julilili42/papers huggingface dataset:
Multi‐trophic guilds respond differently to changing elevation in a subtropical forest
2017-09-07

Negative relationships between species richness and elevation are common and attributed to changes in single environmental properties associated to elevation, such as temperature and habitat area. However, research has lacked taxonomic breadth and comprehensive elevation studies that consider multiple groups from different trophic levels are rare. We thus analysed 24 groups of plants, arthropods, and microorganisms grouped into six trophic guilds (predators, detritivores, herbivores, plants, bacteria and fungi) along a relatively short elevational gradient (~600 m) in a subtropical forest in south‐east China. The total species richness of all organisms was not related to elevation, nor was the richness of plants, herbivores or microorganisms. However, species richness and abundance in two major trophic guilds of arthropods changed with elevation, which was mediated by changes in elevation‐associated habitat properties. Specifically, deadwood mass increased with elevation, which increased detritivore richness indirectly via detritivore abundance, thus supporting the ‘more individuals hypothesis’. In contrast, lower predator richness at higher elevations was directly related to lower mean temperatures, which had no effect on abundance. Our study demonstrates that even along relatively short gradients, elevation can have strong direct and abundance‐mediated effects on species richness, but with effects varying from positive to negative signs depending on local resource availability and the characteristics of groups or trophic guilds. If elevation positively influences local environmental properties that benefit a given group, richness can increase towards higher elevations. Thus, the effect of global change in mountainous regions should be evaluated within the local environmental context using multi‐taxon approaches.
Effects of Sleep on Word Pair Memory in Children – Separating Item and Source Memory Aspects
2017-09-07

Word paired-associate learning is a well-established task to demonstrate sleep-dependent memory consolidation in adults as well as children. Sleep has also been proposed to benefit episodic features of memory, i.e., a memory for an event (item) bound into the spatiotemporal context it has been experienced in (source). We aimed to explore if sleep enhances word pair memory in children by strengthening the episodic features of the memory, in particular. Sixty-one children (8-12 years) studied two lists of word pairs with 1 h in between. Retrieval testing comprised cued recall of the target word of each word pair (item memory) and recalling in which list the word pair had appeared in (source memory). Retrieval was tested either after 1 h (short retention interval) or after 11 h, with this long retention interval covering either nocturnal sleep or daytime wakefulness. Compared with the wake interval, sleep enhanced separate recall of both word pairs and the lists <i>per se</i>, while recall of the combination of the word pair and the list it had appeared in remained unaffected by sleep. An additional comparison with adult controls (<i>n</i> = 37) suggested that item-source bound memory (combined recall of word pair and list) is generally diminished in children. Our results argue against the view that the sleep-induced enhancement in paired-associate learning in children is a consequence of sleep specifically enhancing the episodic features of the memory representation. On the contrary, sleep in children might strengthen item and source representations in isolation, while leaving the episodic memory representations (item-source binding) unaffected.
Dopamine oxidation mediates mitochondrial and lysosomal dysfunction in Parkinson’s disease
2017-09-08

Human-derived neurons provide the answers Pathways involved in energy metabolism and removal of cellular debris by lysosomes play an important role in protecting our brain from degeneration in Parkinson's disease. Burbulla et al. identified a toxic cascade of mitochondrial and lysosomal dysfunction in human neurons derived from patients with Parkinson's. The dysfunction was mediated by accumulation of oxidized dopamine and α-synuclein, but it was not found in Parkinson's mouse models, owing to species-specific differences in dopamine metabolism. Inherent species-specific differences between human and mouse neurons emphasize the value of studying human neurons to identify relevant targets for treatment of Parkinson's disease and related synucleinopathies. Science , this issue p. 1255
The impact of vessel size, orientation and intravascular contribution on the neurovascular fingerprint of BOLD bSSFP fMRI
2017-09-08

Monte Carlo simulations have been used to analyze oxygenation-related signal changes in pass-band balanced steady state free precession (bSSFP) as well as in gradient echo (GE) and spin echo (SE) sequences. Signal changes were calculated for artificial cylinders and neurovascular networks acquired from the mouse parietal cortex by two-photon laser scanning microscopy at 1 μm isotropic resolution. Signal changes as a function of vessel size, blood volume, vessel orientation to the main magnetic field B<sub>0</sub> as well as relations of intra- and extravascular and of micro- and macrovascular contributions have been analyzed. The results show that bSSFP is highly sensitive to extravascular and microvascular components. Furthermore, GE and bSSFP, and to a lesser extent SE, exhibit a strong dependence of their signal change on the orientation of the vessel network to B<sub>0</sub>.
Differential Enzymatic 16O/18O Labeling for the Detection of Cross-Linked Nucleic Acid–Protein Heteroconjugates
2017-09-08

Cross-linking of nucleic acids to proteins in combination with mass spectrometry permits the precise identification of interacting residues between nucleic acid-protein complexes. However, the mass spectrometric identification and characterization of cross-linked nucleic acid-protein heteroconjugates within a complex sample is challenging. Here we establish a novel enzymatic differential <sup>16</sup>O/<sup>18</sup>O-labeling approach, which uniquely labels heteroconjugates. We have developed an automated data analysis workflow based on OpenMS for the identification of differentially isotopically labeled heteroconjugates against a complex background. We validated our method using synthetic model DNA oligonucleotide-peptide heteroconjugates, which were subjected to the labeling reaction and analyzed by high-resolution FTICR mass spectrometry.
A rainfall-manipulation experiment with 517Arabidopsis thalianaaccessions
2017-09-10

The gold standard for studying natural selection and adaptation in the wild is to quantify lifetime fitness of individuals from natural populations that have been grown together in a common garden, or that have been reciprocally transplanted. By combining fitness values with species traits and genome sequences, one can infer selection coefficients at the genetic level. Here we present a rainfall-manipulation experiment with 517 whole-genome sequenced natural accessions of the plant Arabidopsis thaliana spanning the global distribution of the species. The experiments were conducted in two field stations in contrasting climates, in the Mediterranean and in Central Europe, where we built rainout shelters and simulated high and low rainfall. Using custom image analysis we quantified fitness- and phenology-related traits for 23,154 pots, which contained about 14,500 plants growing independently, and over 310,000 plants growing in small populations (max. 30 plants). This large field experiment dataset, which associates fitness and ecologically-relevant traits with genomes, will provide an important resource to test eco-evolutionary genetic theories and to understand the potential evolutionary impacts of future climates on an important plant model species.
Immune mechanisms in heart failure
2017-09-11

Elevated levels of circulating pro‐inflammatory biomarkers in patients with both ischaemic and non‐ischaemic heart failure (HF) correlate with disease severity and prognosis. Experimental studies have shown activation of immune response mechanisms in the heart to provoke cardiac adverse remodelling and cause left ventricular dysfunction. Consequently, most of the clinical trials targeting elements of the immune response in HF attempted to modulate the inflammatory response. Surprisingly, clinical studies targeting immune effectors were either neutral or even increased pre‐specified clinical endpoints, and some studies resulted in worsening of HF. This review discusses immune mediators involved in the pathogenesis and progression of HF and potential therapeutic applications targeting inflammation in HF. Besides more obvious settings featuring immune activation such as inflammatory or ischaemic cardiomyopathy, the relevance of immune activation in acute or chronic HF of other origins, including volume overload or valvular heart disease, is highlighted. Understanding how cell‐specific and molecular mechanisms of the immune response interfere with cardiac remodelling in HF may open new avenues to design biomarkers or druggable targets.
Identifying actionable variants using next generation sequencing in patients with a historical diagnosis of undifferentiated pleomorphic sarcoma
2017-09-11

There are limited data regarding the molecular characterization of undifferentiated pleomorphic sarcomas (UPS; formerly malignant fibrous histiocytoma). This study aimed to investigate the utility of next generation sequencing (NGS) in UPS to identify subsets of patients who harbour actionable mutations. Patients diagnosed with UPS underwent pathological re‐evaluation by a pathologist specializing in sarcoma. Tumor DNA was isolated from archived fresh frozen tissue samples and genotyped using NGS with the Illumina MiSeq TruSeq Amplicon Cancer Panel (48 genes, 212 amplicons). In total, 95 patients initially classified with UPS were identified. Following pathology re‐review the histological subtypes were reclassified to include: Myxofibrosarcoma (MFS, N = 44); UPS( N = 18); and Others ( N = 27; including undifferentiated spindle cell sarcoma ( N = 15) and dedifferentiated liposarcoma ( N = 6)). Seven cases were excluded from further analysis for other reasons. Baseline demographics of the finalized cohort ( N = 88) showed a median age of 66 years (32–95), primarily with stage I–III disease (92%) and high‐grade (86%) lesions. Somatic mutations were identified in 31 cases (35%)(Total mutations = 36: solitary mutation( n = 27); two mutations( = n = 3); three mutations( n = 1)). The most commonly identified mutations were in TP53 ( n = 24), ATM ( n = 3) and PIK3CA (n = 2 ) . Three of 43 patients with MFS and one of 18 patients with UPS had clinically relevant mutations, mainly related to biomarkers of prediction of response; however few had targetable driver mutations. Somatic mutation status did not influence disease free or overall survival. Based on the small number of clinically relevant mutations, these data do not support the routine use of targeted NGS panels outside of research protocols in UPS.
An open‐source biomass pyrolysis reactor
2017-09-11

Abstract Despite its long history of technological development, much charcoal production still relies on polluting and inefficient technologies utilizing traditional kiln designs. In addition to the need for improved charcoal production systems, the growing interest globally in pyrolysis of biomass to generate biochar as a soil fertility improver and for climate change mitigation may drive an increasing demand for such technologies. Accordingly, there is a clear need in developing countries for access to safe, affordable, and efficient open‐source designs and technology that can be fabricated locally. The design described here includes computational fluid dynamics modeling which demonstrated that the design exhibits a stable flow and combustion pattern. A hazard and operability (HAZOP) study, mass and energy modeling, and costing of all components and fabrication were also conducted for a prototype kiln that will accept up to 250 kg biomass h ‐1 . Fabrication and installation costs were estimated using actual commercial quotations based on detailed engineering drawings and design, and were found to be $580 000 for a 250 kg h ‐1 unit. We therefore find that this pyrolysis system promises to be economical on a small scale. It can utilize waste lignocellulosic materials for feedstock, thus alleviating demand pressure on woodlands to provide feedstocks. It was, therefore, concluded that the pyrolysis unit described here promises to provide an affordable and efficient open‐source design that can be fabricated locally in developing countries without licensing restrictions or royalties. © 2017 The Authors Biofuels, Bioproducts and Biorefining published by Society of Industrial Chemistry and John Wiley &amp; Sons Ltd
Geometric analysis of loco-regional recurrences in relation to pre-treatment hypoxia in patients with head and neck cancer
2017-09-11

Our data suggest that loco-regional recurrences after RCT originate from the initial GTV (primary tumor and/or lymph node metastases) containing hypoxic subvolumes, which supports the concept of hypoxia imaging-based dose escalation.
An important question: Which LPS do you use?
2017-09-11

During the last decade the invertebrate Galleria mellonella has successfully been used as a powerful and reliable model host for the analysis of bacterial pathogenesis as it offers an inexpensive a...
Adrenarche in Silver-Russell Syndrome: Timing and Consequences
2017-09-11

Early or premature adrenarche was more frequent in SRS than in the general population and was associated with early age at initiation of rhGH treatment. Response to rhGH treatment and adult height were not compromised by early adrenarche.
A Curious Problem with Using the Colour Checker Dataset for Illuminant Estimation
2017-09-11

In illuminant estimation, we attempt to estimate the RGB of the light. We then use this estimate on an image to correct for the light's colour bias. Illuminant estimation is an essential component of all camera reproduction pipelines. How well an illuminant estimation algorithm works is determined by how well it predicts the ground truth illuminant colour. Typically, the ground truth is the RGB of a white surface placed in a scene. Over a large set of images an estimation error is calculated and different algorithms are then ranked according to their average estimation performance. Perhaps the most widely used publically available dataset used in illuminant estimation is Gehler's Colour Checker set that was reprocessed by Shi and Funt. This image set comprises 568 images of typical everyday scenes. Curiously, we have found three different ground truths for the Shi-Funt Colour Checker image set. In this paper, we investigate whether adopting one ground truth over another results in different rankings of illuminant estimation algorithms. We find that, depending on the ground truth used, the ranking of different algorithms can change, and sometimes dramatically. Indeed, it is entirely possible that much of the recent 'advances' made in illuminant estimation were achieved because authors have switched to using a ground truth where better estimation performance is possible.
XMM–Newton study of the supersoft symbiotic system Draco C1
2017-09-11

We present the results of the analysis of thirty-one XMM–Newton observations of the symbiotic star Draco C1 located in the Draco dwarf spheroidal galaxy. This object had been identified as a supersoft source based on ROSAT data. We analysed X-ray, ultraviolet (UV) and optical data taken with XMM–Newton in order to obtain the physical parameters and the geometry of the system. We have also performed the first X-ray timing analysis of Draco C1. The X-ray spectrum is well fitted with a blackbody model with a temperature of (1.8 ± 0.3) × 105 K. We obtained a bolometric luminosity of ≳1038 erg s−1 for the white dwarf. The X-ray spectrum and luminosity suggest stable nuclear burning on the surface of the white dwarf. The low column density derived from the X-ray spectrum is consistent with the lack of nebular lines found in previous UV studies. The long-term variability in the optical and the UV suggests that the system is not observed face-on and that the variability is caused by the reflection effect. For the red giant companion, we estimate a radius of ∼110 R⊙ and an upper limit ≲1.5 M⊙ for its mass assuming Roche lobe overflow.
Cytokinesis: Membrane Trafficking by Default?
2017-09-11

Abstract The sections in this article are Introduction A Dynamic View of Cell Plate Formation Formation of Cytokinetic Vesicles Delivery of Cytokinetic Vesicles Vesicle Fusion in the Plane of Cell Division What Determines the Specificity of Cytokinetic Vesicle Trafficking? How Can Cytokinesis be Carried out So Fast? Concluding Remarks
Phenol-Soluble Modulin Peptides Contribute to Influenza A Virus-Associated Staphylococcus aureus Pneumonia
2017-09-12

ABSTRACT Influenza A virus (IAV) infection is often followed by secondary bacterial lung infection, which is a major reason for severe, often fatal pneumonia. Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains such as USA300 cause particularly severe and difficult-to-treat cases of IAV-associated pneumonia. CA-MRSA strains are known to produce extraordinarily large amounts of phenol-soluble modulin (PSM) peptides, which are important cytotoxins and proinflammatory molecules that contribute to several types of S. aureus infection. However, their potential role in pneumonia has remained elusive. We determined the impact of PSMs on human lung epithelial cells and found that PSMs are cytotoxic and induce the secretion of the proinflammatory cytokine interleukin-8 (IL-8) in these cells. Both effects were boosted by previous infection with the 2009 swine flu pandemic IAV H1N1 strain, suggesting that PSMs may contribute to lung inflammation and damage in IAV-associated S. aureus pneumonia. Notably, the PSM-producing USA300 strain caused a higher mortality rate than did an isogenic PSM-deficient mutant in a mouse IAV- S. aureus pneumonia coinfection model, indicating that PSMs are major virulence factors in IAV-associated S. aureus pneumonia and may represent important targets for future anti-infective therapies.
Correlative Microscopy Combining Secondary Ion Mass Spectrometry and Electron Microscopy: Comparison of Intensity–Hue–Saturation and Laplacian Pyramid Methods for Image Fusion
2017-09-13

Correlative microscopy combining various imaging modalities offers powerful insights into obtaining a comprehensive understanding of physical, chemical, and biological phenomena. In this article, we investigate two approaches for image fusion in the context of combining the inherently lower-resolution chemical images obtained using secondary ion mass spectrometry (SIMS) with the high-resolution ultrastructural images obtained using electron microscopy (EM). We evaluate the image fusion methods with three different case studies selected to broadly represent the typical samples in life science research: (i) histology (unlabeled tissue), (ii) nanotoxicology, and (iii) metabolism (isotopically labeled tissue). We show that the intensity-hue-saturation fusion method often applied for EM-sharpening can result in serious image artifacts, especially in cases where different contrast mechanisms interplay. Here, we introduce and demonstrate Laplacian pyramid fusion as a powerful and more robust alternative method for image fusion. Both physical and technical aspects of correlative image overlay and image fusion specific to SIMS-based correlative microscopy are discussed in detail alongside the advantages, limitations, and the potential artifacts. Quantitative metrics to evaluate the results of image fusion are also discussed.
Frequent genes in rare diseases: panel‐based next generation sequencing to disclose causal mutations in hereditary neuropathies
2017-09-13

Abstract Hereditary neuropathies comprise a wide variety of chronic diseases associated to more than 80 genes identified to date. We herein examined 612 index patients with either a Charcot‐Marie‐Tooth phenotype, hereditary sensory neuropathy, familial amyloid neuropathy, or small fiber neuropathy using a customized multigene panel based on the next generation sequencing technique. In 121 cases (19.8%), we identified at least one putative pathogenic mutation. Of these, 54.4% showed an autosomal dominant, 33.9% an autosomal recessive, and 11.6% an X‐linked inheritance. The most frequently affected genes were PMP 22 (16.4%), GJB 1 (10.7%), MPZ , and SH 3 TC 2 (both 9.9%), and MFN 2 (8.3%). We further detected likely or known pathogenic variants in HINT 1, HSPB 1, NEFL , PRX , IGHMBP 2, NDRG 1, TTR , EGR 2, FIG 4, GDAP 1, LMNA , LRSAM 1, POLG , TRPV 4, AARS , BIC 2, DHTKD 1, FGD 4, HK 1, INF 2, KIF 5A, PDK 3, REEP 1, SBF 1, SBF 2, SCN 9A, and SPTLC 2 with a declining frequency. Thirty‐four novel variants were considered likely pathogenic not having previously been described in association with any disorder in the literature. In one patient, two homozygous mutations in HK 1 were detected in the multigene panel, but not by whole exome sequencing. A novel missense mutation in KIF 5A was considered pathogenic because of the highly compatible phenotype. In one patient, the plasma sphingolipid profile could functionally prove the pathogenicity of a mutation in SPTLC 2 . One pathogenic mutation in MPZ was identified after being previously missed by Sanger sequencing. We conclude that panel based next generation sequencing is a useful, time‐ and cost‐effective approach to assist clinicians in identifying the correct diagnosis and enable causative treatment considerations. image
Two‐Branch Break‐up Systems by a Single Mantle Plume: Insights from Numerical Modeling
2017-09-13

Abstract Thermomechanical modeling of plume‐induced continental break‐up reveals that the initial location of a mantle anomaly relative to a lithosphere inhomogeneity has a major impact on the geometry and timing of a rift‐to‐spreading system. Models with a warmer Moho temperature are more likely to result in “plume‐centered” mode, where the rift and subsequent spreading axis grow directly above the plume. Models with weak far‐field forcing are inclined to develop a “structural‐inherited” mode, with lithosphere deformation localized at the lateral lithospheric boundary. Models of a third group cultivate two break‐up branches (both “plume‐centered” and “structural inherited”) that form consecutively with a few million years delay. With our experimental setup, this break‐up mode is sensitive to relatively small lateral variations of the initial anomaly position. We argue that one single mantle anomaly can be responsible for nonsimultaneous initiation and development of two rift‐to‐spreading systems in a lithosphere with a lateral strength contrast.