bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human CXCR1 knock-in mice infer functional expression of a murine ortholog
Authors: Fahimi Farnaz , Alam Md Jahangir , Ang Caroline , Adhyatma Galih Prakasa , Xie Liang , Mackay Charles R , Robert Remy 
Published: July 2023

AbstractTargeting CXCR1 and CXCR2 chemokine receptors to block neutrophil migration to sites of inflammation is a promising therapeutic approach for various inflammatory and autoimmune diseases. However, assessing the translational potential of such therapies using mouse models is challenging due to the unclear expression of CXCR1 at the protein level. Although CXCR2 has been well characterized in both mice and humans, the protein-level expression of CXCR1 in mice (mCXCR1) remains controversial. To address this issue, we generated a novel human CXCR1 knock-in (hCXCR1 KI) mouse model in which the transgene is under the control of the native mouse promoter and regulatory elements. Using an anti-human CXCR1 monoclonal antibody (anti-hCXCR1 monoclonal antibody), we found that hCXCR1 was highly expressed on neutrophils in the hCXCR1 KI mice, comparable to levels observed in human neutrophils. This successful expression of hCXCR1 in this mouse model suggests that functional mCXCR1 likely exists. To investigate the functional role of CXCR1, we investigated how antagonizing this receptor using anti-hCXCR1 monoclonal antibody in the arthritis model would affect disease outcomes. Antibody treatment significantly alleviated all signs of joint inflammation. In summary, our newly generated hCXCR1 KI transgenic mice provide a valuable tool to investigate the therapeutic efficacy of small molecules or monoclonal antibodies that antagonize this receptor in neutrophil-mediated pathologies.
Auxins and grass shoot architecture: how the most important hormone makes the most important plants
Authors: Wakeman Alex , Bennett Tom 
Published: July 2023

Abstract
Cereals are a group of grasses cultivated by humans for their grain. It is from these cereal grains that the majority of all calories consumed by humans are derived. The production of these grains is the result of the development of a series of hierarchical reproductive structures that form the distinct shoot architecture of the grasses. Being spatiotemporally complex, the coordination of grass shoot development is tightly controlled by a network of genes and signals, including the key phytohormone auxin. Hormonal manipulation has therefore been identified as a promising potential approach to increasing cereal crop yields and therefore ultimately global food security. Recent work translating the substantial body of auxin research from model plants into cereal crop species is revealing the contribution of auxin biosynthesis, transport, and signalling to the development of grass shoot architecture. This review discusses this still-maturing knowledge base and examines the possibility that changes in auxin biology could have been a causative agent in the evolution of differences in shoot architecture between key grass species, or could underpin the future selective breeding of cereal crops.
Constraining turbulence in protoplanetary discs using the gap contrast: an application to the DSHARP sample
Authors: Pizzati Elia , Rosotti Giovanni P , Tabone Benoît 
Published: July 2023

ABSTRACT
Constraining the strength of gas turbulence in protoplanetary discs is an open problem that has relevant implications for the physics of gas accretion and planet formation. In this work, we gauge the amount of turbulence in six of the discs observed in the DSHARP programme by indirectly measuring the vertical distribution of their dust component. We employ the differences in the gap contrasts observed along the major and the minor axes due to projection effects, and build a radiative transfer model to reproduce these features for different values of the dust scale heights. We find that (a) the scale heights that yield a better agreement with data are generally low ($\lesssim 4\, \mathrm{AU}$ at a radial distance of $100\, \mathrm{AU}$), and in almost all cases we are only able to place upper limits on their exact values; these conclusions imply (assuming an average Stokes number of ≈10−2) low turbulence levels of αSS ≲ 10−3 − 10−4; (b) for the 9 other systems we considered out of the DSHARP sample, our method yields no significant constraints on the disc vertical structure; we conclude that this is because these discs have either a low inclination or gaps that are not deep enough. Based on our analysis we provide an empirical criterion to assess whether a given disc is suitable to measure the vertical scale height.
On the energetics of a tidally oscillating convective flow
Authors: Terquem Caroline 
Published: July 2023

ABSTRACT
This paper examines the energetics of a convective flow subject to an oscillation with a period $t_{\rm osc}$ much smaller than the convective time-scale $t_{\rm conv}$, allowing for compressibility and uniform rotation. We show that the energy of the oscillation is exchanged with the kinetic energy of the convective flow at a rate $D_R$ that couples the Reynolds stress of the oscillation with the convective velocity gradient. For the equilibrium tide and inertial waves, this is the only energy exchange term, whereas for p modes there are also exchanges with the potential and internal energy of the convective flow. Locally, $\left| D_R \right| \sim u^{\prime 2} / t_{\rm conv}$, where $u^{\prime}$ is the oscillating velocity. If $t_{\rm conv} \ll t_{\rm osc}$ and assuming mixing length theory, $\left| D_R \right|$ is $\left( \lambda_{\rm conv} / \lambda_{\rm osc} \right)^2$ smaller, where $\lambda_{\rm conv}$ and $\lambda_{\rm osc}$ are the characteristic scales of convection and the oscillation. Assuming local dissipation, we show that the equilibrium tide lags behind the tidal potential by a phase $\delta(r) \sim r \omega_{\rm osc} / \left( g(r) t_{\rm conv}(r) \right)$, where g is the gravitational acceleration. The equilibrium tide can be described locally as a harmonic oscillator with natural frequency $\left( g/r \right)^{1/2}$ and subject to a damping force $-u^{\prime}/t_{\rm conv}$. Although $\delta(r)$ varies by orders of magnitude through the flow, it is possible to define an average phase shift $\overline{\delta }$ which is in good agreement with observations for Jupiter and some of the moons of Saturn. Finally, $1 / \overline{\delta }$ is shown to be equal to the standard tidal dissipation factor.
The origin of massive compact galaxies: lessons from IllustrisTNG
Authors: Lohmann Felipe S , Schnorr-Müller Allan , Trevisan Marina , Ricci T V , Clerici K Slodkowski 
Published: July 2023

ABSTRACT
We investigate the formation and evolution of z = 0 massive compact galaxies (MCGs) in the IllustrisTNG cosmological simulation. We found that, as in observations, MCGs are mainly old (median age ∼10.8 Gyr), have supersolar metallicities (median log Z/Z⊙ ∼ 0.35), and are α-enhanced (median [α/Fe] ∼ 0.25). The age distribution extends to younger ages, however, and a few MCGs are as young as ∼7 Gyr. In general, MCGs assemble their mass early and accrete low angular momentum gas, significantly increasing their mass while growing their size much slower. A small fraction of MCGs follow another evolutionary path, going through a compaction event, with their sizes shrinking by 40 per cent or more. The accretion of low angular momentum gas leads to enhanced supermassive black hole (SMBH) growth, and MCGs reach the threshold SMBH mass of $\log M_\mathrm{BH}\sim 10^{8.5}\ \mathrm{ M}_\odot$ – when kinetic active galactic nucleus feedback kicks in and quenches the galaxy – earlier than non-compact galaxies. Comparing MCGs to a sample of median-sized quiescent galaxies matched in effective velocity dispersion, we find that their accretion histories are very different. 71 per cent of MCGs do not merge after quenching compared to 37 per cent of median-sized quiescent galaxies. Moreover, tracing these populations back in time, we find that at least a third of median-sized quiescent galaxies do not have a compact progenitor, underscoring that both dry mergers and progenitor bias effects are responsible for the differences in the kinematics and stellar population properties of MCGs and median-sized quiescent galaxies.
Discovery and characterization of two Neptune-mass planets orbiting HD 212729 with TESS
Authors: Armstrong David J , Osborn Ares , Adibekyan Vardan , Delgado-Mena Elisa , Hojjatpanah Saeed , Howell Steve B , Hoyer Sergio , Knierim Henrik , Sousa Sérgio G , Stassun Keivan G , Veras Dimitri , Anderson David R , Bayliss Daniel , Bouchy François , Burke Christopher J , Christiansen Jessie L , Dumusque Xavier , Keniger Marcelo Aron Fetzner , Hadjigeorghiou Andreas , Hawthorn Faith , Helled Ravit , Jenkins Jon M , Latham David W , Lillo-Box Jorge , Nielsen Louise D , Osborn Hugh P , Rodrigues José , Rodriguez David , Santos Nuno C , Seager Sara , Strøm Paul A , Torres Guillermo , Twicken Joseph D , Udry Stephane , Wheatley Peter J , Winn Joshua N 
Published: July 2023

ABSTRACT
We report the discovery of two exoplanets orbiting around HD 212729 (TOI 1052, TIC 317060587), a Teff = 6146 K star with V = 9.51 observed by TESS in Sectors 1 and 13. One exoplanet, TOI-1052b, is Neptune-mass and transits the star, and an additional planet TOI-1052c is observed in radial velocities but not seen to transit. We confirm the planetary nature of TOI-1052b using precise radial velocity observations from HARPS and determined its parameters in a joint RV and photometry analysis. TOI-1052b has a radius of $2.87^{+0.29}_{-0.24}$ R⊕, a mass of 16.9 ± 1.7 M⊕, and an orbital period of 9.14 d. TOI-1052c does not show any transits in the TESS data, and has a minimum mass of $34.3^{+4.1}_{-3.7}$ M⊕ and an orbital period of 35.8 d, placing it just interior to the 4:1 mean-motion resonance. Both planets are best fit by relatively high but only marginally significant eccentricities of $0.18^{+0.09}_{-0.07}$ for planet b and $0.24^{+0.09}_{-0.08}$ for planet c. We perform a dynamical analysis and internal structure model of the planets as well as deriving stellar parameters and chemical abundances. The mean density of TOI-1052b is $3.9^{+1.7}_{-1.3}$ g cm−3 consistent with an internal structure similar to Neptune. A nearby star is observed in Gaia DR3 with the same distance and proper motion as TOI-1052, at a sky projected separation of $\scriptstyle \sim$1500 au, making this a potential wide binary star system.
Association between regional quota program in medical schools and practical clinical competency based on General Medicine In-Training Examination score: a nationwide cross-sectional study of resident physicians in Japan
Authors: Fukui Sho , Shikino Kiyoshi , Nishizaki Yuji , Shimizu Taro , Yamamoto Yu , Kobayashi Hiroyuki , Tokuda Yasuharu 
Published: July 2023

Abstract

Purpose
A regional quota program (RQP) was introduced in Japan to ameliorate the urban–rural imbalance of physicians. Despite concerns about the low learning abilities of RQP graduates, the relationship between the RQP and practical clinical competency after initiating clinical residency has not been evaluated.

Methods
We conducted a nationwide cross-sectional study to assess the association between the RQP and practical clinical competency based on General Medicine In-Training Examination (GM-ITE) scores. We compared the overall and category GM-ITE results between RQP graduates and other resident physicians. The relationship between the RQP and scores was examined using multilevel linear regression analysis.

Results
There were 4978 other resident physicians and 1119 RQP graduates out of 6097 participants from 593 training hospitals. Being younger; preferring internal, general, or emergency medicine; managing fewer inpatients; and having fewer ER shifts were all characteristics of RQP graduates. In multilevel multivariable linear regression analysis, there was no significant association between RQP graduates and total GM-ITE scores (coefficient: 0.26; 95% confidence interval: −0.09, 0.61; P = .15). The associations of RQP graduates with GM-ITE scores in each category and specialty were not clinically relevant. However, in the same multivariable model, the analysis did reveal that total GM-ITE scores demonstrated strong positive associations with younger age and GM preference, both of which were significantly common in RQP graduates.

Conclusion
Practical clinical competency evaluated based on the GM-ITE score showed no clinically relevant differences between RQP graduates and other resident physicians.
Key messages What is already known on this topic Many countries offer unique admission processes to medical schools and special undergraduate programs to increase the supply of physicians in rural areas. Concerns have been raised about the motivation, learning capabilities, and academic performance of the program graduates. What this study adds This nationwide cross-sectional study in Japan revealed clinical competency based on the scores from the General Medicine In-Training Examination showed no clinically relevant differences between graduates of regional quota programs and other resident physicians. How this study might affect research, practice, or policy The study provides evidence to support the Japanese regional quota program from the perspective of clinical competency after initiating clinical practice.
Skeletal traits and otoliths can unravel the relationships within European Gobiidae (Gobius lineage sensu lato)
Authors: Reichenbacher Bettina , Vukić Jasna , Šanda Radek , Schliewen Ulrich K , Esmaeili Hamid R , Kassar Abderrahmane 
Published: July 2023

Abstract
The high diversity of extant gobiids (Gobiidae: Teleostei) makes taxonomic and phylogenetic interpretation of fossil members of the clade a difficult task. To facilitate future taxonomic and systematic work on the group, we have assembled a morphological reference database encompassing skeletal characters, an otolith atlas and otolith morphometric data of 25 present-day species from the European Gobius lineage (s.l.) that represent 18 different genera and include all nine sublineages. We show that: (1) skeletal traits and morphometric otolith variables can be diagnostic for a sublineage; (2) otolith morphology allows identification at the genus and species levels; and (3) the number of anal-fin rays and details of the otolith margins can be used to discriminate closely related dwarf gobies. The skeletal and otolith characters are largely stable in the marine gobies analysed here, whereas freshwater gobies (Padogobius, Ponto-Caspian gobies) are far more variable. This might be related to the conquest by Padogobius and Ponto-Caspian gobies of freshwater and low-salinity habitats, in which environmental conditions can fluctuate widely. We anticipate that the database presented here can be used as a valuable reference tool to assess the relationships of fossil gobiids and increase our knowledge of the evolutionary history of the group as a whole.
Dopaminergic manipulations affect the modulation and meta-modulation of movement speed: evidence from two pharmacological interventions
Authors: Hickman Lydia J. , Sowden Sophie L. , Fraser Dagmar S. , Schuster Bianca A. , Rybicki Alicia J. , Galea Joseph M. , Cook Jennifer L. 
Published: July 2023

AbstractA body of research implicates dopamine in the average speed of simple movements. However, naturalistic movements span a range of different shaped trajectories and rarely proceed at a single constant speed; instead, speed is reduced when drawing“corners”compared to“straights”(i.e., speed-modulation), and the extent of this slowing down is dependent upon the global shape of the movement trajectory (i.e., speed-meta-modulation) – for example whether the shape is an ellipse or a rounded square. By employing two pharmacological intervention studies – individuals with Parkinson’s both ON and OFF dopaminergic medication (N = 32) and members of the general population on a D2 receptor blocker (haloperidol) versus placebo (N = 43) – we implicate dopamine in speed, speed-modulation and speed-meta-modulation. Our findings move beyond vigour models implicating dopamine in average movement speed, and towards a conceptualisation that involves the modulation of speed as a function of contextual information.
Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems
Authors: Moore-Pollard Erika R. , Jones Daniel S. , Mandel Jennifer R. 
Published: July 2023

ABSTRACTPremiseThe sunflower family specific probe set, Compositae-1061, has enabled family-wide phylogenomic studies and investigations at lower-taxonomic levels by targeting 1,000+ genes. However, it generally lacks resolution at the genus to species level, especially in groups with complex evolutionary histories including polyploidy and hybridization.MethodsIn this study, we developed a new Hyb-Seq probe set, Compositae-ParaLoss-1272, designed to target orthologous loci in Asteraceae family members. We tested its efficiency across the family by simulating target-enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in genusPackerawhich has a complex evolutionary and taxonomic history. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 taxa which were previously studied using the Compositae-1061 probe set. Sequences from both probe sets were used to generate phylogenies, compare topologies, and assess node support.ResultsWe report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members. Additionally, Compositae-ParaLoss-1272 had less gene tree discordance, recovered considerably fewer paralogous sequences, and retained longer loci than Compositae-1061.DiscussionGiven the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate this new probe set will provide improved resolution and utility for studies at lower-taxonomic levels and complex groups in the sunflower family.
Pupil size reveals arousal level dynamics in human sleep
Authors: Carro-Domínguez Manuel , Huwiler Stephanie , Oberlin Stella , Oesch Timona Leandra , Badii Gabriela , Lüthi Anita , Wenderoth Nicole , Meissner Sarah Nadine , Lustenberger Caroline 
Published: July 2023

AbstractRecent animal research has revealed the intricate dynamics of arousal levels that are potentially crucial for maintaining proper sleep resilience and memory consolidation. Also in humans, changes in arousal level are believed to be a determining characteristic of healthy and pathological sleep but tracking arousal fluctuations has been methodologically challenging. Here we measured pupil size, an established indicator of arousal levels, during overnight sleep and tested whether the arousal level affects cortical response to auditory stimulation. We show that pupil size dynamics change as a function of sleep macrostructure and microstructural events. In particular, pupil size is inversely related to the occurrence of sleep spindle clusters, a marker of sleep resilience. Additionally, pupil size prior to auditory stimulation influences the evoked response, most notably in delta power, a marker of several restorative and regenerative functions of sleep. Recording pupil size dynamics provides novel insights into the interplay between arousal levels and sleep oscillations, opening new avenues for future research and clinical applications in diagnosing and treating pathological sleep associated with abnormal arousal levels.
Passaging Human Tauopathy Patient Samples in Cells Generates Heterogeneous Fibrils with a Subpopulation Adopting Disease Folds
Authors: Zeng Zhikai , Tsay Karen , Vijayan Vishnu , Frost Matthew P. , Prakash Shikhar , Quddus Athena , Albert Alexa , Vigers Michael , Srivastava Madhur , Woerman Amanda L. , Han Songi 
Published: July 2023

AbstractThe discovery by cryo-electron microscopy (cryo-EM) that the neu-ropathological hallmarks of different tauopathies, including Alzheimer’s disease, corticobasal degeneration (CBD), and progressive supranuclear palsy (PSP), are caused by unique misfolded conformations of the protein tau is among the most profound developments in neurodegenerative disease research. To capitalize on these discoveries for therapeutic development, one must achievein vitroreplication of tau fibrils that adopt the representative tauopathy disease folds, which represents a grand challenge for the field. A widely used approach has been seeded propagation using pathological tau fibrils derived from post-mortem patient samples in biosensor cells that expresses a fragment of the tau protein known as K18, or Tau4RD, containing the microtubule-binding repeat domain of tau as the substrate. The new insights from cryo-EM raised the question of whether the Tau4RD fragment is capable of adopting characteristic tau folds found in CBD and PSP patient fibrils, and whether cell-passaged and amplified tau fibrils can be used as seeds to achieve cell-free assembly of recombinant 4R tau into fibrils without the addition of cofactors. Using Double Electron Electron Resonance (DEER) spectroscopy, we discovered that cell-passaged pathological seeds generate heterogeneous fibrils that are, however, distinct between the CBD and PSP lysate-seeded fibrils, and vastly different from heparin-induced tau fibril structures. Moreover, the lysate-seeded fibrils contain a characteristic sub-population that resembles the disease fold corresponding to the respective starting patient sample. These findings indicate that templated propagation using CBD and PSP patient-derived fibrils is possible with a tau fragment that does not contain the entire pathological fibril core, but also that additional mechanisms must be tuned to converge on a homogeneous fibril population.
Expectancy-related changes in firing of dopamine neurons depend on hippocampus
Authors: Takahashi Yuji K. , Zhang Zhewei , Montesinos-Cartegena Marlian , Kahnt Thorsten , Langdon Angela J. , Schoenbaum Geoffrey 
Published: July 2023

SummaryThe orbitofrontal cortex (OFC) and hippocampus (HC) are both implicated in forming the cognitive or task maps that support flexible behavior. Previously, we used the dopamine neurons as a sensor or tool to measure the functional effects of OFC lesions (Takahashi et al., 2011). We recorded midbrain dopamine neurons as rats performed an odor-based choice task, in which errors in the prediction of reward were induced by manipulating the number or timing of the expected rewards across blocks of trials. We found that OFC lesions ipsilateral to the recording electrodes caused prediction errors to be degraded consistent with a loss in the resolution of the task states, particularly under conditions where hidden information was critical to sharpening the predictions. Here we have repeated this experiment, along with computational modeling of the results, in rats with ipsilateral HC lesions. The results show HC also shapes the map of our task, however unlike OFC, which provides information local to the trial, the HC appears to be necessary for estimating the upper-level hidden states based on the information that is discontinuous or separated by longer timescales. The results contrast the respective roles of the OFC and HC in cognitive mapping and add to evidence that the dopamine neurons access a rich information set from distributed regions regarding the predictive structure of the environment, potentially enabling this powerful teaching signal to support complex learning and behavior.