julilili42/papers huggingface dataset:
In Vivo Regulation of Oligodendrocyte Precursor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2
2018-10-01

The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in vivo during the peak of myelination by targeting the GluA2 subunit. Expression of the unedited (Ca<sup>2+</sup> permeable) or the pore-dead GluA2 subunit of AMPARs triggered proliferation of OPCs and reduced their differentiation into oligodendrocytes. Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit (C-tail), a modification designed to affect the interaction between GluA2 and AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs, decreased the differentiation of OPCs without affecting their proliferation. These findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs, as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in the mouse corpus callosum, are important for balancing the response of OPCs to proliferation and differentiation cues.
Suitability of hepatocyte cell lines HepG2, AML12 and THLE-2 for investigation of insulin signalling and hepatokine gene expression
2018-10-01

Immortal hepatocyte cell lines are widely used to elucidate insulin-dependent signalling pathways and regulation of hepatic metabolism, although the often tumorigenic origin might not represent the metabolic state of healthy hepatocytes. We aimed to investigate if murine cell line AML12 and human cell line THLE-2, which are derived from healthy liver cells, are comparable to hepatoma cell line HepG2 for studying acute insulin signalling and expression of gluconeogenic enzymes and hepatokines. Insulin responsiveness of AML12 and THLE-2 cells was impaired when cells were cultured in the recommended growth medium, but comparable with HepG2 cells by using insulin-deficient medium. THLE-2 cells showed low abundance of insulin receptor, while protein levels in HepG2 and AML12 were comparable. AML12 and THLE-2 cells showed only low or non-detectable transcript levels of G6PC and PCK1 . Expression of ANGPTL4 was regulated similarly in HepG2 and AML12 cells upon peroxisome proliferator-activated receptor δ activation but only HepG2 cells resemble the in vivo regulation of hepatic ANGPTL4 by cAMP. Composition of the culture medium and protein expression levels of key signalling proteins should be considered when AML12 and THLE-2 are used to study insulin signalling. With regard to gluconeogenesis and hepatokine expression, HepG2 cells appear to be closer to the in vivo situation despite the tumorigenic origin.
Tidal Love numbers of neutron stars in f(R) gravity
2018-10-01

The recent detection of gravitational waves from a neutron star merger was a significant step towards constraining the nuclear matter equation of state by using the tidal Love numbers (TLNs) of the merging neutron stars. Measuring or constraining the neutron star TLNs allows us in principle to exclude or constraint many equations of state. This approach, however, has the drawback that many modified theories of gravity could produce deviations from General Relativity similar to the deviations coming from the uncertainties in the equation of state. The first and the most natural step in resolving the mentioned problem is to quantify the effects on the TLNs from the modifications of General Relativity. With this motivation in mind, in the present paper we calculate the TLNs of (non-rotating) neutron stars in <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mi>R</mml:mi> <mml:mn>2</mml:mn></mml:msup> </mml:math> -gravity. More precisely, by solving numerically the perturbation equations, we calculate explicitly the polar and the axial <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>l</mml:mi> <mml:mo>=</mml:mo> <mml:mn>2</mml:mn></mml:mrow> </mml:math> TLNs for three characteristic realistic equations of state and compare the results to General Relativity. Our results show that while the polar TLNs are slightly influenced by the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mi>R</mml:mi> <mml:mn>2</mml:mn></mml:msup> </mml:math> modification of General Relativity, the axial TLNs can be several times larger (in terms of the absolute value) compared to the general relativistic case.
Expanding the Use of Spectral Libraries in Proteomics
2018-10-01

The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.
Chasing discs around O-type (proto)stars
2018-10-01

We present high angular resolution (~0.2′′) continuum and molecular emission line Atacama Large Millimeter/sub-millimeter Array (ALMA) observations of G17.64+0.16 in Band 6 (220−230 GHz) taken as part of a campaign in search of circumstellar discs around (proto)-O-stars. At a resolution of ~400 au the main continuum core is essentially unresolved and isolated from other strong and compact emission peaks. We detect SiO (5–4) emission that is marginally resolved and elongated in a direction perpendicular to the large-scale outflow seen in the 13 CO (2−1) line using the main ALMA array in conjunction with the Atacama Compact Array (ACA). Morphologically, the SiO appearsto represent a disc-like structure. Using parametric models we show that the position-velocity profile of the SiO is consistent with the Keplerian rotation of a disc around an object between 10 and 30 M ⊙ in mass, only if there is also radial expansion from a separate structure. The radial motion component can be interpreted as a disc wind from the disc surface. Models with a central stellar object mass between 20 and 30 M ⊙ are the most consistent with the stellar luminosity (1 × 10 5 L ⊙ ) and indicative of an O-type star. The H30 α millimetre recombination line (231.9 GHz) is also detected, but spatially unresolved, and is indicative of a very compact, hot, ionised region co-spatial with the dust continuum core. The broad line-width of the H30 α emission (full-width-half-maximum = 81.9 km s −1 ) is not dominated by pressure-broadening but is consistent with underlying bulk motions. These velocities match those required for shocks to release silicon from dust grains into the gas phase. CH 3 CN and CH 3 OH thermal emission also shows two arc shaped plumes that curve away from the disc plane. Their coincidence with OH maser emission suggests that they could trace the inner working surfaces of a wide-angle wind driven by G17.64 which impacts the diffuse remnant natal cloud before being redirected into the large-scale outflow direction. Accounting for all observables, we suggest that G17.64 is consistent with a O-type young stellar object in the final stages of protostellar assembly, driving a wind, but that has not yet developed into a compact H II region. The existance and detection of the disc in G17.64 is likely related to its isolated and possibly more evolved nature, traits which may underpin discs in similar sources.
A Study of the Strong Gravity Region of the Black Hole in GS 1354–645
2018-10-01

Abstract It is thought that the spacetime metric around astrophysical black holes is well described by the Kerr solution of Einstein’s gravity. However, robust observational evidence of the Kerr nature of these objects is still lacking. Here we fit the X-ray spectrum of the stellar-mass black hole in GS 1354–645 with a disk reflection model beyond Einstein’s gravity in order test the Kerr black hole hypothesis. We consider the Johannsen metric with the deformation parameters α 13 and α 22 . The Kerr metric is recovered for . For α 22 = 0, our measurements of the black hole spin and of the deformation parameter α 13 are and −0.34 &lt; α 13 &lt; 0.16, respectively. For α 13 = 0, we find a * &gt; 0.975 and −0.09 &lt; α 22 &lt; 0.42. All the reported uncertainties are at 99% of confidence level for two relevant parameters.
Is early silcrete heat treatment a new behavioural proxy in the Middle Stone Age?
2018-10-01

The South African Middle Stone Age (MSA) has in recent years become increasingly important for our understanding of the emergence of 'modern human behaviours'. Several key innovations appeared in this context for the first time, significantly pre-dating their re-invention in the European Upper Palaeolithic. One of these innovations was heat treatment of stone to improve its quality for the production of stone tools. Heat treatment may even be the oldest well-documented technique used to intentionally alter the properties of materials in general. It is commonly thought of as requiring the skilled use of fire, a high degree of planning depth and complex cognitive abilities. However, to work on these fundamental concepts we need to analyse the techniques and procedures used to heat-treat and we need to understand what they imply. In this paper, we present a direct and expedient comparison between the technical complexities of four alternative heat treatment procedures by coding the behaviours required for their set-up in so-called cognigrams, a relatively new method for understanding complexity based on the problem-solution distance. Our results show that although the techniques significantly differ in complexity, the techniques used in the MSA fall within the range of complexities known from other MSA techniques. Heat treatment in above-ground fires, as it was practised during this period in South Africa, was even one of the most complex techniques at the time of its invention. Early heat treatment can therefore be considered an important behavioural proxy that may shed light on the behaviour and socioeconomic structure of past groups. The implications of this are highlighted by the ongoing debate about 'modernity', 'behavioural flexibility' and 'complex cognition' of early anatomically modern humans in Africa.
The Symmetric Tetravalent Sulfhydryl-Specific Linker NATBA Facilitates a Combinatorial “Tool Kit” Strategy for Phage Display-Based Selection of Functionalized Bicyclic Peptides
2018-10-01

The rigid conformation of constrained bicyclic peptides provides a number of advantages over larger protein-based ligands, including better chemical stability, enhanced tissue penetration, and a wider field of possible applications. Selective chemical modification strategies are able to extend the scope of applications not only in a therapeutic manner but also for the development of novel tools for protein capturing, bioimaging, and targeted drug delivery. Herein, we report the synthesis of an adamantane-based, symmetrical, tetravalent, sulfhydryl-specific peptide linker. We have developed an in vitro two-step modification strategy that allows the generation of differently functionalized bicyclic peptides. This "tool kit" strategy was applied to cyclize and functionalize a phage-encoded peptide library bearing the sequence CX<sub>6</sub>CX<sub>6</sub>C. After phage display against a model target, isolated peptides show strong consensus sequences, indicating target-specific binding. The newly developed symmetric tetravalent linker opens new avenues for the combinatorial selection and functionalization of bicyclic peptide ligands with affinity to virtually any target.
Deep XMM-Newton observations of the northern disc of M 31
2018-10-01

Context . We carried out new observations of two fields in the star-forming northern ring of M 31 with XMM-Newton with each one of them consisting of two exposures of about 100 ks each. A previous XMM-Newton survey of the entire M 31 galaxy revealed extended diffuse X-ray emission in these regions. Aims . We study the population of X-ray sources in the northern disc of M 31 by compiling a complete list of X-ray sources down to a sensitivity limit of ∼7 × 10 34 erg s −1 (0.5–2.0 keV) and improve the identification of the X-ray sources. The major objective of the observing programme was the study of the hot phase of the interstellar medium (ISM) in M 31. The analysis of the diffuse emission and the study of the ISM is presented in a separate paper. Methods . We analysed the spectral properties of all detected sources using hardness ratios and spectra if the statistics were high enough. We also checked for variability. In order to classify the sources detected in the new deep XMM-Newton observations, we cross-correlated the source list with the source catalogue of a new survey of the northern disc of M 31 carried out with the Chandra X-ray Observatory and the Hubble Space Telescope (Panchromatic Hubble Andromeda Treasury, PHAT) as well as with other existing catalogues. Results . We detected a total of 389 sources in the two fields of the northern disc of M 31 observed with XMM-Newton . We identified 43 foreground stars and candidates and 50 background sources. Based on a comparison with the results of the Chandra /PHAT survey, we classify 24 hard X-ray sources as new candidates for X-ray binaries. In total, we identified 34 X-ray binaries and candidates and 18 supernova remnants (SNRs) and candidates. We studied the spectral properties of the four brightest SNRs and confirmed five new X-ray SNRs. Three of the four SNRs, for which a spectral analysis was performed, show emission mainly below 2 keV, which is consistent with shocked ISM. The spectra of two of them also require an additional component with a higher temperature. The SNR [SPH11] 1535 has a harder spectrum and might suggest that there is a pulsar-wind nebula inside the SNR. For all SNRs in the observed fields, we measured the X-ray flux or calculated upper limits. We also carried out short-term and long-term variability studies of the X-ray sources and found five new sources showing clear variability. In addition, we studied the spectral properties of the transient source SWIFT J004420.1+413702, which shows significant variation in flux over a period of seven months (June 2015 to January 2016) and associated change in absorption. Based on the likely optical counterpart detected in the Chandra /PHAT survey, the source is classified as a low-mass X-ray binary.
Efficient Map Representations for Multi-Dimensional Normal Distributions Transforms
2018-10-01

Efficient 2D and 3D map representations of both static and dynamic, indoor and outdoor environments are crucial for navigation of driving and flying robots. In this paper, we propose a fast and accurate approach for 2D and 3D Normal Distributions Transform (NDT) mapping based on indexed kd-trees. Similar to other approaches, we also model free space, which allows us to obtain occupancy probabilities. Additionally, we provide optional visibility based updates to enhance map consistency in case of noisy data, e.g. from stereo cameras. Unlike other available implementations, our approach is natively applicable to large-scale environments and in real-time, because our maps are able to grow dynamically. This also offers applicability to exploration tasks. To evaluate our approach, we present experimental results on publicly available datasets and discuss the mapping efficiency in terms of accuracy, runtime and memory management. As an exemplary use case, we apply our maps to Monte Carlo Localization on a well-known large-scale dataset.
A new approach to concept basicness and stability as a window to the robustness of concept list rankings
2018-10-01

Abstract Based on a recently published large-scale lexicostatistical database, we rank 1,016 concepts by their suitability for inclusion in Swadesh-style lists of basic stable concepts. For this, we define separate measures of basicness and stability. Basicness in the sense of morphological simplicity is measured based on information content, a generalization of word length which corrects for distorting effects of phoneme inventory sizes, phonotactics and non-stem morphemes in dictionary forms. Stability against replacement by semantic shift or borrowing is measured by sampling independent language pairs, and correlating the distances between the forms for the concept with the overall language distances. In order to determine the relative importance of basicness and stability, we optimize our combination of the two partial measures towards similarity with existing lists. A comparison with and among existing rankings suggests that concept rankings are highly data-dependent and therefore less well-grounded than previously assumed. To explore this issue, we evaluate the robustness of our ranking against language pair resampling, allowing us to assess how much volatility can be expected, and showing that only about half of the concepts on a list based on our ranking can safely be assumed to belong on the list independently of the data.
Management of Urethral Lesions and Urethrovaginal Fistula Formation Following Placement of a Tension-Free Suburethral Sling: Evaluation From a University Continence and Pelvic Floor Centre
2018-10-01

Abstract Introduction The complication of tape erosion in the urethra following placement of a retropubic (TVT) or transobturator (TOT) tension-free suburethral vaginal sling or an accidental iatrogenic transurethral tape position can result in the formation of a urethrovaginal or vesicovaginal fistula. The objective of the investigation is the evaluation of the management of such rare complications. Patients and Methods Retrospective analysis of 14 patients who were treated for a urethral lesion or urethrovaginal fistula formation status post TVT/TOT placement between June 2011 and February 2018 in the Tübingen University Department of Gynaecology. Results As surgical therapy, 57.1% (n = 8) cases underwent vaginal fistula closure using a Martius flap of the labium majus and in 21.4% (n = 3) using a vaginal rotation skin flap. In 21.4% (n = 3), exclusively vaginal suture reconstruction of the urethra following excision of the tape running transurethrally or tape erosion was performed. 50% (n = 7) of the patients had lasting continence postoperatively without any further need for therapy. In 28.6% (n = 4), there was ongoing stress urinary incontinence, in 21.4% (n = 3) mixed urinary incontinence. Six of the 7 patients with persistent incontinence underwent new placement of a tension-free suburethral retropubic sling (TVT) an average of 8.8 months (5 – 13 months) postoperatively which was uncomplicated in all patients and achieved satisfactory continence. The 3 patients with mixed urinary incontinence and persistent urgency components additionally received anticholinergic medication. During the time period investigated, there were no long-term complications, in particular no recurrent fistulas. Conclusion The rare but relevant complications of a urethral erosion, transurethral tape position or urethrovaginal fistula formation status post TVT/TOT placement can be successfully managed via vaginal surgery. Persistent postoperative urinary incontinence with the need for a two-phase repeat TVT placement following sufficient wound healing must be preoperatively clarified.
The First Anatomically Modern Humans from South-Eastern Europe. Contributions from the Buran-Kaya III Site (Crimea)
2018-10-01

The arrival of modern humans into Europe, their dispersal and their potential interactions with Neanderthals are still in debate. Whereas the first appearance of anatomically modern humans in Western Europe seems to be well understood, the situation is quite different for Eastern Europe, where data are more scarce. The Buran-Kaya III site in Crimea is of key importance to understand the colonization of Europe by anatomically modern humans and their potential contemporaneity with the last Neanderthal occupations. The new radiocarbon dated sequence shows that no Neanderthal settlement existed after 39 ka cal BP and casts doubt on the survival, as previously proposed, of Neanderthal refuge zones in Crimea 28 ka BP ago (34-32 ka cal BP). The human remains from Buran-Kaya III, directly dated to 32450 +250/-230 BP (layer 6-2) and 31900+/-220 BP (layer 6-1) (37.1-35.7 ka cal BP and 36.3-35.2 cal BP respectively), represent some of the oldest evidence of anatomically modern humans in Europe in a unique welldocumented archaeological context (Gravettian). Furthermore, the specimens from layer 6-1 represent the oldest Upper Palaeolithic modern humans from Eastern Europe with evidence of post-mortem treatment of the dead.
Long-term follow-up of early-onset Sneddon syndrome: A case report
2018-10-01

Sneddon syndrome is a rare vasculopathy of small and medium-sized arteries, characterized by the clinical occurrence of livedo racemosa together with ischemic cerebrovascular events.1 First cases of patients with livedo racemosa and neurologic symptoms were reported in the 1950s and 1960s.1-3 This syndrome is rare with an estimated incidence of 4 of 1 million per year and mainly affects young women with a mean onset in the third decade of life.4,5 We present an early-onset idiopathic form of Sneddon syndrome with a long-term follow-up of 19 years in a young male.