bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a T7 phage random peptide library by combining seamless cloning with in vitro translation
Authors: Higashi Katsuaki , Oda Sakiho , Fujii Mai , Nishida Fumiya , Matsumoto Hayato , Morise Jyoji , Oka Shogo , Nonaka Motohiro 
Published: October 2023

Abstract
T7 phage libraries displaying random peptides are powerful tools for screening peptide sequences that bind to various target molecules. The T7 phage system has the advantage of less biased peptide distribution compared to the M13 phage system. However, the construction of T7 phage DNA is challenging due to its long 36 kb linear DNA. Furthermore, the diversity of the libraries depends strongly on the efficiency of commercially available packaging extracts. To address these issues, we examined the combination of seamless cloning with cell-free translation systems. Seamless cloning technologies have been widely used to construct short circular plasmid DNA, and several recent studies showed that cell-free translation can achieve more diverse phage packaging. In this study, we combined these techniques to construct four libraries (CX7C, CX9C, CX11C and CX13C) with different random regions lengths. The libraries thus obtained all showed diversity &gt; 109 plaque forming units (pfu). Evaluating our libraries with an anti-FLAG monoclonal antibody yielded the correct epitope sequence. The results indicate that our libraries are useful for screening peptide epitopes against antibodies. These findings suggest that our system can efficiently construct T7 phage libraries with greater diversity than previous systems.
Refund Psychology
Authors: Yu Tianjiao , Cryder Cynthia , LeBoeuf Robyn A 
Published: October 2023

Abstract
Consumers frequently receive refunds from prior purchases. In this research, we examine if money refunded from previous purchases is more likely to be spent than money that does not go through a refund process. Across nine pre-registered studies, we test how consumers’ willingness to spend depends on the transaction history of their money. We find that, when people receive a refund and do not need to replace the originally purchased item, they are more likely to spend the refunded money on a discretionary purchase than they are to spend non-refunded money that is otherwise identical. We suggest that this pattern arises because refunded money is earmarked as “spending money” at the time of the initial purchase and then retains that earmark even after the refund is issued. When refunds arrive, therefore, they seem free from obligations and easy to spend. This research documents the psychology of purchase refunds, a topic largely unaddressed in the mental accounting literature to date.
Cancer and COVID-19: US cancer incidence rates during the first year of the pandemic
Authors: Howlader Nadia , Bhattacharya Manami , Scoppa Steve , Miller Daniel , Noone Anne-Michelle , Negoita Serban , Cronin Kathy , Mariotto Angela 
Published: October 2023

Abstract

Background
The COVID-19 pandemic has had a profound global impact on health-care systems and patient outcomes. However, the specific effects of the pandemic on cancer incidence rates in the United States during its initial year remain unknown.

Methods
In this study, we analyzed data from the Surveillance, Epidemiology, and End Results–22 registries, which encompass approximately 50% of the US population. We investigated changes in monthly incidence rates stratified by various factors, including cancer type, stage, age group, sex, race and ethnicity, socioeconomic status, rural-urban status, and registry locations. We compared the incidence rates observed during the pandemic with those from the previous year.

Results
Our findings revealed a decline in incidence rates for all cancer sites combined starting in March 2020, coinciding with the implementation of stay-at-home orders. This decline reached its lowest point in April 2020 and persisted at a lower level until May 2020. Notably, compared with April 2019, the incidence rates in April 2020 dropped by 48.1% and did not consistently return to prepandemic levels. The reduction in cancer rates was more pronounced in urban and affluent counties. Across all cancer types, there was a statistically significant decrease in incidence rates during the pandemic, with the largest declines observed in thyroid (71.2%), prostate (57.9%), breast (54.9%), and colon and rectum cancers (54.1%). Furthermore, these decreases were primarily observed in early stage rather than late-stage disease.

Conclusions
The COVID-19 pandemic had a statistically significant impact on cancer outcomes. Monitoring long-term consequences of the pandemic on cancer incidence, stage at diagnosis, and mortality trends will be crucial.
Environmental monitoring for filamentous fungal pathogens in hematopoietic cell transplant units
Authors: Marek Aleksandra , Meijer Eelco F J , Tartari Ermira , Zakhour Johnny , Chowdhary Anuradha , Voss Andreas , Kanj Souha S , Bal Abhijit M 
Published: October 2023

Abstract
The incidence of invasive fungal disease (IFD) is on the rise due to increasing numbers of highly immunocompromized patients. Nosocomial IFD remains common despite our better understanding of its risk factors and pathophysiology. High-efficiency particulate air filtration with or without laminar air flow, frequent air exchanges, a positive pressure care environment, and environmental hygiene, amongst other measures, have been shown to reduce the mould burden in the patient environment. Environmental monitoring for moulds in areas where high-risk patients are cared for, such as hematopoietic cell transplant units, has been considered an adjunct to other routine environmental precautions. As a collaborative effort between authors affiliated to the Infection Prevention and Control Working Group and the Fungal Infection Working Group of the International Society of Antimicrobial Chemotherapy (ISAC), we reviewed the English language literature and international guidance to describe the evidence behind the need for environmental monitoring for filamentous fungi as a quality assurance approach with an emphasis on required additional precautions during periods of construction. Many different clinical sampling approaches have been described for air, water, and surface sampling with significant variation in laboratory methodologies between reports. Importantly, there are no agreed-upon thresholds that correlate with an increase in the clinical risk of mould infections. We highlight important areas for future research to assure a safe environment for highly immunocompromized patients.
FLAMINGO: calibrating large cosmological hydrodynamical simulations with machine learning
Authors: Kugel Roi , Schaye Joop , Schaller Matthieu , Helly John C , Braspenning Joey , Elbers Willem , Frenk Carlos S , McCarthy Ian G , Kwan Juliana , Salcido Jaime , van Daalen Marcel P , Vandenbroucke Bert , Bahé Yannick M , Borrow Josh , Chaikin Evgenii , Huško Filip , Jenkins Adrian , Lacey Cedric G , Nobels Folkert S J , Vernon Ian 
Published: October 2023

ABSTRACT
To fully take advantage of the data provided by large-scale structure surveys, we need to quantify the potential impact of baryonic effects, such as feedback from active galactic nuclei (AGN) and star formation, on cosmological observables. In simulations, feedback processes originate on scales that remain unresolved. Therefore, they need to be sourced via subgrid models that contain free parameters. We use machine learning to calibrate the AGN and stellar feedback models for the FLAMINGO (Fullhydro Large-scale structure simulations with All-sky Mapping for the Interpretation of Next Generation Observations) cosmological hydrodynamical simulations. Using Gaussian process emulators trained on Latin hypercubes of 32 smaller volume simulations, we model how the galaxy stellar mass function (SMF) and cluster gas fractions change as a function of the subgrid parameters. The emulators are then fit to observational data, allowing for the inclusion of potential observational biases. We apply our method to the three different FLAMINGO resolutions, spanning a factor of 64 in particle mass, recovering the observed relations within the respective resolved mass ranges. We also use the emulators, which link changes in subgrid parameters to changes in observables, to find models that skirt or exceed the observationally allowed range for cluster gas fractions and the SMF. Our method enables us to define model variations in terms of the data that they are calibrated to rather than the values of specific subgrid parameters. This approach is useful, because subgrid parameters are typically not directly linked to particular observables, and predictions for a specific observable are influenced by multiple subgrid parameters.
Formation of a wide-orbit giant planet in a gravitationally unstable subsolar-metallicity protoplanetary disc
Authors: Matsukoba Ryoki , Vorobyov Eduard I , Hosokawa Takashi , Guedel Manuel 
Published: October 2023

ABSTRACT
Direct imaging observations of planets revealed that wide-orbit (&gt;10 au) giant planets exist even around subsolar-metallicity host stars and do not require metal-rich environments for their formation. A possible formation mechanism of wide-orbit giant planets in subsolar-metallicity environments is the gravitational fragmentation of massive protoplanetary discs. Here, we follow the long-term evolution of the disc for 1 Myr after its formation, which is comparable to disc lifetime, by way of a two-dimensional thin-disc hydrodynamic simulation with the metallicity of 0.1 $\rm {Z}_{\odot }$. We find a giant protoplanet that survives until the end of the simulation. The protoplanet is formed by the merger of two gaseous clumps at ∼0.5 Myr after disc formation, and then it orbits ∼200 au from the host star for ∼0.5 Myr. The protoplanet’s mass is ∼10 MJ at birth and gradually decreases to 1 MJ due to the tidal effect from the host star. The result provides the minimum mass of 1 MJ for the protoplanet in our simulation. We anticipate that the mass of a protoplanet experiencing reduced mass loss thanks to the protoplanetary contraction in higher resolution simulations can increase to ∼10 MJ. We argue that the disc gravitational fragmentation would be a promising pathway to form wide-orbit giant planets with masses of ≥1 MJ in subsolar-metallicity environments.
Volatiles in the H2O and CO2 ices of comet 67P/Churyumov–Gerasimenko
Authors: Rubin Martin , Altwegg Kathrin , Berthelier Jean-Jacques , Combi Michael R , De Keyser Johan , Fuselier Stephen A , Gombosi Tamas I , Gudipati Murthy S , Hänni Nora , Kipfer Kristina A , Ligterink Niels F W , Müller Daniel R , Shou Yinsi , Wampfler Susanne F 
Published: October 2023

ABSTRACT
European Space Agency’s Rosetta spacecraft at comet 67P/Churyumov–Gerasimenko (67P) was the first mission that accompanied a comet over a substantial fraction of its orbit. On board was the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis mass spectrometer suite to measure the local densities of the volatile species sublimating from the ices inside the comet’s nucleus. Understanding the nature of these ices was a key goal of Rosetta. We analysed the primary cometary molecules at 67P, namely H2O and CO2, together with a suite of minor species for almost the entire mission. Our investigation reveals that the local abundances of highly volatile species, such as CH4 and CO, are reproduced by a linear combination of both H2O and CO2 densities. These findings bear similarities to laboratory-based temperature-programmed desorption experiments of amorphous ices and imply that highly volatile species are trapped in H2O and CO2 ices. Our results do not show the presence of ices dominated by these highly volatile molecules. Most likely, they were lost due to thermal processing of 67P’s interior prior to its deflection to the inner solar system. Deviations in the proportions co-released with H2O and CO2 can only be observed before the inbound equinox, when the comet was still far from the sun and the abundance of highly volatile molecules associated with CO2 outgassing were lower. The corresponding CO2 is likely seasonal frost, which sublimated and lost its trapped highly volatile species before re-freezing during the previous apparition. CO, on the other hand, was elevated during the same time and requires further investigation.
Can Uranus and Neptune form concurrently via pebble, gas, and planetesimal accretion?
Authors: Eriksson Linn E J , Mol Lous Marit A S , Shibata Sho , Helled Ravit 
Published: October 2023

ABSTRACT
The origin of Uranus and Neptune has long been challenging to explain, due to the large orbital distances from the Sun. After a planetary embryo has been formed, the main accretion processes are likely pebble, gas, and planetesimal accretion. Previous studies of Uranus and Neptune formation typically do not consider all three processes; and furthermore, do not investigate how the formation of the outer planet impacts the inner planet. In this paper, we study the concurrent formation of Uranus and Neptune via pebble, gas, and planetesimal accretion. We use a dust-evolution model to predict the size and mass flux of pebbles, and derive our own fit for gas accretion. We do not include migration, but consider a wide range of formation locations between 12 and $40\, \textrm {au}$. If the planetary embryos form at the same time and with the same mass, our formation model with an evolving dust population is unable to produce Uranus and Neptune analogues. This is because the mass difference between the planets and the H–He mass fractions become too high. However, if the outer planetary embryo forms earlier and/or more massive than the inner embryo, the two planets do form in a few instances when the disc is metal-rich and dissipates after a few Myr. Furthermore, our study suggests that in situ formation is rather unlikely. Nevertheless, giant impacts and/or migration could potentially aid in the formation, and future studies including these processes could bring us one step closer to understanding how Uranus and Neptune formed.
Simulations of weakly magnetized turbulent mixing layers
Authors: Zhao Xihui , Bai Xue-Ning 
Published: October 2023

ABSTRACT
Radiative turbulent mixing layers (TMLs) are expected to form pervasively at the phase boundaries in multiphase astrophysical systems. This inherently small-scale structure is dynamically crucial because it directly regulates the mass, momentum, and energy exchanges between adjacent phases. Previous studies on hydrodynamic TMLs have revealed the interactions between cold and hot phases in the context of the circumgalactic medium, offering important insight into the fate of cold clouds traveling through hot galactic winds. However, the role of magnetic field has only been sparsely investigated. We perform a series of 3D magnetohydrodynamics simulations of such mixing layers in the presence of weak to modest background magnetic field. We find that due to field amplification, even relatively weak background magnetic fields can significantly reduce the surface brightness and inflow velocity of the hot gas in the mixing layer. This reduction is attributed to a combination of magnetic pressure support and direct suppression of turbulent mixing, both of which alter the phase structures. Our results are largely independent of thermal conduction and converged with resolution, offering insights on the survival of cold gas in multiphase systems.
Magnetized rotating isothermal winds
Authors: Raives Matthias J , Coleman Matthew S B , Thompson Todd A 
Published: October 2023

ABSTRACT
We consider the general problem of a Parker-type non-relativistic isothermal wind from a rotating and magnetic star. Using the magnetohydrodynamics code athena++, we construct an array of simulations in the stellar rotation rate Ω* and the isothermal sound speed cT, and calculate the mass, angular momentum, and energy loss rates across this parameter space. We also briefly consider the 3D case, with misaligned magnetic and rotation axes. We discuss applications of our results to the spin-down of normal stars, highly irradiated exoplanets, and to nascent highly magnetic and rapidly rotating neutron stars born in massive star core-collapse.
Accretion of ice giant planets from massive protoplanets whose migration is blocked by Jupiter and Saturn
Authors: Benedetti-Rossi G , Ribeiro R , Winter O C , Gaspar H S , Vieira-Neto E 
Published: October 2023

ABSTRACT
The growth and dynamical evolution of protoplanets beyond Saturn through collisions and type I migration typically result in a highly chaotic dynamics, producing a diversity of outcomes depending on the initial conditions. Here we present the results of N-bodies numerical simulations aiming to make a detailed exploration of different initial conditions and potential outcomes for this dynamics. We consider Jupiter and Saturn at the imminence of crossing the 3:2 mean motion resonance in two possible positions based on the final and initial conditions of the Grand Tack and the Nice models, respectively; four different gas disc lifetimes, and a range of population sizes of planetary embryos beyond Saturn with different masses and orbital configurations in a total of 72 different setups. We present statistical analyses of our outcomes including planets that ‘jump’ to interior orbits of Jupiter, the frequency of close encounters between the planetary embryos and Jupiter, the number of ejections and collisions, and the dynamical effects for stabilizing the final planetary system in chains of mean motion resonances. Results show that independently of the initial configuration of Jupiter and Saturn and the gas lifetime, the dynamical evolution goes through three main phases. A few per cent of the simulations successfully produce Uranus and Neptune analogues, which may have implications on the ice giants’ composition and obliquities, the material ejected from the Solar System, and the conditions for the giant planet instability.
Ultracool spectroscopic outliers in Gaia DR3
Authors: Cooper W J , Smart R L , Jones H R A , Sarro L M 
Published: October 2023

ABSTRACT
Gaia DR3 provided a first release of RP spectra and astrophysical parameters for ultracool dwarfs (UCDs). We used these Gaia RP spectra and astrophysical parameters to select the most outlying UCDs. These objects have spectral types of M7 or later and might be young brown dwarfs or low-metallicity objects. This work aimed to find UCDs that have Gaia RP spectra significantly different to the typical population. However, the intrinsic faintness of these UCDs in Gaia means that their spectra were typically rather low signal-to-noise ratio in Gaia DR3. This study is intended as a proof of concept for future iterations of the Gaia data releases. Based on well-studied subdwarfs and young objects, we created a spectral type-specific color ratio, defined using Gaia RP spectra; this ratio is then used to determine which objects are outliers. We then used the objects kinematics and photometry external to Gaia to cut down the list of outliers into a list of ‘prime candidates’. We produce a list of 58 Gaia RP spectra outliers, seven of which we deem as prime candidates. Of these, six are likely subdwarfs and one is a known young stellar object. Four of six subdwarf candidates were known as subdwarfs already. The two other subdwarf candidates, namely 2MASS J03405673 + 2633447 (sdM8.5) and 2MASS J01204397 + 6623543 (sdM9), are new classifications.
Large-scale turbulence cascade in the spiral galaxy NGC 6946
Authors: Nandakumar Meera , Dutta Prasun 
Published: October 2023

ABSTRACT
The generation mechanism of compressible fluid turbulence at kiloparsec scales in the interstellar medium is a long-lasting puzzle. In this work, we explore the nature of large-scale turbulence in the external spiral galaxy NGC 6946. We use the visibility moment estimator to measure the H i column density and line-of-sight turbulent velocity power spectra combining the new observations of A array configuration of Karl G. Jansky Very Large Array (VLA) with the VLA B, C, D array observations from The H i Nearby Galaxy Survey. The estimated power spectra are obeying a power law with a slope of −0.96 ± 0.05 in column density and −1.81 ± 0.07 in line-of-sight velocity in length-scales ranging from 6 kpc to 170 pc. This points towards a forward energy cascade in the plane of the disc with a driving scale at least as large as 6 kpc. The values of the power-law indices indicate a combination of solenoidal and compressive force responsible for driving the measured turbulence. The presence of strong regular magnetic fields from the magnetic spiral arms in the galaxy is possibly contributing to the solenoidal part, while self-gravity or gravitational instability can mostly be the input for the compressive part of the forcing in the driving mechanism.
Slowly rotating close binary stars in Cassini states
Authors: Felce Catherine , Fuller Jim 
Published: October 2023

ABSTRACT
Recent asteroseismic measurements have revealed a small population of stars in close binaries, containing primaries with extremely slow rotation rates. Such stars defy the standard expectation of tidal synchronization in such systems, but they can potentially be explained if they are trapped in a spin-orbit equilibrium known as Cassini state 2 (CS2). This state is maintained by orbital precession due to an outer tertiary star, and it typically results in a very sub-synchronous rotation rate and high degree of spin-orbit misalignment. We examine how CS2 is affected by magnetic braking and different types of tidal dissipation. Magnetic braking results in a slower equilibrium rotation rate, while tidal dissipation via gravity waves can result in a slightly higher rotation rate than predicted by equilibrium tidal theory, and dissipation via inertial waves can result in much slower rotation rates. For seven binary systems with slowly rotating primaries, we predict the location of the outer tertiary predicted by the CS2 theory. In five of these systems, a tertiary companion has already been detected, although it is closer than expected in three of these, potentially indicating tidal dissipation via inertial waves. We also identify a few new candidate systems among a population of eclipsing binaries with rotation measurements via spot modulation.
The exclusionary approach to consciousness
Authors: Paßler Marlo 
Published: October 2023

AbstractThe standard approach in the field of consciousness research involves identifying the neural correlates of consciousness (NCCs) by comparing neural activity between conscious and unconscious trials. However, this method has been met with criticism due to the lack of consensus on how to operationalize and measure consciousness. In this paper, I propose an alternative approach: the exclusionary approach. Rather than utilizing near-threshold conditions to contrast conscious and unconscious trials, this approach leverages the widely accepted notion that subjective reports are reliable under normal conditions. I propose that this can be done by assessing whether consciousness remains stable across trials while manipulating other factors such as reports, tasks, stimulation, or attention. We can use the resulting contrast to exclude certain kinds of neural activity as candidate NCCs. This method produces results that are less contentious, allowing for the establishment of hard criteria for theories of consciousness. Additionally, this approach does not require the development of new research paradigms, but can incorporate existing studies, particularly those aimed at identifying confounding factors in the standard approach. It is important to note, however, that the proposed exclusionary approach does not negate the value of the identification approach. Rather, they should be considered as complementary methods.