bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chameleon: A generalized, connectivity altering software for tackling properties of realistic polymer systems
Authors: Alexiadis Orestis , Cheimarios Nikolaos , Peristeras Loukas D. , Bick Andreas , Mavrantzas Vlasis G. , Theodorou Doros N. , Hill Jörg‐Rüdiger , Krokidis Xenophon 
Published: April 2019

Chameleon, a generalized Monte Carlo software for the phase space analysis of complex, realistic polymer systems is presented. Chameleon implements the so‐called connectivity altering technique applied on polymer chains through Monte Carlo moves that do not mimic actual dynamics. These moves enable an accurate and fast sampling of configuration space and produce a robust environment for the prediction of the polymer's properties. Chameleon's capabilities are presented through a series of computations on well‐studied systems, namely polyethylene (PE), polystyrene (PS) and polyvinyl chloride (PVC) in the melt state. PE, PS and PVC are described via a united atom, coarse grained and all atom representation, respectively. The computed structural and volumetric properties of these systems are compared to experimental data and previous computational works, and found to be in excellent agreement. Finally, the shared memory parallel capabilities of Chameleon are presented and quantified in terms of speedup.This article is categorized under:
Software > Simulation Methods
Structure and Mechanism > Computational Materials Science
Theoretical and Physical Chemistry > Statistical Mechanics
Developmental origins and oncogenic pathways in malignant brain tumors
Authors: Lu Q. Richard , Qian Lily , Zhou Xianyao 
Published: April 2019

Brain tumors such as adult glioblastomas and pediatric high‐grade gliomas or medulloblastomas are among the leading causes of cancer‐related deaths, exhibiting poor prognoses with little improvement in outcomes in the past several decades. These tumors are heterogeneous and can be initiated from various neural cell types, contributing to therapy resistance. How such heterogeneity arises is linked to the tumor cell of origin and their genetic alterations. Brain tumorigenesis and progression recapitulate key features associated with normal neurogenesis; however, the underlying mechanisms are quite dysregulated as tumor cells grow and divide in an uncontrolled manner. Recent comprehensive genomic, transcriptomic, and epigenomic studies at single‐cell resolution have shed new light onto diverse tumor‐driving events, cellular heterogeneity, and cells of origin in different brain tumors. Primary and secondary glioblastomas develop through different genetic alterations and pathways, such as EGFR amplification and IDH1/2 or TP53 mutation, respectively. Mutations such as histone H3K27M impacting epigenetic modifications define a distinct group of pediatric high‐grade gliomas such as diffuse intrinsic pontine glioma. The identification of distinct genetic, epigenomic profiles and cellular heterogeneity has led to new classifications of adult and pediatric brain tumor subtypes, affording insights into molecular and lineage‐specific vulnerabilities for treatment stratification. This review discusses our current understanding of tumor cells of origin, heterogeneity, recurring genetic and epigenetic alterations, oncogenic drivers and signaling pathways for adult glioblastomas, pediatric high‐grade gliomas, and medulloblastomas, the genetically heterogeneous groups of malignant brain tumors.This article is categorized under:

Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics
Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cell Differentiation and Reversion
Signaling Pathways > Cell Fate Signaling
Evaluation of log‐of‐power extremum seeking control for wind turbines using large eddy simulations
Authors: Ciri Umberto , Leonardi Stefano , Rotea Mario A. 
Published: April 2019

AbstractThe extremum seeking control (ESC) algorithm has been proposed to determine operating parameters that maximize power production below rated wind speeds (region II). This is usually done by measuring the turbine's power signal to determine optimal values for parameters of the control law or actuator settings. This paper shows that the standard ESC with power feedback is quite sensitive to variations in mean wind speed, with long convergence time at low wind speeds and aggressive transient response, possibly unstable, at high wind speeds. The paper also evaluates the performance, as measured by the dynamic and steady state response, of the ESC with feedback of the logarithm of the power signal (LP‐ESC). Large eddy simulations (LES) demonstrate that the LP‐ESC, calibrated at a given wind speed, exhibits consistent robust performance at all wind speeds in a typical region II. The LP‐ESC is able to achieve the optimal set‐point within a prescribed settling time, despite variations in the mean wind speed, turbulence, and shear. The LES have been conducted using realistic wind input profiles with shear and turbulence. The ESC and LP‐ESC are implemented in the LES without assuming the availability of analytical gradients.
Optimality of the relaxed polar factors by a characterization of the set of real square roots of real symmetric matrices
Authors: Borisov Lev , Fischle Andreas , Neff Patrizio 
Published: April 2019

AbstractWe consider the problem to determine the optimal rotations which minimize
urn:x-wiley:00442267:media:zamm201800120:zamm201800120-math-0002for a given diagonal matrix with positive entries . The objective function W is the reduced form of the Cosserat shear‐stretch energy, which, in its general form, is a contribution in any geometrically nonlinear, isotropic, and quadratic Cosserat micropolar (extended) continuum model. We characterize the critical points of the energy , determine the global minimizers and compute the global minimum. This proves the correctness of previously obtained formulae for the optimal Cosserat rotations in dimensions two and three. The key to the proof is the result that every real matrix whose square is symmetric can be written in some orthonormal basis as a block‐diagonal matrix with blocks of size at most two.
Race Matters: Income Shares, Income Inequality, and Income Mobility for All U.S. Races
Authors: Akee Randall , Jones Maggie R. , Porter Sonya R. 
Published: April 2019

Abstract
Using unique linked data, we examine income inequality and mobility across racial and ethnic groups in the United States. Our data encompass the universe of income tax filers in the United States for the period 2000–2014, matched with individual-level race and ethnicity information from multiple censuses and American Community Survey data. We document both income inequality and mobility trends over the period. We find significant stratification in terms of average incomes by racial/ethnic group and distinct differences in within-group income inequality. The groups with the highest incomes—whites and Asians—also have the highest levels of within-group inequality and the lowest levels of within-group mobility. The reverse is true for the lowest-income groups: blacks, American Indians, and Hispanics have lower within-group inequality and immobility. On the other hand, low-income groups are also highly immobile in terms of overall, rather than within-group, mobility. These same groups also have a higher probability of experiencing downward mobility compared with whites and Asians. We also find that within-group income inequality increased for all groups between 2000 and 2014, and the increase was especially large for whites. The picture that emerges from our analysis is of a rigid income structure, with mainly whites and Asians positioned at the top and blacks, American Indians, and Hispanics confined to the bottom.
Testing the analytical performance of handheld XRF using marine sediments of IODP Expedition 355
Authors: Hahn A. , Bowen M. G. , Clift P. D. , Kulhanek D. K. , Lyle M. W. 
Published: April 2019

AbstractObtaining geochemical profiles using X-ray fluorescent (XRF) techniques has become a standard procedure in many sediment core studies. The resulting datasets are not only important tools for palaeoclimatic and palaeoceanographic reconstructions, but also for stratigraphic correlation. The International Ocean Discovery Program (IODP) has therefore recently introduced shipboard application of a handheld XRF device, making geochemical data directly available to the science party. In all XRF scanning techniques, the physical properties of wet core halves cause substantial analytical deviations. In order to obtain estimates of element concentrations (e.g. for quantitative analyses of fluxes or mass-balance calculations), a calibration of the scanning data is required. We test whether results from the handheld XRF analysis on discrete samples are suitable for calibrating scanning data. Log-ratios with Ca as a common denominator were calculated. The comparison between the handheld device and conventional measurements show that the latter provide high-quality data describing Al, Si, K, Ca, Ti, Mn, Fe, Zn, Rb and Sr content (R2 compared with conventional measurements: ln(Al/Ca) = 0.99, ln(Si/Ca) = 0.98, ln(K/Ca) = 0.99, ln(Ti/Ca) = 0.99, ln(Mn/Ca) = 0.99, ln(Fe/Ca) = 0.99, ln(Zn/Ca) = 0.99 and ln(Sr/Ca) = 0.99). Our results imply that discrete measurements using the shipboard handheld analyser are suitable for the calibration of XRF scanning data. Our test was performed on downcore sediments from IODP Expedition 355 that display a wide variety of lithologies of both terrestrial and marine origin. The implication is that our findings are valid on a general scale and that shipboard handheld XRF analysis on discrete samples should be used for calibrating XRF scanning data.
Efficient electron transfer across hydrogen bond interfaces by proton-coupled and -uncoupled pathways
Authors: Cheng Tao , Shen Dong Xue , Meng Miao , Mallick Suman , Cao Lijiu , Patmore Nathan J. , Zhang Hong Li , Zou Shan Feng , Chen Huo Wen , Qin Yi , Wu Yi Yang , Liu Chun Y. 
Published: April 2019

AbstractThermal electron transfer through hydrogen bonds remains largely unexplored. Here we report the study of electron transfer through amide-amide hydrogen bonded interfaces in mixed-valence complexes with covalently bonded Mo2units as the electron donor and acceptor. The rate constants for electron transfer through the dual hydrogen bonds across a distance of 12.5 Å are on the order of ∼ 1010 s−1, as determined by optical analysis based on Marcus–Hush theory and simulation of ν(NH) vibrational band broadening, with the electron transfer efficiencies comparable to that of π conjugated bridges. This work demonstrates that electron transfer across a hydrogen bond may proceed via the known proton-coupled pathway, as well as an overlooked proton-uncoupled pathway that does not involve proton transfer. A mechanistic switch between the two pathways can be achieved by manipulation of the strengths of electronic coupling and hydrogen bonding. The knowledge of the non-proton coupled pathway has shed light on charge and energy transport in biological systems.
Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory
Authors: Bertero Alessandro , Fields Paul A. , Ramani Vijay , Bonora Giancarlo , Yardimci Galip G. , Reinecke Hans , Pabon Lil , Noble William S. , Shendure Jay , Murry Charles E. 
Published: April 2019

AbstractFunctional changes in spatial genome organization during human development are poorly understood. Here we report a comprehensive profile of nuclear dynamics during human cardiogenesis from pluripotent stem cells by integrating Hi-C, RNA-seq and ATAC-seq. While chromatin accessibility and gene expression show complex on/off dynamics, large-scale genome architecture changes are mostly unidirectional. Many large cardiac genes transition from a repressive to an active compartment during differentiation, coincident with upregulation. We identify a network of such gene loci that increase their association inter-chromosomally, and are targets of the muscle-specific splicing factor RBM20. Genome editing studies show that TTN pre-mRNA, the main RBM20-regulated transcript in the heart, nucleates RBM20 foci that drive spatial proximity between the TTN locus and other inter-chromosomal RBM20 targets such as CACNA1C and CAMK2D. This mechanism promotes RBM20-dependent alternative splicing of the resulting transcripts, indicating the existence of a cardiac-specific trans-interacting chromatin domain (TID) functioning as a splicing factory.
Enhanced carbon dioxide electrolysis at redox manipulated interfaces
Authors: Wang Wenyuan , Gan Lizhen , Lemmon John P. , Chen Fanglin , Irvine John T. S. , Xie Kui 
Published: April 2019

AbstractUtilization of carbon dioxide from industrial waste streams offers significant reductions in global carbon dioxide emissions. Solid oxide electrolysis is a highly efficient, high temperature approach that reduces polarization losses and best utilizes process heat; however, the technology is relatively unrefined for currently carbon dioxide electrolysis. In most electrochemical systems, the interface between active components are usually of great importance in determining the performance and lifetime of any energy materials application. Here we report a generic approach of interface engineering to achieve active interfaces at nanoscale by a synergistic control of materials functions and interface architectures. We show that the redox-manipulated interfaces facilitate the atomic oxygen transfer from adsorbed carbon dioxide molecules to the cathode lattice that determines carbon dioxide electrolysis at elevated temperatures. The composite cathodes with in situ grown interfaces demonstrate significantly enhanced carbon dioxide electrolysis and improved durability.
Free radical sensors based on inner-cutting graphene field-effect transistors
Authors: Wang Zhen , Yi Kongyang , Lin Qiuyuan , Yang Lei , Chen Xiaosong , Chen Hui , Liu Yunqi , Wei Dacheng 
Published: April 2019

AbstractDue to ultra-high reactivity, direct determination of free radicals, especially hydroxyl radical (•OH) with ultra-short lifetime, by field-effect transistor (FET) sensors remains a challenge, which hampers evaluating the role that free radical plays in physiological and pathological processes. Here, we develop a •OH FET sensor with a graphene channel functionalized by metal ion indicators. At the electrolyte/graphene interface, highly reactive •OH cuts the cysteamine to release the metal ions, resulting in surface charge de-doping and a current response. By this inner-cutting strategy, the •OH is selectively detected with a concentration down to 10−9 M. Quantitative metal ion doping enables modulation of the device sensitivity and a quasi-quantitative detection of •OH generated in aqueous solution or from living cells. Owing to its high sensitivity, selectivity, real-time label-free response, capability for quasi-quantitative detection and user-friendly portable feature, it is valuable in biological research, human health, environmental monitoring, etc.
Surface chromium on Terracotta Army bronze weapons is neither an ancient anti-rust treatment nor the reason for their good preservation
Authors: Martinón-Torres Marcos , Li Xiuzhen , Xia Yin , Benzonelli Agnese , Bevan Andrew , Ma Shengtao , Huang Jianhua , Wang Liang , Lan Desheng , Liu Jiangwei , Liu Siran , Zhao Zhen , Zhao Kun , Rehren Thilo 
Published: April 2019

AbstractFor forty years, there has been a widely held belief that over 2,000 years ago the Chinese Qin developed an advanced chromate conversion coating technology (CCC) to prevent metal corrosion. This belief was based on the detection of chromium traces on the surface of bronze weapons buried with the Chinese Terracotta Army, and the same weapons’ very good preservation. We analysed weapons, lacquer and soils from the site, and conducted experimental replications of CCC and accelerated ageing. Our results show that surface chromium presence is correlated with artefact typology and uncorrelated with bronze preservation. Furthermore we show that the lacquer used to cover warriors and certain parts of weapons is rich in chromium, and we demonstrate that chromium on the metals is contamination from nearby lacquer after burial. The chromium anti-rust treatment theory should therefore be abandoned. The good metal preservation probably results from the moderately alkaline pH and very small particle size of the burial soil, in addition to bronze composition.
A novel generic dictionary-based denoising method for improving noisy and densely packed nuclei segmentation in 3D time-lapse fluorescence microscopy images
Authors: Nasser Lamees , Boudier Thomas 
Published: April 2019

AbstractTime-lapse fluorescence microscopy is an essential technique for quantifying various characteristics of cellular processes, i.e. cell survival, migration, and differentiation. To perform high-throughput quantification of cellular processes, nuclei segmentation and tracking should be performed in an automated manner. Nevertheless, nuclei segmentation and tracking are challenging tasks due to embedded noise, intensity inhomogeneity, shape variation as well as a weak boundary of nuclei. Although several nuclei segmentation approaches have been reported in the literature, dealing with embedded noise remains the most challenging part of any segmentation algorithm. We propose a novel denoising algorithm, based on sparse coding, that can both enhance very faint and noisy nuclei signal but simultaneously detect nuclei position accurately. Furthermore our method is based on a limited number of parameters, with only one being critical, which is the approximate size of the objects of interest. We also show that our denoising method coupled with classical segmentation method works properly in the context of the most challenging cases. To evaluate the performance of the proposed method, we tested our method on two datasets from the cell tracking challenge. Across all datasets, the proposed method achieved satisfactory results with 96:96% recall for the C. elegans dataset. Besides, in the Drosophila dataset, our method achieved very high recall (99:3%).
Glucose-dependent Insulinotropic Polypeptide (GIP) Resistance and β-cell Dysfunction Contribute to Hyperglycaemia in Acromegaly
Authors: Shekhawat Vikram Singh , Bhansali Shobhit , Dutta Pinaki , Mukherjee Kanchan Kumar , Vaiphei Kim , Kochhar Rakesh , Sinha Saroj K. , Sachdeva Naresh , Kurpad Anura V. , Bhat Kishor , Mudaliar Sunder , Bhansali Anil 
Published: April 2019

AbstractImpaired insulin sensitivity (IS) and β-cell dysfunction result in hyperglycaemia in patients of acromegaly. However, alterations in incretins and their impact on glucose-insulin homeostasis in these patients still remain elusive. Twenty patients of active acromegaly (10 each, with and without diabetes) underwent hyperinsulinemic euglycaemic clamp and mixed meal test, before and after surgery, to measure indices of IS, β-cell function, GIP, GLP-1 and glucagon response. Immunohistochemistry (IHC) for GIP and GLP-1 was also done on intestinal biopsies of all acromegalics and healthy controls. Patients of acromegaly, irrespective of presence or absence of hyperglycaemia, had similar degree of insulin resistance, however patients with diabetes exhibited hyperglucagonemia, and compromised β-cell function despite significantly higher GIP levels. After surgery, indices of IS improved, GIP and glucagon levels decreased significantly in both the groups, while there was no significant change in indices of β-cell function in those with hyperglycaemia. IHC positivity for GIP, but not GLP-1, staining cells in duodenum and colon was significantly lower in acromegalics with diabetes as compared to healthy controls possibly because of high K-cell turnover. Chronic GH excess induces an equipoise insulin resistance in patients of acromegaly irrespective of their glycaemic status. Dysglycaemia in these patients is an outcome of β-cell dysfunction consequent to GIP resistance and hyperglucagonemia.
Synthesis and Optimization of Ti/Li/Al Ternary Layered Double Hydroxides for Efficient Photocatalytic Reduction of CO2 to CH4
Authors: Kong Ting-Ting , Huang Jian , Jia Xin-Gang , Wang Wen-Zhen , Zhou Yong 
Published: April 2019

AbstractA series of Ti/Li/Al ternary layered double hydroxides (TiLiAl-LDHs) with different Ti:Li:Al molar ratios were prepared by a coprecipitation method for photocatalytic CO2 reduction. It was demonstrated that the contents of anions between the layers of Ti/Li/Al-LDHs greatly determined the photocatalytic activity for CO2 reduction. With Ti:Li:Al molar ratios optimized to be 1:3:2, the largest contents of $${{\bf{CO}}}_{{\bf{3}}}^{{\bf{2}}}$$

CO

3

2

− anion and hydroxyl group were obtained for the Ti1Li3Al2-LDHs sample, which exhibited the highest photocatalytic activity for CO2 reduction, with CH4 production rate achieving 1.33 mmol h−1 g−1. Moreover, the theoretical calculations show that Ti1Li3Al2-LDHs is a p-type semiconductor with the narrowest band gap among all the obtained TiLiAl-LDHs. After calcined at high temperatures such as 700 °C, and the obtained TiLiAl-700 sample showed much increased photocatalytic activity for CO2 reduction, with CH4 production rate reaching about 1.59 mmol h−1 g−1. This calcination induced photocatalytic enhancement should be related to the cystal structure transformation from hydrotalcite to mixed oxides containing high reactive oxygen species for more efficient CO2 reduction.
Cell cycle genes are downregulated after adipogenic triggering in human adipose tissue-derived stem cells by regulation of mRNA abundance
Authors: Marcon Bruna H. , Shigunov Patrícia , Spangenberg Lucia , Pereira Isabela Tiemy , de Aguiar Alessandra Melo , Amorín Rocío , Rebelatto Carmen K. , Correa Alejandro , Dallagiovanna Bruno 
Published: April 2019

AbstractThe adipogenic process is characterized by the expression of adipocyte differentiation markers that lead to changes in cell metabolism and to the accumulation of lipid droplets. Moreover, during early adipogenesis, cells undergo a strong downregulation of translational activity with a decrease in cell size, proliferation and migration. In the present study, we identified that after 24 hours of adipogenic induction, human adipose tissue-derived stem cells (hASCs) undergo a G1-cell cycle arrest consistent with reduced proliferation, and this effect was correlated with a shift in polysome profile with an enrichment of the monosomal fraction and a reduction of the polysomal fraction. Polysome profiling analysis also revealed that this change in the monosomal/polysomal ratio was related to a strong downregulation of cell cycle and proliferation genes, such as cyclins and cyclin-dependent kinases (CDKs). Comparing total and polysome-associated mRNA sequencing, we also observed that this downregulation was mostly due to a reduction of cell cycle and proliferation transcripts via control of total mRNA abundance, rather than by translational control.
Reabsorption cross section of Nd3+-doped quasi-three-level lasers
Authors: Chen Fei , Sun Junjie , Yan Renpeng , Yu Xin 
Published: April 2019

AbstractThe 4F3/2 → 4I9/2 laser transition of Nd3+-doped crystals emitting at 900 nm is a standard quasi-three-level laser system. The reabsorption effect is one of the factors that restricts laser output power. Based on rate equations, a theoretical model considering the reabsorption effect for continuous-wave Nd3+-doped quasi-three-level lasers is established. The simulation results indicate that the reabsorption effect should be restrained to improve laser characteristics, which are mainly influenced by the Nd3+-doping concentration, laser medium length, pumping beam divergence angle and output mirror transmissivity. The optimal experimental results illustrate the availability of a theoretical model that considers the reabsorption effect. To quantitatively evaluate the reabsorption effect of a Nd3+-doped laser medium, a reabsorption cross section is proposed for the first time to the best of our knowledge. Comparing the experimental results and theoretical calculation results, the reabsorption cross section is estimated for a 912-nm Nd:GdVO4 laser, 914-nm Nd:YVO4 laser and 946-nm Nd:YAG laser.