bluuebunny/crossref_metadata_2025_split huggingface dataset:
Telomere length and survival in primary cutaneous melanoma patients
Authors: Rachakonda Sivaramakrishna , Srinivas Nalini , Mahmoudpour Seyed Hamidreza , Garcia-Casado Zaida , Requena Celia , Traves Victor , Soriano Virtudes , Cardelli Maurizio , Pjanova Dace , Molven Anders , Gruis Nelleke , Nagore Eduardo , Kumar Rajiv 
Published: July 2018

AbstractTelomere repeats at chromosomal ends, critical to genomic integrity, undergo age-dependent attrition. Telomere length, a polygenic trait, has been associated with risk of several disorders including cancers. In contrast to association of long telomeres with increased risk of several cancers, including melanoma, emerging reports suggest that short telomeres predict poor survival in patients with different cancers. In this study based on 1019 stage I and II cutaneous melanoma patients, we show an association between the patients with short telomeres and poor melanoma-specific survival (HR 2.05, 95% CI 1.33–3.16) compared to patients with long telomeres. Due to inverse correlation between age and telomere length (r -0.19, P < 0.0001), we stratified the patients into quantiles based on age at diagnosis and also carried out age-matched analysis. The effect of short telomeres on survival was determined by using multivariate Cox regression that included composite genetic risk score computed from genotyping of the patients for telomere-length associated polymorphisms. The effect of decreased telomere length on poor melanoma-specific survival was particularly strong in patients within the age quantile below 30 years (HR 3.82, 95% CI 1.10–13.30) and between 30–40 years (HR 2.69, 95% CI 1.03–7.03). Our study shows that in contrast to increased melanoma risk associated with increased telomere length, decreased telomere length predicts poor survival in melanoma subgroups.
Long-range non-diffusive spin transfer in a Hall insulator
Authors: Kulik L. V. , Kuznetsov V. A. , Zhuravlev A. S. , Gorbunov A. V. , Solovyev V. V. , Timofeev V. B. , Kukushkin I. V. , Schmult S. 
Published: July 2018

AbstractWe report on optical visualization of spin propagation more than 100 µm. We present an electronic system in a new state of aggregation, the magnetofermionic condensate, in which the lowest-energy spin excitations − photoexcited spin-triplet magnetoexcitons – freely propagate over long distances, in the order of a millimeter, which implies non-diffusion spin transport. Our results open up a completely new system suitable for spintronic devices.
Systematic evaluation of error rates and causes in short samples in next-generation sequencing
Authors: Pfeiffer Franziska , Gröber Carsten , Blank Michael , Händler Kristian , Beyer Marc , Schultze Joachim L. , Mayer Günter 
Published: July 2018

AbstractNext-generation sequencing (NGS) is the method of choice when large numbers of sequences have to be obtained. While the technique is widely applied, varying error rates have been observed. We analysed millions of reads obtained after sequencing of one single sequence on an Illumina sequencer. According to our analysis, the index-PCR for sample preparation has no effect on the observed error rate, even though PCR is traditionally seen as one of the major contributors to enhanced error rates in NGS. In addition, we observed very persistent pre-phasing effects although the base calling software corrects for these. Removal of shortened sequences abolished these effects and allowed analysis of the actual mutations. The average error rate determined was 0.24 ± 0.06% per base and the percentage of mutated sequences was found to be 6.4 ± 1.24%. Constant regions at the 5′- and 3′-end, e.g., primer binding sites used in in vitro selection procedures seem to have no effect on mutation rates and re-sequencing of samples obtains very reproducible results. As phasing effects and other sequencing problems vary between equipment and individual setups, we recommend evaluation of error rates and types to all NGS-users to improve the quality and analysis of NGS data.
Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
Authors: Tyler Andrea D. , Mataseje Laura , Urfano Chantel J. , Schmidt Lisa , Antonation Kym S. , Mulvey Michael R. , Corbett Cindi R. 
Published: July 2018

AbstractThe MinION sequencer (Oxford Nanopore Technologies) is a paradigm shifting device allowing rapid, real time long read sequencing of nucleic acids. Yet external benchmarking of this technologies’ capabilities has not been extensively reported, nor has thorough evaluation of its utility for field-based analysis with sub-optimal sample types been described. The aim of this study was to evaluate the capability of the MinION sequencer for bacterial genomic and metagenomic applications, with specific emphasis placed on the quality, yield, and accuracy of generated sequence data. Two independent laboratories at the National Microbiology Laboratory (Public Health Agency of Canada), sequenced a set of microbes in replicate, using the currently available flowcells, sequencing chemistries, and software available at the time of the experiment. Overall sequencing yield and quality improved through the course of this set of experiments. Sequencing alignment accuracy was high reaching 97% for all 2D experiments, though was slightly lower for 1D sequencing (94%). 1D sequencing provided much longer sequences than 2D. Both sequencing chemistries performed equally well in constructing genomic assemblies. There was evidence of barcode cross-over using both the native and PCR barcoding methods. Despite the sub-optimal nature of samples sequenced in the field, sequences attributable toB. anthracisthe target organism used in this scenario, could none-the-less be detected. Together, this report showcases the rapid advancement in this technology and its utility in the context of genomic sequencing of microbial isolates of importance to public health.
Embryonic germ cell extracts erase imprinted genes and improve the efficiency of induced pluripotent stem cells
Authors: Hu Jing , Zhao Qiaoshi , Feng Yukuan , Li Na , Gu Yanli , Sun Ruizhen , Duan Lian , Wu Yanshuang , Shan Zhiyan , Lei Lei 
Published: July 2018

AbstractPatient-specific induced pluripotent stem cells (iPSCs) have the potential to be useful in the treatment of human diseases. While prior studies have reported multiple methods to generate iPSCs, DNA methylation continues to limit the totipotency and reprogramming efficiency of iPSCs. Here, we first show the competency of embryonic germ cells (EGCs) as a reprogramming catalyst capable of effectively promoting reprogramming induced by four defined factors, including Oct4, Sox2, Klf4 and c-Myc. Combining EGC extracts with these four factors resulted in formation of more embryonic stem cell-like colonies than did factors alone. Notably, expression of imprinted genes was higher with combined induction than with factors alone. Moreover, iPSCs derived from the combined inductors tended to have more global hypomethylation. Our research not only provides evidence that EGC extracts could activate DNA demethylation and reprogram imprinted genes, but also establishes a new way to enhance reprogramming of iPSCs, which remains a critical safety concern for potential use of iPSCs in regenerative medicine.
Interactions of bacteriophage T4 adhesin with selected lipopolysaccharides studied using atomic force microscopy
Authors: Brzozowska Ewa , Leśniewski Adam , Sęk Sławomir , Wieneke Ralph , Tampé Robert , Górska Sabina , Jönsson-Niedziółka Martin , Niedziółka-Jönsson Joanna 
Published: July 2018

AbstractThe interaction between the T4 bacteriophage gp37 adhesin and the bacterial lipopolysaccharide (LPS) is a well-studied system, however, the affinity and strength of the interaction haven’t been analyzed so far. Here, we use atomic force microscopy to determine the strength of the interaction between the adhesin and its receptor, namely LPS taken from a wild strain of E. coli B. As negative controls we used LPSs of E. coli O111:B and Hafnia alvei. To study the interaction an AFM tip modified with the gp37 adhesin was used to scan surfaces of mica covered with one of the three different LPSs. Using the correlation between the surface topography images and the tip-surface interaction we could verify the binding between the specific LPS and the tip in contrast to the very weak interaction between the tip and the non-binding LPSs. Using force spectroscopy we could then measure the binding strength by pulling on the AFM tip until it lifted off from the surface. The force necessary to break the interaction between gp37 and LPS from E. coli B, LPS from E. coli O111:B and LPS from H. alvei were measured to be 70 ± 29 pN, 46 ± 13 pN and 45 ± 14 pN, respectively. The latter values are likely partially due to non-specific interaction between the gp37 and the solid surface, as LPS from E. coli O111:B and LPS from H. alvei have been shown to not bind to gp37, which is confirmed by the low correlation between binding and topography for these samples.
Native point defects of semiconducting layered Bi2O2Se
Authors: Li Huanglong , Xu Xintong , Zhang Yi , Gillen Roland , Shi Luping , Robertson John 
Published: July 2018

AbstractBi2O2Se is an emerging semiconducting, air-stable layered material (Nat. Nanotechnol. 2017, 12, 530; Nano Lett. 2017, 17, 3021), potentially exceeding MoS2 and phosphorene in electron mobility and rivalling typical Van der Waals stacked layered materials in the next-generation high-speed and low-power electronics. Holding the promise of functional versatility, it is arousing rapidly growing interest from various disciplines, including optoelectronics, thermoelectronics and piezoelectronics. In this work, we comprehensively study the electrical properties of the native point defects in Bi2O2Se, as an essential step toward understanding the fundamentals of this material. The defect landscapes dependent on both Fermi energy and the chemical potentials of atomic constituents are investigated. Along with the bulk defect analysis, a complementary inspection of the surface properties, within the simple context of charge neutrality level model, elucidates the observed n-type characteristics of Bi2O2Se based FETs. This work provides important guide to engineer the defects of Bi2O2Se for desired properties, which is key to the successful application of this emerging layered material27.
Rotating magnetocaloric effect and unusual magnetic features in metallic strongly anisotropic geometrically frustrated TmB4
Authors: Orendáč Matúš , Gabáni Slavomír , Gažo Emil , Pristáš Gabriel , Shitsevalova Natalya , Siemensmeyer Konrad , Flachbart Karol 
Published: July 2018

AbstractWe have investigated the rotating magnetocaloric effect (R-MCE) of TmB4 - an anisotropic magnetic system with geometrical frustration of Shastry-Sutherland type. The R-MCE was obtained from detailed temperature dependencies of heat capacity in various magnetic fields of a single crystalline sample for crystal axes orientations c || B and c ⊥ B. The received results exhibit rather complex distributions of positive and negative entropy ΔS(T, B) and temperature ΔT(T, B) differences below and above TN when the direction of the magnetic field changes between directions c || B and c ⊥ B. The calculated results were confirmed by direct R-MCE measurements which, moreover, show an interesting angular dependence of R-MCE in the ordered phase, which seems to be related with the change of the effective magnetic field along the c axis during sample rotation. Thus, our study presents a new type of magnetic refrigerant with a rather large R-MCE for low temperature magnetic refrigeration, and points to further interesting magnetic features in the ordered phase of this frustrated system.
Hierarchical porous N,O Co‐doped carbon/Se composite derived from hydrothermal treated chitosan as Li–Se battery cathode
Authors: Zhao Chenhao , Luo Jiangshui , Hu Zhibiao 
Published: July 2018

Seeking for the porous carbon with suitable structure and morphology has been a key to improve the lithium storage performance of carbon/selenium composite. In this work, the hierarchical porous N,O Co‐doped carbon has been prepared by an initial hydrothermal carbonisation and subsequent activation route using the chitosan as raw material. The carbon obtained at 600°C possessing primary micropores and surface macropores presents high specific surface area (809. 3 m2 g−1) and low porous size, and the selenium with amorphous structure is uniformly encapsulated into the micropores of this carbon to form carbon/selenium composite. As the cathode materials of lithium ion battery, this composite delivers a discharge capacity of 446.9 mAh g−1 at rate of 0.24 C after 100 cycles. At a high rate of 4.8 C, this composite still shows a stable discharge capacity of 342.8 mAh g−1. These results suggest that this composite may be promising for practical applications for lithium‐selenium battery.
Synthesis of columnar‐shaped CeO2 and electrochemical sensor for detecting phenol
Authors: Xiao Xin , Wang YiHui , Zhang DongEn , Gong JunYan , Zhang Ying , Ma JuanJuan , Yang Tao , Tong ZhiWei 
Published: July 2018

Highly uniform columnar‐shaped CeO2 was successfully prepared in large quantities by calcining a precursor, which was prepared by a simple hydrothermal method. The structure and morphology of the precursor and the columnar CeO2 were characterised by X‐ray diffraction and scanning electron microscopy. The columnar CeO2 was fixed on a glassy carbon electrode to obtain a columnar CeO2 sensor for detection of phenol. The anodic peak current was proportional to the phenol concentration in the range of 0.005–0.225 mmol l−1 (R = 0.995) and 0.225–1.125 mmol l−1 (R = 0.998) with the detection limit of 0.9 μmol l−1. This electrochemical method has the advantages of simplicity and ease of fabrication, rapid detection, low cost of the apparatus and wide dynamic ranges.
Effect of sintering temperature on phase transformation and luminescence property of BaAl2Si2O8 :Eu2+ phosphor
Authors: Ma Mingxing , Wang Zhixin , Liang Cun , Zhao Cong , Zhu Dachuan , Han Tao 
Published: July 2018

Sintered at different sintering temperatures, Eu2+ doped BaAl2Si2O8 phosphors were synthesised through one‐step calcination process of precursors prepared by chemical coprecipitation method. Thermal gravity‐differential thermal analysis was used to investigate the initial temperature of phase transition and the optimal sintering temperature of the sample synthesis. The X‐ray diffraction patterns confirmed that the sample calcined at 1200°C possessed a single hexagonal phase of BaAl2Si2O8. Although a little BaAl2Si2O8 phase had been produced, BaAl2O4 phase was dominant in the sample calcined at 1000°C. The morphology of the sample observed by scanning electron microscope showed smooth surfaces and nearly spherical shapes at higher sintering temperature. The emission spectrum of the sample calcined at 1000°C was separated into three Gaussians with the maximum at about 455, 501 and 540 nm, due to the 4f7 →4f6 5d transitions of Eu2+ ions occupying the Ba site of BaAl2Si2O8 and the Ba(1) and Ba(2) site of BaAl2O4, respectively. With the increase of sintering temperature, BaAl2Si2O8 :Eu2+ phosphor exhibited a blue broad emission band peaking at 455 nm with full width at half maximum about 90 nm under near‐ultraviolet excitation at ∼400 nm, and its emission intensity increased considerably due to the improved crystalline and homogeneous distribution of Eu2+ ions.
XMMPZCAT: A catalogue of photometric redshifts for X-ray sources
Authors: Ruiz A. , Corral A. , Mountrichas G. , Georgantopoulos I. 
Published: July 2018

Aims. The third version of the XMM-Newton serendipitous catalogue (3XMM), containing almost half million sources, is now the largest X-ray catalogue. However, its full scientific potential remains untapped due to the lack of distance information (i.e. redshifts) for the majority of its sources. Here we present XMMPZCAT, a catalogue of photometric redshifts (photo-z) for 3XMM sources.
Methods. We searched for optical counterparts of 3XMM-DR6 sources outside the Galactic plane in the SDSS and Pan-STARRS surveys, with the addition of near-(NIR) and mid-infrared (MIR) data whenever possible (2MASS, UKIDSS, VISTA-VHS, and AllWISE). We used this photometry data set in combination with a training sample of 5157 X-ray selected sources and the MLZ-TPZ package, a supervised machine learning algorithm based on decision trees and random forests for the calculation of photo-z.
Results. We have estimated photo-z for 100 178 X-ray sources, about 50% of the total number of 3XMM sources (205 380) in the XMM-Newton fields selected to build this catalogue (4208 out of 9159). The accuracy of our results highly depends on the available photometric data, with a rate of outliers ranging from 4% for sources with data in the optical + NIR + MIR, up to ~40% for sources with only optical data. We also addressed the reliability level of our results by studying the shape of the photo-z probability density distributions.
Bayesian group finder based on marked point processes
Authors: Tempel Elmo , Kruuse Maarja , Kipper Rain , Tuvikene Taavi , Sorce Jenny G. , Stoica Radu S. 
Published: July 2018

Context. Galaxy groups and clusters are formidable cosmological probes. They permit the studying of the environmental effects on galaxy formation. A reliable detection of galaxy groups is an open problem and is important for ongoing and future cosmological surveys.
Aims. We propose a probabilistic galaxy group detection algorithm based on marked point processes with interactions.
Methods. The pattern of galaxy groups in a catalogue is seen as a random set of interacting objects. The positions and the interactions of these objects are governed by a probability density. The parameters of the probability density were chosen using a priori knowledge. The estimator of the unknown cluster pattern is given by the configuration of objects maximising the proposed probability density. Adopting the Bayesian framework, the proposed probability density is maximised using a simulated annealing (SA) algorithm. At fixed temperature, the SA algorithm is a Monte Carlo sampler of the probability density. Hence, the method provides “for free” additional information such as the probabilities that a point or two points in the observation domain belong to the cluster pattern, respectively. These supplementary tools allow the construction of tests and techniques to validate and to refine the detection result.
Results. To test the feasibility of the proposed methodology, we applied it to the well-studied 2MRS data set. Compared to previously published Friends-of-Friends (FoF) group finders, the proposed Bayesian group finder gives overall similar results. However for specific applications, like the reconstruction of the local Universe, the details of the grouping algorithms are important.
Conclusions. The proposed Bayesian group finder is tested on a galaxy redshift survey, but more detailed analyses are needed to understand the actual capabilities of the algorithm regarding upcoming cosmological surveys. The presented mathematical framework permits adapting it easily for other data sets (in astronomy and in other fields of sciences). In cosmology, one promising application is the detection of galaxy groups in photometric galaxy redshift surveys, while taking into account the full photometric redshift posteriors.
Statistical analysis of UV spectra of a quiescent prominence observed by IRIS
Authors: Jejčič S. , Schwartz P. , Heinzel P. , Zapiór M. , Gunár S. 
Published: July 2018

Context. The paper analyzes the structure and dynamics of a quiescent prominence that occurred on October 22, 2013 and was observed by several instruments including the Interface Region Imaging Spectrograph (IRIS).
Aims. We aim to determine the physical characteristics of the observed prominence using Mg II k and h (2796 and 2803 Å), C II (1334 and 1336 Å), and Si IV (1394 Å) lines observed by IRIS. In addition we study the dynamical behavior of the prominence.
Methods. We employed the one-dimensional non-LTE (departures from the local thermodynamic equilibrium – LTE) modeling of Mg II lines assuming static isothermal-isobaric slabs. We selected a large grid of models with realistic input parameters expected for quiescent prominences (temperature, gas pressure, effective thickness, microturbulent velocity, height above the solar surface) and computed synthetic Mg II lines. The method of Scargle periodograms was used to detect possible prominence oscillations.
Results. We analyzed 2160 points of the observed prominence in five different sections along the slit averaged over ten pixels due to low signal to noise ratio in the C II and Si IV lines. We computed the integrated intensity for all studied lines, while the central intensity and reversal ratio was determined only for both Mg II and C II 1334 lines. We plotted several correlations: time evolution of the integrated intensities and central intensities, scatter plots between all combinations of line integrated intensities, and reversal ratio as a function of integrated intensity. We also compared Mg II observations with the models. Results show that more than two-thirds of Mg II profiles and about one-half of C II 1334 profiles are reversed. Profiles of Si IV are generally unreversed. The Mg II and C II lines are optically thick, while the Si IV line is optically thin.
Conclusions. The studied prominence shows no global oscillations in the Mg II and C II lines. Therefore, the observed time variations are caused by random motions of fine structures with velocities up to 10 km s−1. The observed average ratio of Mg II k to Mg II h line intensities can be used to determine the prominence’s characteristic temperature. Certain disagreements between observed and synthetic line intensities of Mg II lines point to the necessity of using more complex two-dimensional multi-thread modeling in the future.
Merkelzellkarzinome der Kopf-Hals-Region
Authors: Steinbichler Teresa B. , Hauser Undine , Schartinger Volker H. , Dudás József , Riechelmann Herbert 
Published: July 2018

ZusammenfassungMerkelzellkarzinome (MCC) sind hochmaligne neuroendokrine Tumore der Haut. Auch wenn sie sehr selten sind, hat sich ihre Inzidenz in den letzten 20 Jahren
verdoppelt. Ihre Mortalität ist höher als die des malignen Melanoms. Risikofaktor ist neben UV-Exposition eine iatrogene oder anderweitige Immunsuppression. MCC
betreffen vor allem Menschen jenseits des 70. Lebensjahrs und treten in der Hälfte der Fälle in der Kopf-Hals-Region auf.
Immunonkologie – ein Überblick
Authors: Kobold Sebastian , Krackhardt Angela , Schlösser Hans , Wolf Dominik 
Published: July 2018

AbstractPioneering work has unraveled the role of the immune system in the development and control of cancer. This knowledge has set the basis for the successful implementation of immunotherapy into the standard of care for a large number of cancer types. Based on response rates and prolongation of overall survival, immunotherapeutic approaches have been approved in a growing number of tumor diseases. Activation or therapeutic utilization of T cells represent the basis of these concepts. Checkpoint inhibitory antibodies inhibiting CTLA-4, PD1 and PD-L1 receptors and ligands induce long-term clinical tumor control in a significant number of cancer patients including metastatic melanoma and non-small cell lung cancer. As an alternative concept of T cell activation, the dual CD19 – CD3 targeting bispecific antibody blinatumomab has been approved for refractory acute lymphatic B-cell leukemia (ALL). Moreover, T cells genetically engineered with an anti-CD19-chimeric antigen receptor have also been approved for ALL and malignant B-cell lymphoma by the food and drug administration (FDA). In all of these immunotherapies, severe side effects may occur and require a well-trained team of physicians. Moreover, the growing number of clinically investigated and validated novel compounds as well as cellular therapeutics accentuate the complexity and challenge of this treatment modality. This review highlights the most prominent recent clinical developments in the field of immuno-oncology.