bluuebunny/crossref_metadata_2025_split huggingface dataset:
The quenching and morphological evolution of central galaxies is facilitated by the feedback-driven expulsion of circumgalactic gas
Authors: Davies Jonathan J , Crain Robert A , Oppenheimer Benjamin D , Schaye Joop 
Published: November 2019

ABSTRACT
We examine the connection between the properties of the circumgalactic medium (CGM) and the quenching and morphological evolution of central galaxies in the EAGLE and IllustrisTNG simulations. The simulations yield very different median CGM mass fractions, fCGM, as a function of halo mass, M200, with low-mass haloes being significantly more gas-rich in IllustrisTNG than in EAGLE. Nonetheless, in both cases scatter in fCGM at fixed M200 is strongly correlated with the specific star formation rate and the kinematic morphology of central galaxies. The correlations are strongest for ∼L⋆ galaxies, corresponding to the mass scale at which AGN feedback becomes efficient. This feedback elevates the CGM cooling time, preventing gas from accreting on to the galaxy to fuel star formation, and thus establishing a preference for quenched, spheroidal galaxies to be hosted by haloes with low fCGM for their mass. In both simulations, fCGM correlates negatively with the host halo’s intrinsic concentration, and hence with its binding energy and formation redshift, primarily because early halo formation fosters the rapid early growth of the central black hole (BH). This leads to a lower fCGM at fixed M200 in EAGLE because the BH reaches high accretion rates sooner, whilst in IllustrisTNG it occurs because the central BH reaches the mass threshold at which AGN feedback is assumed to switch from thermal to kinetic injection earlier. Despite these differences, there is consensus from these state-of-the-art simulations that the expulsion of efficiently cooling gas from the CGM is a crucial step in the quenching and morphological evolution of central galaxies.
Extracting the Global Signal from 21-cm Fluctuations: the Multi-Tracer Approach
Authors: Fialkov Anastasia , Barkana Rennan , Jarvis Matt 
Published: November 2019

Abstract
The multi-tracer technique employs a ratio of densities of two differently biased galaxy samples that trace the same underlying matter density field, and was proposed to alleviate the cosmic variance problem. Here we propose a novel application of this approach, applying it to two different tracers one of which is the 21-cm signal of neutral hydrogen from the epochs of reionization and comic dawn. The second tracer is assumed to be a sample of high-redshift galaxies, but the approach can be generalized and applied to other high-redshift tracers. We show that the anisotropy of the ratio of the two density fields can be used to measure the sky-averaged 21-cm signal, probe the spectral energy distribution of radiative sources that drive this signal, and extract large-scale properties of the second tracer, e.g., the galaxy bias. Using simulated 21-cm maps and mock galaxy samples, we find that the method works well for an idealized galaxy survey. However, in the case of a more realistic galaxy survey which only probes highly biased luminous galaxies, the inevitable Poisson noise makes the reconstruction far more challenging. This difficulty can be mitigated with the greater sensitivity of future telescopes along with larger survey volumes.
Effect of 2-acetylaminofluorene and its genotoxic metabolites on DNA adduct formation and DNA damage in 3D reconstructed human skin tissue models
Authors: Downs Thomas R , Arlt Volker M , Barnett Brenda C , Posgai Ryan , Pfuhler Stefan 
Published: November 2019

AbstractIn vitro genotoxicity assays utilising human skin models are becoming important tools for the safety assessment of chemicals whose primary exposure is via the dermal route. In order to explore metabolic competency and inducibility of CYP450 activating enzymes, 3D reconstructed human skin tissues were topically treated with 2-acetylaminofluorene (2-AAF) and its genotoxic metabolites, N-hydroxy-2-acetylaminofluorene (N-OH-2-AAF) and N-hydroxy-2-aminofluorene (N-OH-2-AF), which primarily cause DNA damage by forming DNA adducts. 2-AAF did not increase DNA damage measured in the reconstructed skin micronucleus (RSMN) assay when administered in multiple applications at 24 h intervals but was detected in the skin comet assay in the presence of the DNA polymerase inhibitor aphidicolin (APC). Similarly, no increase was found with N-OH-2-AAF in the RSMN assay after multiple treatments whereas a single 3 h exposure to N-OH-2-AAF caused a large dose-related increase in the skin comet assay. A significant increase in the RSMN assay was only obtained with the highly reactive N-OH-2-AF metabolite after multiple treatments over 72 h, whereas N-OH-2-AF caused a strong increase after a single 3 h exposure in the skin comet assay. In support of these results, DNA adduct formation, measured by the 32P-postlabelling assay, was examined. Adduct levels after 2-AAF treatment for 3 h were minimal but increased &gt;10-fold after multiple exposures over 48 h, suggesting that enzyme(s) that metabolise 2-AAF are induced in the skin models. As expected, a single 3 h exposure to N-OH-2-AAF and N-OH-2-AF resulted in adduct levels that were at least 10-fold greater than those after multiple exposures to 2-AAF despite ~100-fold lower tested concentrations. Our results demonstrate that DNA damage caused by 2-AAF metabolites is more efficiently detected in the skin comet assay than the RSMN assay and after multiple exposures and enzyme induction, 2-AAF-induced DNA damage can be detected in the APC-modified comet assay.
Requirements for DNA bubble structure for efficient cleavage by helix–two-turn–helix DNA glycosylases
Authors: Makasheva Kristina A , Endutkin Anton V , Zharkov Dmitry O 
Published: November 2019

AbstractOxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix–two-turn–helix (H2TH) structural superfamily, remove oxidised purines and pyrimidines, respectively. Interestingly, the human H2TH family glycosylases, NEIL1, NEIL2 and NEIL3, have been reported to prefer oxidative lesions in DNA bubbles or single-stranded DNA. It had been hypothesised that NEIL2 might be involved in the repair of lesions in transcription bubbles; however, bubble-like structures may appear in other cellular contexts such as displacement loops (D-loops) associated with transcription, recombination or telomere maintenance. The activities of bacterial Fpg and Nei on bubble substrates were not addressed. Also, it is not known whether H2TH enzymes process bubbles containing the third DNA or RNA strand, and how the bubble length and position of the lesion within a bubble affect the excision. We have investigated the removal of 8-oxoguanine (8-oxoG) and 5,6-dihydrouracil (DHU) by Escherichia coli Fpg and Nei and human NEIL1 and NEIL2 from single-strand oligonucleotides, perfect duplexes, bubbles with different numbers of unpaired bases (6–30), bubbles containing the lesion in different positions and D-loops with the third strand made of DNA or RNA. Fpg, NEIL1 and NEIL2 efficiently excised lesions located within bubbles, with NEIL1 and NEIL2 being specific for DHU, and Fpg removing both 8-oxoG and DHU. Nei, in contrast, was significantly active only on DHU located in double-stranded DNA. Fpg and NEIL1 also tolerated the presence of the third strand of either DNA or RNA in D-loops if the lesion was in the single-stranded part, and Fpg, Nei and NEIL1 excised lesions from the double-stranded DNA part of D-loops. The presence of an additional unpaired 5′-tail of DNA or RNA did not affect the activity. No significant position preference for lesions in a 12-mer bubble was found. Overall, the activities of Fpg, NEIL1 and NEIL2 on these non-canonical substrates are consistent with the possibility that these enzymes may participate in the repair in structures arising during transcription or homologous recombination.
Structures of 1:1 and 2:1 complexes of BMVC and MYC promoter G-quadruplex reveal a mechanism of ligand conformation adjustment for G4-recognition
Authors: Liu Wenting , Lin Clement , Wu Guanhui , Dai Jixun , Chang Ta-Chau , Yang Danzhou 
Published: November 2019

AbstractBMVC is the first fluorescent probe designed to detect G-quadruplexes (G4s) in vivo. The MYC oncogene promoter forms a G4 (MycG4) which acts as a transcription silencer. Here, we report the high-affinity and specific binding of BMVC to MycG4 with unusual slow-exchange rates on the NMR timescale. We also show that BMVC represses MYC in cancer cells. We determined the solution structures of the 1:1 and 2:1 BMVC–MycG4 complexes. BMVC first binds the 5′-end of MycG4 to form a 1:1 complex with a well-defined structure. At higher ratio, BMVC also binds the 3′-end to form a second complex. In both complexes, the crescent-shaped BMVC recruits a flanking DNA residue to form a BMVC-base plane stacking over the external G-tetrad. Remarkably, BMVC adjusts its conformation to a contracted form to match the G-tetrad for an optimal stacking interaction. This is the first structural example showing the importance of ligand conformational adjustment in G4 recognition. BMVC binds the more accessible 5′-end with higher affinity, whereas sequence specificity is present at the weaker-binding 3′-site. Our structures provide insights into specific recognition of MycG4 by BMVC and useful information for design of G4-targeted anticancer drugs and fluorescent probes.
Mapping RNA–capsid interactions and RNA secondary structure within virus particles using next-generation sequencing
Authors: Zhou Yiyang , Routh Andrew 
Published: November 2019

Abstract
To characterize RNA–capsid binding sites genome-wide within mature RNA virus particles, we have developed a Next-Generation Sequencing (NGS) platform: viral Photo-Activatable Ribonucleoside CrossLinking (vPAR-CL). In vPAR-CL, 4-thiouridine is incorporated into the encapsidated genomes of virus particles and subsequently UV-crosslinked to adjacent capsid proteins. We demonstrate that vPAR-CL can readily and reliably identify capsid binding sites in genomic viral RNA by detecting crosslink-specific uridine to cytidine transitions in NGS data. Using Flock House virus (FHV) as a model system, we identified highly consistent and significant vPAR-CL signals across virus RNA genome, indicating a clear tropism of the encapsidated RNA genome. Certain interaction sites coincide with previously identified functional RNA motifs. We additionally performed dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to generate a high-resolution profile of single-stranded genomic RNA inside viral particles. Combining vPAR-CL and DMS-MaPseq reveals that the predominant RNA–capsid interaction sites favored double-stranded RNA regions. We disrupted secondary structures associated with vPAR-CL sites using synonymous mutations, resulting in varied effects to virus replication, propagation and packaging. Certain mutations showed substantial deficiency in virus replication, suggesting these RNA–capsid sites are multifunctional. These provide further evidence to support that FHV packaging and replication are highly coordinated and inter-dependent events.
Double-frequency Aharonov-Bohm effect and non-Abelian braiding properties of Jackiw-Rebbi zero-mode
Authors: Wu Yijia , Liu Haiwen , Liu Jie , Jiang Hua , Xie X C 
Published: November 2019

Abstract
Ever since its first proposal in 1976, Jackiw-Rebbi zero-mode has been drawing extensive attention for its charming properties including charge fractionalization, topologically protected zero-energy and possible non-Abelian statistics. We investigate these properties through the Jackiw-Rebbi zero-modes in quantum spin Hall insulators. Though charge fractionalization is not manifested, Jackiw-Rebbi zero-mode's zero-energy nature leads to a double-frequency Aharonov-Bohm effect, implying that it can be viewed as a special case of Majorana zero-mode without particle-hole symmetry. Such relation is strengthened for Jackiw-Rebbi zero-modes also exhibiting non-Abelian properties in the absence of superconductivity. Furthermore, in the condition that the degeneracy of Jackiw-Rebbi zero-modes is lifted, we demonstrate a novel non-Abelian braiding with continuously tunable fusion rule, which is a generalization of Majorana zero-modes’ braiding properties.
Incomplete information and iterated strict dominance
Authors: Bach Christian W , Perea Andrés 
Published: November 2019

Abstract
The solution concept of iterated strict dominance for static games with complete information recursively deletes choices that are inferior. Here, we devise such an algorithm for the more general case of incomplete information. The ensuing solution concept of generalized iterated strict dominance is characterized in terms of common belief in rationality as well as in terms of best response sets. Besides, we provide doxastic conditions that are necessary and sufficient for modelling complete information from a one-person perspective.
Clinical Outcomes Associated With Escherichia coli Infections in Adults With Cystic Fibrosis: A Cohort Study
Authors: Edwards B D , Somayaji R , Greysson-Wong J , Izydorczyk C , Waddell B , Storey D G , Rabin H R , Surette M G , Parkins M D 
Published: November 2019

Abstract

Background
Analysis of “emerging” pathogens in cystic fibrosis (CF) lung disease has focused on unique pathogens that are rare in other human diseases or are drug resistant. Escherichia coli is recovered in the sputum of up to 25% of patients with CF, yet little is known about the epidemiology or clinical impact of infection.

Methods
We studied patients attending a Canadian adult CF clinic who had positive sputum cultures for E coli from 1978 to 2016. Infection was categorized as transient or persistent (≥3 positive sputum cultures, spanning &gt;6 months). Those with persistent infection were matched 2:1 with age, sex, and time-period controls without history of E coli infection, and mixed-effects models were used to assess pulmonary exacerbation (PEx) frequency, lung function decline, hospitalization, and intravenous antibiotic days.

Results
Forty-five patients (12.3%) had E coli recovered from sputum samples between 1978 and 2016, and 18 patients (40%) developed persistent infection. Nine patients (24%) had PEx at incident infection, and increased bioburden was predictive of exacerbation (P = .03). Risk factors for persistent infection included lower nutritional status (P &lt; .001) and lower lung function (P = .009), but chronic infection with Pseudomonas aeruginosa was protective. There was no difference in annual lung function decline, need for hospitalization or intravenous antibiotics, or risk of PEx in patients with persistent infection.

Conclusions
Persistent E coli infection was frequent and was more common in CF patients with low nutritional status and lung function. However, this does not predict clinical decline. Multicenter studies would allow better characterization of the epidemiology and clinical impact of E coli infection.
Formal infectious diseases specialist consultation improves long-term outcome of methicillin-sensitive Staphylococcus aureus bacteremia
Authors: Forsblom E , Frilander H , Ruotsalainen E , Järvinen A 
Published: November 2019

Abstract

Background
Formal infectious diseases specialist (IDS) consultation has been shown to improve short-term outcome of Staphylococcus aureus bacteremia (SAB) but its effect on long-term outcome lacks evaluation.

Methods
Retrospective study of 367 methicillin-sensitive (MS) SAB patients followed for 10 years. The impact of formal IDS consultation on risk for new bacteremia and outcome during long-term follow-up were evaluated. Patients who died within 90 days were excluded to avoid interference from early deceased patients.

Results
304 (83%) patients had formal IDS consultation whereas 63 (17%) received informal or no IDS consultation. Formal consultation, compared to informal or lack of consultation, associated to a reduced risk for a new bacteremia caused by any pathogen within 1-year (OR, 0.39; 95% CI, .18-.84; p=.014; 8% vs. 17%), and within 3-years (OR, 0.39; 95% CI, .19-.80; p=.010; 9% vs. 21%) whereas a trend towards a lower risk was observed within 10-years (OR, 0.56; 95% CI, .29-1.08; p=.079; 16% vs. 25%). Formal consultation, compared to informal or lack of consultation, improved outcome at 1-year (OR, 0.16; 95% CI, .06-.44; p<0.001; 3% vs. 14%), at 3-years (OR, 0.19; 95% CI, .09-.42; p<.001; 5% vs. 22%) and at 10-years (OR, 0.43; 95% CI, .24-.74; p=.002; 27% vs. 46%). Considering all prognostic parameters formal consultation improved outcome (HR, 0.42; 95% CI, .27-.65, p<.001) and lowered risk for any new bacteremia (OR, 0.45; 95% CI, .23-.88, p=.02) during 10-years follow-up.

Conclusion
MS-SAB management by formal IDS consultation, compared to informal or lack of IDS consultation, reduces risk for any new bacteremia episodes and improves long-term prognosis up to ten years.
Far-Lateral Craniotomy for Posterior Inferior Cerebellar Artery to Occipital Artery Bypass: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F 
Published: November 2019

Abstract
Posterior inferior cerebellar artery (PICA) aneurysms are infrequent compared with other intracranial aneurysms and are more commonly distal in origin (35% of PICA aneurysms are distal vs 6.5% of other aneurysms). This makes PICA aneurysms a surgical challenge that requires careful consideration of the patient's angiographic anatomy and perfusion needs before deciding on the appropriate intervention. This patient had a highly calcified left PICA p2 segment aneurysm, which was not favorable for endovascular intervention. An end-to-side anastomosis of the occipital artery to the p3 PICA segment was performed. This anastomosis was achieved with 11-0 suture. A permanent clip was then placed along the vertebral artery occluding both the proximal PICA and the aneurysm. Indocyanine green angiography was performed to demonstrate bypass and PICA patency. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
High-Level Mobility Assessment Tool Normative Values for Children
Authors: Eldridge Beverly J , Galea Mary P , Kissane Anne L , Broder Jonathan C , Brilleman Samuel L , Wolfe Rory , Williams Gavin 
Published: November 2019

Abstract

Background
Physical therapists need to be able to evaluate high-level gross motor skills of children to determine their capacity to engage in activities such as running, jumping, hopping, and stair climbing. The High-Level Mobility Assessment Tool (HiMAT) has excellent interrater and retest reliability and is less susceptible to a ceiling effect than existing mobility scales in children who are 6 to 17 years old and have traumatic brain injury.

Objective
The purposes of this study were to develop normative HiMAT score ranges for Australian children and to investigate the relationship between children’s HiMAT scores and their age, height, weight, and body mass index (BMI).

Design
This study used a cross-sectional design.

Methods
Children included in this study were 5 to 12 years old, had no condition affecting their mobility, could follow 2-stage instructions, and had written informed consent from their parent or guardian. A total 1091 children were assessed at their local school, where their height, weight, and HiMAT score were recorded. The relationships between children’s age, height, weight, and BMI were summarized using Spearman rank correlations. Truncated regression models were used to determine the most appropriate predictor variable for developing sex-specific normative ranges.

Results
There was a positive correlation between children’s HiMAT scores and their age, height, weight, and BMI. Age explained the most variability in HiMAT scores for both boys and girls.

Limitations
The reliability, validity, and responsiveness of the HiMAT have not been tested across a broad range of children with mobility limitations. Normative data reported in this study are for Australian children only.

Conclusions
HiMAT scores for children in this study increased with age, height, weight, and BMI. Age was the most appropriate variable for developing a normative dataset of HiMAT scores for children of primary school age.
DIOPHANTINE APPROXIMATION WITH GAUSSIAN PRIMES
Authors: Harman Glyn 
Published: November 2019

Abstract
In this paper we prove that the exact analogue of the author’s work with real irrationals and rational primes (G. Harman, On the distribution of $\alpha p$ modulo one II, Proc. London Math. Soc. (3) 72, 1996, 241–260) holds for approximating $\alpha \in \mathbb{C}\setminus \mathbb{Q}[i]$ with Gaussian primes. To be precise, we show that for such $\alpha $ and arbitrary complex $\beta $ there are infinitely many solutions in Gaussian primes $p$ to $$\begin{equation*} ||\alpha p + \beta|| <| p|^{-7/22}, \end{equation*}$$where $||\cdot ||$ denotes distance to a nearest member of $\mathbb{Z}[i]$. We shall, in fact, prove a slightly more general result with the Gaussian primes in sectors, and along the way improve a recent result due to Baier (S. Baier, Diophantine approximation on lines in $\mathbb{C}^2$ with Gaussian prime constraints, Eur. J. Math. 3, 2017, 614–649).
Geography, Climate, and Genes in Development Studies
Authors: Klitgaard Robert , Fedderke Johannes W , Napolioni Valerio 
Published: November 2019

AbstractOver the coming decade, much more genetic data will enter into the study of economic development. This paper provides an example and emphasizes the uses and misuses of such information. It has assembled for the first time national frequencies of the ACP1 genetic polymorphism and the Interleukin-6 (IL6-174G) and Interleukin-10 (IL10-1082G) cytokines. These three respond over the centuries to ultraviolet radiation and infectious diseases. The study also looks at a national measure of heterozygotic diversity. In particular, it finds that ACP1 frequencies are significantly related to national outcomes ranging from GDP per capita to type and quality of governance, to measures of national “competitiveness,” to health, to fertility, to measures of satisfaction with life. These associations do not seem explainable by reverse causation nor by the influence of some of the usual variables in studies of long-run development. Nonetheless, these results do not mean that a few genes have a direct causal effect on world development. The ACP1*B variable is surely picking up the influences of many genetic and cultural adaptations over evolutionary time in response to ultraviolet exposure and pathogen burdens. This study's findings thus support other research indicating the importance of disease environments in shaping both genetic and sociocultural adaptations that have influence on development outcomes today. The paper concludes with a discussion of what such strong associations mean and do not mean, in hopes of guiding future studies of genes and other deep roots of economic development.