bluuebunny/crossref_metadata_2025_split huggingface dataset:
A GMRT 150 MHz search for variables and transients in Stripe 82
Authors: Hajela A , Mooley K P , Intema H T , Frail D A 
Published: October 2019

ABSTRACT
We have carried out a dedicated transient survey of 300 deg2 of the SDSS Stripe 82 region using the Giant Metrewave Radio Telescope (GMRT) at 150 MHz. Our multi-epoch observations, together with the TGSS survey, allow us to probe variability and transient activity on four different time-scales, beginning with 4 h and up to 4 yr. Data calibration, RFI flagging, source finding, and transient search were carried out in a semi-automated pipeline incorporating the SPAM recipe. This has enabled us to produce superior-quality images and carry out reliable transient search over the entire survey region in under 48 h post-observation. Among the few thousand unique point sources found in our 5σ single-epoch catalogues (flux density thresholds of about 24, 20, 16, and 18 mJy on the respective time-scales), we find <0.08 per cent, 0.01 per cent, <0.06 per cent, and 0.05 per cent to be variable (beyond a significance of 4σ and fractional variability of 30 per cent) on time-scales of 4 h, 1 d, 1 month, and 4 yr, respectively. This is substantially lower than that in the GHz sky, where ∼1 per cent of the persistent point sources are found to be variable. Although our survey was designed to probe a superior part of the transient phase space, our transient search did not yield any significant candidates. The transient (preferentially extragalactic) rate at 150 MHz is therefore <0.005 on time-scales of 1 month and 4 yr, and <0.002 on time-scales of 1 d and 4 h, beyond 7σ detection threshold. We put these results in perspective with the previous studies and give recommendations for future low-frequency transient surveys.
A simplified model for the secular dynamics of eccentric discs and applications to planet–disc interactions
Authors: Teyssandier Jean , Lai Dong 
Published: October 2019

ABSTRACT
We develop a simplified model for studying the long-term evolution of giant planets in protoplanetary discs. The model accounts for the eccentricity evolution of the planets and the dynamics of eccentric discs under the influences of secular planet–disc interactions and internal disc pressure, self-gravity, and viscosity. Adopting the ansatz that the disc precesses coherently with aligned apsides, the eccentricity evolution equations of the planet–disc system reduce to a set of linearized ordinary differential equations, which allows for fast computation of the evolution of planet–disc eccentricities over long time-scales. Applying our model to ‘giant planet + external disc’ systems, we are able to reproduce and explain the secular behaviours found in previously published hydrodynamical simulations. We re-examine the possibility of eccentricity excitation (due to secular resonance) of multiple planets embedded in a dispersing disc, and find that taking into account the dynamics of eccentric discs can significantly affect the evolution of the planets’ eccentricities.
Gas accretion and galactic fountain flows in the Auriga cosmological simulations: angular momentum and metal redistribution
Authors: Grand Robert J J , van de Voort Freeke , Zjupa Jolanta , Fragkoudi Francesca , Gómez Facundo A , Kauffmann Guinevere , Marinacci Federico , Pakmor Rüdiger , Springel Volker , White Simon D M 
Published: October 2019

ABSTRACT
Using a set of 15 high-resolution magnetohydrodynamic cosmological simulations of Milky Way formation, we investigate the origin of the baryonic material found in stars at redshift zero. We find that roughly half of this material originates from subhalo/satellite systems and half is smoothly accreted from the intergalactic medium. About $90 {{\ \rm per\ cent}}$ of all material has been ejected and re-accreted in galactic winds at least once. The vast majority of smoothly accreted gas enters into a galactic fountain that extends to a median galactocentric distance of ∼20 kpc with a median recycling time-scale of ∼500 Myr. We demonstrate that, in most cases, galactic fountains acquire angular momentum via mixing of low angular momentum, wind-recycled gas with high angular momentum gas in the circumgalactic medium (CGM). Prograde mergers boost this activity by helping to align the disc and CGM rotation axes, whereas retrograde mergers cause the fountain to lose angular momentum. Fountain flows that promote angular momentum growth are conducive to smooth evolution on tracks quasi-parallel to the disc sequence of the stellar mass-specific angular momentum plane, whereas retrograde minor mergers, major mergers, and bar-driven secular evolution move galaxies towards the bulge sequence. Finally, we demonstrate that fountain flows act to flatten and narrow the radial metallicity gradient and metallicity dispersion of disc stars, respectively. Thus, the evolution of galactic fountains depends strongly on the cosmological merger history and is crucial for the chemodynamical evolution of Milky-Way-sized disc galaxies.
Cosmological test of gravity using weak lensing voids
Authors: Davies Christopher T , Cautun Marius , Li Baojiu 
Published: October 2019

ABSTRACT
Modifications to general relativity often incorporate screening mechanisms in order to remain compatible with existing tests of gravity. The screening is less efficient in underdense regions, which suggests that cosmic voids can be a useful cosmological probe for constraining modified gravity models. In particular, weak lensing by voids has been proposed as a promising test of such theories. Usually, voids are identified from galaxy distributions, making them biased tracers of the underlying matter field. An alternative approach is to study voids identified in weak lensing maps – weak lensing voids – which have been shown to better correspond to true underdense regions. In this paper, we study the ability of weak lensing voids to detect the signatures of modified gravity. Focusing on the void abundance and weak lensing profiles, we find that both statistics are sensitive probes of gravity. These are quantified in terms of the signal-to-noise ratios (SNR) with which an LSST-like survey will be able to distinguish between different gravity models. We find that the tangential shear profiles of weak lensing voids are considerably better than galaxy voids at this, though voids have somewhat lower SNR than weak lensing peaks. The abundances of voids and peaks have, respectively, $\rm {SNR} = 50$ and 70 for a popular class of modified gravity in an LSST-like survey.
Inactivation of folylpolyglutamate synthetase Met7 results in genome instability driven by an increased dUTP/dTTP ratio
Authors: Schmidt Tobias T , Sharma Sushma , Reyes Gloria X , Kolodziejczak Anna , Wagner Tina , Luke Brian , Hofer Anders , Chabes Andrei , Hombauer Hans 
Published: October 2019

AbstractThe accumulation of mutations is frequently associated with alterations in gene function leading to the onset of diseases, including cancer. Aiming to find novel genes that contribute to the stability of the genome, we screened the Saccharomyces cerevisiae deletion collection for increased mutator phenotypes. Among the identified genes, we discovered MET7, which encodes folylpolyglutamate synthetase (FPGS), an enzyme that facilitates several folate-dependent reactions including the synthesis of purines, thymidylate (dTMP) and DNA methylation. Here, we found that Met7-deficient strains show elevated mutation rates, but also increased levels of endogenous DNA damage resulting in gross chromosomal rearrangements (GCRs). Quantification of deoxyribonucleotide (dNTP) pools in cell extracts from met7Δ mutant revealed reductions in dTTP and dGTP that cause a constitutively active DNA damage checkpoint. In addition, we found that the absence of Met7 leads to dUTP accumulation, at levels that allowed its detection in yeast extracts for the first time. Consequently, a high dUTP/dTTP ratio promotes uracil incorporation into DNA, followed by futile repair cycles that compromise both mitochondrial and nuclear DNA integrity. In summary, this work highlights the importance of folate polyglutamylation in the maintenance of nucleotide homeostasis and genome stability.
ChimerDB 4.0: an updated and expanded database of fusion genes
Authors: Jang Ye Eun , Jang Insu , Kim Sunkyu , Cho Subin , Kim Daehan , Kim Keonwoo , Kim Jaewon , Hwang Jimin , Kim Sangok , Kim Jaesang , Kang Jaewoo , Lee Byungwook , Lee Sanghyuk 
Published: October 2019

Abstract
Fusion genes represent an important class of biomarkers and therapeutic targets in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data (ChimerSeq) and text mining of publications (ChimerPub) with extensive manual annotations (ChimerKB). In this update, we present all three modules substantially enhanced by incorporating the recent flood of deep sequencing data and related publications. ChimerSeq now covers all 10 565 patients in the TCGA project, with compilation of computational results from two reliable programs of STAR-Fusion and FusionScan with several public resources. In sum, ChimerSeq includes 65 945 fusion candidates, 21 106 of which were predicted by multiple programs (ChimerSeq-Plus). ChimerPub has been upgraded by applying a deep learning method for text mining followed by extensive manual curation, which yielded 1257 fusion genes including 777 cases with experimental supports (ChimerPub-Plus). ChimerKB includes 1597 fusion genes with publication support, experimental evidences and breakpoint information. Importantly, we implemented several new features to aid estimation of functional significance, including the fusion structure viewer with domain information, gene expression plot of fusion positive versus negative patients and a STRING network viewer. The user interface also was greatly enhanced by applying responsive web design. ChimerDB 4.0 is available at http://www.kobic.re.kr/chimerdb/.
Frequent template switching in postreplication gaps: suppression of deleterious consequences by the Escherichia coli Uup and RadD proteins
Authors: Romero Zachary J , Armstrong Thomas J , Henrikus Sarah S , Chen Stefanie H , Glass David J , Ferrazzoli Alexander E , Wood Elizabeth A , Chitteni-Pattu Sindhu , van Oijen Antoine M , Lovett Susan T , Robinson Andrew , Cox Michael M 
Published: October 2019

AbstractWhen replication forks encounter template DNA lesions, the lesion is simply skipped in some cases. The resulting lesion-containing gap must be converted to duplex DNA to permit repair. Some gap filling occurs via template switching, a process that generates recombination-like branched DNA intermediates. The Escherichia coli Uup and RadD proteins function in different pathways to process the branched intermediates. Uup is a UvrA-like ABC family ATPase. RadD is a RecQ-like SF2 family ATPase. Loss of both functions uncovers frequent and RecA-independent deletion events in a plasmid-based assay. Elevated levels of crossing over and repeat expansions accompany these deletion events, indicating that many, if not most, of these events are associated with template switching in postreplication gaps as opposed to simple replication slippage. The deletion data underpin simulations indicating that multiple postreplication gaps may be generated per replication cycle. Both Uup and RadD bind to branched DNAs in vitro. RadD protein suppresses crossovers and Uup prevents nucleoid mis-segregation. Loss of Uup and RadD function increases sensitivity to ciprofloxacin. We present Uup and RadD as genomic guardians. These proteins govern two pathways for resolution of branched DNA intermediates such that potentially deleterious genome rearrangements arising from frequent template switching are averted.
Why is the American South Poorer?
Authors: Baker Regina S 
Published: October 2019

ABSTRACTWhile American poverty research has devoted greater attention to poverty in the Northeast and Midwest, poverty has been persistently higher in the U.S. South than in the other regions. Thus, this study investigates the enduring question of why poverty is higher in the South. Specifically, it demonstrates the role of power resources as an explanation for this regional disparity, yet also considers family demography, economic structure, and racial/ethnic heterogeneity. Using six waves (2000–2016) of U.S. Census Current Population Survey data from the Luxembourg Income Study (N = 1,157,914), this study employs a triangulation of analytic techniques: (1) tests of means and proportion differences, (2) multilevel linear probability models of poverty, and (3) binary decomposition of the South/non-South poverty gap. The comparison of means associated with the power resource hypothesis yields the largest substantive differences between the South and the non-South. In the multilevel models, adjusting for power resources yields the largest declines in the South coefficient. Binary decomposition results indicate power resources are the second most influential factor explaining the South/non-South poverty gap. Overall, power resources are an important source of the South/non-South poverty gap, though economic structure and other factors certainly also play a role. Results also suggest an important interplay between power resources and race. Altogether, these results underscore the importance of macrolevel characteristics of places, including political and economic contexts, in shaping individual poverty and overall patterns of inequality.
Predator and prey detection in two species of water bear (Tardigrada)
Authors: Meyer Harry A , Larsen Hannah E , Akobi Nézira O , Broussard Garret 
Published: October 2019

Abstract
Tardigrade behavioural studies have focused on responses to abiotic environmental conditions. Predator–prey interactions have received some attention, but not how predators and prey might detect one another. Here, we investigate whether a predatory tardigrade species is attracted to, and a potential prey tardigrade avoids, areas previously occupied by the other. In our experiments, Milnesium lagniappe was the predator and Macrobiotus acadianus the prey. Petri dishes with non-nutrient agar were used as experimental arenas. In one treatment, we allowed Macrobiotus to roam over half of the agar for 20 h, while leaving the other half free of Macrobiotus. We then removed the prey and introduced the predator. In the control treatment, no prey were added. Results indicated that Milnesium individuals were significantly concentrated in the area previously occupied by Macrobiotus, whereas no such concentration was evident when Macrobiotus had not been present. A similar protocol was used to test whether Macrobiotus avoided areas previously occupied by the predator. As expected, Macrobiotus were significantly concentrated in the area never occupied by Milnesium, unlike the control treatment. These results suggest that both species can detect the other without physical contact and react accordingly. Given that the experiments were conducted in darkness, detection is probably olfactory.
Two simple criteria to estimate an objective’s performance when imaging in non design tissue clearing solutions
Authors: Asteriti Sabrina , Ricci Valeria , Cangiano Lorenzo 
Published: October 2019

ABSTRACTTissue clearing techniques are undergoing a renaissance motivated by the need to image fluorescence deep in biological samples without physical sectioning. Optical transparency is achieved by equilibrating tissues with high refractive index (RI) solutions, which require expensive optimized objectives to avoid aberrations. One may thus need to assess whether an available objective is suitable for a specific clearing solution, or the impact on imaging of small mismatches between cleared sample and objective design RIs. We derived closed form approximations for image quality degradation versus RI mismatch and other parameters available to the microscopist. We validated them with computed (and experimentally confirmed) aberrated point spread functions, and by imaging fluorescent neurons in high RI solutions. Crucially, we propose two simple numerical criteria to establish: (i) the degradation in image quality (brightness and resolution) from optimal conditions of any clearing solution/objective combination; (ii) which objective, among several, achieves the highest resolution in a given immersion medium. These criteria apply directly to the widefield fluorescent microscope but are also closely relevant to more advanced microscopes.
Cerebellar-recipient motor thalamus drives behavioral context-specific movement initiation
Authors: Dacre Joshua , Colligan Matt , Ammer Julian , Schiemann Julia , Clarke Thomas , Chamosa-Pino Victor , Claudi Federico , Harston J. Alex , Eleftheriou Constantinos , Pakan Janelle M.P. , Huang Cheng-Chiu , Hantman Adam , Rochefort Nathalie L. , Duguid Ian 
Published: October 2019

SummaryTo initiate goal-directed behavior, animals must transform sensory cues into motor commands that generate appropriately timed actions. Sensorimotor transformations along the cerebellar-thalamocortical pathway are thought to shape motor cortical output and movement timing, but whether this pathway initiates goal-directed movement remains poorly understood. Here, we recorded and perturbed activity in cerebellar-recipient regions of motor thalamus (dentate / interpositus nucleus-recipient regions, MThDN/IPN) and primary motor cortex (M1) in mice trained to execute a cued forelimb lever push task for reward. MThDN/IPN population responses were dominated by a time-locked increase in activity immediately prior to movement that was temporally uncoupled from cue presentation, providing a fixed latency feedforward motor timing signal to M1FL. Blocking MThDN/IPN output suppressed cued movement initiation. Stimulating the MThDN/IPN thalamocortical pathway in the absence of the cue recapitulated cue-evoked M1 membrane potential dynamics and forelimb behavior in the learned behavioral context, but generated semi-random movements in an altered behavioral context. Thus, cerebellar-recipient motor thalamocortical input to M1 is indispensable for the generation of motor commands that initiate goal-directed movement, refining our understanding of how the cerebellar-thalamocortical pathway contributes to movement timing.
Deletion of M-opsin prevents “M cone” degeneration in a mouse model of Leber congenital amaurosis
Authors: Xu Hui , Enemchukwu Nduka , Zhong Xiaoyue , Zhang Olivia , Fu Yingbin 
Published: October 2019

AbstractMutations in RPE65 or lecithin-retinol acyltransferase (LRAT) disrupt 11-cis-retinal synthesis and cause Leber congenital amaurosis (LCA). In Lrat−/− mouse model, mislocalized medium (M)-wavelength sensitive opsin was degraded whereas mislocalized short (S)-wavelength sensitive opsin accumulated before the onset of cone degeneration. The mechanism for the foveal medium (M)/long (L)-wavelength-sensitive cone degeneration in LCA is unknown. By crossing Lrat−/− mice with a proteasome reporter mouse line, we showed that M-opsin enriched dorsal cones in Lrat−/− mice exhibit proteasome stress due to the degradation of large amounts of M-opsin. Deletion of M-opsin relieves the proteasome stress and completely prevents “M cone” degeneration in Lrat−/−Opn1sw−/− mice (a pure “M cone” LCA model, Opn1sw−/− encoding S-opsin) for at least 12 months. Our results suggest that M-opsin degradation associated proteasome stress plays a major role in “M cone” degeneration in Lrat−/− model. This finding may represent a general mechanism for “M cone” degeneration for multiple forms of cone degeneration due to M-opsin mislocalization and degradation. Our results have important implications for the current gene therapy strategy for LCA that emphasizes the need for a combinatorial therapy to both improve vision and slow photoreceptor degeneration.
Distribution of members of the Anopheles gambiae complex in selected forested tourist areas of Cross River State, Nigeria
Authors: Oduwole OA , Oduola AO , Oringanje CM , Nwachuku NS , Meremikwu MM , Useh MF , Alaribe AAA 
Published: October 2019

AbstractBackgroundThe Anopheles gambiae mosquitoes are the most abundant, efficient and widely distributed vectors of the malaria parasite in sub-Saharan Africa. In most African countries, where malaria control programmes are focused on the use of long-lasting insecticide treated bed net, there is need to evaluate the biting behaviour and the identity of such mosquitoes to determine the relevance and appropriateness of the control measure implemented.MethodThis study investigated the distribution and molecular characteristics of the Anopheles species in selected forested areas in Cross River State, Nigeria. Mosquitoes were collected using pyrethrum spray catch and Centre for Disease Control light traps modified with yeast and sugar to generate carbon dioxide (CO2). Anopheles gambiae complex was identified using multiplex polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) for molecular forms characterization.ResultsOne hundred and four Anopheles gambiae s.l. were collected during the study. Multiplex PCR showed 75% of the species complex were A. gambiae s.s. and further characterization using PCR-RFLP showed that 53.8% of the A. gambiae s.l. identified were A. gambiae s.s.while 24.4% were A.coluzzii. The two species of the A. gambiae s.l. were found to be most abundant. The study also reported a 1.3% hybrid form of Anopheles gambiae s.s.and Anopheles coluzzii.ConclusionThe findings suggest the first documented evidence of hybrid forms of A. gambiae s.s./A.coluzzii in South Eastern Nigeria although its epidemiological implication is still not clear.
miR-181a Regulates p62/SQSTM1, Parkin and Protein DJ-1 Promoting Mitochondrial Dynamics in Skeletal Muscle Ageing
Authors: Goljanek-Whysall Katarzyna , Soriano-Arroquia Ana , McCormick Rachel , Chinda Caroline , McDonagh Brian 
Published: October 2019

AbstractOne of the key mechanisms underlying skeletal muscle functional deterioration during ageing is disrupted mitochondrial dynamics. Regulation of mitochondrial dynamics is essential to maintain a healthy mitochondrial population and prevent the accumulation of damaged mitochondria, however the regulatory mechanisms are poorly understood. We demonstrated loss of mitochondrial content and disrupted mitochondrial dynamics in muscle during ageing concomitant with dysregulation of miR-181a target interactions. Using functional approaches and mitoQc assay, we have established that miR-181a is an endogenous regulator of mitochondrial dynamics through concerted regulation of Park2, p62/SQSTM1 and DJ-1 in vitro. Downregulation of miR-181a with age was associated with an accumulation of autophagy-related proteins and abnormal mitochondria. Restoring miR-181a levels in old mice prevented accumulation of p62, DJ-1 and PARK2, improved mitochondrial quality and muscle function. These results provide physiological evidence for the potential of microRNA-based interventions for age-related muscle atrophy and of wider significance for diseases with disrupted mitochondrial dynamics.