxymethyl and alkoxycarbonyloxymethyl groups can increase the in vitro activity against asexual blood stages of P. falciparum by more than 1 order of magnitude. We also synthesized double prodrugs by additional esterification of the hydroxamate moiety. Prodrugs with modified hydroxamate moieties are subject to bioactivation in vitro. All prodrugs demonstrated improved antiplasmodial in vitro activity. Selected prodrugs and parent compounds were also tested for their cytotoxicity toward HeLa cells and in vivo in a Plasmodium berghei malaria model as well as in the SCID mouse P. falciparum model.
Back Cover: {Sn10[Si(SiMe3)3]4}2−: A Highly Reactive Metalloid Tin Cluster with an Open Ligand Shell (Chem. Eur. J. 7/2015)
2015-01-29

The metalloid tin cluster {Sn10[Si(SiMe3)3]4}2− was obtained in good yield by the reaction of a SnICl solution with LiSi(SiMe3)3. The centaur polyhedral arrangement of the ten tin atoms is in line with 26 bonding electrons in the cluster core. The high reactivity of the cluster in solution can be traced back to the open ligand shell, opening the door for further investigations into the chemical properties of metalloid cluster compounds of tin. For more details, see the Full Paper by A. Schnepf et al. on page 2992 ff.
GAME: GRB AND ALL-SKY MONITOR EXPERIMENT
2015-01-29

We describe the GRB and all-sky monitor experiment (GAME) mission submitted by a large international collaboration (Italy, Germany, Czech Republic, Slovenia, Brazil) in response to the 2012 ESA call for a small mission opportunity for a launch in 2017 and presently under further investigation for subsequent opportunities. The general scientific objective is to perform measurements of key importance for GRB science and to provide the wide astrophysical community of an advanced X-ray all-sky monitoring system. The proposed payload was based on silicon drift detectors (~1–50 keV), CdZnTe (CZT) detectors (~15–200 keV) and crystal scintillators in phoswich (NaI/CsI) configuration (~20 keV–20 MeV), three well established technologies, for a total weight of ~250 kg and a required power of ~240 W. Such instrumentation allows a unique, unprecedented and very powerful combination of large field of view (3–4 sr), a broad energy band extending from ~1 keV up to ~20 MeV, an energy resolution as good as ~250 eV in the 1–30 keV energy range, a source location accuracy of ~1 arcmin. The mission profile included a launch (e.g. by Vega) into a low Earth orbit, a baseline sky scanning mode plus pointed observations of regions of particular interest, data transmission to ground via X-band (4.8 Gb/orbit, Alcantara and Malindi ground stations), and prompt transmission of GRB/transient triggers.
The Arab East and the Bedouin Component in Pre-modern History: Approaching Textual Representations and Their Changing Settings in Life
2015-01-30

Article The Arab East and the Bedouin Component in Pre-modern History: Approaching Textual Representations and Their Changing Settings in Life was published on April 30, 2015 in the journal Der Islam (volume 92, issue 1).
Network-based interactive navigation and analysis of large biological datasets
2015-01-30

Abstract Over the last decade, advances in high-throughput technologies have resulted in a flood of new biological data. Here, individual samples can extend up into terabyte size. While potential applications are broad, ranging from biotechnology to medical applications, the analysis of these datasets poses massive challenges. In order to make use of the produced terabytes of data, these datasets need to be integrated, need to be mapped onto existing biological knowledge, and need to be explored by experts. We present UniPAX and BiNA, a scalable system for the integration and analysis of high-throughput data (genomics, transcriptomics, proteomics, and metabolomics) in a network context. A central data warehouse holds the core dataset. A flexible middleware can execute custom queries on this dataset and communicate with our visual analytics tool BiNA, the Biological Network Analyzer. We demonstrate how the combination of these tools permits an efficient analysis of large-scale datasets for medical applications.