bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel non-phosphorylative pathway of pentose metabolism from bacteria
Authors: Watanabe Seiya , Fukumori Fumiyasu , Nishiwaki Hisashi , Sakurai Yasuhiro , Tajima Kunihiko , Watanabe Yasuo 
Published: January 2019

AbstractPentoses, including D-xylose, L-arabinose, and D-arabinose, are generally phosphorylated to D-xylulose 5-phosphate in bacteria and fungi. However, in non-phosphorylative pathways analogous to the Entner-Dodoroff pathway in bacteria and archaea, such pentoses can be converted to pyruvate and glycolaldehyde (Route I) or α-ketoglutarate (Route II) via a 2-keto-3-deoxypentonate (KDP) intermediate. Putative gene clusters related to these metabolic pathways were identified on the genome of Herbaspirillum huttiense IAM 15032 using a bioinformatic analysis. The biochemical characterization of C785_RS13685, one of the components encoded to D-arabinonate dehydratase, differed from the known acid-sugar dehydratases. The biochemical characterization of the remaining components and a genetic expression analysis revealed that D- and L-KDP were converted not only to α-ketoglutarate, but also pyruvate and glycolate through the participation of dehydrogenase and hydrolase (Route III). Further analyses revealed that the Route II pathway of D-arabinose metabolism was not evolutionally related to the analogous pathway from archaea.
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

Abstract
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.
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.
What is powerful knowledge in school history? Learning from the South African and Rwandan school curriculum documents
Authors: Bertram Carol 
Published: January 2019

AbstractThis 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

Abstract

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

Abstract

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

AbstractRecently, 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

Abstract
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 $|u|^ru, 2\leq r &lt; 4,$ 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

Abstract
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.