julilili42/papers huggingface dataset:
Closer view of the IGR J11014-6103 outflows
2016-06-21

<ext-link ext-link-type="aoi">IGR J11014-6103</ext-link> (also known as the Lighthouse Nebula) is composed of a bow-shock pulsar wind nebula (PWN) and large-scale X-ray jet-like features, all powered by PSR J1101-6101. Previous observations suggest that the jet features stem from a ballistic jet of relativistic particles. In order to confirm the nature of the jet and the counter-jet, we obtained a new deep 250 ks Chandra observation of the Lighthouse Nebula. We performed detailed spatial and spectral analysis of all X-ray components of the system. The X-ray PWN is now better resolved and shows a peculiar morphology resembling the shape of an arrow. The overall helical pattern of the main jet is confirmed. However, there are large deviations from a simple helical model at small and large scales. Significant extended emission is now detected, encompassing the main jet all along its length. The presence of an apparent gap along the main jet at ~50′′ distance from the pulsar is confirmed; however, the surrounding extended emission prevents conclusions on the coherence at this position of the jet. The counter-jet is now detected at high statistical significance. In addition, we found two small-scale arcs departing from the pulsar towards the jets. We also looked for possible bow-shock emission due to the pulsar motion, with a short VLT/FORS2 H-α observation. No clear emission is found, most likely because of the contamination from a diffuse nebulosity. The results of our X-ray analysis show that both a ballistic jet scenario and an alternative scenario involving the diffusion of particles along pre-existing interstellar magnetic field lines are able to satisfactorily explain some of the observational evidence, but cannot fully reproduce the observations. \\n
Quantitative chest CT analysis in patients with systemic sclerosis before and after autologous stem cell transplantation: comparison of results with those of pulmonary function tests and clinical tests
2016-06-21

CT quantification of lung volume and parenchymal attenuation in SSc patients presenting with alveolitis and fibrosis that undergo autologous SCT yields parameters that match well with those of pulmonary function and even clinical tests. It might therefore be used as a substitute marker in patients who are unable to adequately perform lung function tests.
Access to photon fragmentation functions in hadronic jet production
2016-06-21

We argue that the process , for which a photon\\nis observed inside a fully reconstructed jet and is treated as part of the jet,\\noffers new probes of the so far little known fragmentation functions for\\nphotons. We present a next-to-leading-order QCD calculation of the cross\\nsection for this process in the limit that the jet is relatively narrow. We\\nalso investigate the background resulting from the two-photon decay of neutral\\npions. We present numerical results relevant for possible measurements at the\\nLHC and at RHIC. These suggest that should\\nprovide clean access to the photon fragmentation functions, provided an\\nefficient suppression of the background is available in experiment.\\n
Adaptive immune response to lipoproteins of Staphylococcus aureus in healthy subjects
2016-06-21

Staphylococcus aureus is a frequent commensal but also a dangerous pathogen, causing many forms of infection ranging from mild to life‐threatening conditions. Among its virulence factors are lipoproteins, which are anchored in the bacterial cell membrane. Lipoproteins perform various functions in colonization, immune evasion, and immunomodulation. These proteins are potent activators of innate immune receptors termed Toll‐like receptors 2 and 6. This study addressed the specific B‐cell and T‐cell responses directed to lipoproteins in human S. aureus carriers and non‐carriers. 2D immune proteomics and ELISA approaches revealed that titers of antibodies (IgG) binding to S. aureus lipoproteins were very low. Proliferation assays and cytokine profiling data showed only subtle responses of T cells; some lipoproteins did not elicit proliferation. Hence, the robust activation of the innate immune system by S. aureus lipoproteins does not translate into a strong adaptive immune response. Reasons for this may include inaccessibility of lipoproteins for B cells as well as ineffective processing and presentation of the antigens to T cells.
Neutron stars in Horndeski gravity
2016-06-22

Horndeski's theory of gravity is the most general scalar-tensor theory with a\\nsingle scalar whose equations of motion contain at most second-order\\nderivatives. A subsector of Horndeski's theory known as "Fab Four" gravity\\nallows for dynamical self-tuning of the quantum vacuum energy, and therefore it\\nhas received particular attention in cosmology as a possible alternative to the\\n CDM model. Here we study compact stars in Fab Four gravity, which\\nincludes as special cases general relativity ("George"),\\nEinstein-dilaton-Gauss-Bonnet gravity ("Ringo"), theories with a nonminimal\\ncoupling with the Einstein tensor ("John") and theories involving the\\ndouble-dual of the Riemann tensor ("Paul"). We generalize and extend previous\\nresults in theories of the John class and were not able to find realistic\\ncompact stars in theories involving the Paul class.\\n
Prodromal Markers in Parkinson’s Disease: Limitations in Longitudinal Studies and Lessons Learned
2016-06-22

A growing body of evidence supports a prodromal neurodegenerative process preceding the clinical onset of Parkinson's disease (PD). Studies have identified several different prodromal markers that may have the potential to predict the conversion from healthy to clinical PD but use considerably different approaches. We systematically reviewed 35 longitudinal studies reporting prodromal PD features and evaluated the methodological quality across 10 different predefined domains. We found limitations in the following domains: PD diagnosis (57% of studies), prodromal marker assessments (51%), temporal information on prodromal markers or PD diagnosis (34%), generalizability of results (17%), statistical methods (accounting for at least age as confounder; 17%), study design (14%), and sample size (9%). However, no limitations regarding drop-out (or bias investigation), or report of inclusion/exclusion criteria or prodromal marker associations were revealed. Lessons learned from these limitations and additional aspects of current prodromal marker studies in PD are discussed to provide a basis for the evaluation of findings and the improvement of future research in prodromal PD. The observed heterogeneity of studies, limitations and analyses might be addressed in future longitudinal studies using a, yet to be established, modular minimal set of assessments improving comparability of findings and enabling data sharing and combined analyses across studies.
Counteracting Implicit Conflicts by Electrical Inhibition of the Prefrontal Cortex
2016-06-22

Abstract Cognitive conflicts and distractions by task-irrelevant information often counteract effective and goal-directed behaviors. In some cases, conflicting information can even emerge implicitly, without an overt distractor, by the automatic activation of mental representations. For instance, during number processing, magnitude information automatically elicits spatial associations resembling a mental number line. This spatial–numerical association of response codes (SNARC) effect can modulate cognitive-behavioral performance but is also highly flexible and context-dependent, which points toward a critical involvement of working memory functions. Transcranial direct current stimulation to the PFC, in turn, has been effective in modulating working memory-related cognitive performance. In a series of experiments, we here demonstrate that decreasing activity of the left PFC by cathodal transcranial direct current stimulation consistently and specifically eliminates implicit cognitive conflicts based on the SNARC effect, but explicit conflicts based on visuospatial distraction remain unaffected. This dissociation is polarity-specific and appears unrelated to functional magnitude processing as classified by regular numerical distance effects. These data demonstrate a causal involvement of the left PFC in implicit cognitive conflicts based on the automatic activation of spatial–numerical processing. Corroborating the critical interaction of brain stimulation and neurocognitive functions, our findings suggest that distraction from goal-directed behavior by automatic activation of implicit, task-irrelevant information can be blocked by the inhibition of prefrontal activity.
Sex differences in number line estimation: The role of numerical estimation
2016-06-22

Sex differences in mathematical performance have frequently been examined over the last decades indicating an advantage for males especially when numerical problems cannot be solved by (classroom‐)learnt strategies and/or estimation. Even in basic numerical tasks such as number line estimation, males were found to outperform females – with sex differences argued to emerge from different solution strategies applied by males and females. We evaluated the latter using two versions of the number line estimation task: a bounded and an unbounded task version. Assuming that women tend more strongly to apply known procedures, we expected them to be at a particular disadvantage in the unbounded number line estimation task, which is less prone to be solved by specific strategies such as proportion judgement but requires numerical estimation. Results confirmed more pronounced sex differences for unbounded number line estimation with males performing significantly more accurately in this task version. This further adds to recent evidence suggesting that estimation performance in the bounded task version may reflect solution strategies rather than numerical estimation. Additionally, it indicates that sex differences regarding the spatial representation of number magnitude may not be universal, but associated with spatial–numerical estimations in particular.
Closed-Loop Neuroprosthesis for Reach-to-Grasp Assistance: Combining Adaptive Multi-channel Neuromuscular Stimulation with a Multi-joint Arm Exoskeleton
2016-06-23

Stroke patients with severe motor deficits cannot execute task-oriented rehabilitation exercises with their affected upper extremity. Advanced rehabilitation technology may support them in performing such reach-to-grasp movements. The challenge is, however, to provide assistance as needed, while maintaining the participants' commitment during the exercises. In this feasibility study, we introduced a closed-loop neuroprosthesis for reach-to-grasp assistance which combines adaptive multi-channel neuromuscular stimulation with a multi-joint arm exoskeleton. Eighteen severely affected chronic stroke patients were assisted by a gravity-compensating, seven-degree-of-freedom exoskeleton which was attached to the paretic arm for performing reach-to-grasp exercises resembling activities of daily living in a virtual environment. During the exercises, adaptive electrical stimulation was applied to seven different muscles of the upper extremity in a performance-dependent way to enhance the task-oriented movement trajectory. The stimulation intensity was individualized for each targeted muscle and remained subthreshold, i.e., induced no overt support. Closed-loop neuromuscular stimulation could be well integrated into the exoskeleton-based training, and increased the task-related range of motion (p = 0.0004) and movement velocity (p = 0.015), while preserving accuracy. The highest relative stimulation intensity was required to facilitate the grasping function. The facilitated range of motion correlated with the upper extremity Fugl-Meyer Assessment score of the patients (p = 0.028). Combining adaptive multi-channel neuromuscular stimulation with antigravity assistance amplifies the residual motor capabilities of severely affected stroke patients during rehabilitation exercises and may thus provide a customized training environment for patient-tailored support while preserving the participants' engagement.
Co-infections in Visceral Pentastomiasis, Democratic Republic of the Congo
2016-06-23

Snakeborne Armillifer pentastomiasis is an emerging human parasitic infection in rural tropical areas where snake meat is eaten. After a series of severe ocular A. grandis larval infections and anecdotal abdominal infection in Sankuru District, Democratic Republic of the Congo, during 2014-2015, we systematically investigated possible pentastomid etiology in patients who underwent surgery in the region. Histologic and molecular analyses by established pentastomid 18S rDNA- and newly developed Armillifer-specific cytochrome oxidase PCRs revealed larval pentastomid lesions in 3.7% of patients. Some persons had A. armillatus and A. grandis co-infections. Another pentastomid larva, Raillietiella sp., was molecularly detected in 1 patient who had concomitant A. grandis and A. armillatus infection. The PCRs used were suitable for detecting pentastomid species even in highly necrotic tissues. Phylogenetic analyses of Armillifer cytochrome oxidase genes detected multiple local strains.
Comparison of Preparation Methods of Bacterial Cell-Mineral Aggregates for SEM Imaging and Analysis Using the Model System of Acidovorax sp. BoFeN1
2016-06-23

Innovative microanalytical methods are valuable tools in geomicrobiology. They often require the use of dried samples, demanding a challenging sample preparation. Since geomicrobiological samples typically have a strongly heterogeneous composition, choosing a preparation method is not straightforward. We therefore compared how different drying methods (critical point drying, hexamethyldisilazane drying, air drying and freeze drying) influence the structure of bacterial cell-mineral aggregates. Each method proved suitable for a specific purpose, but none was able to completely preserve the sample structure. Additional information was obtained on surface alterations by sputter coating and on preservation of extracellular polymeric substances during resin embedding.
Chemosensitization of Prostate Carcinoma Cells with a Receptor-directed Smac Conjugate
2016-06-23

Caspase 3/7 apoptosis tests after induction of apoptosis with staurosporine or UV irradiation showed that the coupling of SmacN7 with undecylic aldehyde resulted in a greatly increased adjuvant pro-apoptotic effect compared to the separate components and a mutant SmacN7 peptide sequence in the LNCaP prostate carcinoma cells compared to the benign prostate hyperplasia (BPH) cells and the human embryonal kidney (HEK) cells.
Live and let die: a REM complex promotes fertilization through synergid cell death in Arabidopsis
2016-06-24

Fertilization in flowering plants requires a complex series of coordinated events involving interaction between the male and female gametophyte. We report here molecular data on one of the key events underpinning this process – the death of the receptive synergid cell and the coincident bursting of the pollen tube inside the ovule to release the sperm. We show that two REM transcription factors, VALKYRIE (VAL) and VERDANDI (VDD), both targets of the ovule identity MADS-box complex SEEDSTICK-SEPALLATA3, interact to control the death of the receptive synergid cell. In vdd-1/+ mutants and VAL_RNAi lines, we find that GAMETOPHYTIC FACTOR 2 (GFA2), which is required for synergid degeneration, is downregulated, whereas expression of FERONIA (FER) and MYB98, which are necessary for pollen tube attraction and perception, remain unaffected. We also demonstrate that the vdd-1/+ phenotype can be rescued by expressing VDD or GFA2 in the synergid cells. Taken together, our findings reveal that the death of the receptive synergid cell is essential for maintenance of the following generations, and that a complex comprising VDD and VAL regulates this event.
Treatment of graft failure with TNI‐based reconditioning and haploidentical stem cells in paediatric patients
2016-06-24

Summary Graft failure is a life‐threatening complication after allogeneic haematopoietic stem cell transplantation ( HSCT ). We report a cohort of 19 consecutive patients (median age: 8·5 years) with acute leukaemias ( n = 14) and non‐malignant diseases ( n = 5) who experienced graft failure after previous HSCT from matched ( n = 3) or haploidentical donors ( n = 16) between 2003 and 2012. After total nodal irradiation ( TNI )‐based reconditioning combined with fludarabine, thiotepa and anti‐T cell serotherapy, all patients received T cell‐depleted peripheral blood stem cell grafts from a second, haploidentical donor. Median time between graft failure and retransplantation was 14 d (range 7–40). Sustained engraftment (median: 10 d, range 9–32) and complete donor chimerism was observed in all evaluable patients. 5 patients additionally received donor lymphocyte infusions. Graft‐versus‐host disease (Gv HD ) grade II and III occurred in 1 patient each (22%); no Gv HD grade IV was observed. 2 patients had transient chronic Gv HD . The regimen was well tolerated with transient interstitial pneumonitis in one patient. Treatment‐related mortality after one year was 11%. Event‐free survival and overall survival 3 years after retransplantation were 63% and 68%. Thus, a TNI ‐based reconditioning regimen followed by transplantation of haploidentical stem cells is an option to rescue patients with graft failure within a short time span and with low toxicity.
Evidence of local adaptation to fine‐ and coarse‐grained environmental variability inPoa alpinain the Swiss Alps
2016-06-24

Summary In the alpine landscape, characterized by high spatiotemporal heterogeneity and barriers, divergent selection is likely to lead to local adaptation of plant populations either through adaptive genetic differentiation or through phenotypic plasticity. The relative importance of these processes has rarely been investigated in relation to the spatial scale of environmental heterogeneity. In this study, we used reciprocal transplantation experiments of populations across nearby and distant field sites to shed light on these complementary processes. We reciprocally transplanted populations of the widespread alpine grass, Poa alpina , within and across regions in the Swiss Alps. We inferred local adaptation at the metapopulation level by comparing fitness of plants transplanted to their site of origin and to nearby or distant novel sites. Additionally, we measured specific leaf area ( SLA ) and performed selection analyses to investigate directional selection on mean trait value at each field site and on the degree of plasticity of this trait to assess whether plastic responses were adaptive. In parallel, all populations were genotyped with microsatellite markers to assess neutral molecular differentiation. Molecular differentiation was high among populations within and among regions, indicating restricted gene flow among P. alpina populations. Reproductive biomass was highest in individuals grown in their region of origin, revealing local adaptation to coarse‐grained environmental variability. Similarly, inflorescence height, associated with reproductive biomass, reflected adaptation to fine‐ and coarse‐grained environmental variability. Furthermore, we found evidence that plasticity in SLA across coarse‐grained habitats was correlated with plant fitness, suggesting that plasticity in this trait is adaptive. Synthesis . Our results revealed adaptive genetic differentiation between P. alpina populations in the Swiss Alps reflecting local adaptation. Furthermore, high phenotypic plasticity in SLA contributed to the maintenance of fitness homoeostasis across habitats. Hence, adaptive genetic differentiation and phenotypic plasticity play a complementary role for adaption of P. alpina to environmental heterogeneity in the Swiss Alps and both may be critical to mitigate local extinction risk under rapid climate change.
PDK1 Determines Collagen-Dependent Platelet Ca 2+ Signaling and Is Critical to Development of Ischemic Stroke In Vivo
2016-06-24

Objective— Activation of platelets by subendothelial collagen results in an increase of cytosolic Ca 2+ concentration ([Ca 2+ ] i ) and is followed by platelet activation and thrombus formation that may lead to vascular occlusion. The present study determined the role of phosphoinositide-dependent protein kinase 1 (PDK1) in collagen-dependent platelet Ca 2+ signaling and ischemic stroke in vivo. Approach and Results— Platelet activation with collagen receptor glycoprotein VI agonists collagen-related peptide or convulxin resulted in a significant increase in PDK1 activity independent of second-wave signaling. PDK1 deficiency was associated with reduced platelet phospholipase Cγ2–dependent inositol-1,4,5-trisphosphate production and intracellular [Ca 2+ ] i in response to stimulation with collagen-related peptide or convulxin. The defective increase of [Ca 2+ ] i resulted in a substantial defect in activation-dependent platelet secretion and aggregation on collagen-related peptide stimulation. Furthermore, Rac1 activation and spreading, adhesion to collagen, and thrombus formation under high arterial shear rates were significantly diminished in PDK1-deficient platelets. Mice with PDK1-deficient platelets were protected against arterial thrombotic occlusion after FeCl 3 -induced mesenteric arterioles injury and ischemic stroke in vivo. These mice had significantly reduced brain infarct volumes, with a significantly increased survival of 7 days after transient middle cerebral artery occlusion without increase of intracerebral hemorrhage. Tail bleeding time was prolonged in pdk1 −/− mice, reflecting an important role of PDK1 in primary hemostasis. Conclusions— PDK1 is required for Ca 2+ -dependent platelet activation on stimulation of collagen receptor glycoprotein VI, arterial thrombotic occlusion, and ischemic stroke in vivo.
Task-Related Edge Density (TED)—A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain
2016-06-24

The formation of transient networks in response to external stimuli or as a reflection of internal cognitive processes is a hallmark of human brain function. However, its identification in fMRI data of the human brain is notoriously difficult. Here we propose a new method of fMRI data analysis that tackles this problem by considering large-scale, task-related synchronisation networks. Networks consist of nodes and edges connecting them, where nodes correspond to voxels in fMRI data, and the weight of an edge is determined via task-related changes in dynamic synchronisation between their respective times series. Based on these definitions, we developed a new data analysis algorithm that identifies edges that show differing levels of synchrony between two distinct task conditions and that occur in dense packs with similar characteristics. Hence, we call this approach "Task-related Edge Density" (TED). TED proved to be a very strong marker for dynamic network formation that easily lends itself to statistical analysis using large scale statistical inference. A major advantage of TED compared to other methods is that it does not depend on any specific hemodynamic response model, and it also does not require a presegmentation of the data for dimensionality reduction as it can handle large networks consisting of tens of thousands of voxels. We applied TED to fMRI data of a fingertapping and an emotion processing task provided by the Human Connectome Project. TED revealed network-based involvement of a large number of brain areas that evaded detection using traditional GLM-based analysis. We show that our proposed method provides an entirely new window into the immense complexity of human brain function.