bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel miRNA identified in GRSF1 complex drives the metastasis via the PIK3R3/AKT/NF-κB and TIMP3/MMP9 pathways in cervical cancer cells
Authors: Sun Qi , Yang Zhen , Li Pu , Wang Xu , Sun Lu , Wang Shixing , Liu Min , Tang Hua 
Published: September 2019

AbstractmicroRNAs (miRNAs) play an important role in carcinogenesis. Typically, miRNAs downregulate the target expression by binding to the 3′ UTR of mRNAs. However, recent studies have demonstrated that miRNAs can upregulate target gene expression, but its mechanism is not fully understood. We previously found that G-rich RNA sequence binding protein (GRSF1) mediates upregulation of miR-346 on hTERT gene. To explore whether GRSF1 mediate other miRNA’s upregulation on their target genes, we obtained profile of GRSF1-bound miRNAs by Flag-GRSF1-RIP-deep sequencing and found 12 novel miRNAs, named miR-G. In this study, we focused on miR-G-10, which is highly expressed in cervical cancer tissues and cell lines and serum from patients with metastatic cervical cancer. miR-G-10 in cervical cancer cells significantly promoted migration/invasion and anoikis resistance in vitro and lung metastasis in vivo. Furthermore, miR-G-10 bound to the 3′ UTR of PIK3R3 and upregulated its expression to activate the AKT/NF-κB signal pathway in a GRSF1-dependent manner, whereas miR-G-10 suppressed TIMP3 in the AGO2 complex to modulate the MMP9 signaling pathway in cervical cancer cells. Taken together, our findings may provide a new insight into the upregulation mechanism mediated by miRNAs and a potential biomarker for cervical cancer.
Main spectral features of meteors studied using a terawatt-class high-power laser
Authors: Ferus M. , Kubelík P. , Petera L. , Lenža L. , Koukal J. , Křivková A. , Laitl V. , Knížek A. , Saeidfirozeh H. , Pastorek A. , Kalvoda T. , Juha L. , Dudžák R. , Civiš S. , Chatzitheodoridis E. , Krůs M. 
Published: September 2019

Context. Meteor spectra are commonly interpreted using data from databases and tables. Several studies have demonstrated very sophisticated calculations of elemental compositions of meteoroid bodies based on the computation of synthetic meteor spectra or on the spectral analysis of airglow plasma containing evaporated, atomized, and ionized meteoroid matter. However, considering accuracy, reliability of computations, lack of laboratory experimental data in this field, as well as the complicated physical structure of meteor plasma, such qualitative assignment or quantitative calculations are still extensively discussed in the scientific community. Even on the laboratory level, many studies have shown the high complexity of the acquisition and interpretation of the data that are recorded with techniques of emission spectroscopy that are in fashion and philosophy similar to the spectral analysis of meteor plasma, that is, detection and quantification of the elements that are ablated from complicated multicomponent matrices.
Aims. The current study is focused on the application of terawatt-class laser-induced breakdown spectroscopy (TC-LIBS) of real samples of chondritic meteorites. We recorded emission spectra with high resolution and high precision that contain spectral lines that are typical for real meteoric spectra. Experimental data were compiled in a form that is convenient for the meteoric spectra interpretation and calibration.
Methods. TC-LIBS was carried out by a high-power terawatt-class laser facility, the Prague Asterix Laser System (PALS). The spectra were simultaneously recorded by an echelle high-resolution spectrograph in the UV/VIS spectral ranges and by a low-resolution spectrograph that was used for real observation of meteor spectra. We also present calculated synthetic spectra based on data from the NIST atomic spectra database.
Results. We assembled etalon qualitative tables of major meteoric spectral features that can be used both for the spectral wavelength calibration of low-resolution observational instruments and for the exact interpretation of meteor spectra. The data are compared with real meteor spectra.
Pudding Economics: Franklin’s “The Way to Wealth” and the Transactional Self
Authors: Horwitz Howard 
Published: September 2019

Abstract
Benjamin Franklin’s preface to the 1758 edition of Poor Richard’s Almanack, usually titled “The Way to Wealth,” is generally regarded as a sermon on frugality. The very form of the 1758 Preface, with Richard Saunders’s voice framing Father Abraham’s “Harangue,” ironizes Father Abraham’s doctrine of frugality. The effect of this literary performance is to illustrate or even stimulate desire for social interaction that is not frugal in any strict sense, but rather manifests an impulse to expand intercourse. The 1758 preface and Franklin’s extensive writings on economics present an expansive vision of capital formation. Commerce must grow incessantly, not for the accumulation of capital per se but for the prospect of endless growth, to spur and sustain what Adam Smith called “the progressive state.” Franklin’s economic writings delineate the constitution of the subject populating progressive society. Identity and ultimately the character of society are fabricated through ongoing, visible, and expanding transactions. Expansive or progressive identity is not illusory, but constitutive. Self and society must be creditable. This conceptualization was central to economic policy-making in the new nation; it straddles neoliberal critiques of subjectification in late capitalism.
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning
Authors: Hanson Jack , Litfin Thomas , Paliwal Kuldip , Zhou Yaoqi 
Published: September 2019

AbstractMotivationProtein intrinsic disorder describes the tendency of sequence residues to not fold into a rigid three-dimensional shape by themselves. However, some of these disordered regions can transition from disorder to order when interacting with another molecule in segments known as molecular recognition features (MoRFs). Previous analysis has shown that these MoRF regions are indirectly encoded within the prediction of residue disorder as low-confidence predictions [i.e. in a semi-disordered state P(D)≈0.5]. Thus, what has been learned for disorder prediction may be transferable to MoRF prediction. Transferring the internal characterization of protein disorder for the prediction of MoRF residues would allow us to take advantage of the large training set available for disorder prediction, enabling the training of larger analytical models than is currently feasible on the small number of currently available annotated MoRF proteins. In this paper, we propose a new method for MoRF prediction by transfer learning from the SPOT-Disorder2 ensemble models built for disorder prediction.ResultsWe confirm that directly training on the MoRF set with a randomly initialized model yields substantially poorer performance on independent test sets than by using the transfer-learning-based method SPOT-MoRF, for both deep and simple networks. Its comparison to current state-of-the-art techniques reveals its superior performance in identifying MoRF binding regions in proteins across two independent testing sets, including our new dataset of &gt;800 protein chains. These test chains share &lt;30% sequence similarity to all training and validation proteins used in SPOT-Disorder2 and SPOT-MoRF, and provide a much-needed large-scale update on the performance of current MoRF predictors. The method is expected to be useful in locating functional disordered regions in proteins.Availability and implementationSPOT-MoRF and its data are available as a web server and as a standalone program at: http://sparks-lab.org/jack/server/SPOT-MoRF/index.php.Supplementary informationSupplementary data are available at Bioinformatics online.
Rising Powers and Grassroots Image Management: Confucius Institutes and China in the Media
Authors: Brazys Samuel , Dukalskis Alexander 
Published: September 2019

Abstract
This article proposes and tests a mechanism of grassroots image management to explain how rising powers craft an international environment more conducive to their interests. The aim is to promote the state’s foreign policy goals by influencing the perceptions of ordinary foreign citizens. To test this mechanism, we examine the impact of China’s Confucius Institutes (CIs) as an observable instrument of China’s grassroots image management strategy. Using data from the Global Database of Events, Language, and Tone (GDELT), we employ a spatial–temporal approach which finds that proximity to an active CI significantly and substantively improves the tone of media reporting about events relevant to China in that locality. The finding is robust to different specifications and estimation strategies, and is qualitatively consistent with results generated using household opinion data from Afrobarometer surveys. Theoretically, our results suggest the importance of systematically examining presentations and perceptions about rising powers at the popular level, in addition to focusing on elite attitudes, to understand discursive change. More directly, our findings reveal that CIs are helping to improve how China is viewed among foreign publics.
Predominance of soil vs root effect in rhizosphere microbiota reassembly
Authors: Zhao Mengli , Yuan Jun , Shen Zongzhuan , Dong Menghui , Liu Hongjun , Wen Tao , Li Rong , Shen Qirong 
Published: September 2019

ABSTRACTRhizosphere community assembly is simultaneously affected by both plants and bulk soils and is vital for plant health. However, it is still unclear how and to what extent disease-suppressive rhizosphere microbiota can be constructed from bulk soil, and the underlying agents involved in the process that render the rhizosphere suppressive against pathogenic microbes remain elusive. In this study, the evolutionary processes of the rhizosphere microbiome were explored based on transplanting plants previously growing in distinct disease-incidence soils to one disease-suppressive soil. Our results showed that distinct rhizoplane bacterial communities were assembled on account of the original bulk soil communities with different disease incidences. Furthermore, the bacterial communities in the transplanted rhizosphere were noticeably influenced by the second disease-suppressive microbial pool, rather than that of original formed rhizoplane microbiota and homogenous nontransplanted rhizosphere microbiome, contributing to a significant decrease in the pathogen population. In addition, Spearman's correlations between relative abundances of bacterial taxa and the abundance of Ralstonia solanacearum indicated Anoxybacillus, Flavobacterium, Permianibacter and Pseudomonas were predicted to be associated with disease-suppressive function formation. Altogether, our results showed that bulk soil played an important role in the process of assembling and reassembling the rhizosphere microbiome of plants.
Construction of conformal maps based on the locations of singularities for improving the double exponential formula
Authors: Kyoya Shunki , Tanaka Ken’ichiro 
Published: September 2019

Abstract
The double exponential formula, or DE formula, is a high-precision integration formula using a change of variables called a DE transformation; it has the disadvantage that it is sensitive to singularities of an integrand near the real axis. To overcome this disadvantage, Slevinsky & Olver (2015, On the use of conformal maps for the acceleration of convergence of the trapezoidal rule and Sinc numerical methods. SIAM J. Sci. Comput., 37, A676–A700) attempted to improve the formula by constructing conformal maps based on the locations of singularities. Based on their ideas, we construct a new transformation formula. Our method employs special types of the Schwarz–Christoffel transformation for which we can derive the explicit form. The new transformation formula can be regarded as a generalization of DE transformations. We confirm its effectiveness by numerical experiments.
Nonsmooth algorithms for minimizing the largest eigenvalue with applications to inner numerical radius
Authors: Kangal Fatih , Mengi Emre 
Published: September 2019

Abstract
Nonsmoothness at optimal points is a common phenomenon in many eigenvalue optimization problems. We consider two recent algorithms to minimize the largest eigenvalue of a Hermitian matrix dependent on one parameter, both proven to be globally convergent unaffected by nonsmoothness. One of these algorithms models the eigenvalue function with a piece-wise quadratic function and is effective in dealing with nonconvex problems. The other algorithm projects the Hermitian matrix into subspaces formed of eigenvectors and is effective in dealing with large-scale problems. We generalize the latter slightly to cope with nonsmoothness. For both algorithms we analyze the rate of convergence in the nonsmooth setting, when the largest eigenvalue is multiple at the minimizer and zero is strictly in the interior of the generalized Clarke derivative, and prove that both algorithms converge rapidly. The algorithms are applied to, and the deduced results are illustrated on the computation of the inner numerical radius, the modulus of the point on the boundary of the field of values closest to the origin, which carries significance for instance for the numerical solution of a symmetric definite generalized eigenvalue problem and the iterative solution of a saddle point linear system.
Sonic ‘Detheatricalization’: Jean Cocteau, Film Music, and ‘Les Parents Terribles’
Authors: Anderson Laura 
Published: September 2019

Abstract
Jean Cocteau’s adaptation of his controversial play Les Parents terribles for the screen stands out in his oeuvre as an attempt to reconcile theatre and cinema. It also presented a challenge in preparing a soundscape for a work that did not have any music in its original form. Parents occupies a unique, Janus-like position in the history of French film music, as forward-looking in its anticipation of New Wave treatment of music as material as it is representative of the turn to adapting stage plays for the screen that started in the 1930s. Drawing on production sketchbooks and testimonies, this article considers the development of Cocteau’s working method and his collaboration with Georges Auric, fuelled by the director’s desire to take control of sonic matters. The resulting employment of a monothematic score was not only a new solution to the famous problem of filmed theatre, ‘detheatricalizing’ Parents sonically and visually, it contributed considerably to the development of Cocteau’s status as film auteur—one whose role now extended to adapting musical material. Furthermore, the effect of this compositional technique in Parents suggests that it can be fruitfully situated in relation to recent work in film music studies on issues of anempathetic scoring practices.
From the far-ultraviolet to the far-infrared – galaxy emission at 0 ≤ z ≤ 10 in the shark semi-analytic model
Authors: Lagos Claudia del P , Robotham Aaron S G , Trayford James W , Tobar Rodrigo , Bravo Matías , Bellstedt Sabine , Davies Luke J M , Driver Simon P , Elahi Pascal J , Obreschkow Danail , Power Chris 
Published: September 2019

ABSTRACT
We combine the shark semi-analytic model of galaxy formation with the prospect software tool for spectral energy distribution (SED) generation to study the multiwavelength emission of galaxies from the far-ultraviolet (FUV) to the far-infrared (FIR) at 0 ≤ z ≤ 10. We produce a physical model for the attenuation of galaxies across cosmic time by combining a local Universe empirical relation to compute the dust mass of galaxies from their gas metallicity and mass, attenuation curves derived from radiative transfer calculations of galaxies in the eagle hydrodynamic simulation suite, and the properties of shark galaxies. We are able to produce a wide range of galaxies, from the z = 8 star-forming galaxies with almost no extinction, z = 2 submillimetre galaxies, down to the normal star-forming and red-sequence galaxies at z = 0. Quantitatively, we find that shark reproduces the observed (i) z = 0 FUV-to-FIR, (ii) 0 ≤ z ≤ 3 rest-frame K-band, and (iii) 0 ≤ z ≤ 10 rest-frame FUV luminosity functions, (iv) z ≤ 8 UV slopes, (v) the FUV-to-FIR number counts (including the widely disputed 850 μm), (vi) redshift distribution of bright $850\, \mu$m galaxies, and (vii) the integrated cosmic SED from z = 0 to 1 to an unprecedented level. This is achieved without the need to invoke changes in the stellar initial mass function, dust-to-metal mass ratio, or metal enrichment time-scales. Our model predicts star formation in galaxy discs to dominate in the FUV-to-optical, while bulges dominate at the NIR at all redshifts. The FIR sees a strong evolution in which discs dominate at z ≤ 1 and starbursts (triggered by both galaxy mergers and disc instabilities, in an even mix) dominate at higher redshifts, even out to z = 10.
Progenitors and explosion properties of supernova remnants hosting central compact objects: I. RCW 103 associated with the peculiar source 1E 161348−5055
Authors: Braun C , Safi-Harb S , Fryer C L 
Published: September 2019

ABSTRACT
We present a Chandra and XMM–Newton imaging and spectroscopic study of the supernova remnant (SNR) RCW 103 (G332.4−00.4) containing the central compact object 1E 161348−5055. The high-resolution Chandra X-ray images reveal enhanced emission in the south-eastern and north-western regions. Equivalent width line images of Fe L, Mg, Si, and S using XMM–Newton data were used to map the distribution of ejecta. The SNR was sectioned into 56 regions best characterized by two-component thermal models. The harder component (kT ∼ 0.6 keV) is adequately fitted by the VPSHOCK non-equilibrium ionization model with an ionization time-scale net ∼ 1011–1012 cm−3 s, and slightly enhanced abundances over solar values. The soft component (kT ∼ 0.2 keV), fitted by the APEC model, is well described by plasma in collisional ionization equilibrium with abundances consistent with solar values. Assuming a distance of 3.1 kpc and a Sedov phase of expansion into a uniform medium, we estimate an SNR age of 4.4 kyr, a swept-up mass Msw = 16$f_\mathrm{ s}^{-1/2}$ D$_{3.1}^{5/2}$ M⊙, and a low explosion energy E* = 3.7 × 1049 $f_\mathrm{ s}^{-1/2}$ D$_{3.1}^{5/2}$ erg. This energy could be an order of magnitude higher if we relax the Sedov assumption, the plasma has a low filling factor, the plasma temperature is underestimated, or if the SNR is expanding into the progenitor’s wind-blown bubble. Standard explosion models did not match the ejecta yields. By comparing the fitted abundances to the most recent core-collapse nucleosynthesis models, our best estimate yields a low-mass progenitor of around 12–13 M⊙, lower than previously reported. We discuss degeneracies in the model fitting, particularly the effect of altering the explosion energy on the progenitor mass estimate.
A protein architecture guided screen for modification dependent restriction endonucleases
Authors: Lutz Thomas , Flodman Kiersten , Copelas Alyssa , Czapinska Honorata , Mabuchi Megumu , Fomenkov Alexey , He Xinyi , Bochtler Matthias , Xu Shuang-yong 
Published: September 2019

AbstractModification dependent restriction endonucleases (MDREs) often have separate catalytic and modification dependent domains. We systematically looked for previously uncharacterized fusion proteins featuring a PUA or DUF3427 domain and HNH or PD-(D/E)XK catalytic domain. The enzymes were clustered by similarity of their putative modification sensing domains into several groups. The TspA15I (VcaM4I, CmeDI), ScoA3IV (MsiJI, VcaCI) and YenY4I groups, all featuring a PUA superfamily domain, preferentially cleaved DNA containing 5-methylcytosine or 5-hydroxymethylcytosine. ScoA3V, also featuring a PUA superfamily domain, but of a different clade, exhibited 6-methyladenine stimulated nicking activity. With few exceptions, ORFs for PUA-superfamily domain containing endonucleases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activity of the endonucleases. DUF3427 domain containing fusion proteins had very little or no endonuclease activity, despite the presence of a putative PD-(D/E)XK catalytic domain. However, their expression potently restricted phage T4gt in Escherichia coli cells. In contrast to the ORFs for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found in defense islands, often also featuring DNA methyltransferases.
Oxazinomycin arrests RNA polymerase at the polythymidine sequences
Authors: Prajapati Ranjit K , Rosenqvist Petja , Palmu Kaisa , Mäkinen Janne J , Malinen Anssi M , Virta Pasi , Metsä-Ketelä Mikko , Belogurov Georgiy A 
Published: September 2019

AbstractOxazinomycin is a C-nucleoside antibiotic that is produced by Streptomyces hygroscopicus and closely resembles uridine. Here, we show that the oxazinomycin triphosphate is a good substrate for bacterial and eukaryotic RNA polymerases (RNAPs) and that a single incorporated oxazinomycin is rapidly extended by the next nucleotide. However, the incorporation of several successive oxazinomycins or a single oxazinomycin in a certain sequence context arrested a fraction of the transcribing RNAP. The addition of Gre RNA cleavage factors eliminated the transcriptional arrest at a single oxazinomycin and shortened the nascent RNAs arrested at the polythymidine sequences suggesting that the transcriptional arrest was caused by backtracking of RNAP along the DNA template. We further demonstrate that the ubiquitous C-nucleoside pseudouridine is also a good substrate for RNA polymerases in a triphosphorylated form but does not inhibit transcription of the polythymidine sequences. Our results collectively suggest that oxazinomycin functions as a Trojan horse substrate and its inhibitory effect is attributable to the oxygen atom in the position corresponding to carbon five of the uracil ring.
Conventional MRI radiomics in patients with suspected early- or pseudo-progression
Authors: Bani-Sadr Alexandre , Eker Omer Faruk , Berner Lise-Prune , Ameli Roxana , Hermier Marc , Barritault Marc , Meyronet David , Guyotat Jacques , Jouanneau Emmanuel , Honnorat Jerome , Ducray François , Berthezene Yves 
Published: September 2019

Abstract

Background
After radiochemotherapy, 30% of patients with early worsening MRI experience pseudoprogression (Psp) which is not distinguishable from early progression (EP). We aimed to assess the diagnostic value of radiomics in patients with suspected EP or Psp.

Methods
Radiomics features (RF) of 76 patients (53 EP and 23 Psp) retrospectively identified were extracted from conventional MRI based on four volumes-of-interest. Subjects were randomly assigned into training and validation groups. Classification model (EP versus Psp) consisted of a random forest algorithm after univariate filtering. Overall (OS) and progression-free survivals (PFS) were predicted using a semi-supervised principal component analysis, and forecasts were evaluated using C-index and integrated Brier scores (IBS).

Results
Using 11 RFs, radiomics classified patients with 75.0% and 76.0% accuracy, 81.6% and 94.1% sensitivity, 50.0% and 37.5% specificity, respectively, in training and validation phases. Addition of MGMT promoter status improved accuracy to 83% and 79.2%, and specificity to 63.6% and 75%. OS model included 14 RFs and stratified low- and high-risk patients both in the training (hazard ratio [HR], 3.63; P = .002) and the validation (HR, 3.76; P = .001) phases. Similarly, PFS model stratified patients during training (HR, 2.58; P = .005) and validation (HR, 3.58; P = .004) phases using 5 RF. OS and PFS forecasts had C-index of 0.65 and 0.69, and IBS of 0.122 and 0.147, respectively.

Conclusions
Conventional MRI radiomics has promising diagnostic value, especially when combined with MGMT promoter status, but with moderate specificity. In addition, our results suggest a potential for predicting OS and PFS.