bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships
Authors: Hishamuddin Muhammad Syahmi , Lee Shiou Yih , Ng Wei Lun , Ramlee Shairul Izan , Lamasudin Dhilia Udie , Mohamed Rozi 
Published: August 2020

AbstractAquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.
The dynamics of free and phosphopeptide-bound Grb2-SH2 reveals two dynamically independent subdomains and an encounter complex with fuzzy interactions
Authors: Sanches Karoline , Caruso Icaro P. , Almeida Fabio C. L. , Melo Fernando A. 
Published: August 2020

AbstractThe growth factor receptor-bound protein 2 (Grb2) is a key factor in the regulation of cell survival, proliferation, differentiation, and metabolism. In its structure, the central Src homology 2 (SH2) domain is flanked by two Src homology 3 (SH3). SH2 is the most important domain in the recognition of phosphotyrosines. Here, we present the first dynamical characterization of Grb2-SH2 domain in the free state and in the presence of phosphopeptide EpYINSQV at multiple timescales, which revealed valuable information to the understanding of phophotyrosine sensing mechanism. Grb2-SH2 presented two dynamically independent subdomains, subdomain I involved in pY recognition and subdomain II is the pY + 2 specificity pocket. Under semi-saturated concentrations of pY-pep we observed fuzzy interactions, which led to chemical exchange observed by NMR. This information was used to describe the encounter complex. The association with pY-pep is dynamic, involving fuzzy interactions and multiple conformations of pY-pep with negative and hydrophobic residues, creating an electrostatic-potential that drives the binding of pY-pep. The recognition face is wider than the binding site, with many residues beyond the central SH2 binding site participating in the association complex, which contribute to explain previously reported capability of Grb2 to recognize remote pY.
Fabrication of fluorescent pH-responsive protein–textile composites
Authors: Saldanha Dalia Jane , Abdali Zahra , Modafferi Daniel , Janfeshan Bita , Dorval Courchesne Noémie-Manuelle 
Published: August 2020

AbstractWearable pH sensors are useful tools in the healthcare and fitness industries, allowing consumers to access information related to their health in a convenient manner via the monitoring of body fluids. In this work, we tailored novel protein–textile composites to fluorescently respond to changing pH. To do so, we used amyloid curli fibers, a key component in the extracellular matrix ofEscherichia coli, as genetic scaffold to fuse a pH-responsive fluorescent protein, pHuji. Engineered amyloids form macroscopic and environmentally resistant aggregates that we isolated to use as stand-alone hydrogel-based sensors, and that we trapped within textile matrices to create responsive bio-composites. We showed that these composites were mechanically robust and vapor-permeable, thus exhibiting favorable characteristics for wearable platforms. CsgA–pHuji fibers integrated in the textile allowed the final device to respond to pH changes and distinguish between alkaline and acidic solutions. We demonstrated that the resulting composites could sustain their fluorescence response over days, and that their sensing ability was reversible for at least 10 high/low pH cycles, highlighting their potential for continuous monitoring. Overall, we introduced a biosynthesized amyloid-based textile composite that could be used as biosensing patch for a variety of applications in the smart textile industry.
Upcycling of Fe-bearing sludge: preparation of erdite-bearing particles for treating pharmaceutical manufacture wastewater
Authors: Hu Tongke , Wang Huaimin , Ning Ruyan , Qiao Xueling , Liu Yanwen , Dong Wenqing , Zhu Suiyi 
Published: August 2020

AbstractGroundwater treatment sludge is a type of solid waste with 9.0–28.9% wt.% Fe content and is precipitated in large quantity from backwash wastewater in groundwater treatment. The sludge is mainly composed of fine particles containing Fe, Si and Al oxides, such as ferrihydrite, quartz and boehmite. The Fe oxides mostly originate from the oxidation of ferrous Fe in groundwater, whilst the silicate/aluminium compounds mainly originate from the broken quartz sand filter in the backwash step. In general, the sludge is firstly coagulated, dewatered by filter pressing and finally undergoes harmless solidification before it is sent to landfills. However, this process is costly (approximately US$66.1/t) and complicated. In this study, groundwater treatment sludge was effectively recycled to prepare novel erdite-bearing particles via a one-step hydrothermal method by adding only Na2S·9H2O. After hydrothermal treatment, the quartz and boehmite of the sludge were dissolved and recrystallised to sodalite, whilst ferrihydrite was converted to an erdite nanorod at 160 °C and a hematite at 240 °C. SP160 was prepared as fine nanorod particles with 200 nm diameter and 2–5 μm length at a hydrothermal temperature of 160 °C. Nearly 100% OTC and its derivatives in pharmaceutical manufacture wastewater were removed by adding 0.1 g SP160. The major mechanism for the removal was the spontaneous hydrolysis of erdite in SP160 to generate Fe oxyhydroxide and use many hydroxyl groups for coordinating OTC and its derivatives. This study presents a novel method for the resource reutilisation of waste groundwater treatment sludge and reports efficient erdite-bearing particles for pharmaceutical manufacture wastewater treatment.
Vasoactive intestinal peptide axis is dysfunctional in patients with Graves’ disease
Authors: Carrión M. , Ramos-Leví A. M. , Seoane I. V. , Martínez-Hernández R. , Serrano-Somavilla A. , Castro D. , Juarranz Y. , González-Álvaro I. , Gomariz Rosa P. , Marazuela Mónica 
Published: August 2020

AbstractVasoactive intestinal peptide (VIP) is a neuropeptide with potent immunoregulatory properties. Reduced serum VIP levels and alterations in VIP receptors/signaling on immune cells have been associated with different inflammatory/autoimmune diseases. However, its role in autoimmune thyroid diseases (AITD) remains unknown. This study examined the interrelationship between VIP system, autoimmune background and thyroid hormones in peripheral immune cells in patients with AITD. Only Graves’ disease (GD) patients showed significantly lower serum VIP levels when compared to healthy subjects and to Hashimoto’s thyroiditis patients. Serum VIP levels were lower at the onset of GD, showing a significant negative correlation with thyroid hormone levels. The expression of VIP receptors, VPAC1 and VPAC2, was significantly upregulated in peripheral blood mononuclear cells (PBMC) from GD patients. There was an impairment of VIP signalling in these patients, probably attributable to a dysfunction of VPAC1 with preservation of VPAC2. The correlation between VPAC1 and thyroid hormone receptor expression in PBMC from healthy subjects was lost in GD patients. In summary, the VIP system is altered in peripheral immune cells of GD patients and this finding is associated with different thyroid hormone receptor patterns, showing a dynamic inter-regulation and a prominent role of VIP in this setting.
Small cell transformation of ROS1 fusion-positive lung cancer resistant to ROS1 inhibition
Authors: Lin Jessica J. , Langenbucher Adam , Gupta Pranav , Yoda Satoshi , Fetter Isobel J. , Rooney Marguerite , Do Andrew , Kem Marina , Chang Kylie Prutisto , Oh Audris Y. , Chin Emily , Juric Dejan , Corcoran Ryan B. , Dagogo-Jack Ibiayi , Gainor Justin F. , Stone James R. , Lennerz Jochen K. , Lawrence Michael S. , Hata Aaron N. , Mino-Kenudson Mari , Shaw Alice T. 
Published: August 2020

AbstractHistologic transformation from non-small cell to small cell lung cancer has been reported as a resistance mechanism to targeted therapy in EGFR-mutant and ALK fusion-positive lung cancers. Whether small cell transformation occurs in other oncogene-driven lung cancers remains unknown. Here we analyzed the genomic landscape of two pre-mortem and 11 post-mortem metastatic tumors collected from an advanced, ROS1 fusion-positive lung cancer patient, who had received sequential ROS1 inhibitors. Evidence of small cell transformation was observed in all metastatic sites at autopsy, with inactivation of RB1 and TP53, and loss of ROS1 fusion expression. Whole-exome sequencing revealed minimal mutational and copy number heterogeneity, suggestive of “hard” clonal sweep. Patient-derived models generated from autopsy retained features consistent with small cell lung cancer and demonstrated resistance to ROS1 inhibitors. This case supports small cell transformation as a recurring resistance mechanism, and underscores the importance of elucidating its biology to expand therapeutic opportunities.
Development and validation of nomogram to predict risk of survival in patients with laryngeal squamous cell carcinoma
Authors: Cui Jie , Wang Liping , Zhong Waisheng , Chen Zhen , Tan Xiaojun , Yang Hong , Chen Jie , Liu Genglong 
Published: August 2020

Abstract
To the best of our knowledge, this is the first study established a nomogram to predict survival probability in Asian patients with LSCC. A risk prediction nomogram for patients with LSCC, incorporating easily assessable clinicopathologic factors, generates more precise estimations of the survival probability when compared TNM stage alone, but still need additional data before being used in clinical application.
Background: Due to a wide variation of tumor behavior, prediction of survival in laryngeal squamous cell carcinoma (LSCC) patients received curative-intent surgery is an important but formidable challenge. We attempted to establish a nomogram to precisely predict survival probability in LSCC patients.
Methods: A total of 369 consecutive LSCC patients underwent curative resection between 2008 and 2012 at Hunan Province Cancer Hospital were included in the present study. Subsequently, 369 LSCC patients were assigned to a training set (N=261) and a validation set (N=108) at random. On the basis of multivariable Cox regression analysis results, we developed a nomogram. The predictive accuracy and discriminative ability of the nomogram were confirmed by calibration curve and a concordance index (C-index), and compared with TNM stage system by C-index, receiver operating characteristic (ROC) analysis.
Results: Six independent parameters to predict prognosis were age, pack years, N-stage, lymph node ratio (LNR), anemia and albumin, which were all assembled into the nomogram. The calibration curve verified excellent models’ concordance. The C-index of the nomogram was 0.73 (0.68–0.78), and the area under curve (AUC) of nomogram in predicting overall survival (OS) was 0.766, which were significantly higher than traditional TNM stage. Decision curve analysis further demonstrated that our nomogram had a larger net benefit than the TNM stage.
Conclusion: A risk prediction nomogram for patients with LSCC, incorporating easily assessable clinicopathologic factors, generates more precise estimations of the survival probability when compared TNM stage alone, but still need additional data before being used in clinical application.
Mining novel cell glycolysis related gene markers that can predict the survival of colon adenocarcinoma patients
Authors: Chen Sihan , Cao Guodong , Wu Wei , Lu Yida , He Xiaobo , Yang Lei , Chen Ke , Chen Bo , Xiong MaoMing 
Published: August 2020

Abstract
Colon adenocarcinoma (COAD) is a malignant gastrointestinal tumor, often occurring in the left colon, which is regulated by glycolysis-related processes. In past studies, multiple genes that influence the prognosis for survival have been discovered through bioinformatics analysis. However, the prediction of disease prognosis using a single gene is not an accurate method. In the present study, a mechanistic model was established to achieve better prediction for the prognosis of COAD. COAD-related data downloaded from The Cancer Genome Atlas (TCGA) were correlated with the glycolysis process using gene set enrichment analysis (GSEA) to determine the glycolysis-related genes that regulate COAD. Using COX regression analysis, glycolysis-related genes associated with the prognosis of COAD were identified, and the genes screened to establish a predictive model. The risk scores of this model were correlated with relevant clinical data to obtain a connection diagram between the model and survival rate, tumor characteristic data, etc. Finally, genes in the model were correlated with cells in the tumor microenvironment, finding that they affected specific immune cells in the model. Seven genes related to glycolysis were identified (PPARGC1A, DLAT, 6PC2, P4HA1, STC2, ANKZF1, and GPC1), which affect the prognosis of patients with COAD and constitute the model for prediction of survival of COAD patients.
Association of variant on the promoter of cluster of differentiation 74 in graves disease and graves ophthalmopathy
Authors: Liu Yu-Huei , Shen Chiou-Yuan , Tsai Fuu-Jen 
Published: August 2020

Abstract
The macrophage migration inhibitory factor (MIF)/cluster of differentiation 74 (CD74) plays a role in immunological functions. The present study aims to investigate whether single-nucleotide polymorphisms (SNPs) in the MIF and CD74 are risk factors for developing Graves ophthalmopathy (GO) in patients with Graves disease (GD). A case–control study enrolled 484 patients with GD (203 with and 281 without GO) and 1000 healthy individuals. SNPs were discriminated using real-time polymerase chain reaction. Hardy–Weinberg equilibrium, as well as frequencies of allele and genotype between GD patients with and without GO, were estimated using the Chi-square test. The effects of CD74 on adipocyte proliferation and differentiation were evaluated using 3T3-L1 preadipocytes. Quantitative DNA-immunoprecipitation was used to detect the binding capacity of NR3C1 and FOXP3 to A/G oligonucleotides. The results showed that individuals carrying the GG genotype at rs2569103 in the CD74 had a decreased risk of developing GD (P=3.390 × 10−11, odds ratio (OR) = 0.021, 95% confidence interval (CI) = 0.003–0.154); however, patients with GD carrying the AG genotype at rs2569103 in the CD74 had an increased risk of developing GO (P=0.009, OR = 1.707, 95% CI = 1.168–2.495). The knockdown of CD74 reduced adipocyte proliferation and differentiation. NR3C1 had a higher affinity for A, whereas FOXP3 had a higher affinity for G of rs2569103. The results suggested the existence of a link between the genetic variation of CD74 promoter and the risk for developing GD and GO, which should be considered in clinical practice.
ROSINA ion zoo at Comet 67P
Authors: Beth A. , Altwegg K. , Balsiger H. , Berthelier J.-J. , Combi M. R. , De Keyser J. , Fiethe B. , Fuselier S. A. , Galand M. , Gombosi T. I. , Rubin M. , Sémon T. 
Published: August 2020

Context.The Rosetta spacecraft escorted Comet 67P/Churyumov-Gerasimenko for 2 yr along its journey through the Solar System between 3.8 and 1.24 au. Thanks to the high resolution mass spectrometer on board Rosetta, the detailed ion composition within a coma has been accurately assessed in situ for the very first time.Aims.Previous cometary missions, such asGiotto, did not have the instrumental capabilities to identify the exact nature of the plasma in a coma because the mass resolution of the spectrometers onboard was too low to separate ion species with similar masses. In contrast, the Double Focusing Mass Spectrometer (DFMS), part of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis on board Rosetta (ROSINA), with its high mass resolution mode, outperformed all of them, revealing the diversity of cometary ions.Methods.We calibrated and analysed the set of spectra acquired by DFMS in ion mode from October 2014 to April 2016. In particular, we focused on the range from 13–39 u q−1. The high mass resolution of DFMS allows for accurate identifications of ions with quasi-similar masses, separating13C+from CH+, for instance.Results.We confirm the presence in situ of predicted cations at comets, such as CHm+(m= 1−4), HnO+(n= 1−3), O+, Na+, and several ionised and protonated molecules. Prior to Rosetta, only a fraction of them had been confirmed from Earth-based observations. In addition, we report for the first time the unambiguous presence of a molecular dication in the gas envelope of a Solar System body, namely CO2++.
Dust and gas absorption in the high mass X-ray binary IGR J16318−4848
Authors: Ballhausen Ralf , Lorenz Maximilian , Fürst Felix , Pottschmidt Katja , Corrales Lia , Tomsick John A. , Bissinger né Kühnel Matthias , Kretschmar Peter , Kallman Timothy R. , Grinberg Victoria , Hell Natalie , Psadaraki Ioanna , Rogantini Daniele , Wilms Jörn 
Published: August 2020

Context.With an absorption column density on the order of 1024cm−2, IGR J16318−4848 is one of the most extreme cases of a highly obscured high mass X-ray binary. In addition to the overall continuum absorption, the source spectrum exhibits a strong iron and nickel fluorescence line complex at 6.4 keV. Previous empirical modeling of these features and comparison with radiative transfer simulations raised questions about the structure and covering fraction of the absorber and the profile of the fluorescence lines.Aims.We aim at a self-consistent description of the continuum absorption, the absorption edges, and the fluorescence lines to constrain the properties of the absorbing material, such as ionization structure and geometry. We further investigate the effects of dust absorption on the observed spectra and the possibility of fluorescence emission from dust grains.Methods.We usedXMM-NewtonandNuSTARspectra to first empirically constrain the incident continuum and fluorescence lines. Next we usedXSTARto construct a customized photoionization model where we vary the ionization parameter, column density, and covering fraction. In the third step we modeled the absorption and fluorescence in a dusty olivine absorber and employed both a simple analytical model for the fluorescence line emission and a Monte Carlo simulation of radiative transfer that generates line fluxes, which are very close to the observational data.Results.Our empirical spectral modeling is in agreement with previous works. Our second model, the single gas absorber does not describe the observational data. In particular, irrespective of the ionization state or column density of the absorber, a much higher covering fraction than previously estimated is needed to produce the strong fluorescence lines and the large continuum absorption. A dusty, spherical absorber (modeled as consisting of olivine dust, although the nature of dust cannot be constrained) is able to produce the observed continuum absorption and edges.Conclusions.A dense, dusty absorber in the direct vicinity of the source consisting of dust offers a consistent description of both the strong continuum absorption and the strong emission features in the X-ray spectrum of IGR J16318−4848. In particular, for low optical depth of individual grains, which is the case for typical volume densities and grain size distribution models, the dust will contribute significantly to the fluorescence emission.
A wide field-of-view low-resolution spectrometer at APEX: Instrument design and scientific forecast
Authors:   The CONCERTO Collaboration, Ade P. , Aravena M. , Barria E. , Beelen A. , Benoit A. , Béthermin M. , Bounmy J. , Bourrion O. , Bres G. , De Breuck C. , Calvo M. , Cao Y. , Catalano A. , Désert F.-X. , Durán C.A. , Fasano A. , Fenouillet T. , Garcia J. , Garde G. , Goupy J. , Groppi C. , Hoarau C. , Lagache G. , Lambert J.-C. , Leggeri J.-P. , Levy-Bertrand F. , Macías-Pérez J. , Mani H. , Marpaud J. , Mauskopf P. , Monfardini A. , Pisano G. , Ponthieu N. , Prieur L. , Roni S. , Roudier S. , Tourres D. , Tucker C. 
Published: August 2020

Context.Characterising the large-scale structure in the Universe from present times to the high redshift epoch of reionisation is essential to constraining the cosmology, the history of star formation, and reionisation, to measuring the gas content of the Universe, and to obtaining a better understanding of the physical processes that drive galaxy formation and evolution. Using the integrated emission from unresolved galaxies or gas clouds, line intensity mapping (LIM) provides a new observational window to measure the larger properties of structures. This very promising technique motivates the community to plan for LIM experiments.Aims.We describe the development of a large field-of-view instrument, named CONCERTO (for CarbON CII line in post-rEionisation and ReionisaTiOn epoch), operating in the range 130–310 GHz from the APEX 12-m telescope (5100 m above sea level). CONCERTO is a low-resolution spectrometer based on the lumped element kinetic inductance detectors (LEKID) technology. Spectra are obtained using a fast Fourier transform spectrometer (FTS), coupled to a dilution cryostat with a base temperature of 0.1 K. Two two kilo-pixel arrays of LEKID are mounted inside the cryostat that also contains the cold optics and the front-end electronics.Methods.We present, in detail, the technological choices leading to the instrumental concept, together with the design and fabrication of the instrument and preliminary laboratory tests on the detectors. We also give our best estimates for CONCERTO sensitivity and give predictions for two of the main scientific goals of CONCERTO, that is, a [CII]-intensity mapping survey and observations of galaxy clusters.Results.We provide a detailed description of the instrument design. Based on realistic comparisons with existing instruments developed by our group (NIKA, NIKA2, and KISS), and on the laboratory characterisation of our detectors, we provide an estimate for CONCERTO sensitivity on the sky. Finally, we describe, in detail, two of the main scientific goals offered by CONCERTO at APEX.
Homöopathie und Weisheitszähne
Authors: Elies Michael K.H. 
Published: August 2020

ZusammenfassungWeisheitszähne zeigen einerseits eine sehr individuelle Entwicklung, andererseits lassen sich Störungsmuster aufzeigen, die mit den Weisheitszähnen in Verbindung stehen und miasmatisch der Tuberkulinie zuzuordnen sind. Therapeutisch kommen häufig sogenannte kleine Arzneimittel zur Anwendung. Bewährte homöopathische Arzneien bei schwierigen Weisheitszahnverhältnissen sowie Komplikationen einer Weisheitszahnentfernung werden dargestellt.