bluuebunny/crossref_metadata_2025 huggingface dataset:
Constraints on the extragalactic magnetic field strength from blazar spectra based on 145 months of Fermi-LAT observations
Authors: Podlesnyi E I , Dzhatdoev T A , Galkin V I
Published: September 2022

Properties of the extragalactic magnetic field (EGMF) outside of clusters and filaments of the large-scale structure are essentially unknown. The EGMF could be probed with γ-ray observations of distant (redshift z > 0.1) blazars. TeV γ-rays from these sources are strongly absorbed on extragalactic background light photons; secondary electrons and positrons produce cascade γ-rays with the observable flux dependent on EGMF parameters. We put constraints on the EGMF strength using 145 months of Fermi-LAT observations of the blazars 1ES 1218+304, 1ES 1101−232, and 1ES 0347−121, and imaging atmospheric Cherenkov telescope observations of the same sources. We perform a series of full direct Monte Carlo simulations of intergalactic electromagnetic cascades with the elmag 3.01 code and construct a model of the observable spectra inside the point spread functions of the observing instruments for a range of EGMF strengths. We compare the observed spectra with the models for various values of the EGMF strength B and calculate the exclusion statistical significance for every value of B. We find that the values of the EGMF strength B ≤ 10−17 G are excluded at a high level of the statistical significance Z > 4σ for all the four options of the intrinsic spectral shape considered (power law, power law with exponential cutoff, log-parabola, and log-parabola with exponential cutoff). The value of B = 10−16 G is not excluded; it is still a viable option of the EGMF strength. These results were obtained for the case of steady sources.
The merger and assembly histories of Milky Way- and M31-like galaxies with TNG50: disc survival through mergers
Authors: Sotillo-Ramos Diego , Pillepich Annalisa , Donnari Martina , Nelson Dylan , Eisert Lukas , Rodriguez-Gomez Vicente , Joshi Gandhali , Vogelsberger Mark , Hernquist Lars
Published: September 2022

We analyse the merger and assembly histories of Milky Way (MW) and Andromeda (M31)-like galaxies to quantify how, and how often, disc galaxies of this mass can survive recent major mergers (stellar mass ratio ≥ 1:4). For this, we use the cosmological magneto-hydrodynamical simulation TNG50 and identify 198 analog galaxies, selected based on their z = 0 stellar mass ($10^{10.5-11.2}\, \rm {M}_{\odot }$), discy stellar morphology and local environment. First, major mergers are common: 85 per cent (168) of MW/M31-like galaxies in TNG50 have undergone at least one major merger across their lifetime. In fact, 31 galaxies (16 per cent) have undergone a recent major merger, i.e. in the last 5 Gyr. The gas available during the merger suffices to either induce starbursts at pericentric passages or to sustain prolonged star formation after coalescence: in roughly half of the cases, the pre-existing stellar disc is destroyed because of the merger but reforms thanks to star formation. Moreover, higher merger mass ratios are more likely to destroy the stellar discs. In comparison to those with more ancient massive mergers, MW/M31-like galaxies with recent major mergers have, on average, somewhat thicker stellar discs, more massive and somewhat shallower stellar haloes, larger stellar ex situ mass fractions, but similarly massive kinematically defined bulges. All this is qualitatively consistent with the different observed properties of the Galaxy and Andromeda and with the constraints on their most recent major mergers, 8–11 and  2 Gyr ago, respectively. According to contemporary cosmological simulations, a recent quiet merger history is not a pre-requisite for obtaining a relatively thin stellar disc at z = 0.
Properties beyond mass for unresolved haloes across redshift and cosmology using correlations with local halo environment
Authors: Ramakrishnan Sujatha , Velmani Premvijay
Published: September 2022

The structural and dynamic properties of the dark matter haloes, though an important ingredient in understanding large-scale structure formation, require more conservative particle resolution than those required by halo mass alone in a simulation. This reduces the parameter space of the simulations, more severely for high redshift and large-volume mocks, which are required by the next-generation large-sky surveys. Here, we incorporate redshift and cosmology dependence into an algorithm that assigns accurate halo properties such as concentration, spin, velocity, and spatial distribution to the subresolution haloes in a simulation. By focusing on getting the right correlations with halo mass and local tidal anisotropy α measured at 4 × halo radius, our method will also recover the correlations of these small-scale structural properties with the large-scale environment, i.e. the halo assembly bias at all scales greater than 5 × halo radius. We find that the distribution of halo properties is universal with redshift and cosmology. By applying the algorithm to a large-volume simulation $(600\, h^{-1}\, {\rm Mpc})^3$, we can access the 30–500 particle haloes, thus gaining an order of magnitude in halo mass and two to three orders of magnitude in number density at z = 2–4. This technique reduces the cost of mocks required for the estimation of covariance matrices, weak lensing studies, or any large-scale clustering analysis with less massive haloes.
The SAMI–Fornax Dwarfs Survey – II. The Stellar Mass Fundamental Plane and the dark matter fraction of dwarf galaxies
Authors: Eftekhari F Sara , Peletier Reynier F , Scott Nicholas , Mieske Steffen , Bland-Hawthorn Joss , Bryant Julia J , Cantiello Michele , Croom Scott M , Drinkwater Michael J , Falcón-Barroso Jésus , Hilker Michael , Iodice Enrichetta , Napolitano Nicola R , Spavone Marilena , Valentijn Edwin A , van de Ven Glenn , Venhola Aku
Published: September 2022

We explore the kinematic scaling relations of 38 dwarf galaxies in the Fornax Cluster using observations from the SAMI integral field spectrograph. We focus on the Fundamental Plane (FP), defined by the physical properties of the objects (scale length, surface brightness, and velocity dispersion) and the Stellar Mass (Fundamental) Plane, where surface brightness is replaced by stellar mass, and investigate their dynamical-to-stellar-mass ratio. We confirm earlier results that the Fornax dEs are significantly offset above the FP defined by massive, hot stellar systems. For the Stellar Mass (Fundamental) Plane, which shows much lower scatter, we find that young and old dwarf galaxies lie at about the same distance from the plane, all with comparable scatter. We introduce the perpendicular deviation of dwarf galaxies from the Stellar Mass Plane defined by giant early-types as a robust estimate of their DM fraction, and find that the faintest dwarfs are systematically offset above the plane, implying that they have a higher dark matter fraction. This result is confirmed when estimating the dynamical mass of our dEs using a virial mass estimator, tracing the onset of dark matter domination in low mass stellar systems. We find that the position of our galaxies on the Stellar Mass FP agrees with the galaxies in the Local Group. This seems to imply that the processes determining the position of dwarf galaxies on the FP depend on the environment in the same way, whether the galaxy is situated in the Local Group or in the Fornax Cluster.
FastChem 2
: an improved computer program to determine the gas-phase chemical equilibrium composition for arbitrary element distributions
Authors: Stock Joachim W , Kitzmann Daniel , Patzer A Beate C
Published: September 2022

The computation of complex neutral/ionized chemical equilibrium compositions is invaluable to obtain scientific insights of, for example, the atmospheres of extrasolar planets and cool stars. We present FastChem 2 , a new version of the established semi-analytical thermochemical equilibrium code FastChem. Whereas the original version is limited to atmospheres containing a significant amount of hydrogen, FastChem 2 is also applicable to chemical mixtures dominated by any other species, such as CO2 or N2. The new c++ code and an optional python module are publicly available under the GPLv3 license. The program is backward compatible so that the previous version can be easily substituted. We updated the thermochemical data base by adding HNC, FeH, TiH, Ca−, and some organic molecules. In total 523 species are now in the thermochemical data base including 28 chemical elements. The user can reduce the total number of species to, for example, increase the computation performance or can add further species if the thermochemical data are available. The program is validated against its previous version and extensively tested over an extended pressure–temperature grid with pressures ranging from $10^{-13}$ up to $10^3\, \mathrm{bar}$ and temperatures between $100$ and $6000\, \mathrm{K}$. FastChem 2 is successfully applied to a number of different scenarios including nitrogen-, carbon-, and oxygen-dominated atmospheres and test cases without hydrogen and helium. Averaged over the extended pressure–temperature grid FastChem 2 is up to 50 times faster than the previous version and is also applicable to situations not treatable with version 1.
Do periods of decayless kink oscillations of solar coronal loops depend on noise?
Authors: Nakariakov Valery M , Kolotkov Dmitrii Y , Zhong Sihui
Published: September 2022

Decayless kink oscillations of solar coronal loops are studied in terms of a low-dimensional model based on a randomly driven Rayleigh oscillator with coefficients experiencing random fluctuations. The model considers kink oscillations as natural modes of coronal loops, decaying by linear resonant absorption. The damping is counteracted by random motions of the loop footpoints and the interaction of the loop with external quasi-steady flows with random fluctuations. In other words, the model combines the self-oscillatory and randomly driven mechanisms for the decayless behaviour. The random signals are taken to be of the stationary red noise nature. In the noiseless case, the model has an asymptotically stationary oscillatory solution, i.e. a kink self-oscillation. It is established that the kink oscillation period is practically independent of noise. This finding justifies the seismological estimations of the kink and Alfvén speeds, and the magnetic field in an oscillating loop by kink oscillations, based on the observed oscillation period. The oscillatory patterns are found to be almost harmonic. Noisy fluctuations of external flows modulate the amplitude of the almost monochromatic oscillatory pattern symmetrically, while random motions of the loop footpoints cause antisymmetric amplitude modulation. Such modulations are also consistent with the observed behaviour.
Characterizing non-thermal equilibrium contact binaries
Authors: Wang Z H , Zhu L Y , Yuan K
Published: September 2022

Formation and evolution of marginal contact binaries with larger temperature difference between their two components remain inexplicable to date. To get a better understanding of the nature of such population we investigate on an individual, NSVS 7358116, by analysing observational data obtained from ground-based and space-based telescopes. It is found that NSVS 7358116 is a marginal contact totally eclipsing binary with a small fill-out factor by 3 per cent but large temperature difference by 2000 K or t-ratio by 0.3. This suggests that its two components are in poor thermal contact. By collecting all available targets in literature, we compiled a table of 80 non-thermal equilibrium contact binaries (nTCBs) including 39 STRONG t-ratio samples and 41 WEAK t-ratio samples. We performed statistical distribution analysis on physical parameters which reveals that STRONG t-ratio samples will evolve to WEAK t-ratio samples through heat and mass transfer along with angular momentum loss, meanwhile thickening their common envelop. This current investigation is acted as only an appetizer, because more exploration on nTCBs and its evolutionary connection with related populations will follow.
MRI turbulence in accretion discs at large magnetic Prandtl numbers
Authors: Held Loren E , Mamatsashvili George
Published: September 2022

The effect of large magnetic Prandtl number Pm (the ratio of viscosity to resistivity) on the turbulent transport and energetics of the magnetorotational instability (MRI) is poorly understood, despite the realization of this regime in astrophysical environments as disparate as discs from binary neutron star (BNS) mergers, the inner regions of low-mass X-ray binaries and active galactic nuclei, and the interiors of protoneutron stars. We investigate the MRI dynamo and associated turbulence in the regime Pm > 1 by carrying out fully compressible, 3D MHD-shearing box simulations using the finite-volume code pluto, focusing mostly on the case of Keplerian shear relevant to accretion discs. We find that when the magnetic Reynolds number is kept fixed, the turbulent transport (as parameterized by α, the ratio of stress to thermal pressure) scales with the magnetic Prandtl number as α ∼ Pmδ, with δ ∼ 0.5−0.7 up to Pm ∼ 128. However, this scaling weakens as the magnetic Reynolds number is increased. Importantly, compared to previous studies, we find a new effect at very large Pm – the turbulent energy and stress begin to plateau, no longer depending on Pm. To understand these results we have carried out a detailed analysis of the turbulent dynamics in Fourier space, focusing on the effect of increasing Pm on the transverse cascade – a key non-linear process induced by the disc shear flow that is responsible for the sustenance of MRI turbulence. Finally, we find that α–Pm scaling is sensitive to the box vertical-to-radial aspect ratio, as well as to the background shear.
Equation of state for hot hyperonic neutron star matter
Authors: Kochankovski Hristijan , Ramos Angels , Tolos Laura
Published: September 2022

The FSU2H equation-of-state model, originally developed to describe cold neutron star matter with hyperonic cores, is extended to finite temperature. Results are presented for a wide range of temperatures and lepton fractions, which cover the conditions met in protoneutron star matter, neutron star mergers, and supernova explosions. It is found that the temperature effects on the thermodynamical observables and the composition of the neutron star core are stronger when the hyperonic degrees of freedom are considered. An evaluation of the temperature and density dependence of the thermal index leads to the observation that the so-called Γ law, widely used in neutron star merger simulations, is not appropriate to reproduce the true thermal effects, specially when hyperons start to be abundant in the neutron star core. To make finite temperature equations of state easily accessible, simple parametrizations of the thermal index for nucleonic and hyperonic β-stable neutrino-free matter are provided.
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma
Authors: Showpnil Iftekhar A , Selich-Anderson Julia , Taslim Cenny , Boone Megann A , Crow Jesse C , Theisen Emily R , Lessnick Stephen L
Published: September 2022

Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or a highly related FET/ETS chimera. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma cells using a well-validated ‘knock-down/rescue’ model of EWS/FLI function in combination with next generation sequencing assays to evaluate how the chromatin landscape changes with loss, and recovery, of EWS/FLI expression. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. This EWS/FLI binding signature is associated with establishment of topologically-associated domain (TAD) boundaries, compartment activation, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. In addition, EWS/FLI co-localizes with the loop-extrusion factor cohesin to promote chromatin loops and TAD boundaries. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators of three-dimensional reprogramming of chromatin.
Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding
Authors: Hyjek-Składanowska Malwina , Anderson Brooke A , Mykhaylyk Vitaliy , Orr Christian , Wagner Armin , Poznański Jarosław T , Skowronek Krzysztof , Seth Punit , Nowotny Marcin
Published: September 2022

The introduction of phosphorothioate (PS) linkages to the backbone of therapeutic nucleic acids substantially increases their stability and potency. It also affects their interactions with cellular proteins, but the molecular mechanisms that underlie this effect are poorly understood. Here, we report structural and biochemical studies of interactions between annexin A2, a protein that does not possess any known canonical DNA binding domains, and phosphorothioate-modified antisense oligonucleotides. We show that a unique mode of hydrophobic interactions between a sulfur atom of the phosphorothioate group and lysine and arginine residues account for the enhanced affinity of modified nucleic acid for the protein. Our results demonstrate that this mechanism of interaction is observed not only for nucleic acid-binding proteins but can also account for the association of PS oligonucleotides with other proteins. Using the anomalous diffraction of sulfur, we showed that preference for phosphorothioate stereoisomers is determined by the hydrophobic environment around the PS linkage that comes not only from protein but also from additional structural features within the ASO such as 5-Me groups on cytosine nucleobases.
Predicting Risk of Multidrug-Resistant Enterobacterales Infections Among People With HIV
Authors: Henderson Heather I , Napravnik Sonia , Kosorok Michael R , Gower Emily W , Kinlaw Alan C , Aiello Allison E , Williams Billy , Wohl David A , van Duin David
Published: September 2022

Background

Medically vulnerable individuals are at increased risk of acquiring multidrug-resistant Enterobacterales (MDR-E) infections. People with HIV (PWH) experience a greater burden of comorbidities and may be more susceptible to MDR-E due to HIV-specific factors.

Methods

We performed an observational study of PWH participating in an HIV clinical cohort and engaged in care at a tertiary care center in the Southeastern United States from 2000 to 2018. We evaluated demographic and clinical predictors of MDR-E by estimating prevalence ratios (PRs) and employing machine learning classification algorithms. In addition, we created a predictive model to estimate risk of MDR-E among PWH using a machine learning approach.

Results

Among 4734 study participants, MDR-E was isolated from 1.6% (95% CI, 1.2%–2.1%). In unadjusted analyses, MDR-E was strongly associated with nadir CD4 cell count ≤200 cells/mm3 (PR, 4.0; 95% CI, 2.3–7.4), history of an AIDS-defining clinical condition (PR, 3.7; 95% CI, 2.3–6.2), and hospital admission in the prior 12 months (PR, 5.0; 95% CI, 3.2–7.9). With all variables included in machine learning algorithms, the most important clinical predictors of MDR-E were hospitalization, history of renal disease, history of an AIDS-defining clinical condition, CD4 cell count nadir ≤200 cells/mm3, and current CD4 cell count 201–500 cells/mm3. Female gender was the most important demographic predictor.

Conclusions

PWH are at risk for MDR-E infection due to HIV-specific factors, in addition to established risk factors. Early HIV diagnosis, linkage to care, and antiretroviral therapy to prevent immunosuppression, comorbidities, and coinfections protect against antimicrobial-resistant bacterial infections.
Roman Catholic Theology
Authors: Phan Peter C.
Published: September 2022

Although the Roman Catholic Church claims historical continuity with Jesus Christ himself and regards the subsequent Christian development as its own, it acquired distinctive features in matters of doctrine, worship, ethics, spirituality, and organization since the Reformation in opposition to the Protestant churches (and to a lesser extent also to the Orthodox church since 1054). “Roman Catholic theology” refers to the doctrinal development that has taken place in the Roman Catholic Church from the sixteenth century (commonly referred to as the Counter-Reformation) until today. Since it is characteristic of Roman Catholic theology to accord a special authority to the official teachings of the church (the magisterium), especially of ecumenical councils and bishops (in particular the bishop of Rome and his immediate collaborators), this article begins with an exposition of the magisterium's teaching on eschatology. Next, it expounds the eschatology of some of the most influential contemporary Roman Catholic theologians such as Karl Rahner, Hans Urs von Balthasar, Ladislaus Boros, Edward Schillebeeckx, and Joseph Ratzinger. It also discusses Catholic official teachings on eternal life and contemporary Catholic eschatologies.
Process Eschatology
Authors: Griffin David Ray
Published: September 2022

This article discusses eschatology from the perspective of process theology, a theological movement that employs the “process philosophy” of Alfred North Whitehead and Charles Hartshorne. It considers the question of whether process theology can do justice to the basic dimensions of the eschatology of Jesus Christ. Salvation for Jesus involved four dimensions: salvation from the threat of meaninglessness through confidence that we are known and loved by our Creator; an ultimate salvation in a resurrected life beyond bodily death; a salvation that would be realized on earth with the coming political reign of God; and a reign of God in the individual heart and in social relations (which is made possible by faith in the first three dimensions of salvation). Modern liberal theology has generally denied the second and third dimensions and sometimes even the first, thereby leaving the fourth dimension—often called “realized eschatology”—with little, if any, basis. This article also examines subjective immortality and sanctification in a life beyond bodily death.
Liberation Theology: A Latitudinal Perspective
Authors: Westhelle Vítor
Published: September 2022

Liberation theology (LT) is a plural concept but a catalytic notion for theologies that challenge the hegemonic theological canon. Hegemony is a concept borrowed by LT from Italian philosopher Antonio Gramsci. It designates a certain ruling order that combines power and consent. Liberation theologies can be broadly defined as an indisposition toward the hegemonic canons of Western theology. In this sense, they manifest in an array of theological expressions which include along with third world theologies, North American black theology, feminist theology, womanist theology, and many other adjectival or genitive theologies that challenge the dominant Western academic theological productions. This article discusses LT from a latitudinal perspective, eschatology and paradigms for eschatological thinking, Christianity and post-colonialism, the incoming reign of God and the signs of places, and eschaton.
Death, Final Judgment, and the Meaning of Life
Authors: Hart David Bentley
Published: September 2022

The ancient injunction memento mori—whispered by a slave into the ear of a victorious general in his triumphal chariot or by a monk to his own heart in the solitude of his cell—has frequently been translated as “remember that thou art mortal,” which may be faithful to the phrase's special hortatory import; but the literal meaning of the injunction is “remember to die.” However, we cannot easily remember to die because death runs contrary to the whole orientation of human consciousness. In Christian thought sacrifice and judgment, life from death, and the life of the age to come converge in a way that radically transforms them. Indeed, one might even say that, on the cross of Christ, two distinct orders of sacrifice uniquely coincide and that at Easter one order triumphs completely over the other. This article discusses death, final judgment, and the meaning of life. It examines religion and meaning without an afterlife, the reorientation of religious consciousness, and the radical transformation of judgment in light of Easter.
Time, Eternity, and Eschatology
Authors: Craig William Lane
Published: September 2022

Time is that dimension of reality whose constituent elements are ordered by relations of “earlier than,” “simultaneous with,” and “later than”, and are experienced by us as past, present, and future. This much, at least, is common property among almost all disputants in debates about the nature of time. Beyond that point, philosophers are deeply divided about the nature of time. The controversy most relevant to the concerns of eschatology is the debate over whether time is tensed or tenseless. We are all familiar with tense as it plays a role in natural languages. Philosophers and theologians are also deeply divided over the nature of divine eternity, debating whether God's eternity is to be construed as a state of timelessness or of infinite, omnitemporal duration. Theories of time intersect crucially with theories of divine eternity and with cosmogony. This is also the case with eschatology, in particular with physical eschatology. This article explores the interface of time, eternity, and eschatology and discusses perdurantism.
Holographic index calculation for Argyres–Douglas and Minahan–Nemeschansky theories
Authors: Imamura Yosuke , Murayama Shuichi
Published: September 2022

We calculate the superconformal indices of the $\mathcal {N}=2$ superconformal field theories realized on N coincident D3-branes in 7-brane backgrounds with constant axiodilaton via the anti-de Sitter/conformal field theory correspondence. We include the finite-N corrections as the contribution of D3-branes wrapped around 3-cycles in the internal space. We take only single-wrapping contributions into account for simplicity. We also determine the orders of the next-to-leading corrections that we do not calculate. The orders are relatively high, and we obtain many trustworthy terms. We give the results for N = 1, 2, 3 explicitly, and find nice agreement with known results.
Response of the underground environment of the KAGRA observatory against the air pressure disturbance from the Tonga volcanic eruption on January 15, 2022
Authors: Washimi Tatsuki , Yokozawa Takaaki , Takamori Akiteru , Araya Akito , Hoshino Sota , Itoh Yousuke , Kobayashi Yuichiro , Kume Jun’ya , Miyo Kouseki , Ohkawa Masashi , Oshino Shoichi , Tomaru Takayuki , Yokoyama Jun’ichi , Yuzurihara Hirotaka
Published: September 2022

On January 15, 2022, at 04:14:45 (UTC), the Hunga Tonga-Funga Ha’apai, a submarine volcano in the Tongan archipelago in the southern Pacific Ocean, erupted and generated global seismic, shock, and electromagnetic waves, which also reached Japan, situated more than 8000 km away. KAGRA is a gravitational wave telescope located in an underground facility in Kamioka, Japan. It has a wide variety of auxiliary sensors to monitor environmental disturbances that obstruct the observation of gravitational waves. The effects of the volcanic eruption were observed by these environmental sensors both inside and outside of the underground facility. In particular, the shock waves made it possible to evaluate the transfer functions from the air pressure wave in the atmosphere to the underground environmental disturbances (air pressure and seismic motion).
Colorectal Cancer in Childhood-onset Inflammatory Bowel Disease: A Scandinavian Register-based Cohort Study, 1969–2017
Authors: Everhov Åsa H. , Ludvigsson Jonas F. , Järås Jacob , Erichsen Rune , Pedersen Lars , Halfvarson Jonas , Askling Johan , Ekbom Anders , Sørensen Henrik Toft , Olén Ola
Published: September 2022

Through linkage of data from Danish and Swedish national registers we identified 6937 patients with childhood (<18 years)-onset Crohn disease (CD), 8514 patients with childhood-onset ulcerative colitis (UC) and up to 10 times as many matched (sex, age, residence) reference individuals 1969–2017. During follow-up to a median age of 27 (interquartile range = 21–39) years, 25 (0.36%) CD patients were diagnosed with colorectal cancer (CRC) versus 43 (0.06%) reference individuals, and 113 (1.33%) UC patients versus 45 (0.05%) reference individuals. The hazard ratio (HR) for CRC was 6.46 (95% CI = 3.95–10.6) in CD and 32.5 (95% CI = 23.0–45.9) in UC and increased with decreasing age at diagnosis. The HR for CRC was increased for all phenotypes, but with higher estimates for colonic CD [17.9 (95% CI = 7.43–43.3)] and UC with extensive/pancolitis [36.3 (95% CI = 22.8–57.8)]. The relative risk of CRC was increased for all phenotypes of childhood-onset inflammatory bowel disease. Age at onset may be considered an additional risk factor when implementing surveillance programs.
Patient Perspectives after Trapeziectomy and Ligament Reconstruction Tendon Interposition: A Qualitative Analysis
Authors: Stepan Jeffrey G. , Rolf Liz , Zhu Eric , Brody Madison , Landau Andrew J. , Calfee Ryan P. , Dy Christopher J.
Published: September 2022

Background:

We aimed to explore patients’ perioperative experience after trapeziectomy and ligament reconstruction tendon interposition (LRTI) through semi-structured patient interviews to identify deficiencies in our preoperative patient counseling.

Methods:

We conducted semi-structured interviews with 14 patients who had undergone LRTI either 10-14 weeks or 9-12 months post-op at the time of their interview. The semi-structured interview guide was developed by a fellowship-trained hand surgeon and a qualitative research specialist to discuss each patient’s perioperative experience. Inductive and deductive qualitative coding strategies were used to develop a codebook. All transcripts were then double coded and discussed to develop recurrent major themes from the patient interviews.

Results:

Our interviews identified three major themes discussed consistently on the patient perioperative experience. 1) Despite specific counseling about a 3-6 month postoperative rehabilitation period, patients were still surprised at the length of recovery process in regaining function, range of motion, and strength. 2) Patients repeatedly outlined that surgery on the dominant hand imparted specific limitations that made the postoperative course difficult. 3) Patients discussed the importance of hand therapy both in rehabilitation and guiding patient postoperative expectations.

Conclusions:

Preoperative counseling is of vital importance to set patient expectations in terms of overall expected outcomes, but also regarding early limitations, expectations, and overall recovery length. These themes have influenced how we counsel our patients about recovery after thumb CMC surgery and may help other surgeons identify areas for improvement in their discussions with patients.
Drivers of within- and among-individual variation in risk-taking behaviour during reproduction in a long-lived bird
Authors: Mohring Bertille , Angelier Frédéric , Jaatinen Kim , Steele Ben , Lönnberg Elin , Öst Markus
Published: September 2022

Plastic and selective mechanisms govern parental investment adjustments to predation threat. We investigated the relative importance of plasticity and selection in risk-taking propensity of incubating female common eidersSomateria mollissimafacing unprecedented predation in SW Finland, Baltic Sea. Using a 12-year individual-based dataset, we examined within- and among-individual variation in flight initiation distance (FID), in relation to predation risk, nest detectability, individual traits and reproductive investment (NFID= 1009;Nindividual= 559). We expected females nesting in riskier environments (higher predation risk, lower nest concealment) to mitigate environmentally imposed risk by exhibiting longer FIDs, and females investing more in current reproduction (older, in better condition or laying larger clutches) to display shorter FIDs. The target of predation—adult or offspring—affected the mechanisms adapting risk-taking propensity; females plastically increased their FID under higher adult predation risk, while risk-avoiding breeders were predominant on islands with higher nest predation risk. Risk-taking females selected thicker nest cover, consistent with personality-matching habitat choice. Females plastically attenuated their anti-predator response (shorter FIDs) with advancing age, and females in better body condition were more risk-taking, a result explained by selection processes. Future research should consider predator type when investigating the fitness consequences of risk-taking strategies.
New members of the family Eggerthellaceae isolated from Marmota himalayana: Xiamenia xianingshaonis gen. nov., sp. nov., from intestinal contents, and Berryella wangjianweii sp. nov., from trachea
Authors: Zhang Gui , Lv Xianglian , Cheng Yanpeng , Lai Xin-He , Yang Jing , Jin Dong , Lu Shan , Pu Ji , Liu Liyun , Xu Jianguo
Published: September 2022

Four strictly anaerobic, Gram-stain-positive, urease-, oxidase- and catalase-negative, rod-shaped strains (zg-886T/zg-887 and zg-1050T/zg-1084) were isolated from Marmota himalayana. Comparison analysis of 16S rRNA genes showed that the two strain pairs belong to the family

Eggerthellaceae

: zg-1050T and zg-1084 were most closely related to

Berryella intestinalis

68-1-3T (97.2 %), while zg-886T/zg-887 had the highest similarity to

Slackia piriformis

YIT 12062T (91.6 %), followed by

Paraeggerthella hongkongensis

DSM 16106T (91.4 %) and

Gordonibacter urolithinfaciens

DSM 27213T (91.4 %). Phylogenetic analyses based on 16S rRNA genes and genomes showed that the two strain pairs represent two different lineages within the family

Eggerthellaceae

. The genomic G+C contents of strains zg-886T and zg-1050T were 63.0 and 66.3 mol%, respectively. The values of digital DNA–DNA hybridization, average nucleotide identity, average amino acid identity and the percentage of conserved proteins between the two new type strains and members of the family

Eggerthellaceae

were lower than the respective thresholds for delineation of a species or genus. In contrast to the absence of any known quinones in strain zg-1050T, strain zg-886T contained MK-6 (42.5 %), MMK-6 (25.0 %) and DMMK-6 (32.5 %). The four strains grew optimally at pH 7.0, 37 ºC and 0.5 % NaCl (w/v). According to these polyphasic analyses, two new members within the family

Eggerthellaceae

are proposed, Xiamenia xianingshaonis gen. nov., sp. nov. (zg-886T=JCM 34097T=GDMCC 1.1710T) and Berryella wangjianweii sp. nov. (zg-1050T=GDMCC 1.2426T=JCM 34748T).
Adaptive compensation of arcuate fasciculus lateralization in developmental dyslexia
Authors: Zhao Jingjing , Zhao Yueye , Song Zujun , de Schotten Michel Thiebaut , Altarelli Irene , Ramus Franck
Published: September 2022

Previous studies have reported anomalies in the arcuate fasciculus (AF) lateralization in developmental dyslexia (DD). Still, the relationship between AF lateralization and literacy skills in DD remains largely unknown. The purpose of our study is to investigate the relationship between the lateralization of the AF anterior segment (AFAS), AF long segment (AFLS), and AF posterior segment (AFPS) in connection to literacy skills in DD. The participants included 26 children with dyslexia and 31 age-matched children in the control group. High angular diffusion imaging, combined with spherical deconvolution tractography, was used to reconstruct the AF. Connectivity measures of hindrance-modulated oriented anisotropy (HMOA) were computed for each of the three segments of the AF: anterior segment (AFAS), long segment (AFLS), and posterior segment (AFPS). The lateralization index (LI) of each AF segment was calculated by (right HMOA - left HMOA) / (right HMOA + left HMOA). Results showed that the LIs of AFAS and AFLS were positively correlated with reading accuracy in children with dyslexia. Specifically, the LI of AFAS was positively correlated with text and nonword reading accuracy, while the LI of AFLS accounted for word reading accuracy. The results suggest adaptive compensation of arcuate fasciculus lateralization in developmental dyslexia and functional dissociation of the anterior segment and long segment in the compensation.
Additional Evidence Implicating GPD1L in the Pathogenesis of Brugada Syndrome in A Large Multi-generational Family
Authors: Greiner Alexander , Mehdi Haider , Cevan Chloe , Gutmann Rebecca , London Barry
Published: September 2022

Background

Brugada Syndrome (BrS) is an inherited arrhythmia syndrome in which mutations in SCN5A account for 20% of cases. Mutations in other ion channels or channel-modifying genes may account for an additional 10% of cases, though recent analysis has suggested that SCN5A should be regarded as the sole monogenic cause of BrS.

Objective

We sought to re-assess the genetic underpinnings of BrS in a large mutligenerational family with a putative GPD1L-A280V mutation.

Methods

Fine linkage mapping was performed in the family using the Illumina Global Screening array. Whole exome sequencing of the proband was performed to identify rare variants and mutations, and Sanger sequencing was used to assay previously-reported risk single nucleotide polymorphsims (SNPs) for BrS.

Results

Linkage analysis decreased the size of the previously-reported microsatellite linkage region to ∼3 megabases. GPD1L-A280V was the only rare coding non-synonymous variation present at <1% allele frequency in the proband within the linkage region. Other variants were either synonymous, or in genes not known to play a role in BrS and that failed to co-segregate with BrS in the large family. Risk SNPs known to predispose to BrS were overrepresented in affected members of the family.

Conclusion

Together, our linkage and sequencing data suggest GPD1L-A280V remains the most likely cause of BrS in this large mutligenerational family. While care should be taken in interpreting variant pathogenicity given the genetic uncertainty of BrS, our data support inclusion of other putative BrS in clinical genetic panels.
Dysregulation of mTOR Signaling Mediates Common Neurite and Migration Defects in Both Idiopathic and 16p11.2 Deletion Autism Neural Precursor Cells
Authors: Prem Smrithi , Dev Bharati , Peng Cynthia , Mehta Monal , Alibutud Rohan , Connacher Robert J. , Thomas Madeline St , Zhou Xiaofeng , Matteson Paul , Xing Jinchuan , Millonig James H. , DiCicco-Bloom Emanuel
Published: September 2022

Autism spectrum disorder (ASD) is defined by common behavioral characteristics, raising the possibility of shared pathogenic mechanisms. Yet, vast clinical and etiological heterogeneity suggests personalized phenotypes. Surprisingly, our iPSC studies find that six individuals from two distinct ASD-subtypes, idiopathic and 16p11.2 deletion, have common reductions in neural precursor cell (NPC) neurite outgrowth and migration even though whole genome sequencing demonstrates no genetic overlap between the datasets. To identify signaling differences that may contribute to these developmental defects, an unbiased phospho-(p)-proteome screen was performed. Surprisingly despite the genetic heterogeneity, hundreds of shared p-peptides were identified between autism subtypes including the mTOR pathway. mTOR signaling alterations were confirmed in all NPCs across both ASD-subtypes, and mTOR modulation rescued ASD phenotypes and reproduced autism defects in controls. Thus, our studies demonstrate that genetically distinct ASD subtypes have common defects in neurite outgrowth and migration which are driven by the shared pathogenic mechanism of mTOR signaling dysregulation.
Whole genome sequencing of ‘mutation-negative’ individuals with Cornelia de Lange Syndrome
Authors: Ansari Morad , Halachev Mihail , Parry David , Campos Jose L. , D’Souza Elston N. , Barnett Christopher , Wilkie Andrew O. M. , Barnicoat Angela , Patel Chirag V. , Sukarova-Angelovska Elena , Girisha Katta M. , Firth Helen V. , Prescott Katrina , Wilson Louise C. , McEntagart Meriel , Davidson Rosemarie , Lynch Sally Ann , Joss Shelagh , Holden Simon T. , Lam Wayne K. , Sisodiya Sanjay M. , Green Andrew J. , Poke Gemma , Whiffin Nicola , FitzPatrick David R. , Meynert Alison
Published: September 2022

Aims

This study assesses the diagnostic utility of whole genome sequence analysis in a well-characterised research cohort of individuals referred with a clinical suspicion of Cornelia de Lange syndrome (CdLS) in whom prior genetic testing had not identified a causative variant.

Methods

Short read, whole genome sequencing was performed in 195 individuals from 105 families, 108 of whom were affected. 100/108 of the affected individuals had prior relevant genetic testing with no pathogenic variant being identified. The study group comprised 42 trios (affected individuals with both unaffected parents), 61 singletons (unrelated affected individuals) and two families with more than one affected individual.

Results

32/105 (30.5%) unrelated probands had likely causative coding region disrupting variants. 4 loci were identified in >1 proband; NIPBL (10), ANKRD11 (6), EP300 (3), EHMT1 (2). Single alleles were detected in the remaining genes (EBF3, KMT2A, MED13L, NLGN3, NR2F1, PHIP, PUF60, SET, SETD5, SMC1A, TBL1XR1). Possibly causative variants in non-coding regions of NIPBL were identified in four individuals. Single de novo variants were identified in five genes not previously reported to be associated with any developmental disorder: ARID3A, PIK3C3, MCM7, MIS18BP1 and WDR18.

Conclusions

Clustering of de novo non-coding variants implicate a single uORF and a small region in intron 21 in NIPBL regulation. Causative variants in genes encoding chromatin-associated proteins, with no defined influence on cohesin function, appear to result in CdLS-like clinical features.
Effects of the Variance in Prevalence of the DASH Diet in Nursing Homes on Seniors With Elevated Blood Pressure or Hypertension
Authors: Liu Ryan , Chui Tsz-Kiu
Published: September 2022

1.

The DASH diet is a dietary pattern designed to help treat or prevent hypertension. The diet includes foods rich in potassium, calcium, and magnesium while limiting foods high in sodium, saturated fat, and added sugars. The DASH diet’s relationship with hypertension in adults is well defined, but the effect of its variance in prevalence in nursing homes on seniors is not. We performed a mixed-methods observational study incorporating a survey collecting anonymized nursing home data regarding the number of servings of various food groups provided to senior residents per day. The data were analyzed using the Fung et al. DASH diet scoring method. We then conducted an interview with nursing home dieticians to investigate the public health effect of the DASH diet on hypertension in residents. Lastly, a content analysis was performed of nursing home menus to support the data from the surveys. In a pool of 11 nursing homes, 100% of the facilities incorporated some aspect of the DASH diet, and in a pool of five nursing homes, 60% achieved high adherence to the DASH diet. We additionally confirmed a previously observed negative relationship between red meat consumption in seniors to higher risk and poorer prognosis of hypertension. These analyses bolster the DASH diet’s potential role as a hypertension prevention mechanism in nursing homes, suggesting that future DASH diet interventions may hold promise.
Are the relevant risk factors being adequately captured in empirical studies of smoking initiation? A machine learning analysis based on the Population Assessment of Tobacco and Health study
Authors: Le Thuy T. T. , Issabakhsh Mona , Li Yameng , Sánchez-Romero Luz María , Tan Jiale , Meza Rafael , Levy David , Mendez David
Published: September 2022

Cigarette smoking continues to pose a threat to public health. Identifying individual risk factors for smoking initiation is essential to further mitigate this epidemic. To our knowledge, no study today has used Machine Learning (ML) techniques to automatically uncover informative predictors of smoking onset among adults using the Population Assessment of Tobacco and Health (PATH) study. In this work, we employed Random Forest paired with Recursive Feature Elimination to identify relevant PATH variables that predict smoking initiation among adult never smokers at baseline between two consecutive PATH waves. We included all potentially informative baseline variables in wave 1 (wave 4) to predict past 30-day smoking status in wave 2 (wave 5). Using the first and most recent pairs of PATH waves was found sufficient to identify the key risk factors of smoking initiation and test their robustness over time. As a result, classification models suggested about 60 informative PATH variables among more than 200 candidate variables in each baseline wave. With these selected predictors, the resulting models have a high discriminatory power with the area under the Specificity-Sensitivity curves of around 80%. We examined the chosen variables and discovered important features. Across the considered waves, three factors, (i) BMI, (ii) dental/oral health status, and (iii) taking anti-inflammatory or pain medication, robustly appeared as significant predictors of smoking initiation, besides other well-established predictors. Our work demonstrates that ML methods are useful to predict smoking initiation with high accuracy, identify novel smoking initiation predictors, and enhance our understanding of tobacco use behaviors.