bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the correspondence between nested calculi and semantic systems for intuitionistic logics
Authors: Lyon Tim 
Published: December 2020

AbstractThis paper studies the relationship between labelled and nested calculi for propositional intuitionistic logic, first-order intuitionistic logic with non-constant domains and first-order intuitionistic logic with constant domains. It is shown that Fitting’s nested calculi naturally arise from their corresponding labelled calculi—for each of the aforementioned logics—via the elimination of structural rules in labelled derivations. The translational correspondence between the two types of systems is leveraged to show that the nested calculi inherit proof-theoretic properties from their associated labelled calculi, such as completeness, invertibility of rules and cut admissibility. Since labelled calculi are easily obtained via a logic’s semantics, the method presented in this paper can be seen as one whereby refined versions of labelled calculi (containing nested calculi as fragments) with favourable properties are derived directly from a logic’s semantics.
Early Childhood Outcomes Among Infants Born by Vaginal Birth After Cesarean and Repeat Cesarean Delivery in the Military Health System
Authors: Kikuchi Jacqueline , Ranjit Anju , Jiang Wei , Witkop Catherine , Hamlin Lynette , Koehlmoos Tracey Perez 
Published: December 2020

ABSTRACT

Objective
This study examines whether children delivered by repeat cesarean section experience higher incidences of otitis media, respiratory infections, and allergic diseases than children delivered by vaginal birth after cesarean section (VBAC) in the Military Health System.

Study Design
This is a retrospective cohort study from the Military Health System Data Repository of women who underwent repeat cesarean section or VBAC between 2006 and 2012 and their offspring through 2014.

Results
About 11,659 infants with 2 years of follow-up were identified. Infants delivered by VBAC had lower odds of developing respiratory illness (P &lt; .000), otitis media (P &lt; .001), and allergies (P = .022) compared with infants born by repeat cesarean section. There were no differences in the development of food allergies.

Conclusion
Emerging data regarding early childhood health are additional factors that can influence the mother’s decision on mode of birth after a primary cesarean section.
Hydrogen and helium escape on Venus via energy transfer from hot oxygen atoms
Authors: Gu Hao , Cui Jun , Niu Dandan , Yu Jiang 
Published: December 2020

ABSTRACT
Due to the relatively strong gravity on Venus, heavy atmospheric neutrals are difficult to accelerate to the escape velocity. However, a variety of processes, such as the dissociative recombination of ionospheric O$_2^+$, are able to produce hot atoms which could deliver a significant amount of energy to light neutrals and drive their escape. In this study, we construct a Monte Carlo model to simulate atmospheric escape of three light species, H, H2, and He, on Venus via such a knock-on process. Two Venusian background atmosphere models are adopted, appropriate for solar minimum and maximum conditions. Various energy-dependent and species-dependent cross-sections, along with a common strongly forward scattering angle distribution, are used in our calculations. Our model results suggest that knock-on by hot O likely plays the dominant role in driving total atmospheric hydrogen and helium escape on Venus at the present epoch, with a significant portion contributed from regions below the exobase. Substantial variations are also revealed by our calculations. Of special interest is the modelled reduction in escape flux at high solar activities for all species, mainly associated with the enhancement in thermal O concentration near the exobase at high solar activities which hinders escape. Finally, model uncertainties due to several controlling factors, including the distribution of relevant light species in the background atmosphere, the plane-parallel approximation, and the finite O energy distribution, are evaluated.
Spatially resolved direct method metallicity in a high-redshift analogue local galaxy: temperature structure impact on metallicity gradients
Authors: Cameron Alex J , Yuan Tiantian , Trenti Michele , Nicholls David C , Kewley Lisa J 
Published: December 2020

Abstract
We investigate how H ii region temperature structure assumptions affect “direct-method” spatially-resolved metallicity observations using multispecies auroral lines in a galaxy from the SAMI Galaxy Survey. SAMI609396B, at redshift z = 0.018, is a low-mass galaxy in a minor merger with intense star formation, analogous to conditions at high redshifts. We use three methods to derive direct metallicities and compare with strong-line diagnostics. The spatial metallicity trends show significant differences among the three direct methods. Our first method is based on the commonly used electron temperature Te([O iii]) from the [O iii]λ4363 auroral line and a traditional Te([O ii]) – Te([O iii]) calibration. The second method applies a recent empirical correction to the O+ abundance from the [O iii]/[O ii] strong-line ratio. The third method infers the Te([O ii]) from the [S ii]λλ4069,76 auroral lines. The first method favours a positive metallicity gradient along SAMI609396B, whereas the second and third methods yield flattened gradients. Strong-line diagnostics produce mostly flat gradients, albeit with unquantified contamination from shocked regions. We conclude that overlooked assumptions about the internal temperature structure of H ii regions in the direct method can lead to large discrepancies in metallicity gradient studies. Our detailed analysis of SAMI609396B underlines that high-accuracy metallicity gradient measurements require a wide array of emission lines and improved spatial resolutions in order to properly constrain excitation sources, physical conditions, and temperature structures of the emitting gas. Integral-field spectroscopic studies with future facilities such as JWST/NIRSpec and ground-based ELTs will be crucial in minimising systematic effects on measured gradients in distant galaxies.
Non-thermal filaments from the tidal destruction of clouds in the Galactic centre
Authors: Coughlin Eric R , Nixon C J , Ginsburg Adam 
Published: December 2020

ABSTRACT
Synchrotron-emitting, non-thermal filaments (NTFs) have been observed near the Galactic centre for nearly four decades, yet their physical origin remains unclear. Here we investigate the possibility that NTFs are produced by the destruction of molecular clouds by the gravitational potential of the Galactic centre. We show that this model predicts the formation of a filamentary structure with length on the order of tens to hundreds of pc, a highly ordered magnetic field along the axis of the filament, and conditions conducive to magnetic reconnection that result in particle acceleration. This model therefore yields the observed magnetic properties of NTFs and a population of relativistic electrons, without the need to appeal to a dipolar, ∼mG, Galactic magnetic field. As the clouds can be both completely or partially disrupted, this model provides a means of establishing the connection between filamentary structures and molecular clouds that is observed in some, but not all, cases.
Giant planet scatterings and collisions: hydrodynamics, merger-ejection branching ratio, and properties of the remnants
Authors: Li Jiaru , Lai Dong , Anderson Kassandra R , Pu Bonan 
Published: December 2020

ABSTRACT
Planetary systems with sufficiently small orbital spacings can experience planetary mergers and ejections. The branching ratio of mergers versus ejections depends sensitively on the treatment of planetary close encounters. Previous works have adopted a simple ‘sticky-sphere’ prescription, whose validity is questionable. We apply both smoothed particle hydrodynamics and N-body integrations to investigate the fluid effects in close encounters between gas giants and the long-term evolution of closely packed planetary systems. Focusing on parabolic encounters between Jupiter-like planets with MJ and 2MJ, we find that quick mergers occur when the impact parameter rp (the pericentre separation between the planets) is less than 2RJ, and the merger conserved at least 97 per cent of the initial mass. Strong tidal effects can affect the ‘binary-planet’ orbit when rp is between 2RJ and 4RJ. We quantify these effects using a set of fitting formulae that can be implemented in N-body codes. We run a suite of N-body simulations with and without the formulae for systems of two giant planets initially in unstable, nearly circular and coplanar orbits. The fluid (tidal) effects significantly increase the branching ratio of planetary mergers relative to ejections by doubling the effective collision radius. While the fluid effects do not change the distributions of semimajor axis and eccentricity of each type of remnant planets (mergers versus surviving planets in ejections), the overall orbital properties of planet scattering remnants are strongly affected due to the branching ratio change. We also find that the merger products have broad distributions of spin magnitudes and obliquities.
Measuring the evolution of intergalactic gas from z = 0 to 5 using the kinematic Sunyaev–Zel’dovich effect
Authors: Chaves-Montero Jonás , Hernández-Monteagudo Carlos , Angulo Raúl E , Emberson J D 
Published: December 2020

ABSTRACT
A complete census of baryons in the late Universe is a long-standing challenge due to the intermediate temperate and rarefied character of the majority of cosmic gas. To gain insight into this problem, we extract measurements of the kinematic Sunyaev–Zel’dovich (kSZ) effect from the cross-correlation of angular redshift fluctuations maps, which contain precise information about the cosmic density and velocity fields, and cosmic microwave background maps high-pass filtered using aperture photometry; we refer to this technique as angular redshift fluctuations (ARF)–kSZ tomography. Remarkably, we detect significant cross-correlation for a wide range of redshifts and filter apertures using 6dF galaxies, BOSS galaxies, and SDSS quasars as tracers, yielding a 11σ detection of the kSZ effect. We then leverage these measurements to set constraints on the location, density, and abundance of gas inducing the kSZ effect, finding that this gas resides outside dark matter haloes, presents densities ranging from 10 to 250 times the cosmic average, and comprises half of cosmic baryons. Taken together, these findings indicate that ARF–kSZ tomography provides a nearly complete census of intergalactic gas from z = 0 to 5.
Chemical abundances in Seyfert galaxies – V. The discovery of shocked emission outside the AGN ionization axis
Authors: Riffel R A , Dors O L , Armah M , Storchi-Bergmann T , Feltre A , Hägele G F , Cardaci M V , Ruschel-Dutra D , Krabbe A C , Pérez-Montero E , Zakamska N L , Freitas I C 
Published: December 2020

ABSTRACT
We present maps for the electron temperature in the inner kpc of three luminous Seyfert galaxies: Mrk 79, Mrk 348, and Mrk 607 obtained from Gemini Multi-Object Spectrograph-integral field unit observations at spatial resolutions of ∼110–280 pc. We study the distributions of electron temperature in active galaxies and find temperatures varying in the range from ∼8000 to $\gtrsim 30\, 000\,$K. Shocks due to gas outflows play an important role in the observed temperature distributions of Mrk 79 and Mrk 348, while standard photoionization models reproduce the derived temperature values for Mrk 607. In Mrk 79 and Mrk 348, we find direct evidence for shock ionization with overall orientation orthogonal to the ionization axis, where shocks can be easily observed as the active galactic nuclei radiation field is shielded by the nuclear dusty torus. This also indicates that even when the ionization cones are narrow, the shocks can be much wider angle.
A pan-cancer atlas of somatic mutations in miRNA biogenesis genes
Authors: Galka-Marciniak Paulina , Urbanek-Trzeciak Martyna Olga , Nawrocka Paulina Maria , Kozlowski Piotr 
Published: December 2020

AbstractIt is a well-known and intensively studied phenomenon that the levels of many miRNAs are differentiated in cancer. miRNA biogenesis and functional expression are complex processes orchestrated by many proteins cumulatively called miRNA biogenesis proteins. To characterize cancer somatic mutations in the miRNA biogenesis genes and investigate their potential impact on the levels of miRNAs, we analyzed whole-exome sequencing datasets of over 10 000 cancer/normal sample pairs deposited within the TCGA repository. We identified and characterized over 3600 somatic mutations in 29 miRNA biogenesis genes and showed that some of the genes are overmutated in specific cancers and/or have recurrent hotspot mutations (e.g. SMAD4 in PAAD, COAD and READ; DICER1 in UCEC; PRKRA in OV and LIN28B in SKCM). We identified a list of miRNAs whose level is affected by particular types of mutations in either SMAD4, SMAD2 or DICER1 and showed that hotspot mutations in the RNase domains in DICER1 not only decrease the level of 5p-miRNAs but also increase the level of 3p-miRNAs, including many well-known cancer-related miRNAs. We also showed an association of the mutations with patient survival. Eventually, we created an atlas/compendium of miRNA biogenesis alterations providing a useful resource for different aspects of biomedical research.
A ubiquitin switch controls autocatalytic inactivation of the DNA–protein crosslink repair protease SPRTN
Authors: Zhao Shubo , Kieser Anja , Li Hao-Yi , Reinking Hannah K , Weickert Pedro , Euteneuer Simon , Yaneva Denitsa , Acampora Aleida C , Götz Maximilian J , Feederle Regina , Stingele Julian 
Published: December 2020

Abstract
Repair of covalent DNA–protein crosslinks (DPCs) by the metalloprotease SPRTN prevents genome instability, premature aging and carcinogenesis. SPRTN is specifically activated by DNA structures containing single- and double-stranded features, but degrades the protein components of DPCs promiscuously and independent of amino acid sequence. This lack of specificity is useful to target diverse protein adducts, however, it requires tight control in return, in order to prohibit uncontrolled proteolysis of chromatin proteins. Here, we discover the components and principles of a ubiquitin switch, which negatively regulates SPRTN. We demonstrate that monoubiquitylation is induced in an E3 ligase-independent manner and, in contrast to previous assumptions, does not control chromatin access of the enzyme. Data obtained in cells and in vitro reveal that monoubiquitylation induces inactivation of the enzyme by triggering autocatalytic cleavage in trans while also priming SPRTN for proteasomal degradation in cis. Finally, we show that the deubiquitylating enzyme USP7 antagonizes this negative control of SPRTN in the presence of DPCs.
Intestinal differentiation involves cleavage of histone H3 N-terminal tails by multiple proteases
Authors: Ferrari Karin Johanna , Amato Simona , Noberini Roberta , Toscani Cecilia , Fernández-Pérez Daniel , Rossi Alessandra , Conforti Pasquale , Zanotti Marika , Bonaldi Tiziana , Tamburri Simone , Pasini Diego 
Published: December 2020

AbstractThe proteolytic cleavage of histone tails, also termed histone clipping, has been described as a mechanism for permanent removal of post-translational modifications (PTMs) from histone proteins. Such activity has been ascribed to ensure regulatory function in key cellular processes such as differentiation, senescence and transcriptional control, for which different histone-specific proteases have been described. However, all these studies were exclusively performed using cell lines cultured in vitro and no clear evidence that histone clipping is regulated in vivo has been reported. Here we show that histone H3 N-terminal tails undergo extensive cleavage in the differentiated cells of the villi in mouse intestinal epithelium. Combining biochemical methods, 3D organoid cultures and in vivo approaches, we demonstrate that intestinal H3 clipping is the result of multiple proteolytic activities. We identified Trypsins and Cathepsin L as specific H3 tail proteases active in small intestinal differentiated cells and showed that their proteolytic activity is differentially affected by the PTM pattern of histone H3 tails. Together, our findings provide in vivo evidence of H3 tail proteolysis in mammalian tissues, directly linking H3 clipping to cell differentiation.
Dynapaenia and sarcopaenia in chronic haemodialysis patients: do muscle weakness and atrophy similarly influence poor outcome?
Authors: Souweine Jean-Sébastien , Pasquier Grégoire , Kuster Nils , Rodriguez Annie , Patrier Laure , Morena Marion , Badia Eric , Raynaud Fabrice , Chalabi Lotfi , Raynal Nathalie , Ohresser Isabelle , Hayot Maurice , Mercier Jacques , Quintrec Moglie Le , Gouzi Fares , Cristol Jean-Paul 
Published: December 2020

Abstract

Background
Sarcopaenia, defined as a decline in both muscle mass and function, has been recognized as a major determinant of poor outcome in haemodialysis (HD) patients. It is generally assumed that sarcopaenia is driven by muscle atrophy related to protein-energy wasting. However, dynapaenia, defined as weakness without atrophy, has been characterized by a different disease phenotype from sarcopaenia. The aim of this study was to compare the characteristics and prognosis of sarcopaenic and dynapaenic patients among a prospective cohort of chronic HD (CHD) patients.

Methods
Two hundred and thirty-two CHD patients were enrolled from January to July 2016 and then followed prospectively until December 2018. At inclusion, weakness and atrophy were, respectively, evaluated by maximal voluntary force (MVF) and creatinine index (CI). Sarcopaenia was defined as the association of weakness and atrophy (MVF and CI below the median) while dynapaenia was defined as weakness not related to atrophy (MVF below the median, and CI above the median).

Results
From a total of 187 prevalent CHD patients [65% of men, age 65.3 (49.7–82.0) years], 44 died during the follow-up period of 23.7 (12.4–34.9) months. Sarcopaenia and dynapaenia were observed in 33.7 and 16% of the patients, respectively. Compared with patients with sarcopaenia, patients with dynapaenia were younger and with a lower Charlson score. In contrast, mortality rate was similar in both groups (38 and 27%, respectively). After adjustment for age, sex, lean tissue index, serum albumin, high-sensitivity C-reactive protein (hs-CRP), haemoglobin (Hb), normalized protein catabolic rate (nPCR), dialysis vintage and Charlson score, only patients with dynapaenia were at increased risk of death [hazard ratio (HR) = 2.99, confidence interval 1.18–7.61; P = 0.02].

Conclusions
Screening for muscle functionality is highly warranted to identify patients with muscle functional impairment without muscle atrophy. In contrast to sarcopaenia, dynapaenia should appear as a phenotype induced by uraemic milieu, characterized by young patients with low Charlson score and poor prognosis outcome independently of serum albumin, hs-CRP, Hb, nPCR and dialysis vintage.
Home and facility haemodialysis patients: a comparison of outcomes in a matched cohort
Authors: Yeung Emily K , Polkinghorne Kevan R , Kerr Peter G 
Published: December 2020

AbstractBackgroundHome haemodialysis (HHD) is utilized significantly less often than facility HD globally with few exceptions, despite being associated with improved survival and better quality of life. Previously HHD was exclusively offered to younger patients with a few comorbidities. However, with the increasing burden of end-stage kidney disease (ESKD) alongside an ageing population, increasing numbers of older patients are being treated with HHD. This study aims to re-evaluate survival and related outcomes in the context of this epidemiological shift.MethodsA matched cohort design was used to compare all-cause mortality, transplantation, average biochemical values and graft survival 6 months post-transplant between HHD and facility HD patients. A total of 181 HHD patients from a major hospital network were included with 413 facility HD patients from the Australia and New Zealand Dialysis and Transplant Registry matched by age, gender and cause of ESKD. Survival analysis and competing risks analysis (for transplantation) were performed.ResultsAfter adjusting for body mass index, smoking status, racial group and comorbidities, HHD was associated with a significantly reduced risk of death compared with facility HD patients [hazard ratio 0.47 (95% confidence interval 0.30–0.74)]. Transplantation rates were comparable, with high rates of graft survival at 6 months in both groups. Haemoglobin, calcium and parathyroid hormone levels did not vary significantly. However, HHD patients had significantly lower phosphate levels.ConclusionsIn this study, improved survival outcomes were observed in patients on home compared with facility dialysis, with comparable rates of transplantation, graft survival and biochemical control.
Microbiological Outcomes Associated With Low Leukocyte Counts in Cerebrospinal Fluid
Authors: Wald Mathieu , Merisor Simona , Zachary Pierre , Augereau Olivier , Gravier Simon , Jaulhac Benoit , De Briel Dominique , Velay Aurélie , Gregorowicz Guillaume , Martinot Martin 
Published: December 2020

Abstract
The significance of low leukocyte counts in cerebrospinal fluid (CSF) remains unclear. We performed a 2-year retrospective study to examine microbiological outcomes associated with CSF leukocytes at 6–10/mm3. Of the 178 samples examined, we detected positive results for 11 samples, including 5 cases of tick-borne encephalitis virus infection.
Capital Obsolescence and Agricultural Productivity*
Authors: Caunedo Julieta , Keller Elisa 
Published: December 2020

AbstractThis article argues that accounting for capital-embodied technology greatly increases the importance of capital in explaining cross-country differences in agricultural labor productivity. To do so, we draw on a novel data set of agricultural capital prices. We document that new capital is more expensive in richer countries, both in absolute terms and relative to old capital. A model of endogenous adoption of capital of different quality links these price differences to the path of capital-embodied technology. In particular, our model recovers the level of embodied technology from the price of new capital and the growth rate of embodied technology from the price of new capital relative to old capital. We then measure the stocks of quality-adjusted capital in agriculture for a sample of 16 countries at different stages of development. We find that adjusting for differences in quality almost doubles the importance of capital in accounting for cross-country differences in agricultural labor productivity: from 21% to 37%. In addition, improvements in capital quality have been an important source of agricultural labor productivity growth over the past 25 years, accounting for 21% and 35% of the productivity growth in poor and rich countries, respectively.