bluuebunny/crossref_metadata_2025_split huggingface dataset:
Translation elongation factor P (EF-P)
Authors: Hummels Katherine R , Kearns Daniel B 
Published: January 2020

ABSTRACTTranslation elongation factor P (EF-P) is conserved in all three domains of life (called eIF5A and aIF5A in eukaryotes and archaea, respectively) and functions to alleviate ribosome pausing during the translation of specific sequences, including consecutive proline residues. EF-P was identified in 1975 as a factor that stimulated the peptidyltransferase reaction in vitro but its involvement in the translation of tandem proline residues was not uncovered until 2013. Throughout the four decades of EF-P research, perceptions of EF-P function have changed dramatically. In particular, while EF-P was thought to potentiate the formation of the first peptide bond in a protein, it is now broadly accepted to act throughout translation elongation. Further, EF-P was initially reported to be essential, but recent work has shown that the requirement of EF-P for growth is conditional. Finally, it is thought that post-translational modification of EF-P is strictly required for its function but recent studies suggest that EF-P modification may play a more nuanced role in EF-P activity. Here, we review the history of EF-P research, with an emphasis on its initial isolation and characterization as well as the discoveries that altered our perceptions of its function.
Yeast synthetic biology for designed cell factories producing secretory recombinant proteins
Authors: Thak Eun Jung , Yoo Su Jin , Moon Hye Yun , Kang Hyun Ah 
Published: January 2020

ABSTRACT
Yeasts are prominent hosts for the production of recombinant proteins from industrial enzymes to therapeutic proteins. Particularly, the similarity of protein secretion pathways between these unicellular eukaryotic microorganisms and higher eukaryotic organisms has made them a preferential host to produce secretory recombinant proteins. However, there are several bottlenecks, in terms of quality and quantity, restricting their use as secretory recombinant protein production hosts. In this mini-review, we discuss recent developments in synthetic biology approaches to constructing yeast cell factories endowed with enhanced capacities of protein folding and secretion as well as designed targeted post-translational modification process functions. We focus on the new genetic tools for optimizing secretory protein expression, such as codon-optimized synthetic genes, combinatory synthetic signal peptides and copy number-controllable integration systems, and the advanced cellular engineering strategies, including endoplasmic reticulum and protein trafficking pathway engineering, synthetic glycosylation, and cell wall engineering, for improving the quality and yield of secretory recombinant proteins.
Accelerating numerical wave propagation using wavefield adapted meshes. Part I: forward and adjoint modelling
Authors: van Driel M , Boehm C , Krischer L , Afanasiev M 
Published: January 2020

SUMMARYAn order of magnitude speed-up in finite-element modelling of wave propagation can be achieved by adapting the mesh to the anticipated space-dependent complexity and smoothness of the waves. This can be achieved by designing the mesh not only to respect the local wavelengths, but also the propagation direction of the waves depending on the source location, hence by anisotropic adaptive mesh refinement. Discrete gradients with respect to material properties as needed in full waveform inversion can still be computed exactly, but at greatly reduced computational cost. In order to do this, we explicitly distinguish the discretization of the model space from the discretization of the wavefield and derive the necessary expressions to map the discrete gradient into the model space. While the idea is applicable to any wave propagation problem that retains predictable smoothness in the solution, we highlight the idea of this approach with instructive 2-D examples of forward as well as inverse elastic wave propagation. Furthermore, we apply the method to 3-D global seismic wave simulations and demonstrate how meshes can be constructed that take advantage of high-order mappings from the reference coordinates of the finite elements to physical coordinates. Error level and speed-ups are estimated based on convergence tests with 1-D and 3-D models.
Basic Sets for Unipotent Blocks of Finite Reductive Groups in Bad Characteristic
Authors: Chaneb Reda 
Published: January 2020

Abstract
We show the existence of a unitriangular basic set for unipotent blocks of simple reductive groups of classical type in bad characteristic with some exceptions. Then, we introduce an algorithm to count unipotent irreducible Brauer characters and we verify that this algorithm is effective for exceptional adjoint groups.
Trumping International Law?
Authors: Birdsall Andrea , Sanders Rebecca 
Published: January 2020

AbstractFrom bringing back waterboarding, to violating treaty obligations, to banning Muslims, Donald J. Trump has proposed numerous extralegal policies. We examine the implications of this disdain for legality, arguing that Trump's frequent hostility and indifference to legal rules and institutions paradoxically impede his capacity to enact his promises and damage international law. To situate Trump's legal politics, we draw comparisons with the Bush and Obama administrations. As constructivists note, the vitality of legal norms is dependent not just on one state's actions, but crucially on others’ reactions. While Trump has gone beyond his predecessors in rhetorically attacking international law, the backlash he generates limits the realization of his agenda in part due to his failure to convince others to violate the law or revise legal rules in novel ways. When the administration does reluctantly pursue legal justifications for controversial policies, it is better able to overcome legal constraints and political opposition.
Downregulated long non-coding RNA LINC01093 in liver fibrosis promotes hepatocyte apoptosis via increasing ubiquitination of SIRT1
Authors: Tang Yinhe , Ma Naijing , Luo Hao , Chen Shizuan , Yu Fuxiang 
Published: January 2020

Abstract
The apoptosis of hepatocytes contributes to the activation of hepatic stellate cells (HSCs), thus promoting the accumulation of extracellular matrix proteins and aggravating liver fibrosis. Silent information regulator 1 (SIRT1) is an anti-fibrotic protein whose downregulation induces hepatocyte apoptosis. This study aims to identify whether SIRT1 is regulated by long non-coding RNA LINC01093 and explore its underlying mechanisms. Liver fibrosis was induced in mice using CCl4, and the differential expressions of several fibrosis-related long noncoding RNAs were detected in liver tissues. The effect of LINC01093 on cell apoptosis and viability of hepatocytes were investigated after LINC01093 overexpression or knockdown using flow cytometry and MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay. The anti-fibrotic effect of LINC01093 overexpression was observed in vivo. LncRNA LINC01093 is downregulated in CCl4-induced liver tissues and TGF-β1-stimulated hepatocytes. Downregulated LINC01093 promoted cell apoptosis and inhibited cell viability of hepatocytes. The co-culture between LINC01093-knockdown hepatocytes and HSCs increased the expressions of pro-fibrotic proteins. Downregulated LINC01093 promoted hepatocyte apoptosis via promoting degradation and ubiquitination of SIRT1 under TGF-β1 stimulation. The injection of LINC01093-overexpressing vectors alleviated liver fibrosis in vivo. In liver fibrosis, the downregulated LINC01093 promoted hepatocyte apoptosis, which is mediated by increasing the degradation and ubiquitination of SIRT1.
Achieving Justice for Child Survivors of Conflict-related Sexual Violence in the Democratic Republic of the Congo
Authors: Perissi Daniele , Naimer Karen 
Published: January 2020

Abstract
In March 2015, the first major conference, or États Généraux, of the Congolese justice system was held in Kinshasa, Democratic Republic of the Congo. The conference, the mandate of which was to evaluate the functioning of the judicial system and formulate recommendations about reforms and actions to be implemented, pledged to strengthen national investigations and prosecutions of international crimes as a matter of priority. This development was significant in a country where widespread impunity for perpetrators of mass crimes, in particular conflict-related sexual violence, is rampant and exacerbates the trauma suffered by survivors. Among the cases deemed a ‘priority’, the Kavumu case was especially important. In that case, the Military Court of South Kivu found that the accused were part of an armed group, controlled by provincial lawmaker Frédéric Batumike, and together they were responsible for the rape of over 40 young girls over a three-year period. After a long and complex process, in December 2017, a mobile military court convicted 11 militia members, including the parliamentarian, of rape as a crime against humanity and sentenced them to life. In July 2018, the High Military Court confirmed the verdict. This article will provide an overview of the Kavumu case as well as the main milestones of the proceedings. The article will then discuss three features of the case that exemplify innovations and best practices — as well as pending challenges — in the prosecution of conflict-related sexual violence, including the issue of domestic immunities for international crimes; the unique, interdisciplinary protections undertaken for child victims of sexual violence in legal proceedings; and the effective collaborations among the network of medical, legal, and civil society actors supporting national efforts to combat impunity. The Kavumu case aptly illustrates how national justice institutions, working alongside international and local partners, can lead the way in achieving progress and overcoming complex challenges to advance accountability and set important precedents in the fight against impunity for conflict-related sexual violence.
Prophylactic donor lymphocyte infusion for relapse prevention: a meta-analysis
Authors: Poonsombudlert Kittika , Kewcharoen Jakrin , Prueksapraopong Chattip , Limpruttidham Nath 
Published: January 2020

Abstract

Objective
Primary disease relapse (PDR) of malignant hematologic conditions after standard hematopoietic stem cell transplant (HSCT) is one of the most challenging diseases; therefore ongoing researches are aiming at relapse prevention and minimizing the transplant-related side effects. Prophylactic donor lymphocytes (pDLI) had been proposed as a valuable strategy for PDR prevention, but early studies had been discouraging due to the limited benefit and possible association with acute graft-versus-host disease (aGVHD). Therefore, we conducted a meta-analysis to evaluate the association between pDLI use, PDR, aGVHD and OS.

Method
We performed a comprehensive literature search in MEDLINE, Cochrane library and Embase database from inception to May 2019 for studies that evaluated the association between pDLI and PDR. We conducted a random effect meta-analysis of 9 studies involving a total of 748 participants (pDLI = 398, non-pDLI = 350) and reported the pooled odd ratio (OR) for association of pDLI use, PDR, aGVHD and OS.

Result
We found a significant decreased odd of PDR in the pDLI group (pooled OR = 0.42, 95% CI 0.30–0.58, I2 = 0%), but there was no significant increased odd of aGVHD (pooled OR of 0.98, 95% CI 0.56–1.72, I2 = 0.8%). We also found that there was an increased odd of overall survival (OS) (pooled OR 3.17, 95% CI 1.85–5.45, I2 = 50.2%).

Conclusion
There are significantly decreased odd of PDR and increased odd of OS in the pDLI group compared to the control group, but there is no statistically significant increased odd of aGVHD as suggested by previous studies. We concluded that pDLI is a potentially valuable method for post-transplant PDR prevention.
LYMESIM 2.0: An Updated Simulation of Blacklegged Tick (Acari: Ixodidae) Population Dynamics and Enzootic Transmission of Borrelia burgdorferi (Spirochaetales: Spirochaetaceae)
Authors: Gaff Holly , Eisen Rebecca J , Eisen Lars , Nadolny Robyn , Bjork Jenna , Monaghan Andrew J 
Published: January 2020

AbstractLyme disease is the most commonly reported vector-borne disease in the United States, and the number of cases reported each year continues to rise. The complex nature of the relationships between the pathogen (Borrelia burgdorferi sensu stricto), the tick vector (Ixodes scapularis Say), multiple vertebrate hosts, and numerous environmental factors creates challenges for understanding and predicting tick population and pathogen transmission dynamics. LYMESIM is a mechanistic model developed in the late 1990s to simulate the life-history of I. scapularis and transmission dynamics of B. burgdorferi s.s. Here we present LYMESIM 2.0, a modernized version of LYMESIM, that includes several modifications to enhance the biological realism of the model and to generate outcomes that are more readily measured under field conditions. The model is tested for three geographically distinct locations in New York, Minnesota, and Virginia. Model-simulated timing and densities of questing nymphs, infected nymphs, and abundances of nymphs feeding on hosts are consistent with field observations and reports for these locations. Sensitivity analysis highlighted the importance of temperature in host finding for the density of nymphs, the importance of transmission from small mammals to ticks on the density of infected nymphs, and temperature-related tick survival for both density of nymphs and infected nymphs. A key challenge for accurate modeling of these metrics is the need for regionally representative inputs for host populations and their fluctuations. LYMESIM 2.0 is a useful public health tool that downstream can be used to evaluate tick control interventions and can be adapted for other ticks and pathogens.
‘This ‘Merikay War’: Poetic Responses in Lancashire to the American Civil War
Authors: Rennie Simon 
Published: January 2020

Abstract
This article examines Lancashire commentary on the American Civil War during the Cotton Famine of 1861–65 through poetry which has recently been recovered from local newspapers. The complexity and variety of the often labouring-class subjectivities figured in the texts works to further disrupt the conventional historical view of a region united in moral and political sympathy with the Union cause, as exemplified by discourses surrounding Lincoln’s letter to the region in 1863. Much of this poetry displays an acute awareness of its place in the world. Labouring-class Lancashire people were forced by economic circumstances to confront the nature of a Victorian globalization which had proved its instability, and many began to see themselves in terms of a global subjectivity for the first time. This poetic discourse may have been materially and culturally adjacent to journalistic comment on the crisis, but poetry’s imaginative freedom and ability to compress language and hence cultural meaning often represented an amplification, distortion, or even contradiction of implied editorial comment. Nowhere was this more apparent than in the sometimes febrile context of Lancashire commentary on the American Civil War and its domestic effects. Even when no particular resolution was offered as an option the ability of Lancashire poets to represent the voice of their fellow sufferers with some degree of authenticity served to reflect the ever more intimate relationship between the Victorian global and the local which the effects of the American war demonstrated in such stark terms.
Constraining planet formation around 6–8 M⊙ stars
Authors: Veras Dimitri , Tremblay Pier-Emmanuel , Hermes J J , McDonald Catriona H , Kennedy Grant M , Meru Farzana , Gänsicke Boris T 
Published: January 2020

ABSTRACT
Identifying planets around O-type and B-type stars is inherently difficult; the most massive known planet host has a mass of only about $3\, \mathrm{M}_{\odot }$. However, planetary systems which survive the transformation of their host stars into white dwarfs can be detected via photospheric trace metals, circumstellar dusty and gaseous discs, and transits of planetary debris crossing our line of sight. These signatures offer the potential to explore the efficiency of planet formation for host stars with masses up to the core-collapse boundary at $\approx 8\, \mathrm{M}_{\odot }$, a mass regime rarely investigated in planet formation theory. Here, we establish limits on where both major and minor planets must reside around $\approx 6\rm {-}8\, \mathrm{M}_{\odot }$ stars in order to survive into the white dwarf phase. For this mass range, we find that intact terrestrial or giant planets need to leave the main sequence beyond approximate minimum star–planet separations of, respectively, about 3 and 6 au. In these systems, rubble pile minor planets of radii 10, 1.0, and 0.1 km would have been shorn apart by giant branch radiative YORP spin-up if they formed and remained within, respectively, tens, hundreds, and thousands of au. These boundary values would help distinguish the nature of the progenitor of metal pollution in white dwarf atmospheres. We find that planet formation around the highest mass white dwarf progenitors may be feasible, and hence encourage both dedicated planet formation investigations for these systems and spectroscopic analyses of the highest mass white dwarfs.
Secular evolution of close-in planets: the effects of general relativity
Authors: Marzari F , Nagasawa M 
Published: January 2020

ABSTRACT
Pairs of planets in a system may end up close to their host star on eccentric orbits as a consequence of planet–planet scattering, Kozai, or secular migration. In this scenario, general relativity and secular perturbations have comparable time-scales and may interfere with each other with relevant effects on the eccentricity and pericenter evolution of the two planets. We explore, both analytically and via numerical integration, how the secular evolution is changed by general relativity for a wide range of different initial conditions. We find that when the faster secular frequency approaches the general relativity precession rate, which typically occurs when the outer planet moves away from the inner one, it relaxes to it and a significant damping of the proper eccentricity of the inner planet occurs. The proper eccentricity of the outer planet is reduced as well due to the changes in the secular interaction of the bodies. The lowering of the peak eccentricities of the two planets during their secular evolution has important implications on their stability. A significant number of two-planet systems, otherwise chaotic because of the mutual secular perturbations, are found stable when general relativity is included.
Measuring stellar magnetic helicity density
Authors: Lund K , Jardine M , Lehmann L T , Mackay D H , See V , Vidotto A A , Donati J-F , Fares R , Folsom C P , Jeffers S V , Marsden S C , Morin J , Petit P 
Published: January 2020

ABSTRACT
Helicity is a fundamental property of a magnetic field but to date it has only been possible to observe its evolution in one star – the Sun. In this paper, we provide a simple technique for mapping the large-scale helicity density across the surface of any star using only observable quantities: the poloidal and toroidal magnetic field components (which can be determined from Zeeman–Doppler imaging) and the stellar radius. We use a sample of 51 stars across a mass range of 0.1–1.34 M⊙ to show how the helicity density relates to stellar mass, Rossby number, magnetic energy, and age. We find that the large-scale helicity density increases with decreasing Rossby number Ro, peaking at Ro ≃ 0.1, with a saturation or decrease below that. For both fully and partially convective stars, we find that the mean absolute helicity density scales with the mean squared toroidal magnetic flux density according to the power law: $|\langle {h\, }\rangle |$ ∝ $\langle {\rm {{\it B}_{tor}}^2_{}\, \rangle }^{0.86\, \pm \, 0.04}$. The scatter in this relation is consistent with the variation across a solar cycle, which we compute using simulations and observations across solar cycles 23 and 24, respectively. We find a significant decrease in helicity density with age.
The dynamical history of the evaporating or disrupted ice giant planet around white dwarf WD J0914+1914
Authors: Veras Dimitri , Fuller Jim 
Published: January 2020

ABSTRACT
Robust evidence of an ice giant planet shedding its atmosphere around the white dwarf WD J0914+1914 represents a milestone in exoplanetary science, allowing us to finally supplement our knowledge of white dwarf metal pollution, debris discs, and minor planets with the presence of a major planet. Here, we discuss the possible dynamical origins of this planet, WD J0914+1914 b. The very young cooling age of the host white dwarf (13 Myr) combined with the currently estimated planet–star separation of about 0.07 au imposes particularly intriguing and restrictive coupled constraints on its current orbit and its tidal dissipation characteristics. The planet must have been scattered from a distance of at least a few au to its current location, requiring the current or former presence of at least one more major planet in the system in the absence of a hidden binary companion. We show that WD J0914+1914 b could not have subsequently shrunk its orbit through chaotic f-mode tidal excitation (characteristic of such highly eccentric orbits) unless the planet was or is highly inflated and possibly had partially thermally self-disrupted from mode-based energy release. We also demonstrate that if the planet is currently assumed to reside on a near-circular orbit at 0.07 au, then non-chaotic equilibrium tides impose unrealistic values for the planet’s tidal quality factor. We conclude that WD J0914+1914 b either (i) actually resides interior to 0.07 au, (ii) resembles a disrupted ‘Super-Puff’ whose remains reside on a circular orbit, or (iii) resembles a larger or denser ice giant on a currently eccentric orbit. Distinguishing these three possibilities strongly motivates follow-up observations.
Faint Standards for ZYJHK from the UKIDSS and VISTA Surveys
Authors: Leggett S K , Cross Nicholas J G , Hambly Nigel C 
Published: January 2020

ABSTRACT
The currently defined ‘United Kingdom Infrared Telescope (UKIRT) Faint Standards’ have JHK magnitudes between 10 and 15, with Kmedian = 11.2. These stars will be too bright for the next generation of large telescopes. We have used multi-epoch observations taken as part of the UKIRT Infrared Deep Sky Survey (UKIDSS) and the Visible and Infrared Survey Telescope for Astronomy (VISTA) surveys to identify non-variable stars with JHK magnitudes in the range 16–19. The stars were selected from the UKIDSS Deep Extragalactic Survey and Ultra Deep Survey, the WFCAM calibration data (WFCAMCAL08B), the VISTA Deep Extragalactic Observations (VIDEO), and UltraVISTA. Sources selected from the near-infrared databases were paired with the Pan-STARRS Data Release 2 of optical to near-infrared photometry and the Gaia astrometric Data Release 2. Colour indices and other measurements were used to exclude sources that did not appear to be simple single stars. From an initial selection of 169 sources, we present a final sample of 81 standard stars with ZYJHK magnitudes, or a subset, each with 20 to 600 observations in each filter. The new standards have Ksmedian = 17.5. The relative photometric uncertainty for the sample is &lt;0.006 mag and the absolute uncertainty is estimated to be ≲ 0.02 mag. The sources are distributed equatorially and are accessible from both hemispheres.