pinecone/core-2020-05-10-deduplication huggingface dataset:
Intracluster light properties in the CLASH-VLT cluster MACS J1206.2-0847

International audienceAims. We aim constrain the assembly history of clusters by studying the intracluster light (ICL) properties, estimating its contribution to the fraction of baryons in stars, f∗, and understanding possible systematics or bias using different ICL detection techniques.Methods. We developed an automated method, GALtoICL, based on the software GALAPAGOS, to obtain a refined version of typical BCG+ICL maps. We applied this method to our test case MACS J1206.2-0847, a massive cluster located at z ~ 0.44, which is part of the CLASH sample. Using deep multiband Subaru images, we extracted the surface brightness (SB) profile of the BCG+ICL and studied the ICL morphology, color, and contribution to f∗ out to R500. We repeated the same analysis using a different definition of the ICL, SBlimit method, i.e., a SB cut-off level, to compare the results.Results. The most peculiar feature of the ICL in MACS1206 is its asymmetric radial distribution, with an excess in the SE direction and extending toward the second brightest cluster galaxy, which is a post starburst galaxy. This suggests an interaction between the BCG and this galaxy that dates back to τ ≤ 1.5 Gyr. The BCG+ICL stellar content is ~8% of M∗,500, and the (de-) projected baryon fraction in stars is f∗ = 0.0177(0.0116), in excellent agreement with recent results. The SBlimit method provides systematically higher ICL fractions and this effect is stronger at lower SB  limits. This is due to the light from the outer envelopes of member galaxies that contaminate the ICL. Though more time consuming, the GALtoICL method provides safer ICL detections that are almost free of this contamination. This is one of the few ICL study at redshift z > 0.3. At completion, the CLASH/VLT program will allow us to extend this analysis to a statistically significant cluster sample spanning a wide redshift range: 0.2 ≲ z ≲ 0.6
Long-Term Durum Wheat-Based Cropping Systems Result in the Rapid Saturation of Soil Carbon in the Mediterranean Semi-arid Environment

Climate, soil physical-chemical characteristics, land management, and carbon (C) input from crop residues greatly affect soil organic carbon (SOC) sequestration. According to the concept of SOC saturation, the ability of SOC to increase with C input decreases as SOC increases and approaches a SOC saturation level. In a 12-year experiment, six semi-arid cropping systems characterized by different rates of C input to soil were compared for ability to sequester SOC, SOC saturation level, and the time necessary to reach the SOC saturation level. SOC stocks, soil aggregate sizes, and C inputs were measured in durum wheat monocropping with (Ws) and without (W) return of aboveground residue to the soil and in the following cropping systems without return of aboveground residue to soil: durum wheat/fallow (Wfall), durum wheat/berseem clover, durum wheat/barley/faba bean, and durum wheat/Hedysarum coronarium. The C sequestration rate and SOC content were lowest in Wfall plots but did not differ among the other cropping systems. The C sequestration rate ranged from 0.47MgC ha-1y-1 in Ws plots to 0.66MgCha-1y-1 in W plots but was negative (-0.06MgCha-1y-1) in Wfall plots. Increases in SOC were related to C input up to a SOC saturation value; over this value, further C inputs did not lead to SOC increase. Across all cropping systems, the C saturation value for the experimental soil was 57.7Mgha-1, which was reached with a cumulative C input of 15Mgha-1
Polymerization of lignosulfonates by the laccase-HBT (1-hydroxybenzotriazole) system improves dispersibility

The ability of laccases from Trametes villosa (TvL), Myceliophthora thermophila (MtL), Trametes hirsuta (ThL) and Bacillus subtilis (BsL) to improve the dispersion properties of calcium lignosulfonates 398 in the presence of HBT as a mediator was investigated. Size exclusion chromatography showed an extensive increase in molecular weight of the samples incubated with TvL and ThL by 107% and 572% from 28400 Da after 17 h of incubation, respectively. Interestingly, FTIR spectroscopy, 13C NMR and Py-GC/MS analysis of the treated samples suggested no substantial changes in the aromatic signal of the lignosulfonates, a good indication of the ability of TvL/ThL-HBT systems to limit their effect on functional groups without degrading the lignin backbone. Further, the enzymatic treatments led to a general increase in the dispersion properties, indeed a welcome development for its application in polymer blends.Financial support from the BIORENEW EU-project (NMP2-CT-2006-26456), Austrian Academic Exchange Programme (OEAD) and the Spanish projects BIO2007-28720-E, BIO2008-01533, and AGL2008-00709 is acknowledged
Production of curcuminoids from tyrosine by a metabolically engineered Escherichia coli using caffeic acid as an intermediate

Curcuminoids are phenylpropanoids with high pharmaceutical potential. Herein, we report an engineered artificial pathway in Escherichia coli to produce natural curcuminoids through caffeic acid. Arabidopsis thaliana 4-coumaroyl-CoA ligase (4CL1) and Curcuma longa diketide-CoA synthase (DCS) and curcumin synthase (CURS1) were used to produce curcuminoids and 70 mg/L of curcumin was obtained from ferulic acid. Bisdemethoxycurcumin and demethoxycurcumin were also produced, but in lower concentrations, by feeding p-coumaric acid or a mixture of p-coumaric acid and ferulic acid, respectively. Additionally, curcuminoids were produced from tyrosine through the caffeic acid pathway. To produce caffeic acid, tyrosine ammonia lyase (TAL) from Rhodotorula glutinis and 4-coumarate 3-hydroxylase (C3H) from Saccharothrix espanaensis were used. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) from Medicago sativa was used to convert caffeoyl-CoA to feruloyl-CoA. Using caffeic acid, p-coumaric acid or tyrosine as a substrate, 3.9 mg/L, 0.3 mg/L and 0.2 mg/L of curcumin were produced, respectively. This is the first time DCS and CURS1 were used in vivo to produce curcuminoids and that curcumin was produced by feeding tyrosine. We have shown that curcumin can be produced using a pathway through caffeic acid. This alternative pathway represents a step forward in the heterologous production of curcumin using E. coli.This work was supported by FEDER funds through the COMPETE and ON2 program and through National funds of FCT in the scope of the project FCOMP-01-0124-FEDER-027462, PEst-OE/EQB/LA0023/2013, NORTE-07-0124-FEDER-000028, and NORTE-07-0124-FEDER-000027. Financial support for this work was provided by FCT grant SFRH/BD/51187/2010 and SYNBIOBACTHER project (PTDC/EBB-BIO/102863/2008)
Comparing palliative care in care homes across Europe (PACE) : protocol of a cross-sectional study of deceased residents in 6 EU countries

Objectives: Although a growing number of older people are dying in care homes, palliative care has developed in these settings only recently. Cross-country representative comparative research hardly exists in this area. As part of a large EU-funded project, we aim to undertake representative comparative research in care homes in Europe, to describe and compare 6 countries in terms of (1) resident outcomes, quality and costs of palliative and end-of-life care; and (2) palliative care structures and staff knowledge and attitudes toward palliative care. We also aim to explore country, facility, staff, patient, and care characteristics related to better outcomes at resident level. 

Design and Methods: To obtain a representative nationwide sample, we will conduct a large-scale cross-sectional study of deceased residents in care homes in Belgium, Finland, Italy, the Netherlands, Poland, and the United Kingdom, using proportional stratified random sampling (taking into account region, facility type and bed capacity). In each country, all participating care homes retrospectively report all deaths of residents in and outside the facilities over the previous 3-month period. For each case, structured questionnaires, including validated instruments, are sent to (1) the administrator/manager, (2) staff member most involved in care, (3) treating physician (general practitioner or elderly care physician), and (4) a closely involved relative. It is estimated that, per country, 50 care homes are needed on average to obtain a minimum of 200 deceased residents. Collected data include clinical and socio-demographic characteristics, quality of dying, quality and costs of palliative care and end-of-life care, and palliative care structures at the facility level and country level. To obtain a representative view of staff knowledge and attitudes regarding palliative care, PACE will conduct a cross-sectional study of staff working in the participating care homes. 

Conclusion: Considering the growing challenges associated with aging in all European countries, there is an urgent need to build a robust international comparative evidence base that can inform the development of policies to target improved palliative care in care homes. By describing this research protocol, we hope to inform international research in care homes on how to perform representative end-of-life care research in these settings and better understand which systems are associated with better outcomes
Aspects of the UV/IR correspondence: energy broadening and string fluctuations

We show that a source which radiates in the vacuum of the strongly coupled N = 4=4 SYM theory produces an energy distribution which, in the supergravity approximation, has the same space-time pattern as the corresponding classical distribution: the radiation propagates at the speed of light without broadening. We illustrate this on the basis of several examples: a small perturbation propagating down a steady string, a massless particle falling into AdS5, and the decay of a time-like wave-packet. A similar observation was made in Phys. Rev. D81 (2010) 126001 for the case of a rotating string. In all these cases, the absence of broadening is related to the fact that the energy backreaction on the boundary arises exclusively from the bulk perturbation at, or near, the boundary. This is so since bulk sources which propagate in AdS5 at the speed of light do not generate any energy on the boundary. We interpret these features as an artifact of the supergravity approximation, which fails to encode quantum mechanical fluctuations that should be present even in the strong coupling limit. We argue that such fluctuations should enter the dual string theory as longitudinal string fluctuations, which are not suppressed at strong coupling. We heuristically estimate the effects of such fluctuations and argue that they restore the broadening of the radiation, in agreement with expectations from both quantum mechanics and the ultraviolet/infrared correspondence
A fully discrete BEM-FEM method for an exterior elasticity system in the plane

The final publication is available http://dx.doi.org/10.1016/S0377-0427(00)00533-1[Abstract] We present a modified version of the usual BEM–FEM coupling for the exterior elasticity problem in the plane (cf. Costabel and Stephan, SIAM J. Numer. Anal. 27 (1990) 1212–1226). This new formulation allows us to take advantage of techniques from Hsiao et al., Computing 25 (1980) 557–566 to compute the boundary integral terms using simple quadrature formulas. We provide error estimates for the Galerkin method and prove that the corresponding fully discrete scheme preserves the optimal rates of convergen
Molecular mechanisms of imatinib resistance in gastrointestinal stromal tumor with focus on microRNAs

Gastrointestinal stromal tumor (GIST) is mainly initialized by mutations in receptor tyrosine kinase genes KIT or PDGFRA. The development of imatinib, a small molecule inhibitor that targets these tyrosine kinase receptors, remarkably improved patient outcome. However, imatinib resistance remains a major therapeutic challenge in GIST therapy, and its underlying mechanisms are still not completely understood. This thesis work aimed to explore the role of microRNAs (miRNAs) and DOG1 in imatinib resistance of GIST.



In Paper I, we identified specific miRNA signatures associated with imatinib resistance, metastatic disease, KIT mutational status and survival in GIST patients treated with neoadjuvant imatinib. Importantly, we demonstrate that miR-125a-5p modulates imatinib response in the single KIT-mutated GIST882 cells through PTPN18 regulation. This study highlights the clinical impact of miRNAs in GIST patients treated with imatinib pre-operatively, and suggests the important role of miR-125a-5p and PTPN18 in imatinib resistance of GISTs.



In Paper II, we tested our hypothesis that miR-125a-5p overexpression in imatinib-resistant GISTs suppresses PTPN18 expression that subsequently leads to defective FAK dephosphorylation. Indeed, we demonstrate that silencing of PTPN18 increased FAK phosphorylation in GIST cells, and the acquired imatinib-resistant GIST882R cells exhibited higher pFAK and lower PTPN18 expressions than the imatinib-sensitive parental cells. FAK and pFAK expressions are also associated with imatinib resistance in GIST specimens. This study highlights the potential role of PTPN18 and pFAK in imatinib resistance of GIST.



In Paper III, we found that miR-320a and miR-320b are upregulated and their potential target MCL1 is downregulated in imatinib-treated GISTs. Imatinib treatment affects MCL1 and miR-320 levels in GIST882 cells, and the imatinib-resistant GIST882R cells showed higher levels of the anti-apoptotic MCL1L isoform and lower expression of miR-320a/b as compared to GIST882 cells. This study suggests that miR-320a/b and MCL1 play a role in imatinib-induced cell death and resistance in GIST.



In Paper IV, we evaluated the functional role of DOG1 in imatinib-resistant GIST48 and –sensitive GIST882 cells using specific DOG1 activator and inhibitor. We showed that DOG1 is localized in different cellular compartments in imatinib-resistant and -sensitive GIST cells. Pharmacological modulation of DOG1 activity has subtle effect on cell viability and proliferation, but may shift early apoptotic cells to late apoptotic stages in GIST48 cells. 
Overall, this thesis work describes the role of miRNAs in cell viability and resistance to imatinib treatment in GIST
Unraveling the pattern of the XYZ mesons

We present a plausible mechanism for the origin of the XYZ mesons in the heavy meson spectra within a standard quark-model picture. We discuss the conditions required for the existence of four-quark bound states or resonances contributing to the heavy meson spectra, being either compact or molecular. We concentrate on charmonium and bottomonium spectra, where several new states, difficult to understand as simple quark-antiquark pairs, have been reported by different experimental collaborations. The pivotal role played by entangled meson-meson thresholds is emphasized
Cosmic expansion history from SNe Ia data via information field theory
  -- the charm code

We present charm (cosmic history agnostic reconstruction method), a novel
inference algorithm that reconstructs the cosmic expansion history as encoded
in the Hubble parameter $H(z)$ from SNe Ia data. The novelty of the approach
lies in the usage of information field theory, a statistical field theory that
is very well suited for the construction of optimal signal recovery algorithms.
The charm algorithm infers non-parametrically
$s(a)=\ln(\rho(a)/\rho_{\mathrm{crit}0})$, the density evolution which
determines $H(z)$, without assuming an analytical form of $\rho(a)$ but only
its smoothness with the scale factor $a=(1+z)^{-1}$. The inference problem of
recovering the signal $s(a)$ from the data is formulated in a fully Bayesian
way. In detail, we have rewritten the signal as the sum of a background
cosmology and a perturbation. This allows us to determine the maximum a
posteriory estimate of the signal by an iterative Wiener filter method.
Applying charm to the Union2.1 supernova compilation, we have recovered a
cosmic expansion history that is fully compatible with the standard
$\Lambda$CDM cosmological expansion history with parameter values consistent
with the results of the Planck mission
Complex network based computational techniques for edgetic modelling of mutations implicated with human diseases

Complex networks are a graph theoretic method that can model genetic mutations, in particular single nucleotide polymorphisms (snp’s) which are genetic variations that only occur at single position in a DNA sequence. These can potentially cause the amino acids to be changed and may affect protein function and thus structural stability which can contribute to developing diseases. We show how snp’s can be represented by complex graph structures, the connectivity patterns if represented by graphs can be related to human diseases,  where the proteins are the nodes (vertices) and the interactions between them are represented by links (edges). Disruptions caused by mutations can be explained as loss of connectivity such as the deletion of nodes or edges in the network (hence the term edgetics). Furthermore, diseases appear to be interlinked with hub genes causing multiple problems and this has led to the concept of the human disease network or diseasome. Edgetics is a relatively new concept which is proving effective for modelling the relationships between genes, diseases and drugs which were previously considered intractable problems
The challenges of amblyopia treatment.

The treatment of amblyopia, particularly anisometropic (difference in refractive correction) and/or strabismic (turn of one eye) amblyopia has long been a challenge for many clinicians. Achieving optimum outcomes, where the amblyopic eye reaches a visual acuity similar to the fellow eye, is often impossible in many patients. Part of this challenge has resulted from a previous lack of scientific evidence for amblyopia treatment that was highlight by a systematic review by Snowdon et al. in 1998. Since this review, a number of publications have revealed new findings in the treatment of amblyopia. This includes the finding that less intensive occlusion treatments can be successful in treating amblyopia. A relationship between adherence to treatment and visual acuity has also been established and has been shown to be influenced by the use of intervention material. In addition, there is growing evidence of that a period of glasses wearing only can significantly improve visual acuity alone without any other modes of treatment. This review article reports findings since the Snowdon's report.The Ulverscroft Foundation.\ud
Open Access funded by Chang Gung UniversityPeer-reviewedPublisher Versio
Genome-wide analyses of aggressiveness in attention-deficit hyperactivity disorder

Aggressiveness is a behavioral trait that has the potential to be harmful to individuals and society. With an estimated heritability of about 40%, genetics is important in its development. We performed an exploratory genome-wide association (GWA) analysis of childhood aggressiveness in attention deficit hyperactivity disorder (ADHD) to gain insight into the underlying biological processes associated with this trait. Our primary sample consisted of 1,060 adult ADHD patients (aADHD). To further explore the genetic architecture of childhood aggressiveness, we performed enrichment analyses of suggestive genome-wide associations observed in aADHD among GWA signals of dimensions of oppositionality (defiant/vindictive and irritable dimensions) in childhood ADHD (cADHD). No single polymorphism reached genome-wide significance (P < 5.00E-08). The strongest signal in aADHD was observed at rs10826548, within a long noncoding RNA gene (beta = -1.66, standard error (SE) = 0.34, P = 1.07E-06), closely followed by rs35974940 in the neurotrimin gene (beta = 3.23, SE = 0.67, P = 1.26E-06). The top GWA SNPs observed in aADHD showed significant enrichment of signals from both the defiant/vindictive dimension (Fisher's P-value = 2.28E-06) and the irritable dimension in cADHD (Fisher's P-value = 0.0061). In sum, our results identify a number of biologically interesting markers possibly underlying childhood aggressiveness and provide targets for further genetic exploration of aggressiveness across psychiatric disorders. © 2016 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc
An extreme [O III] emitter at z = 3.2: A low metallicity Lyman continuum source

Aims. Cosmic reionization is an important process occurring in the early epochs of the Universe. However, because of observational limitations due to the opacity of the intergalactic medium to Lyman continuum photons, the nature of ionizing sources is still not well constrained. While high-redshift star-forming galaxies are thought to be the main contributors to the ionizing background at z > 6, it is impossible to directly detect their ionizing emission. Therefore, looking at intermediate redshift analogues (z ∼ 2?4) can provide useful hints about cosmic reionization. Methods. We investigate the physical properties of one of the best Lyman continuum emitter candidate at z = 3.212 found in the GOODS-S/CANDELS field with photometric coverage from the U to the MIPS 24 ?m band and VIMOS/VLT and MOSFIRE/Keck spectroscopy. These observations allow us to derive physical properties such as stellar mass, star formation rate, age of the stellar population, dust attenuation, metallicity, and ionization parameter, and to determine how these parameters are related to the Lyman continuum emission. Results. Investigation of the UV spectrum confirms a direct spectroscopic detection of the Lyman continuum emission with S/N > 5. Non-zero Lyaα flux at the systemic redshift and high Lyman-aα ESCape fraction (f(Lyaα) ≥ 0.78) suggest a low H i column density. The weak C and Si low-ionization absorption lines are also consistent with a low covering fraction along the line of sight. The subsolar abundances are consistent with a young and extreme starburst. The [O iii] iiiλλ4959, 5007+Hβ equivalent width (EW) is one of the largest reported for a galaxy at z > 3 (EW([O iii] λλ4959, 5007 + Hβ) ≈1600 Å, rest-frame; 6700 Å observed-frame) and the near-infrared spectrum shows that this is mainly due to an extremely strong [O iii] emission. The large observed [O iii]/[O ii] ratio (>10) and high ionization parameter are consistent with prediction from photoionization models in the case of a density-bounded nebula scenario. Furthermore, the EW([O iiiλλ4959, 5007+Hβ) is comparable to recent measurements reported at z ∼ 7?9, in the reionization epoch. We also investigate the possibility of an AGN contribution to explain the ionizing emission but most of the AGN identification diagnostics suggest that stellar emission dominates instead. Conclusions. This source is currently the first high-z example of a Lyman continuum emitter exhibiting indirect and direct evidences of a Lyman continuum leakage and having physical properties consistent with theoretical expectation from Lyman continuum emission from a density-bounded nebula. A low H i column density, low covering fraction, compact star formation activity, and a possible interaction/merging of two systems may contribute to the Lyman continuum photon leakage. © 2015 ESO.We acknowledge the financial contribution from PRIN-INAF 2012.Peer Reviewe