julilili42/papers huggingface dataset:
Hydrodynamics of embedded planets’ first atmospheres – III. The role of radiation transport for super-Earth planets
2017-07-26

The population of close-in super-Earths, with gas mass fractions of up to 10 per cent represents a challenge for planet formation theory: how did they avoid runaway gas accretion and collapsing to hot Jupiters despite their core masses being in the critical range of Mc ≃ 10 M⊕? Previous three-dimensional (3D) hydrodynamical simulations indicate that atmospheres of low-mass planets cannot be considered isolated from the protoplanetary disc, contrary to what is assumed in 1D-evolutionary calculations. This finding is referred to as the recycling hypothesis. In this paper, we investigate the recycling hypothesis for super-Earth planets, accounting for realistic 3D radiation hydrodynamics. Also, we conduct a direct comparison in terms of the evolution of the entropy between 1D and 3D geometries. We clearly see that 3D atmospheres maintain higher entropy: although gas in the atmosphere loses entropy through radiative cooling, the advection of high-entropy gas from the disc into the Bondi/Hill sphere slows down Kelvin-Helmholtz contraction, potentially arresting envelope growth at a sub-critical gas mass fraction. Recycling, therefore, operates vigorously, in line with results by previous studies. However, we also identify an `inner core' - in size ≈25 per cent of the Bondi radius - where streamlines are more circular and entropies are much lower than in the outer atmosphere. Future studies at higher resolutions are needed to assess whether this region can become hydrodynamically isolated on long time-scales.
Voxel‐based magnetic resonance image postprocessing in epilepsy
2017-07-26

Summary Objective Although the general utility of voxel‐based processing of structural magnetic resonance imaging ( MRI ) data for detecting occult lesions in focal epilepsy is established, many differences exist among studies, and it is unclear which processing method is preferable. The aim of this study was to compare the ability of commonly used methods to detect epileptogenic lesions in magnetic resonance MRI ‐positive and MRI‐negative patients, and to estimate their diagnostic yield. Methods We identified 144 presurgical focal epilepsy patients, 15 of whom had a histopathologically proven and MRI ‐visible focal cortical dysplasia; 129 patients were MRI negative with a clinical hypothesis of seizure origin, 27 of whom had resections. We applied four types of voxel‐based morphometry ( VBM ), three based on T1 images (gray matter volume, gray matter concentration, junction map [ JM ]) and one based on normalized fluid‐attenuated inversion recovery ( nFSI ). Specificity was derived from analysis of 50 healthy controls. Results The four maps had different sensitivity and specificity profiles. All maps showed detection rates for focal cortical dysplasia patients ( MRI positive and negative) of &gt;30% at a strict threshold of p &lt; 0.05 (family‐wise error) and &gt;60% with a liberal threshold of p &lt; 0.0001 (uncorrected), except for gray matter volume (14% and 27% detection rate). All maps except nFSI showed poor specificity, with high rates of false‐positive findings in controls. In the MRI ‐negative patients, absolute detection rates were lower. A concordant nFSI finding had a significant positive odds ratio of 7.33 for a favorable postsurgical outcome in the MRI ‐negative group. Spatial colocalization of JM and nFSI was rare, yet showed good specificity throughout the thresholds. Significance All VBM variants had specific diagnostic properties that need to be considered for an adequate interpretation of the results. Overall, structural postprocessing can be a useful tool in presurgical diagnostics, but the low specificity of some maps has to be taken into consideration.
Automated Analysis of Flow Cytometry Data to Reduce Inter-Lab Variation in the Detection of Major Histocompatibility Complex Multimer-Binding T Cells
2017-07-26

Manual analysis of flow cytometry data and subjective gate-border decisions taken by individuals continue to be a source of variation in the assessment of antigen-specific T cells when comparing data across laboratories, and also over time in individual labs. Therefore, strategies to provide automated analysis of major histocompatibility complex (MHC) multimer-binding T cells represent an attractive solution to decrease subjectivity and technical variation. The challenge of using an automated analysis approach is that MHC multimer-binding T cell populations are often rare and therefore difficult to detect. We used a highly heterogeneous dataset from a recent MHC multimer proficiency panel to assess if MHC multimer-binding CD8<sup>+</sup> T cells could be analyzed with computational solutions currently available, and if such analyses would reduce the technical variation across different laboratories. We used three different methods, FLOw Clustering without K (FLOCK), Scalable Weighted Iterative Flow-clustering Technique (SWIFT), and ReFlow to analyze flow cytometry data files from 28 laboratories. Each laboratory screened for antigen-responsive T cell populations with frequency ranging from 0.01 to 1.5% of lymphocytes within samples from two donors. Experience from this analysis shows that all three programs can be used for the identification of high to intermediate frequency of MHC multimer-binding T cell populations, with results very similar to that of manual gating. For the less frequent populations (<0.1% of live, single lymphocytes), SWIFT outperformed the other tools. As used in this study, none of the algorithms offered a completely automated pipeline for identification of MHC multimer populations, as varying degrees of human interventions were needed to complete the analysis. In this study, we demonstrate the feasibility of using automated analysis pipelines for assessing and identifying even rare populations of antigen-responsive T cells and discuss the main properties, differences, and advantages of the different methods tested.
The BIF Domain in Plant bHLH Proteins Is an ACT-Like Domain
2017-07-26

Basic helix-loop-helix (bHLH) proteins, are important regulators of eukaryotic transcription and are particularly numerous in plants, playing roles in development and environmental responses ([Pires and Dolan, 2010][1]; [Feller et al., 2011][2]). Members of this family of transcription factors are
Ionization spectra of highly Stark-shifted rubidium Rydberg states
2017-07-26

We report on the observation and numerical calculation of ionization spectra\\nof highly Stark-shifted Rydberg states of rubidium beyond the classical\\nionization threshold. In the numerical calculations, a complex absorbing\\npotential (CAP) allows us to predict the energy levels and ionization rates of\\nRydberg states in this regime. Our approach of adjusting the CAP to the\\nexternal electric field reduces the number of free parameters from one per\\nresonance to a single one. Furthermore, we have measured the ionization spectra\\nof magneto-optically trapped rubidium atoms which are excited to principal\\nquantum numbers of 43 and 70 at various electric fields. The emerging ions are\\ndetected using an ion optics. We find good agreement between the numerically\\nand experimentally obtained spectra.\\n
External validation of a rectal cancer outcome prediction model with a cohort of patients treated with preoperative radiochemotherapy and deep regional hyperthermia
2017-07-26

The nomogram showed reasonable performance when deep regional hyperthermia is incorporated into preoperative therapy. The higher than predicted rates seen for OS and DMFS in particular in the high-risk groups warrant further prospective validation and subsequent investigation of the underlying mechanisms.
The wide genetic landscape of clinical frontotemporal dementia: systematic combined sequencing of 121 consecutive subjects
2017-07-27

PurposeTo define the genetic spectrum and relative gene frequencies underlying clinical frontotemporal dementia (FTD).MethodsWe investigated the frequencies and mutations in neurodegenerative disease genes in 121 consecutive FTD subjects using an unbiased, combined sequencing approach, complemented by cerebrospinal fluid Aβ<sub>1-42</sub> and serum progranulin measurements. Subjects were screened for C9orf72 repeat expansions, GRN and MAPT mutations, and, if negative, mutations in other neurodegenerative disease genes, by whole-exome sequencing (WES) (n = 108), including WES-based copy-number variant (CNV) analysis.ResultsPathogenic and likely pathogenic mutations were identified in 19% of the subjects, including mutations in C9orf72 (n = 8), GRN (n = 7, one 11-exon macro-deletion) and, more rarely, CHCHD10, TARDBP, SQSTM1 and UBQLN2 (each n = 1), but not in MAPT or TBK1. WES also unraveled pathogenic mutations in genes not commonly linked to FTD, including mutations in Alzheimer (PSEN1, PSEN2), lysosomal (CTSF, 7-exon macro-deletion) and cholesterol homeostasis pathways (CYP27A1).ConclusionOur unbiased approach reveals a wide genetic spectrum underlying clinical FTD, including 11% of seemingly sporadic FTD. It unravels several mutations and CNVs in genes and pathways hitherto not linked to FTD. This suggests that clinical FTD might be the converging downstream result of a delicate susceptibility of frontotemporal brain networks to insults in various pathways.
Prevalence and Distribution of Diabetes Mellitus in a Maximum Care Hospital: Urgent Need for HbA1c-Screening
2017-07-27

Abstract Objective Diabetes mellitus affects almost one in 10 individuals in Germany. So far, little is known about the diabetes prevalence in maximum care hospitals. We assessed the diabetes prevalence, proportion of undiagnosed cases, the effectiveness of diabetes screening in a university hospital, the consequences for hospital stay and acquired complications. Research Design and Methods Over a 4 week period we determined HbA1c from 3 733 adult patients which were hospitalized at the university hospital of Tuebingen and had an available blood sample. Diabetes diagnosis was defined as HbA1c≥6.5% and/or previously documented diabetes diagnosis, prediabetes was defined as HbA1c≥5.7% and &lt;6.5% without history of previous diabetes. Results 23.68% of the patients had prediabetes and 22.15% had diabetes with a high variation between the specialised departments (range 5–43%). The rate of unknown diabetes was 3.7%, the number needed to screen was 17 in patients older than 50 years. Patients with diabetes had a prolonged hospital stay compared to the mean length of stay for their diagnosis related group (diabetes: 1.47±0.24 days; no diabetes: −0.18±0.13 days, p=0.0133). The prevalence of hospital acquired complications was higher in diabetic patients (diabetes: 197 of 630; no diabetes: 447 of 2 459, p&lt;0.0001). Conclusions Every fourth patient in the university hospital had diabetes and every second had either prediabetes or diabetes. It is also worthwhile to screen for unknown diabetes in patients over the age of 50. The high prevalence and negative consequences of diabetes require screening and intensified specialized diabetes treatment in hospitals.
Neural correlates of moral judgment in pedophilia
2017-07-27

Pedophilia is a sexual preference that is often associated with child sex offending (CSO). Sexual urges towards prepubescent children and specifically acting upon those urges are universally regarded as immoral. However, up until now, it is completely unknown whether moral processing of sexual offenses is altered in pedophiles. A total of 31 pedophilic men and 19 healthy controls were assessed by using functional magnetic resonance imaging (fMRI) in combination with a moral judgment paradigm consisting of 36 scenarios describing different types of offenses.Scenarios depicting sexual offenses against children compared to those depicting adults were associated with higher pattern of activation in the left temporo-parietal-junction (TPJ) and left posterior insular cortex, the posterior cingulate gyrus as well as the precuneus in controls relative to pedophiles, and vice versa. Moreover, brain activation in these areas were positively associated with ratings of moral reprehensibility and negatively associated with decision durations, but only in controls. Brain activation, found in key areas related to the broad network of moral judgment, theory of mind and (socio-)moral disgust - point to different moral processing of sexual offenses in pedophilia in general. The lack of associations between brain activation and behavioral responses in pedophiles further suggest a biased response pattern or dissected implicit valuation processes.
DPP4 gene variation affects GLP-1 secretion, insulin secretion, and glucose tolerance in humans with high body adiposity
2017-07-27

A common variant, i.e., SNP rs6741949, in the DPP4 gene interacts with body adiposity and negatively affects glucose-stimulated GLP-1 levels, insulin secretion, and glucose tolerance. Whether this SNP underlies the reported inter-individual variance in responsiveness to DPP-4 inhibitors, at least in subjects with high body fat content, remains to be shown.
Planet-disc interaction in laminar and turbulent discs
2017-07-27

\\n In weakly ionised discs turbulence can be generated through the vertical shear instability (VSI). Embedded planets are affected by a stochastic component in the torques acting on them, which can impact their migration. In this work we study the interplay between a growing planet embedded in a protoplanetary disc and the VSI turbulence. We performed a series of 3D hydrodynamical simulations for locally isothermal discs with embedded planets in the mass range from 5 to 100 Earth masses. We study planets embedded in an inviscid disc that is VSI unstable, becomes turbulent, and generates angular momentum transport with an effective α = 5 × 10-4. This is compared to the corresponding viscous disc using exactly this α-value. In general we find that the planets have only a weak impact on the disc turbulence. Only for the largest planet (100 M⊕) does the turbulent activity become enhanced inside of the planet. The depth and width of a gap created by the more massive planets (30,100 M⊕) in the turbulent disc equal exactly that of the corresponding viscous case, leading to very similar torque strengths acting on the planet, with small stochastic fluctuations for the VSI disc. At the gap edges vortices are generated that are stronger and longer-lived in the VSI disc. Low mass planets (with Mp ≤ 10 M⊕) do not open gaps in the disc in either case, but generate for the turbulent disc an overdensity behind the planet that exerts a significant negative torque. This can boost the inward migration in VSI turbulent discs well above the Type I rate. Owing to the finite turbulence level in realistic 3D discs the gap depth will always be limited and migration will not stall in inviscid discs. \\n
Hitting probabilities for the Greenwood model and relations to near constancy oscillation
2017-07-27

We derive some properties of the Greenwood epidemic Galton–Watson branching model. Formulas for the probability that the associated Markov chain hits state when started from state are obtained. For , it follows that slightly oscillates with varying and has infinitely many accumulation points. In particular, does not converge as . It is shown that there exists a Markov chain which is Siegmund dual to the chain . The hitting probabilities of the dual Markov chain are investigated.
Beyond Logic. Proceedings of the Conference held in Cerisy-la-Salle, 22-27 May 2017
2017-07-27

The project "Beyond Logic" is devoted to what hypothetical reasoning is all about when we go beyond the realm of "pure" logic into the world where logic is applied. As such extralogical areas we have chosen philosophy of science as an application within philosophy, informatics as an application within the formal sciences, and law as an application within the field of social interaction. The aim of the conference was to allow philosophers, logicians and computer scientists to present their work in connection with these three areas. The conference took place 22-27 May, 2017 in Cerisy-la-Salle at the Centre Culturel International de Cerisy. The proceedings collect abstracts, slides and papers of the presentations given, as well as a contribution from a speaker who was unable to attend.
SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution
2017-07-27

ABSTRACT Summary Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-friendly SplitsTree software package. However, to give the user the option to adjust and extend these approaches and to facilitate their integration into analysis pipelines, there is a need for robust, open-source implementations of associated data structures and algorithms. Here we present SPECTRE, a readily available, open-source library of data structures written in Java, that comes complete with new implementations of several pre-published algorithms and a basic interactive graphical interface for visualizing planar split networks. SPECTRE also supports the use of longer running algorithms by providing command line interfaces, which can be executed on servers or in High Performance Computing (HPC) environments. Availability Full source code is available under the GPLv3 license at: https://github.com/maplesond/SPECTRE SPECTRE’s core library is available from Maven Central at: https://mvnrepository.com/artifactuk.ac.uea.cmp.spectre/core Documentation is available at: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/ Contact sarah.bastkowski@earlham.ac.uk Supplementary Information (SI) Supplementary information is available at Bioinformatics online.
Fibroblast Growth Factor 21—Metabolic Role in Mice and Men
2017-07-28

Since its identification in 2000, the interest of scientists in the hepatokine fibroblast growth factor (FGF) 21 has tremendously grown, and still remains high, due to a wealth of very robust data documenting this factor's favorable effects on glucose and lipid metabolism in mice. For more than ten years now, intense in vivo and ex vivo experimentation addressed the physiological functions of FGF21 in humans as well as its pathophysiological role and pharmacological effects in human metabolic disease. This work produced a comprehensive collection of data revealing overlaps in FGF21 expression and function but also significant differences between mice and humans that have to be considered before translation from bench to bedside can be successful. This review summarizes what is known about FGF21 in mice and humans with a special focus on this factor's role in glucose and lipid metabolism and in metabolic diseases, such as obesity and type 2 diabetes mellitus. We highlight the discrepancies between mice and humans and try to decipher their underlying reasons.
Genomic insights into specialized metabolism in the marine actinomycete Salinispora
2017-07-28

Summary Comparative genomics is providing new opportunities to address the diversity and distributions of genes encoding the biosynthesis of specialized metabolites. An analysis of 119 genome sequences representing three closely related species of the marine actinomycete genus Salinispora reveals extraordinary biosynthetic diversity in the form of 176 distinct biosynthetic gene clusters (BGCs) of which only 24 have been linked to their products. Remarkably, more than half of the BGCs were observed in only one or two strains, suggesting they were acquired relatively recently in the evolutionary history of the genus. These acquired gene clusters are concentrated in specific genomic islands, which represent hot spots for BGC acquisition. While most BGCs are stable in terms of their chromosomal position, others migrated to different locations or were exchanged with unrelated gene clusters suggesting a plug and play type model of evolution that provides a mechanism to test the relative fitness effects of specialized metabolites. Transcriptome analyses were used to address the relationships between BGC abundance, chromosomal position and product discovery. The results indicate that recently acquired BGCs can be functional and that complex evolutionary processes shape the micro‐diversity of specialized metabolism observed in closely related environmental bacteria.
Ultra compact stars: reconstructing the perturbation potential
2017-07-28

In this work we demonstrate how different semi-classical methods can be\\ncombined in a novel way to reconstruct the perturbation potential of ultra\\ncompact stars. Besides rather general assumptions, the only specific\\ninformation entering this approach is the spectrum of the \\naxial quasi-normal modes. In general it is not possible to find a unique\\nsolution for the potential in the inverse problem, but instead a family of\\npotentials producing the same spectrum. Nevertheless, this already determines\\nimportant properties of the involved potential and can be used to rule out many\\ncandidate models. A unique solution was found based on the additional natural\\nassumption that the exterior part ( ) is described by the\\nRegge-Wheeler potential. This is true in general relativity for any\\nnon-rotating spherically symmetric object. This technique can be potentially\\napplied for the study of deviations from general relativity. The methods we\\ndemonstrate are easy to implement and rather general, therefore we expect them\\nalso to be interesting for other fields where inverse spectrum problems are\\nstudied, e.g. quantum physics and molecular spectroscopy.\\n
ADPase CD39 Fused to Glycoprotein VI‐Fc Boosts Local Antithrombotic Effects at Vascular Lesions
2017-07-28

Background GPVI (Glycoprotein VI) is the essential platelet collagen receptor in atherothrombosis. Dimeric GPVI ‐Fc (Revacept) binds to GPVI binding sites on plaque collagen. As expected, it did not increase bleeding in clinical studies. GPVI ‐Fc is a potent inhibitor of atherosclerotic plaque‐induced platelet aggregation at high shear flow, but its inhibition at low shear flow is limited. We sought to increase the platelet inhibitory potential by fusing GPVI ‐Fc to the ectonucleotidase CD 39 (fusion protein GPVI‐CD39), which inhibits local ADP accumulation at vascular plaques, and thus to create a lesion‐directed dual antiplatelet therapy that is expected to lack systemic bleeding risks. Methods and Results GPVI ‐ CD 39 effectively stimulated local ADP degradation and, compared with GPVI ‐Fc alone, led to significantly increased inhibition of ADP ‐, collagen‐, and human plaque–induced platelet aggregation in Multiplate aggregometry and plaque‐induced platelet thrombus formation under arterial flow conditions. GPVI ‐ CD 39 did not increase bleeding time in an in vitro assay simulating primary hemostasis. In a mouse model of ferric chloride–induced arterial thrombosis, GPVI ‐ CD 39 effectively delayed vascular thrombosis but did not increase tail bleeding time in vivo. Conclusions GPVI‐CD39 is a novel approach to increase local antithrombotic activity at sites of atherosclerotic plaque rupture or injury. It enhances GPVI ‐Fc–mediated platelet inhibition and presents a potentially effective and safe molecule for the treatment of acute atherothrombotic events, with a favorable risk–benefit ratio.