bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of pore surfaces on the electronic states of metal complexes formed on bipyridine periodic mesoporous organosilica
Authors: Shirai Soichi , Waki Minoru , Maegawa Yoshifumi , Yamada Yuri , Inagaki Shinji
Published: January 2019

A combined experimental–theoretical study clarifies correlations between the pore-surface structures and the electronic properties of metal complexes on BPy-PMO.
Double -shelled hollow ZnO/carbon nanocubes as an efficient solid-phase microextraction coating for the extraction of broad-spectrum pollutants
Authors: Hu Xingru , Wang Chaohai , Luo Rui , Liu Chao , Qi Junwen , Sun Xiuyun , Shen Jinyou , Han Weiqing , Wang Lianjun , Li Jiansheng
Published: January 2019

Efficient extraction of pollutants with different chemical properties from environmental samples has attracted great attention in the development of analytical chemistry.
Acidity-triggered zwitterionic prodrug nano-carriers with AIE properties and amplification of oxidative stress for mitochondria-targeted cancer theranostics
Authors: Xu Junhuai , Yan Bin , Du Xiaosheng , Xiong Junjie , Zhou Mi , Wang Haibo , Du Zongliang
Published: January 2019

A TPE-based polyurethane prodrug has been established for mitochondria-targeting drug delivery and real-time monitoring.
Aromatic C–H amination in hexafluoroisopropanol
Authors: D'Amato Erica M. , Börgel Jonas , Ritter Tobias
Published: January 2019

We report direct amination of electron-poor arenes and evaluate the crucial factors for the enhanced reactivity in hexafluoroisopropanol.
Retraction: Comprehensive insights into the charge dynamics process and excellent photoelectric properties of heterojunction solar cells
Authors: Liu Xiangyang , Wang Shun , Zheng Haiwu , Cheng Xiuying , Gu Yuzong
Published: January 2019

Retraction of ‘Comprehensive insights into the charge dynamics process and excellent photoelectric properties of heterojunction solar cells’ by Xiangyang Liu et al., Phys. Chem. Chem. Phys., 2016, 18, 24299–24306.
Niclosamide-induced Wnt signaling inhibition in colorectal cancer is mediated by autophagy
Authors: Wang Jiangbo , Ren Xiu-rong , Piao Hailan , Zhao Shengli , Osada Takuya , Premont Richard T. , Mook Robert A. , Morse Michael A. , Lyerly Herbert Kim , Chen Wei
Published: January 2019

The Wnt signaling pathway, known for regulating genes critical to normal embryonic development and tissue homeostasis, is dysregulated in many types of cancer. Previously, we identified that the anthelmintic drug niclosamide inhibited Wnt signaling by promoting internalization of Wnt receptor Frizzled 1 and degradation of Wnt signaling pathway proteins, Dishevelled 2 and β-catenin, contributing to suppression of colorectal cancer growth in vitro and in vivo. Here, we provide evidence that niclosamide-mediated inhibition of Wnt signaling is mediated through autophagosomes induced by niclosamide. Specifically, niclosamide promotes the co-localization of Frizzled 1 or β-catenin with LC3, an autophagosome marker. Niclosamide inhibition of Wnt signaling is attenuated in autophagosome-deficient ATG5−/− MEF cells or cells expressing shRNA targeting Beclin1, a critical constituent of autophagosome. Treatment with the autophagosome inhibitor 3MA blocks niclosamide-mediated Frizzled 1 degradation. The sensitivity of colorectal cancer cells to growth inhibition by niclosamide is correlated with autophagosome formation induced by niclosamide. Niclosamide inhibits mTORC1 and ULK1 activities and induces LC3B expression in niclosamide-sensitive cell lines, but not in the niclosamide-resistant cell lines tested. Interestingly, niclosamide is a less effective inhibitor of Wnt-responsive genes (β-catenin, c-Myc, and Survivin) in the niclosamide-resistant cells than in the niclosamide-sensitive cells, suggesting that deficient autophagy induction by niclosamide compromises the effect of niclosamide on Wnt signaling. Our findings provide a mechanistic understanding of the role of autophagosomes in the inhibition of Wnt signaling by niclosamide and may provide biomarkers to assist selection of patients whose tumors are likely to respond to niclosamide.
The Value of Electroencephalogram in Assessing Children With Speech and Language Impairments
Authors: Systad Silje , Bjørnvold Marit , Sørensen Christiane , Lyster Solveig-Alma Halaas
Published: January 2019

Purpose

We sought to estimate the prevalence of isolated epileptiform activity (IEA) in children with speech and language impairments and discuss the utility of an electroencephalogram (EEG) in assessing these children.

Method

We conducted a systematic review and searched for eligible studies in 8 databases. All languages were included, and meta-analyses were performed.

Results

We found 55 prevalence estimates (8 with control group). The odds of having IEA were 6 times greater for children with speech and language impairments than for typically developing children. The overall pooled prevalence of IEA was 27.3%. A wide variation between the prevalence estimates was, to a certain degree, explained by type of impairment (8.1% in speech impairments, 25.8% in language impairments, and 51.5% in language regression). Sleep EEGs detected a significantly higher prevalence than awake EEGs. Although the presence of epilepsy gave a significantly higher prevalence than if epilepsy was not present, 33.5% of children with language impairment but without epilepsy were found to have IEA in sleep EEGs.

Conclusions

This systematic review shows that IEA is 6 times more prevalent in children with speech and language impairment than in typically developing children. However, the prevalence rates vary to a great extent. Uncovering IEA will, in addition to information from other clinical assessments, provide a more comprehensive understanding of the child's impairments. We argue that, although EEG is of questionable value when assessing children with speech impairments, sleep EEG could be valuable when assessing children with language impairments and, in particular, children who experience language regression.
Advantage of prediction and mental imagery for goal‐directed behaviour in agents and robots
Authors: Krichmar Jeffrey L. , Hwu Tiffany , Zou Xinyun , Hylton Todd
Published: January 2019

Mental imagery and planning are important aspects of cognitive behaviour. Being able to predict outcomes through mental simulation can increase environmental fitness and reduce uncertainty. Such predictions reduce surprise and fit with thermodynamically driven theories of brain function by attempting to reduce entropy. In the present work, the authors tested these ideas in a predator–prey scenario where agents with a limited energy budget had to maximise food intake, while avoiding a predator. Forward planning agents, with the ability to mentalise, to Actor Critic agents that do not plan beyond the current state were also compared. The authors show that the ability to mentalise has distinct advantages when in noisy, uncertain stimuli. These advantages are even more prevalent when tested in the real world on physical robots. The authors’ results highlight the importance of taking into consideration mental imagery and embodiment when constructing artificial cognitive systems.
Fault recoverability analysis of interconnected systems
Authors: Huang Chengkai , Yang Hao , Ren Wenjing , Jiang Bin
Published: January 2019

Fault recoverability (FR) property reflects the capability of the system to accommodate faults through control reconfiguration under admissible input energy constraints. This study analyses the FR of interconnected non‐linear and linear systems. Several explicit bounds of the amount of control energy required to drive the initial states of the interconnected system to the origin are computed. This helps to evaluate the FR under both centralised and distributed control schemes. The new results are further applied to meta aircraft configuration to verify the effectiveness.
The potential of combining MATISSE and ALMA observations: constraining the structure of the innermost region in protoplanetary discs
Authors: Kobus J. , Wolf S. , Brunngräber R.
Published: January 2019

Context. In order to study the initial conditions of planet formation, it is crucial to obtain spatially resolved multi-wavelength observations of the innermost region of protoplanetary discs.

Aims. We evaluate the advantage of combining observations with MATISSE/VLTI and ALMA to constrain the radial and vertical structure of the dust in the innermost region of circumstellar discs in nearby star-forming regions.

Methods. Based on a disc model with a parameterized dust density distribution, we apply 3D radiative-transfer simulations to obtain ideal intensity maps. These are used to derive the corresponding wavelength-dependent visibilities we would obtain with MATISSE as well as ALMA maps simulated with CASA.

Results. Within the considered parameter space, we find that constraining the dust density structure in the innermost 5 au around the central star is challenging with MATISSE alone, whereas ALMA observations with reasonable integration times allow us to derive significant constraints on the disc surface density. However, we find that the estimation of the different disc parameters can be considerably improved by combining MATISSE and ALMA observations. For example, combining a 30-min ALMA observation (at 310 GHz with an angular resolution of 0.03′′) for MATISSE observations in the L and M bands (with visibility accuracies of about 3%) allows the radial density slope and the dust surface density profile to be constrained to within Δα = 0.3 and Δ(α − β) = 0.15, respectively. For an accuracy of ~1% even the disc flaring can be constrained to within Δβ = 0.1. To constrain the scale height to within 5 au, M band accuracies of 0.8% are required. While ALMA is sensitive to the number of large dust grains settled to the disc midplane we find that the impact of the surface density distribution of the large grains on the observed quantities is small.
Asymmetric jet production in the active galactic nucleus of NGC 1052
Authors: Baczko A.-K. , Schulz R. , Kadler M. , Ros E. , Perucho M. , Fromm C. M. , Wilms J.
Published: January 2019

Context. Few active galactic nuclei (AGN) reveal double-sided jet systems. However, these systems are crucial to understand basic physical properties of extragalactic jets.

Aims. We address the questions whether jets in AGN are symmetric in nature, how well they are collimated on small scales, and how they evolve with time.

Methods. We monitored the sub-parsec scale morphology of NGC 1052 with the Very Long Baseline Array at 43 GHz from 2005 to 2009.

Results. A detailed study of 29 epochs show a remarkable asymmetry between both jets. A kinematic analysis of the outflows reveals higher apparent velocities for the eastern (approaching) jet as compared to the western (receding) jet, i.e., βej = 0.529 ± 0.038 and βwj = 0.343 ± 0.037, respectively. Contradictory to previous studies, we find higher flux densities for the western jet as compared to the eastern. The distribution of brightness temperature and jet width features well-collimated jets up to 1 mas distance to the dynamic center and a nearly conical outflow further outward. By combining flux density ratios and velocities of the jet flows, we were unable to find a combination of intrinsic velocities and inclination angles of the jets that is consistent for all four years of observation; this contradicts findings for symmetrically evolving jets. Spectral index maps between quasi-simultaneous 22 GHz and 43 GHz observations support the existence of an optically thick absorber covering the innermost ≃1.6 mas around the 43 GHz central feature and an optically thin jet emission with a spectral index of ≤−1.

Conclusions. Our results fit into a picture in which we expect larger internal energy and/or magnetic flux in the western jet and higher kinetic energy in the eastern jet. Previous observations at lower frequencies have found slower velocities of the moving jet features as compared to this work. Considering the different velocities in different areas, we suggest a spine-sheath structure with a faster inner layer and slower outer layer.
Molecular gas in radio galaxies in dense megaparsec-scale environments at z = 0.4–2.6
Authors: Castignani G. , Combes F. , Salomé P. , Benoist C. , Chiaberge M. , Freundlich J. , De Zotti G.
Published: January 2019

Context. Low luminosity radio galaxies (LLRGs) typically reside in dense megaparsec-scale environments and are often associated with brightest cluster galaxies (BCGs). They are an excellent tool to study the evolution of molecular gas reservoirs in giant ellipticals, even close to the active galactic nucleus.

Aims. We investigate the role of dense megaparsec-scale environment in processing molecular gas in LLRGs in the cores of galaxy (proto-)clusters. To this aim we selected within the COSMOS and DES surveys a sample of five LLRGs at z = 0.4−2.6 that show evidence of ongoing star formation on the basis of their far-infrared (FIR) emission.

Methods. We assembled and modeled the FIR-to-UV spectral energy distributions (SEDs) of the five radio sources to characterize their host galaxies in terms of stellar mass and star formation rate. We observed the LLRGs with the IRAM-30 m telescope to search for CO emission. We then searched for dense megaparsec-scale overdensities associated with the LLRGs using photometric redshifts of galaxies and the Poisson Probability Method, which we have upgraded using an approach based on the wavelet-transform (wPPM), to ultimately characterize the overdensity in the projected space and estimate the radio galaxy miscentering. Color-color and color-magnitude plots were then derived for the fiducial cluster members, selected using photometric redshifts.

Results. Our IRAM-30 m observations yielded upper limits to the CO emission of the LLRGs, at z = 0.39, 0.61, 0.91, 0.97, and 2.6. For the most distant radio source, COSMOS-FRI 70 at z = 2.6, a hint of CO(7→6) emission is found at 2.2σ. The upper limits found for the molecular gas content M(H2)/M⋆ <  0.11, 0.09, 1.8, 1.5, and 0.29, respectively, and depletion time τdep ≲ (0.2−7) Gyr of the five LLRGs are overall consistent with the corresponding values of main sequence field galaxies. Our SED modeling implies large stellar-mass estimates in the range log(M⋆/M⊙) = 10.9−11.5, typical for giant ellipticals. Both our wPPM analysis and the cross-matching of the LLRGs with existing cluster/group catalogs suggest that the megaparsec-scale overdensities around our LLRGs are rich (≲1014 M⊙) groups and show a complex morphology. The color-color and color-magnitude plots suggest that the LLRGs are consistent with being star forming and on the high-luminosity tail of the red sequence. The present study thus increases the still limited statistics of distant cluster core galaxies with CO observations.

Conclusions. The radio galaxies of this work are excellent targets for ALMA as well as next-generation telescopes such as the James Webb Space Telescope.
Small-scale physical and chemical structure of diffuse and translucent molecular clouds along the line of sight to Sgr B2
Authors: Thiel V. , Belloche A. , Menten K. M. , Giannetti A. , Wiesemeyer H. , Winkel B. , Gratier P. , Müller H. S. P. , Colombo D. , Garrod R. T.
Published: January 2019

Context. The diffuse and translucent molecular clouds traced in absorption along the line of sight to strong background sources have so far been investigated mainly in the spectral domain because of limited angular resolution or small sizes of the background sources.

Aims. We aim to resolve and investigate the spatial structure of molecular clouds traced by several molecules detected in absorption along the line of sight to Sgr B2(N).

Methods. We have used spectral line data from the EMoCA survey performed with the Atacama Large Millimeter/submillimeter Array (ALMA), taking advantage of its high sensitivity and angular resolution. The velocity structure across the field of view is investigated by automatically fitting synthetic spectra to the detected absorption features, which allows us to decompose them into individual clouds located in the Galactic centre (GC) region and in spiral arms along the line of sight. We compute opacity maps for all detected molecules. We investigated the spatial and kinematical structure of the individual clouds with statistical methods and perform a principal component analysis to search for correlations between the detected molecules. To investigate the nature of the molecular clouds along the line of sight to Sgr B2, we also used archival Mopra data.

Results. We identify, on the basis of c-C3H2, 15 main velocity components along the line of sight to Sgr B2(N) and several components associated with the envelope of Sgr B2 itself. The c-C3H2 column densities reveal two categories of clouds. Clouds in Category I (3 kpc arm, 4 kpc arm, and some GC clouds) have smaller c-C3H2 column densities, smaller linewidths, and smaller widths of their column density PDFs than clouds in Category II (Scutum arm, Sgr arm, and other GC clouds). We derive opacity maps for the following molecules: c-C3H2, H13CO+, 13CO, HNC and its isotopologue HN13C, HC15N, CS and its isotopologues C34S and 13CS, SiO, SO, and CH3OH. These maps reveal that most molecules trace relatively homogeneous structures that are more extended than the field of view defined by the background continuum emission (about 15′′, that is 0.08–0.6 pc depending on the distance). SO and SiO show more complex structures with smaller clumps of size ~5–8′′. Our analysis suggests that the driving of the turbulence is mainly solenoidal in the investigated clouds.

Conclusions. On the basis of HCO+, we conclude that most line-of-sight clouds towards Sgr B2 are translucent, including all clouds where complex organic molecules were recently detected. We also conclude that CCH and CH are good probes of H2 in both diffuse and translucent clouds, while HCO+ and c-C3H2 in translucent clouds depart from the correlations with H2 found in diffuse clouds.
Combined methods of moment vectors and Stokes parameters to analyze tomographic image of plasma turbulence
Authors: Fujisawa A. , Nagashima Y. , Yamasaki K. , Inagaki S. , Yamada T. , Sasaki M.
Published: January 2019

Plasma turbulence tomography is now working to show a two dimensional structure and dynamics of plasma turbulence in a cylindrical plasma device, PANTA. A new method, the Stokes parameter analysis on moment vectors, is being developed to treat the image of plasma turbulence and extract hidden characteristics of polarization or rotation of spatial patterns created in turbulent plasmas. The article presents the explanation of the method and the application results obtained from a PANTA plasma.
Equations of motion for position-dependent coarse-grain mappings obtained with Mori-Zwanzig theory
Authors: Lynn Hudson , Thachuk Mark
Published: January 2019

A position-dependent transformation is introduced for mapping a system of atomistic particles to a system of coarse-grained (CG) variables, which under some circumstances might be considered particles. This CG mapping allows atomistic particles to simultaneously contribute to more than a single CG particle and to change in time the CG particle they are associated with. That is, the CG mapping is dynamic. Mori-Zwanzig theory is then used to obtain the equations of motion for this CG mapping, resulting in conservative, dissipative, and random force terms in generalized, non-Markovian Langevin equations. In addition to the usual forces arising from the effective CG potential derived from atomistic interactions, new forces arise from the dynamic changes in the CG mapping itself. These new forces effectively account for changes arising from fluxes of atomistic particles into and out of CG ones as time progresses. Several examples are given showing the range of problems that can be addressed with this new CG mapping. These range from the usual case where atomistic particles are grouped into large molecular-like chunks, with mappings that remain fixed in time and for which an atomistic particle is part of only a single CG one, to the case where CG particles resemble fluid elements, containing many hundreds of independent atomistic particles. The new CG mapping also allows for hybrid descriptions, in which a part of the system remains atomistic or molecular-like and a part is highly coarse-grained to mesoscopic fluid element-like particles, for example. In the latter case, the equations of motion then provide the correct formalism for determining the forces, beyond the usual conservative ones. This provides a theoretical foundation upon which approximate equations of motion can be formulated to thus build numerical algorithms for expanded applications of accurate CG molecular dynamics.
Spin-dependent scattering and magnetic proximity effect in Ni-doped Co/Cu multilayers as a probe of atomic magnetism
Authors: Tykhonenko-Polishchuk Yu. O. , Polishchuk D. M. , Polek T. I. , Yaremkevych D. D. , Kravets A. F. , Tovstolytkin A. I. , Timoshevskii A. N. , Korenivski V.
Published: January 2019

We investigate the spin transport and ferromagnetic resonance properties of giant magnetoresistance (GMR) Co/Cu-Ni multilayers with variable levels of Ni doping in the Cu spacer. We present an experimental evidence for a magnetic-to-diamagnetic transition in the atomic magnetic moment of Ni in the Cu matrix for concentrations below 15 at. % Ni. As its concentration is increased, Ni atoms turn into spin scattering centers, which is manifested experimentally as a step-like change in the GMR of the multilayers. This behavior is observed in multilayers with gradient-doped Cu spacers, where only the inner region was doped with Ni. In the uniformly doped spacers, the GMR decreases monotonously with increasing Ni content, indicating that Ni atoms are magnetic and act as spin relaxation centers in the entire dopant-concentration range studied. We explain the difference in the observed GMR behavior due to a strong magnetic proximity effect in the uniform spacers, which is efficiently suppressed in the gradient spacers. The observed magnetic phase transition is fully supported by our detailed ab initio calculations, taking into consideration structural relaxation in the system as well as potential Ni clustering. Controlling the loss or gain of the atomic magnetism for a specific dopant can be a tool in probing and controlling spin relaxation in materials and devices for spin-valve and spin-torque based applications.
One dimensional Cherenkov processes in ferromagnetic insulator
Authors: Wei Tongli , Li Yaojin , Ma Decheng , Jia Chenglong
Published: January 2019

One dimensional Cherenkov processes in ferromagnetic insulators are studied with perturbation theory under the constraint condition of conservation of energy and momentum. It is shown that the magnon-phonon interaction channels are limited and wave number dependent, which result in, respectively, 1/k2 and 1/k4 dependence of the lifetime and the relaxation time of long wavelength magnons. The reciprocal of relaxation time between magnons and phonons, 1/τmp, is found to be a linearly increasing function of the temperature in the high temperature regime. Based on the Sanders-Walton model, we further show that when a thermal (phonon) gradient is applied along the system, the temperature difference between the phonon bath and the magnons with wave-vector k becomes more pronounced as k decreases.
Spin-orbit torque-induced switching of in-plane magnetized elliptic nanodot arrays with various easy-axis directions measured by differential planar Hall resistance
Authors: Takahashi Yu , Takeuchi Yutaro , Zhang Chaoliang , Jinnai Butsurin , Fukami Shunsuke , Ohno Hideo
Published: January 2019

Spin-orbit torque-induced switching of an elliptical nanomagnet with an in-plane easy axis allows sub-ns and field-free operation. Since its properties crucially depend on the design of the nanomagnet such as the easy-axis direction, it is of high importance to systematically elucidate the dependence of performance on various parameters of the nanomagnet towards magnetoresistive random access memory applications. Here, we show a scheme to statistically evaluate the switching properties of in-plane nanomagnets in a short turnaround time. We use devices with an array of CoFeB/MgO nanomagnets formed on a cross-shaped Ta/W Hall bar, and the differential planar Hall resistance is measured to study the magnetization switching. Using the scheme, we investigate the easy-axis angle dependence of switching properties at zero magnetic fields for various current pulse widths from 100 ms to 1.7 ns. We show that the dependence of threshold switching current on the easy-axis direction significantly varies with the pulse width.
What is powerful knowledge in school history? Learning from the South African and Rwandan school curriculum documents
Authors: Bertram Carol
Published: January 2019

This paper explores the question of what is powerful knowledge in school history, drawing on an analysis of secondary school history curriculum documents from South Africa and Rwanda. The paper engages with how these official curricula make selections regarding history topics, and how conceptual relationships are structured, and then interrogates to what extent the curricula might give learners access to powerful historical knowledge. The post‐apartheid South African history curriculum chose a disciplinary focus, which aims for learners to develop the skills to analyse historical sources and evidence and to recognise that there are different interpretations of particular events. In contrast, the Rwandan history curriculum takes a collective, memory‐history approach which does not focus on historical enquiry and has a strong focus on nation‐building and citizenship. I engage with the implications of what this means for the idea of powerful knowledge in school history and argue that the socialisation aspect of school history cannot be ignored.
The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides
Authors: Tschaplinski Timothy James , Abraham Paul E , Jawdy Sara S , Gunter Lee E , Martin Madhavi Z , Engle Nancy L , Yang Xiaohan , Tuskan Gerald A
Published: January 2019

Background and Aims

The use of woody crops for Quad-level (approx. 1 × 1018 J) energy production will require marginal agricultural lands that experience recurrent periods of water stress. Populus species have the capacity to increase dehydration tolerance by lowering osmotic potential via osmotic adjustment. The aim of this study was to investigate how the inherent genetic potential of a Populus clone to respond to drought interacts with the nature of the drought to determine the degree of biochemical response.

Methods

A greenhouse drought stress study was conducted on Populus deltoides ‘WV94’ and the resulting metabolite profiles of leaves were determined by gas chromatography–mass spectrometry following trimethylsilylation for plants subjected to cyclic mild (–0.5 MPa pre-dawn leaf water potential) drought vs. cyclic severe (–1.26 MPa) drought in contrast to well-watered controls (–0.1 MPa) after two or four drought cycles, and in contrast to plants subjected to acute drought, where plants were desiccated for up to 8 d.

Key Results

The nature of drought (cyclic vs. acute), frequency of drought (number of cycles) and the severity of drought (mild vs. severe) all dictated the degree of osmotic adjustment and the nature of the organic solutes that accumulated. Whereas cyclic drought induced the largest responses in primary metabolism (soluble sugars, organic acids and amino acids), acute onset of prolonged drought induced the greatest osmotic adjustment and largest responses in secondary metabolism, especially populosides (hydroxycinnamic acid conjugates of salicin).

Conclusions

The differential adaptive metabolite responses in cyclic vs. acute drought suggest that stress acclimation occurs via primary metabolism in response to cyclic drought, whereas expanded metabolic plasticity occurs via secondary metabolism following severe, acute drought. The shift in carbon partitioning to aromatic metabolism with the production of a diverse suite of higher order salicylates lowers osmotic potential and increases the probability of post-stress recovery.
ClusterMap: compare multiple single cell RNA-Seq datasets across different experimental conditions
Authors: Gao Xin , Hu Deqing , Gogol Madelaine , Li Hua
Published: January 2019

Motivation

Single cell RNA-Seq (scRNA-Seq) facilitates the characterization of cell type heterogeneity and developmental processes. Further study of single cell profiles across different conditions enables the understanding of biological processes and underlying mechanisms at the sub-population level. However, developing proper methodology to compare multiple scRNA-Seq datasets remains challenging.

Results

We have developed ClusterMap, a systematic method and workflow to facilitate the comparison of scRNA-seq profiles across distinct biological contexts. Using hierarchical clustering of the marker genes of each sub-group, ClusterMap matches the sub-types of cells across different samples and provides ‘similarity’ as a metric to quantify the quality of the match. We introduce a purity tree cut method designed specifically for this matching problem. We use Circos plot and regrouping method to visualize the results concisely. Furthermore, we propose a new metric ‘separability’ to summarize sub-population changes among all sample pairs. In the case studies, we demonstrate that ClusterMap has the ability to provide us further insight into the different molecular mechanisms of cellular sub-populations across different conditions.

Availability and implementation

ClusterMap is implemented in R and available at https://github.com/xgaoo/ClusterMap.

Supplementary information

Supplementary data are available at Bioinformatics online.
A rapid-based improvement on some mesh refinement strategies in solving optimal control problems
Authors: Souzban Maedeh , Solaymani Fard Omid , Borzabadi Akbar H
Published: January 2019

Recently, a mesh refinement strategy is presented on pseudospectral methods for solving optimal control problems by using the relative curvature of the state approximation to choose the type of discretization change in each iteration. Nevertheless, this criterion requires a large amount of computational cost in terms of CPU time. The main goal of this paper is to draw attention to select a suitable criterion with fewer computational cost. To this end, we use the arc length of the state approximation in the mesh interval based on the relative error estimate that was recently provided. We also update the number of mesh intervals and the location of mesh points according to the behaviour of the arc length. Indeed, by implementing this criterion, we do not need to solve an optimization problem anymore, and so significantly reduce the computational time as well as CPU times. Finally, we illustrate the accuracy, efficiency and ability of the arc length criterion in comparison with the curvature by offering some numerical examples.
On the Nonlinear Wave Equation with Time-periodic Potential
Authors: Petkov Vesselin , Tzvetkov Nikolay
Published: January 2019

It is known that for some time-periodic potentials $q(t, x) \geq 0$ having compact support with respect to $x$ some solutions of the Cauchy problem for the wave equation $\partial _t^2 u - \Delta _x u + q(t,x)u = 0$ have exponentially increasing energy as $t \to \infty $. We show that if one adds a nonlinear defocusing interaction $|u|^ru, 2\leq r < 4,$ then the solution of the nonlinear wave equation exists for all $t \in{\mathbb R}$, and its energy is polynomially bounded as $t \to \infty $ for every choice of $q$. Moreover, we prove that the zero solution of the nonlinear wave equation is instable if the corresponding linear equation has the property mentioned above.
Does the Presence of Foreign Firms Reduce Domestic Firms’ Financial Constraints in Sub-Saharan Africa?†
Authors: Edjigu Habtamu Tesfaye , Sim Nicholas
Published: January 2019

Firms in the SSAs (sub-Saharan African countries for short) face severe financial constraints. Because financial markets in the SSAs are underdeveloped, policymakers have sought after the establishment of foreign-owned firms in their countries to help, among others, alleviate the financial constraints faced by domestic firms. However, there is no empirical evidence that speaks to the association between foreign firm presence and domestic firms’ financial constraint. Using firm-level data spanning across 36 SSAs from the World Bank Enterprise Survey, we show that the increase in foreign firm presence can ease the financial constraints of domestic firms in the SSAs. One reason is that foreign-owned firms are not only less financially constrained, they are also less likely to apply for bank loans. Therefore, an increase in foreign firm presence may reduce the competition for loans and ease the financial constraints of domestic firms by improving their borrowing success.
Trial2rev: Combining machine learning and crowd-sourcing to create a shared space for updating systematic reviews
Authors: Martin Paige , Surian Didi , Bashir Rabia , Bourgeois Florence T , Dunn Adam G
Published: January 2019

Objectives

Systematic reviews of clinical trials could be updated faster by automatically monitoring relevant trials as they are registered, completed, and reported. Our aim was to provide a public interface to a database of curated links between systematic reviews and trial registrations.

Materials and Methods

We developed the server-side system components in Python, connected them to a PostgreSQL database, and implemented the web-based user interface using Javascript, HTML, and CSS. All code is available on GitHub under an open source MIT license and registered users can access and download all available data.

Results

The trial2rev system is a web-based interface to a database that collates and augments information from multiple sources including bibliographic databases, the ClinicalTrials.gov registry, and the actions of registered users. Users interact with the system by browsing, searching, or adding systematic reviews, verifying links to trials included in the review, and adding or voting on trials that they would expect to include in an update of the systematic review. The system can trigger the actions of software agents that add or vote on included and relevant trials, in response to user interactions or by scheduling updates from external resources.

Discussion and Conclusion

We designed a publicly-accessible resource to help systematic reviewers make decisions about systematic review updates. Where previous approaches have sought to reactively filter published reports of trials for inclusion in systematic reviews, our approach is to proactively monitor for relevant trials as they are registered and completed.
Maternal nutrition and stage of early pregnancy in beef heifers: impacts on hexose and AA concentrations in maternal and fetal fluids1
Authors: Crouse Matthew S , Greseth Nathaniel P , McLean Kyle J , Crosswhite Mellissa R , Pereira Nicolas Negrin , Ward Alison K , Reynolds Lawrence P , Dahlen Carl R , Neville Bryan W , Borowicz Pawel P , Caton Joel S
Published: January 2019

We examined the hypothesis that maternal nutrition and day of gestation would affect the concentrations of AAs and hexoses in bovine utero-placental fluids and maternal serum from days 16 to 50 of gestation. Forty-nine cross-bred Angus heifers were bred via artificial insemination and fed a control diet (CON = 100% of requirements for growth) or a restricted diet (RES = 60% of CON) and ovariohysterectomized on days 16, 34, or 50 of gestation; nonpregnant controls were not bred and ovariohysterectomized on day 16 of the synchronized estrous cycle. The resulting design was a completely randomized design with a 2 × 3 factorial + 1 arrangement of treatments. Maternal serum, histotroph, allantoic fluid, and amniotic fluid were collected at time of ovariohysterectomy. Samples were then analyzed for concentrations of AAs and intermediary metabolites: alanine (Ala), arginine, asparagine (Asn), aspartate (Asp), citrulline, cysteine, glutamine, glutamate (Glu), glycine (Gly), histidine, isoleucine, leucine (Leu), lysine, methionine (Met), ornithine, phenylalanine (Phe), proline (Pro), serine (Ser), threonine (Thr), tryptophan, tyrosine (Tyr), and valine (Val). The concentrations of Gly, Ser, and Thr in maternal serum were greater (P ≤ 0.05) in CON compared with RES. Furthermore, day of gestation affected (P ≤ 0.05) concentrations of Asn, Glu, Phe, Thr, and Tyr in maternal serum. Status of maternal nutrition affected the Asp concentration of histotroph where RES was greater (P = 0.02) than CON. In histotroph, Ala, Leu, Met, and Val concentrations were greater (P ≤ 0.05) on day 50 compared with day 16. Additionally, Glu and Pro concentrations in histotroph were greater (P < 0.01) on days 34 and 50 compared with day 16. A day × treatment interaction was observed for the concentration of Val in allantoic fluid where day 34 CON was greater (P = 0.05) than all other days and nutritional treatments. In addition, the concentration of Gln in amniotic fluid experienced a day × treatment interaction where day 34 RES was greater (P ≤ 0.05) than day 34 CON, which was greater (P ≤ 0.05) than day 50 CON and RES. These data support our hypothesis that day of gestation and maternal nutrition affect the concentrations of various neutral and acidic AA in beef heifer utero-placental fluids and maternal serum from days 16 to 50 of gestation.
Respiratory Illness Associated With Emergent Human Adenovirus Genome Type 7d, New Jersey, 2016–2017
Authors: Killerby Marie E , Rozwadowski Faye , Lu Xiaoyan , Caulcrick-Grimes Mardea , McHugh Lisa , Haldeman Ann Marie , Fulton Tara , Schneider Eileen , Sakthivel Senthilkumar K , Bhatnagar Julu , Rabeneck Demi B , Zaki Sherif , Gerber Susan I , Watson John T
Published: January 2019

Background

Human adenoviruses (HAdVs) are known causes of respiratory illness outbreaks in congregate settings, but cases and clusters are less well described from community settings in the United States. During December 2016–February 2017, the New Jersey Department of Health received reports of HAdV infections from 3 sources in 3 adjacent counties. We investigated to characterize the epidemiologic, laboratory, and clinical features of this HAdV outbreak.

Methods

A case was defined as a New Jersey resident with acute respiratory illness during December 1, 2016–March 31, 2017 with laboratory identification of HAdV genome type 7d (HAdV-7d). Human adenovirus was detected by real-time and conventional polymerase chain reaction and molecular typed by partial hexon capsid protein gene sequencing. The HAdV genome type was identified by whole genome sequencing analysis. Available medical, public health, and surveillance records were reviewed.

Results

We identified 12 cases, including 3 treatment facility patients, 7 college students, and 2 cases at a tertiary-care hospital. Four cases died; all had underlying comorbidities. Nine HAdV-7d whole genome sequences obtained from all 3 sites were nearly identical.

Conclusions

Transmission of HAdV-7d occurred in community and congregate settings across 3 counties and resulted in severe morbidity and mortality in some cases with underlying comorbidities. Clinicians and local and state health departments should consider HAdV in patients with severe respiratory infection.
Cervical Template to Optimize the Plate-to-Disc Distance in Instrumented Anterior Cervical Discectomies and Fusions: Instrumentation Assessment
Authors: Tumialán Luis M
Published: January 2019

BACKGROUND

An increased incidence of adjacent segment degeneration in the cervical spine has been associated with a plate-to-disc distance (PDD) of <5 mm.

OBJECTIVE

To introduce a template to size, position, and secure a cervical plate and ensure a 5-mm minimum PDD.

METHODS

A prospective observational study was performed on 50 consecutive patients who had single-level anterior cervical discectomy and fusion (ACDF) using a cervical template. The cervical template was secured into the interbody spacer and assessed for length, PDD, and adequate vertebral body coverage. Holes were drilled through the template, which was then removed for cervical plate placement. Postoperative radiographs were assessed for PDD to adjacent segments, the angle from the vertical axis of the spine, and distance from midline. Neck Disability Index and visual analog scale scores for the neck and arm were obtained preoperatively and at 30-d and 90-d follow-up.

RESULTS

Fifty patients underwent single-level ACDFs. The mean angle from the long axis of the spine was 2.4 (0.0-4.4) degrees; mean distance from midline was 1.3 (0.0-2.8) mm; and mean distance from the plate ends to the adjacent segments above was 5.4 (4.6-6.2) mm, and below, 5.1 (4.3-5.8) mm.

CONCLUSION

A cervical template can reliably secure the midline and predetermine the size of the shortest cervical plate for adequately stabilizing the segment for arthrodesis. Use of a template standardizes the process of maximizing the PDD.
A new large cynodont from the Late Permian (Lopingian) of the South African Karoo Basin and its phylogenetic significance
Authors: Abdala Fernando , Gaetano Leandro C , Smith Roger M H , Rubidge Bruce S
Published: January 2019

The Karoo Basin of South Africa has the best global record of Lopingian (Late Permian) non-mammaliaform cynodonts, currently represented by five species. We describe Vetusodon elikhulu gen. et sp. nov., documented by four specimens from the Daptocephalus Assemblage Zone. With a basal skull length of ~18 cm, it is the largest Lopingian cynodont and is also larger than Induan representatives of the group. Vetusodon elikhulu has a cranial morphology that departs notably from that previously documented for Permo-Triassic cynodonts. It features a short and extremely wide snout, resembling that of the contemporaneous therocephalian Moschorhinus, and has large incisors and canines that contrast with the small unicusped postcanines, suggesting a more important role of the anterior dentition for feeding. The dentary is extremely long and robust, with the posterior margin located closer to the craniomandibular joint than in other Lopingian and Induan cynodonts (e.g. Thrinaxodon). The secondary palate morphology of V. elikhulu is unique, being short and incomplete and with the posterior portion of the maxilla partly covering the vomer. A phylogenetic analysis suggests that V. elikhulu is the sister taxon of Eucynodontia and thus the most derived of the Lopingian to Induan cynodonts yet discovered.
A direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone inDrosophila
Authors: Uyehara Christopher M. , McKay Daniel J.
Published: January 2019

The ecdysone pathway was amongst the first experimental systems employed to study the impact of steroid hormones on the genome. InDrosophilaand other insects, ecdysone coordinates developmental transitions, including wholesale transformation of the larva into the adult during metamorphosis. Like other hormones, ecdysone controls gene expression through a nuclear receptor, which functions as a ligand-dependent transcription factor. Although it is clear that ecdysone elicits distinct transcriptional responses within its different target tissues, the role of its receptor, EcR, in regulating target gene expression is incompletely understood. In particular, EcR initiates a cascade of transcription factor expression in response to ecdysone, making it unclear which ecdysone-responsive genes are direct EcR targets. Here, we use the larval-to-prepupal transition of developing wings to examine the role of EcR in gene regulation. Genome-wide DNA binding profiles reveal that EcR exhibits widespread binding across the genome, including at many canonical ecdysone-response genes. However, the majority of its binding sites reside at genes with wing-specific functions. We also find that EcR binding is temporally dynamic, with thousands of binding sites changing over time. RNA-seq reveals that EcR acts as both a temporal gate to block precocious entry to the next developmental stage as well as a temporal trigger to promote the subsequent program. Finally, transgenic reporter analysis indicates that EcR regulates not only temporal changes in target enhancer activity but also spatial patterns. Together, these studies define EcR as a multipurpose, direct regulator of gene expression, greatly expanding its role in coordinating developmental transitions.

SIGNIFICANCE

Nuclear receptors (NRs) are sequence-specific DNA binding proteins that act as intracellular receptors for small molecules such as hormones. Prior work has shown that NRs function as ligand-dependent switches that initiate a cascade of gene expression changes. The extent to which NRs function as direct regulators of downstream genes in these hierarchies remains incompletely understood. Here, we study the role of the NR EcR in metamorphosis of theDrosophilawing. We find that EcR directly regulates many genes at the top of the hierarchy as well as at downstream genes. Further, we find that EcR binds distinct sets of target genes at different developmental times. This work helps inform how hormones elicit tissue- and temporal-specific responses in target tissues.
Dimensions of neighborhood tracts and their associations with mental health problems
Authors: Forthman Katherine L. , Yeh Hung-wen , Kuplicki Rayus , Paulus Martin P.
Published: January 2019

Objective

Neighborhood characteristics can have profound effects on resident health. The aim of this study was to use an unsupervised learning approach to reduce the multi-dimensional assessment of a neighborhood using American Community Survey (ACS) data to simplify the assessment of neighborhood influence on health.

Method

Multivariate quantitative characterization of the neighborhood was derived by performing a factor analysis on the 2011-2015 ACS data. The utility of the latent variables was examined by determining the association of these factors with poor mental health measures from the 500 Cities Project 2017 release.

Results

A five-factor model provided the best fit for the data and the latent factors quantified the following characteristics of the census tract: (1) affluence, (2) proportion of singletons in neighborhood, (3) proportion of African-Americans in neighborhood, (4) proportion of seniors in neighborhood, and (5) proportion of noncitizens in neighborhood. African-Americans (R2 = 0.67) in neighborhood and Affluence (R2 = 0.83) were strongly associated with poor mental health.

Conclusions

These findings indicate the importance of this factor model in future research focused on the relationship between neighborhood characteristics and resident health.
2-((E)-{[3-(1H-Imidazol-1-yl)propyl]imino}methyl)-4-[(E)-(4-methylphenyl)diazenyl]phenol
Authors: Slassi Siham , Stetsiuk Oleh , Amine Amina , Aarjane Mohammed , El-Ghayoury Abdelkrim , Zouihri Hafid , Yamni Khalid
Published: January 2019

In the title compound, C20H21N5O, the dihedral angles between the central phenol ring and pendant toluyl and imidazole rings are 3.20 (16) and 81.44 (14)°, respectively; the dihedral angle between the pendant rings is 84.39 (16)°. An intramolecular O—H...N hydrogen bond occurs. A Hirshfeld fingerprint analysis indicates that H...H contacts account for 48.6% of the surface.
Policy and planning of research data management in university libraries of Pakistan
Authors: Piracha Haseeb Ahmad , Ameen Kanwal
Published: January 2019

Purpose

This paper aims to assess the policy framework and planning regarding research data management (RDM) in university libraries of Pakistan.

Design/methodology/approach

Data were collected from 30 Higher Education Commission high ranking university libraries by using mixed method explanatory sequential design.

Findings

The results indicate that library heads just heard about RDM, but there was lack of knowledge and awareness. Few libraries were at the planning stage. Other major challenges including lack of willingness, motivation and coordination with researchers, non-availability of skillful professional and support staff, poor infrastructure and networking were found in this regard.

Originality/value

This is the first study of its kind that explores the planning and policy development regarding RDM in university libraries of Pakistan.